TEST BANK for Biochemistry The Molecular Basis of Life 7th Edition by James R. McKee; Trudy McKee

CHAPTER ONE BIOCHEMISTRY: AN INTRODUCTION 1) The ultimate source of energy for life on earth is __________.

A) The sun B) Geothermal heat C) Carbohydrates D) Fats E) Other organisms Ans A 2) Which of the following is not a common component of biomolecules?

A) Carbon B) Hydrogen C) Oxygen D) Nitrogen E) Chlorine Ans E 3) Which of the following is the basic structural unit of living organisms?

A) Nucleus B) Cell membrane C) Tissue D) Cell E) Cytoskeleton Ans D 4) Which of the following is not an organelle?

A) Mitochondria B) Chloroplast C) Nucleus D) Plasma membrane E) Golgi complex Ans D 5) Which of the following is not a role played by carbohydrates in living cells?

A) Energy source B) Structural support C) Intercellular communication D) Both A and B are correct E) All are roles played by carbohydrates in living cells Ans D 6) Metabolism is best defined as the _________.

A) Reactions of living cells B) Reactions that synthesize large molecules in living cells C) Reactions that degrade molecules in living cells D) Conversion of food molecules to energy E) Reactions that synthesize and degrade molecules in living cells Ans E 7) The average life span of a species is about ________years A) One million B) Ten million C) Five hundred thousand D) Five million E) One hundred thousand Ans A 8) Which of the following is not a waste product of living organisms A) Carbon dioxide B) Water C) Urea D) Ammonia E) Glycine Ans E 9) Biochemistry is defined as A) The study of life processes B) The study of the molecular basis of life C) The study of living organisms

D) The study of organic compounds in living organisms E) The study of living compounds Ans B 10) One of the principal methods that organisms use to obtain energy from chemical bonds is by ___________.

A) Substitution reactions B) Dehydration reactions C) Oxidation/reduction reactions D) Hydration reactions E) Addition reactions Ans C 11) The following is an example of which reaction class?

CH3Br + HSCH2CH(NH2)COOH → CH3SCH2CH(NH2)COOH + Br- + H+ A) Substitution B) Elimination C) Addition D) Isomerization E) Oxidation/Reduction Ans A 12 The following is an example of which reaction class HOOCCH=CHCOOH + H2O → HOOCCH2CH(OH)COOH A) Substitution B) Elimination C) Addition D) Isomerization E) Oxidation/Reduction Ans C 13) The following is an example of which reaction class?

CH3CH2OH → CH3CHO + H2O A) Substitution

B) Elimination C) Addition D) Isomerization E) Oxidation/Reduction Ans E 14) Which of the following is not a component of nucleic acid?

A) Nucleotides B) Glucose C) Phosphate group D) Purines E) Pyrimidines Ans B 15) The largest molecules in living organisms are _________.

A) proteins B) lipids C) nucleic acids D) carbohydrates E) steroids Ans C 16) All of the following classes of compounds are lipids except _______.

A) fats B) sterols C) fatty acids D) phosphoglycerides E) nucleotides Ans E 17) Which of the following classes of biomolecules are the most abundant in nature?

A) Lipids B) Amino acids C) Carbohydrates

D) Proteins E) Nucleotides Ans C 18) Consider the following molecule. Which arrow is pointing to a peptide bond?

A) A B) B C) C D) D E) E Ans C 19) The following molecule is an example of which single class of compounds?

CH3CH2CH(NH2)COOH A) Amine B) Acid C) Ester D) Amino acid E) Alcohol Ans D 20) The following molecule is an example of which class of compounds?

CH3CH2CH2COOCH2CH3 A) Hydrocarbon B) Acid

C) Ester D) Ether E) Aldehyde Ans C 21) The following molecule is an example of which class of compounds?

CH3CH2CH2COOH A) Hydrocarbon B) Acid C) Alcohol D) Aldehyde E) Ketone Ans B 22) The chemical properties of organic molecules are determined by specific arrangements of atoms called _____________.

A) Structure B) Bonds C) Functional groups D) Radicals E) Molecules Ans C 23) Which of the following classes of compounds make up most of the mass of an organism?

A) Amino acids B) Proteins C) Lipids D) Carbohydrates E) Water Ans E 24) Which of the following is not a basic element of life?

A) Phosphorous B) Hydrogen

C) Nitrogen D) Oxygen E) All of the above are basic elements of life Ans E 25) Most biomolecules can be considered to be derivatives of A) Amino acids B) Carbohydrates C) Fats D) Hydrocarbons E) Alcohols Ans D 26) Which of the following amino acids contain a hydrophobic side chain A) Leucine B) Arginine C) Glutamine D) Glutamic acid E) Aspartic acid Ans A 27) Which of the following small molecules do not form biopolymers A) Amino acids B) Sugars C) Fatty acids D) Nucleotides E) C and D Ans C 28) Choose the amino acid that can function as a neurotransmitter A) Glutamic acid B) Alanine C) Tyrosine D) Lysine E) Cysteine

Ans A 29) A constant source of _______ is required for maintenance of a cell’s ordered state.

A) Heat B) Oxygen C) Energy D) Stimulus E) Water Ans C 30) Which of the following is not true of life?

A) Life is cellular B) Life is information based C) Life is complex and dynamic D) All living things produce energy using mitochondria E) Life adapts and evolves Ans D 31) Which of the following classes of compounds contain the same functional group as an ester?

A) Amino acids B) Fatty acids C) Carbohydrates D) Proteins E) Fats Ans E 32) Which of the following is not a component of DNA A) Uracil B) Adenine C) Cytosine D) Guanidine E) Thymine Ans A 33) The sum total of all reactions of an organism is called

A) Life B) Metabolism C) Biosynthesis D) Anabolism E) Energetics Ans B 34) Which of the following is not characteristic of an autopoietic system?

A) Autonomous B) Self-organizing C) Self-maintaining D) Intelligent E) B and D Ans D 35) The assumption that a complete understanding of a living organism can be obtained solely by investigating all of its components is called _________.

A) Systems biology B) Reductionism C) Emergence D) Robustness E) Feedback control Ans B 36) Which of the following is not a core principle of systems biology?

A) Emergence B) Robustness C) Redundancy D) Modularity E) Limit of resolution Ans E 37) The field of study associated with the investigation of gene expression patterns is called: A) Proteomics

B) Bioinformatics C) Genomics D) Functional genomics E) Synomics Ans D 38) Which of the following is not an example of a macromolecule?

A) Nucleic acid B) Protein C) Polysaccharide D) Enzyme E) Amino acid Ans E 39) Which of the following is not considered a class of small biomolecule?

A) Amino acid B) Sugar C) Nucleic Acid D) Fatty acid E) Nucleotide Ans C 40) The functional group present in the following molecule is called:

A) Amine B) Ketone C) Amide D) Ester E) Acid

Ans C 41) The majority of Earth’s species belong to which of the following classifications?

A) Eukaryotes B) Prokaryotes C) Viruses D) Mammals E) Archea Ans B 42) The conversion of earths atmosphere from anerobic to aerobic was due to the development of _________________ by cyanobacteria.

A) Photosynthesis B) Metabolism C) Chemosynthesis D) Oxidation of iron E) Fixation of nitrogen as cyanide Ans A 43) The largest mass extinction also known as the great dying was called the A) Cenezoic extinction B) Permian extinction C) Mesozoic event D) Great ice age E) The great plague Ans B 44) The most prominent function of RNA is A) Energy source B) Nutrient source C) Protein synthesis D) Structural elements E) B and C Ans C

45) An organism’s entire set of DNA is called A) Genome B) Genetic sequence C) Polynucleotide sequence D) Gene E) Inheritance Ans A 46) The major function of carbohydrates is A) Catalysts and structural elements B) Energy sources and structural elements C) Genetic information D) Protein synthesis E) Insulation Ans B

SHORT ANSWER 47) What is meant by the term biomolecule?

Ans A biomolecule is a molecule synthesized by living organisms.

48) What is meant by the term metabolism?

Ans Metabolism is the sum total of all reactions in a living organism.

49) What is meant by the term hydrophobic?

Ans Hydrophobic molecules are incapable of hydrogen bonding with polar molecules including water.

50) What is meant by the term sugar?

Ans Sugars are polyhydoxy aldehydes and ketones that are the basic unit of a carbohydrate.

51) Define the term fatty acid.

Ans Fatty acids are monocarboxylic acids represented by the formula R-COOH in which R is an alkyl group that contains carbon and hydrogen.

52) Define the term nucleotide.

Ans A Nucleotide is composed of a 5-carbon sugar (ribose or deoxyribose), a nitrogenous base, and one or more phosphate groups.

53) Why is DNA sometimes referred to as the double helix?

Ans DNA is sometimes referred to as the double helix because it is composed of two antiparallel polynucleotide strands wound around each other.

54) Identify the functional groups in the following molecule.

Ans The functional groups present in the above molecule are two carboxylic acid groups and an amino group.

55) Identify the functional group in the following molecule.

Ans The functional group present in the above molecule is an amide group.

56) Name four classes of small biomolecules. In what larger biomolecules are they found?

Ans Amino acids occur in peptides and proteins. Sugars occur in oligosaccharides and polysaccharides. Nucleotides are the components of nucleic acids. Fatty acids are components of several types of lipid molecules (e.g., triacylglycerols and phospholipids).

57) What are the functions of fatty acids?

Ans The functions of fatty acids include energy storage and components of membrane.

Some fatty acids are also precursors to hormone-like molecules.

58) What are two functions of nucleotides?

Ans Nucleotides are involved in energy transformations. They are also components of DNA and RNA. 59) Compare the features of an airplane autopilot system with a biological system in terms of robustness, control mechanisms and redundancy.

Ans Both an airplane autopilot system and a biological system are robust (i.e., they have

the ability to maintain stability despite changes in the environment or other events that threaten the continuation of system functions). They both have feedback control mechanisms, in which information regarding internal processes is used to adjust functions to maximize performance. The actual failsafe mechanisms differ in that human-made

systems have redundancy (duplicate parts) while biological systems have degeneracy, in which duplicate (or similar) functions may be carried out by different parts of the system.

60) How do plants dispose of waste products?

Ans Plants dispose of waste products either by degradation or by storage in vacuoles or cell walls.

64) To what major class of biomolecules does the following molecule belong?

Ans Amino acid 61) To what major class of biomolecules does the following molecule belong?

Ans Nucleoside 62) What are the primary functions of metabolism?

Ans The primary functions of metabolism are acquisition and utilization of energy, synthesis of biomolecules, and removal of waste products.

ESSAY QUESTIONS 63) Compare and contrast the general features of human-designed complex systems and living systems.

Ans Both human-designed complex systems (such as machines or factories) and living systems require raw materials (nutrients) and energy to manufacture components; systems of both types also produce waste products and heat. Machines can be designed to self-regulate upon receiving feedback from the environment (e.g., by monitoring temperature to determine heating or cooling needs). In contrast, living systems are selfsustaining; that is, they produce and repair all of their own structural and functional components and, via nucleic acids, they build the machines (enzymes) that make the components. Even the nucleic acids themselves are reproduced by living systems. This level of self-sustainability is not present in human-designed complex systems.

64) Biochemistry and molecular biology are often thought of as very similar fields. In what ways do they differ?

Ans Biochemistry is the study of the chemical transformations occurring in living systems that are controlled by enzymes and regulatory mechanisms. Molecular biology, the study of the genome and its expression in a living system, is concerned with the formation, structure and function of the nucleic acids DNA and RNA. 65) Humans synthesize most of the cholesterol required for cell membranes and for the synthesis of vitamin D and steroid hormones. What would you expect to happen if a person’s diet is high in cholesterol. Provide a reason for your response.

Ans The capacity of healthy bodies to adapt to high-cholesterol diets by inhibiting cholesterol synthesis is an example of the means by which living organisms regulate their metabolic processes.

66) DNA structure must be stable because it acts as an organism’s repository of genetic information. However, it is equally important that DNA is not completely stable. Explain.

Ans If DNA were completely stable no variation in the organism would take place and evolution would be impossible. Species would not have the possibility to adapt to environmental changes, a circumstance that would inevitably lead to extinction.

67) Describe the significance of the phrase “robust yet fragile”.

Ans Complex control mechanisms and protective systems allow living organisms to withstand various physical and/or chemical challenges, e.g. multiple fail-safe mechanisms exist that protect against fluctuations in temperature, availability of nutrients, and energy needs. As such, living organisms are robust, yet they are fragile in their vulnerability to unusual or rare events that cause irreparable damage. For example, a bleeding cut will clot and heal, but exposure to high levels of carbon monoxide can cause death.

68) Comment on the statement that carbon is not the most abundant element in the body by weight.

Ans While carbon containing compounds are essential for life, the body is largely composed of water. As a result, oxygen is the most abundant element in the body.

69) Why do anabolic processes consume energy and catabolic processes release energy?

Ans Anabolic processes involve the formation of new carbon-carbon bonds, which is an endothermic process that requires an external source of energy. Catabolic processes involve bond cleavage, in which bond energy is released and in some cases captured so as to drive anabolic reactions.

70) Comment on the statement that a species whose organisms are composed of exceptionally robust systems will most likely become extinct.

Ans Adaptation to new environmental conditions requires the capacity to change existing systems. If a robust system is resistant to change, as the environment changes the species cannot adapt and will eventually become extinct.

71) When insulin binds to the insulin receptor, information is exchanged. Explain.

Ans Insulin is released when glucose concentrations in the blood have increased. The binding of the insulin molecule to its receptor, made possible by the complementary three-dimensional structures of insulin and its receptor, triggers a signal transduction process that allows the target cell to remove glucose from the blood stream and alters the expression of insulin-sensitive genes.

CHAPTER TWO LIVING CELLS 1) During exocytosis membrane-bound vesicles migrate from the Golgi apparatus to the __________.

A) Lysosome B) Smooth endoplasmic reticulum C) Cell wall D) Plasma membrane E) More than one answer is correct Ans D 2) Notable features of eukaryotes include all of the following except ________.

A) Rapid cell division B) Larger size C) A complex internal structure D) An endomembrane system E) Organelles Ans A 3) Gram-negative bacteria lack _________.

A) Cell walls B) Peptidoglycans in the cell wall C) An outer coat of lipid bound proteins D) DNA E) Carbohydrate containing polymers in the cell wall Ans E 4) The plasma membrane _________.

A) Provides support B) Is present only in eukaryotes C) Controls the flow of substances in and out of the cell D) Is present only in prokaryotes E) Both A and C are correct Ans E 5) Structural features that make phospholipids suited for their biological role are:

A) A hydrophilic head group B) Branched carbon chains C) A hydrophobic group D) A and C are correct E) None of the above is true Ans D 6) The grainy appearance of prokaryotic cytoplasm is due in part to ________.

A) A large number of ribosomes B) Plasmids C) Nucleolus D) DNA E) RNA Ans A 7) Which of the following types of molecules is not hydrophilic A) Sodium chloride B) Glucose C) Amino acids D) Fats E) Both A and B are correct.

Ans D 8) The basic structure of biological membranes is provided by what class of compounds?

A) Proteins B) Lipids C) Carbohydrates D) Steroids E) Peptidoglycans Ans B 9) Which of the following is not true of the nucleus?

A) It is found in both eukaryotes and prokaryotes B) It contains the cell’s “genetic blueprint” C) It exerts a profound influence over all cellular metabolic functions D) It contains chromatin fibers E) It is bounded by membrane

Ans A 10) Which of the following statements is not true of the endoplasmic reticulum?

A) It often constitutes more than half of the cell’s total membrane B) It exists in two forms: rough and smooth C) Rough ER is responsible for protein synthesis D) Smooth ER is responsible for lipid synthesis E) Rough ER ribosomes are responsible for biotransformation.

Ans E 11) Which of the following is not true of eukaryotic ribosomes?

A) They are macromolecular machines B) They function in the biosynthesis of proteins C) They contain ribosomal RNA D) They consist of two unequally sized subunits E) They are attached to the smooth ER Ans E 12) Which of the following statements is not true of the Golgi apparatus?

A) The analogous plant structure is referred to as a dictyosome B) It has two faces C) The cisterna or forming face usually projects toward the ER D) It is involved in the packaging and secretion of cell products E) It is usually located near the plasma membrane Ans E 13) Which of the following statements is not true of the lysosome?

A) It functions in intercellular digestion B) Both ER and Golgi apparatus are involved in its formation C) It is capable of degrading most biomolecules D) It is involved in the packaging and secretion of cell products E) It is involved in pathological conditions such as gout and rheumatoid arthritis Ans D 14) Acid hydrolases are found in ___________.

A) Ribosomes B) Lysosomes C) Golgi Apparatus D) Dictyosomes E) Smooth ER Ans B 15) The main role of peroxisomes is _____________.

A) Anaerobic respiration B) Aerobic respiration C) Lipid oxidation D) Generation and destruction of peroxides E) Carbohydrate oxidation Ans D 16) Biological machines are derived from which class of compounds A) Fats B) Proteins C) Carbohydrates D) Ribosomes E) B and C Ans B 17) Which of the following organelles is involved in aerobic metabolism?

A) Mitochondria B) Peroxisomes C) Glyoxysomes D) Ribosomes E) Lysosomes Ans A 18) Respiratory assemblies are responsible for the synthesis of ___________.

A) ATP

B) NADH C) GTP D) Hydrogen peroxide E) ADP Ans A 19) The two membranes of the mitochondria create two separate compartments called the intermembrane space and the __________.

A) Cristae B) Matrix C) Lumen D) Cisternae E) Vesicle Ans B 20) Which of the following statements is not true of the mitochondrial matrix?

A) It contains enzymes responsible for nucleotide metabolism B) It contains circular DNA molecules C) It contains all of the necessary compounds for protein synthesis D) It has a gel-like consistency E) It has a high concentration of enzymes and ions Ans A

21) The excluded volume of a cell varies between _____ and ______%.

A) 5–10 B) 10–20 C) 20–40 D) 40–50 E) 0–5 Ans C 22) Plastids are plant structures similar to what organelle found in animals?

A) Ribosomes B) Leucoplasts C) Golgi apparatus

D) Peroxisomes E) None of the above is correct Ans E 23) The stroma of plastids is analogous to what structure of mitochondria?

A) Grana B) Matrix C) Inner membrane D) Outer membrane E) Cisternal space Ans B 24) Which of the following help make up the cytoskeleton?

A) Microtubules B) Microfilaments C) Intermediate fibers D) B and C are correct E) All are correct Ans E 25) Mitochondria and _________ consume molecular oxygen.

A) Plastids B) Ribosomes C) Peroxisomes D) Lysosome E) Golgi apparatus Ans C 26) Which of the following is present only in prokaryotic cells?

A) Nucleus B) Endoplasmic reticulum C) Plasma membrane D) Nucleolus E) None of the above is correct

Ans E 27) Biotransformation is defined as: A) The preparation of water-insoluble substances for excretion B) Oxidation of organic molecules C) Transformation of food molecules to ATP D) Reactions occurring within a living system E) Conversion of harmless compounds to toxins Ans A 28) In place of a nucleus a prokaryotic cell has a __________.

A) Mesosome B) Nucleoid C) Centrosome D) Nucleosome E) Reticulosome Ans B 29) Which of the following eukaryotic organelles is a key regulator of apoptosis?

A) Mitochondria B) Flagella C) Chloroplasts D) Cilia E) Ribosomes Ans A 30) Which of the following is not a role of transmembrane proteins?

A) Transport of ions B) Structural support C) Transport of nutrients D) Receptors E) Enzymes Ans B

31) Which of the following is not a membrane protein?

A) Channel protein B) Carrier protein C) Receptors D) Integral proteins E) Motor proteins Ans E 32) Examples of eukaryotic signal molecules are: A) Neurotransmitters B) Hormones C) Cytokines D) Both A and B are correct E) All of the above are correct Ans E 33) Which of the following is not a phase of the information processing mechanism?

A) Reception B) Transduction C) Response D) Transformation E) Both A and C are correct Ans D 34) Which of the following is not a component of the endomembrane system?

A) Plasma membrane B) Endoplasmic reticulum C) Golgi apparatus D) Lysosomes E) Ribosomes Ans E 35) The carbohydrate coat of a cell is called the:

A) Extracellular matrix B) Glycocalyx C) Cell cortex D) Fibroblast E) Both A and C are correct Ans B 36) The perinuclear space is: A) The space between the nucleus and the cytoplasm B) The space between the membranes of the nuclear envelope C) The space between the nucleus and the nucleous D) The space between DNA and histones E) Both A and B are correct Ans B 37) Which of the following organelles are involved in autophagy?

A) Mitochondria B) Lysosomes C) Chloroplasts D) Golgi apparatus E) Both B and C are correct Ans B 38) Which of the following molecules is not an example of a type of eukaryotic signal molecule?

A) Neurotransmitter B) Hormone C) Cytokinin D) Endotoxin E) Both A and B are correct Ans D 39 Of the approximately100 trillion cells in the human body how many are actually human cells?

A) All of them B) 50 Trillion C) 90 Trillion D) 10 Trillion E) 80 Trillion Ans D 40) Analysis of the RNA of prokaryotes reveals that there are ______ distinct types of prokaryotes.

A) One B) Two C) Three D) Four E) Five Ans B 41) Which of the following are microbiota A) Bacteria B) Fungi C) Archea D) A and B E) A, B and C Ans E 42) Which of the following are techniques used by the body to protect itself against indigenous microbiota A) Impenetrable epithelial tissue B) Immune system cells C) Antimicrobial proteins D) Beta defensins E) All of the above Ans E

43) Which of the following is a superorganism A) Streptococcus B) Lactobacillus C) Homo sapiens D) Corynebacterium E) Klebsiella Ans C 44) The endocytic cycle is A) A means of remodeling plasma membrane B) A form a signal transduction C) Cycling of sodium and potassium ions through the cell membrane D) Continuous recycling of membrane through endocytosis and exocytosis E) A and D Ans A

SHORT ANSWER 46) Define the term organelle?

Ans An organelle is large subcellular compartment in a eukaryotic cell that is specialized for a specific task.

47) Define the term eukaryotes.

Ans Eukaryotes are composed of cells that have a nucleus and other membrane-bound compartments.

48) What is an integral protein?

Ans An integral protein is a protein that is embedded within a membrane.

49) What is a peripheral protein?

Ans A peripheral protein is a protein that is not embedded within a membrane but is attached by covalent or noncovalent bonds to a membrane protein or lipid.

50) What is a ligand?

Ans A ligand is a molecule that binds to a protein or receptor.

51) What is the function of a motor protein?

Ans Motor proteins are nucleotide binding components of protein complexes that

function as biological machines. Nucleotide hydrolysis drives precise changes in the conformation of the biological machine that permit the accomplishment of the machines task.

52) What is meant by the term macromolecular crowding?

Ans Macromolecular crowding refers to the large number of different proteins at low concentrations within the interior of cells.

53) What is an endotoxin?

Ans An endotoxin is a toxic molecule that is released from membrane-bound lipids when a pathogenic Gram-positive bacterial cell disintegrates.

54) Define the term hormone.

Ans A hormone is a signaling molecule produced by glandular cells that influences the behavior of distant target cells.

55) What is the slime layer?

Ans The slime layer, also known as biofilm, is a disorganized accumulation of polysaccharides that form when bacteria adhere to surfaces.

56) Explain why the term “crowded” rather than “concentrated” is used to describe the densely packed molecules on the interior of living cells?

Ans Macromolecules of each type usually are present in low numbers. The concentration of any one macromolecule is low but adds to the overall number of molecules. This results in crowding.

57) Describe how noncovalent interactions promote the self-assembly of supramolecular structures in living organisms.

Ans Intricately shaped functional groups on the surface of biomolecules, form noncovalent interactions with biomolecules with complementary structures. These interactions facilitate the formation of supramolecular structures that have properties that are similar (e.g., hydrogen bonding) or complementary (e.g., oppositely charged ions). As these noncovalent interactions form, more of the molecules’ surfaces are drawn closer to each other, making further interactions possible. Large numbers of noncovalent interactions stabilize the complexes formed from these molecules.

58) How do lysosomes participate in the life of the cell?

Ans In their roles in endocytosis (destruction of biomolecules) and autophagy (worn out cell components) lysosomes digest biomolecules of all types. In addition, lysosomes destroy the components of foreign cells and other exogenous extracellular materials.

59) What functions does the cytoskeleton perform in living cells?

Ans The highly developed framework of the cytoskeleton performs the following functions in eukaryotic cells: (1) maintenance of overall cell shape, (2) facilitation of coherent cellular movement, (3) provision of a supporting structure that guides the movement of organelles within the cell, and (4) service as a platform for enzyme and signal cascade complexes.

60) What roles do plasma membrane proteins play in living cells?

Ans Among the roles of plasma membrane proteins are transport, response to stimuli, cell-cell contact, and catalytic functions.

61) What are two essential functions of the nucleus?

Ans The nucleus is the repository of the cell’s hereditary information. The nucleus also exerts a profound influence over all of the cell’s metabolic activities through the expression of that information.

62) Describe the functions of the Golgi apparatus.

Ans The Golgi apparatus processes, sorts, and packages protein and lipid molecules for distribution to other regions of the cell or for export.

63) List three environmental signals detected by primary cilia.

Ans Examples of environmental signals detected by primary cilia include urine flow, wound healing, and sight.

64) Describe the function of kinesins and dyneins in intraflagellar transport.

Ans The kinesins are motor proteins that move particles along the outer pair of

micotubules of cilia and flagella toward the cell periphery. Dyneins move molecules along microtubules in the opposite direction.

ESSAY QUESTIONS 65) Humans have been described as superorganisms consisting of human cells in combination with a larger number of microorganisms. Explain. Is this a symbiotic relationship? What effect can the consumption of antibiotics have on this relationship?

Ans It would appear to be obvious that a human consists of only human cells. It should be recognized, however, that human cells are thousands of times larger than the smaller prokaryotic organisms that cohabit the body. The human body is in a symbiotic relationship with most of its nonhuman inhabitants because it provides a stable source of warmth, moisture and nutrients. In turn, some of these microorganisms defend against invading pathogens, and perform special services such as aiding food digestion and providing us with essential nutrients. The importance of symbiotic organisms can be seen in the effect of mistreatment with antibiotics that disrupts the normal intestinal flora, allowing the overgrowth of pathogenic bacteria normally kept in check by beneficial organisms.

66) Biological membranes are held together by weak noncovalent forces. Why is it important that weak forces hold membranes together? What would happen if membrane structure involved stronger covalent bonding?

Ans Although individual bonds are weak, large numbers of such interactions provide considerable stability. The greater strength of covalent bonds would prevent the most essential feature of biological membranes, the capacity of membrane components to move within the membrane. For example, membrane proteins must be able to diffuse through the membrane to perform their functions.

67) What effect does macromolecular crowding have on the traditional analysis of reaction rates?

Ans The interior of cells was once thought to have a soup-like consistency thereby justifying the belief that reactant and product diffusion is a factor that influences reaction rates. It has since been learned that the cell is actually a thick gel in which reactant diffusion has little effect on reaction rates. Instead, the enzymes in several biochemical pathways have been found to exist in structures where they are arranged so that a reaction product is released into the active site of the enzyme catalyzing the next reaction.

68) Eukaryotic cells are much larger cells than prokaryotic cells. What factors of internal structure make this increase in size possible?

Ans Eukaryotic cells are larger than prokaryotes because their increased structural complexity makes possible better use of raw materials and disposal of waste, and allows an efficient integration of metabolism that sustains the cell. In addition, eukaryotic cells possess numerous mitochondria, which provide the large amounts of energy required for maintaining such a high level of complexity.

69) Comment on the statement that the cytoplasm is just a soup containing organelles.

Ans The “soup” model was the original view of a cell in which reactions are diffusion controlled with many water-soluble molecules randomly moving through the cytoplasm until they reach their target sites. A more careful examination of the interior of a cell shows that cytoplasm is actually a semisolid gel in which there is very little free diffusion.

70) The interior of living cells is highly organized and this organization is maintained over long periods of time. Entropy, a measure of the disorder or randomness of the system, predicts that highly organized systems should become progressively disorganized. How does a living cell evade entropy?

Ans Entropy is a spontaneous process. In the absence of energy and nutrients a cell would indeed become progressively disorganized (i.e. it would die). Entropy can be evaded (at least locally) by the input of energy. The cell uses the energy derived from the oxidation of nutrient molecules to reverse the spontaneous effects of entropy. It is only when this energy generation breaks down that disorder increases and the cell dies.

71) The surface of the eukaryotic cell is coated with carbohydrate groups attached to protein and lipid molecules. What structural feature of the carbohydrate molecule accounts for this phenomenon?

Ans Carbohydrate molecules, which can be composed of an almost infinite variety of arrangements of several different sugars, allows the encoding of a vast amount of information. As a result, the cell surface contains a large number of molecules (e.g., glycoproteins and glycolipids) whose complex structure allow them to perform a diverse array of functions. For example, hormone receptor proteins bind only to a specific hormone and not other molecules.

72) Mitochondria are one of many types of organelles. What features of mitochondria argue most strongly for their descent from a free living ancestor?

Ans Numerous features of mitochondria resemble those of prokaryotic cells. Examples include their size, shape, and capacity to undergo binary fission. Mitochondria also possess circular DNA molecules and perform protein synthesis with components that resemble their prokaryotic counterparts.

73) In eukaryotes the DNA remains within the nucleus and RNA, synthesized within the nucleus, is used to transfer information to the rest of the cell. Why use RNA for this purpose and why not just use DNA directly?

Ans DNA, the master template of the cell’s genetic information, resides within the nucleus where its is protected from damage such as cleavage by nucleases. If RNA molecules are damaged or destroyed new copies can be made quickly by transcription from DNA. 74) In density gradient centrifugation the products are removed from the bottom of the centrifuge tube. Why not remove them from the top of the tube?

Ans If the layers in a centrifuge tube were withdrawn from the top of the centrifuge tube, there would be unavoidable mixing, thereby destroying the integrity of the sample. By draining slowly from the bottom through a small hole this problem is avoided.

CALCULATIONS 75) The dimensions of a prokaryotic ribosome are approximately 14 nm x 20 nm. If ribosomes occupy 20% of the volume of a bacterial cell calculate how many ribosomes are in a typical cell such as E. coli. Assume that the shape of a ribosome is approximately that of a cylinder. A typical bacterial cell volume is 1.6 um3.

Ans The volume of a ribosome is calculated as follows: r2h = (3.14)(0.007 m)2(0.02 m) = 3  10–6 m3 The volume of a bacterial cell is 1.6 m3. The number of ribosomes that can fit in a bacterial cell is 1.6/3  10-6 = 5  105, because they occupy only 20% of the cell’s volume, divide 5 x 105 ribosomes in a cell by 5 to give 1  105 ribosomes per bacterial cell.

76) The E. coli cell is 2 m long and 1 m in diameter, while a typical eukaryotic cell is 20 m in diameter. Assuming that the E. coli cell is a perfect cylinder and the eukaryotic cell is a perfect sphere, calculate the surface-to-volume ratio for each cell type [cylinder volume V = r2h; cylinder area A = 2r2 + 2rh; sphere volume V = 4/3(r3); sphere area 4r2].What do these numbers tell you about the evolutionary changes that would have to occur to generate an efficient eukaryotic cell considering that most biochemical processes depend on membrane-bound processes.

Ans The volume of the E. coli cell is given by V = rh = (3.14)(0.5 m)2(2 m) =

1.57 m3.

The surface area is: A = 2r2 + 2rh = (2)(3.14)(0.5 m)2 + (2)(3.14)(0.5 m)(2 m) = 1.57 m2 + 6.28 m2 = 7.85 m2.

The E. coli surface-to-volume ratio = 7.85 m2/1.57 m3 = 5.0 m-1.

The volume of the eukaryotic cell is V = (4/3)(3.14)(10)3 = 4189 m3.

The surface area of the eukaryotic cell is 4r2 = 4(3.14)(10)2 = 1256 m2.

The eukaryotic cell surface-to-volume ratio = 1256 m2/4189 m3 = 3.0 m-1.

The eukaryotic cell has a much smaller surface-to-volume ratio than does the E. coli. In order to import enough material to sustain the functions of the cell, the membrane must become more efficient. Eukaryotes have significantly greater membrane transport capacity because of membrane transport proteins that are more sophisticated and present in exceptionally large numbers and extensive membrane folding, which increases the surface-to-volume ratio. Note that the loss of the prokaryote cell wall allowed membrane folding.

CHAPTER THREE WATER: THE MATRIX OF LIFE 1) How many hydrogen bonds can water form?

A) One B) Two C) Three D) Four E) Five Ans D 2) A hydrogen bond is best defined as: A) A strong chemical bond between hydrogen and another element B) A weak chemical bond between hydrogen and another element C) A relatively strong electrostatic bond between hydrogen and oxygen or nitrogen D) A weak electrostatic bond between hydrogen and oxygen or nitrogen E) A bond between two hydrogens Ans C 3) Which of the following compounds are capable of hydrogen bonding with like molecules?

A) CH3CH2CH2CH2CH3 B) CH3CH2OCH2CH3 C) CH3NH2 D) HOCH2CH2OH E) Both C and D are correct Ans E 4) Which of the following is not a type of van der Waals force?

A) Dipole-dipole interactions B) Dipole-induced dipole interactions C) Induced dipole – induced dipole interactions D) Chemical bonds E) Hydrogen bonds Ans D 5) Which of the following is not an example of noncovalent interactions between molecules?

A) Salt bridges B) Hydrogen bonds C) Hydrophobic interactions D) Ionic bonds E) Chemical bonds Ans E 6) Which of the following factors is responsible for the fact that water is a liquid at room temperature?

A) Covalent O-H bonds B) Ionic bonds C) Hydrogen bonds D) Hydrophobic bonding between water molecules E) The molecular weight of water Ans C 7) Which of the following properties of water promotes the relatively constant climate of earth?

A) High heat of fusion B) High surface tension C) High heat of vaporization D) High heat capacity E) A, C, and D are all important Ans E 8) Which of the following compounds is amphipathic?

A) H2O B) CH3CH2CH2CH2CH3 C) HOOCCOOH D) CH3CH2CH2CH2COOH E) Both A and D are correct Ans D 9) Which of the following is a hydronium ion?

A) H3O+ B) OHC) HOOH D) CH3OH2+ E) H4O++ Ans A 10) Which of the following is the conjugate acid of the bicarbonate ion?

A)

B)

C)

D)

E)

Ans B

11) Which of the following statements is true of weak acids dissolved in water?

A) They are completely ionized in water B) They are totally unionized in water C) They are partially ionized in water D) The dissociation constant is a function of pH E) The dissociation constant is a function of solute concentration Ans C 12) What is the pH of a solution where the concentration of hydrogen ions is 2 x 10-5 molar?

A) 5 B) 2.5 C) 2 D) 4.7 E) 5.3 Ans D 13) Which of the following would not form a suitable buffer?

A) Acetic acid/ acetate B) Carbonic acid/ bicarbonate C) Bicarbonate/ carbonate D) Hydrochloric acid/ chloride E) Phosphoric acid/ dihydrogen phosphate Ans D 14) Buffering capacity is directly proportional to which of the following factors?

A) Molecular weight of the buffer B) Concentration of the conjugate acid of the buffer C) Concentration of the conjugate base of the buffer D) Concentration of both components of the buffer E) The acid or base to be buffered against Ans D

15) The sodium acetate/acetic acid buffer is 0.1 molar in sodium acetate and 0.5 molar in acetic acid. What is the concentration of the buffer?

A) 0.1 molar B) 0.5 molar C) 0.6 molar D) 0.4 molar E) Either A or B depending on whether acid or base is being added to the buffer.

Ans C 16) The pH of a solution that is 0.25 molar in acetic acid and 0.1 molar in sodium acetate is 4.36. What is the pKa of acetic acid?

A) 4.36 B) 4.76 C) 7.76 D) 3.76 E) 5.76 Ans B 17) The most important buffer in blood is __________.

A) Carbonate/bicarbonate buffer B) Protein buffer C) Phosphate buffer D) Lactate buffer E) Tartrate buffer Ans A 18) When an individual breathes very rapidly, large amounts of carbon dioxide are exhaled. What effect does this have on blood pH? A) Acidosis B) Alkalosis C) No change D) First acidosis then rebounding alkalosis E) First alkalosis then rebounding acidosos Ans B

19) Salt bridges in proteins are an example of _________.

A) Hydrogen bonds B) Ionic interactions C) Hydrophobic interactions D) van der Waals forces E) London dispersion forces Ans B 20) What is the osmolarity of a solution that is 0.25 molar in trisodium phosphate?

A) 0.25 osmolar B) 0.5 osmolar C) 0.75 osmolar D) 1.0 osmolar E) None of the above is correct Ans D 21) Red blood cells are isotonic to a solution that is 0.9% sodium chloride. These same cells are _______________ to a solution that is 0.9% sodium sulfate.

A) Isotonic B) Hypertonic C) Hypotonic D) Tonic E) Nontonic Ans C 22) Which of the following molecules would have a dipole moment?

A) CCl4 B) CH3CH3 C) H2 D) CHCl3 E) I2 Ans D

23) Which of the following molecules would form a micelle?

A) NaCl B) CH3COOH C) CH3CH2CH2CH2CH2CH3 D) H3PO4 E) CH3(CH2)10COO- Na + Ans E 24) Which of the following molecules are weak acids?

A) HCl B) CO3-2 C) HNO3 D) HCO3E) Both B and D Ans D 25) Which of the following ions would have the largest hydration sphere?

A) Li+ B) Na+ C) K+ D) Cs+ E) All would have the same size hydration sphere Ans A 26) Hydration is best defined as A) Covalent interaction between water and a solute B) Noncovalent interaction between water and a solute C) Salt formation in water D) Ionization of a base to produce hydroxide ions E) Both C and D are correct Ans B 27) The noncovalent interaction between an amide and an alcohol would be which of the following?

A) Salt bridges B) Hydrophobic C) Hydrogen bonding D) Both A and C are correct E) All of the above are true Ans C 28) Crenation would result when cells are placed in a ___________ solution.

A) Hypertonic B) Hypotonic C) Isotonic D) Nontonic E) Nonaqueous solvent Ans A 29) Which of the following is not an important noncovalent interaction of living organisms?

A) Ionic interactions B) Van der Waals interactions C) Hydrogen bonds D) Carbon hydrogen bonds E) All are important Ans D 30) Which of the following molecules would have unusually high heat capacities?

A) Ammonia B) Methane C) Methyl alcohol D) Benzene E) Both A and C are correct Ans E 31) The hybridization of the water molecule is: A) Sp3 B) Sp2 C) Sp

D) Unhybridized E) Planar Ans A 32) Which of the following is the strongest type of non-covalent force?

A) Dipole-Dipole B) Dipole-Induced Dipole C) Induced Dipole–Induced Dipole D) London dispersion forces E) Hydrogen bond Ans E 33) Which of the following ions would have the strongest tendency to form an ion pair with carboxylate groups on the surface of a protein?

A) Lithium B) Sodium C) Potassium D) All have the same tendency E) These ions do not associate with proteins Ans C 34) Which of the following species would form a buffer with HPO4-2?

A) H3PO4 B) H2PO4-1 C) CO3-2 D) All would form buffers with HPO4-2 E) Both A and B Ans B 35) Water can form how many hydrogen bonds?

A) One B) Two C) Three D) Four E) Five

Ans D 36) Which of the following solutions will be isotonic with 3M sucrose?

A) 3M NaCl B) 1 M Sodium sulfate C) 1.5 M Proline D) 2 M Sodium chloride E) 1 M Magnesium sulfate Ans B 37) Which of the following molecules is hydrophobic?

A) Sodium chloride B) Ethyl alcohol C) Hexane D) Sucrose E) Ammonia Ans C 38) In biological systems buffers usually contain an excess of __________.

A) Weak base B) Weak acid C) The two components of the buffer are present in equal amounts D) It would depend on the system E) None of the above is correct Ans A 39) The tendency of nonpolar molecules to aggregate in a water medium is called ________.

A) Crenation B) Hydrophobic effect C) Hydrophillic effect D) Micellular effect E) Amphiatic

Ans B 40) The high heat of fusion of water is due to its _______________.

A) Hydrogen bonding B) High surface tension C) High heat of vaporization D) High heat capacity E) A, C, and D are all important Ans A 41) Which of the following is not a role of water in the body A) Nutrient absorption B) Nutrient transport C) Waste product excretion D) Temperature regulation E) All are roles of water Ans E 42) Which of the following species can form a buffer system?

A) Hydrochloric acid / Acetic acid B) Acetic acid / Sodium chloride C) Acetic acid / Ammonium chloride D) Acetic acid/ Sodium acetate E) Phosphoric acid / Sodium phosphate Ans D 43) Which of the following are unusual properties of water that suit it to be the matrix of life?

A) Tetrahedral hybridization B) Presence of oxygen C) Thermal properties D) Solvent characteristics E) C and D Ans E

44) What percentage of the world’s water is drinkable A) 100% B) 60% C) 3% D) 1% E) 97% Ans C 45) The immediate effect of deforestation is A) Drought B) Erosion C) Formation of grasslands D) Formation of deserts E) Increase in the water table Ans B 46) Which of the following is not an effect of hydrogen bonding on the physical properties of water?

A) Increased boiling point B) Increased heat of fusion C) Increased melting point D) Increased heat of vaporization E) All are effects of hydrogen bonding Ans E SHORT ANSWER 47) What is a salt bridge?

Ans A salt bridge forms as a result of the attraction between positively and negatively charged amino acid side chains.

48) Describe an isotonic solution.

Ans. An isotonic solution is a solution that contains the same concentration of solute and water on both sides of a selectively permeable membrane.

49) Define the term hydrophobic effect.

Ans The hydrophobic effect is a phenomenon in which nonpolar molecules are attracted to each other by van der Waals forces and are unable to hydrogen bond with water, resulting in a water cage surrounding the nonpolar molecules.

50) Define the term alkalosis.

Ans Alkalosis is a condition that arises when the human blood pH rises above 7.45.

51) How many hydrogen bonds can methanol form with water?

Ans

Three hydrogen bonds form between the OH group of

methanol and surrounding water molecules.

52) Bicarbonate is the principle buffer of the blood and phosphate is the principle buffer within cells. Explain.

Ans Carbon dioxide is present in the blood in sufficient quantities to make the bicarbonate buffer effective as a buffer. Phosphate concentration in blood is too low for this compound to be an effective buffer. Within cells the phosphate concentration is relatively higher and can therefore be an effective buffer.

53) What is the effect of hyperventilation on blood pH?

Ans Hyperventillation drives the transfer of carbon dioxide from the blood. This process, which shifts the following equilibrium to the left, consumes protons, thereby making the blood more alkaline.

CO2 + H2O → H2CO3 → HCO3- + H+ 54) Is it possible to prepare a buffer consisting of only carbonic acid and sodium carbonate?

Ans No. The carbonic acid and carbonate react to produce bicarbonate. It is possible to have either a buffer system of carbonic acid and bicarbonate or a buffer of bicarbonate and carbonate.

55) Many molecules are polar but they do not form significant hydrogen bonds. What is unusual about water that hydrogen bonding becomes possible?

Ans The extreme electronegativity of the oxygen polarizes the O-H bond of water and makes the hydrogen atom electron deficient. Because the unshared pairs of electrons on the oxygen are available for bonding, an electrostatic interaction with hydrogen occurs.

56) If the total concentration of a buffer is known (and not the individual concentrations of the weak acid and its conjugate base) can the pH of the buffer be calculated?

Ans No. Calculation of the pH of a buffer requires knowing the pKa of the buffer and the concentration of the weak acid and the conjugate base.

57) What is the maximum number of hydrogen bonds that water can form?

Ans Water can form a total of four hydrogen bonds.

58) Describe how you would increase the buffering capacity of a 0.1 M acetate buffer.

Ans The buffering capacity of a system is increased by raising the concentrations of both buffer components but not changing their ratio ([A-]/[HA]). Increasing the concentration of the weak acid for example, would increase the buffer capacity for added base, but would lower the buffer capacity for added acid.

59) What is a micelle? How do micelles form?

Ans A micelle is an aggregation of amphipathic molecules, with a polar and a nonpolar components. Micelles form when these molecules are mixed with water with the polar surface exposed to water and the nonpolar components internalized.

60) What is the hydronium ion?

Ans A hydronium ion (H3O+) forms when a proton combines with a water molecule.

61) Pure sugars are often crystalline solids. Frequently, the process used to concentrate aqueous solutions of sugars produces syrups rather than crystals. Explain.

Ans The syrup is actually a mixture of the sugar and small amounts of water that remain tightly held by hydrogen bonds to the OH groups of the sugars. Such tightly held water molecules prevent the direct hydrogen bonding between –OH groups in the sugar molecules required for crystallization.

62) Water forms stronger hydrogen bonds than ammonia. Suggest a reason for this.

Ans Oxygen is a smaller molecule than nitrogen. As a result, the hydrogens of the water molecule can approach the oxygen in other water molecules more closely to form stronger bonds. Oxygen is also more electronegative than nitrogen, resulting in an O-H bond being more polar than an N-H bond.

63) Water has been described as the universal solvent. If this was strictly true could life have arisen in this medium? Explain Ans The structure of living cells is based on the phase separation of hydrophobic and hydrophilic substances. The function of cell membrane is possible only because lipids are insoluble in water. If water dissolved every molecule, living organisms would not be able to create a barrier between themselves and their surroundings and living organisms would not be possible.

64) Why can’t seawater be used to water plants?

Ans The salts dissolved in the seawater (a hypertonic solution) pull water out of plants and will cause them to die. This is the reverse of the normal flow of water from the environment into the plant.

65) The pH scale is valid only for water. Explain.

Ans The pH scale is derived using the ionization constant of water. To establish the pH scale for another solvent, the ionization constant of that solvent would have to be used.

The resulting pH scale for the solvent would be different from the pH scale for water.

ESSAY QUESTIONS 66) Compounds such as the sugar trehalose are used as compatible solutes (i.e., water replacements) in desiccated organisms. What are the requirements for a substance that is to be used in this manner?

Ans For a substance to be used as a compatible solute it must have solvent properties (polarity, ability to hydrogen bond) that are similar to those of water. In addition it must be nontoxic even at high concentrations and provide freezing point depression and

osmoprotection. Finally and it must interact with structured water in a way that stabilizes the three-dimensional structures of the cell membrane and proteins.

67) When salt is spread on Jello (a mixture of gelatin and water), its consistency changes from a solid into a liquid. Explain.

Ans The sodium and chloride ions form stronger hydration spheres with water molecules than they do with gelatin. As a result Jello, a colloid, breaks down to form a solution of salt, water, and gelatin molecules.

68) Explain why water has an unusually high heat capacity.

Ans Heat capacity, the energy required to raise the temperature of one gram of a material one degree centigrade, is high for water because of this molecule’s extensive hydrogen bonding. Raising water’s temperature involves breaking a very large number of hydrogen bonds. As a result, more energy is required than for other molecules with similar molecular mass.

69) Give an example of a molecule without an OH group that would be expected to have an unusually high heat capacity.

Ans Molecules with high heat capacity must be capable of hydrogen bonding. The best candidate for this would be ammonia (NH3).

70) Ammonia and water are both capable of forming hydrogen bonds. Why is water better at forming these bonds than ammonia?

Ans The oxygen in water is more electronegative than the nitrogen in ammonia so it will tend to attract the electrons of the nearby hydrogens more strongly. Oxygen also has two unshared pairs of electrons available for hydrogen bonding. Ammonia has only one pair of electrons and so, therefore, cannot form as many hydrogen bonds.

71) What is the major ionic structure for tyrosine at pH 7?

Tyrosine NH2 pKa = 9.11

COOH pKa 2.2

OH pKa = 10.07

Ans Since the carboxyl group of tyrosine has a pka value of 2.2, it will be unprotonated at pH 7. With a pKa of 9.11 the amino group will be protonated at ph 7.

Tyrosine at pH = 7

72) In water fatty acids form a micelle with the COO- groups on the surface. The hydrophobic hydrocarbon tails are directed to the interior of the micelle. Explain.

Ans The carboxylate anion of the fatty acid forms hydrogen bonds with the surrounding water molecules. The hydrophobic hydrocarbon tails exclude water, thereby moving into the water-free interior of the micelle.

73) Explain why soaps that form micelles lower the surface tension of the water.

Ans Surface tension is a measure of the force required to penetrate the surface of a liquid.

The water molecules are not only interacting with themselves with relatively strong hydrogen bonds, but also with the outer polar groups of the micelle molecules. The micelle-water interactions are not as strong as the water–water interactions and the surface tension becomes weaker.

74) If the osmotic pressure of a concentrated solution of sodium chloride is measured it is less than the calculated value. As the concentration of the sodium chloride is reduced the value of the osmotic pressure becomes closer and closer to the calculated value. Explain.

Ans Osmotic pressure is dependent on the number of particles in a solution. At high concentrations some of the sodium and chloride ions associate with each other thereby reducing the number of particles and lowering the observed osmotic pressure. As the concentration of sodium chloride is reduced, the degree of this association decreases and observed osmotic pressures value approaches that of the calculated value.

75) Glucose is stored in cells as glycogen, an insoluble polymer. Hormone- triggered hydrolysis of glycogen produces glucose on demand. What advantages does this method of storage have for the cell?

Ans As an insoluble macromolecule glycogen does not affect the osmotic pressure of the cell. An equivalent amount of free glucose would cause the cell to burst from the influx of water. Glycogen can be easily converted to glucose on demand at a rate slow enough for the cell to adapt to any osmotic pressure changes.

76) When plants are exposed to seawater they wilt and die. Explain.

Ans Exposure to the high salt concentration of seawater causes water to flow down its concentration gradient out of the plants cells, causing them to shrink, a process called crenation.

CALCULATIONS 77) What is the osmolarity of a 1.3 M solution of sodium phosphate (Na3PO4)? Assume 85% ionization for this solution.

Ans Osmolarity is equal to the molarity multiplied by the extent of ionization (the number of ions produced per ionic compound). Na3PO4 dissociates into four ions.

Assuming 85% ionization, the osmolarity of the solution therefore is (1.3)(4)(0.85) = 4.4 osmolar.

78) What is the hydrogen ion concentration in a solution at pH 8.3?

Ans pH = -log [H+] 8.3 = - log [H+] [H+] = 10-8.3 = 5.0 X 10 -9 M 79) A solution that is 0.1M in acetic acid and 0.1 M in sodium acetate has a pH of 4.76.

Determine the pKa of acetic acid. What is the Ka for acetic acid?

Ans pH = pKa + log [acetate]/[acetic acid] 4.76 = pKa + log [0.1]/[0.1] 4.76 = pKa + log 1 4.76 = pKa

pKa = log Ka taking the antilog of both sides 4.76 = Ka 0.0000173 = Ka 1.73 x10-5 = Ka 80) Calculate the ratio of dihydrogen phosphate to hydrogen phosphate in blood at a pH 7.4. The Ka is 6.3 x10-8.

Ans Ka = 6.3 × 10−8, therefore, pKa = 7.2 pH = pKa + log[A−]/[HA] (where A− = conjugate base of the weak acid HA) 7.4 = 7.2 + log[A−]/[HA] log[A−]/[HA] = 7.4 − 7.2 = 0.2 [A−]/[HA] = 1.58:1 or 1.6:1

81) What would be the pH of 1L of water if 1 ml of 1M HCl is added?

Ans When 1 mL of 1 M HCl is added to 1 L of water the new [H+] becomes: (0.001 L) (1M H+) = 0.001 mol H+ (0.001 mol H+)/(1.001L total) = 9.99 x10-4M H+ pH = -log [H+] = - log (9.99x10-4 M H+)

pH = 3 82) Sketch the titration curve of the amino acid tyrosine starting with the following structure:

The pKa values are as follows: amino group 9.11, carboxyl group = 2.2 and side chain hydroxyl group = 10.07.

Ans The titration curve for tyrosine is as follows:

CHAPTER FOUR ENERGY 1) The course of chemical reactions is determined by three factors. These are enthalpy, entropy, and A) Heat of reaction B) Free energy C) States of matter D) Bond energy E) Both A and B are correct Ans B 2) Which of the following statements is true of an open system?

A) There is an exchange of energy only with the surroundings B) There is an exchange of matter only with the surroundings C) There is an exchange of both matter and energy with the surroundings D) In an open system either matter or energy, but not both may be exchanged with the surroundings E) Energy flows only into the system: matter flows out of the system Ans C 3) Which of the following statements is true of a closed system?

A) There is an exchange of energy only with the surroundings B) There is an exchange of matter only with the surroundings C) There is an exchange of both matter and energy with the surroundings D) In a closed system either matter or energy, but not both may be exchanged with the surroundings E) Energy flows only into the system: matter flows out of the system Ans A 4) Which of the following thermodynamic properties is a state function?

A) Work B) Heat C) Enthalpy D) Entropy E) Both C and D are correct Ans E

5) The first law of thermodynamics is described by which of the following equations?

A) E = Q+W B) Q = E-W C) W = Q-W D) Both B and C are correct E) All of the above are correct Ans A 6) Which of the following statements is not true of a spontaneous process?

A) The enthalpy value is negative B) The entropy value is negative C) The free energy value is positive D) The work value is negative E) The enthalpy value is positive Ans C 7) Which of the following is not a standard condition for standard free energy?

A) 25 0C B) 1 Atm. pressure C) Concentration of reactants = 1 molar D) Concentration of products = 1 molar E) pH = 7 Ans E 8) The ionization constant of acetic acid is 1x10-5. What is Go for the reaction?

A) –6500 cal/mol B) 3250 cal/mol C) 6500 cal/mol D) 6000 cal/mol E) 1624 cal/mol Ans C

9) Under standard conditions is the ionization of a carboxylic acid spontaneous or not? A typical carboxylic acid has a pKa of 4.

A) It is spontaneous B) It is not spontaneous C) Not enough information is provided Ans B 10) In order for two reactions to be coupled what conditions must be met?

A) They must both be spontaneous B) One of the reactions must be spontaneous C) A product of one of the reactions must be a reactant in the second reaction D) They both must have ATP as a reactant E) Both B and C must be true Ans E 11) When water and hydrophobic molecules are mixed all of the following are true except: A) The hydrophobic molecules aggregate B) The free energy of dissolving molecules is unfavorable C) -TS becomes negative D) Water’s hydrogen-bonded interactions are disrupted E) All of the above are true Ans E 12) The oxidation of food molecules to form CO2 and H2O is a (n) _______ process.

A) Exergonic B) Endergonic C) Isothermic D) Lithotropic E) Spontaneous Ans A 13) The most important direct source of the energy that drives reactions in the body is: A) ATP B) ADP

C) GTP D) Glucose E) Fatty acids Ans A 14) The law of the conservation of energy states that A) The total energy of the universe is constant B) Entropy of a system increases C) There are three laws of thermodynamics D) The work that can be performed by a system is a constant E) The energy of a system’s surroundings is constant Ans A 15) Which of the following is a low quality energy source A) Electromagnetic radiation B) Heat C) Electrical Energy D) Chemical Energy E) B and C Ans B 16) Which of the following statements regarding free energy changes is true?

A) At equilibrium G0 = O B) For the reaction to be spontaneous Go must be positive C) Free energy is a state function D) Both A and C are true E) All of the above are true Ans D 17) Which of the following compounds would liberate the most free energy on hydrolysis?

A) ATP B) Phosphoenolpyruvate C) PPi D) ADP E) GTP

Ans B 18) Which of the following thermodynamic properties is the most useful criterion of spontaneity?

A) Entropy B) Free energy C) Standard free energy D) Enthalpy E) Change in temperature Ans B 19) For a reaction to be spontaneous which of the following statements must be true? ) Suniv= O ) Suniv = positive C) Siniv = negative D) A or B E) Entropy has no effect on the spontaneity of a process Ans B 20) Which of the following processes are driven by the hydrolysis of ATP? A) Biosynthesis of biomolecules B) Active transport of substances across membranes C) Mechanical work such as muscle contraction D) Both A and B are correct E) All of the above are correct Ans E 21) The study of reaction rates is called ___________.

A) Reactions B) Thermodynamics C) Kinetics D) Mechanics E) Entropics

Ans C 22) Which of the following is described by the first law of thermodynamics?

A) EnthalpY B) Entropy C) Free energy D)A and B E) A, B and Ans A 23) Which of the following is described by the second law of thermodynamics?

A) Enthalpy B) Entropy C) Free energy D) A and B E) A, B, and C Ans B 24) What type of bond is being cleaved during the conversion of ATP to ADP? A) Ester B) Ether C) Hydrogen D) Anhydride E) Amide Ans D 25) The tendency of ATP to undergo hydrolysis is called __________.

A) Free energy of hydrolysis B) Cleavage rate C) Phosphoryl group transfer potential D) High energy bond potential E) None of the above is correct Ans A

26) The products of the hydrolysis of ATP are more stable than ATP itself. This circumstance is due to __________.

A) pH effects B) Relief of charge-charge repulsions C) Resonance stabilization of the products D) Relief of steric strain E) Both B and C are correct Ans E 27) A living organism is what type of thermodynamic system?

A) Closed B) Open C) A system at equilibrium D) A system with negative entropy E) Both C and D are correct Ans B 28) Which of the following thermodynamic properties is pathway dependent?

A) Free energy B) Entropy C) Enthalpy D) Work E) Both B and C are correct Ans D 29) A Kelvin is _________.

A) A unit of temperature measurement B) A unit of entropy measurement C) A measurement of the density of a system D) An index of the spontaneity of a reaction E) A unit of heat Ans A

30) The rate of a reaction can be determined from which of the following?

A) Free energy B) Enthalpy C) Entropy D) All of the above are correct E) None of the above is correct Ans E 31) To maintain a system far from equilibrium a constant input of _______ is required.

A) Entropy B) Energy C) Only systems at equilibrium are stable D) Disorganized energy E) Both A and B are correct Ans B 32) Systems far from equilibrium are referred to as _________ systems.

A) Spontaneous B) Dissipative C) Critical D) Entropic E) Heterotropic Ans B 33) An organism at equilibrium is said to be __________.

A) At rest B) Dissipative C) Organized D) Dead E) Dormant Ans D 34) The following statement is made by which law of thermodynamics?

“At absolute zero the disorder of a perfect crystal approaches zero”.

A) First Law B) Second Law C) Third Law D) A and B E) All make this statement Ans C 35) A measure of a system’s internal energy is A) Enthalpy B) Entropy C)Free energy D) Work E) Heat Ans A 36) In living organisms where does the increase in entropy takes place?

A) Cell B) Surroundings C) Either A or B D) Entropy does not change E) Entropy does not apply to living things Ans B 37) How many molecules of oxygen are required to completely oxidize one mole of stearic acid, (C17H35COOH)?

A) 18 B) 9 C) 34 D) 45 E) 53 Ans E

38) Given the following H values, calculate the H for the complete combustion of stearic acid. H (Kcal/mol.)

Compound

-211.4

C17H35COO

0

Oxygen

-94

Carbon dioxide

-68.4

Water

A) –49 Kcal B) –2096.2 Kcal C) –2711.8 Kcal D) 0 Kcal E) 3071.8 Kcal Ans C 39) Magnesium ion (Mg++) forms complexes with ATP. What would happen to the stability of ATP if the magnesium was removed?

A) There would be no change in stability B) The ATP would be more stable C) The ATP would be less stable D) The effect on stability would depend on specific conditions E) Either A or B is correct Ans C 40) Choose the molecule with the highest phosphate transfer potential.

A) Phosphoenolpyruvate B) ATP C) PPi D) Glucose-1-phosphate E)Carbamoyl phosphate Ans A

41) Biogeochemical cycles are pathways driven by which of the following?

A) Nuclear B) Solar C) Geothermal energy D) Tectonic movements E) B and C Ans E 42) Which of the following moves through a system in a biogeochemical cycle?

A) Chemical compounds B) Heat C) Light D)Energy E) All of the above Ans E 43) In classical thermodynamics which of the following is true?

A) All systems are at or near equilibrium B) All materials are at low concentration C) The system is far from equilibrium D) The systems are always open E) A and B Ans E 44) A Benard cell is an example of: A) A classical thermodynamic system B) A system at equilibrium C) A dissipative system D) A system at uniform temperature E) B and C Ans C 45) The evolution of living organisms is driven by: A) Size of the energy gradient to be dissipated

B) First law of thermodynamics C) Second law of thermodynamics D) Attainment of equilibrium E) A and C Ans E 46) A process is spontaneous when ) G0 = 0 ) G0 > 0 C)G0 < 0 D) Energy is absorbed E) Entropy is negative Ans C SHORT ANSWER 47) Explain why entropy is a state function.

Ans A state function must be independent of path. This is true of entropy.

48) What is a chemolithotrophe?

Ans Chemolithotrophs are heterotrophs that generate ATP by oxidizing inorganic compounds.

49) Define the thermodynamic term work. Provide two physiological examples of work.

Ans Work is defined as a change in energy that produces a physical change.

Physiological examples include biomolecule synthesis, active transport across membranes and muscle contraction.

50) At what temperature is G0’ = H for all conditions?

Ans G0’ = H when T = 0 K 51) In some biochemical processes a reaction will not occur by itself unless its product is a reactant in a more favorable reaction. What principle is involved in this phenomenon?

Ans A reaction with an unfavorable free energy value (+G) can be pulled to completion if it is coupled to a reaction with a sufficiently negative free energy value, that is if the product of the reaction is the reactant in a reaction with a favorable free energy value and the sum of the two free energy values is negative.

52) Describe why ATP, the molecule that serves as the energy currency for the body, has an intermediate phosphoryl group transfer potential.

Ans ATP has an intermediate phosphoryl group transfer potential because it can accept a phosphate group from compounds that have a higher phosphoryl group transfer potential and transfer it to lower energy compounds.

53) Magnesium ion (Mg++) forms complexes with the negative charges of the phosphate in ATP. In the absence of Mg++ would ATP have more, less or the same stability as when the ion is present?

Ans In the absence of Mg2+ increased repulsion between adjacent negative charges of ATP would cause it to have less stability than ATP associated with Mg2+.

54) What factor makes the hydrolysis of AMP less energetic than the hydrolysis of ATP or ADP? Ans AMP hydrolysis involves cleavage of an ester bond and therefore releases the least energy. Hydrolysis of the two other phosphoryl linkages involves the hydrolysis of an anhydride.

55) The law of the conservation of energy is an alternate statement of which law of thermodynamics?

Ans It is an alternate statement of the first law.

56) Frequently when salts dissolve in water, the solution becomes warm. Such a process is exothermic. When other salts, such as ammonium chloride, dissolve in water, the solution becomes cold, indicating an endothermic process. Because endothermic processes are generally not spontaneous, why does ammonium chloride dissolve in water?

Ans In the case of endothermic solutions, the enthalpy may be negative but the entropy is sufficiently positive to make the overall G relationship favorable to dissolving in water.

57) What is a biogeochemical cycle?

Ans A biogeochemical cycle is a pathway driven by solar and geothermal energy in which a chemical element moves through Earth’s biotic and abiotic compartments.

58) Define the term thermodynamics.

Ans Thermodynamics is the study of heat and energy transformations.

59) Why is free energy a better measure of the spontaneity of a reaction than any of the three laws?

Ans Free energy takes into consideration both entropy and enthalpy.

60) Reactions that occur only if there is sufficient energy available to the system are said to be __________________.

Ans Kinetically favorable.

61) What conditions are necessary for two reactions to be coupled?

Ans In order for two reactions to be coupled they must have a common intermediate.

62) What two processes are involved in the exchange of energy between a system and its surroundings?

Ans The two processes are heat and work.

63) What happens when the energy flow in a living organism reaches equilibrium?

Ans The organism dies.

64) What is meant by the term endergonic reaction?

Ans An endergonic reaction is a chemical reaction that absorbs energy (i.e. it has a positive free energy change).

65) What is an isothermic process?

Ans In an isothermic process, there is no heat exchanged with the surroundings.

66) What are the energy currency molecules in cells?

Ans ATP, NADH, NADPH, and FADH2 have the necessary reducing power (i.e. the ability to donate high-energy electrons in cellular redox processes) to be cellular energy currency molecules.

67) What two categories of reactions provide the energy to drive metabolic processes?

Ans Phosphorylation reactions and redox (oxidation/reduction) reactions provide cellular energy necessary to drive metabolic processes.

ESSAY QUESTIONS 68) In order for the carbon cycle to function there must also be a silica cycle. Explain.

Ans Silicates such as calcium silicate react with carbon dioxide to produce calcium carbonate and silicon dioxide. As the calcium carbonate and silicon dioxide are cycled into the crust the high temperature of the interior produces calcium silicate and carbon dioxide. The carbon dioxide is then vented via volcanoes to the surface.

69) All of the energy captured by living organisms is stored as redox energy. Explain in reference to photosynthesis and cell respiration.

Ans Light energy captured by photosynthesizing organisms results in the formation of new carbon-carbon and carbon-hydrogen bonds from carbon dioxide and water, and the waste product oxygen. During this process valence changes occur in carbon and oxygen.

Release of the bond energy of biomolecules in a valence change process called cell respiration involves the breaking of carbon-carbon and carbon-hydrogen bonds yielding carbon dioxide and water.

70) The total energy of an isolated system is constant. Explain.

Ans If the system is isolated nothing can move in or out and the total energy must remain unchanged.

71) The first law of thermodynamics states that H = E + PV + VP . In living systems PV and VP are negligible. Explain.

Ans In living systems significant changes in volume and pressure do not occur to any appreciable extent. Consequently, the values of the V and P terms approach zero.

72) According to the first law of thermodynamics, it is theoretically possible for CO2 and H2O to spontaneously react to form a hydrocarbon. Explain why this process is not observed.

Ans The hydrocarbon-forming reaction also requires the input of a large amount of energy. Since this excess energy is not available at room temperature and standard pressure, the reaction does not occur. However, when the right conditions are present, hydrocarbons can be formed. For example, carbon-hydrogen bonds are formed during photosynthesis.

73) In a living cell S is always positive, whereas in a dead cell S is zero. Explain.

Ans In a living system a constant input of energy ensures that order is constantly being maintained by exporting entropy to the surroundings (S> 0). In a dead system the living processes are at equilibrium and there is no flow of energy, hence S = 0.

74) Of the three thermodynamic quantities H, G and S which provides the most useful criterion of spontaneity in a reaction. Explain.

Ans ΔG is the most useful criterion of spontaneity because it reflects the change in entropy, which must increase for a reaction to be spontaneous.

75) In chemical reactions it is possible to have conditions where E or H = 0. Is it ever possible to have a condition where S = 0?

Ans No. During a reaction, the entropy of the universe always increases.

76) Phosphoenolpyruvate has a very high free energy of hydrolysis but only one phosphate group. Why does it have such a high free energy value?

Ans The hydrolysis of phosphoenolpyruvate is really two reactions. The first reaction is the release of the phosphate group from the enol form of a pyruvate molecule that does not have a very large free energy value. The second reaction, the conversion of the enol form of pyruvate into its stable keto form, has a high measured free energy change that is the sum of both of these reactions.

77) What are the first and second laws of thermodynamics and what are their defining equations?

Ans The first law of thermodynamics concerns the conservation of energy, where energy cannot be created or destroyed. Energy can be transformed from one form to another. E = q+w Where E = the change in energy of the system q = the heat absorbed or released by the system w = the work done by or to the system The second law of thermodynamics concerns the spontaneity of reactions where spontaneous reactions occur in the direction that increase the total disorder of the universe. Suniv = S surr + S sys Where S is entropy in the universe (univ), surroundings (surr) and system (sys).

CALCULATIONS

78) The Ka for the ionization of formic acid is 1.8 X 10-4. Calculate Go for this reaction. ns Go = RTlnKeq G0 = -(8.315J/molK)(298K)ln(1.8x10-4) G0 = 8.315(298K)(-8.62)J/mol G0 = + 21.266J/mol or+ 21.3 kJ/mol 79) The equilibrium constant for the ionization of acetic acid is 1.8X10-5. Calculate Go for this reaction.

Ans Given that the ionization constant for acetic acid is 1.8x10-5, the G0 for the reaction would be calculated as follows: G0 = -RTlnKeq G0 =-(8.315J/molK)(298K)(ln1.8x10-5) = -27.071 or - 27.1 kJ/mol 80) Consider the following reaction Glucose-1-phosphate → Glucose-6-phosphate Go’ = -7.1 kJ/mol What is the equilibrium constant for this reaction at 25 oC Ans G0’ + -RTlnKeq

-7,100 J/mol = - (8.315J/molK)(298K)(lnKeq) lnKeq =2.865 Keq = 17.56

81) Pyruvate oxidation to form carbon dioxide and water liberates energy at the rate of 1142.2 kJ/mol. If pyruvate is oxidized by cell respiration approximately 12.5 ATP molecules per mole are produced. The free energy of hydrolysis of ATP is -30.5 kJ/mol.

What is the apparent efficiency of ATP production?

Ans The energy generated by the hydrolysis of 12.5 ATP is (12.5mol)(-30.5 kJ/mol) = 381.3 kJ The energy required to produce 12.5 mol of ATP is 1142.2 kJ. The apparent efficiency of the process is (381.3/1142.2) x 100 = 33.4%

82) Given the following data, calculate Keq for the denaturation reaction of -lactoglobin at 25oC. H0 = -88 kJ/mol

S0 = - 0.3 kJ/mol

T = 298 K

ns G0 = H0 –TS0 G0 = (-88kJ/mol)-(298K)(0.3kJ/molK)

=(-88-89.4)kJ/molK = -177.4kJ/mol G0 =-RTlnKeq = (-177.4kJ/mol)(1000J/kJ) = 8.315J/molK)(298K)lnKeq 76.1 = lnKeq and Keq = 1.2x1031 The Keq value indicates that the denaturation of the protein is virtually irreversible.

CHAPTER FIVE AMINO ACIDS, PEPTIDES, AND PROTEINS 1) Which of the following is a function of proteins?

A) Defense B) Metabolic regulation C) Transport D) Catalysis E) All of the above are correct Ans E 2) The term protein refers to amino acid polymers with greater than ________amino acids.

A) 10 B) 20 C) 50 D) 70 E) 90 Ans C 3) Which of the following is a nonstandard amino acid?

A) Glycine B) Cysteine C) 5-Hydroxyproline D) Valine E) Alanine Ans C 4) Which of the following is a heterocyclic amino acid?

A) Alanine B) Valine C) Proline D) Tyrosine E) Cystine Ans C 5) Which of the following is not a class of amino acid?

A) Nonpolar and neutral B) Polar and neutral C) Acidic D) Basic E) Asymmetric Ans E 6) Which of the following amino acids lacks a center of asymmetry?

A) Alanine B) Glycine C) Valine D) Isoleucine E) Aspartic acid Ans B 7) Given the following pK’s what is the principal form of serine at pH 5? pKa1 = 2.21 A)

B)

C)

D)

E)

pKa2 = 9.15

pKR = 13

Ans E 8) Given the following pKa’s, the isoelectric point of serine is ________. pK1 = 2.21 pK2 = 9.15 pKR = 13 A) 2.21 B) 5.68 C) 9.15 D) 6.62 E)11.36 Ans B 9) Consider the following dipeptide. Which letter indicates an amide bond?

A) A B) B C) C D) D E) E Ans C

10) The amino acid sequence of a polypeptide is referred to as ________structure.

A) Primary B) Secondary C) Tertiary

D) Quaternary E) Peptide Ans A 11) The overall three-dimensional structure of a polypeptide is referred to as _________ structure.

A) Primary B) Secondary C) Tertiary D) Quaternary E) Peptide Ans C 12) Invariant amino acids in a protein are presumed: A) To be unimportant in the structure and function of the protein B) To be essential to the structure and function of the protein C) Always to occur at the beginning of the amino acid sequence of an enzyme D) Always to occur at the end of the amino acid sequence of an enzyme E) To be part of the prosthetic group Ans B 13) -pleated sheets are associated with what level of protein structure?

A) Primary B) Secondary C) Tertiary D) Quaternary E) Superquaternary Ans B 14) Which of the following amino acids would foster an -helix?

A) Glycine B) Alanine C) Proline D) Tyrosine E) Serine

Ans B 15) The Greek key is associated with which of the following?

A) -helix B) Parallel -pleated sheets C) Antiparallel -pleated sheets D) Disulfide bridges E) Salt bridges Ans C 16) Which of the following interactions does not stabilize tertiary structure?

A) Hydrophobic interactions B) Electrostatic interactions C) Hydrogen bonds D) Covalent bonds E) None of the above Ans E 17) Detergents denature proteins by disrupting which of the following?

A) Hydrogen bonds B) Disulfide bridges C) Hydrophobic interactions D) Salt bridges E) Both A and B are correct Ans C 18) Fibrous proteins typically have large amounts of: A) -Helix B) -Pleated sheets C) Disulfide bridges D) Salt bridges E) Both A and B are correct Ans E

19) The identity and arrangement of amino acids on the surface of a globular protein are important because they may: A) Interact to form specific binding cavities B) Stabilize the tertiary structure of the protein C) Bind regulatory molecules D) Both A and C are correct E) All of the above are correct Ans E 20) Which of the following statements regarding cooperative binding is true?

A) Two or more proteins aid the binding of a ligand.

B) The binding of one ligand aids the binding of a second ligand C) The folding of part of a protein aids in the folding of the remainder of the protein D) All proteins engage in cooperative binding E) The binding of a cofactor to a protein aids in the binding of a ligand.

Ans B 21) Which of the following statements is true of the Bohr effect?

A) Oxygen is delivered to cells in proportion to their needs B) Binding of protons to hemoglobin molecules facilitates the binding of oxygen C) Metabolic waste products bond to oxyhemoglobin D) A and B are both true E) All of the above are true Ans A 22) A polypeptide has a high pI value. Which of the following amino acids are likely to be present?

A) Glycine B) Serine C) Valine D) Aspartic acid E) Arginine Ans E

23) Structural proteins “freeze” large amounts of water. Which of the following interactions is not likely to be involved in the binding of water?

A) Salt bridges B) Hydrogen bonding C) Hydrophilic interactions D) Disulfide bridges E) Both C and D are correct Ans D 24) Why is the peptide bond stronger than the ester bond?

A) Greater electronegativity of nitrogen B) Greater electronegativity of oxygen C) Resonance stabilization of the amide bond D) Increased basicity of nitrogen E) Size of the nitrogen atom compared to the oxygen atom Ans C 25) Which of the following amino acids would be classified as a nonstandard amino acid?

A)Tyrosine B)Lysine C)Cystine D)Glycine E)Arginine Ans C 26) Given that pK1 = 2.35 and pK2 = 9.69 for alanine. What is its isoelectric point?

A) 9.69 B) 2.34 C) 6.02 D) 12.03 E) 7.00 Ans C 27) When not at the terminal of a protein, which of the following amino acids cannot contribute to the pI of a protein?

A) Arginine B) Lysine C) Cysteine D) Tyrosine E) Alanine Ans E 28) When part of a polypeptide chain, other than the N-terminus, which of the following amino acids can form an aldimine?

A)Glycine B)Alanine C)Proline D)Histidine E)Lysine Ans E 29) Collagen is classified as which of the following types of protein?

A) Enzyme B) Structural C) Movement D) Defense E) Regulatory Ans B 30) A prosthetic group is a: A) Repair enzyme B) Group other than an amino acid that is part of a protein C) Group that generates the native form of a protein D) Disulfide link E) Group that reduces enzyme activity Ans B 31) The major component of the dry weight of cells is _______.

A) Carbohydrate

B) Protein C) Fats D) Minerals E) The major component will vary from organism to organism Ans B 32) The total number of proteins that can be produced from any 10 amino acids is?

A) 1020 B) 2010 C) 100 D) 200 E) 1010 Ans B 33) Schiff bases are also referred to as: A) Aldimines B) Amines C) Carbinolamines D) Amino acids E) Both A and C are correct Ans A 34) Which of the following amino acids would be found in a -turn?

A) Proline B) Alanine C) Phenylalanine D) Lysine E) Tyrosine Ans A 35) Which of the following is not a function of IUPs? A) Signal transduction B) Transcription C) Translation D) Cell proliferation E) Oxygen transport

Ans E 36) The source of energy for motor proteins in addition to ATP is: A) NAD+ B) GTP C) PEP D) ADP E) PPi Ans B 37) Keratin is classified as which of the following types of protein?

A) Enzyme B) Structural C) Movement D) Defense E) Regulatory Ans B 38) In which of the following mechanical properties does spider silk exceed all synthetic fibers?

A) Toughness B) Tensile strength C) Elasticity D) Resilience E) All of the above Ans E 39) Which of the following is a hydrophobic amino acid?

A) Glycine B) Serine C) Lysine D) Phenylalanine E) Both C and D are hydrophobic Ans D

40) A conjugated protein consists of a simple protein combined with a _________.

A) Apoprotein B) Holoprotein C) Prosthetic group D) Answers B and C are correct E) All of the above are correct Ans C 41) Which of the following amino acids is not one of the twenty standard amino acids?

A) Glycine B) Phenylalanine C) Tyrosine D) Cystine E) Arginine Ans D 42) How many standard amino acids are there?

A) 5 B) 17 C) 20 D) 12 E) 32 Ans C 43) How many octapeptides containing only two amino acids are possible?

A) 8 B) 148 C) 16 D) 256 E) 35 Ans D

44) Amino acid polymers with a molecular weight between several thousand and several million Daltons are called A) Dipeptides B) Polypeptides C) Proteins D) Peptides E) None of the above Ans C 45) Which of the following is not a function of proteins?

A) Structural materials B) Catalyst C) Metabolic regulation D) Transport E) All of the above are functions of proteins Ans E 46) Which of the following is a polar amino acid?

A) Phenylalanine B) Tyrosine C) Methionine D) Tryptophan E) Proline Ans B SHORT ANSWER 47) Describe the term protomer.

Ans A protomer is the individual subunit of a multisubunit protein.

48) What is a zwitterion?

Ans A zwitterion is a molecule that possesses both positive and negative charges.

49) Describe the term hormone. Give an example.

Ans A hormone is a chemical signal molecule, produced in one cell that regulates the function of other cells. Many hormones are polypeptides such as insulin.

50) What is a Schiff base? Give an example of a reaction involving a Schiff base.

Ans A Schiff base is the imine product of the reaction between amine and carbonyl groups. Schiff bases are intermediates that form during a transamination reaction.

A Schiff Base 51) What is a moonlighting protein? Give an example.

Ans “Moonlighting” is a term sometimes used to describe multifunction proteins.

Glyceraldehyde-3-phosphate dehydrogenase is an enzyme in glucose metabolism that also functions in processes such as DNA replication and repair and microtubule bundling.

52) Define the term molecular disease.

Ans Molecular diseases result from function-altering mutations in genes that code for proteins such as hemoglobin.

53) List six functions of proteins in the body.

Ans Examples of the major functions of protein in the body include catalysis, structure, movement, defense, regulation, transport, stress response and storage.

54) In what level of protein structure do disulfide bond occur?

Ans Disulfide bonds are a common covalent bond in tertiary structure of proteins.

55) What type of secondary structure would the following amino acid sequence be most likely to have ?

Ala-Val-Ala-Val-Ala-ValAns The secondary structure would be an  helix which can form because alanine and valine have side chains that are not bulky in size or bear a charge.

56) What type of secondary structure would poly-L form? What type of structures would poly-D-alanine form?

Ans Poly L-alanine forms a right handed -helix and poly D-alanine forms a left handed -helix.

57) Why do some proteins require molecular chaperones to fold into their active conformations, while others do not?

Ans The structure and folding difficulties of each protein is different. Simple single domain proteins such as ribonuclease A spontaneously fold without the help of molecular chaperons. More complex multi-domain proteins tend to require assistance.

58) Of the naturally occurring amino acids Gly, Val, Phe, His, and Ser, which would be likely to form coordination compounds with metals when part of a peptide chain?

Ans Glycine, valine, histidine and serine residues would all form weak coordination compounds using their amino nitrogens and carboxylate anions. More significant coordination would be expected with histidine and serine using the side chain nitrogen and oxygen.

59) Which amino acid is the precursor of the following molecule called serotonin?

Ans Serotonin is derived from tryptophan.

60) Which amino acid is the precursor of the following molecule called dopamine.

Ans Dopamine is derived from tyrosine.

61) The peptide bond is a stronger bond than that of esters. What structural feature of the peptide bond gives it additional bond strength?

Ans The peptide bond is stronger than the ester bond for two reasons. The N is closer to the size of C than the O is which makes for greater covalency in the bond. Also, because the O and N differ in electronegativity and both have lone pair(s) of electrons, the amide has resonance hybridization. The amide bond, therefore, has partial double bond character.

62) What would be the products of the acid hydrolysis of the following decapeptide?

Gly-Phe-Tyr-Asn-Tyr-Met-Ser-His-Val-Leu

Ans The products are glycine, phenylalanine, tyrosine, methionine, valine, leucine, serine, histidine and aspartic acid. The asparagine would be changed to aspartic acid by the hydrolysis conditions.

63) A polypeptide has a high pI value. Suggest which amino acids might comprise it.

Ans Amino acids with basic side chains such as lysine, arginine or tyrosine would contribute to a high pI value.

64) Distinguish between proteins, peptides and polypeptides.

Ans A polypeptide is a polymer containing more than 50 amino acid residues. A protein is composed of one or more polypeptide chains. A peptide is a polymer with fewer than 50 amino acids.

ESSAY QUESTIONS 65) Describe the forces involved in protein folding.

Ans The primary driving force in protein folding is the requirement to achieve a low energy state despite the decrease in entropy that occurs as the proteins three-dimensional structure becomes more ordered. Key considerations include the energy associated with different bond angles and bond rotations, the chemical properties of the amino acid side chains (e.g. whether or not the side chain will be charged at the cellular pH), and interactions between side chains. Hydrophobic interactions are particularly important.

Recall that hydrophobic interactions are driven in part by the increase in entropy in the surrounding water molecules.)

66) The amino acid glutamine is not isolated when proteins containing glutamine are hydrolysed in acid or base. Explain.

Ans Glutamine contains a side chain group with an amide bond, which is easily hydrolysed in the presence of acid or base, thereby yielding glutamate.

67) Hydrolysis of proteins containing cysteine often produce considerable amounts of cystine on hydrolysis. Explain.

Ans Air oxidation of the SH group of cysteine to yield the disulfide converts two cysteine molecules to cystine.

68) Which of the standard amino acids would not survive acid hydrolysis?

Ans Serine and threonine would be partially degraded by reaction of the OH group with the acid. The amide group of asparagine and glutamine would hydrolyze to yield a carboxylic acid. Arginine’s uriedo group would also be converted to a carboxylic acid by strong hot acid.

69) Tryptophan is the precursor of serotonin. What chemical reaction must take place to effect this change?

Ans Serotinin is the product of trypthophan decarboxylation.

70) A mutational change alters a polypeptide by substituting three adjacent prolines for three glycines. What possible effect will this event have on the proteins structure?

Ans A glycine residue with its small R group (an H atom) within a peptide molecule increases the molecule’s rotational freedom. A polypeptide with a series of three chainstiffening prolines in the positions ordinarily occupied by three glycine residues would become less flexible, a circumstance that would cause a change in conformation and probably loss of function.

71) Proteins containing L-amino acids form right-handed helices, whereas proteins containing D-amino acids form left-handed helices. Would a racemic mixture (equal amounts of D and L-amino acids) form a helix?

Ans In order to form a helix, a protein must have a constant twist in the same direction composed of helix favoring amino acids. Mixtures of D- and L-amino acids would disrupt any helical structure.

72) Phosphoserine is a modified amino acid. How many inflection points would there be in a titration of this molecule?

Phosphoserine Ans There would be an inflection point for each titratiable acid group, in this case three: one each for the phosphoric acid followed by the carboxylic acid and finally the ammonium ion.

73) Mutations in protein structure are either lethal, inconsequential or beneficial. Explain.

Ans Mutations in the amino acid sequence of proteins have the following effects: Most proteins contain only a few amino acids residues whose presence is absolutely required for biological activity. If a protein in which there is a change in one of these amino acids is important for survival then such a change may have lethal consequences.

Changes in the amino acid residues that perform nonspecific roles in a protein often have no observable effect, i.e. they are inconsequential. In extremely rare circumstances an amino acid residue change may have survival value.

74) Is it possible for a multifunctional protein to improve its activity for one function without affecting the activity of another function?

Ans Improvement of one function may not affect the other if the two active sites involved in the functions are remote enough from each other so that each is unaffected by conformational changes in the other.

75) The initial estimate for protein coding genes in humans was 100,000 instead of the approximately 20,000 genes that have been confirmed. What factors explain this discrepancy?

Ans Several protein products (proteoforms) can result from a single protein-coding gene due to genome-dependent single amino acid polymorphisms, alternative splicing of mRNAs, and posttranslational modifications of proteins.

CALCULATIONS 76) Arginine has the following pKa values pK1 = 2.17 , pK2 = 9.04 pKR = 12.48 Give the net charge at the following pH’s 1, 2, 4, 7, 10 Ans pH = 1, charge = +1 pH = 4, charge = 0 pH = 10, charge = -1 77) Consider the following tripeptide Gly-Ala-Val

pH= 7, charge = 0

Glycine pK1 = 2.34 pK2 = 9.60

Alanine pK1 = 2.34 pK2 = 9.69

Valine pK1 = 2.32 pK2 = 9.62 (a) What is its approximate isoelectric point of this molecule?

Ans The pI is calculated by taking the average of the pK2 of glycine and the pk1 of Valine (2.32 + 9.60)/2 = 5.97 (b) In which direction will the tripeptide move if placed in an electric field at pH 1, 5, 10, and 12 At pH’s below the pI the peptide will move toward the negative pole At pH’s above the pI the peptide will move toward the positive pole.

78) The pKa values for tyrosine are as follows: pK1 2.20 pK2 9.11 pKR 10.07 What is the pI of tyrosine?

Ans pI = (pKa1 + pKa2)/2 = (2.2 + 9.11)/2 = 5.65

CHAPTER NINE AEROBIC METABOLISM I 1) Place the following reaction intermediates of the citric acid cycle in chronological order: i. malate, ii. fumarate, iii. succinyl-CoA, iv. citrate, v. -ketoglutarate.

A), i, ii, iv, v, iii B) iv, v, iii, i, ii C) iv, i, v, iii, ii D) v, iii, i, ii, iv E) iv, v, iii, ii, i Ans E 2) Oxalosuccinate is a transient intermediate formed during which of the following reactions?

A) Citrate → Isocitrate B) Isocitrate → -ketoglutarate C) Pyruvate → Acetyl-CoA D) Malate → Oxaloacetate E) Succinyl CoA→ Succinate Ans B 3) FADH2 is a product of which of the following reactions?

A) Pyruvate → Acetyl CoA B) Malate → Oxaloacetate C) Succinyl-CoA → Succinate D) Succinate → Fumarate E) Succinate → Malate Ans D 4) NADH is produced in which of the following reactions?

A) Malate → Fumarate B) Succinate → Fumarate C) -Ketoglutarate → Succinyl-CoA D) Succinyl-CoA → Fumarate E) Oxaloacetate → Citrate Ans C

5) In the glyoxylate cycle two-carbon molecules are converted to precursors of which of the following?

A) Acetyl-CoA B) Glucose C) Pyruvate D) Succinate E) Carbon dioxide Ans B 6) Which of the following enzymes is unique to the glyoxylate cycle __________?

A) Aconitase B) Malate dehydrogenase C) Fumarase D) Succinate dehydrogenase E) Isocitrate lyase Ans E 7) The regulated enzymes of the citric acid cycle include _________.

A) Malate dehydrogenase B) Fumarase C) Citrate lyase D) -Ketoglutarate dehydrogenase E) Succinate thiokinase Ans D 8) The enzymes involved in citrate metabolism include all of the following except _______.

A) Citrate synthase B) Citrate lyase C) Pyruvate carboxylase D) Malate synthase E) Malic enzyme

Ans D 9) Redox potential is best defined as A) The tendency of one species to gain electrons B) The tendency of one species to lose electrons C) The tendency of a species to gain or lose electrons D) The entropy of a reaction expressed as a voltage difference E) None of the above is correct Ans C 10) In order to determine the standard voltage of a reaction A) The individual reaction reduction potentials must be added B) The standard cells must be written as they occur in the reaction and the voltages are added.

C) All the reactions must be written as oxidations and the voltages are added.

D) The voltages of the individual reactions at pH = 7 must be calculated and the resultant voltages are added.

E) A standard voltage for a reaction must be determined experimentally.

Ans B 11) Which of the following reactions is an oxidation reaction?

A) NaOH +HCl → NaCl + H2O B) CH3COOH → CH3COO- +H+ C) CH3CHO → CH3CH2OH D) CH3CH2OH → CH3CHO +H2O E) CH2=CH2 + H2O → CH3CH2OH Ans D 12) Which of the following reactions has an oxidized product?

A) Carboxylic acid → aldehyde B) R-SH + RSH → R-S-S-R C) Alcohol → Ketone D) Glutamate → -Ketoglutarate E) None of the above are correct Ans E

13) In any redox reaction, an electron donor is A) The reducing agent B) The oxidizing agent C) Reduced as it accepts electrons D) All of the above are correct E) None of the above are correct Ans A 14) In a redox reaction, an electron acceptor is A) Oxidized as it accepts one or more electrons B) The reducing agent C) Converted to an electron donor with the gain of one or more electrons D) All of the above are correct E) None of the above are correct Ans C 15) Each turn of the citric acid cycle produces how many moles of CO2?

A) 1 B) 2 C) 3 D) 4 E) 5 Ans B 16) Acetyl-CoA that is consumed by the citric acid cycle is produced from which of the following biochemical pathways?

A) Glycolysis B) Fatty acid oxidation C) Purine catabolism D) Urea cycle E) Both A and B are correct Ans E

17) Which of the following is the strongest reducing agent? (The standard reduction potential of each species is provided in parentheses.)

A) FADH2 (+0.22V) B) H2 (+0.424V) C) Cytochrome a-Fe+2 (-0.29V) D) Lactate ( + 0.19 V) E) H2O (+0.82V) Ans B 18) Which of the following reacts with Acetyl-CoA to form citrate?

A) Succinate B) Oxaloacetate C) -Ketoglutarate D) Fumarate E) Malate Ans B 19) The redox reaction in which succinate is converted to fumarate uses FAD rather than NAD+ because A) FAD is a stronger oxidizing agent than NAD+ B) NAD+ is a stronger oxidizing agent than FAD C) FAD is required for the oxidation of carboxylic acids D) Only FAD can penetrate into mitochondria E) NAD is not found in the cytoplasm.

Ans A 20) Most of the energy released during the electron transport system is used to drive ______ synthesis.

A) ATP B) ADP C) NADH D) NADPH E) Fatty acids Ans A 21) Which of the following reactions requires GDP A) Fumarate → Malate

B) Succinyl-CoA → Succinate C) Malate → Oxaloacetate D) Citrate → Isocitrate E) -Ketoglutarate → Succinyl-CoA Ans B 22) How many oxidations steps are there in the citric acid cycle?

A) 1 B) 2 C) 3 D) 4 E) 5 Ans D 23) The product of the first reaction of the citric acid cycle is ________.

A) Acetyl-CoA B) Oxaloacetate C) Pyruvate D) Lactate E) Citrate Ans E 24) Which of the following reactions involves a substrate level phosphorylation?

A) Pyruvate → Acetyl-CoA B) Succinyl-CoA → Succinate C) Citrate → Isocitrate D) Fumarate → Malate E) Malate → Oxaloacetate Ans B 25) The carbon skeletons of which of the following are direct precursors of amino acids?

A) Malate B) Succinate C) -Ketoglutarate D) Oxaloacetate

E) Both C and D are correct Ans E 26) Which of the following is not directly required for the activity of pyruvate dehydrogenase?

A) CoASH B) Lipoic acid C) NAD+ D) ATP E) None of the above is correct Ans D 27) Which of the following is a positive effector of isocitrate dehydrogenase?

A) ADP B) FAD C) NADH D) Succinyl–CoA E) Both A and C are correct Ans A 28) Consider the following reaction: Pyruvate + NADH + H+ --→ Lactate + NAD+ The half cell reaction (with their standard reduction potentials) are Pyruvate + 2H+ + 2e- → Lactate (-0.19V) NAD+ + H+ + 2e- → NADH (-0.32V) What is the reduction potential for the overall reaction?

A) + 0.00V B) + 0.03 V C) + 0.13 V D) +0.22 V E) +0.15 V Ans C

29) The overall reaction catalyzed by pyruvate dehydrogenase is which of the following?

A) CH3COCHO + NAD+ + CoASH → CH3CHOSCoA + NADH B) CH3COCOO- + FAD +CoASH → CH3CHSCoA + NADH C) CH3COCOO- + NAD+ + CoASH → CH3COSCoA + NADH D) CH3CH(OH)COO- + NADH + CoASH → CH3CH(OH)COSCoA + NAD+ E) None of the above is correct Ans C 30) The citric acid cycle is a component of aerobic respiration. Molecular oxygen A) Is directly involved in the reactions of the cycle B) Is only indirectly involved in the reactions of the cycle C) Is an important substrate for the cycle D) Both A and C are true E) None of the above are true.

Ans B 31) The main toxic effect of oxygen is due to which of the following?

A) Sulfate formation B) ROS C) Heat production during oxidation D) Protons E) Hydroxide ion Ans B 32) The primordial reductive branch of the citric acid cycle was a means of producing which of the following?

A) ATP B) NADP+ C) NADPH D) NADH E) None of the above is correct Ans E

33) The primordial oxidation branch of the citric acid cycle used which of the following as the ultimate electron acceptor?

A) Pyruvate B) Carbon dioxide C) Oxygen D) Sulfur E) NAD+ Ans D 34) The enzyme, which links the two branches of the citric acid cycle, is which of the following A) -Ketoglutarate dehydrogenase B) Lactate dehydrogenase C) Malate dehydrogenase D) Fumatate reductase E) Fumarase Ans A 35) The glyoxylate cycle is a mechanism whereby plants manufacture carbohydrate from ___________.

A) Other carbohydrates B) Amino acids C) Fatty acids D) Carbon dioxide E) Phospholipids Ans C

36) In biological systems most energy generating redox reactions involve hydride ion transfer or hydrogen atom transfer using which of the following?

A) NADH B) FADH2 C) Pyruvate D) NADPH E) Both A and B are correct

Ans E 37) Which of the following coenzymes function as an acetyl group carrier?

A) Thiamine pyrophosphate B) Lipoic Acid C) NADH D) FADH2 E) Coenzyme A Ans E 38) The first of two molecules of carbon dioxide is released from which of the following compounds in the citric acid cycle?

A) Isocitrate B) Citrate C) -Ketoglutarate D) Succinate E) Fumarate Ans A 39) The high-energy molecule produced in the conversion of succinyl-CoA to succinate is which of the following?

A) ATP B) GTP C) AMP D) NADH E) Both A and B are correct Ans E 40) Which of the following conversions is an anaplerotic reaction of the citric acid cycle?

A) Pyruvate to oxaloacetate B) Certain amino acids to succinyl CoA C) Glutamate to -ketoglutarate D) Aspartate to oxaloacetate E) All of the above are correct Ans E

41) Oxygen is useful for energy generation because A) It is soluble in the cell membrane B) It is abundant C) It is a powerful reducing agent D) It is a powerful oxidizing agent E) A, B and D Ans E 42) The most pivotal event in the history of life on earth was: A) The development of DNA B) The development of RNA C) Emergence of the water splitting complex in Photosystem II D) Development of photosynthesis E) Adaptation to life on land Ans C 43) After the evolution of oxygenic photosynthesis the release of oxygen was not immediately followed by the accumulation of oxygen in the atmosphere. This was true because A) It was incorporated into organic molecules B) It remained dissolved in water C) It was consumed by oxidizable materials such as iron and ammonia D) A and C E) A, B and C Ans C 44) Obligate anaerobes are: A) Organisms that possess antioxidant molecules that detoxify ROS B) Grow only in the absence of oxygen C) Can use oxygen when it is available D) Require oxygen to grow E) Release oxygen Ans B

45) Facultative anaerobes: A) Organisms that possess antioxidant molecules that detoxify ROS B) Grow only in the absence of oxygen C) Can use oxygen when it is available D) Require oxygen to grow E) Release oxygen Ans C 46) In eukaryotes citrate synthetase rate is controlled primarily by: A) Availability of oxaloacetate B) Allosteric regulators C) Concentration of malate D) The NADH/NAD+ ratio E) Succinyl-CoA availability Ans A SHORT ANSWER 47) What is the difference between aerotolerant anaerobes and obligate anaerobes?

Ans An obligate anaerobe grows only in the absence of oxygen, An aerotolerant anaerobe has mechanisms to protect it from oxygen in the environment.

48) Describe two important roles of the citric acid cycle.

Ans The citric acid cycle is an important component of aerobic respiration. The NADH and FADH2 produced during oxidation-reduction reactions of the cycle donate electrons to the mitochondrial ETC. Citric acid cycle intermediates are also used as biosynthetic precursors and as end products of amino acid degradation.

49) Acetyl-CoA is manufactured in the mitochondria and used in the cytoplasm to synthesize fatty acids. However acetyl-CoA cannot penetrate the mitochondrial membrane. How is this problem solved?

Ans When present in excess citrate, produced in the mitochondria by the citric acid cycle, is transported across the mitochondrial membrane into the cytoplasm. Once in the cytoplasm, citrate is cleaved by citrate lyase to acetyl-CoA and oxaloacetate. The acetylCoA is then used to synthesize fatty acids as well as other biomolecules.

50) How does the glyoxylate cycle differ from the citric acid cycle?

Ans The glyoxylate cycle is a modified version of the citric acid cycle in which the two reactions that release carbon dioxide are bypassed. As a result organisms that have the glyoxylate cycle can use two carbon compounds such as acetate and acetyl-CoA to produce glucose via gluconeogenesis.

51) Write the net equation for the citric acid cycle.

Ans The net equation for the citric acid cycle is: Acetyl-CoA + 3NAD+ + FAD + GDP (or ADP) + Pi + 2H2O  2CO2 + 3NADH + FADH2 + CoASH + GTP (or ATP) + 2H+

52) What are the two stages of the citric acid cycle? List the products of each stage.

Ans In the citric acid cycle, stage I, reactions 1-4, two carbon atoms enter the cycle as acetyl-CoA, and two carbon atoms leave the cycle as two molecules of CO2. The products of stage I are: succinyl-CoA, 2NADH, 2CO2, and H+. In stage II, reactions 5-8, oxaloacetate is regenerated from succinyl-CoA. The products of stage II are: Loxaloacetate, CoASH, FADH2, NADH, H+, and either ATP or GTP.

53) Lactic acidosis occurs as a result of shock. Explain why low oxygen levels promote lactate production.

Ans When oxygen levels are reduced products of the citric acid cycle accumulate.

Energy generation is primarily by glycolysis, the end product of which is pyruvate. In order to regenerate the NAD+ required for the reaction pyruvate is reduced to lactate.

54) Describe in detail the structure of the pyruvate dehydrogenase complex.

Ans Pyruvate dehydrogenase complex is a large multienzyme complex that contains three enzyme activities, each of which is present in multiple copies. E1 is pyruvate dehydrogenase (or pyruvate decarboxylase) with TPP, E2 is dihydrolipoyl transacetylase with lipoic acid and CoASH, and E3 is dihydrolipoyl dehydrogenase, with NAD+ and FAD. The pyruvate dehydrogenase complex in mammalian cells contains 60 copies of E2 and 20–30 copies each of E1 and E3.

55) What is an amphibolic pathway? Provide an example.

Ans An amphibolic pathway is a metabolic pathway that functions in both anabolism and catabolism. The citric acid cycle is an example of an amphibolic pathway since it is used to generate energy and metabolic intermediates such as -ketoglutarate and oxaloacetate.

56) Outline the steps of the glyoxylate cycle.

Ans The first two reactions of the glyoxylate cycle, catalyzed by citrate synthase and aconitase, also occur in the citric acid cycle. In the next two reactions isocitrate is split into succinate and glyoxylate. Glyoxylate reacts with acetyl-CoA to form malate. The cycle is completed when malate is converted to oxaloacetate by malate dehydrogenase.

57) List the biochemical processes involved in aerobic metabolism.

Ans Aerobic metabolism consists of the citric acid cycle, the electron transport system and oxidative phosphorylation, 58) What is meant by the term reduction potential?

Ans Redox (reduction potential) is a measure of the tendency of an electron donor in a redox pair to lose an electron.

59) What is an anaplerotic reaction? Give an example.

Ans An anaplerotic reaction is a reaction that replenishes a substrate needed for a biochemical pathway. The conversion of glutamate and aspartate to -ketoglutarate and oxaloacetate, respectively are examples of an anaplerotic reaction.

60) What is a glyoxosome? What is its function?

Ans A glyoxosome is essentially a peroxisome in germinating seed. Glyoxysome enzymes contribute to the conversion of TG reserves to carbohydrate molecules.

61) Define the term reactive oxygen species. Provide examples.

Ans Reactive oxygen species are derivative of molecular oxygen. Examples include superoxide radicals, hydrogen peroxide, the hydroxyl radical, and singlet oxygen.

62) What is the function of nucleoside diphosphate kinase?

Ans Nucleoside diphosphate kinase is an enzyme that catalyzes the reversible transfer of a phosphoryl group between a nucleoside triphosphate and nucleoside diphosphate.

63) Explain why animals cannot produce glucose from two-carbon molecules such as acetate or ethanol.

Ans Unlike organisms that are capable of the glyoxylate pathway, animals cannot use two carbon molecules as precursors in gluconeogenesis. One pathway to gluconeogenesis begins with pyruvate reacting to form oxaloacetate, then phosphoenolpyruvate. Since the decarboxylation of pyruvate for form acetyl-CoA is irreversible, and there is no biosynthetic pathway from acetyl-CoA to pyruvate, glucose cannot be formed from twocarbon molecules such as acetate. In the citric acid cycle oxaloacetate cannot be synthesized solely from acetyl-CoA. When acetyl-CoA enters the citric acid cycle by reacting with oxaloacetate, it adds two carbons to the cycle. If oxaloacetate is used for gluconeogenesis it must be replenished via citric acid cycle intermediates larger than acetyl-CoA or by its synthesis from certain amino acids. The glyoxylate cycle, not present in animals, does allow gluconeogenesis from 2-carbon molecules because it bypasses the citric acid cycle reactions that liberate carbon dioxide.

ESSAY QUESTIONS 64) Dichloroacetate inhibits the enzyme pyruvate dehydrogenase kinase. As a result, this compound has been used with limited success to treat lactic acidosis. Phosphorylation of the -subunit of the pyruvate dehydrogenase component of pyruvate dehydrogenase complex by pyruvate dehydrogenase kinase causes complete loss of enzymatic activity.

Describe the theory behind the clinical use of dichloroacetate.

Ans Inhibition of pyruvate dehydrogenase kinase, an enzyme that contributes to the regulation of pyruvate dehydrogenase, has the effect of increasing the conversion of pyruvate molecules to acetyl-CoA, thereby decreasing lactate levels.

65) A runner needs a tremendous amount of energy during a race. Explain how the use of ATP by contracting muscle affects the citric acid cycle.

Ans Contracting muscle converts large amounts of ATP to ADP. The drop in ATP concentration stimulates two key regulatory enzymes in the citric acid cycle. Isocitrate dehydrogenase, a citric acid cycle enzyme that which converts isocitrate to ketoglutarate, is inhibited by high concentrations of ATP and activated by high concentrations of ADP. A reduced ATP concentration also stimulates the conversion of pyruvate to acetyl-CoA catalyzed by pyruvate dehydrogenase.

66) The citric acid cycle operates only when oxygen is present, yet oxygen is not a substrate for the cycle. Explain.

Ans As a terminal electron acceptor oxygen is required for the function of the electron transport chain (ETC).

O2 + NADH + H+ → H2O + NAD+ Without oxygen, the ETC shuts down, and NADH accumulates at the expense of NAD+.

Both high NADH and low NAD+ levels inhibit the citric acid cycle. Low NAD+ levels would also impact the two key regulatory enzymes the utilize NAD+ as a substrate.

67) Discuss the mechanism of control of the irreversible steps in the citric acid cycle.

Ans The three mechanisms of control of the irreversible reactions of the citric acid cycle are: substrate availability, product inhibition, and competitive feedback inhibition. Citrate synthase is sensitive to availability of substrates oxaloacetate and acetyl-CoA. In many gram-negative bacteria such as E. coli, ATP, NADH, and succinyl-CoA allosterically inhibit citrate synthase. Isocitrate dehydrogenase, which catalyzes the next irreversible reaction is activated by high ADP and NAD+ and inhibited by ATP and NADH. The third irreversible reaction is catalyzed by -ketoglutarate dehydrogenase, which is activated by AMP, and inhibited by products succinyl-CoA and NADH.

68) If a small amount of [1-14C] glucose is added to an aerobic yeast culture, where will the 14C initially appear in the citrate molecules?

Ans If a small amount of [1-14C]glucose is added to an aerobic yeast culture, the radiolabel will appear in citrate molecules at the carboxyl carbon that is attached to citrate’s third carbon atom. In glycolysis, the [1-14C]glucose is split into two molecules of pyruvate, one of which contains the 14C at its carboxyl carbon (C1). If the 14C-labeled pyruvate is converted to acetyl-CoA by pyruvate dehydrogenase, the carboxyl carbon will be released as 14CO2. However, if the pyruvate is carboxylated to form oxaloacetate, the 14

C will be C1 in oxaloacetate. Upon further reaction with acetyl-CoA, the 14C becomes

the carboxyl carbon attached to C3 of citrate.

69) You have just consumed a piece of fruit. Trace the carbon atoms in the glucose in the fruit through the biochemical pathways between their uptake into liver cells and their conversion to carbon dioxide.

Ans After glucose has been absorbed from the intestine, it is transported to the liver, where it is converted to glucose-6-phosphate. Glucose-6-phosphate then enters the glycolytic cycle and is eventually transformed into two molecules of pyruvate. Pyruvate is converted to acetyl-CoA and carbon dioxide. Acetyl-CoA which then enters the citric acid cycle where two more carbon dioxide are released.

70) What is the significance of substrate-level phosphorylation reactions? Which of the reactions of the citric acid cycle involve substrate-level phosphorylations?

Ans In substrate level phosphorylation, a nucleoside diphosphate such as ADP is converted to a nucleoside triphosphate such as ATP by the direct transfer of a phosphoryl group from a high energy compound. The only reaction in the citric acid cycle that involves this type of reaction is the cleavage of succinyl-CoA to form succinate, CoASH, and GTP.

71) One of the many effects of chronic alcohol abuse is thiamine deficiency, caused by impaired absorption of the vitamin through the intestinal wall and diminished storage in a damaged liver. When thiamine levels are inadequate, cellular energy generation is diminished. List three enzymes involved in cellular metabolism that require thiamine.

Describe the metabolic consequences of inadequate thiamine levels.

Ans Three enzymes that require thiamine are pyruvate dehydrogenase, -ketoglutarate dehydrogenase, and transketolase. Thiamine is involved in decarboxylation and acyl group transfer reactions. Absence of decarboxylation reactions would prevent pyruvate from being decarboxylated to form acetyl-CoA. The body would then lack two carbon units for synthesis and energy production. Pyruvate accumulates as lactate. The overall results of thiamine deficiency are lack of energy, muscle wasting and acidosis.

72) Malonate poisons the citric acid cycle because it inhibits succinate dehydrogenase.

After reviewing its structure describe how the inhibitory effect of malonate can be overcome.

Malonic Acid

Ans Malonate is a competitive inhibitor of succinate dehydrogenase because it competes reversibly with succinate for the active site in the enzyme. Increasing the concentration of succinate should reverse the effect of the malonate.

73) Fatty acid degradation stimulates the citric acid cycle through the activation of pyruvate carboxylase by acetyl-CoA. Why would the activation of pyruvate carboxylase increase energy generation from fatty acids?

Ans Carboxylation of pyruvate produces oxaloacetate, a citric acid cycle intermediate.

Increasing the concentration of one of the intermediates stimulates the cycle and more energy is produced.

74) Describe in general terms how the appearance of molecular oxygen in Earth’s atmosphere about 3 billion years ago affected the history of living organisms.

Ans Ancient Earth possessed an atmosphere that contained methane, ammonia and was devoid of oxygen. With the development of photosynthesis, oxygen was released into the atmosphere in ever increasing amounts. Subsequently, this oxygen reacted with methane to form carbon dioxide and with ammonia to form molecular nitrogen. The continued release of oxygen produced an oxidizing atmosphere consisting of primarily oxygen, nitrogen, and carbon dioxide. Some living organisms were able to adapt to an oxygen atmosphere by developing mechanisms for preventing oxygen radical induced damage.

Eventually, certain organisms evolved to use oxygen as an electron acceptor in energy generation. This circumstance made multicellular organisms possible.

75) Which steps in the citric acid cycle are regulated? Why are they regulated?

Ans The steps in the citric acid cycle that are regulated are those catalyzed by citrate synthase, which converts acetyl-CoA and oxaloacetate into citrate; isocitrate dehydrogenase, which converts isocitrate to α-ketoglutarate; and α-ketoglutarate dehydrogenase, which forms succinyl-CoA. These steps represent important metabolic branch points. Citrate synthase is stimulated by substrate availability, and inhibited by its product citrate. Because citrate can penetrate the mitochondrial membrane and be cleaved to form acetyl-CoA and oxaloacetate, it therefore can be used to transport acetyl-CoA out of the mitochondrion for fatty acid synthesis. Citrate also inhibits PFK-1 in glycolysis, and it also activates the first step in fatty acid synthesis. α-Ketoglutarate a molecule that plays an important role in amino acid metabolism and other metabolic processes and is the product of isocitrate dehydrogenase an enzyme that has an important role in

metabolism. When the enzyme is inhibited by ATP and NADH, citrate levels rise, which is followed by its transport into the cytoplasm. The activity of -ketoglutarate dehydrogenase is inhibited by NADH, (high NADH levels are an indication of high energy levels) and succinyl-CoA. CALCULATIONS 76) Calculate the free energy change that occurs in the following reaction 1/2O2 + NADH + H+ →H20 + NAD+

Ans The free energy changes are as follows:

1/2O2 + NADH + H+ → H2O = NAD+ E0 = 0.82V + 0.32V = 1.14V G0 = 2(96485J/molV)(1.14V) =219985 J/mol =220 kJ/mol 77) Determine the standard free energy for the following reaction Cytochrome c (Fe+2) + 1/2O2 → cytochrome c (Fe+3) + H2O Ans Cyt c (Fe2+) + 1/2 O2 → Cyt c (Fe3+) + H2O ΔE0′ = 0.58 V ΔG0′ = (−2)(96,485J/V • mol)(+0.58 V) = −112 kJ/mol

CHAPTER ELEVEN LIPIDS AND MEMBRANES 1) Fatty acid groups are referred to as ________ groups.

A) Acetyl B) Acyl C) Prenyl D) Isoprenoid E) Isopentenyl Ans B 2) The double bonds in naturally occurring fatty acids are usually _______ isomers.

A) Cis B) Trans C) Both cis and trans D) Essential E) Nonessential Ans A 3) The essential fatty acids are A) Arachidonic acid B) Linoleic acid C) Linolenic acid D) Both A and B are correct E) Both B and C are correct Ans E 4) Fatty acids react with alcohols to form _____.

A) Amides B) Ethers C) Anhydrides D) Epoxides E) Esters Ans E 5) Prostaglandins are involved in _________.

A) Ovulation B) Inflammation C) Digestion D) Both A and B are correct E) All of the above are correct Ans D 6) The functions of fat include A) Insulation B) Energy storage C) Water-repellent properties D) Both A and B are correct E) All of the above are correct Ans E 7) Waxes A) Are complex mixtures of nonpolar lipids B) Are esters formed from long-chain fatty acids and long-chain alcohols C) Contain hydrocarbons, sterols, and alcohols D) Both A and B are correct E) Both A and C are correct Ans E 8) Phospholipids are A) Structural components of membranes B) Surface active agents C) Rich energy sources D) Both A and B are correct E) All of the above are correct Ans D 9) Phosphatidylcholine is sometimes referred to as ______.

A) PIP2 B) Cephalin C) Ceramide

D) Cardiolipin E) None of the above is correct Ans E 10) The myelin sheath A) Surrounds nerve cell axons B) Contains large amounts of cardiolipin C) Facilitates nerve impulse transmission D) Both A and B are correct E) Both A and C are correct Ans E 11) All of the following are glycolipids except _________.

A) Sulfatides B) Cerebrosides C) Gangliosides D) Both A and B are correct E) None of the above is correct Ans E 12) The role of very low density lipoproteins is A) Scavenging the cholesterol from cell membranes B) Transporting of lipids from liver to tissues C) Transporting of cholesterol esters to the liver D) Both A and B are correct E) All of the above are correct Ans B 13) Which of the following statements concerning carotenoids is not true?

A) Carotenoids are the only examples of the monoterpenes B) The carotenes are hydrocarbon members of the carotenoids C) Xanthophylls are oxygenated derivatives of the carotenes D) Carotenoids are orange-colored pigments E) None of the above is true Ans A

14) Which of the following molecules is not a lipid?

A) Fatty acids B) Steroids C) Isoprenoids D) Waxes E) All of the above are lipids Ans E 15) The basic structure of biological membranes is a consequence of the physical properties of _______.

A) Proteins B) Phospholipids C) Cholesterol D) Water E) None of the above is correct Ans B 16) A membrane’s fluidity is largely determined by the percentage of A) Phosphatidylcholine B) Phosphatidylethanolamine C) Wax esters D) Cardiolipin E) Unsaturated fatty acids Ans E

17) In the fluid mosaic model of membrane structure A) Proteins form an inner layer between two layers of lipid B) Proteins coat an inner layer of lipids C) Proteins float in a lipid bilayer D) Proteins are covalently bonded to the lipid bilayer E) All of the above are true Ans C

18) Which of the following statements concerning the anion channel protein is not true?

A) It plays an important role in carbon dioxide transport in blood B) It facilitates the chloride shift C) Bicarbonate and chloride exchange occurs through the anion channel protein D) The N-terminal methionine residue of the anion channel protein is prenylated E) All of the above statements are true.

Ans D 19) Energy requiring transport mechanisms include A) Primary active transport B) Diffusion C) Facilitated diffusion D) Both A and B are correct E) Both A and C are correct Ans A 20) In simple diffusion a solute A) Is propelled by random molecular motion B) Moves up its concentration gradient C) Moves across a membrane because of an input of free energy.

D) Both A and B are correct E) All of the above are correct Ans A 21) Which of the following statements is not true?

A) Membrane potential is an electrical gradient across a membrane.

B) A decrease in membrane potential is referred to as membrane depolarization.

C) The term repolarization is defined as the reestablishment of the original membrane potential.

D) The diffusion of potassium ions out of a nerve cell make the inside of the membrane negative.

E) The sodium channel in muscle and nerve cells is a voltage-gated channel.

Ans D 22) In muscle cells, local depolarization caused by acetylcholine binding leads to the opening of the voltage gated _____channels.

A) Chloride B) Potassium C) Proton D) Sodium E) Glucose permease Ans D 23) The function of glucose permease is an example of A) Primary active transport B) Secondary active transport C) Facilitated diffusion D) Simple diffusion E) None of the above is true Ans B 24) -6 Fatty acids A) Have a double bond six carbon atoms from the carbonyl end of the chain B) Have a double bond six carbon atoms from the methyl end of the chain C) Have six double bonds in the molecule D) Have three more double bonds than -3 fatty acids E) Contain six trans double bonds in the molecule Ans B 25) Membrane receptors are transmembrane molecules or membrane molecular complexes that A) Monitor and respond to changes in the cell’s environment.

B) Bind to hormones or neurotransmitters C) Are involved in embryonic and fetal development D) Initiate an intracellular response when they bind an appropriate molecule E) All of the above are correct Ans E 26) Patients with familial hypercholesterolemia A) Possess depressed levels of plasma cholesterol B) Have missing or defective LDL receptors C) Are homozygous or heterozygous for a nonfunctional LDL receptor gene D) Have very high levels of serum cholesterol E) B, C, and D are correct

Ans E 27) Indicate which of the following compounds is an endocannabinoid.

A) Oleic acid B) Arachidonic acid C) Anandamide D) Prostaglandin E) -3 Fatty acids Ans C 28) Low fat diets deficient in essential fatty acids are characterized by which of the following?

A) Poor wound healing B) Alopecia C) Dental caries D Ketone bodies E) Both A and B are correct Ans E 29) Which of the following structural features is not characteristic of TXA2?

A) An ether ring B) One OH group C) Two double bonds D) One double bond E) Is derived from arachidonic acid Ans D 30) Neutral fats belong to which of the following?

A) Phospholipids B) Glycolipids C) Prostaglandins D) Triacylglycerols E) Free fatty acids Ans D

31) In addition to the prostaglandins and leukotrienes the autocrine regulators include: A) Arachidonic acid B) Linoleic acid C) Thromboxanes D) Steroids E) All of the above are correct Ans C 32) Choose the lipid class that acts as surfactants.

A) Triacylglycerols B) Fatty acids C) Waxes D) Phospholipids E) Both A and B are correct Ans D 33) Peripheral membrane proteins are linked to anchor molecules through a ___________ link A) Ether B) Ester C) Amide D) Amino E) Plasma Ans C 34) Glycolipids differ from sphingolipids in that they contain no _________.

A) Carbohydrate B) Phosphate C) Fatty acid D) Choline E) Both B and C are correct Ans B 35) Which of the following is not likely to be a naturally occurring fatty acid?

A) C13H27COOH B) C14H29COOH C) C15H31COOH D) C17H35COOH E) C19H39COOH Ans B 35) How many isoprene units does a diterpene contain?

A) 1 B) 2 C) 3 D) 4 E) 5 Ans D 36) The function of dolichols is to A) Transport sugars in glycoprotein synthesis B) Bind carbohydrate on the cell surface of bacteria C) Bind to oxygenated carotenes D) Serve as precursors of carotenoids E) They are degradation products of steroids Ans A 37) Plasma lipoproteins transport _______ through the blood from one organ to another.

A) Triacylglycerols B) Phospholipids C) Cholesteryl esters D) Both A and C are correct E) All of the above are correct Ans E 38) _________ are the principal transporters of cholesteryl esters to tissues.

A) Chylomicrons B) Very low density lipoprotein C) Intermediate density lipoprotein

D) Low density lipoprotein E) All of the above are true Ans D 39) Individuals with cystic fibrosis have a defective _______ ion channel in their epithelial membrane A) Water B) Chloride C) Potassium D) Protein E) Sodium Ans B 40) A consequence of replacing dietary fat content with sugars is A) No effect on body weight B) An increase in body weight C) A small loss of body weight D) A large decrease in body weight E) An initial loss of weight followed by a large increase in body weight Ans B 41) Which of the following is not a consequence of a low fat diet?

A) Low levels of fat soluble vitamins B) Low levels of essential fatty acids C) Brittle hair D) Poor would healing E) Low blood pressure Ans E 43) Phospholipase B hydrolyzes ______ ester bonds in phospholipids A) C-1 B) C-2 C) C-3 D) Both C-1 and C-2 E) All of the above

Ans D 44) Which of the following is not a function of phospholipases?

A) Membrane remodeling B) Signal transduction C) Energy storage D) Digestion E) Toxicity Ans C 45) Membranes become more rigid when they contain A) Large amounts of glycolipids B) Large amounts of unsaturated fatty acids C) Large amounts of saturated fatty acids D) Large amounts of water E) Both A and B are correct Ans C 46) Flippase transfers _________ from the outer to inner membrane leaflet A) Phospholipids B) Cholesterol C) Triacylglycerols D) Glycolipids E) Water Ans A SHORT ANSWER 47) What does the word saturated mean in the term saturated fatty acid?

Ans A saturated fatty acid is saturated in hydrogen. There are no carbon-carbon double bonds.

48) Where is the first carbon-carbon double bond in an -3 fatty acid?

Ans. The first carbon-carbon double bond in this molecule is between the third and fourth carbons relative to the terminal methyl group.

49) What is the major function of waxes?

Ans. Waxes act as protective coatings on the surface of plants or the skin and hair of animals.

50) What is the major function of cholesterol?

Ans. Cholesterol is an important component of animal cell membranes and a precursor for all steroid hormones.

51) Why do plasma lipoproteins require a protein component to accomplish their role?

Ans The protein component of plasma lipoproteins serves to solubilize the lipoproteins in the blood. It also binds to cell surface receptors that permit uptake of lipoproteins by body cells.

52) What role do bile salts play in the body?

Ans The bile salts are used to emulsify dietary fat and oils so they may be digested and then absorbed.

53) What do the abbreviations ACAT and LCAT stand for? What functions do these molecules serve in lipid metabolism?

Ans. ACAT is an abbreviation for Acyl-CoA: cholesterol acyltransferase, the enzyme responsible for converting cholesterol to its acyl ester which is stored within cells. LCAT is an abbreviation for the plasma enzyme lecithin: cholesterol acyltransferase, which

transfers a fatty acid residue from lecithin to cholesterol. The cholesterol ester product is then sequestered within a plasma lipoprotein.

54) From what fatty acids are most eicosanoids derived? What is the medical importance of eicosanoids? Provide an example.

Ans Many eicosanoids are derived from arachidonic acid. The treatment of several medical conditions requires the suppression of the synthesis of eicosanoids. Examples include anaphylaxis, allergies, pain, injury-induced inflammation caused, and high fever.

55) What is the difference between an autocrine regulator and a hormone?

Ans An autocrine regulator is a hormone-like molecule that triggers a response within the same cell that produces it. A hormone is a molecule produced by one type of cell that elicits a response in target cells in another part of the body 56) How do water molecules move through hydrophobic cell membranes?

Ans Water molecules can penetrate through hydrophobic cell membrane by moving through water channel complexes called the aquaporins.

57) To which class of terpenes does the following molecule belong?

Ans The indicated compound is a monoterpene because it contains two isoprene units.

58) How does the function of HDL promote the reduction of risk for coronary artery disease?

Ans HDL is believed to scavenge free cholesterol and transport it to the liver. where it is converted to bile acids and excreted. The resulting reduction in total cholesterol in the serum helps prevent plaque formation.

59) What change would you make in the structure of a cell membrane to increase the cell’s resistance to mechanical stress?

Ans An increase in a membranes content of cholesterol and cardiolipin (two phospholipids linked by glycerol) increases its resistance to mechanical stress.

60) List three mediator proteins that move phospholipid molecules from one side of a membrane to the other. What are the functions of each?

Ans There are three proteins that facilitate the movement of phospholipid molecules from one side of a membrane to another. Flippase transfers phospholipids from the outer to the inner membrane leaflet. Floppase transfers phospholipids from the inner to the outer leaflet. Scramblase is nonspecific, energy-independent redistributor of phospholipids across membranes.

61) Describe how glucose is transported across membranes in the kidney. What type of transport is involved?

Ans The sodium gradient created by the Na+-K+-ATPase in the plasma membrane of kidney tubule cells enables glucose transport. This is an example of secondary active transport.

62) Describe and give specific examples of a facilitated diffusion process.

Ans In facilitated diffusion, polar, charged, or large molecules that normally cannot penetrate the cell membrane diffuse across the membrane through protein channels or carriers that "facilitate" this diffusion. Because facilitated diffusion occurs with (or down) a concentration gradient, this is a spontaneous process. Examples include the glucose transporter and anion channels in the red blood cell membrane.

63) Describe the general structure of lipoproteins. How does this structure allow the transport of water-insoluble lipid molecules in the bloodstream?

Ans The outer layer of lipoproteins consist of a single layer of phospholipids and proteins. The hydrophobic hydrocarbon chains of the phospholipids face inward, towards the neutral lipids contained within. The hydrophilic group of the phospholipids face outward and are solvated by water molecules, allowing the lipoprotein to dissolve in the bloodstream.

64) Suggest a reason why elevated LDL levels are a risk factor for coronary artery disease.

Ans Most of the cholesterol in plaque results from the ingestion of dLDL by the foam cells that infiltrate the arterial wall. High blood plasma dLDL therefore promotes atherosclerosis. Because the coronary arteries are narrow, they are especially prone to occlusion by atherosclerotic plaque.

65) Mammals in the Arctic Circle (e.g., reindeer) have higher levels of unsaturated fatty acids in their legs than in the rest of their bodies. Suggest a reason for this phenomena.

Does it have a survival advantage?

Ans The hooves and lungs of cold adapted animals are subjected to much lower temperatures than the rest of the body. At these low temperatures the membrane must be modified so that the membranes remain fluid. This can be done by increasing the unsaturation of the nonpolar tails of the membrane phospholipids.

66) Plants often produce waxes on the surface of their leaves to prevent dehydration and protect against insects. What structural feature of waxes makes them more suitable for this task than carbohydrates or proteins?

Ans Both carbohydrates and proteins contain large numbers of atoms capable of hydrogen bonding (oxygen and nitrogen). In the presence of water these materials would either dissolve or swell. Waxes on the other hand are composed of hydrophobic molecules that ere resistant to the penetration of water from the leaf interior. A relatively thick waxy layer prevents insect penetration.

ESSAY QUESTIONS

67) Describe the possible consequences of a low fat diet.

Ans Diets in which there are insufficient fats and oils can have serious health consequences. Among these are deficiencies in fat soluble vitamins (A, D, E, and K) and the essential fatty acids linoleic and linolenic acids. Consequences of a low fat diet include dry skin, brittle hair, fatigue, high blood pressure, atherosclerosis, depressed immunity, poor wound healing, and depression. In children essential fatty acid deficiencies have been linked to impaired brain development.

68) Explain why the bilayer translocation movement of phospholipids in cell membranes is relatively slow.

Ans For a phospholipid to move from one side of the bilayer to the other, the polar head must move through the hydrophobic portion of the phospholipid membrane. This process requires a significant amount of energy and is therefore relatively slow.

69) Suggest a reason why trans fatty acids have melting points similar to analogous saturated fatty acids.

Ans Like saturated fatty acids, trans fatty acids can have fully extended chains that pack together well, resulting in an increased melting point relative to unsaturated fatty acids that contain cis-double bonds.

70) Describe what cellular processes lipid rafts are involved in.

Ans Lipid rafts are plasma membrane microdomains are enriched in cholesterol, sphingolipids and certain membrane proteins, which make them more rigid than the surrounding membrane. Lipid rafts have been implicated in such cellular processes as exocytosis, endocytosis, and signal transduction 71) Changes in temperature affect membrane properties. How would you expect the lipid composition of thermophile membranes to differ from those of prokaryotes that live at more normal temperatures?

Ans High temperatures destabilize the membranes of prokaryotes adapted to “normal” temperatures. The membranes of thermophilic prokaryotes are resistant to high temperatures because they contain longer, saturated fatty acyl groups that pack closely together and lipids such as sterols or similar molecules that act as stiffening agents. In addition, they also contain glycero-ether lipids, which are difficult to hydrolyze.

72) Detergents are synthetic soap-like substances that researchers use to disrupt membranes and extract membrane proteins. Explain how this process works.

Ans The hydrophobic and hydrophilic components of detergents disrupt membranes thus allowing the extraction of previously inaccessible membrane proteins.

73) Explain why triacylglycerols are not components of lipid bilayers.

Ans To form bilayers, molecules need to be amphipathic. Although triacylglycerols have three polar ester bonds, their three hydrocarbon chains are sufficiently long to cause these molecules to be nonpolar overall. Their hydrophobic nature causes them to coalesce into droplets rather than form bilayers.

74) Explain why entropy increases when a lipid bilayer forms from phospholipid molecules.

Ans The ordered water molecules surrounding each phospholipid molecule are released from the polar heads as the bilayer forms. Order is lost and entropy increases.

75) Animal cells are enclosed in a cell membrane. According to the fluid mosaic model this membrane is held together by hydrophobic interactions. Considering the shear forces involved why does this membrane not break from shear stress.

Ans The fluidity of the membrane allows for flexible movement. Any breaks that do occur expose the hydrophobic core of the membrane to an aqueous environment.

Hydrophobic interactions spontaneously move the broken ends together and, in combination with certain other components of cell membrane resealing mechanisms (e.g., cytoskeleton and calcium ions), the membrane reseals.

76) Glycolipids are nonionic lipids that can orient themselves into bilayers as phospholipids do. They accomplish this feat although they lack an ionic group like that of the phospholipids. Suggest a reason why this is possible.

Ans The carbohydrate portion of the glycolipid can form hydrogen bonds with the water.

This carbohydrate component is the polar group, and it is thus analogous to the charged portion of the phospholipid.

CHAPTER TWELVE LIPID METABOLISM 1) How many acetyl-CoA’s are required to synthesize one molecule of isopentenyl pyrophosphate?

A) 1 B) 2 C) 3 D) 4 E) 5 Ans C 2) ___________ is used to transport fatty acids into the mitochondria.

A) Carrone B) Phytate C) Creatine D) Carnitine E) Acyl carrier protein Ans D 3) The -oxidation of fatty acids requires_________.

A) Coenzyme A B) FAD C) NAD+ D) Both A and C are correct E) All of the above are correct Ans E 4) _________, a product of the oxidation of odd-chain fatty acids, is converted to succinyl-CoA. A) Malonyl-CoA B) Propionyl-CoA C) Acetyl-CoA D) Oxaloacetate E) Acyl carnitine Ans B

5) _______ derive a substantial amount of energy from the oxidation of odd-chain fatty acids.

A) Plants B) Fungi C) Ruminants D) Humans E) Microorganisms Ans C 6) The carbon atoms of cholesterol are derived from _______.

A) Oxaloacetate B) Succinyl CoA C) Erythrose D) Acetyl CoA E) More than one response is correct Ans D 7) The following reaction requires the presence of _________.

A) Carnitine B) CoASH C) NAD+ D) FAD E) Water Ans C 8) In animals the function of peroxisomal -oxidation appears to be A) Energy generation B) Gluconeogenesis

C) Synthesis of very long fatty acids D) Degradation of branch chain fatty acids E) Shortening of very long chain fatty acids Ans E 9) The acetyl-CoA derived from glyoxysomal -oxidation is converted to carbohydrate via A) The glyoxylate cycle B) The citric acid cycle C) Gluconeogenesis D) Both A and B are correct E) Both A and C are correct Ans E 10) Refsum’s disease results from a buildup of ________in nerve tissue.

A) Epoxides B) Ketone bodies C) Odd chain fatty acids D) Phytanic acids E) Carnitine Ans D 11) Which of the following is not one of the ketone bodies?

A) Acetoacetate B) -Hydroxybutyrate C) -Methylglutarate D) Acetone E) None of the above is correct Ans C 12) Most eicosanoids are derived from ________acid.

A) Stearic B) Monohydroperoxyeicosatetraenoic C) Linolenic D) Arachidonic E) Arachidic

Ans D 13) Glycerol from the hydrolysis of triacylglycerols is transported by the blood to the ____ A) Intestine B) Stomach C) Liver D) Pancreas E) A and B Ans C 14) The intermediates in fatty acid synthesis are linked through a ________linkage to ACP. A) Thioester B) Amide C) Ester D) Acetal E) Ether Ans A 15) Saturated fatty acids containing up to 16 carbon atoms are assembled in ________.

A) Mitochondria B) Rough endoplasmic reticulum C) Smooth endoplasmic reticulum D) Peroxisomes E) Cytoplasm Ans E 16) Fatty acid synthesis begins with the carboxylation of acetyl CoA to form ________.

A) Propionyl-CoA B) Acetoacetyl-CoA C) Malonyl-CoA D) Butyryl-CoA E) None of the above is correct

Ans C 17) All of the following are enzymatic activities found in fatty acid synthase except A) -Ketoacyl-ACP reductase B) Malonyl/acetyl transferase C) Thioesterase D) Lipoxygenase E) -Hydroxyacyl-ACP dehydratase Ans D 18) Desaturation of fatty acids involves all of the following except A) Oxygen B) NADH C) Cytochrome b5 D) Cytochrome b5 reductase E) None of the above is correct Ans E 19 Which of the following types of fatty acid oxidation produces a dicarboxylic acid?

A) Alpha B) Beta C) Delta D) Omega E) A and D Ans D 20) The conversion of acetyl-CoA to malonyl-CoA is inhibited by ________.

A) Glucagon B) Epinephrine C) Palmitoyl-CoA D) All of the above are correct E) None of the above is correct Ans D 21) The conversion of acyl-CoA to acylcarnitine is inhibited by __________.

A) Malonyl-CoA B) Citrate C) Acetyl-CoA D) Insulin E) Both A and B are correct Ans A 22) In conjugation reactions A) An insoluble molecule is converted to a precipitate B) A soluble molecule is excreted C) An insoluble molecule is made soluble by conversion to a derivative with a water soluble functional group D) Both A and B are correct E) None of the above is correct.

Ans C 23) Depending on an animal’s metabolic needs, fatty acids may be converted to triacylglycerols, energy, or __________.

A) Converted to glycerol B) Stored as terpenes C) Used in membrane synthesis D) Both B and C are correct E) Stored as fatty acids Ans C 24) Membrane remodeling A) Requires phospholipases B) Requires acyl transferases C) Occurs only when cells are under stress D) Both A and B are correct E) All of the above are correct Ans D 25) The conversion of phosphatidylethanolamine to phosphatidylcholine requires ______ A) SAH B) SAM C) Acyl carrier protein D) Serine

E) Base exchange enzyme Ans B 26) The sulfatides are synthesized when ________ reacts with 3-phosphoadenosine-5’-phosphosulfate.

A) Phosphatidylceramide B) Phosphatidylcholine C) Galactocerebroside D) Sphingomyelin E) UDP-glucose Ans C 27) __________ is the rate-limiting enzyme in cholesterol synthesis.

A) HMG-CoA reductase phosphatase B) HMG-CoA reductase kinase C) Mevalonate kinase D) Phosphomevalonate kinase E) None of the above is correct Ans E 28) The conversion of squalene to cholesterol requires ________.

A) Oxygen B) Isopentenyl pyrophosphate C) NADPH D) Both A and B are correct E) Both A and C are correct Ans C 29) Cholesterol is a precursor of _________.

A) Aldosterone B) Cortisol C) Testosterone D) Estrogen E) All of the above are correct

Ans E 30) Most bile acids are conjugated with ________.

A) Glycine B) Glucuronate C) Taurine D) Both A and B are correct E) Both A and C are correct Ans E 31) Which of the following tissues cannot use fatty acids as a fuel?

A) Brain B) Muscle C) Heart D) Liver E) All tissues use fatty acids Ans A 32) Lipolysis is used to A) Degrade triacylglycerols B) Prepare triacylglycerols for excretion C) Remove lipid from membrane D) Cleave fatty acids into two carbon units E) Convert fatty acids to glucose Ans A 33) Oxidation of the carbon farthest from the carbonyl group of a fatty acid is called A)  oxidation B) -oxidation C) -oxidation D) The reaction does not occur E) Either A or B are correct depending on the point of reference Ans C

34) In the process of thiolytic cleavage the following occurs: A) A cis double bond is produced B) A trans double bond is produced C) An acetyl CoA molecule is released when the bond between C and C of an acylCoA is broken D) A fatty acid reacts with CoA to produce an acetyl-CoA E) Hydrogen sulfide is used to cleave the carbon-carbon double bond Ans C 35) How many FADH2 molecules would be produced in the oxidation of palmitic acid?

A) 1 B) 3 C) 5 D) 7 E) 9 Ans D 36) The rate limiting step in fatty acid synthesis is A) Acetyl-CoA carboxylation B) Reduction of a cis double bond C) Conversion of the trans double bond to a cis double bond D) Reduction of the ketoester to the hydroxyl ester E) Desaturation of the fatty acid to form trans double bonds Ans A 37) Which of the following lipids have signaling functions?

A) Triacylglycerols B) Steroids C) Bile salts D) Prostaglandins E) -tocopherol Ans D 38) What form of oxidation is characteristic of branched chain fatty acids

A) -oxidation B) −oxidation C) -oxidation D) -oxidation E) -oxidation Ans A 39) The metabolism of fatty acids is regulated in the short term by allosteric modulators, covalent modification and _________.

A) Fluctuating nutrient availability B) Energy demands C) Changes in gene expression D) Hormones E) A, B, and C are all correct Ans D

40) The most important mechanism for degrading and eliminating cholesterol is the synthesis of A) Fatty acids B) Bile acids C) Squalene D) Taurine E) Isoprene Ans B 41) The absorption of triglycerides and other lipid nutrients and their distribution to body tissues is referred to as the A) Endogenous pathway B) Exogenous pathway C) Apolipoprotein pathway D) Chylomicron distribution pathway E) Triacylglycerol absorption pathway Ans B

42) The pathway in which lipoproteins are transported from the liver to cells is referred to A) Endogenous pathway B) Exogenous pathway C) Apolipoprotein pathway D) Chylomicron distribution pathway E) Triacylglycerol absorption pathway Ans A

43) Which of the following is not a function of lipids A) Energy storage B) Components of biological membranes C) Insulation D) Source of acetyl-CoA E) All of the above are functions of lipids Ans E 44) The triacylglycerol cycle is A) A mechanism for releasing amino acids to the liver B) A mechanism that regulates the level of fatty acids that are available for energy generation.

C) A mechanism that hydrolyses triacylglycerol D) Converts fatty acids to triacylglycerol E) B, C, and D Ans E 45) The principal means of producing glycerol in the body A) The triacylglycerol cycle B) Glyceroneogenesis C) Gluconeogenesis D) Lipolysis E) Liponeogenesis Ans B

46) The recycling rate of triacylglycerols to fatty acids is inhibited by A) Epinephrine B) Norepinephrine C) Insulin D) Lipase E) A and B Ans C SHORT ANSWER 47) What is an enterocyte? What is its function?

Ans An enterocyte is a intestinal wall cell. Enterocytes absorb nutrients digested within the lumen of the small intestine.

48) Define ketogenesis.

Ans Ketogenesis is the condition in which excess acetyl-CoA molecules are converted to acetoacetate, -hydroxybutyrate and acetone, which are known collectively as the ketone bodies 49) Define ketosis.

Ans Ketosis is an accumulation of ketone bodies in the blood and tissues.

50) What are the differences between -oxidation in mitochondria and peroxisomes?

Ans Peroxisomes have -oxidation enzymes that are specific for long-chain fatty acids, whereas mitochondria possess enzymes that are specific for short-and moderate-chain length fatty acids. In addition, the first reaction in the peroxisomal pathway is catalyzed by a different enzyme than the mitochondrial pathway. The FADH2 produced in the first

peroxisomal reaction donates its electrons to oxygen directly (forming hydrogen peroxide) instead of UQ as in the mitochondria.

51) List three differences between fatty acid synthesis and -oxidation Ans The differences between fatty acid synthesis and  oxidation are: (1) The two pathways take place in different cell compartments. Synthesis occurs in the cytoplasm and -oxidation is within the mitochondria, (2) The intermediates of fatty acid synthesis and -oxidation are linked through thioester linkages to ACP and CoASH, respectively and 3) The electron carrier for fatty acid synthesis is NADPH whereas the electron carriers for -oxidation are NADH and FADH2.

52) Explain how hormones act to modify the metabolism of fatty acids in both the short and long term. Give examples.

Ans In the short term, hormones alter the activity of preexisting regulatory enzyme molecules. For example, glucagon inhibits acetyl-CoA carboxylase. Long-term effects of hormones usually involve changes in the pattern of enzyme synthesis in target cells. For example, insulin promotes the synthesis of enzymes involved in lipogenesis (e.g., acetylCoA carboxylase and fatty acid synthase).

53) Define the term thiolytic cleavage. In what biochemical process does it occur?

Ans A thiolytic cleavage is a reaction in which a bond to a sulfur is broken. In the oxidation of fatty acids the final reaction (C-C cleavage), catalyzed by thiolase is described as thiolytic cleavage. The products of the reaction are acetyl-CoA and acylCoA with two fewer carbon atoms.

54) How do cells adjust the fluidity of their membranes?

Ans Cell adjust the fluidity of their membranes with membrane remodeling, a process in which phospholipases and acyl transferases alter the fatty acid composition of membrane lipid molecules. The replacement of saturated fatty acids with unsaturated fatty acids increases membrane fluidity.

55) Describe the difference between LDLs and IDLs. Ans After the TG content of a VLDL (very low density lipoprotein) has been depleted the lipoprotein is referred to as IDL (intermediate density) lipoprotein.

56) -Oxidation of naturally occurring monounsaturated fatty acids requires an additional enzyme. What is this enzyme and how does it accomplish its task?

Ans Enoyl-CoA isomerase converts the naturally occurring cis double bond at 3 to a trans double bond at 2, the correct position for the next round of -oxidation.

57) What is the function of a glucocorticoid?

Ans A glucocorticoid is a steroid hormone that affects carbohydrate, protein and lipid metabolism.

58) What is the function of a Phase I reaction?

Ans A Phase I reaction in a biotransformation process introduces a water soluble functional group into a hydrophobic molecule.

59) How would you describe the three phases of biotransformation?

Ans In phase 1 of biotransformation, reactions catalyzed by oxidoreductases and hydrolases convert hydrophobic substances into more polar molecules. In phase II functional groups on substrate molecules are conjugated with water-soluble substances

such as glutathione, glutamate, sulfate or glucuronate, which promote rapid excretion. In animals the term phase III is used to describe the excretory process.

60) What is the function of ACP? Ans ACP (acyl carrier protein), a component of fatty acid synthase, is a protein that contains a phosphopantetheine prosthetic group. The acyl intermediates in fatty acid synthesis are linked to phosphopantetheine via a thioester bond, analogous to CoASH in -oxidation.

61) What is the function of conjugation reactions in the biotransformation process?

Ans Conjugation reactions usually improve the water solubility of substrate molecules with OH groups that can be esterified with glucuronate or sulfate.

62) Under severe starvation conditions people develop “acetone breath”. Explain.

Ans During periods of prolonged starvation, when there is an excess of acetyl-CoA (from the -oxidation of fatty acids) and very low reserves of glucose, excess ketone bodies are formed. When the concentration of acetoacetate is high, it decarboxylates to form acetone, which may be detected in the breath.

63) Describe the role of insulin in lipid metabolism.

Ans Insulin promotes the uptake of fatty acids and their storage via triacylglycerol synthesis. Specifically insulin decreases intracellular cAMP and inactivates the adipocyte adipose triglyceride lipase to prevent the hydrolysis of fats to glycerol and fatty acids.

Insulin also stimulates the release of VLDL from the liver, and activates lipoprotein lipase synthesis and the transport of fatty acids to the endothelial cells in fat and muscle tissue.

ESSAY QUESTIONS 64) Describe the possible effects of low levels of carnitine on a person’s metabolism.

Ans Carnitine is required for the transport of fatty acids into mitochondrial matrix where they are oxidized to generate energy. When carnitine levels are low, fat metabolism is impaired. Although glucose metabolism accelerates, an energy deficit occurs. In addition accumulating acyl-CoA molecules become substrates for competing processes such as peroxisomal -oxidation and triacylglycerol synthesis.

65) When the production of acetyl-CoA exceeds the body’s capacity to oxidize it, acetoacetate, -hyroxybutyrate and acetone accumulate. When generated in large amounts, these substances can exceed the blood’s buffering capacity. As the blood pH falls, the ability of red blood cells to carry oxygen is affected. Subsequently, the brain can be starved of oxygen and a fatal coma can result. Explain how severe dieting can produce this condition.

Ans Severe dieting (less than 600 calories per day) causes the oxidation of large amounts of fatty acids from the body’s TG reserves. Ketone body production increases dramatically with the effect of causing acidosis. Brain cells are damaged by the acidosis and by the ketone bodies themselves, especially the organic solvent acetone.

66) There is an unusually high concentration of phosphatidylcholine on the lumenal side of the ER. What structural feature of phosphatidylcholine is responsible? Explain how this structural feature produces this effect.

Ans Membrane phospholipids are synthesized on the cytoplasmic side of the SER membrane. Because the polar head groups of phospholipid molecules make transport across the hydrophobic core of a membrane an unlikely event, a translocation mechanism

is used to transfer phospholipids across the membrane to ensure balanced growth.

Choline-containing phospholipids are found in high concentration on the luminal side of the ER membrane because a prominent phospholipid translocator protein called flippase preferentially transfers this class of molecule.

67) During periods of stress or fasting, fatty acids are released by adipocytes. Explain.

Ans As a result of stress or fasting energy levels are low,the release of epinephrine and norepinephrine results in the elevation of cAMP and triggers the hydrolysis of triglycerides. The products of lipolysis, fatty acids and glycerol, are then released into the blood.

68) Pharmaceuticals in a class called statins inhibit the enzyme HMG-CoA reductase.

What is the primary effect of this drug on patients?

Ans The primary effect of the statins is the competitive inhibition of the HMG-CoA reductase, the rate limiting enzyme in cholesterol biosynthesis. The result is lower blood cholesterol levels.

69) Describe the role of the three proteins that facilitate the movement of phospholipid across a membrane.

Ans The three proteins that facilitate the movement of phospholipid molecules from one side of a membrane to another are as follows. Flippase transfers phospholipids from the outer to the inner membrane leaflet. Floppase transfers phospholipids from the outer to the inner leaflet. Scaramblase is a nonspecific energy-dependent redistributor of phospholipids across membranes.

70) Provide an explanation for the fact that most fatty acids are 16 to 18 carbons long.

Ans Fatty acids are assembled from by fatty acid synthase from acetyl groups in a process that ends at C16. Although, there is a robust capacity to elongate fatty acids, the most abundant fatty acids are C16 and C18, the product of one round of the elongation process.

71) How are lipid molecules such as estrogen and -carotene related to each other?What biosynthesis reaction do these specific molecules have in common?

Ans Both estrogen and -carotene are isoprenoids. They are originally synthesized from the isoprene units in isopentenyl pyrophosphate molecules. These and other isoprenoid molecules are assembled by head-to-tail condensations of these groups.

72) Provide an explanation for the intracellular separation of fatty acid metabolic processes Ans Fatty acid biosynthesis occurs in the cytoplasm, whereas fatty acid catabolism takes place in mitochondria and peroxisomes so that these pathways may be regulated independently and energy-wasting futile cycles may be prevented.

CALCULATIONS 73) Butyric acid, a simple four-carbon fatty acid, is oxidized by -oxidation. Calculate the number of FADH2 and NADH molecules that are produced in this reaction. How many acetyl-CoA molecules are produced?

Ans In the oxidation of butyric acid by the -oxidation pathway, 1 FADH2 and 1 NADH and two acetyl-CoA are produced.

74) The adaptation of desert animals to their environment requires water conservation mechanisms. A number of these organisms conserve water so successfully that they never

actually drink it. They depend instead on water generated during metabolism. Determine how much water can be obtained by the oxidation of one mole of palmitic acid.

Ans The reaction for the oxidation of one mole of palmitic acid is; CH3(CH2)14COOH + 23O2 -> 16CO2 + 16H2O One mole of palmitic acid produces a yield of 16 moles of water molecules. From this number must be subtracted 8 moles of water of which 7 moles are used in the hydration reaction of each round of -oxidation spiral and 1 mole is used for the hydrolysis of pyrophosphate, the reaction that drives the activation of the palmitic acid molecule to completion. The net reaction, therefore, yields a total of 8 molecules of water.

75) Compare the energy content of a stearic acid molecule with that of glucose.

Ans The yield of ATP from the oxidation of stearic acid is 122 (8FADH2 x 1.5 ATP, 8NADH x 2.5 ATP and 9 acetyl-CoA x 10 ATP). Since the formation of stearoyl-CoA requires two ATP equivalents the net synthesis is 120ATP. Stearic acid yields 120/18 or 6.6 ATP per carbon atom. Recall that the ratio for glucose is 5.2 ATP per carbon.

CHAPTER THIRTEEN PHOTOSYNTHESIS 1) The membrane component that mediates the conversion of light energy into chemical energy is called a __________.

A) Chromophore B) Granum C) Antenna pigment D) Stromal lamella E) Reaction center Ans E 2) Photosystem I contains _______.

A) P700 B) P680 C) D1/D2 dimer D) Cyt B559 E) All of the above Ans A 3) PSII is found in the A) Thylakoid membrane directly exposed to the stroma B) Thylakoid membrane that is not exposed to the stroma C) Stroma D) Inner membrane of chloroplasts E) All of the above are correct Ans B 4) The CF1 component of the ATP synthase A) Possesses an ATP synthesizing activity B) Possesses a proton-conducting channel C) Projects into the stroma D) Both A and C are correct E) Both B and C are correct Ans D

5) All of the following statements concerning light are true except A) High frequency radiation such as gamma rays and X-rays, which have long wavelengths, are high energy.

B) A wavelength is the distance from the crest of one wave to the crest of the next wave.

C)  = c/ D) When light interacts with matter, it does so in discrete packets of energy called photons.

E) The intensity of electromagnetic radiation is proportional to a2.

Ans A 6) As long as the spins of two unpaired electrons remain antiparallel, a molecule which has absorbed light energy, is said to be A) In the ground state B) An excited chromophore C) In an excited singlet state D) Both A and C are correct E) None of the above are correct Ans C 7) In _______ a molecule’s excited state decays as it emits a photon.

A) Oxidation-reduction B) Radiationless decay C) Resonance energy transfer D) Both A and C are correct E) None of the above are correct Ans E 8) All of the following statements concerning the oxygen-evolving complex in chloroplasts are true except A) It is found in PSI B) It is found in PSII C) It consists of a “clock” mechanism D) It consists of five oxidation states E) The evolution of one O2 requires the splitting of two waters

Ans A 9) Which of the following is a component of PSI? A) D1/D2 dimer B) Pheophytin a C) Ferredoxin D) Plastoquinone E) Rubisco Ans C 10) Pheophytin a is a molecule whose structure is similar to that of ______ A) -carotene B) Lutein C) Plastocyanin D) Chlorophyll E) Plastoquinone Ans D 11) Cyclic electron transport occurs when A) ATP synthesis is excessive B) Oxygen evolution is suppressed C) A chloroplast has a high NADPH/NADP+ D) The D1/D1 dimer is damaged E) None of the above are correct Ans C 12) In photosynthesis there is A) Splitting of water to form oxygen B) Synthesis of sugar C) Excitation of chromophores D) Production of a proton gradient E) All of the above are correct Ans E

13) __________allows photosynthesizing cells to reemit photons in a protective overflow mechanism.

A) Oxidation-reduction B) Radiationless decay C) Fluorescence D) Resonance energy transfer E) Photorespiration Ans C 14) The Calvin cycle is sometimes referred to as A) The dark reactions B) Light independent reactions C) Reductive pentose phosphate pathway D) Both A and B are correct E) All of the above are correct Ans E 15) Ribulose –1,5-bisphosphate carboxylase catalyzes the carboxylation of ribulose-1,5-bisphosphate to form A) One molecule of sucrose B) One molecule of glucose C) Two molecules of glyceraldehyde-3-phosphate D) Two molecules of glycerate-3-phosphate E) Two molecules of dihydroxyacetone phosphate Ans D 16) The reaction in photosynthesis catalyzed by glyceraldehyde-3-phosphate dehydrogenase is similar to a reaction in A) Sucrose synthesis B) Gluconeogenesis C) Citric acid cycle D) Glycogenesis E) Glycogenolysis Ans B 17) The net production of “fixed” carbon in the Calvin cycle is

A) One molecule of glyceraldehyde-3-phosphate B) One molecule of glycerate-3-phosphate C) Two molecules of glycerate-3-phosphate D) Two molecules of eythrose-4-phosphate E) One molecule of ribulose-1,5-bisphosphate Ans A 18) Most of the carbon translocated throughout plants is in the form of A) Starch B) Sucrose C) Ribulose-1,5-bisphosphate D) Glyceraldehyde-3-phosphate E) Dihydroxyacetone phosphate Ans B 19) During photosynthesis light energy captured by an organism’s photosystem is transduced into which of the following?

A) P B) Water C) Oxygen D) Carbon dioxide E) Glucose Ans A 20) The process of photorespiration is suppressed in A) C3 metabolism B) C4 metabolism C) CAM metabolism D) Both B and C are correct E) All of the above are correct Ans B 21) Phosphoenolpyruvate carboxylase catalyzes a key reaction in A) Sucrose metabolism B) The Calvin cycle

C) The Hatch-Slack pathway D) Gluconeogenisis E) The PCR cycle Ans C 22) Features of light regulation of photosynthesis-associated enzymes include all of the following except __________.

A) pH B) Phytochrome C) Mg++ concentration D) Fluorescence E) Ferredoxin-threodoxin system Ans D 23) The active form of phytochrome is ________.

A) Pr B) Pfr C) Blue form D) Both A and C are correct E) Both B and C are correct Ans B 24) Examples of phytochrome-mediated process include all of the following except A) Seed germination B) Chloroplast development C) Stem elongation D) Intracellular Ca++ level changes E) None of the above are correct Ans E 25) When adequate light is available, the overall rate of photosynthesis is dependent on the rate of A) Ca++ levels B) Sucrose accumulation C) Starch accumulation

D) Phytochrome concentration E) Carbon dioxide fixation Ans E 26) In addition to an inner and outer membrane chloroplasts contain a third membrane called A) Thylakoid lumen B) Stroma C) Thylakoid membrane D) Stromal llamella E) Grana Ans C 27) In photorespiration which of the following molecules are consumed?

A) Carbon dioxide B) Oxygen C) NADH D) ATP E) B, C, and D are correct Ans E 28) The chlorophylls absorb little light between A) 400 and 500 nm B) 500 and 600 nm C) 600 and 700 nm D) Bot A and B are correct E) None of the above is correct Ans B 29) The most abundant enzyme on earth is A) Alcohol dehydrogenase B) Rubisco C) Sucrose synthase D) Citrate synthase E) Glucose-6-phosphate dehydrogenase

Ans B 30) Which of the following statements concerning photorespiration is not true?

A) High oxygen concentration and high temperatures promote photorespiration.

B) Photorespiration is a serious problem of C4 plants in hot dry environments.

C) When the rates of carbon dioxide release and fixation are equal, the carbon dioxide compensation point has been reached.

D) Photorespiration is depressed by carbon dioxide concentrations above 0.2%.

E) The lower the value of the carbon dioxide compensation point the less photorespiration takes place.

Ans B 31) There are three mechanisms for fixing carbon dioxide in plants: C4 metabolism, C3 photosynthesis and ___________.

A) Photorespiration B) Calvin Cycle C) Crassulacean acid metabolism D) Light independent reaction E) Dark reaction Ans C 32) In C4 plants carbon dioxide is initially incorporated into _________.

A) Oxaloacetate B) Malate C) Pyruvate D) Succinate E) Acetate Ans A 33) CAM plants are mostly A) Grasses B) Succulents C) Conifers D) Blue green algae E) Both A and C are correct Ans B

34) The principal regulator of photosynthesis is ___________.

A) Light B) Oxygen C) Carbon dioxide D) Oxaloacetate E) Water Ans A 35) During the light-dependent reactions which of the following takes place?

A) Oxygen is evolved B) ATP is produced C) NADPH is produced D) Carbon dioxide is fixed E) Both A and B are correct Ans E 36) The most important enzyme in photosynthesis is ____________.

A) Ribulose-1,5-bisphosphate carboxylase B) ATP synthase C) Pheophytin D) Ferredoxin- NADP oxidoreductase E) Dehydrogenase Ans A 37) What is the final electron acceptor of photosynthesis?

A) Carbon dioxide B) Water C) Oxygen D) Glucose E) ATP Ans A 38) The principal metals involved in photosynthesis include all of the following except

A) Mn B) Ca C) Mg D) Fe E) Cu Ans E 39) The three phases of the Calvin Cycle are carbon fixation, regeneration and __________ A) Photorespiration B) ATP synthesis C) Reduction D) NADP synthesis E) Both A and B are correct Ans C 40) Which of the following is not a biofuel A) Ethanol from petroleum B) Biodiesel C) Hydrogen D) Methane E) A and D Ans A 41) In photosynthesis captured light energy is used to initially synthesize A) ATP B) NADH C) NADPH D) Glucose E) A and C Ans E 42) Which of the following is not found in the water splitting complex?

A) Manganese B) Calcium C) Magnesium

D) Amino acid residues E) A and B Ans C 43) In the reduction phase of the Calvin Cycle aldolase catalyzes the reaction between dihydroxyacetone and glyceraldehyde-3-phospate to form A) Glucose B) Fructose-1,6-bisphosphate C) Dihydroxyacetone phosphate D) Fructose-6-phosphate E) Fructose-1-phosphate Ans B 44) Which of the following is not a consequence of global warming as predicted by the vast majority of the world’s climate scientists?

A) Increased frequency of insect born diseases B) Increased intensity of drought C) Food shortages D) Higher temperatures E) Drop in ocean levels Ans E 45) Which of the following fuels cannot be carbon neutral?

A) Hydrogen B) Natural gas C) Ethanol produced by fermentation D) Biodiesel E) A and B Ans B SHORT ANSWER 46) What processes occur in the light-dependent reaction of photosynthesis?

Ans In light-dependent reactions electrons are energized by light energy and subsequently used in ATP and NADPH synthesis.

47) What processes occur in the light-independent reaction of photosynthesis?

AnsLight-independent reactions, also referred to as the Calvin Cycle, are a photosynthetic pathway in which carbon dioxide is incorporated into carbohydrate molecules, They can occur in the absence of light.

48) What is a Rieske protein and what is its function?

Ans A Rieske protein is a iron-sulfur protein in the b6f complex in thylakoid membrane that accepts electrons from the electron carrier PQ and donates them to PC. 49) What is the most significant contribution of early photosynthetic organisms to Earth’s environment?

Ans The most significant contribution of early photosynthesizing organisms to the Earth’s environment was the conversion of a reducing atmosphere (ammonia and methane) to an oxidizing atmosphere.

50) List the three primary photosynthetic pigments and describe the role of each in photosynthesis.

Ans The three primary photosynthetic pigments are the chlorophylls, the carotenoids and pheophytin. Chlorophyll a absorbs light energy and is involved in light harvesting.

Chlorophyll b is a light harvesting pigment that passes light energy to chlorophyll a. The carotenoids function as light-harvesting pigments to protect against over-excitation and ROS. Pheophytin is an electron transfer molecule in PSII. 51) List three ways that chloroplasts resemble mitochondria.

Ans Chloroplasts resemble mitochondria in the following ways: (1) they are both similar in size and structure to modern prokaryotes; (2) they both reproduce by binary fission; (3) the generic information (a circular DNA molecule) of both chloroplasts and mitochondria are similar to that of prokaryotes: (4) the ribosomes of chloroplasts and mitochondria is similar in size and function; and (5) they are both thought to have arisen from ancient free living prokaryotes.

52 What is lutein?

Ans Lutein is a light-absorbing and antioxidant carotenoid found in thylakoid membrane.

53) What is the final electron acceptor in photosynthesis when the NADPH/NADP+ ratio is low?

Ans The final electron acceptor in photosynthesis is carbon dioxide, regardless of the NADPH/NADP+ ratio.

54) What are the principal products that are produced during the light-dependent reactions of photosynthesis?

Ans During the light reactions of photosynthesis, light-driven electron transport results in ATP and NADPH synthesis.

55) What is the net production of one cycle of the dark reactions?

Ans The net production of one cycle of the dark reactions is one molecule of glyceraldehyde-3-phosphate.

56) Carbon dioxide and water are substrates for photosynthesis. Which of these is the source of molecular oxygen?

Ans Oxygen molecules are generated from oxygen atoms extracted from water.

57) Why is the oxygen-evolving system referred to as a clock?

Ans The oxygen-evolving system is referred to as a clock because it involves five oxidation-reduction reactions that must be completed in order.

58) In reference to photosynthesis what is a special pair and how does it function?

Ans A special pair is composed of two special chlorophyll a molecules that reside within a reaction center. In PSI the special pair is referred to as P700 because it absorbs light at 700 nm. In PSII the special pair of chlorophyll a molecules are referred to as P680.

59) Why is the term dark reactions misleading?

Ans The term “dark reaction” is misleading because it implies that carbon fixation occurs only in the absence of light. The term light-independent is used instead.

60) Plants actively engaged in photosynthesis also evolve carbon dioxide. Explain.

Ans Rubisco, the enzyme that catalyzes carbon fixation can bind both carbon dioxide or oxygen in its active site. Photorespiration, the reaction of ribulose-1,5-bisphosphate with oxygen (a waste product of the light reactions), converts fixed carbon to carbon dioxide.

Photorespiration is favored when susceptible plants are exposed to high temperatures and conditions that cause low carbon dioxide and/or high oxygen concentration.

61) List four consequences of global warming.

Ans The consequences of global warming include rising ocean levels, economic damage from increasingly more powerful hurricanes, drought and flood-caused food and water shortages and the increased prevalence of insect-borne diseases.

62) List three criteria for sustainable biofuel production.

Ans The criteria for sustainable biofuel production are: (1) economically viable production of large quantities of energy, (2) noncompetition with food production ( e.g., no use of arable land), and (3) neutral effects on the environment.

63) List the types of metal that are components of the photosynthesis mechanisms. What functions do they serve?

Ans Among the most notable metals present in photosynthesizing systems are magnesium, manganese, iron and copper. Magnesium stabilizes the porphyrin ring of chlorophyll molecules during the reduction of water to yield oxygen. Manganese acts as a redox canter in the transfer of electrons from the quinone electron carriers to the terminal electron acceptors in photosynthesis. Finally, copper acts as the terminal electron acceptor in PSII before the electrons are transferred to P700 in PSI. 64) Where does carbon dioxide fixation take place in the cell?

Ans Carbon dioxide fixation occurs in the stroma of the chloroplasts.

65) Why does carbon dioxide repress photorespiration?

Ans The first reaction in both photosynthesis and photorespiration is catalyzed by rubisco, which has both carboxylase and oxidase activity. Carbon dioxide and oxygen compete for the enzyme’s active site. Higher levels of CO2 enables it to out-compete O2,, and photosynthesis will occur at the the expense of photorespiration 66) What are triose phosphates? Where are they formed in plant carbohydrate metabolism?

Ans The term triose phosphate is used to describe the molecules glyceraldehyde-3phosphate and dihydroxyacetone phosphate. Formed during the Calvin cycle, the triose phosphates are used in plants in biosynthetic processes such as the formation of sucrose, polysaccharides, fatty acids, and amino acids.

ESSAY QUESTIONS 67) If the rate of photosynthesis is plotted versus the incident wavelength of light, an action spectrum is obtained. How can the action spectrum provide information about the nature of the light-absorbing pigments involved in photosynthesis?

Ans The maximum rate of photosynthesis will occur at the max of the photosynthesizing system. This absorption maximum should match the absorption maxima of the light absorbing pigments.

68) What is the net reaction for photosynthesis? What is the origin of the oxygen molecules in glucose?

Ans The net reaction for photosynthesis is 3CO2 + 6NADPH + 9ATP → glyceraldehyde-3-phosphate + 6NADP+ + 9ADP +8Pi The fixation of six carbon dioxide into glucose occurs at the expense of 12 NADPH and 18 ATP. The source of the oxygen atoms in glucose is carbon dioxide.

69) Deforestation greatly decreases the plant biomass in any area. What impact will deforestation have on the quality of life in the region?

Ans Deforestation has numerous negative effects on the local environment. Among thse are disrupted water cycle (the local climate becomes drier because of the loss of

transpiration by trees), significantly increased water runoff and erosion (tree roots absorb rain water and ground water), and a degraded environment with reduced biodiversity.

70) Explain the following observation. When a photosynthetic system is exposed to a brief flash of light no oxygen is evolved. It is only after several bursts of light that oxygen is evolved.

Ans The oxygen evolving complex of PSII exists in five transient oxidation states (S0 trough S4) and is collectively referred to as a clock. Because the absorption of four photos is required to remove an electron from a water molecule oxygen evolution occurs only when the S4 state as been reached, several light bursts are required.

71) If a C3 plant and a C4 plant are placed in separate sealed containers and provided with adequate light and water, both will survive. If both plants are placed in a single sealed container the C3 plant will die. Explain.

Ans C4 plants are resistant to photorespiration. As a consequence, the total energy that\they expend in carbon dioxide fixation is less. Therefore, C4 plants are more efficient and can out compete the C3 plants for carbon.

72) Herbicides that act by promoting photorespiration are lethal to C3 plants but do not affect C4 plants. Explain.

Ans Because of the capacity of C4 plants to avoid the process of photorespiration, herbicides that promote photorespiration do not affect these organisms.

73) What is the end product of photosynthesis when hydrogen sulfide is the source of hydrogen atoms?

Ans When hydrogen sulfide (H2S) is the source of hydrogen atoms, the end products of photosynthesis are glucose and the element sulfur.

74) What effect would you expect dinitrophenol to have on photosynthesis?

Ans Dinitrophenol is an uncoupler molecule that destroys the proton gradient required for ATP synthesis. The resulting loss of ATP causes photosynthesis to come to a halt.

75) The burning of fossil fuels releases carbon dioxide into the atmosphere and is detrimental to Earth’s ecosystems. Explain why the use of biofuels, which also release carbon dioxide into the atmosphere, is an improvement over fossil fuels.

Ans Biofuels are an improvement over fossil fuels because they are renewable and carbon neutral (the combustion of biofuels is offset by the carbon dioxide they remove from the atmosphere).

76) In the absence of carbon dioxide, chlorophyll fluoresces. How does carbon dioxide prevent this fluorescence?

Ans The electrons energized by light absorption are used to generate NADPH. This NADPH is then used in carbon fixation reactions to yield carbohydrate molecules. If carbon dioxide is not available, NADPH accumulates and the chlorophyll molecules do not have electron transfer available as a way to return t the relaxed state. One avenue available is to release the energy. Fluorescence allows the release of each energized electrons energy as a photon.

CHAPTER FOURTEEN NITROGEN METABOLISM I: SYNTHESIS 1) The glutamate family of amino acids includes all of the following except _____.

A) Glutamine B) Arginine C) Lysine D) Proline E) None of the above is correct Ans C 2) Which of the following is an example of an excitatory neurotransmitter?

A) Serotonin B) Glycine C) Glutamine D) Glutamate E) None of the above is correct Ans D 3) All of the following are referred to collectively as the branched chain amino acids except _________.

A) Valine B) Glycine C) Leucine D) Isoleucine E) None of the above is correct Ans B 4) Which of the following is an example of an inhibitory neurotransmitter?

A) Glycine B) -Aminobutyrate C) Glutamate D) Both A and B are correct E) All of the above are correct Ans D

5) Glycine is used as a precursor molecule in the synthesis of all of the following except _______.

A) Glutathione B) Heme C) Purine bases D) Chlorophyll E) Carnitine Ans E 6) In plants fixed nitrogen is assimilated into __________.

A) Serine B) Glutathione C) Lysine D) Threonine E) Glutamine Ans E 7) -Ketoisovalerate is an intermediate formed during the synthesis of _________.

A) Leucine B) Lysine C) Threonine D) Both A and B are correct E) Both A and C are correct Ans A 8) The group of molecules called the catecholamines include all of the following except _________.

A) Histamine B) Epinephrine C) Dopamine D) Norepinephrine E) Both A and C are correct Ans A 9) Tryptophan is a precursor in the synthesis of _________.

A) Carnitine B) NAD C) GABA D) Both A and B are correct E) All of the above are correct Ans B 10) Chorismate is a precursor in the synthesis of all of the following except _______.

A) Phenylalanine B) Tryptophan C) Ubiquinone D) Tyrosine E) Guanidoacetate Ans E 11) Molecules involved in histidine synthesis include ________.

A) Phosphoribosylpyrophosphate B) ATP C) Glutamate D) Both A and C are correct E) All of the above are correct Ans E 12) All of the following statements concerning folic acid are true except: A) N5,N10-methylene THF is a product of the cleavage of glycine.

B) Vitamin B12 is required for the N5-methyl THF-dependent conversion of homocysteine to methionine.

C) N10-formyl THF, CO2, and aspartate are precursors in the synthesis of hypoxanthine D) Folic acid is a B vitamin.

E) Folic acid requires intrinsic factor for its absorption in the intestine.

Ans E 13) SAM is a methyl donor in the synthesis of ______.

A) Methionine B) Creatine C) Phosphatidylcholine D) Both A and C are correct

E) All of the above are correct Ans E 14) Amethopterin is a structural analogue of _________.

A) Thiamine B) GABA C) Folate D) MPPP E) Mercapturic acid Ans C 15) The transport of GSH out of cells serves all of the following functions except ______.

A) Protection of the plasma membrane B) Amino acid transport C) Transfer of sulfur atoms out of cells D) Formation of mercapturic acid derivatives of organic contaminants E) None of the above is correct Ans E 16) All of the following are purine bases except _____.

A) Guanine B) Thymine C) Adenine D) Hypoxanthine E) All of the above are purine bases Ans B 17) Deficiency of _______ causes Lesch-Nyhan syndrome.

A) Folic acid B) Carbamoyl phosphate synthetase II C) UMP synthase D) HGPRT E) Mg-Protoporphyrin methylesterase Ans D

18) All of the following are directly involved in the synthesis of deoxyribonucleic acid except _______.

A) Thioredoxin B) NADPH C) Ribonucleotide reductase D) Thioredoxin reductase E) HGPRT Ans E 19) Inorganic nitrogen is initially assimilated into which of the following amino acids A) Glycine B) Alanine C) Serine D) Glutamine E) Leucine Ans D 20) The amino acids serine and _______ are preferentially used to synthesize glucose for export from the liver A) Lysine B) Histidine C) Alanine D)Tryptophan E) Glycine Ans C 21) Nitrogen fixation requires iron and ________ as cofactors.

A) Cu B) Zn C) Mo D) Ba E) Mg Ans C 22) One-carbon carriers in metabolism include

A) Biotin B) Folate C) SAM D) Both B and C are correct E) All of the above are correct Ans E 23) Which of the following is an -keto acid/-amino acid pair used in transamination?

A) Pyruvate/leucine B) Oxaloacetate/aspartate C) Oxaloacetate/glutamate D) -Ketoglutarate/aspartate E) -Keto--hydroxybutyrate/phenylalanine Ans B 24) In plants the pathway by which most ammonium ion is incorporated into organic molecules requires A) Glutamate synthetase B) Glutamine synthetase C) Reduced ferredoxin or NADPH D) Both B and C are correct E) All of the above are correct Ans E 25) Asparagine is formed from aspartic acid and _________ .

A) SAM B) Glutamine C) Ammonium ions D) Both A and C are correct E) All of the above are correct Ans B 26) The benzene ring of the aromatic amino acids is formed by the A) Dehydrogenation of cyclohexane B) Deamination of dietary phenylalanine C) Shikimate pathway D) Dehydroxylation of tyrosine

E) Transamination of -keto--methylvalerate Ans C 27) The oxidation state of the methenyl group (-CH=) is comparable to that of ____.

A) Methanol B) Formaldehyde C) Formate D) Both A and B are correct E) All of the above are correct Ans C 28) The methylated product of _______ is creatine.

A) Norepinephrine B) -Aminobutyric acid C) Guanidinoacetate D) Phosphoribosylglycinamide E) Hemin Ans C 29) The fixation of nitrogen requires _______.

A) Fe-Mo protein B) Fe protein C) Ferredoxin D) Both A and B are correct E) All of the above are correct Ans E 30) Most aminotransferases utilize ________as the recipient -keto acid.

A) -Ketoglutarate B) Pyruvate C) Oxaloacetate D) Phenylpyruvate E) Imidazolpyruvate Ans A 31) The primary energy source for enterocytes is:

A) Glucose B) Fatty acids C) Glutamine D) Lysine E) Alanine Ans C 32) ________ ATP molecules are required to convert one mole of nitrogen to two ammonia molecules.

A) 1 B) 5 C) 8 D) 16 E) 20 Ans D 33) The first step in nitrogen fixation is ________.

A) Binding of nitrogen to the Fe-S complex B) Binding of nitrogen to the Mo-Fe complex C) Transfer of electrons to ferredoxin from NADPH D) Conversion of nitrogen to H-N=N—H E) Conversion of nitrogen to hydrazine Ans C 34) The major form of regulation of nitrogen fixation is _______.

A) ATP levels B) NADPH levels C) Transcriptional control of the nitrogen fixation genes D) Ammonia levels E) Nitrogen availability Ans C 35) The first amino acid containing newly fixed nitrogen is _______.

A) Glutamine

B) Glycine C) Proline D) Asparagine E) Alanine Ans A 36) Which of the following is not a gasotransmitter?

A) NO B) CO2 C) CO D) H2S E) Both A and D are correct Ans B 37) Which of the following compounds is not present in the normal process of nitrogen fixation A) Elemental nitrogen B) HN=NH C) NH2OH D) H2NNH2 E) None of the above Ans C 38) Hydrogen sulfide is produced from A) SAM B) Cysteine C) Cystine D) Both B and C are correct D) All of the above are correct Ans D 39) The six families of amino acids are glutamate, aromatic, serine, aspartate, pyruvate, and _______.

A) Glycine B) Histidine C) Tyrosine

D) Tryptophan E) Ketogenic Ans B 40) Which of the following neurotransmitters are derived from amino acids?

A) Histamine B) NADH C) Catecholamines D) SAM E) Both A and C are correct Ans E 41) In ocean water phytoplankton growth is limited by temperature and low levels of nutrients containing A) Sodium B) Carbon dioxide C) Nitrogen D) Potassium E) Calcium Ans C 42) Hypoxic water is characterized by A) High levels of ammonia B) Low levels of oxygen C) High levels of oxygen D) Excessive warmth E) Excessive nutrients Ans B 43) The ultimate products of mineralization of organic nitrogen is A) Ammonia B) Nitrate C) Nitrite D) Dinitrogen E) Amino acids

Ans D 44) The most common intracellular reducing agent is A) NADP B) NADPH C) Ammonia D) Glutathione E) Cysteine Ans D 45) In nitrogen fixation by microorganisms what gas other than ammonia is produced?

A) Hydrazine B) Carbon dioxide C) Water vapor D) Hydrogen E) Oxygen Ans D 46) Which of the following is not a function of glutathione A) Antioxidant B) Cofactor for antioxidant enzymes C) Protect cells from xenobiotics D) Maintain sulfhydryl groups in reduced form E) Provides reducing equivalents for nitrogen fixation Ans E

SHORT ANSWER 47) What is meant by the term amino acid pool?

Ans The term amino acid pool refers to those amino acid molecules that are immediately available in an organism for use in metabolic processes.

48) What is an essential amino acid?

Ans An essential amino acids is an amino acid that cannot be synthesized by the body and must be obtained from the diet.

49) What is the blood brain barrier?

Ans The blood brain barrier is a physical barrier between the cells of the brain and blood vessels that prevents many polar molecules and ions from being transported from brain capillaries into brain cells.

50) What is a retrograde neurotransmitter?

Ans A retrograde neurotransmitter is a neurotransmitter molecule that once released from the presynaptic cells binds to the presynaptic cell to potentiate its activity.

51) What is meant by the term one-carbon metabolism?

Ans One-carbon metabolism is a set of reactions in which single carbon atoms are transferred from one molecule to another.

52) The concentration of serine differs significantly in blood flowing from the liver to the rest of the body and the nutrients entering the enterocyte. Explain why the concentrations change.

Ans The concentration of serine is typically higher in the nutrients entering the enterocytes than in the blood leaving the liver because the liver uses serine to manufacture glucose for transport.

53) Why are nitrogen compounds limited in the biosphere? Give two reasons.

Ans While nitrogen incorporation into organic molecules is thermodynamically favored, the conditions in the biosphere (temperature, pressure and pH) are such that the reactions have low kinetic probability. Only a few organisms possess the molecular machinery to surpass the energy barrier to achieve nitrogen compound synthesis.

54) The concentration of alanine differs significantly in blood flowing from the liver to the rest of the body and the nutrients entering the enterocyte. Explain why the concentrations change.

Ans The concentration of alanine is typically higher in the nutrient pool entering the enterocytes than in the blood leaving the liver because the liver uses alanine to synthesize glucose via gluconeogenesis.

55) Why are transamination reactions important in both the synthesis and degradation of amino acids?

Ans Transamination reactions are a mechanism for conserving valuable nitrogen reserves. The reaction is reversible and can be used to convert -keto acids produced by metabolic reactions into nonessential -amino acids that may be in short supply. Surplus amino acids present in larger amounts than required by current metabolic needs are used as the source of the amino group.

56) What are the two major classes of neurotransmitters in terms of their effects on postsynaptic cells? How do their modes of action differ? Give examples of each type of neurotransmitter.

Ans Neurotransmitters are either excitatory or inhibitory. Excitatory neurotransmitters (e.g., glutamate and acetylcholine) promote the depolarization of a postsynaptic cell.

Inhibitory neurotransmitters (e.g., glycine) inhibit the action potentials in postsynaptic cells i.e., they make the membrane potential more negative.

57) List the major reactions in the synthesis of arginine from glutamate.

Ans Arginine is produced in the following series of reactions: Glutamate + Acetyl-CoA -> N-acetylglutamate + CoASH N-acetylglutamate -> -> -> L-ornithine L-ornithine -> -> L-arginine 58) Illustrate the pathway to synthesize glycine.

Ans Glycine is produced in the following series of reactions: 3-Phosphoglycerate + NAD+ -> 3-Phosphohydroxypyurvate + NADH + H+ 3-Phosphohydroxypyruvate + Glutamate -> 3-Phosphoserine + -Ketoglutarate 3-Phosphoserine + H2O –> Serine + Pi Serine + THF -> Glycine + N5N10-methylene THF + H2O 59) What are the most important carriers in one-carbon metabolism? Give two examples of processes in which each one participates.

Ans The two most prominent one-carbon carriers are THF (tetrahydrofolate, the biologically active derivative of folic acid) and SAM (S-adenosylmethionine). THF plays important roles in the synthesis of several amino acids and the nucleotides. SAM which contains an activated methyl thioether group, is a major methyl donor in the synthesis of numerous biomolecules such a phosphatidylcholine, epinephrine, and carnitine.

60) Glutathione is an important intracellular thiol. List five functions of glutathione in the body.

Ans Glutathione is involved in the synthesis of DNA, RNA and the eicosanoids. It is also utilized as a reducing agent that protects cells from radicals, oxygen, and as a conjugating agent for environmental toxins. Glutathione is also believed to play a role in amino acid transport.

61) Discuss the roles of branched-chain amino acids (BCAAs) in protein structure and synthesis.

Ans The BCAAs (leucine, isoleucine, and valine) are essential amino acids and provide critical hydrophobic side chains in protein structure. BCAAs also represent a major transport form of amino nitrogen from the liver to other tissues, where they are used in protein synthesis, as well as various amino acid derivatives.

62) Through what intermediates do nitrogen atoms pass during its reduction by nitrogenase?

Ans The following intermediates occur during the reduction of molecular nitrogen to yield ammonia: diimine (HN=NH) and hydrazine (H2NNH2).

63) Tetrahydrofolate, a biologically active form of folic acid is shown below. How is it formed?

Folic Acid

Ans. THF is formed by the reduction of folic acid with NADPH in two reaction catalyzed by dihydrofolate reductase.

Tetrahydrofolate

64) Identify the following molecule. What is its metabolic role?

Ans S-adenosylmethionine is a methyl transfer agent.

65 What carbon in uracil is derived from carbon dioxide?

Ans The carbon at position two of the uracil ring is derived from carbon dioxide.

66) In the nitrogen reductase system for every molecule of ammonia released one molecule of hydrogen gas is also produced. What is the source of the hydrogen gas?

Ans The source of the hydrogen gas produced by the nitrogen reductase system is NADPH. ESSAY QUESTIONS 67 Nitrogenase complexes are irreversibly inactivated by oxygen. Explain how the nitrogen-fixing bacteria solve this problem.

Ans Nitrogen-fixing organisms solve the problem of oxygen inactivation of nitrogenase in several ways. Anaerobic organisms prevent exposure to oxygen by living only in anaerobic soil. Other organisms physically separate oxygen from the nitrogenase complex. For example, many of the cyanobacteria produce specialized nitrogenasecontaining cells called heterocysts. The thick walls of the heterocysts isolate the enzymes from atmospheric oxygen. In addition, legumes produce an oxygen binding protein called leghemoglobin, which traps oxygen before it can interact with the nitrogenase complex.

68) In pyrimidine nucleosides the anti conformation predominates because of steric interactions with pentose. Do the purine nucleotides have similar interactions?

Ans Surprisingly, the larger purine base does not have similar steric interactions with the pentose. Even though the pyrimidine has only one ring, its carbonyl group interferes sterically with the pentose ring to hinder the formation of the syn conformation. In contrast, the shape and functionality of the purine rings are such that steric interactions with the pentose are minimal when in the syn conformation, in spite of the overall larger size of the purines.

69) Vegans (individuals who do not consume meat or meat products such as milk and eggs) may develop pernicious anemia if they take antibiotics. Explain.

Ans Vegans are at risk for a vitamin B12 deficiency because of their diet. If significant amounts of antibiotics are also consumed, normal intestinal microorganisms, some of which synthesize vitamin B12, may be eliminated. With the loss of the last source of the vitamin, the body becomes so depleted that the symptoms of pernicious anemia will manifest themselves.

70) The amino acids glutamine and glutamate are central to amino acid metabolism.

Explain.

Ans Glutamate plays a central role in amino acid metabolism because it and ketoglutarate constitute one of the most common -amino acid/-keto acid pairs used in transamination reactions. Glutamate also serves as a precursor of several amino acids and as a component of polypeptides. Glutamine serves as the amino group donor in numerous biosynthetic reactions (e.g., purine, pyrimidine, and amino sugar synthesis) as a safe storage and transport form of ammonia, and as a component of polypeptides.

71) Both oxygen and nitrogen are present in the atmosphere as gases. Oxygen is reactive and nitrogen is relatively inert. What features of the two molecules account for this difference?

Ans Atmospheric nitrogen contains a nonpolar triple bond that must be broken to reduce nitrogen to ammonia. In contrast diatomic oxygen is a unstable diradical, which is much more reactive (e.g., ready to accept electrons in a redox reaction) than the stable nitrogen triple bond.

72) Although they are consumed by animals in the diet, the purine and pyrimidine bases (unlike fatty acids and sugars) are not used to generate energy. How does the body use them? What is the ultimate fate of dietary nitrogenous bases?

Ans Purine and pyrimidine bases are recycled in salvage pathways. Instead of being degraded to form precursors for catabolic pathways they are oxidized and excreted as nitrogenous waste products.

73) Tyrosine is a nonessential amino acid in humans. Under what circumstances would it become an essential amino acid?

Ans Tyrosine becomes an essential amino acid if its precursor the EAA phenylalanine is excluded from the diet, the enzyme phenylalanine-4-monoxygenase is missing or defective, or the coenzyme BH4 is not available.

74) The antibiotic sulfanilamide is an analogue of the para-aminobenzoic acid component of folate. Why would certain microorganisms die when exposed to sulfanilamide?

Ans Microorganisms synthesize folic acid from its precursors. This pathway is blocked if the para-aminobenzoic acid analogue sulfanilamide is present since it is a competitive inhibitor of the bacterial enzyme used to synthesize folate. Sulfanilamide does not kill susceptible infectious microorganisms. Instead it stops their growth, thus limiting their numbers so that the immune system can effectively destroy them.

75) Why do marathon runners prefer beverages with glucose instead of amino acids during a long run?

Ans Running is a physical activity that requires the rapid metabolism of both fatty acids and glucose. The most rapidly utilized source of glucose is blood glucose. Although certain amino acids can be absorbed in the intestine and used as substrates in gluconeogenesis in the liver this process is slower then the immediate absorption of glucose into the blood.

76) By definition essential amino acids are not synthesized by an organism. Arginine is classified as an essential amino acid in infants even though it is part of the urea cycle.

Explain.

Ans Arginine is normally synthesized by the urea cycle. In small children, the urea cycle is not fully functional. Consequently, arginine must be obtained from external sources.

CHAPTER FIFTEEN NITROGEN METABOLISM II: DEGRADATION 1) In addition to urea, humans also excrete waste nitrogen as A) Uric acid B) Ammonia C) Nitrous oxide D) Guanidine E) Elemental nitrogen Ans A 2) Stress proteins A) Are only produced when cells are exposed to high temperatures B) Act solely as molecular chaperones C) Are referred to as heat shock proteins D) Both A and C are correct E) None of the above is correct Ans C 3) The ammonia that is incorporated into urea molecules is produced in reactions catalyzed by all of the following enzymes except A) Urease activity possessed by intestinal bacteria B) Serine dehydratase C) Glutamate dehydrogenase D) Serine hydroxymethyltransferase E) L-Amino acid transferase Ans D 4) N-Acetylglutamate is A) Produced from glutamate and acetyl-CoA B) Stimulates the activity of carbamoyl synthetase I C) Inhibits the activity of carbamoyl synthetase I D) Both A and B are true E) Both A and C are true Ans D

5) Amino acids whose degradation yields acetyl-CoA include all of the following except ________.

A) Threonine B) Glycine C) Glutamate D) Alanine E) Cysteine Ans C 6) Homogentisate is an intermediate in the degradation of __________.

A) Threonine B) Lysine C) Arginine D) Tryptophan E) Tyrosine Ans E 7) -Ketoadipate is an intermediate in the degradation of ________.

A) Lysine B) Valine C) Proline D) Leucine E) Tyrosine Ans A 8) In addition to phenylalanine-4-monooxygenase the conversion of phenylalanine to tyrosine requires ________.

A) Oxygen B) BH4 C) NADPH D) Both A and C are correct E) All of the above are correct Ans E

9) Amino acids whose degradation yields -ketoglutarate include all of the following except _________.

A) Arginine B) Glutamine C) Leucine D) Histidine E) None of the above is correct Ans C 10) Glutamate--semialdehyde is an intermediate in the degradation of _________.

A) Proline B) Glutamate C) Leucine D) Histidine E) Methionine Ans A 11) Amino acids whose degradation yields succinyl-CoA includes all of the following except ________.

A) Methionine B) Isoleucine C) Valine D) Histidine E) None of the above is correct Ans D 12) Alkaptonuria is caused by a deficiency of A) Phenylalanine hydroxylase B) Catechol-o-methyltransferase C) Aldehyde dehydrogenase D) Monoamine oxidase E) Homogentisate oxidase Ans E 13) Albinism is caused by the absence of A) Phenylalanine hydroxylase B) Tyrosinase

C) Branched chain -ketodehydrogenase D) Cyanocobalamin E) Monoamine oxidase Ans B 14) The major route for protein degradation is A) Cytoplasmic proteolytic enzymes B) Lysosomes C) UPS D) Both A and B are correct E) All of the above are correct Ans C 15) Which of the following reactions require SAM? A) Synthesis of dopamine B) Synthesis of norepinephrine C) Conversion of tryptophan to serotonin D) Conversion of norepinephrine to epinephrine E) None of the above is correct Ans D 16) The production of antibodies A) Occurs in B cells and is referred to as humoral immunity B) Occurs in T cells and is referred to as cellular immunity C) Occurs in B cells and is referred to as cellular immunity D) Occurs in T cells and is referred to as humoral immunity E) None of the above is correct Ans A 17) Which of the following is not a characteristic N-terminal amino acid residue of longlived proteins?

A) Sulfur containing amino acids B) Bulky hydrophobic amino acids C) Hydroxy containing amino acids D) Non bulky hydrophobic amino acids E) A and C

Ans B 18) Covalently bound chains with _________ or more ubiquitin monomers are required to transfer a protein to the proteosome.

A) 1 B) 2 C) 3 D) 4 E) 5 Ans D 19) Which of the following amino acids reacts with HOCl to form a nontoxic product during respiratory bursts?

A) Glycine B) Phenylalanine C) Taurine D) Aspartate E) Isoleucine Ans C 20) The end product of uracil degradation is ________.

A) Urea B) Ammonium ions C) Allantoate D) -Alanine E) -Aminoisobutryate Ans D 21) The end product of thymine degradation is _______.

A) Urea B) Ammonium ions C) Allantoate D) -Alanine E) -Aminoisobutryate

Ans E 22) Dihydropyrimidine dehydrogenase catalyzes the conversion of A) Uridine to uracil B) Uracil to dihydrouracil C) Thymine to dihydrothymine D) Both A and B are correct E) Both B and C are correct Ans E 23) The glucogenic amino acids include all of the following except ______.

A) Glycine B) Cysteine C) Tyrosine D) Serine E) Alanine Ans C 24) Components of the transulfuration pathway include all of the following except ________.

A) SAM B) Cysteine C) Homocysteine D) ATP E) BH4 Ans E 25) In adenosine deaminase deficiency large concentrations of dATP result in the inhibition of _____________.

A) Xanthine oxidase B) Purine nucleoside phosphorylase C) Aminohydrolase D) 5’-nucleotidase E) Ribonucleotide reductase

Ans E 26) Which of the following tissues can only replenish citric acid cycle intermediates by the purine nucleotide cycle?

A) Muscle B) Brain C) Heart D) Liver E) Kidney Ans A 27) All of the following are directly involved in protein turnover except _______.

A) Hsp B) Calpains C) Cathepsin D) Proteosome E) None of the above is correct Ans E 28) Propionyl-CoA and L-methylmalonyl-CoA are intermediates in the conversion of ________ to succinyl-CoA A) Histidine B) Isoleucine C) Valine D) Both A and B are correct E) Both B and C are correct Ans E 29) The end products of the transulfuration pathway are sulfate and _______.

A) ATP B) Serine C) Aspartate D) Pyruvate E) Oxaloacetate Ans D 30) Methylmalonic acidemia results from a deficiency of

A) Branched chain -keto acid dehydrogenase B) Methylmalonate dehydrogenase C) Vitamin B12 D) Vitamin B6 E) None of the above is correct Ans C 31) The main nitrogen storage molecule in animals is A) Carbohydrates B) Amino acids C) Nucleic acids D) Fats E) None of the above Ans E 32) Decomposers convert organic nitrogen to ________.

A) Ammonia B) Nitrate C) Nitrite D) Dinitrogen E) All of the above are correct Ans E 33) In general, catabolism of amino acids begins with A) Removal of the amino group B) Decarboxylation C) -Oxidation D) Conversion to the CoA derivative E) Conversion to pyruvate Ans A 34) In muscle excess amino groups are transferred to _________ to produce glutamate A) Pyruvate B) Oxaloacetate

C) -Ketoglutarate D) Glutamine E) Oxalomalonate Ans C 35) Ammonia is transferred to the liver as A) Urea B) Ammonia C) Glutamine D) Pyruvate E) Aspartate Ans C 36) Urea is synthesized in which organ?

A) Liver B) Heart C) Kidney D) Muscle E) All of the above Ans A 37) In patients with alkaptonuria the urine is colored _________.

A) Yellow B) Clear C) Black D) Blue E) Both answers C and D are correct Ans C 38) High phenylalanine blood levels from phenylketonuria results in damage to which organ?

A) Brain B) Heart C) Kidney D) Live

E) Muscle Ans A 39) Which of the following conditions result in a buildup of -ketoacids derived from branched chain amino acids?

A) Alkaptonuria B) Albinism C) Phenylketonuria D) Maple syrup urine disease E) Methyl-malonate acidemia Ans D 40) A buildup of uric acid is characteristic of which of the following diseases?

A) Gout B) Adenosine deaminase deficiency C) Purine nucleoside phosphorylase deficiency D) Albinism E) Both A and C are correct Ans A 41) Autophagy is A) B) C) D) E)

Used to degrade extracellular material Another term for phagocytosis Used to degrade worn out intracellular components Used to degrade secreted intercellular components Another term for endocytosis

Ans C 42) Phagocytosis is A) Used to degrade extracellular material B) Another term for autophagy C) Involved in the degradation of intercellular material D) Another term for exocytosis E) None of the above Ans A

43) Proteosomal digestion of what type of protein does not require ubiquination A) Globular B) Highly oxidized C) Denatured D) Structural E) Intercellular Ans B 44) Autophagy is triggered by A) Hypoxia B) Oxidative stress C) Nutrient deprivation D) High temperature E) All of the above Ans E 45) The ultimate products of autophagy include A) Carbon dioxide B) Fatty acids C) Amino acids D) Sugars E) B, C, and D Ans E

46) The major catabolic mechanism used by eukaryotic cells to maintain optimal function and respond to changing environmental conditions is A) Microautophagy B) Macroautophagy C) Chaperone-mediated autophagy D) Phagocytosis E) Endocytosis Ans B

SHORT ANSWER 47) What is maple syrup urine disease?

Ans Maple syrup urine disease is an illness with symptoms that include convulsions, brain damage and mental retardation. It is caused by a deficiency in the enzyme complex branched-chain -keto acid dehydrogenase, which results in the accumulation of toxic keto acids derived from leucine, isoleucine, and valine.

48) What is phenylketonuria?

Ans Phenylketonuria is an illness caused by a deficiency of phenylalanine hydroxylase.

Toxic levels of phenylalanine accumulate in the blood, which results in the disruption of amino acid transport into the brain. Symptoms include brain damage and mental retardation.

49) What are T cells?

Ans T cells or T lymphocyte are a white blood cells that bear antibody-like molecules on thier surfaces. T cells destroy foreign cells in cellular immunity.

50) What are  cells?

Ans B cells or B lymphocyte are white blood cells that produce and secrete antibodies, the proteins that initiate the destruction of foreign substances or cells in the humoral immune response.

51) What are the major nitrogenous waste products of metabolism in humans?

Ans The major nitrogen containing waste molecules are ammonia, urea and uric acid.

52) What are three purposes served by protein turnover?

Ans The process of protein turnover promotes metabolic flexibility, protects the cell from the accumulation of abnormal proteins, and is a key feature for organismal developmental processes.

53) What are the structural features of proteins that mark them for destruction?

Ans The structural features that apparently mark proteins for destruction are (1) certain N-terminal amino acid residues (e.g., methionine or alanine), (2) peptide motif sequences (e.g., amino acid sequences with proline, glutamic acid, serine, and threonine), and (3) oxidized amino acid residues (amino acids residues whose side chains have been oxidized by oxidases or ROS).

54) What are the seven metabolic products produced by the degradation of amino acids?

Ans The metabolic products of amino acid degradation are acetyl-CoA, acetoacetyl-CoA, pyruvate -ketoglutarate, succinyl-CoA, fumarate and oxaloacetate, Ammonia is also a product of amino acid degradation.

55) In humans the purine ring cannot be degraded. How is it excreted?

Ans Purines are degraded to xanthine, which is then oxidized to yield the ring-containing molecule uric acid. A significant percentage of uric acid is excreted in the urine.

56) Describe how glutamate is degraded.

Ans Glutamate is converted to the citric acid cycle intermediate -ketoglutarate by glutamate dehydrogenase or by transamination.

57) Describe how the glucose-alanine cycle acts to transport ammonia to the liver.

Ans Amino groups of amino acids derived from muscle protein are transferred to pyruvate via a transamination reaction to yield alanine. Alanine is then transferred to the liver where it is reconverted to pyruvate by transferring its amino group to ketoglutarate to form glutamate. Pyruvate is then converted to glucose via gluconeogenesis.

58) What are the metabolic intermediates in alanine degradation?

Ans Alanine transfers its amino group to -ketoglutarate to form pyruvate and glutamate.

The glutamate is then oxidatively deaminated to form ammonia and −ketoglutarate.

Pyruvate and -ketoglutarate are degraded by the citric acid cycle.

59) Describe the Krebs bicycle. What compound links the citric acid and urea cycles?

Ans The term Krebs bicycle refers to two interlocking cyclic pathways: the citric acid cycle and the urea cycle. The aspartate-arginosuccinate shunt of the citric acid cycle is responsible for regenerating the aspartate needed for the urea cycle from fumarate. The molecule the two cycles have in common is arginosuccinate.

60) Describe how a protein is targeted for degradation by ubiquitination.

Ans In ubiquitination, the major mechanism of protein degradation, the small protein ubiquitin is covalently attached to lysine residues of a protein with structural features such as oxidized amino acids residues that mark it for destruction. Once the protein is ubiquitinated it is degraded by proteases.

61) Which of the following compounds yield uric acid when degraded: DNA, FAD, CTP, PRPP, -Alanine, urea, NAD+.

Ans When they are degraded, the purine containing molecules DNA, FAD, and NAD+ yield uric acid.

62) Describe how tyrosine is degraded.

Ans Tyrosine is catabolized in five reactions to acetoacetate and fumarate. The resulting acetoacetate is then converted to acetoacetyl-CoA, and then to acetyl-CoA. Acetyl-CoA is then catabolized in the TCA cycle.

63) Explain why the amino acid tryptophan is both ketogenic and glucogenic.

Ans Tryptophan is ketogenic because its catabolic pathway results in the formation of ketoadipate, which reacts further to form acetoacetyl-CoA and then acetyl-CoA. Tryptophan is glucogenic in that one. If its catabolic reactions along this pathway also produces alanine, which is converted to pyruvate (a substrate for gluconeogenesis) via a transamination reaction.

64) Explain how tyrosinase deficiency causes albinism.

Ans Tyrosinase catalyzes the conversion of DOPA to dopaquinone, a highly reactive molecule that is the precursor of the pigment molecule melanin. In the absence of tyrosinease, melanin can’t be synthesized, thus resulting in albinism.

65) Why can’t humans degrade purine rings?

Ans Humans can’t degrade purine rings because they do not synthesize the enzymes urate oxidase and allantoinase. These enzymes catalyze the conversion of uric acid to allantoate, the first product of purine degradation that does not contain a ring.

ESSAY QUESTIONS

66) The urea cycle occurs partially in the cytoplasm and partially in the mitochondrion.

Discuss the urea cycle reactions with reference to these cellular locations.

Ans The first two reactions in the biochemical pathway that converts ammonium ion to urea (i.e., the formation of carbamoyl phosphate and citrulline) occur in the mitochondrial matrix. The urea cycle continues as citrulline is transported into the cytoplasm. The products of the subsequent reactions are urea and ornithine. The latter molecule, ornithine is transported back into the mitochondrial matrix where it reacts with another molecule of carbamoyl phosphate to yield citrulline.

67) In individuals with PKU, is tyrosine an essential amino acid?

Ans Individuals with PKU lack phenylalanine hydroxylase (phenylalanine-4monooxygenase) activity, so they cannot synthesize tyrosine from phenylalanine.

Tyrosine is therefore an essential amino acid for these patients.

68) Most amino acids are degraded in the liver. This is not true of the branch-chain amino acids, most of which degraded in extrahepatic tissues with high protein turnover. What is the primary tissue that uses branched chain amino acids?

Ans The branched chain amino acids (leu, ile, val) are metabolized primarily in muscle tissue, where they are used to synthesize nonessential amino acids.

69) Explain why providing domestic cats with a vegetarian diet is a bad idea.

Ans Domestic cats cannot synthesize taurine and they must obtain it by consuming meat.

Without taurine, domestic cats become listless and die prematurely.

70) Alkaptonuria, albinism, phenylketonuria are all examples of which kind of defiency?

Ans These conditions are all genetic diseases in which mutations result in deficiencies of single enzymes and/or amino acid metabolism.

71) Why can’t humans simply excrete waste nitrogen atoms as ammonia rather than utilize the energetically expensive process of urea synthesis?

Ans Humans cannot excrete waste nitrogen atoms as ammonia because of its toxicity.

Urea is also toxic but much less so than ammonia. The conversion of ammonia to urea not only allows the nitrogen to be transported and excreted in a much less toxic form but also prevents the large water loss that would be required by the excretion of ammonia.

72) Phenylketonuria can be caused by deficiencies in phenylalanine hydroxylase and by enzymes catalyzing the formation and regeneration of 5,6,7,8,-tetrahydrobiopterin. How can this second deficit cause the symptoms of PKU? Ans Tetrahyrobiopterin is a cofactor in the oxidation of phenylalanine to form tyrosine.

The sustained absence of this cofactor would result in an increased blood level of phenylalanine and the appearance of the symptoms of PKU. 73) In their in vitro studies using liver slices, Krebs and Henseleit observed that urea formation was stimulated by the addition of ornithine, citrulline, and arginine. Other amino acids had no effect. Explain these observations.

Ans Ornithine, citrullene, and arginine are intermediates in the urea cycle, Increased concentration of these substrate biomolecules stimulates the formation of urea.

74) Caffeine, a methylated xanthine found in chocolate, coffee, and tea is excreted as uric acid. Use your knowledge of the metabolism of other purine compound to suggest how caffeine is metabolized.

Caffeine Ans Because of the structural similarities to purine, caffeine is converted to a variety of derivatives by xanthine oxidase (e.g., 1-methyluric acid, and 7-methylxanthine).

75) Discuss and compare the three forms of autophagy.

Ans The three forms of autophagy, a cellular degradation pathway in which cellular components are degraded by hydrolytic enzymes in lysosomes, are chaperone-mediated autophagy, microautophagy, and macroautophagy. Chaperone-mediated autophagy is a receptor-mediated process in which specific proteins are bound to a chaperone complex are unfolded and transported in lysosomes, where microautophagy and macroautophagy apply to small amounts and bulk degradation of cytoplasmic components, respectively.

CALCULATIONS 76) Urea formation is energetically expensive, requiring the expenditure of 4 mol of ATP per mole of urea formed. However NADH is produced when fumarate is reconverted to aspartate. How many ATP molecules are produced by the mitochondrial oxidation of the NADH? What is the net ATP requirement for urea synthesis?

Ans The NADH formed during the conversion of fumarate to aspartate results in the synthesis of approximately 2.5 ATP. Therefore, the net ATP requirement for urea synthesis (4ATP-2.5 ATP) is approximately 1.5 moles of ATP per mole of urea.

CHAPTER SEVENTEEN NUCLEIC ACIDS 1) Which of the following is/are differences between DNA and RNA A) DNA is single stranded B) RNA is double stranded C) RNA contains uracil D) RNA is single stranded E) Both D and E are correct Ans E 2) Which of the following describes the flow of genetic information as stated in the central dogma of molecular biology?

A) RNA → Protein → DNA B) DNA → RNA → Protein C) DNA → Protein → RNA D) Protein → RNA → DNA E) None of the above is correct Ans B 3) The DNA “backbone” is composed of A) An amide bond between deoxyribose and a nitrogenous base B) A glycosidic bond between deoxyribose and a nitrogenous base C) A phosphodiester bond between 3! and 5! hydroxyl groups of adjacent deoxyribose residues D) A phosphodiester bond between 2! and 5! hydroxyl groups of adjacent deoxyribose residues E) None of the above is correct Ans C

4) Nucleosomes are composed of all of the following except ________.

A) H1 B) H2 C) H3 D) H4

E) H5 Ans E

5) There are approximately _________ human genes.

A) 10,000 B) 20,000 C) 100,000 D) 1,000,000 E) 10.000.000 Ans B 6)______ are gene sequences that code for a gene product.

A) Introns B) Exons C) Nucleosomes D) Cruciforms E) Snurps Ans B 7) A genome is A) The sequence that contains the base sequence information necessary to code for a gene product B) The complete DNA base sequence in an organism C) The complementary pairing of purine and pyrimidine bases D) A base pair E) A newly synthesized RNA molecule Ans B 8) Protein synthesis is called A) Translation B) Transcription C) Replication D) A metabolome

E) Proteome Ans A 9) The entire set of proteins synthesized by a cell is called A) Metabolome B) Genome C) Proteome D) Epigenome E) Transcriptome Ans C 10) The polyamines assist in the compression of eukaryotic chromosome structure because they A) Contain functional groups that bond to DNA B) Assist in the formation of telomeres C) Possess positive charges that interact with the negative charges of DNA D) Promote chemical modification of the histones E) None of the above is correct Ans C 11) In nucleosome structure the histone ________ aids in stabilizing the wrapping of DNA around the protein octomer.

A) H1 B) H2A C) H2B D) H3 E) H4 Ans A 12) Chromatin contains several levels of structure which include A) Nucleosomes B) 200 nm filaments C) 30 nm fiber D) Both B and C are correct E) All of the above are correct Ans E

13) D loops and variable loops are found in _______ A mRNA B) rRNA C) tRNA D) hnRNA E) snRNA Ans C 14) Which of the following are involved in the splicing of RNA molecules?

A) Snurps B) snRNA C) rRNA D) Both A and B are correct E) None of the above is correct Ans D 15) The DNA strand that acts as a template during transcription is referred to as the ______ strand.

A) Sense B) Antisense C) Transcribed D) All of the above are correct E) None of the above is correct Ans B 16) Determine the mRNA sequence for the following DNA sequence.

5’-GCCATTTCCCGTTA-3’ A) 5’-CGGTAAAGGGCAAT-3’ B) 5’-CGGUAAAGGGCAAU-3’ C) 5’-TAACGGCAAATGGC-3’ D) 5’-UAACGGCAAAUGGC-3’ E) 5’-UAACGGGAAAUGGC-3’ Ans E

17) Which of the following does not contribute to the noncovalent interactions that stabilize the helical strands of DNA A) Hydrophobic interactions B) Phosphodiester bonds C) Hydrogen bonds D) Base stacking E) Hydration Ans B 18) During a transition mutation which of the following bases would be substituted for cytosine?

A) Thymine B) Adenine C) Guanine D) Both B and C are correct E) All of the above are true Ans A 19) The polyamines are a class of DNA binding molecules that include ______.

A) Spermine B) Speruline C) Spermidine D) Both A and C are correct E) All of the above are correct Ans D 20) _______ are structures that occur at the ends of chromosomes A) Cistrons B) Telomeres C) Cruciforms D) Centromeres E) Capsids Ans B

21) HIV infection of a susceptible cell is initiated when the gp120 envelope protein binds the _______ antigen.

A) T4 B) C4 C) T2 D) C2 E) None of the above is correct Ans E 22) HIV is a type of A) Pox virus B) Rhabdovirus C) Herpes virus D) Papilloma virus E) Retrovirus Ans E 23) HIV possesses a ________ genome A) ssDNA B) dsDNA C) ssRNA D) dsRNA E) None of the above is correct Ans C 24) Hydroxyapatite A) Is a calcium phosphate gel B) Binds to double stranded DNA C) Is used in column chromatography D) Both A and C are correct E) All of the above are correct Ans E 25) Southern blotting

A) Is a technique used to identify specific genes B) Utilizes restriction enzymes C) Is a chain terminating method D) Both A and B are correct E) All of the above are correct Ans D 26) The genetic variations observed in DNA fingerprinting are referred to as ______.

A) RFLPs B) RLFPs C) FRLPs D) DFLPs E) DLFPs Ans A 27) The extraction and purification of bacterial DNA involves the use of which of the following.

A) RNase B) Lysozyme C) Phenol and chloroform D) Both A and B are correct E) All of the above are correct Ans E 28) Palindromes A) Form cruciforms B) Contain inverted repeats C) Are sequences that provide the same information whether they are read forward or backwards D) Play a role in the function of restriction enzymes E) All of the above are correct Ans E 29) The denaturation of DNA is

A) Promoted by heat, low salt concentration, and extremes of pH B) Reversible C) Monitored by measuring the absorbance at 300 nm D) Both A and B are correct E) All of the above are correct Ans D 30) The chain terminating method for sequencing DNA was developed by A) Maxam and Gilbert B) Frederick Sanger C) Watson and Crick D) Hershey and Chase E) None of the above is correct Ans B 31) In a transversion mutation A) A purine base is substituted for a pyrimidine base B) A pyrimidine base is substituted for a purine base C) A purine or pyrimidine base is frame shifted D) Both A and B are correct E) All of the above are correct Ans D 32) A nucleoid is: A) Supercoiled DNA attached to a protein core B) Negatively supercoiled DNA C) Positively supercoiled DNA D) Relaxed DNA E) Either B or C depending on the organism Ans A 33) Chromatin is: A) Supercoiled DNA B) DNA complexed with histones C) Linear uncoiled DNA D) Relaxed DNA

E) Genes Ans B 34) Intergenic sequences are A) DNA segments that do not code for gene product B) Junk DNA C) DNA that codes for more than one product D) DNA which stabilizes the nucleosome E) Both A and B are correct Ans E 35) Restriction enzymes A) Prevent DNA synthesis B) Prevent RNA synthesis C) Prevent protein synthesis D) Cut DNA at specific base sequences E) Both A and B are correct Ans D 36) The hypochromic effect is A) The aggregation of chromatin into large clusters B) The shift of light absorption to longer wavelengths C) The formation of chromatin-histone complexes D) The conversion of B-DNA to Z-DNA E) The shift of light to shorter wavelengths Ans B 37) Which of the following is the largest and most complex structure?

A) Genes B) Nucleotides C) Nucleosomes D) Chromosomes E) Chromatin Ans D

38) Which of the following is not a function of RNA? A) Regulation of gene expression B) Cell differentiation C) Catalysis D) Both A and C are functions of RNA E) All of the above are functions of RNA Ans E 39) Which of the following statements is not true of mRNA? A) Prokaryotic mRNAs are mainly polycistronic B) Eukaryotic mRNAs are mainly monocistronic C) Eukaryotic mRNAs are extensively modified after synthesis D) Prokaryotic mRNAs are immediately transmitted into protein without covalent modifications E) Prokaryotic mRNAs are capped with 7-methylguanosine Ans E 40) Lysogeny is: A) Cleavage of the cellular RNA B) Infection of the host cell by a virus C) Integration of the virus genome into the host chromosome D) Formation of the prophage from the virus coat E) None of the above is correct Ans C 41) A defect in which of the following HAR’s can result in microcephaly?

A) ASPM B) FOXP2 C) AMY1 D) LCT E) HAR1 Ans A 42) The change of a single base pair in a DNA chain is referred to as:

A) Transversion mutation B) Silent mutation C) Missense mutation D) Point mutation E) Nonsense mutation Ans D 43) A mutation caused by an alkylating agent is referred to as A) Transversion mutation B) Silent mutation C) Missing mutation D) Point mutation E) Nonsense mutation Ans A 44) A point mutation that converts the code for an amino acid to a premature stop signal is referred to as A) Transversion mutation B) Silent mutation C) Missing mutation D) Point mutation E) Nonsense mutation Ans E 45) Which of the following is not an endogenous cause of DNA damage?

A) Tautomeric shift B) Radiation C) Deamination D) Depurination E) ROS induced oxidation Ans B 46) Point mutations that occur in a population to any extent are referred to as

A) Silent mutations B) Nonsense mutation C) Transition mutation D) Single nucleotide polymorphisms E) Missense mutation Ans D

SHORT ANSWER 47) What is molecular biology?

Ans Molecular biology is the science devoted to elucidating the structure and functional properties of genomes.

48) What is the metabolome?

Ans The metabolome is the complete set of organic metabolites that are produced within a cell.

49) What is a transversion mutation?

Ans A transversion mutation is a type of point mutation in which a pyrimidine is substituted for a purine or vice versa.

50) What is a point mutation?

Ans A point mutation is a change of a single nucleotide base in a DNA sequence.

51) What is a silent mutation?

Ans A silent mutation is a change in DNA sequence that has no discernible effect on an organism.

52) What are Chargaff’s rules?

Ans Chargaff’s Rules describe the base composition of DNA. The concentrations of adenine and thymine are equal and the concentrations of cytosine and guanine are equal.

53) What is meant by the term single nucleotide polymorphism?

Ans Single nucleotide polymorphism (SNPs) are single nucleotide variations or point mutations that occur in at least 1% of the population 54) List three differences between eukaryotic and prokaryotic DNA. Ans Eukaryotic genomes are larger than those of prokaryotes. In contrast to prokaryote genomes, which consist entirely of protein coding genes, the majority of eukaryotic DNA sequences do no appear to have protein coding functions. Unlike prokaryotic genes, most eukaryotic genes are not continuous (i.e. they usually contain introns).

55) List three biological properties facilitated by supercoiling.

Ans Biological processes that are facilitated by supercoiling include packaging of DNA into compact forms (e.g., chromosomes), DNA replication and transcription.

56) Describe the structural differences between RNA and DNA. Ans RNA molecules differ from DNA in the following ways: (1) RNA contains ribose instead of deoxyribose. (2) the nitrogenous bases in RNA differ from those of DNA (e.g.,

uracil replaces thymine and several RNA bases are chemically modified), and (3) in contrast to the double helix of DNA, RNA is single-stranded.

57) What are the three most prominent forms of RNA? What roles do they play in cell function?

Ans The three major types of RNA are ribosomal RNA (a component of ribosomes), transfer RNA (each molecule transports a specific amino acid to the ribosome for assembly into proteins), and messenger RNA (each molecule specifies the sequence of amino acids in a polypeptide).

58)What features of the Z-DNA molecule allow the distinctive Zig Zag conformation to form?

Ans The transition from B-DNA to Z-DNA can occur when the nucleotide base sequence is composed of alternating purine and pyrimidine (e.g., CGCGCG). Because alternate nucleotides can assume different conformations (syn or anti), these DNA segments form a left-handed helix. The phosphate groups in the backbone of this DNA conformation form a zizzag pattern hence the name Z-DNA. 59) The melting point of a DNA molecule increases as the GC content increases. Explain.

Ans Guanine-cytosine pairs contain three hydrogen bonds, whereas adenine-thymine pairs contain only two. The proportion of GC pairs, i.e., the greater the number of hydrogen bonds holding the DNA strands together the higher the melting point will be.

60) Provide the complementary strand and the RNA transcription product for the following DNA template segment: 5’- AGGGGCCGTTATCGTT-3’

Ans The complementary DNA strand (written in the standard 5’ to 3’ direction is 5’AACGATAACGGCCCCT-3’. The RNA strand is 5’-AACGAUAACGGCCCCU-3’

61) Describe the structural features that stabilize RNA molecules.

Ans Single-stranded RNA forms three-dimensional structures by coiling back on itself, allowing it to form double-stranded regions with stabilizing features that are analogous to DNA, namely, short segments with hydrogen bonding between complementary base pairs (A-U, G-U, and G-C) and base stacking. These double-stranded regions in RNA are primarily intrachain, but may occur between adjacent molecules. Additional stabilizing interactions may occur between double-stranded regions and free loops of RNA. 62) Describe how DNA cell methylation patterns are retained from one cell generation to the next.

Ans The stable inheritance of DNA methylation patterns from one cell generation to the next is made possible by a class of enzymes called maintenance methyltransferases. They methylate the cytosines in CpG rich regions in newly synthesized DNA strands. The enzymes methylate the cytosines on the new strand at sites opposite to the methylated cytosines on the parental strand.

63) What error would cause more damage to a cell: A DNA replication error or a DNA transcription error.

Ans Unless it is corrected by DNA repair a DNA replication error will continue to be propagated as the replicated strands themselves undergo replication in the next cell cycle.

A transcription error is transient and will result in only a small number of defective gene products. Replication errors would therefore potentially cause more cellular damage.

64) When an aromatic hydrocarbon intercalates between two stacked base pairs, what effect may there be on DNA structure?

Ans When an aromatic hydrocarbon intercalates between two stacked pairs, either adjacent base pairs are deleted or new base pairs are inserted during replication.

Intercalating agents may also cause chromosomes to break.

65) Chargaff’s rules apply to DNA but not RNA. Explain.

Ans Chargaff’s rules do not apply to RNA because RNA is single stranded.

66) Describe how water affects DNA structure.

Ans Water stabilizes DNA structure by binding to phosphate groups, deoxyribose, 3- and 5- oxygen atoms and electronegative atoms in the nucleotide basses. Also, the increased entropy of surrounding water molecules drives the hydrophobic interactions between the nucleotide bases within the helix.

ESSAY QUESTIONS 67 Under physiological conditions DNA ordinarily forms B-DNA, However, RNA hairpins and DNA-RNA hybrids adopt the structure of A-DNA. Considering the structural differences between DNA and RNA explain this phenomena.

Ans The principle structural difference between DNA and RNA is the 2’-OH group of ribose in RNA molecules. In DNA which lacks the 2’-OH group in the deoxyribose sugar, hydrogen-bonded complimentary strands can easily adopt the B-form double helix.

In contrast, double-stranded regions of RNA molecules cannot adopt this conformation because of steric hindrance. Instead they adopt the less compact A-helical form in which there are 11 bp per turn and the base pairs tilt 200 away from the horizontal.

68) Jerome Vinograd found that when circular DNA from a polyoma virus is subjected to cesium chloride gradient centrifugation, it separates into two distinct bands, one

consisting of supercoiled DNA and the other of relaxed DNA. Explain how you would identify each band.

Ans Relaxed circular DNA has a strand is less compact than supercoiled circular DNA and so has a lower effective density. As a result the relaxed DNA will not migrate as far in the centrifuge tube as the supercoiled DNA. 69) 5-Bromouracil is an analogue of thymine which usually pairs with adenine.

However, 5-bromouracil frequently pairs with guanine. Explain.

Ans The electron withdrawing effect of bromine increases the likelihood of enol formation of uracil. The enol mimics the hydrogen bonding pattern of cytosine.

Therefore, 5-bromouracil can be paired with guanine.

70) The flow of genetic information is from DNA to RNA to protein. In certain viruses, the flow of information is from RNA to DNA. Is it possible for genetic information flow to begin with proteins? Explain.

Ans Because nucleotide base sequences and amino acid sequences are such completely different ‘languages” a complex mechanism is required for the “translation” of one type of information into another. In the absence of any evidence to the contrary it does not appear likely that there is a mechanism for transforming information expressed in proteins can be utilized to direct the synthesis of nucleic acids.

71) Your research requires the isolation of mitochondrial DNA without contamination with nuclear DNA. Describe how you would accomplish this task.

Ans Nuclei and mitochondria are separately obtained from source tissue by means of cell homogenization followed by density gradient centrifugation. The nucleic acids in each organellar fraction are then extracted with the aid of detergents, solvents and proteases

(to remove proteins). RNA is removed by treating with each sample with RNase. The DNA from each type of organelle is then further purified by centrifugation.

72) The set of mRNA’s present within a cell changes over time. Explain.

Ans Each cell is constantly receiving information from the environment. Cells adapt to changing conditions as information in the form of nutrients, hormones, growth factors, and other types of molecules triggers changes in the signal transduction mechanisms that ultimately cause changes in gene expression. The transcriptome, the set of mRNA molecules produced under specified conditions, is a measure of the current status of gene expression.

73) Some organisms are under considerable strain to streamline their genomes for the sake of more efficient operation. As a result, the mitochondria of eukaryotic species have lost the overwhelming majority of their genes, of which several hundred were transferred to the nuclear genome. Yet mitochondria still retain a genome with the capacity to produce several electron transport proteins. Suggest a reason why these energygenerating organelles retained the genes to produce this set of molecules.

Ans The protein components of the electron transport system are located in the inner membrane of mitochondria. When these components are damaged by ROS they need to be replaced immediately. If the genes coding for these molecules are in the mitochondria then they can be easily synthesized as needed. If the genes were in the cell nucleus a time-consuming signal mechanism would be required to initiate gene expression. The newly synthesized proteins would then have to be delivered back to the mitochondrion and then transported across the outer mitochondrial membrane and inserted into the inner membrane.

74) The suggestion has been made that DNA extracted from ancient fossils could be cloned and used to resurrect an extinct species. Comment on the practicality of this idea.

Ans DNA degrades with time. Ancient fossils have little intact DNA with which to reconstruct the organism. In addition, although intact DNA is vitally important for organismal function, it is only the operating system of the organism. Without access to a living example of such an organism, it would be impossible to reconstitute the physiological structure and functional properties that are unique to a species.

75) Fluorouracil is a structural analogue of thymine. The fluorine promotes enolization.

How is this effect used in the treatment of cancer?

Ans The enolization of the fluorouracil allows it to hydrogen bond with guanine rather than adenine and thereby cause a transition mutation. As these mutations accumulate rapidly dividing cells (the majority of which are cancer cells) are fatally damaged.

CALCULATIONS 76) There are six million base pairs in the human genome. Each bp is 0.3 nm in length.

Calculate the total length of the DNA in a single cell. Assuming that there are 1014cells in the human body calculate the total length of the DNA. How does this estimate compare to the distance from the earth to the sun (1.5 x 108 km)?

Ans The total length of DNA in a single cell is approximately 2m (six million x 0.34 nm). Assuming that there are 1014 body cells, the total length of the DNA in the human body is approximately 2 X 1011 km. This estimated length is about 1000 times greater that the distance from the earth to the sun, (Note that 1 nm = 10-9 m,)

77) A DNA sample contains 21% adenine. What is the complete percentage composition of the bases in DNA? Ans According to Chargaff’s rules if a DNA sample contains 21% adenine then it also contains 21% thymine. If the AT content is 42% then the C-G content is 58%.

Consequently, the guanine and cytosine percentages are both 29% in the DNA sample.

CHAPTER EIGHTEEN GENETIC INFORMATION 1) The replisome consists of all of the following proteins except _________.

A) DNA polymerase B) DNA topoisomerase C) Primase D) Catabolic gene activator protein E) Helicase Ans D 2) The experiment that demonstrated the mechanism whereby DNA is synthesized was performed by A) Avery, MacLeod and McCarty B) Watson and Crick C) Linus Pauling D) Meselson and Stahl E) Maurice Wilkins Ans D 3) The _____ are enzymes that catalyze the unwinding of duplex DNA. A) Topoisomerases B) Helicases C) Ligases D) Primases E) Unwindases Ans B 4) SSB are A) A series of nucleases that degrade RNA primers B) Substrates for DNA ligase C) Proteins that bind to single-stranded DNA D) Enzymes that catalyze Okazaki fragment formation E) Molecules that bind to DNA Ans C

5) The background rate of spontaneous mutations is approximately ________ mutations per gene per million gametes A) 0.01 to 0.1 B) 0.1 to 1 C) 1 to 10 D) 10 to 100 E) None of the above are correct Ans B 6) DNA polymerase  is believed to be involved in A) Eukaryotic DNA repair B) Mitochondrial DNA replication C) Chloroplast DNA replication D) Prokaryotic DNA synthesis E) Chloroplast DNA repair Ans A 7) Mutations are caused by all of the following except ________.

A) Depurinations B) Radiation C) Viruses D) Oxidative Damage E) None of the above are correct Ans E 8) DNA molecules are copied or replicated by a _______ mechanism.

A) Conservative B) Semiconservative C) Dispersive

D) More than one answer is correct E) All of the above are correct Ans B 9) The tangling of DNA strands during replication is prevented by _________.

A) Topoisomerases B) Helicases C) Ligases D) Primases E) Unwindases Ans A 10) The rate of DNA synthesis in eukaryotes is approximately_________ nucleotides per ________ per replication fork.

A) 10/ second B) 50 / second C) 100 / second D) 50 / minute E) 100/ minute Ans B 11) In the eukaryotic cell cycle the M(itosis) phase occurs after the ______ phase.

A) Go B) G1 C) G2 D) S E) None of the above is correct Ans C 12) _______ is a form of intermicrobial DNA transfer that occurs when bacteriophage inadvertently serve as carriers of bacterial DNA to the recipient cell.

A) Transposition B) Conjugation C) Transformation D) Transduction E) Recombination

Ans D 13) The initiation of transcription involves the binding of RNA polymerase to a specific sequence called a __________.

A) Delta repeat B) Consensus sequence C) Promoter D) Primer E) Long terminal repeat Ans C 14) All of the following gene products are coded for by constitutive genes except ______.

A) Histone B) Aconitase C) Pyruvate dehydrogenase D) Lactose E) rRNA Ans D 15) The reassortment of DNA sequences is called A) Duplication B) Replication C) Recombination D) Decoding E) Reconstitution Ans C 16) _______ are tumors that arise in connective tissue.

A) Lymphomas B) Leukemias C) Carcinomas D) Sarcomas E) None of the above is correct Ans D 17) ______ is a protooncogene that codes for a GTP-binding protein.

A) Sis B) Src C) Jun D) Myc E) None of the above is correct Ans E 18) ______ is a protooncogene that codes for platelet-derived growth factor.

A) Sis B) Src C) Jun D) Myc E) None of the above is correct Ans A 19) _______ is a product of a delayed response gene.

A) Cyclin B) Jun C) Fos D) AP-1 E) Myc Ans A 20) ______ is an enzyme that catalyzes a critical step in replicative transposition.

A) Unwindase B) Replicase C) Resolvase D) Primase E) Catabolic gene activation protein Ans C 21) DNA synthesis is called A) Transcription B) Replication C) Translation

D) Transformation E) Transposition Ans B 22) _______ catalyzes the transcription of the precursor of the tRNAs and 5S rRNA. A) RNA polymerase I B) RNA polymerase II C) RNA polymerase III D) RNA directed DNA polymerase E) None of the above is correct Ans C 23) DNA transposition can cause gene ______.

A) Duplication B) Deletion C) Transcription D) Both A and B are correct E) All of the above are correct Ans D 24) Many promoters for RNA polymerase II contain a consensus sequence call the _______.

A) CAAT box B) GC box C) Pribnow box D) TATA box E) Okazaki box Ans D 25) Place the following steps of general recombination in chronological order i. DNA ligase seals the cut ends ii A second series of DNA strand cuts occurs opposite the first crossover strands iii Two homologous DNA molecules become paired iv DNA polymerase fills any gaps and DNA ligase seals the cut strands v Two of the DNA strands are cleaved

vi The two strand segments cross over A) i, iii, v, iv, ii, vi B) iii, iv, vi, i, vi, iii C) iv, ii, v, i, ii, iv D) iii, v, vi, i, ii, iv E) v, vi, i, ii, iv, iii Ans D 26) Most of the carcinogenic effects of radiation are believed to be the result of _______.

A) Viruses B) Transposition C) ROS D) Transduction E) Alkylation Ans C 27) DNA is synthesized in which of the following directions A) In the 5’→ 3’ direction on the leading strand and 3’ → 5’ direction on the lagging strand B) In the 3’→ 5” direction on the leading strand and the 5’→ 3’ direction on the lagging strand C) In the 5’→ 3’ direction on both DNA strands D) The direction differs depending on the genes being duplicated E) None of the above is correct Ans C

28) All of the following play a role in DNA repair except ________.

A) Light B) PR enzyme C) Ribozymes D) Endonuclease E) Pol I Ans C

29) In the absence of its inducer the lac operon remains repressed because of the binding of lac repressor to the _______.

A) Promoter B) Regulatory gene C) Catabolic gene activator protein D) Operator E) CAP site Ans D 30) Eukaryotic gene expression is affected by all of the following except ______.

A) RNA processing B) Translational control C)) Gene rearrangements D) Transcriptional control E) None of the above is correct Ans E 31) The majority of genetic variations arise from A) Mutations B) Genetic recombination C) Base deletion D) Tautomerism E) Both A and B are correct Ans B 32) Topoisomerases A) Join DNA strands together B) Prevent tangling of DNA strands C) Relieve torque in replicating DNA D) Change the supercoiling of DNA E) All of the above are correct Ans E 33) Type II topoisomerases

A) Produce double stranded breaks in DNA B) Replicate only the lagging strand C) Replicate only the leading strand D) Relieve torque ahead of the replicating machinery E) Both A and B are correct Ans A 34) In higher eukaryotes replication begins with the A) Origin of replication complex (ORC) B) Assembly of pre-initiation replication complex (preRC) C) Recruiting of the MCM complex to the replication site D) Stabilizing of the DNA strands by replication protein A (RPA) E) Attachment of DNA polymerase  to each DNA strand Ans B 35) Light-induced repair will correct which of the following mutations A) Deamination of adenine B) Reversion of thymine dimers C) Tautomerism of uracil D) Removal of nucleotides E) Breaks in the phosphodiester linkage Ans B 36) In nucleotide excision repair A) Single bases are removed and replaced B) Bulky lesions are removed C) Thymine dimers are replaced D) Gaps are repaired by DNA polymerase E) Nucleotides are removed and new ones inserted Ans B 37) Insertion of viral DNA into a host cell’s genome is an example of A) Transformation B) Transduction C) Conjugation D) Site specific recombination

E) Myosis Ans D 38) Genomic libraries are produced by A) Colony hybridization techniques B) Polymerase chain reactions C) Electroporation D) Shotgun cloning E) Cosmids Ans D 39) Homology modeling facilitates A) Protein structure prediction B) Open reading frames synthesis C) Stop codons deletion D) Protein function E) Start codon initiation Ans A 40) Protooncogenes are A) Normal genes that code for transcription factors B) Normal genes that if mutated can promote carcinogenesis C) Tumor suppressor genes D) Growth factor receptor genes E) All of the above are correct Ans B 41) An exonuclease is an enzyme that A) Depolymerizes RNA only B) Polymerizes DNA and RNA C) Removes nucleotides from the end of a polynucleotide strand D) Add nucleotides to the end of a polynucleotide strand E) Depolymerizes DNA only

Ans C 42) Repair of DNA by the SOS system has a major disadvantage A) Repair is slow B) Repair is error prone C) Repair cannot replace missing nucleotide sequences D) Frequently fragments the DNA chain E) C and D Ans B

43) A difference between prokaryotic and eukaryotic DNA polymerases is: A) Polymerizes DNA from opposite ends of the DNA chain B) Eukaryotic DNA polymerases do not remove RNA primers C) Prokaryotic polymerases work with both DNA and RNA chains D) Prokaryotic DNA polymerases do not require an RNA primer E) There are no differences Ans B 44) The average natural mutation rate for plants and animals is one mutation per ______ genes/generation.

A) 10,000 B) 50,000 C) 100,000 D) 1,000,000 Ans C 45) ____________ repair occurs only on a strand actively being transcribed, A) Mismatch repair B) Transcription coupling repair C) Replication slippage D) DNA E) RNA

Ans B 46) __________ corrects replication proofreading errors.

A) Mismatch repair B) Transcription coupling repair C) Reading repair D) Transcription coupling repair factor E) Isomerase repair factor Ans A SHORT ANSWER 47) What is a replication fork?

Ans A replication fork is the Y shaped region of an unwinding DNA double helix that is undergoing replication.

48) What is an Okazaki fragment?

Ans. An Okazaki fragment is any of a series of deoxyribonucleotide strand segments that are formed during the discontinuous replication of the lagging DNA strand as the leading strand is continuously replicated.

49) What is mismatch repair?

Ans Mismatch repair is a single-strand DNA repair mechanism involving three proteins (MutS, MutL, and Mut H) that corrects helix-distorting base mispairings.

50) What is an insertional element?

Ans An insertional element is a short DNA sequence involved in site specific recombination; also called an IS element or att site.

51) What is a cosmid?

Ans A cosmid is a cloning vehicle that contains the -bacteriophage COS sites incorporated into plasmid DNA sequences with one or more selectable markers.

52) What is a consensus sequence?

Ans A consensus sequence is the average of several similar DNA sequences. For example the consensus sequence of the -10 box of E. coli promoter is TATAAT. 53) What is a riboswitch?

Ans A riboswitch is a bacterial RNA-based control mechanism made up of a specific untranslated sequence within an mRNA. Usually the action of the riboswitch is triggered by a change in tertiary structure inducing by binding to a ligand that represses gene expression.

54) How does negative supercoiling promote the initiation of replication?

Ans Negative supercoiling facilitates the unzipping of DNA during the initiation phase of replication.

55) Mustard gas is an extremely toxic substance that severely damages lung tissue. In small amounts, mustard gas is a mutagen and carcinogen. Considering that mustard gas is a bifunctional alkylating agent, explain how it mutates genes and impacts DNA replication.

Ans Mustard gas cross links the strands in DNA with permanent covalent bonds thereby

blocking normal replication.

56) Indicate what types of mutation that ROS causes.

Ans ROS may cause single and double stranded breaks, pyrimidine dimer formation and the loss of purine and pyrimidine bases.

57) What types of mutations are caused by small alkylating agents?

Ans Small alkylating agents attach to the nitrogen atoms of the purines and pyrimidines, destabilizing glycoside linkages (leading to depurination). They also interfere with hydrogen bonding thereby promoting both transversion and transition mutations.

58) What type of mutations would nitrous acid cause?

Ans Nitrous acid deaminates bases. For example, cytosine is converted to uracil.

59) How can viruses cause mutations?

Ans Viruses can cause mutations by inserting their genomes into host cell regulatory sequences, thereby inactivating them.

60) Explain the significance of “jumping genes.”

Ans “Jumping genes” is the popular name for transposons. First discovered by Barbara McClintock, transposons (transposable elements) are DNA sequences that can move around the genome.

61) Describe two forms of genetic recombination. What functions do they fulfill?

Ans General recombination, a process in which segments of homologous DNA molecules are exchanged, is most commonly observed during meiosis. In site-specific recombination, protein-DNA interactions promote the recombination of nonhomologous

DNA. Transposition is an example of site-specific recombination. Genetic recombination promotes species diversity.

62) Within cells, cytosine slowly converts to uracil. What type of mutation would this lead to? What impact would the same modification have if it occurred at the RNA or gene product level?

Ans In DNA, when cytosine is converted to uracil, an AT base pair is substituted for a GC base pair. Such a change in RNA is not as important because RNA molecules are short-lived and disposable. In contrast, because DNA molecules are the cell’s permanent repository of genetic information, any change in base sequence may affect an organism’s viability.

63) A correlation has been found among species between life span and efficiency of DNA repair systems. Suggest a reason why this is so.

Ans Because DNA is constantly exposed to disruptive processes, its structural integrity is highly dependent on efficient repair mechanisms. The life span of an organism is dependent on the health of the constituent cells, which is in turn dependent on the timely and accurate expression of genetic information. Consequently, the capacity of the organisms in a species to maintain the integrity to DNA molecules is an important factor in determining life span.

64) Describe the advantages for organisms to arrange genes in operons.

Ans In relatively simple genomes, such as those in bacteria, operons provide a convenient mechanism for regulating genes. Proteins required in the same metabolic pathway or functional process are synthesized together because their genes are controlled by the same promoter.

65) Many genes generate different products depending on the type of the cell expressing the gene. How is this phenomenon accomplished?

Ans Mechanisms to regulate gene expression differently in different cells include genomic control (including gene rearrangements and selective gene amplification), RNA processing, (alternative splicing) RNA editing.

66) RNA molecules are more reactive than DNA molecules explain.

Ans RNA molecules are more reactive than DNA molecules because of the presence of the 2’-OH group of ribose. In addition, the complexity of RNA’s three-dimensional structures that result from single-stranded molecules coiling back on themselves provides opportunities for more diverse intermolecular interactions and binding than does DNA. ESSAY QUESTIONS 67) Although genetic variation is required for species to adapt to changes in their environment, most genetic changes are detrimental. Explain why mutations are rarely beneficial.

Ans Most mutations that do affect the functioning of an organism, are deleterious because of the complex nature of living processes. Change in the properties of any of the thousands of different gene products is potentially disruptive. Only on rare occasions, usually as a result of a change in the environment, does a mutation improve the viability of an individual organism.

68) During certain stages of development, the requirement for certain gene products may require gene amplification. What purpose does gene amplification serve?

Ans The purpose of gene amplification is to rapidly produce multiple copies of specific gene products that are required in greater quantities during certain stages in a cell's development.

69) There appears to be insufficient genetic material to direct all the activities of certain types of eukaryotic cell. Provide one example whereby genetic recombination is used to solve this problem.

Ans Genetic recombination can allow cells to alter gene expression and expand their repertoire of proteins. Antibody production in lymphocytes is a prominent example. The rearrangement of several possible choices for each of a number of antibody gene segments by site specific recombination results in the generation of an extremely large number of different antibody molecules.

70) Adjacent pyrimidine bases in DNA form dimers with high efficiency after exposure to UV light. If these dimers are not repaired, skin cancers can result. Melanin is a natural sunscreen produced by melanocytes, a type of skin cell, when the skin is exposed to sunlight. Individuals who spend long periods over many years developing a tan eventually acquire thick and highly wrinkled skin. Such individuals are also at high risk for skin cancer. Can you explain, in general terms why these phenomena are related?

Ans The tanning process, which occurs in response to overexposure to sunlight, is triggered by DNA damage. Over time skin cells undergo an accelerated aging process that is manifested in a thickened and wrinkled skin. DNA damage may also inactivate tumor suppressor genes and/or cause mutations to protooncogenes, thus increasing the skin cancer risk.

71) Phorbol esters have been observed to reduce the transcription of AP-1 genes. Explain how this process could occur. What are the consequences of AP-1 transcription? What role does intermittent exposure to phorbol esters have on an individual’s health?

Ans Phorbol esters mimic the action of DAG, the normal cell metabolite that activates protein kinase C (PKC). PKC initiates a phosphorylation cascade that results in the activation of numerous molecules involved in cell growth and division, including jun and fos which then combine to form AP-1. AP-1is a transcription factor whose presence promotes cell division. Phorbol esters cause an affected cell to have a growth advantage over nearby cells. Because phorbol esters are tumor promoters any exposure to them increases the risk that initiated cells may progress to a cancerous state.

72) Because of overuse of antibiotics and/or weakened government surveillance of infectious disease, several diseases that had been thought to be no longer a threat to human health are rapidly becoming unmanageable (e.g. antibiotic resistant tuberculosis).

Superbugs (microorganisms that are resistant to almost all known antibiotics) have also been detected. How did this circumstance arise? What will happen if the process continues?

Ans Antibiotic resistance arises because the overuse of antibiotics acts as a selection pressure, (i.e., they provide a growth advantage for disease-causing organisms that possess resistance genes). Superbugs are organisms that are resistant to several types of antibiotics because they possess resistance gene-containing plasmids. If the circumstances that cause antibiotic resistance continue, antibiotics may eventually become ineffective against most infectious diseases.

73) Explain the difference between the potential effects on an individual organism of errors made during the replication and those made during transcription.

Ans Errors that occur during DNA replication have the potential to become permanent if repair processes fail. Errors made during transcription affect only a few RNA molecules and are temporary.

74) Explain how a reverse transcriptase activity within a cell can result in gene amplification.

Ans Gene amplification, the selective duplication of certain genes, can occur via a reverse transcriptase mediated event. The creation of one or more cDNA’s from mRNA is followed by insertion of these sequences into the genome.

75) It was originally thought that the DNA polymerase machinery moves along the DNA in the manner analogous to a train on a track. Current evidence indicates that the polymerizing machinery is instead stationary, and DNA strands are pumped through the complex. What advantages does this stationary machinery have?

Ans The DNA polymerase enzyme complex is a sophisticated machine that is composed of a large number of fragile components. By keeping the complex stationary, cells protect it from mechanical damage that would occur if it moved through the crowded nucleoplasm.

CALCULATIONS 76) Determine the magnitude of amplification of a single DNA molecule that can be attained with PCR during five cycles.

Ans The amplification of a single DNA molecule during five cycles yields 25 or 32 molecules.

CHAPTER NINETEEN PROTEIN SYNTHESIS 1)The Shine-Dalgarno sequence is a A) Prokaryotic mRNA sequence that binds IF-3 B) Prokaryotic mRNA sequence that binds 16S rRNA of the small ribosomal subunit C) Prokaryotic mRNA sequence that binds the 16S RNA of the large ribosomal subunit D) Eukaryotic rRNA sequence that binds the AUG codon of mRNA E) None of the above are correct Ans B 2) The initiation phase of prokaryotic translation ends as the GTP molecule bound to ________ is hydrolyzed to GDP and Pi A) IF-1 B) IF-2 C) IF-3 D) IF-4 E) None of the above is correct Ans B 3) During the elongation phase of prokaryotic translation the aminoacyl-tRNA must first bind _________ before it can be positioned in the A site.

A) EF-Ts B) EF-Tu C) EF-Ts-GDP D) EF-Ts-GTP E) EF-Tu-GTP Ans E

4)________ is an enzymatic activity that hydrolyses the bond linking the completed polypeptide chain and the P site tRNA A) RF-1 B) EF-G C) Peptidyl transferase D) Ribosomal esterase E) Signal peptidase

Ans C 5) Prominent prokaryotic posttranslational modifications include all of the following except __________.

A) Glycosylation B) Methylation C) Proteolytic processing D) Prenylation E) Phosphorylation Ans D

6) In prokaryotes most of the control of protein synthesis occurs at the level of ______.

A) Translation B) Transcription C) Replication D) Reverse transcription E) Posttranslational modification Ans B

7) The enzymatic activities coded by the lac operon include all of the following except: A) Thiogalactoside transacylase B) Lactose transferase Χ) -Galactosidase D) Galactose permease E) None of the above is correct Ans B 8) Translocation in eukaryotes requires _____, which is a GTP binding protein.

A) eEF-1 B) eEF-2 C) eEF-3 D) eEF-4 E) None of the above is correct Ans B

9) In eukaryotic translation the 40S complex binds the 60S subunit to form the _______ initiation complex.

A) 80S B) 88S C) 90S D) 100S E) 108S Ans A

10) ________ provides the energy needed to move the ribosome along an mRNA. A) ATP B) GTP C) UTP D) TTP E) All of the above are correct Ans B 11) Polypeptides containing signal peptides are called ________.

A) Zymogens B) Preproproteins C) Proproteins D) All of the above are correct E) None of the above is correct Ans B

12) Phosphorylated dolichol, a polyisoprenoid found in ER membrane, is involved in A) Polypeptide synthesis B) Proteolytic cleavage reactions C) Lipophilic modification reactions D) Hydroxylation reactions E) Glycosylation reactions

Ans E

13) All of the following are involved in signal peptide processing except A) Ribosomal polypeptide translocation factor B) SRP receptor protein C) Docking protein D) Translocon E) Stop transfer signal Ans A 14) The phrase “global control” refers to: A) Large alterations in mRNA translation patterns B) Large alterations in mRNA synthesis patterns C) Specific changes in rRNA synthesis D) Specific changes in mRNA synthesis E) Changes in transcript localization patterns Ans A

15) Translational frame shifting A) Results in the synthesis of more than one polypeptide from a single mRNA B) Has been observed in cells infected by retroviruses C) Is the result of a +1 or –1 change in the reading frame of an mRNA D) Both A and C are correct E) All of the above are correct Ans E

16) All of the following statements concerning eukaryotic mRNA are true except A) Only a small portion of mRNA enters the cytoplasm B) Most hnRNA is processed into mRNA C) Export of mRNA through nuclear pores is carefully controlled D) mRNA export usually requires a 5’-cap and a 3’-poly A tail E) None of the above is correct Ans B

17) Eukaryotic mRNA stability involves: A) Reversible adenylation B) The length of poly (A) tails C) The binding of specific proteins to certain mRNA sequences D) The action of various nucleases E) All of the above are correct Ans E

18) _______ are a group of molecules that mediate protein folding.

A) Hsp 70s B) Chaperonins C) Docking protein D) Both A and B are correct E) All of the above are correct Ans D

19) The mRNA that codes for ________ possesses an iron response element.

A) Collagen B) Elastin C) Globin D) Ferritin E) Thiogalactoside transacetylase Ans D

20) Chloramphenicol is an antibiotic that: A) Inhibits prokaryotic peptidyl transferase B) Causes mRNA misreading via binding to the 30S subunit C) Interferes with aminoacyl-tRNA binding via binding to 30S subunit D) Inhibits eukaryotic peptidyl transferase E) Inhibits prokaryotic peptide chain elongation Ans A

21) Cycloheximide is an antibiotic that

A) Inhibits prokaryotic peptidyl transferase B) Causes mRNA misreading via binding to 30s subunit C) Interferes with aminoacyl-tRNA binding via binding to the 30S subunit D) Inhibits eukaryotic peptidyl transferase E) Inhibits prokaryotic peptide chain elongation Ans D 22) Tetracycline is an antibiotic that A) Inhibits prokaryotic peptidyl transferase B) Causes mRNA misreading via binding to 30S subunit C) Interferes with aminoacyl-tRNA binding to the 30S subunit D) Inhibits eukaryotic peptidyl transferase E) Inhibits prokaryotic peptide chain elongation Ans C

23) Erythromycin is an antibiotic that A) Inhibits prokaryotic peptidyl transferase B) Causes mRNA misreading via binding to 30S subunit C)Interferes with aminoacyl-tRNA binding via binding to the 30S subunit D) Inhibits eukaryotic peptidyl transferase E) Inhibits prokaryotic peptide chain elongation Ans E 24) Which of the following antibiotics would be most toxic for humans A) Tetracycline B) Chloramphenicol C) Streptomcyin D) Cycloheximide E) Erythromycin Ans D 25) Ribonucleoprotein particles A) Contain an mRNA B) Contain several types of protein C) Are found only in prokaryotes D) Both A and B are correct E) All of the above are correct

Ans D

26) ________ is a translation factor that possesses a unique histidine residue that can be modified to form diphthamide A) IF-2 B) EF-Tu C) EF-Ts D) eEF-1 E) eEF-2 Ans E

27) Hydroxylation is a posttranslational modification that A) Requires ascorbic acid B) Is catalyzed by several mixed function oxidases C) Is required for the structural integrity of globin D) Both A and B are correct E) All of the above are correct Ans D 28) In prokaryotes posttranslational methylation reactions are associated with A) Signal transduction B) Chemotaxis C) S-Adenosylmethionine D) All of the above are correct E) None of the above is correct Ans D 29) The half-lives of prokaryotic mRNA usually varies between A) 1 and 3 seconds B) 1 and 3 minutes C) 1 and 3 hours D) 3 and 10 hours E) None of the above is correct Ans B

30) Peptidyl transferase is an enzymatic activity that A) Catalyzes the release of polypeptides from the ribosomes B) Is found in an rRNA component of ribosomes C) Catalyzes the nucleophilic attack of the A site -amino group on the carbonyl carbon of the P side amino acid D) Catalyses peptide bond formation E) All of the above are correct Ans E

31) Unlike the protein synthesis mechanism in the cytoplasm of eukaryotic cells, mitochondria have _______ stop codes.

A) 1 B) 2 C) 3 D) 4 E) 5 Ans D

32) An analysis of the wobble hypothesis suggests that a minimum of _______ RNA’s are required to translate all 61 codons plus one for a start codon.

A) 22 B) 32 C) 16 D) 62 E) 30 Ans B

33) Translation begins with A) Elongation B) Initiation C) Termination D) Targeting E) tRNA synthesis Ans B

34) Which of the following is a type of posttranslational modification?

A) Removal of signal peptides B) Carboxylation C) Methylation D) Phosphorylation E) All of the above Ans E

35) Protein synthesis requires _____ high energy phosphate bonds per peptide bond.

A) 1 B) 2 C) 3 D) 4 E) 5 Ans D

36) An amino acid coded for by a stop signal is A) Pyrrolysine B) Lysine C) Cysteine D) Selenocysteine E) Both A and D are correct Ans E

37) In eukaryotes which of the following amino acids is often hydroxylated after protein synthesis?

A) Proline B) Tyrosine C) Arginine D) Methionine E) All of the above Ans A

38) Which of the following amino acids is sometimes carboxylated after protein synthesis in eukaryotes A) Glutamate B) Aspartate C) Phenylalanine D) Lysine E) Arginine Ans A

39) Prokaryotes exclusively use which of the following translational control mechanisms?

A) Negative translational control of ribosomal proteins B) Global controls C) RNA specific controls D) Allosteric modifications of ribosomes E) Energy depletion Ans A 40) Which of the following is a synonymous codon with UCU? A) AAU B) UCA C) GAU D) AAA E) CUG Ans B

41) Protein synthesis in bacteria involves six functional centers. Which of the following is not one of those centers?

A) Decoding center B) Aminase transfer center C) Pepidyl transfer center D) GTPase associated region E) A site Ans B

42) The peptide emerging from the exit tunnel first encounters a molecular factor called A) Trigger factor B) Signal factor C) Linkage chaperone D) P-site E) Translation factor Ans A 43) Eukaryotic initiation begins with the assembly of ________________.

A) Preinitiation complex B) Cap-binding complex C) Poly-binding complex D) 48S Initiation complex E) Translational initiation complex Ans A

44) Which of the following compounds is referred to as the twenty-first amino acid?

A) Selenocysteine B) Glucolysine C) Cysteine D) Dehydroxyalinine E) D-Lysine Ans A

45) During synthesis of secreted proteins, binding of the ribosome to the ER membrane is mediated by A) The translocon B) SRP and SRP receptor protein C) Signal peptidase D) Co-translational transfer E) Posttranslational translocation Ans B

SHORT ANSWER 46) What is the wobble Hypothesis?

Ans The wobble hypothesis is an explanation of the observation that cells often have fewer tRNAs than expected. Freedom in the pairing of the third base of the codon to the first base of the anticodon allows some tRNA’s to pair with several codons.

47) What is a Shine-Dalgarno sequence?

Ans A Shine-Dalgarno sequence is a purine rich sequence on the mRNA close to AUG (the initiation codon) that binds to a complementary sequence on the 30S ribosome subunit thereby promoting the formation of the correct preinitiation complex.

48) List the major translational control mechanisms of eukaryotes.

Ans Eukaryotic translation is controlled by (1) the metabolic status of a cell (primarily via the mTORC1 signaling pathway); (2) mRNA export through nuclear pores; (3) mRNA stability (e.g., presence or absence of nuclease resistant sequences such as palindromes and poly(A) tails; and (4) negative translation controls in which in certain circumstances repressor proteins bind to sequences near the mRNA’s 5’end.

49) What are the goals of proteomic researchers?

Ans The goal of proteomic researchers is to identify the structural and functional properties of all the proteins produced in a living organism.

50) List and describe four properties of the genetic code.

Ans The genetic code is degenerate (several codons have the same meaning), specific (each codon specifies only one amino acid) and universal (with few exceptions each codon always specifies the same amino acid). In addition the genetic code is nonoverlapping and without punctuation (i.e., the open reading frame of an mRNA is read as a continuous coding sequence).

51) What are the “wobble rules”? What are the consequences of the wobble rules in protein synthesis?

Ans The wobble rules are (1) the first two base pairings in a codon-anticodon interaction confer most of the specificity required during translation, and (2) the interactions between the third codon and anticodon nucleotides are less stringent.

Because of the “wobble rules” only a minimum of 31 tRNA’s are required for the translation of all 61 codons.

52) What are the major differences between eukaryotic and prokaryotic translation?

Ans The major differences between eukaryotic and prokaryotic translation are speed (the prokaryotic processes are significantly faster), location (encased within a nucleus,the eukaryotic process is not directly coupled to transcription as prokaryotic translation is), complexity (eukaryotes possess more complex mechanisms for regulating protein synthesis), and posttranslational modifications (eukaryotic reactions are significantly more complex than those of prokaryotes).

53) Briefly outline the steps in the elongation cycle.of protein synthesis.

Ans During the elongation phase of protein synthesis, the second aminoacyl-RNA becomes bound to the ribosome in the A site. Peptide bond formation between the A and P site amino acids is then catalyzed by peptidyl transferase. Subsequently, the ribosome is moved along the mRNA by a GTP-requiring mechanism referred to as translocation.

54) Describe the structure and function of the signal recognition particle.

Ans A signal recognition particle (SRP) is a large complex composed of protein and RNA that binds to a ribosome that has begun translating a polypeptide possessing a signal peptide segment. Once the SRP has bound to the ribosome, translation is temporarily arrested. The SRP then mediates ribosomal binding to docking proteins on the surface of a membrane (e.g. RER membrane). Translation subsequently recommences and the growing polypeptide inserts into the membrane.

55) Why are tRNA’s described as adaptor molecules?

Ans tRNA’s are adaptor molecules because they bind to specific amino acids molecules and then position those molecules in the ribosome according to the base sequence of an mRNA. In other words, they bridge the gap between the base code of nucleic acids and the amino acid sequence of polypeptides.

56) Explain the roles of the large and small subunits of ribosomes.

Ans The large ribosomal subunit contains the catalytic site for peptide bond formation. The small ribosomal subunit serves as a guide for the translation factors required to regulate protein synthesis. Together the two subunits come together and

form a molecular machine that polymerizes amino acids in a sequence specified by the base sequence in an mRNA molecule.

57) List and describe the major classes of eukaryotic posttranslational modifications.

Ans The major classes of eukaryotic posttranslational modification are proteolytic cleavage (the hydrolysis of specific peptide bonds), glycosylation (attachment of sugar residues to specific amino acid residues), phosphorylation ( the addition of phosphate groups to specific amino acid residues on a protein), lipophilic modification (covalent attachment of lipid groups to a protein), methylation (attachment of methyl groups), and disulfide bond formation (formation of –S-Sbonds between cysteine residues).

58) Explain the importance of proper targeting of nascent polypeptides.

Ans It is necessary to have a targeting mechanism to ensure that proteins end up in a location appropriate to their function in a timely and predictable way. Specific localization sequences and/or posttranslational modification of the product protein then ensures delivery of the protein to its target location.

59) Eukaryotic protein synthesis is considerably slower than synthesis of prokaryotes.

Explain.

Ans Features of eukaryotic protein synthesis that account for the increased time required (as opposed to prokaryotic translation) include the greater quantity, variety and functioning of eukaryotic translation factors (e.g., at least 12 IF’s vs 3 for prokaryotes), additional processing of mRNA (addition of a 5'-cap and a poly (A) tail

and the removal of introns), and the increasing quantity and variety of eukaryotic posttranslational modifications, (e.g. hydroxylation and disulfide bond formation).

60) Explain the significance of the following statement: The functioning of the aminoacyl-tRNA synthesis is referred to as the second genetic code.

Ans Because the accuracy of protein synthesis depends directly on codon-anticodon interactions, the specificity with which t RNAs are linked to amino acids is critically important. The process in which the amino acid-tRNA synthetases catalyze the covalent binding of each of the t RNAs with its correct amino acid has, therefore, been referred to as the second genetic code.

61) Indicate the phase of protein synthesis during which the polypeptide is actually synthesized.

Ans The phase during which a polypeptide is synthesized is called elongation.

62) What is the energy source used to move mRNA in a ribosome during protein synthesis.

Ans GTP hydrolysis us the energy source used to drive translocation, the movement of mRNA codons through the ribosome.

63) Indicate the phase of protein synthesis during which the ribosome dissociates into subunits.

Ans The termination step is the phase of protein synthesis in which the nascent polypeptide is released from the ribosome which then dissociates into its subunits.

64) Explain the critically important role of aminoacyl-tRNA synthetases in protein synthesis.

Ans Each aminoacyl-tRNA synthetases correctly attaches a specific amino acid to its cognate tRNA. Then some of these enzymes also proofread the product. This process increases the accuracy of protein synthesis.

65) Given that the amino acid sequence for a polypeptide, can the base sequence for the mRNA that codes for it be predicted?

Ans The precise base sequence for such a polypeptide cannot be predicted because of the degeneracy of the genetic code.

THOUGHT QUESTIONS

66) Compare and contrast the coding reassignment mechanisms whereby selenocysteine and pyrolysine are linked to their cognate tRNA’s. Explain.

Ans The coding reassignment mechanisms for selenoysteine and pyrolysine are similar in many respects (e.g., the use of the reassignment sequences SECIS and PYLIS, and specific tRNA’s and acyl-tRNA synthetases). A major difference between these two examples of coding reassignment is the mechanism whereby the two nonstandard amino acids are linked to their respective tRNA’s. Selenocysteine tRNA is produced from a specialized seryl-tRNA. The seryl group is converted after

linkage to the tRNA to a selenocysteinyl group. In contrast, pyrolysine is synthesized before it is linked to its tRNA.

67) Despite considerable species differences in the amino acid and nucleotide sequences of ribosomal proteins and RNA, respectively, the three-dimensional structures of ribosomal protein and ribosomal RNA are remarkably similar among species. Suggest reasons for these similarities.

Ans, The overall three-dimensional structures of ribosomal protein and ribosomal RNA are remarkably similar among species because of high selection pressure. In other words, ribosomal function is such an important factor in species viability that evolution has conserved their tertiary structure despite mutation.

68) Describe how the base pairing between the Shine-Dalgarno sequence and the 30S subunit provide the means by which a start codon is distinguished from a methionine codon. What is the eukaryotic version of this mechanism?

Ans The prokaryotic Shine-Dalgarno sequence promotes the correct alignment of the start codon on the ribosome (as opposed to a methionine codon) because it binds to a nearby complementary sequence in the 16S tRNA component of the 30S ribosome.

Eukaryotic ribosomes identify the initiating AUG codon by binding to the capped 5’ end of the mRNA and then scanning for a translation start site.

69) Some aminoacyl-tRNA synthetases that link amino acids with similar side chains (e.g. isoleucine and valine) to their cognate RNA’s possess proofreading sites. What sets of amino acids whose structural similarities might also require proofreading?

Ans Sets of amino acids with similar side chains, which might require proofreading include phenylalanine/tyrosine, serine/threonine, aspartate/glutamate, asparagine/glutamine, isoleucine/leucine and glycine/alanine.

70) What advantages are there for synthesizing an inactive protein that must be subsequently activated by prostranslational modifications?

Ans The activation of an inactive protein by proteolytic cleavage or other posttranslational modifications ensures that the protein is active only when it has been successfully diverted to its site of function.

71) What factors insure accuracy of protein synthesis? How does the level of accuracy usually attained in protein synthesis compare with that of DNA replication or transcription?

Ans The principal factors that ensure accuracy in protein synthesis are codonanticodon base pairing and the mechanism by which amino acids are linked to their cognate tRNAs. The level of accuracy of protein synthesis, while quite high, is still less than that achieved during replication or transcription.

72) Can you suggest a reason why ribosomes in all living organisms consist of two subunits and not one supramolecular complex?

Ans A two subunit ribosome is essential to ensure that all of the required elements are in place before the translational process begins. This is a physical ordering process much like an assembly line; the parts must be in place before the enzymatic activities are set in motion.

73) A prokaryotic species is facing a new environmental stress that can be ameliorated by a catalytic activity that requires the side chain of a unique amino acid derivative called pyrovaline. What molecule and mechanism would be required for the incorporation of this nonstandard amino acid into a protein molecule?

Ans Assuming that the pyrovaline is available from a metabolic pathway, the following circumstances must occur: (1) A codon is assigned to pyrovaline, (2) A tRNA with the requisite codon is available, (3) An aminoacyl tRNA synthetase binds pyrovaline to its cognate tRNA, (4) A stem-loop or similar structure upstream of the newly assigned codon in the mRNA promotes the codon reassignment.(5) The tRNA bound to pyrovaline would then enter the ribosome where its amino acid is incorporated into the protein.

CALCULATIONS:

74) There are four serine codons in the genetic code. A peptide sequence is composed of 10 serine residues. Determine how many different mRNA sequences could code for this molecule?

Ans Since there are four serine codons and assuming that there is no codon usage bias the total number of different mRNA sequences would be 410 or 1,048,576.

75) Determine the total number of nucleotides that must be hydrolysed in the synthesis of Lys-Ala-Ser-Val.

Ans The total amount of nucleotide bond energy that is required to synthesize LysAla-Ser-Val is equivalent to the hydrolysis of 16 or 17 phosphoryl groups from ATP or GTP determined as follows: 1 GTP to form the complete ribosome and initiate translation, 8 ATP to create 4 aminoacyl-tRNAs, 2 ATP equivalents per amino acid 6 GTP to create 3 peptide bonds (1 GTP for elongation and 1 GTP for translocation for each peptide bond formed),1 or 2 GTP to terminate translation (1 GTP in eukaryotes, 2 GTP in prokaryotes).

76) Estimate the minimum number of ATP and GTP molecules required to polymerize 200 amino acids.

Ans Four high-energy phosphate bonds are required to incorporate each amino acid into a polypeptide (i.e., 2 GTP and 2 ATP ) The polymerization of 200 amino acids requires 400 GTP and 400 ATP.

77) How many possibilities are there for the codon sequence of the peptide sequence glycylserylcysteinylarginylalanine? How many possibilities are there?

The number of possible codons for the amino acids in this peptide sequence is as follows: glycine (4), serine (6), cysteine (2), arginine (6) and alanine (4).

Ans. The total number of possible codon sequences for this peptide is calculated by multiplying the numbers of codons for the amino acid residues by the number of amino acids. 4 x 6 x 2 x 6 x 4 = 2304

CHAPTER SIX ENZYMES 1. The minimum amount of energy required to bring about a chemical reaction is called __________.

A) activation energy B) enthalpy of reaction C) free energy D) standard free energy E) transition state Ans A 2. Which of the following is not a property of enzymes?

A) Capable of being regulated B) Reaction rates high in comparison to uncatalyzed reaction C) Highly specific D) Side products of reactions are rare.

E) All of the above are correct.

Ans E 3. Consider the following reaction diagram. Which letter indicates the transition state?

A) A B) B C) C D) D E) E Ans C 4. In contrast to inorganic catalysts, enzymes have an intricately shaped surface called the __________.

A) substrate B) cofactor C) active site D) apoenzyme E) holoenzyme

Ans C 5. The lock and key model of enzyme activity proposes that each __________.

A) enzyme can react with only a single substrate B) enzyme has a cofactor that promotes the catalytic activity C) substrate has a specific cofactor that binds it to the enzyme D) enzyme binds a specific substrate because the active site and substrate have complementary structures.

E) Both A and B are correct.

Ans D 6. The synthesis of enzymes in response to changing metabolic needs is referred to as __________.

A) enzyme induction B) allosteric regulation C) negative feedback D) zymogen activation E) cooperative binding Ans A 7. Which of the following is a coenzyme?

A) NADP+ B) Zn++ C) Cu++ D) Insulin E) Oxytocin Ans A 8. Alcohol dehydrogenase without NAD+ is called a __________.

A) apoenzyme B) holoenzyme C) substrate D) cofactor E) coenzyme Ans A 9. The term synthetase is included in which class of enzymes?

A) Ligases B) Hydrolases C) Transferases D) Lyases E) Isomerases Ans A 10. Which of the following is not a type of oxidoreductase?

A) Peroxidase B) Hydroxylase C) Reductase D) Dehydrogenase E) Peptidase Ans E 11. Which of the following classes of enzymes catalyze reactions involving the cleavage of bonds by the addition of water?

A) Transferase B) Hydrolase C) Lyase D) Ligase E) Isomerase Ans B 12. Consider the following reaction data.

Alanylanine + water → alanine [alanylanine] [water] Rate 0.1 0.1 1×10-4 0.2 0.1 2×10-4 0.1 0.2 2×10-4 0.2 0.2 4×10-4 The reaction is __________ order overall.

A zero B) first C) second D) third E) fourth Ans C

13. The steady state assumption states that if k1 = the rate constant for ES formation k2 = the rate constant for ES dissociation k3 = the rate constant for product formation A) k2 is highly negligible compared with k3 B) The rate of formation of ES is equal to the rate of its degradation over the course of the reaction.

C) The rate of formation of ES exceeds the rate of degradation over the course of the reaction.

D) k3 is negligible when compared to k2.

E) Product concentration at the beginning of the reaction is low.

Ans B 14. The expression of the Michaelis constant is equal to A) (K2 + K3)/K1 B) (K2 + K1./K3 C) (K1 + K2)/K3 D) (K3 + K1) + K3 E) (K2/K1) + K3 Where K1 = the rate constant for ES formation K2 = the rate constant for ES dissociation K3 = the rate constant for product formation Ans A 15. Specific activity is defined as __________.

A) enzyme concentration that converts 1  mole of substrate to product per minute.

B) enzyme concentration that converts 1 mole of substrate to product per minute C) the number of I.U. per mg of protein D) the number of I. U. per gram of protein E) enzyme concentration that converts 1 mm of substrate to product per minute.

Ans C 16. In the Lineweaver-Burk double reciprocal plot the slope is equal to __________.

A) 1/[S] B) 1/V C) Km/Vmax D) 1/Vmax

E) –1/Km Ans C 17. In the Lineweaver-Burk double reciprocal plot the vertical intercept is equal to __________.

A) 1/[S] B) 1/V C) Km/Vmax D) 1/Vmax E) –1/Km Ans D 18. In the Lineweaver-Burk double reciprocal plot the horizontal intercept is equal to __________.

A) 1/[S] B) 1/V C) Km/Vmax D) 1/Vmax E) –1/Km Ans E 19. In competitive inhibition, increasing the concentration of substrate __________ A) decreases the overall rate of the reaction B) increases the overall rate of the reaction C) is without effect D) the observed effect depends on the inhibitor E) competitive inhibitors do not affect the rate of the reaction Ans B 20. Which of the following amino acids is capable of acting as a general acid or general base at physiological pH? A) Glycine B) Histidine C) Tyrosine D) Tryptophan E) Proline Ans B

21. Which of the following amino acids can participate in covalent catalysis?

A) Tryptophan B) Alanine C) Serine D) Histidine E) Both C and D are correct.

Ans E 22. Which of the following is a feature of transition metals that makes them efficient cofactors?

A) Have a high concentration of positive charge B) Can act as a Lewis acid C) Have directed valences D) Can exist as a variety of valence states E) All of the above are correct.

Ans E 23. NADPH and NADH are coenzymes found in which class of enzymes?

A) Dehydrogenases B) Ligases C) Hydrolases D) Transferases E) Both C and D are correct.

Ans A 24. Which of the following is not present in the active site of alcohol dehydrogenase?

A) Zn++ B) Histidine C) Cysteine D) NAD+ E) Proline Ans E 25. Enzyme control is accomplished in which of the following ways?

A) Genetic control B) Covalent modification

C) Allosteric regulation D) Compartmentation E) All of the above are correct.

Ans E 26. Zymogens are a feature of what type of enzymatic control?

A) Genetic control B) Covalent modification C) Allosteric regulation D) Compartmentation E) Both B and C are correct.

Ans B 27. Regulatory enzymes are a feature of what type of enzymatic control?

A) Genetic control B) Covalent modification C) Allosteric regulation D) Compartmentation E) Both B and C are correct.

Ans C 28. Positive cooperativity is a feature of what type of enzymatic control?

A) Genetic control B) Covalent modification C) Allosteric regulation D) Compartmentation E) Both B and C are correct.

Ans C 29. Segregation of biochemical pathways into different organelles in an example of which type of enzymatic regulation?

A) Genetic control B) Covalent modification C) Allosteric regulation D) Compartmentation E) Both B and C are correct.

Ans D

30. Catalysts are effective because they __________.

A) decrease the rate of the reverse reaction B) stabilize the transition state C) decrease the activation energy of a reaction D) increase the energy released during a reaction E) Both B and C are correct.

Ans E 31. Enzymes act by __________.

A) decreasing the energy of activation of a reaction B) increasing the energy of activation of a reaction C) raising the temperature of a reaction D) providing a surface to favorably orient the reactants E) Both A and D are correct.

Ans E 32. Enzyme studies are best carried out in __________.

A) dilute aqueous solution B) highly concentrated solutions of the enzyme C) highly concentrated solutions of the substrate D) the presence of an inert crowding agent E) the presence of a membrane Ans D 33. Alcohol dehydrogenase is an example of which of the following classes of enzymes?

A) Oxidoreductases B) Transferase C) Hydrolase D) Lyase E) Isomerase Ans A 34. Which of the following is not an assumption of the law of mass action?

A) Forward reaction is linear.

B) Reverse reaction is linear.

C) System is homogenous.

D) Interacting molecules move randomly and independently of each other.

E) All are assumptions of the law of mass action.

Ans E 35. Metabolons are defined as __________.

A) multifunction enzymes B) complexes that channel product molecules from one active site to another C) metabolic intermediates D) effector molecules E) rate of flow of metabolites from one point to another Ans B 36. Metabolic flux is best defined as a __________.

A) lubrication enzyme that promotes the flow of reactants B) rate of flow of metabolites from one point to another in a pathway C) rate of a reaction D) promoter molecule E) Both A and D are correct.

Ans B 37. An enzyme without it cofactor is called __________.

A) coenzyme B) apoenzyme C) holoenzyme D) noncatalytic E) isoenzyme Ans B 38. Which of the following amino acids cannot actively participate in a catalytic site?

A) Serine B) Threonine C) Tyrosine D) Glycine E) Glutamine Ans D

39. In addition to serine and aspartate which of the following amino acids is a member of the serine triad?

A) Threonine B) Tyrosine C) Glutamine D) Histidine E) Glycine Ans D 40. Which of the following is not an important metal in biological systems?

A) Na+ B) K+ C) Mg++ D) Cu++ E) Ba++ Ans E 41. The major site of alcohol detoxification is __________.

A) intestine B) kidney C) pancreas D) liver E) stomach Ans D 42. The main enzyme used to detoxify alcohol in humans is __________.

A) ADH1 B) ADH2 C) ADH3 D) ADH4 E) All of the above are correct.

Ans A 43. Consider the following diagram. What constitutes the activation energy for the forward reaction?

A) C–A B) C–E C) E–A D) C–B E) E–D Ans A 44. Which of the following statements is not true of enzymes?

A) Increase the reaction rate B) Obey the laws of thermodynamics C) Catalyze the forward reaction only D) Do not affect the position of equilibrium E) Not consumed by the reaction Ans C 45. Hexokinase is an example of which class of enzymes?

A) Hydrolase B) Lyase C) Isomerase D) Transferase E) Ligase Ans D 46. Pyruvate carboxylase is an example of which class of enzymes?

A) Oxidoreductase B) Transferase C) Hydrolase D) Ligase E) Lyase Ans D SHORT ANSWER 47. What is meant by the term activation energy?

Ans Activation energy is the threshold energy required to produce a chemical reaction.

48. What is meant by the term active site?

Ans An active site is the cleft in the surface of an enzyme where a substrate binds.

49. Describe the term coenzyme. Give two examples.

Ans A coenzyme is a small organic molecule required in the catalytic mechanism of a certain enzyme. Examples include NAD+ and FAD. 50. What is meant by the term turnover number?

Ans Turnover number is the number of molecules of a substrate converted to product in each second per mole of enzyme.

51. What is a noncompetitive inhibitor?

Ans A noncompetitive inhibitor is an inhibitor that binds to both the free enzyme and the enzyme-substrate complex but not in the active site.

52. What is a reaction intermediate?

Ans A reaction intermediate is a species that exists for a finite length of time and is then transformed into product.

53. What is a proenzyme ?

Ans A proenzyme is the inactive precursor of an enzyme.

54. List four important properties of enzymes.

Ans The important properties of enzymes include high catalytic rates, a high degree of substrate specificity, negligible formation of side products, and capacity for regulation.

55. Describe negative feedback inhibition.

Ans Negative feedback inhibition is a process in which the product of a pathway inhibits the activity of the pacemaker enzyme, usually the first enzyme in the pathway.

56. What properties of transition metals make them useful as enzyme cofactors?

Ans Transition metal ions are useful as enzyme cofactors because they have concentrations of positive charge, can act as Lewis acids, and can bind to two or more ligands at the same time.

57. Explain why enzyme kinetics measurement are made at the start of a reaction.

Ans At the start of a reaction, the concentrations of the reactants and products can be known precisely. Because equilibrium has not yet been established presumably only the forward reaction is taking place.

58. Describe the relationship between the law of mass action, solute concentration and effective concentration.

Ans The law of mass action assumes linear reaction rates with respect to solute concentrations, a homogeneous reaction system, and random, independent interactions between molecules. However, macromolecular crowding increases the effective concentration, which impacts binding affinities, reaction rates, equilibrium constants, and diffusion rates. As a result, catalytic activities of enzymes in vivo are typically not predictable based upon in vitro studies of enzyme activity in dilute solutions.

59. Catalysts are believed to lower the activation energy of the transition state in a chemical reaction. How do they accomplish this task?

Ans The amount of energy required for the transition state to be reached during an enzyme-catalyzed reaction is lowered in part because the enzyme’s active site constrains the motions and allowed conformations of the substrate. The active site, which optimally orients the substrate, forces it to adopt a conformation similar to that of the transition state. The energy gained upon substrate binding is also used to lower the activation energy.

60. Transition metals can act as Lewis acids. Explain.

Ans Transition metals can act as Lewis acids because they can accept electrons.

61. Is a reaction mechanism altered by the presence of a catalyst? Explain.

Ans Catalysts do alter the reaction mechanism. A metal catalyst does so because it binds reactants on its surface thereby orienting them to maximize their reactivity. Enzymes do so because amino acid side chains and other catalytic species actively participate in the reaction. Catalysts provide a different pathway for the reaction to occur.

62. Explain the difference between the energy of reaction and energy of activation.

Ans The energy of a reaction is the difference between the energy of the reactants and product. The energy of activation is the energy difference between the reactants and the transition state.

63. Mercuric ion and methyl alcohol are inhibitors of alcohol dehydrogenase. Explain.

Ans Mercuric ion inactivates the enzyme by reacting with sulfhydryl groups. Methanol, whose structure is very similar to that of ethanol, acts as a competitive inhibitor.

64. Describe the difference between reversible and irreversible inhibitors. Give an example of each.

Ans Reversible inhibition does not destroy the enzyme. Adding substrate or removing the inhibitor can remove the inhibitory effect. Malonate, whose structure resembles that of succinate, is a reversible competitive inhibitor of succinate dehydrogenase. An irreversible inhibitor binds permanently (usually covalently) to the enzyme and destroys its catalytic ability. Removing irreversible inhibitors will not restore enzyme activity.

Iodoacetate is an irreversible inhibitor that alkylates glyceraldehyde-3-phosphate dehydrogenase.

65. List three enzymatic dyads.

Ans The most commonly observed enzymatic dyads are arginine-arginine, carboxylatecarboxylate and carboxylate-histidine.

66. How does an enzyme attain catalytic perfection?

Ans An enzyme achieves catalytic perfection if it converts every substrate molecule that enters the active site into a product molecule.

ESSAY QUESTIONS 67. Water is often excluded from the active site of enzymes. Under these circumstances an amino nitrogen becomes much more nucleophilic. Explain.

Ans In the presence of water the amino group is hydrated and shielded from the substrate.

68. How does an enzyme lower the activation energy of a reaction?

Ans The shape and charge distribution of an enzyme’s active site optimally orients substrate molecules and forces them to change their conformation to that of the transition state. The reactants are brought into proximity with each other and held in a reactive conformation by interactions with the enzyme.

69. Can an activity coefficient ever be greater than one?

Ans An activity coefficient of greater than one is impossible since a value of one indicates that there is complete dissociation of the ions.

70. Why do many enzymes require cofactors?

Ans The metals and coenzymes used by some enzymes provide structural and chemical properties that are not provided by amino acid side chains within the active site.

71. Is catalytic perfection a function of concentration?

Ans Catalytic perfection occurs when an enzyme converts substrate to product every time that a substrate molecule enters the active site. Once a catalytically perfect enzyme is saturated with substrate, the rate of product formation does not increase.

72. Freeze drying is a useful technique for isolating enzymes. If the pH is not carefully controlled, however, the enzyme frequently becomes denatured. Explain.

Ans When ice forms, any solutes remaining in the water phase become concentrated. If the enzyme solution is acidic or basic as the ice forms, pH values may be altered sufficiently that the enzyme will become denatured. The use of an appropriate buffer controls the pH, thereby preventing denaturation.

73. An enzyme is a large complex molecule much of which is seemingly uninvolved in the enzyme’s catalytic function. Would it be possible to eliminate excess polypeptide segments and still retain activity?

Ans An enzyme’s large size is required for catalytic activity because it’s complicated folding pattern ensures that the structure and catalytic function of the active site is maintained. In addition, enzymes often have sites other than the active site that are involved in the molecule’s regulation.

74. Some enzymes exist in the body as an inactive form (proenzymes) that are activated only when needed. What advantage do inactive precursors provide?

Ans The conversion of inactive precursors into active enzymes allows a fast response to changing conditions. It also protects the cells from potential damage. Consider, for example, the secretion of precursors of powerful proteolytic enzymes by the pancreas.

75. Most enzymes are amino acid polymers. Would the replacement of the nitrogen in the peptide bond and side chains with oxygen be possible?

Ans Oxygen is a better leaving group than nitrogen. As a result, the polymer would undergo hydrolysis more easily and be less stable. Nitrogen is also more basic than oxygen. Loss of nitrogen would mean that there would be no basic side groups eliminating much of the catalytic acid-base reactions of proteins. Finally, the ester bond is not capable of the resonance of the amide bond. As a result, certain structural features of proteins would either not be possible at all or they would be less stable.

76. How does aspirin inhibit the perception of pain?

Ans Aspirin reduces inflammation and pain perception by preventing the conversion of arachidonic acid into PGG2 (prostaglandin G2) by inhibiting an enzyme called prostaglandin endoperoxide synthase (PTGS). PTGS contains two active sites, cyclooxygenase and peroxidase; aspirin inhibits the enzyme by acetylating the serine residue within cyclooxygenase.

CALCULATIONS 77. Catalase has a Km of 25 mM and a kcat of 4×107sec-1 with H2O2 as a substrate.

Carbonic anhydrase has a Km of 26mM and a kcat of 4×105 sec-1. What does this data tell you about these two enzymes?

Ans Catalase has a higher affinity for the substrate and a higher turnover number than does the carbonic anhydrase.

78. The km and kcat for fumarase the enzyme that catalyzes the conversion of fumarate to malate are 5×10-6M and 8×102 s-1respectively. What does the data tell you about the operation of this enzyme in the citric acid cycle?

Ans This enzyme has a greater tendency to dehydrate malate to fumarate than the reverse reaction. In order for the citric acid cycle to operate with the enzyme-catalyzed production of malate, malate concentrations must be very low.

79. Consider the following reaction along with its rate information A+B→C [A] (mM) [B] (mM) Rate (mM/s) 0.05 0.05 2×107 0.10 0.05 4×107 0.05 0.1 4×107 0.1 0.1 8×107 What is the overall rate expression for this reaction? What is the order of the reaction?

Ans Doubling the concentration of A while holding B constant results in a doubling of the rate of the reaction. The reaction is first order in both A and B. The overall rate expression is: Rate = k[A][B] The overall reaction is second order.

80. Consider the following data for an enzyme-catalyzed hydrolysis reaction in the presence and absence of inhibitor I using a Michaelis-Menton plot determine Km for both inhibited and uninhibited reactions [Substrate](M) o (umol/min) o1 (moles/min) 6×10-6 20.8 4.2 -5 1×10 29 5.8 2×10-5 45 9 -5 6×10 67.9 13.6

1.8×10-4 Ans

87

16.2

Note the difficulty in estimating Vmax for the uninhibited reaction. If 95 μmol/min is chosen for the maximum velocity, then Km is 20 μM (the substrate concentration, [S], at half Vmax, or 45 μmol/min). However, if 100 μmol/min is the maximum velocity, then Km = 25 μM. The inhibited reaction appears to have a Vmax of 16 μmol/min; Km=15 μM.

The data from this graph is transformed into a Lineweaver-Burk plot. The X intercept is –1/Km and the y intercept is 1/vmax 81. The table represents a specific substrate concentrations for an enzyme that displays classical Michaelis-Menten kinetics. Two sets of inhibitor data are also included.

Determine the Km and Vmax for the uninhibited enzyme.

[S](mM) 1.3 2.6 6.5 13.0 26.0

Without Inhibitor 2.50 4.00 6.30 7.60 9.00

Ans Vmax = 10 μm/s Km = 5 μm

Vo(mM/s) With Inhibitor A With Inhibitor B 1.17 0.62 2.10 1.42 4.00 2.65 5.70 3.12 7.20 3.58

The x intercept is –1/Km and the y intercept is 1/Vmax.

CHAPTER SEVEN CARBOHYDRATES 1. Which of the following is not a carbohydrate?

A)

B)

C)

D)

E)

Ans B 2. Which of the following carbohydrates does not belong to the family of naturally occurring sugars?

A)

B)

C)

D)

E)

Ans D 3. The compound

is an epimer of which of the following molecules?

A) B) C) D)

E)

Ans A 4. Which of the following structures is the -anomer of D-glucose?

A)

B)

C)

D

E)

Ans B 5. Which of the following is a -lactone?

A)

B)

C)

D)

E)

Ans C 6. Which of the following is an aldonic acid?

A)

B)

C)

D)

E)

Ans B 7. Which of the following compounds is an aldaric acid?

A)

B)

C)

D)

E)

Ans E 8. Which of the following is an alditol?

A)

B)

C)

D)

E)

Ans E 9. Which of the following is a glycoside?

A)

B)

C)

D)

E)

Ans B 10. Which of the following carbohydrates is a nonreducing sugar?

A) Glucose B) Fructose C) Lactose D) Sucrose E) Ribose Ans D 11. The preferred energy source of the brain is __________.

A) fructose B) glucose C) arabinose D) maltose E) sucrose

Ans B 12. The two most common deoxy sugars are deoxyribose and __________.

A) L-fucose B) deoxyglucose C) deoxyarabinose D) L-sorbose E) D-sorbose Ans A 13. Which of the following sugars contains a -1,4-linkage?

A) Cellulose B) Glucose C) Amylose D) Sucrose E) Maltose Ans A 14. Oligosaccharides usually contain between __________ and __________ simple sugar units.

A) 6, 8 B) 2, 10 C) 1, 10 D) 3, 10 E) 7, 10 Ans B 15. Amylopectin is a form of __________.

A) cellulose B) lactose C) starch D) glycogen E) amylose Ans C 16. The most abundant organic substance on earth is __________.

A) starch B) cellulose C) sucrose D) glucose E) Both B and D are correct.

Ans B 17. Which of the following is not a homoglycan?

A) Cellulose B) Glycogen C) Starch D) Heparin E) Amylose Ans D 18. Which of the following polysaccharides can bind exceptionally large amounts of water?

A) Cellulose B) Glycogen C) Starch D) Heparin E) Amylose Ans D 19. Carbohydrate is thought to enhance the stability of protein molecules by __________.

A) changing the protein’s shape to better resist denaturation B) protecting the underlying protein from the action of proteolytic enzymes C) using hydrogen bonding to increase the stability of the protein D) Both A and B are correct.

E) All the above are correct.

Ans B 20. In glycoproteins carbohydrate is most often linked to threonine, asparagine or __________.

A) serine B) lysine C) valine D) aspartic acid

E) tyrosine Ans A 21. Cellulose is indigestible to most animals because __________ A) cellulose is not soluble in water B) animals lack the enzymes required to hydrolyze the  links of the cellulose C) cellulose has no food value and therefore cannot be digested D) Both A and B are correct.

E) None of the above are correct.

Ans B 22. A glycosidic link is chemically an __________.

A) ether B) ester C) amide D) aldehyde E) ketone Ans A 23. Which of the following yields N-acetyl-D-glucosamine on hydrolysis?

A) Cellulose B) Heparin C) Chitin D) Amylopectin E) Amylose Ans C 24. Glycoproteins lack which of the following groups typically found in proteoglycans?

A) Uronic acids B) Sulfate groups C) N-Glycosidic linkages D) Both A and B are correct.

E) All of the above are correct.

Ans D 25. Glycogen is __________.

A) the main energy storage molecule of animals B) the main carbohydrate reserve of animals C) the main carbohydrate found in seeds D) a form of plant starch E) Both C and D are correct.

Ans B 26. Lactose intolerance arises from __________.

A) bacteria in the intestine that produce toxic metabolites B) the inability of intestinal enzymes to cleave the lactose C) a sensitivity to galactose D) a sensitivity to glucose E) an allergic reaction to glucose Ans B 27. Glycoconjugates result from the covalent linkage of carbohydrate to proteins or __________.

A) amino acids B) lipids C) nucleotides D) Both A and B are correct.

E) None of the above are correct.

Ans B 28. The three most common homoglycans found in nature are cellulose, starch, and __________.

A) amylose B) lactose C) fructose D) glycogen E) sucrose Ans D 29. The two polysaccharides used to store glucose as an energy reserve are starch and __________.

A) glycogen B) cellulose C) fructose

D) sucrose E) maltose Ans A 30. The principal structural carbohydrate of plants is __________.

A) starch B) glycogen C) cellulose D) amylose E) xylulose Ans C 31. The accumulation of AGEs is linked to which of the following diseases?

A) Atherosclerosis B) Arthritis C) Diabetes D) Both A and B are correct.

E) All of the above are correct.

Ans E 32. N-Glycans are linked via a(n) __________ link between the carbohydrate and the amino acid.

A) -Glycosidic B) -Glucosidic C) ester D) amide E) Both A and B are correct.

Ans B 33. Which of the following is not a common sugar found in N-glycans?

A) Mannose B) Glucose C) Maltose D) Fucose E) Galactose Ans C

34. Which of the following is an example of posttranslational modification of proteins?

A) Phosphorylation B) Acetylation C) Proteolytic cleavage D) Glycosylation E) All of the above are examples of posttranslational modification.

Ans E 35. The glycome is the __________.

A) total set of sugars and glycans that an organism produces B) total set of sugars that an organism produces C) total set of glycans that an organism produces D) glycoforms produced by a single sugar E) None of the above are correct.

Ans A 36. The production of the glycan components of each type of glycoprotein as a series of slightly different forms is referred to as __________ A) glycoformation B) glycolation C) microheterogeneity D) posttranslational modification E) alternative splicing Ans C 37. Translation of the sugar code requires which of the following?

A) Glycoforms B) Lectins C) RNA D) DNA E) Integrins Ans B 38. How many stereoisomers are possible for an aldohexose?

A) 4 B) 8 C) 12

D) 16 E) 32 Ans D 39. Reaction of an amino acid with C1 of a cyclic aldose produces which of the following linkages?

A) Ester B) Amide C) Glycosidic D) Imine E) Schiff base Ans C 40. Which of the following terms is not associated with glycation reactions?

A) AGEs B) Amadori products C) Adduct D) Lactose E) Maillard reaction Ans D 41. The principle means of protection of plants against herbivores is __________.

A) taste B) smell C) poison D) mimicry E) color Ans A 42. Of the following primary types of taste perception which is the most important in identifying calorie-dense foods?

A) Sweet B) Savory C) Sour D) Salty E) A and B are correct.

Ans A

43. Savory taste detects which of the following?

A) Sugars B) Amino acids C) Toxicity D) Electrolytes E) Acids Ans B 44. Glycomics is defined as __________.

A) the investigation of the structure and function of all glycans in a cell.

B) glycosidology C) glycology D) lipology E) saccariology Ans A 45. In an aldohexopyranose how many methyl groups will be incorporated on treatment with methyl iodide?

A) One B) Two C) Three D) Four E) Five Ans E 46. Which of the following sugars lacks a chiral center?

A) Glucose B) Glyceraldehyde C) Dihydroxyacetone D) Ribose E) Fructose Ans C SHORT ANSWER

47. Define the term diastereomers.

Ans Diastereomers are non-superimposable nonmirror image stereoisomers.

48. What is an enediol?

Ans An enediol is the intermediate formed during the reversible isomerization of sugars that results in an intermolecular shift of a hydrogen atom and a relocation of a double bond.

49. What is a reducing sugar?

Ans A reducing sugar is a sugar that can be oxidized by a weak oxidizing agent.

50. What structural relationship is indicated by the term D-sugar?

Ans In D-family sugars, the OH on the chiral carbon farthest from the carbonyl group is on the right side in a Fischer projection formula. So both (+)-glucose and (−)-fructose are D-sugars despite their rotation of plane-polarized light in opposite directions.

51. What is the difference between a heteroglycan and a homoglycan? Give an example of each.

Ans Heteroglycans can be made up of more than one type of monosaccharide residue but homoglycans contain only one type. Examples of homoglycans and heteroglycans are starch and hyaluronic acid, respectively.

52. What is a function of glycogen?

Ans Glycogen is a storage form of glucose.

53. The polymer chains of glycosaminoglycans are widely spread apart and bind large amounts of water. What functional groups of the polymer are responsible for this phenomenon?

Ans GAGs are widely spread apart and attract large amounts of water because of charge repulsion caused by negatively charged and hydrophilic sulfate and carboxylate groups.

54. What role do carbohydrate groups play in maintaining glycoprotein stability?

Ans Numerous carbohydrate groups protect glycoproteins from denaturation because they are hydrophilic groups that surround the protein and protect against proteasecatalyzed peptide bond cleavage.

55. What are function of proteoglycans?

Ans Proteoglycans provide strength, support, and elasticity to tissue.

56. Classify D-glyceraldehyde and dihydroxyacetone as enantiomers, diastereomers, epimers or an aldose-ketose pair.

Ans Glyceraldehyde and dihydroxyacetone phosphate are an aldose-ketose pair.

57. Classify D-glucose and D-mannose as enantiomers, diastereomers, epimers, or an aldose ketose pair.

Ans D-glucose and D-mannose are epimers.

58. Raffinose, the most abundant trisaccharide in nature, occurs in whole grains and numerous vegetables. It is the -galactosyl derivative of sucrose. Is raffinose a reducing or nonreducing sugar?

Ans Raffinsoe is a reducing sugar because the galactosyl ring can open.

59. Define the term reducing sugar. What structural feature does a reducing sugar have?

Ans A reducing sugar reduces Cu(II) in Benedict’s reagent. This reduction takes place because the hemiacetal portion of a sugar can form an aldehyde functional group, which can be oxidized to a carboxylic acid.

60. What structural differences characterize cellulose, glycogen and starch?

Ans Amylopectin, at type of starch and glycogen are both homoglycans containing glucose monomers linked by α-(1,4) glycosidic bonds with branch points connected by α(1,6) glycosidic bonds. Glycogen, however, is much more highly branched than amylopectin. Cellulose is a linear polymer of glucose linked by β-(1,4) glycosidic bonds.

61. Phosphate esters can form at position 2 to 6 of an aldohexose but not in position 1.

Explain.

Ans Phosphate esters can form at positions 2–6 of an aldohexose because all these carbons bear alcoholic OH groups. In contrast, a phosphate at the anomeric carbon would be a mixed anhydride.

62. Suggest a reason why sorbitol prevents water loss in candy.

Ans Moisture loss is prevented because of hydrogen bonding between the OH groups of sorbitol and water.

63. What sugar is produced by the epimerization of galactose?

Ans Three sugars are possible. Talose is the sugar produced by the epimerization of galactose at C2. The C4 epimer is glucose, and the C3 epimer is galactose.

64. Sucrose does not undergo mutarotation. Explain.

Ans In order for the sugar to undergo mutarotation there must be a hemiacetal or hemiketal as part of the structure. Sucrose’s anomeric carbons are linked in a full acetal linkage.

65. Treatment of fructose with methyl iodide produces 1,3,4,6,-tetra-O-methylfructose What does this information tell you about the ring structure of fructose?

Ans The information provided reveals that the fructose molecule has a five-membered ring since the hydroxyl at carbon six is methylated.

66. Why is it advantageous for a plant toxin to elicit a bitter taste when an animal eats the plant rather than a bland or sweet taste?

Ans A bitter taste is sufficiently unpleasant that the animal will immediately make the connection between the type of plant and the unpleasant sensation. As a result the animal will stop eating and then avoid the offending plant in the future. If the toxin’s taste is neutral or sweet sufficient time may elapse between consuming the toxin and the onset of any unplesant effects. The animal may continue to eat the plant, thereby defeating the toxin’s purpose.

67. How does glycosylation improve the water solubility of a water-insoluble molecule?

Ans The OH groups of the sugar interact with the water via hydrogen bonding to improve the solubility of the entire molecule.

ESSAY QUESTIONS 68. Toxic compounds in plants frequently have bitter tastes that are detectable at very low concentrations. The sweet taste of carbohydrates is only detectable at much higher levels.

Can you suggest a reason why this is true?

Ans Certain plants contain toxic molecules that protect them from foraging animals. It is therefore highly desirable for animals to detect plant toxins at very low levels. Sweet taste is a signal that food is rich in calories and is not toxic. A higher detection limit for sweet taste assures consumption of only those foods that have a high caloric content.

69. The simplest chiral aldose has three carbon atoms, but the simplest chiral ketose has four carbons. Explain. Include structures in your answer.

Ans Chiral molecules must have a carbon center bearing four different groups. This is possible for a three carbon aldehyde where the carbonyl is at the end of the chain. In a

ketose the carbonyl is in the body of the chain and can therefore only possess a chiral carbon center when the molecule has at least four carbons.

Aldotriose

Ketotetrose

70. Normally, the formation of an acetal requires the incorporation of two alcohol units.

Formation of a sugar acetal requires only the incorporation of one additional molecule of alcohol. Explain.

Ans A sugar is actually a polyalcohol that forms a cyclic hemiacetal when one of these sugar alcohol groups is used. Acetal formation requires that one additional alcohol unit react with the cyclic hemiacetal.

71. 1-Methylglucose is a nonreducing sugar, whereas 2-methylglucose is a reducing sugar. Explain.

Ans The methyl group in 1-methylglucose is part of a full acetal which is not capable of acting as a reducing sugar. Since 2-methylglucose has a free aldehyde group it is capable of acting as a reducing sugar.

72. How does glycation of red blood cells serve as a measure of long term blood glucose levels?

Ans The amino groups of hemoglobin within red blood cells form covalent bonds with sugar molecules. Since this is a nonenzymatic process it takes time. Glycated hemoglobin levels therefore are an indicator of blood glucose control over an extended period of time.

73. What is the smallest ketose that can form a stable ring?

Ans Stable ketose rings contain five or greater atoms, one of which is an oxygen. Since the ketone group must be at least one carbon in from the end of the chain a ketopentose would be the smallest ketose capable of forming a stable ring.

74. Five- and six-membered ring carbohydrate hemiacetals and hemiketals are reasonably stable and can be easily isolated in contrast to a typical organic acetal. Account for this difference in stability.

Ans Carbohydrate acetals have an OH in close proximity to the carbonyl group and easily form a five or six membered rings. This is not true of simple aldehydes and ketones.

75. Polysaccharides can form stable gels that contain immobilized water. How does the polysaccharide immobilize the water?

Ans The many OH groups of the polysaccharide interact with water molecules through hydrogen bonding. Hydrogen bonds can be formed between a single water molecule and several carbohydrate groups effectively immobilizing the polymer.

76. There are two chemically distinct forms of glucose. How is it possible for a single molecule to behave as two distinct molecules?

Ans Glucose can form a ring and in so doing generate a new chiral center. The two ring forms of the glucose that can form the straight chain molecule are diastereomers (nonsuperimposable nonmirror image stereoisomers) and as such have distinct chemical and physical properties.

CHAPTER EIGHT CARBOHYDRATE METABOLISM 1. Both glycogenesis and glycogenolysis are controlled primarily by the interplay between the two hormones insulin and __________.

A) glycogen synthetase B) glucagon C) fructose kinase D) glucose hydrolyase E) pentose kinase Ans B 2. Hexokinase D is found in the __________.

A) kidney B) liver C) heart D) muscle E) intestine Ans B 3. An enzyme family called the __________ catalyzes the phosphorylation of hexoses in the body.

A) hexolysases B) phosphorolyases C) hexokinases D) glucokinases E) phosphofructokinases Ans C 4. The conversion of glucose-1-phosphate to UDP-glucose has a G0’ near zero. Which of the following reactions is coupled with the previous reaction to drive it to completion?

A) Hydrolysis of PPi B) Hydrolysis of ATP C) Hydrolysis of ADP D) Hydrolysis of UDP E) Hydrolysis of UTP Ans A

5. Which of the following is required for the conversion of UDP-glucose to glycogen?

A) Glycogen synthase B) Branching enzyme C) Glucose phosphorylase D) Debranching enzyme E) Both A and B are correct.

Ans E 6. A glycogen molecule that has been degraded to its branch points is called __________.

A) dextrin B) glucose C) amylose D) limit dextrin E) Both A and B are correct.

Ans D 7. Regulation of glycolysis involves all of the following except __________.

A) insulin B) glucagon C) SREBP1c D) AMPK E) None of the above are correct.

Ans E 8. The binding of insulin to receptors on the surface of muscle cells stimulates which of the following processes?

A) Glycogenolysis B) Glycogenesis C) Release of ATP D) Formation of cyclic AMP E) Release of glucagon Ans B 9. Under stressful conditions epinephrine is released from the adrenal medulla. The release of epinephrine has which of the following effects on glucose metabolism?

A) Glycogenolysis is stimulated.

B) Glycogenesis is inhibited.

C) Adenylate cyclase is activated.

D) Both A and B are correct.

E) All the above are correct.

Ans E 10. Phosphorylase kinase __________.

A) converts inactive phosphorylase to active phosphorylase B) converts active phosphorylase to inactive phosphorylase C) phosphorylates glycogen synthase D) converts ADP to ATP E) Both B and C are correct.

Ans A 11. Cori’s disease is caused by __________.

A) lack of insulin B) lack of phosphorylase b C) lack of glucagons D) a deficiency of debranching enzyme E) deficient chromium receptors on the cell surface Ans D 12. Which of the following activates phosphoprotein phosphatase?

A) Insulin B) Epinephrine C) Glucagon D) ATP E) Both A and B are correct.

Ans A 13. Glucose-6-phosphate is a substrate in which of the following processes?

A) Gluconeogenesis B) Glycolysis C) Photosynthesis D) Glycogenolysis E) Both A and B are correct.

Ans E

14. Fructose-2,6-bisphosphate __________.

A) is an indicator of high cellular glucose concentration B) is formed by PFK-1 C) activates aldolase D) Both A and B are correct.

E) All of the above are correct.

Ans A 15. The Embden-Myerhof pathway is also referred to as __________.

A) gluconeogenesis B) glycogenolysis C) glycolysis D) glycogenesis E) citric acid cycle Ans C 16. In glycolysis __________ moles of ATP are produced per mole of glucose consumed.

A) one B) two C) three D) four E) five Ans B 17. In glycolysis __________ moles of NADH are produced per mole of glucose consumed.

A) one B) two C) three D) four E) five Ans B 18. The presence of which of the following molecules indicates that the cell has sufficient energy reserves?

A) ATP

B) Citrate C) ADP D) Fructose-1,6-biphosphate E) Both A and B are correct.

Ans E 19. Which of the following enzymes is an oxidoreductase?

A) Aldolase B) Triose phosphate isomerase C) Glyceraldehyde-3-phosphate dehdyrogenase D) Phosphofructokinase E) Phosphoglucoisomerase Ans C 20. The first reaction in the oxidative phase of the pentose phosphate pathway is catalyzed by __________.

A) ribulose-5-phosphate dehydrogenase B) transketolase C) glucose-6-phosphatase D) glucose-6-phosphate dehydrogenase E) hexokinase Ans D 21. Which of the following enzymes catalyzes an irreversible process?

A) Pyruvate kinase B) Aldolase C) Enolase D) Phosphoglycerate mutase E) Glyceraldehyde-3-phosphate dehydrogenase Ans A 22. In anaerobic organisms pyruvate is used to regenerate cellular __________.

A) NADP+ B) FADH C) FAD D) NAD+ E) ADP

Ans D 23. Allosteric regulation of which of the following enzymes is important in the regulation of glycolysis?

A) Hexokinase B) PFK-1 C) Pyruvate kinase D) Both A and C are correct.

E) All of the above are correct.

Ans E 24. Gluconeogenesis occurs primarily in the __________.

A) brain B) muscle C) liver D) heart E) pancreas Ans C 25. Which of the following molecules can be used to synthesize glucose via gluconeogenesis?

A) Lactate B) Pyruvate C) Glycerol D) Keto acids E) All of the above are correct.

Ans E 26. Which of the following is the most important glucogenic amino acid?

A) Aspartate B) Alanine C) Glycine D) Glutamate E) All are equally important.

Ans B 27. Gluconeogenesis is stimulated by high concentrations of which of the following compounds?

A) Lactate B) Glycerol C) Amino acid D) Both A and B are correct E) All of the above are correct Ans E 28. Which of the following is an oxidizing agent in fermentation?

A) Lactate B) Glucose C) NADH D) Pyruvate E) ADP Ans D 29. In addition to glucose which of the following sugars are important in the human diet?

A) Fructose B) Galactose C) Mannose D) Sucrose E) Both A and D are correct.

Ans D 30. Intermediates in the nonoxidative phase of the pentose phosphate pathway include all of the following except __________.

A) dihydroxyacetone phosphate B) sedoheptulose-7-phosphate C) fructose-6-phosphate D) xylulose-5-phosphate E) erythrose-4-phosphate Ans A 31. The use of a highly exergonic reaction in the beginning of a catabolic pathway is referred to as __________.

A) bioactivation B) turbo design C) activation D) glycolysis

E) Both A and C are correct.

Ans B 32. Aldol cleavage of which of the following sugars will produce one mole each of dihydroxyacetone and glyceraldehyde?

A) Fructose B) Glucose C) Ribose D) Maltose E) Trehalose Ans A 33. Which of the following is a second messenger in glycogenolysis?

A) Glucagon B) Insulin C) Glucose D) ATP E) cAMP Ans E 34. In animals excess glucose is converted into its storage form, __________.

A) starch B) chitin C) glycogen D) amylose E) amylopectin Ans C 35. The major carbohydrate fuel for most organisms is __________.

A) glucose B) fructose C) ribose D) sucrose E) All of the above are correct.

Ans A 36. Which of the following enzymes is not required in gluconeogenesis?

A) Phosphoenolpyruvate carboxykinase B) Phosphofructokinase C) Pyruvate kinase D) Fructose-1,6-bisphosphatase E) Pyruvate carboxylase Ans B 37. The final product of glycolysis is __________.

A) dihydroxyacetone phosphate B) pyruvate C) ethanol D) acetyl-CoA E) acetaldehyde Ans B 38. The principal products of the pentose phosphate pathway include __________.

A) NADH B) NADPH C) ATP D) ribose-5-phosphate E) Both B and D are correct.

Ans E 39. Flux of which of the following sugars into the glycolytic pathway is essentially unregulated.

A) Glucose B) Fructose C) Glucose-1-phosphate D) Both A and C are correct E) None of the above are correct Ans B 40. Conversion of fructose-6-phosphate to fructose-1,6-bisphosphate has two purposes.

One is the commitment of the molecule to glycolysis; the second is __________.

A) raising the free energy of the system B) making possible the formation of a second mole of ATP C) preventing the cleavage products of the next step from diffusing out of the cell D) preventing the reverse reaction E) enolization of the product

Ans C 41. Which of the following enzymes will catalyze the first committed step in glycolysis?

A) Phosphofructoisomerase B) Aldolase C) Triose phosphate isomerase D) Phosphofructokinase 1 E) Phosphoglucooisomerase Ans D 42. The Crabtree effect in yeast is __________.

A) fermentation of glucose B) repression of aerobic metabolism by glucose C) repression of glycolysis by oxygen D) repression of glucose metabolism by ethyl alcohol E) fermentation of ethyl alcohol Ans B 43. The Pasteur effect is __________.

A) fermentation of glucose B) repression of aerobic metabolism by glucose C) repression of glycolysis by oxygen D) repression of glucose metabolism by ethyl alcohol E) fermentation of ethyl alcohol Ans C 44. A diauxic shift is __________.

A) a significant change in gene expression B) shifting from aerobic to anerobic respiration C) shifting from anerobic to aerobic respiration D) change in composition of microbes in a sample E) change in the amount of ATP used to ferment glucose Ans A 45. The phosphorylation of glucose when it enters a cell accomplishes which of the following?

A) Makes the glucose more water soluble

B) Prevents back diffusion out of the cell C) Isomerize the glucose D) Activates the glucose for further reaction E) Both B and D are correct.

Ans E 46. Which of the following compounds is an end product of anaerobic respiration?

A) Carbon dioxide B) Ethanol C) Water D) Glycogen E) Acetaldehyde Ans B SHORT ANSWER 47. In which reaction in glycolysis does a dehydration occur?

Ans In glycolysis, a dehydration occurs in the conversion of 2-phosphoglycerate to phosphoenolpyruvate, catalyzed by enolase.

48. Upon entering a cell, glucose is phosphorylated. Give two reasons why this reaction is required.

Ans Phosphorylation of glucose upon entry into the cells prevents leakage of the molecule out of the cell and facilitates its binding to the active sites of enzymes.

49. What reaction is catalyzed by aldolase?

Ans . Aldolase catalyzes the reversible conversion of fructose-1,6-bisphosphate to DHAP and glyceraldehyde-3-phosphate.

50. What reaction is catalyzed by hexokinase?

Ans Hexokinase catalyzes the phosphorylation of glucose to yield glucose-6-phosphate.

51. What reaction is catalyzed by phosphoglucomutase?

Ans Phosphoglucomutase catalyzes the reversible conversion of glucose-1-phosphate and glucose-6-phosphate.

52. Suggest a reason why glycolysis produces NADH and the pentose phosphate pathway produces NADPH.

Ans If either NADPH or NADH were the sole hydrogen carrier it would be impossible to determine the need for carbon units in either the pentose phosphate pathway or glycolysis. A decrease in the concentration of either reducing agent activates enzymes that shunt carbon into its respective pathway.

53. What is the principle reason that organisms such as yeast produce alcohol?

Ans Such organisms utilize acetaldehyde as a hydrogen acceptor in order to regenerate NAD+. Ethanol is the product of the reduction of acetaldehyde.

54. What happens to pyruvate under anaerobic conditions in aerobic cells? + Ans Under anaerobic conditions, pyruvate is reduced to lactate to regenerate NAD .

55. Glycolysis occurs in two stages. Describe what is accomplished in each stage.

Ans In the first stage glucose is phosphorylated twice and then cleaved to from two molecules of glyceraldehyde-3-phosphate. In stage 2 each glyceraldehyde-3-phosphate is converted to pyruvate with a net production of one NADH and two ATP. 56. Compare the entry-level substrates, products and metabolic purposes of glycolysis and gluconeogenesis.

Ans In glycolysis, the entry level substrates are sugars and the product is pyruvate. The main purposes of glycolysis are to provide the cell with energy and/or several metabolic intermediates. The substrates for gluconeogenesis are pyruvate, lactate, glycerol, and several amino or -keto acids. Gluconeogenesis provides the body with glucose when blood glucose levels are low.

57. Why is severe hypoglycemia so dangerous?

Ans Severe hypoglycemia is so dangerous because brain cells and red blood cells rely solely on glucose for their energy needs. Severe hypoglycemia causes fainting, and requires immediate medical attention. When the condition is prolonged and/or recurrent, it may also result in long-term brain impairment or dysfunction.

58. Describe the effect of insulin and glucagon on blood glucose.

Ans Insulin is released in response to high blood glucose levels. In the liver insulin inhibits glycogenolysis and activates glycogenesis resulting in a decrease in blood glucose levels. Insulin also causes an increased cellular uptake (adipocytes and muscle cells) of glucose. Glucagon is released in response to low blood glucose levels. In the liver glucagon inhibits glycogenesis and the activates glycogenolysis resulting in the release of glucose into the bloodstream.

59. Describe the Cori cycle; what is its physiological function?

Ans In the Cori cycle, lactate produced under anaerobic conditions in exercising skeletal

muscle, is transported to the liver, where it is converted back to pyruvate by transamination and then to glucose via gluconeogenesis, which is then returned to muscle. In muscle, glucose undergoes glycolysis to form pyruvate, which reacts with NADH to form lactate and NAD+. The physiological function of the Cori cycle is to convert lactate, a waste product of anabolic muscle metabolism, into glucose.

60. Describe the effects of insulin and glucagon on glycogen metabolism.

Ans The general effect of insulin is to lower blood glucose levels by initiating a process that leads to the inhibition of glycogenolysis and the activation of glycogenesis.

Glucagon has the opposite effect. It raises blood glucose levels by initiating a process that leads to the activation of glycogenolysis and the inhibition of glycogenesis.

61. What cell types produce insulin, glucagon, epinephrine, and cortisol?

Ans Insulin and glucagon are produced within pancreatic  and  cells respectively.

Epinephrine and cortisol are produced by cells in the adrenal glands in response to stress.

62. Describe the different functions of glycogen in muscle and liver.

Ans In muscle, glycogen is synthesized to store glucose for energy and metabolized when energy is needed. In the liver, glycogenesis (glycogen synthesis) and glycogenolysis (glycogen hydrolysis) are regulated to maintain blood glucose levels.

63. Glycogen synthesis requires a short primer chain. Explain how new glycogen molecules are synthesized given this limitation.

Ans In the synthesis of new glycogen molecules, a primer protein called glycogenin is used to initiate glycogen formation. Glucose is transferred from UDP-glucose to a specific tyrosine residue of the glycogenin. This glucose then serves as the starting point for a new growing glycogen molecule.

64. Why does PEP have such a high phosphoryl group transfer potential?

Ans Phosphoenolpyruvate has a high phosphoryl group transfer potential because the transfer of the enol phosphate to another molecule produces an unsaturated alcohol (pyruvate in its enol form) vinyl alcohol. The enol form of pyruvate tautomerizes rapidly to the keto-form making the transfer almost irreversible.

65. In aerobic metabolism oxygen is the ultimate oxidizing agent (electron acceptor).

What is the oxidizing agent in anaerobic fermentation?

Ans The common oxidizing agent in anaerobic metabolism is NAD+.

66. How does phosphorylation increase the reactivity of glucose?

Ans The OH group itself is not very easily displaced. However conversion of an OH group to a phosphate ester is very easily accomplished. These esters are good leaving groups and when displaced have the same effect as if an OH had reacted.

ESSAY QUESTIONS: 67. Explain and contrast the Pasteur and Crabtree effects.

Ans In the Pasteur effect, oxygen inhibits glucose oxidation via glycolysis. In other words glucose is oxidized more rapidly in aerobic cells that are deprived of oxygen compared to when oxygen is available. In the Crabtree effect, which is observed in S. cerevisiae, glucose represses aerobic metabolism (the opposite of what occurs in the Pasteur effect) Excess pyruvate is converted to ethanol, which is then excreted into the environment, where it kills microbial competitors.

68. Explain the role of glycogenin in glycogen synthesis.

Ans Glycogenin is a primer protein that is required for glycogen synthesis. Each glycogen chain is synthesized by glycogen synthase by extending a preexisting tetrasaccharide, which is linked to a specific tyrosine residue in glycogenin.

69. Describe the physiological condition that activates gluconeogenesis. What prevents competition between gluconeogenesis and glycolysis?

Ans Gluconeogenesis occurs mainly in the liver. It is activated by processes that deplete blood glucose, such as fasting and exercise. Futile cycles are prevented by having the forward and reverse reactions catalyzed by different enzymes, both independently regulated.

70. An individual has a genetic condition that prevents the production of glucokinase.

Following a carbohydrate meal do you expect blood glucose levels to be high, low or about normal? What organ accumulates glycogen under these circumstances?

Ans In such an individual, following a carbohydrate meal blood glucose levels would be higher than normal. Recall that the kinetic properties of glucokinase allow the liver to remove excess glucose from blood. Skeletal muscle would accumulate some additional glycogen, but most excess glucose would be used to synthesize triacylglycerol in adipocytes, a process that is promoted by insulin. A significant amount of liver glycogen is synthesized from glucose produced by gluconeogenesis.

71. Why is fructose metabolized more rapidly than glucose?

Ans In the liver fructose is metabolized more rapidly than glucose because its metabolism bypasses two regulatory steps in the glycolytic pathway: the conversions of glucose to glucose-6-phosphate and fructose-6-phosphate to fructose-1,6-bisphosphate.

72. Why is it important that gluconeogenesis not be the exact reverse of glycolysis?

Ans If gluconeogenesis and glycolysis were exactly the reverse of one another, futile cycles would be established and much energy would be wasted. In addition, it would be impossible for the body to store glycogen or release glucose into the blood as needed.

73. Severe dieting results in both the reduction of fat stores and the loss of muscle mass.

Trace the conversion of muscle protein to glucose production.

Ans Once muscle protein has been degraded to amino acids, a large percentage of them are converted to either oxaloacetate or pyruvate. Both of these molecules are substrates for the gluconeogenesis pathway.

74. Both glycogen and triacylglycerols are energy sources used by the body. Suggest a reason why both are needed.

Ans Glycogen and triacylglycerols differ in the speed with which energy can be mobilized. Glycogen can be converted into glucose and diverted into production very quickly (instant energy). It takes longer to mobilize the fat reserves, but once activated they provide the energy for sustained effort.

75. List the three principle hormones that regulate glucose metabolism. Briefly explain the effects these molecules have on carbohydrate metabolism.

Ans The three principle hormones that regulate glucose metabolism are insulin, glucagon and epinephrine. Insulin is an anabolic hormone that causes target cells to take up glucose from the blood and stimulates glycogenesis in liver and muscle and glycolysis in the liver. Glucagon is released when blood glucose levels are low. It stimulates liver glycogenolysis and gluconeogenesis, both of which produce glucose, which is then released into the blood. Epinephrine, released under stressful conditions, raises blood glucose levels by triggering liver glycogenolysis.

CHAPTER TEN AEROBIC METABOLISM II 1. Molecules involved in the conversion of oxidized proteins to their functional reduced sulfhydryl form include all of the following except __________.

A) thioredoxin B) NADPH C) catalase D) thioredoxin reductase E) None of the above are correct.

Ans C 2. All of the following are components of the electron transport chain except __________.

A) coenzyme Q B) succinate dehydrogenase C) coenzyme A D) cytochrome c E) NADH dehydrogenase Ans C 3. The ETC component that transfers electrons directly to oxygen is __________.

A) cyt c B) UQ C) cyt bc1 D) cytochrome oxidase E) succinate dehydrogenase Ans D 4. During the oxidation of NADH there are several steps in which Eo’ is sufficient for ATP synthesis. These occur within __________.

A) Complexes I, II, and III B) Complexes I, III, and IV C) Complexes II, III, and IV D) Complexes III, IV, and V E) Complexes I, II, and IV Ans B

5. Which of the following molecules inhibits Complex I of the electron transport chain?

A) Azide B) Amytal C) Cyanide D) Arsenic E) Carbon monoxide Ans B 6. ATP synthesis and mitochondrial electron transport are coupled by __________.

A) protonmotive force B) high energy intermediates C) proton gradient D) Both A and C are correct.

E) All of the above are correct.

Ans D 7. Evidence supporting the chemiosmotic theory includes all of the following except __________.

A) inhibitors of ATP synthesis have been shown to dissipate the proton gradient B) mitochondria with disrupted membranes cannot synthesize ATP C) ATP synthesis is depressed when mitochondrial swelling occurs as a result of osmotic changes D) the pH of a weakly buffered suspension of mitochondria rises when O2 added.

E) actively respiring mitochondria expel protons Ans D 8. Examples of uncouplers include __________.

A) DNP B) antimycin C) gramicidin D) Both A and B are correct.

E) Both A and C are correct.

Ans E 9. In the ATP synthase, the Fo factor __________.

A) has three types of subunits B) possesses ATPase activity

C) is a transmembrane proton channel D) Both A and B are correct.

E) Both A and C are correct.

Ans E 10. The maximum P/O ratio of FADH2 is __________.

A) 1.5 B) 1.75 C) 2.0 D) 2.5 E) 3.0 Ans A 11. The control of aerobic respiration by __________ is referred to as respiratory control.

A) HPO4-2 B) NADH C) FADH2 D) citrate E) ADP Ans E 12. The first ROS formed during the reduction of oxygen is __________.

A) hydrogen peroxide B) hydroxyl radical C) singlet oxygen D) superoxide radical E) None of the above are correct.

Ans D 13. The reaction of Fe+2 with H2O2 results in the production of __________.

A) hydroxyl radical B) hydroxide ion C) superoxide radical D) Both A and B are correct.

E) Both A and C are correct.

Ans D

14. ROS are generated during __________.

A) xenobiotic metabolism B) respiratory burst C) ionizing radiation D) Both A and B are correct.

E) All the above are correct.

Ans E 15. Glutathione peroxidase __________.

A) converts organic peroxides into alcohols B) generates GSH from GSSG C) reduces H2O2 into H2O D) Both A and B are correct.

E) Both A and C are correct.

Ans E 16. The NADPH required for the generation of GSH from GSSG in synthesized by the reactions of __________.

A) the pentose phosphate pathway B) glycolysis C) the citric acid cycle D) Both A and B are correct.

E) Both A and C are correct.

Ans A 17. Glutathione peroxidase requires __________ for full activity.

A) sulfur B) copper C) iron D) selenium E) magnesium Ans D 18. Examples of antioxidants include all of the following except __________.

A) ascorbic acid B) −carotene C) -tocopherol D) hydroquinone E) gramicidin

Ans E 19. One of the mechanisms by which vitamin C protects membrane is by __________.

A) regenerating reduced -tocopherol B) reacting with proline C) reacting with peroxyl radicals D) Both A and B are correct.

E) Both A and C are correct.

Ans E 20. The ultimate electron acceptor of the mitochondrial electron transport system is __________.

A) coenzyme Q B) NADPH C) O2 D) H2O E) Both C and D are correct.

Ans C 21. The major sources of NADH that reduce Complex I of the ETC include __________.

A) fatty acid oxidation B) CoQ C) pentose phosphate pathway D) the citric acid cycle E) Both A and D are correct.

Ans E 22. In Complex III, electrons are transferred from UQH2 to __________.

A) O2 B) coenzyme Q C) cytochrome c D) FAD E) NADH Ans C 23. __________ is a metal cofactor of the cytochromes.

A) Fe B) S C) Co D) Zn E) Ca Ans A 24. Carbon monoxide inhibits which of the following?

A) NADH dehydrogenase B) Ubiquinone C) Cytochrome oxidase D) Succinate dehydrogenase E) None of above are correct.

Ans C 25. Which of the following is the best reducing agent?

A) H2O B) O2 C) FADH2 D) FMNH2 E) NADH Ans E 26. The final product of oxidative phosphorylation is __________.

A) water B) ADP C) NADPH D) ATP E) FMNH2 Ans D 27. __________ are hydrophobic molecules that dissipate ionic gradients.

A) Uncouplers B) Ionophores C) Xenobiotics D) Radicals E) None of the above are correct.

Ans B 28. The return of __________ into the mitochondrion is coupled to the formation of __________.

A) Ca+2; cAMP B) Fe+2; CoQ C) ADP; NADH D) ADP; CoASH E) H+; ATP Ans E 29. The energy that is captured by the electron transport system is in the form of __________.

A) NADH B) FADH2 C) ATP D) Both A and B are correct.

E) All the above are correct.

Ans D 30. The reducing power generated in the cytoplasm can be transferred into the mitochondrion by which of the following processes?

A) Glycerol phosphate shuttle B) Malate-aspartate shuttle C) The phosphate shuttle D) A and B are correct.

E) All the above are correct.

Ans D 31. The cytochromes contain which type of prosthetic group?

A) FADH B) Heme C) TPP D) Zinc++ E) NAD + Ans B

32. The function of complex III is the transfer of electrons from __________.

A) coenzyme Q to Cyt c B) NADH to CoQ C) succinate to UQ D) CoQ to NADH E) UQ to succinate Ans A 33. Which of the following complexes contain copper?

A) Complex I B) Complex II C) Complex III D) Complex IV E) Complex V Ans D 34. Which of the following acts as an allosteric inhibitor of complex IV? A) FMN B) NADH C) FADH2 D) ATP E) ADP Ans D 35. Which of the following is not a step in the ATP synthesizing process?

A) ADP + Pi bind to the L site.

B) ATP is synthesized as the L conformation converts to the T conformation.

C) ATP is released as the T conformation converts to the O confirmation.

D) The O conformation binds ADP and Pi. E) All of the above are correct.

Ans D 36. Nonshivering thermogenesis is regulated by which of the following?

A) Norepinephrine B) Thermogenin C) UCP2 D) ATP

E) GTP Ans A 37. The primary function of catalase is to __________, A) detoxify peroxides B) reduce the disulfide group C) convert hydrogen peroxide to water D) generate ROS E) oxidize heme Ans C 38. How many ATP are generated during the oxidation of one NADH? A) 1 B) 2 C) 2.5 D) 3 E) 3.5 Ans C 39. Which of the following would not be classified as a ROS? A) Oxygen B) CH3O. C) H-O-O. D) Hydroxide ion E) None of the above are correct (all are ROS).

Ans D 40. The principal sources of electrons for the electron transport system is (are) which of the following?

A) Glycolysis B) Citric acid cycle C) Fatty acid oxidation D) Both A and B are correct.

E) All the above are correct.

Ans E

41. The statement aerobic organisms use oxygen to generate energy required to maintain metabolic processes yet they risk damage caused by highly reactive oxygen molecules can be referred to as __________.

A) oxidation B) reactive oxygen species C) oxygen paradox D) metabolic damage E) thermodynamic inconsistency Ans C 42. The ultimate waste products of aerobic cellular metabolism of oxygen include __________.

A) pyruvate B) ethyl alcohol C) carbon dioxide D) carbon monoxide E) Either A or B is correct.

Ans C 43. According to the solid state model of electron transport, electron transfer is efficient because __________.

A) electron transfer is the result of random collisions B) there are short diffusion distances between components for mobile electron carriers C) UQ is abundant D) cytochrome c diffuses rapidly E) electron carriers are mobile Ans B 44. How many protons are required to drive the phosphorylation of ADP by the mitochondrial ATP synthase?

A) One B) Two C) Three D) Four E) Five Ans D

45. A respiratory burst is initiated when NADPH reacts with oxygen to produce which of the following?

A) Superoxide anion B) Water C) Hydrogen peroxide D) Hydroxyl radical E) Peroxide radical Ans A 46. Antimycin A inhibits cyt b in complex III. If this inhibitor is added to a suspension of mitochondria which of the following will increase in concentration?

A) NADH B) Reduced cytochrome c1 C) Reduced cytochrome c D) NAD+ E) A and D are correct.

Ans A SHORT ANSWER 47. Describe the proton motive force?

Ans The protonmotive force is the force arising from a gradient of protons across a membrane and a membrane potential.

48. What is the glycerol phosphate shuttle?

Ans The glycerol phosphate shuttle is a metabolic process that uses glycerol-3-phosphate to transfer electrons from NADH in the cytosol to mitochondrial FAD to yield FADH2..

49. What is a respiratory burst?

Ans A respiratory burst is an oxygen-consuming process in scavenger cells such as macrophages in which ROS are generated and used to kill foreign or damaged cells.

50. Describe the principle features of the chemiosmotic theory.

Ans The chemiosmotic coupling theory has the following principal features: As electrons pass through the electron transport chain (ETC), energy is captured and used to transport protons from the matrix into the inner membrane space. As a result, an electrical potential () and a proton gradient (pH) are created across the inner membrane. The

electrochemical proton gradient is sometimes referred to as the protonmotive force (p).

Protons, which are present in the intermembrane space in great excess, can pass through the inner membrane and back into the matrix down their concentration gradient only through the proton-translocating ATP synthase.

51. What are the principle sources of electrons for the electron transport system?

Ans The principle sources of electrons for the mitochondrial electron transport system are NADH and FADH2, generated in the citric acid cycle and fatty acid oxidation.

52. How does nitrophenol inhibit ATP synthesis?

Ans ATP synthesis requires the presence of a proton gradient across the mitochondrial membrane. Dinitrophenol, which has an ionizable hydrogen, can diffuse across the mitochondrial membrane. As it diffuses across the membrane, protons are transported from one side of the mitochondrial membrane to the other, thereby disrupting the proton gradient and interfering with ATP synthesis.

53. Compare the amount of energy captured from a mole of glucose from glycolysis alone with that of oxidative phosphorylation.

Ans In glycolysis, the net production of energy from one mole of glucose is two moles of ATP. If the two molecules of pyruvate are further oxidized by oxidative phosphorylation mechanism the total number of ATPs generated from the mole of glucose will be 29.5 to 31, depending on the shuttle mechanism used to transfer the electrons from the two cytoplasmic NADHs to the mitochondrial ETC. 54. Describe the enzymatic activities used by cells to protect themselves from oxidative damage.

Ans The major enzyme defenses against oxidative stress are provided by superoxide dismutase, catalase and glutathione peroxidase.

55. Describe the types of cellular damage produced by ROS. Ans ROS damage cells by inactivating enzymes, depolymerizing polysaccharides,

breaking DNA, and destroying membranes.

56. What material accumulates when azide (N3-) is added to actively respiring mitochondria?

Ans When added to actively respiring mitochondria, azide inhibits cytochrome oxidase, resulting in the accumulation of H+ on the matrix side, and reduced cytochrome c in the intermembrane space.

57. When rotenone is added to actively respiring mitochondria the ratio of NADH to NAD+ increases, but the FADH2/FAD remains unchanged. What step in the system is being inhibited?

Ans NADH dehydrogenase (Complex I) oxidizes NADH to NAD+. When Complex I is inhibited NADH accumulates (resulting in an increased NADH/NAD+ ratio) and FADH2 which is oxidized in Complex II is unaffected.

58. List some of the causes of reperfusion triggered cardiac cell damage.

Ans Reperfusion-induced cardiac cell damage is primarily the result of ROS production, acidosis, and the opening of MPTP. ROS are generated by a reenergized mitochondrial ETC, the neutrophil enzymes NADPH oxidase and xanthine oxidase, and iron-induced hydroxyl ion production. Acidosis is caused by lactate accumulation, which is triggered by increased oxygen unloaded by hemoglobin. Reperfusion also promotes increased nitric oxide synthesis. MPTP opening causes the mitochondrial membrane potential to collapse.

59. Explain why rotenone inhibits oxidative phosphorylation when the substrate is pyruvate but not when succinate is used.

Ans Rotenone inhibits complex I which oxidizes NADH. NADH is provided by the citric

acid cycle with acetyl-CoA, a derivative of pyruvate, as the substrate. Succinate, the substrate for complex II, enters the series below the point where rotenone inhibits.

60. Describe the processes that are driven by mitochondrial electron transport.

Ans In addition to ATP synthesis, the mitochondrial electron transport-driven proton gradient also drives transport of substances across the inner membrane (e.g., phosphate, ADP and ATP). When the proton gradient is diminished heat generation (nonshivering thermogenesis) results.

61. What would be the end products when the following substances are final electron acceptors in the electron transport system: nitrate, ferric ion, carbon dioxide, sulfate and sulfur?

Ans Although the end products of the following substances in an electron transport

system are not named specifically in the text, we can speculate based upon the most reduced forms of the atom with the highest oxidation state. The nitrogen atom in nitrate (NO3–) has an oxidation state of +5; possible reduction products include: NO2–, NO, N2, with NH3 being the most reduced form. The ferric ion (Fe3+) may reduce to ferrous ion (Fe2+) or metallic iron. With carbon dioxide, CH4 is the most reduced form of carbon.

The most reduced form of sulfur, sulfide, (S2–), would likely be the final product of the reduction of both sulfate (SO42–) and elemental sulfur.

62. What advantages does dioxygen have over nitrate, ferric ion, carbon dioxide, sulfate and sulfur as final electron acceptors in the electron transport system?

Ans The advantage of dioxygen over the charged oxidizing species such as NO3, Fe+3, and SO42- is that O2 readily diffuses across cell membranes. Unlike CO2, which also diffuses across cell membranes, dioxygen is highly reactive and readily accepts electrons.

Finally O2 is found almost everywhere on Earth’s surface and is much more readily accessible that oxidizing agents such as sulfur.

63. Describe the mechanism whereby uncoupling agents disrupt phosphorylation.

Ans Uncoupling agents disrupt phosphorylation by reducing (or collapsing) the proton

gradient across the inner mitochondrial membrane. Uncoupling proteins such as UCP1 form a proton channel across this membrane, while other uncoupling agents such as dinitrophenol carry protons across the membrane. Both types of uncouplers provide a mechanism for protons to move across the membrane in a way that bypasses ATPase.

The energy captured by the electron transport system is dissipated as heat instead of being used to do work, (e.g., ATP synthesis). UCP1 is activated by fatty acids that are produced by the hydrolysis of fats in brown adipose tissue. Fat hydrolysis in brown fat tissue is initiated by a cascade mechanism, which is triggered by the neurotransmitter norepinephrine.

64. The electron transport system consists of a series of oxidations rather than one reaction. Why is this an important feature of energy capture?

Ans The net reaction of the electron system is highly exergonic. Using a series of oxidations rather than one reaction allows of a more controlled, more efficient capture of this energy, avoiding the liberation of a great deal of heat.

65. Describe the role of UCP1 in nonshivering thermogenesis.

Ans In nonshivering thermogenesis the energy generated by the oxidation of fatty acids is

released as heat. UCP1, a protein dimer with a proton channel, dissipates the proton gradient across the inner membrane, thereby causing reduced ATP synthesis and the release of heat.

66. What is the respirasome?

Ans The respirasome is functional aerobic respiration unit in the inner mitochondrial membrane; the I , III2, IV1-2 supercomplex has been identified in animals, plants, and fungi.

ESSAY 67. A previous explanation of the mechanism of ATP synthesis referred to as the chemical coupling hypothesis, postulated that ATP synthesis occurs as s substrate level

phosphorylation via a phosphate containing intermediate. The chemical coupling hypothesis failed to explain why mitochondrial membrane must be intact during ATP synthesis. How does the chemiosmotic theory account for this phenomena?

Ans According to the chemiosmotic theory, an intact inner mitochondrial membrane is required to maintain the proton gradient required for ATP synthesis.

68. Valinomycin is an ionophore antibiotic that renders biological membranes permeable to K+. Its side effects in patients with bacterial infections include a rise in body temperature and sweating. Explain.

Ans The passage of K+ across a membrane through an ionophore such as valinomycin lowers the electrical potential gradient. As a result, some of the energy that would have been used to synthesize ATP is dissipated as heat. This explains the rise in body temperature and sweating upon treatment with valinomycin.

69. When taken in appropriate amounts Vitamin E protects the body from ROS. However when it is taken in excessive amounts Vitamin E can potentially make the body more susceptible to ROS. Explain.

Ans In small quantities ROS act as signal molecules. Excessive amounts of dietary antioxidants such as vitamin E compromise the ROS-triggered defense mechanisms that induce increased synthesis of antioxidant enzymes.

70. Proteins with ionizable cysteine thiol groups undergo reversible redox reactions.

These proteins are referred to collectively as the cysteine proteome. Discuss the role of redox switches in the context of the cysteine proteome.

Ans. Metabolic processes are linked to protein structure and function by kinetically controlled redox switches; in the cysteine proteome, these are sulfur redox switches.

Active-site cysteines are oxidized/reduced thereby causing changes in signal transduction until the active-site cysteine oxidation/reduction is reversed. Current understanding of these relationships can be described by the redox code, a set of four principles that together describe the relationships between NAD(P)+/NAD(P)H, GSH/GSSG, the cysteine proteome, and other redox molecules.

71. According to the chemiosmotic theory, what would be the effect on oxidative phosphorylation of allowing other positive ions to diffuse across the inner mitochondrial membrane?

Ans Other ions such as sodium or potassium moving across the membrane would disrupt the electrical potential reducing or eliminating oxidative phosphorylation.

72. Cyanide causes an irreversible inhibition of electron transport that prevents ATP synthesis, whereas the inhibitory effect of small amounts of dinitrophenol on ATP synthesis is reversible. Explain the difference.

Ans Cyanide binds to cytochrome oxidase irreversibly. All the cytochromes in the ETC become reduced and ATP synthesis ceases. In the case of dinitrophenol, the acidic phenol disrupts the proton gradient by shuttling protons across the membrane. None of the parts of the electron transport system are irreversibly altered by dinitrophenol. The timely removal of the phenol allows the system to restore itself.

73. Explain why an inhibitor of complex I will not only cause an increase in the ratio of NADH to NAD+ but also an increase in the UQ/UQH ratio.

Ans Complex I transfers protons from NADH to UQ. Inhibition of this process will

prevent the oxidation of NADH to NAD+. However, NADH will accumulate and the NADH/NAD ratio will increase. UQH2 will be oxidized by the remainder of the cytochrome system thus generating more UQ. As a result the UQ/UQH2 ratio will also increase.

74. Suppose that the mitochondrial complexes were not imbedded within the inner mitochondrial membrane. According to the chemiosmotic theory, what would be the consequences?

Ans If the cytochrome complexes were not embedded in the mitochondrial inner membrane the proton gradient could not be established and ATP synthesis would not occur.

75. What is the minimum voltage drop for individual electron transfer events in the mitochondrial electron transport system that is necessary for ATP synthesis?

Ans The minimum voltage drop for individual electron transfer events in the mitochondrial electron transport system that is necessary for ATP synthesis are as follows: Complex I = +0.42V, Complex III = +0.18 V and Complex IV = 0.52V. Note that of the three steps in the oxidation of NADH that account for the synthesis of an ATP molecule, the minimum voltage drop (+0.18V) occurs between UQH2 and cyt c (Complex III).

CALCULATIONS 76. Ethanol is oxidized in the liver to form acetate, which is converted to acetyl-CoA. Determine how many molecules of ATP are produced from one mole of ethanol. Note that 2 mol of NADH are produced when ethanol is oxidized to form acetate.

Ans The oxidation of one mole of ethanol to acetyl-CoA produces two moles of NADH.

The conversion of acetate to carbon dioxide and water through the citric acid cycle produces 3 NADH, 1 FADH2, and 1 GTP. Assuming that the aspartate-malate shuttle is in operation, each cytoplasmic NADH yields 2.25 ATP for a total of 4.5 ATP. Each mitochondrial NADH yields 2.5 ATP for a total of 7.5 ATP. Each molecule of FADH2

yields 1.5 ATP for a total of 1.5 ATP. Each GTP yields 0.75 ATP for a total of 0.75 ATP. The total ATP produced by the oxidation of ethanol is therefore 14.25 ATP.

CHAPTER SIXTEEN INTEGRATION OF METABOLISM 1. The endocrine system uniquely produces __________.

A) hormones B) phermones C) adipocytes D) LDLs E) urea Ans A 2. During fasting and prolonged starvation, skeletal muscle __________.

A) is degraded to provide amino acids to the liver for gluconeogenesis B) is released as fat into the blood for storage in adipose tissue C) is synthesized from blood lactate D) converts glutamine molecules to proline E) None of the above are correct.

Ans A 3. The cells that line the small intestine, which are responsible for the absorption of nutrients into the body, are called __________.

A) adipocytes B) tubule cells C) hepatocytes D) enterocytes E) epithelial cells Ans D 4. Which of the following organs is responsible for pH regulation?

A) Liver B) Lungs C) Intestine D) Muscle E) Kidney Ans E 5. The most distinctive characteristic of living organisms is __________.

A) cellular structure

B) the autonomous capacity to sustain adequate operating conditions C) utilization of carbon compounds as food D) complex cellular mechanisms E) utilizing environmental materials as energy sources Ans B 6. A simple system for information flow is composed of three components: reception, transduction and response. In multicellular organisms hormones play a role in which phase?

A) Reception B) Transduction C) Response D) Hormones are not involved in the process of information flow.

E) Both A and B are correct.

Ans A 7. In a metabolic steady state the rate of anabolic processes is approximately equal to __________.

A) catabolic processes B) cellular energy needs C) nutrient intake D) cellular repair and growth E) Both B and C are correct.

Ans A 8. In animals, the vast majority of water-soluble hormones are __________.

A) peptides B) steroids C) polypeptides D) carbohydrates E) Both A and C are correct.

Ans E 9. The molecules that mediate the growth-promoting actions of GH are referred to as the __________.

A) interferons B) mitogens C) insulin-like growth factors

D) Both B and C are correct.

E) None of the above are correct.

Ans C 10. Symptoms of uncontrolled diabetes mellitus include all of the following except __________.

A) hyperosmolar hyperglycemic nonketosis B) hypoglycemia C) hyperlipoproteinemia D) ketoacidosis E) polyuria Ans B 11. Steroid hormones __________.

A) are transported in blood attached to transport proteins B) bind to intracellular receptors C) diffuse through the plasma membrane of target cells D) Both A and B are correct.

E) All of the above are correct.

Ans E 12. Which of the following is not a major source of extracellular signal molecules?

A) Steroids B) Modified amino acids C) Carbohydrates D) Fatty acids E) Proteins Ans C 13. The biological effects of atrial natriuretic factor appear to be mediated by __________.

A) cAMP B) cGMP C) PIP2 D) AG E) IP3 Ans B

14. In animals, the __________ system(s) has/have a primary responsibility for coordinating metabolism.

A) nervous B) lymphatic C) hepatic D) endocrine E) Both A and D are correct.

Ans E 15. The IP3 receptor __________.

A) binds cGMP B) is associated with Gi C) is a calcium channel D) Both B and C are correct.

E) All of the above are correct.

Ans C 16. A DNA segment that binds a hormone-receptor complex is called a __________.

A) DRE B) DAG C) EGF D) HRE E) IGF Ans D 17. Calmodulin is a __________.

A) transmembrane receptor B) calcium-binding protein C) HSP D) plant hormone E) A, B, and C are correct.

Ans B 18. Insulin resistance is __________.

A) a risk factor for Type I diabetes B) a risk factor for Type II diabetes

C) caused by excessive production of ANF D) Associated with damage to the adrenal gland E) None of the above are correct.

Ans B 19. Receptors for most water soluble hormones are located in what part of the cell?

A) Plasma membrane B) Endoplasmic reticulum C) Nucleus D) Cytoplasm E) Nuclear membrane Ans A 20. Which of the following is not a second messenger molecule?

A cGMP B) cAMP C) Calcium D) Steroids E) Inositol-phospholipid system Ans D 21. The most prominent mechanism to prevent excessive hormone synthesis is __________.

A) desensitization B) down regulation C) feedback inhibition D) target cell stimulation E) sensitization Ans C 22. Enterocytes require large amounts of energy supplied by __________.

A) glucose oxidase B) fatty acid degradation C) lactose oxidation D) glutamine E) alanine Ans D

23. The organ responsible for processing most foreign molecules is __________.

A) intestine B) stomach C) liver D) kidney E) blood Ans C 24. Insulin-resistance is associated with all of the following except __________.

A) obesity B) desensitization C) down-regulation D) IDDM E) NIDDM Ans D 25. Biochemical signal molecules include __________.

A) amino acids B) fatty acid derivatives C) steroids D) peptides E) All of the above are correct.

Ans E 26. Receptor tyrosine kinases are transmembrane receptors that bind ligands such as __________.

A) insulin B) epidermal growth factor C) platelet derived growth factor D) insulin-like growth factor E) All of the above are correct.

Ans E 27. Which of the following molecules is a second messenger?

A) TSH B) cGMP

C) Proline D) Calcium E) Both B and D are correct.

Ans E 28 The organ responsible for the regulation of blood pH is __________.

A) liver B) kidney C) intestine D) brain E) stomach Ans B 29. Most diabetic complications are the result of __________.

A) glycation B) hyperglycemia C) damage to the vascular system D) Both A and B are correct.

E) All of the above are correct.

Ans E 30. The principle target tissues of insulin include __________.

A) skeletal muscle B) liver C) adipose tissue D) Both B and C are correct.

E) All of the above are correct.

Ans E 31. Animals employing several mechanisms to prevent excessive hormone action and release. Examples include which of the following?

A) Genetic regulation B) Feedback inhibition C) Desensitization D) Down regulation E) All of the above are true.

Ans E

32. Which of the following molecules do GPCRs not respond to?

A) Catecholamines B) Oxytocin C) Light D) Dopamine E) Insulin Ans E 33. Which of the following is a role of PKB? A) Stimulation of glycogen synthesis B) Inhibition of lipolysis C) Glucose transport into adipocytes D) Activation of mTOR E) All of the above are roles of PKB. Ans E 34. An example of a cytokine is __________.

A) epidermal growth factor B) interleukins C) interferons D) insulin-like growth factors E) Both B and C are correct.

Ans E 35. The most serious acute symptom of Type 1 diabetes is __________.

A) anemia B) ketoacidosis C) hypoglycemia D) insulin resistance E) Both A and C are correct.

Ans B 36. Hyperosmolar hyperglycemic nonketosis can occur in ___________ diabetes.

A) Type I B) Type II C) Insulin-dependent diabetes

D) all forms of diabetes E) None of the above are correct (it is not a symptom of diabetes).

Ans B 37. During periods of starvation muscle reduces its consumption of glucose. This spares its use for which of the following organs?

A) Liver B) Heart C) Kidneys D) Brain E) Lungs Ans D 38. Leptin is secreted by which of the following tissues?

A) Brain B) Liver C) Adipose tissue D) Muscle E) Gastrointestinal tract Ans C 39. The brain consumes about __________% of the body’s energy.

A) 10 B) 20 C) 30 D) 40 E) 50 Ans B 40.The phosphatidylinositol cycle mediates the action of all of the following except __________.

A) acetylcholine B) insulin C) glucagon D) vasopressin E) GRH Ans C

41. Metabolism of fructose in the liver rapidly depletes which of the following?

A) NADPH B) ATP C) Triose phosphate D) AMP E) Glucose Ans B 42. An autoimmune disease caused by the destruction of the insulin producing beta cells of the pancreas is called __________.

A) hyperglycemia B) dyslipidemia C) glucosuria D) Type II diabetes E) Type I diabetes Ans E 43. Extreme thirst and frequent urination in diabetics is directly caused by __________.

A) osmotic diuresis B) hyperglycemia C) dyslipidemia D) glucosuria E) adipoisledimia Ans D 44. Type II diabetes is uniquely characterized by __________.

A) hyperinsulinemia B) depressed insulin levels C) insulin resistance D) depressed glucose levels E) Both A and C are correct.

Ans A 45. Which of the following carbohydrates is a major contributing cause of dyslipidemia non-alcoholic fatty liver disease?

A) Glucose

B) Ribose C) Fructose D) Galactose E) Xylose Ans C 46. Urea synthesis is the responsibility of which organ of the body?

A) Kidney B) Liver C) Intestine D) Stomach E) Lung Ans B SHORT ANSWER 47. What is meant by the term insulin resistance?

Ans Insulin resistance is the insensitivity of target cells to insulin. A common cause is the down regulation of insulin receptors.

48. What is the body mass index (BMI)?

Ans BMI is a measure of a person’s body composition, based on weight and height.

49. What is a phorbol ester?

Ans Phorbol esters are tumor-promoting compounds found in croton oil. They mimic the action of DAG. 50. What is metabolic syndrome Ans Metabolic syndrome is a cluster of clinical disorders that include obesity, hypertension, dyslipidemia and insulin resistance.

51. What is a tumor promoter?

Ans A tumor promoter is a molecule that provides cells with a growth advantage over nearby cells.

52. What is meant by the term ketoacidosis?

Ans Ketoacidosis is an elevated concentration of ketone bodies in the blood, occurs in Type II diabetics as the result of unrestrained fatty acid oxidation.

53. What is the source and action of the PDGF? Ans Platelet-derived growth factor, secreted by blood platelets, stimulates mitosis during wound healing.

54. List three examples of steroid transport proteins.

Ans Steroid transport proteins include corticosteroid-binding globulin, sex hormonebinding protein, and albumin.

55. Body builders often take anabolic steroids to increase their muscle mass. How do these steroids achieve their effect?

Ans Anabolic steroid hormones change the expression of a specific set of genes that code for proteins (e.g., enzymes that increase protein synthesis in skeletal muscle, among other metabolic changes), when they bind to specific DNA sequences called hormone response elements.

56. Extreme thirst is a characteristic symptom of diabetes. Explain.

Ans In uncontrolled diabetes large amounts of glucose are excreted in the urine.

Excessive urine flow is caused when large amounts of water are excreted along with the glucose. The resulting dehydration then triggers the thirst response.

57. What is meant by the term osmotic diuresis?

Ans Osmotic diuresis is a process in which solutes in the urinary filtrate causes excessive loss of water and electrolytes.

58. During periods of fasting some muscle protein is depleted. How is this process initiated, and what happens to the amino acids in the proteins?

Ans During the initial phase of a prolonged fast, blood glucose and insulin levels fall, and glucagon release is triggered. Glucagon acts to prevent hypoglycemia by promoting glycogenolysis and gluconeogenesis. The amino acids derived from muscle protein are a major source of the carbon skeleton substrates for gluconeogenesis.

59. What is meant by the term GLUT4?

Ans GLUT4 is an insulin sensitive glucose transporter found in the plasma membrane of muscle and adipose tissue cells.

60. Hemoglobin molecules exposed to high levels of glucose are converted to glycated products. The most common, referred to as hemoglobin A1c (HbA1c), contains a  chain

glycated adduct. Because red blood cells last about 3 months, HbA1c concentration is a useful measure of a patient’s blood sugar control. In general terms describe why and how HbA1c forms.

Ans HBA1c formation is a consequence of nonenzymatic glycation of hemoglobin that occurs in the presence of high blood glucose levels. In the Maillard reaction, the aldehyde group of glucose condenses with a free amino group in a protein to form a Schiff base, the Amadori product. The Amadori product subsequently destabilizes to form a reactive carbonyl-containing product that reacts with hemoglobin to form the adduct.

61. What are the sites on protein that are phosphorylated during signal transduction cascades?

Ans The sites on proteins that are phosphorylated during signal transduction cascades are the hydroxyl groups of serine and tyrosine.

62. Because the prime early symptom of diabetes is a high level of blood glucose, insulin is often associated primarily with carbohydrate metabolism. List several other processes that are insulin-dependent.

Ans In addition to carbohydrate metabolism, insulin also impacts lipid and protein metabolism by triggering several processes that are anabolic and/or ensure nutrient storage. These processes include stimulating fat synthesis in the liver and fat storage in adipocytes, promoting amino acid uptake by cells (especially liver and muscle cells), stimulating protein synthesis in most tissues, decreasing lipolysis, promoting satiety by inhibiting NPY/AgRP neurons and activating POMC neurons in the hypothalamus.

63. Hormones can be assigned to what three general classes based on the molecules they are derived from.

Ans Hormones can be classified as peptides or polypeptides (composed of amino acids), amino acid derivatives, or as steroids (derived from cholesterol).

ESSAY QUESTIONS 64. During periods of prolonged exercise muscles burn fatty acids released from adipocytes in addition to glucose. Explain how the need for additional fatty acids by muscle is communicated to the adipocytes.

Ans One consequence of physical activity is the activation of the sympathetic nervous system, which in turn stimulates the adrenal gland to secrete epinephrine and norepinephrine. These hormones then activate the enzymes that catalyze the hydrolysis of triacylglycerol to form the fatty acids used to drive muscle contraction.

65. How do phorbol esters promote tumor growth?

Ans Phorbol esters, found in croton oil, activate protein kinase C, an action that stimulates cell growth and division. However, unlike DAG, the molecule that they mimic, phorbol esters continue to activate protein kinase C for a prolonged time. This circumstance provides the affected cell with an advantage over unstimulated cells.

Phorbol esters may contribute to the transformation of a cell previously exposed to a carcinogenic initiating event into a cancerous cell whose unrestricted proliferation creates a tumor.

66. In severely diabetic patients the blood glucose level is so high that the sugar appears in the urine. Before the development of blood tests by modern medical research, diabetics could often be recognized by the appearance of flies around their feet. Suggest a reason for this observation.

Ans Flies are well known for their preference for sugar. If urine has detectable sugar in it, flies will be attracted.

67. Explain why obese individuals are often insulin resistant.

Ans Release of fatty acids by enlarged adipocytes and their subsequent nonspecific insertion in cell membranes cause the disruption of signal transduction pathways such as the insulin receptor pathway.

68. Dieters frequently fast in an attempt to reduce their weight. During these fasts, they often lose considerable muscle mass rather than fat. Explain.

Ans Increased mobilization of fatty acids provides an alternate energy source for muscle, thereby sparing glucose for the brain. In addition, glucagon stimulates gluconeogenesis, a pathway that utilizes amino acids derived from muscle.

69. Discuss the relationship between the inflammatory response, obesity, and type-2 diabetes.

Ans Obesity is a strong risk factor for type-2 diabetes because excess lipid accumulation in adipose tissue, combined with other cellular stresses, results in low-grade inflammation. This inflammatory response causes adipocytes to release proinflammatory cytokines (e.g. tumor necrosis factor-a (TNF-a)) which, in turn, induce the phosphorylation of IRS-1 serine residues. These phosphorylated IRS-1 serine residues interfere with insulin signaling which causes depressed glucose transport and increased lipolysis.

70. Why is it important for hormones to act at low concentrations and be degraded quickly?

Ans To ensure proper control of metabolism, powerful hormones are synthesized in small quantities. Hormones also elicit responses in only specific target cells. They are inactivated quickly to ensure the precision of metabolic regulation.

71. Hormones are often synthesized and stored within secretory vesicles. Secretion occurs only when the hormone-producing cell is stimulated. Explain the advantage that this process has over making the hormone molecules as they are needed.

Ans The storage of preformed secretory molecules in secretory vesicles allows for a rapid response of the hormone producing cells to metabolic signals. As soon as the appropriate signal is received the vesicles fuse with plasma membrane and release their contents (via exocytosis) to the bloodstream.

72. Skeletal muscle cannot synthesize fatty acids yet it produces the enzyme acetyl-CoA carboxylase. Explain the role of this enzyme.

Ans While muscle cells do not synthesize fatty acids they do oxidize them. The product of the carboxylation of acetyl-CoA is malonyl-CoA. When cellular ATP and NADH levels are high, malonyl-CoA has the effect of inhibiting the oxidation of fatty acids because it inhibits carnitine acyl transferase I, the enzyme involved in the transport of fatty acids into the mitochondria.

73. Animals can convert glucose to fat but not the reverse. Explain.

Ans The fatty acid components of triacylglycerol molecules cannot be converted into glucose molecules in animals because these organisms lack the glyoxylate cycle enzymes isocitrate lyase and malate synthase. These enzymes convert the two carbon molecule acetyl-CoA to malate. Malate is then converted to oxaloacetate, the three carbon molecule that is a substrate for gluconeogenesis.

74. Ketoacidosis is a common feature of insulin-dependent diabetes mellitus, but not of insulin-independent diabetes mellitus. Explain.

Ans In Type I diabetes (insulin–dependent diabetes mellitus), little or no insulin is produced and the action of glucagon is unopposed. Glucagon causes an increase in lipolysis in adipocytes, leading to an excess of acetyl-CoA molecules, which are then converted to ketone bodies. Ketoacidosis (an excess of ketone bodies in the blood with low pH) does not occur in type II diabetes (insulin independent diabetes mellitus) in which blood levels of insulin are normal or elevated but cells are resistant to insulin.

Since the action of glucagon is not completely unopposed, and, lipolysis is not activated as it is in type I diabetes, and the excess production of ketone bodies does not occur.

75. Type II diabetics are often obese. Explain how obesity contributes to the onset of diabetes.

Ans Obesity contributes to the onset of diabetes by promoting tissue insensitivity to insulin. Specifically, this process begins as enlarged adipocytes release free fatty acids into the bloodstream and are taken up by the membranes of other cells, causing the disruption of signal transduction pathways. Consequences include: lipotoxicity, high blood insulin levels, excess glucose production (liver), inhibited insulin-mediated glucose uptake by muscle, and further release of fatty acids from adipocytes that have developed insulin resistance. Adipose tissue in the obese develops a low-level chronic inflammation, and as a result, adipocytes experience ER stress and oxidative stress and release inflammatory cytokines that increases insulin resistance further. All of these factors contribute to the onset of diabetes.

76. During the first week of a prolonged diet there is a relatively rapid weight loss. What is the major source of weight loss during this period?

Ans The major contributing factor to the relatively rapid weight loss during the first week of a prolonged diet is depletion of glycogen stores, which is accompanied by the loss of water bound to glycogen, loss of muscle protein, and lipolysis of triacylglycerol in adipocytes. Also contributing to weight loss is large amounts of amino acids from muscle protein needed to provide glucoseπ (via gluconeogenesis in the liver), the preferred energy source for the brain. Lipolysis releases fatty acids to provide an alternate energy source to glucose. Also, a molecule of water is required to hydrolyze each glycosidic, ester, and peptide bond.