
Course Introduction
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Course Introduction
Structural Biology explores the molecular structure and dynamics of biological macromolecules such as proteins, nucleic acids, and complexes, and investigates how these structures determine their function within the cell. The course introduces key experimental techniques including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy, providing students with the tools to analyze and interpret structural data. Through the integration of theoretical concepts and practical case studies, students gain an understanding of structure-function relationships and the significance of structural information in drug design, molecular medicine, and biotechnology.
Recommended Textbook
Biochemistry 4th Edition by Christopher K. Mathews
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Q1) Which of the following best describes homeostasis?
A)a non-equilibrium,non-steady state
B)a non-equilibrium steady state
C)an equilibrium-controlled,non-steady state
D)an equilibrium-controlled steady state
E)none of the above
Answer: B
Q2) Which of the following macromolecules is considered a homopolymer?
A)polypeptides
B)ribonucleic acids
C)deoxyribonucleic acids
D)starch
E)all of the above
Answer: D
Q3) The molecule pyruvic acid is found at the crossroads of several biochemical pathways.Pyruvic acid is also known as 2-oxopropanoic acid.Based upon this name,draw the molecule.
Answer: 11ea8a11_436d_60c5_8b44_bfd5f6b258f9_TB4872_00
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Q1) Lysine contains two amine groups (pK<sub>a</sub> values of 9.0 and 10.0)and a carboxylic acid group (pK<sub>a</sub> 2.2).In a solution of pH 9.5,which of the following would best describe the protonation and charge state of lysine?
A)carboxylic acid: deprotonated and neutral;both amines: protonated and positive
B)carboxylic acid: deprotonated and negative;both amines: deprotonated and neutral
C)carboxylic acid: deprotonated and negative;amine (pK<sub>a</sub> 9.0): deprotonated and neutral;amine (pK<sub>a</sub> 10.0): protonated and positive
D)carboxylic acid: deprotonated and negative;amine (pK<sub>a</sub> 9.0): protonated and positive;amine (pK<sub>a</sub> 10.0): deprotonated and neutral
E)carboxylic acid: deprotonated and neutral;amine (pK<sub>a</sub> 9.0): deprotonated and neutral;amine (pK<sub>a</sub> 10.0): protonated and positive
Answer: C
Q2) Imidazole is a commonly used buffer in biochemistry labs.With a pK<sub>a</sub> of 7.0,what would be the ratio of base to acid at pH 7.4?
Answer: 2.5 11ea8a11_436e_4b29_8b44_234f570e4c48_TB4872_00
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Q1) The highly exergonic nature of ATP hydrolysis is explained by which of the following?
A)the resulting orthophosphate is stabilized by resonance
B)electrostatic repulsion occurs between phosphate groups and the adenine base of ATP
C)the resulting product undergoes tautomerization to the keto form of ADP
D)the bond that is hydrolyzed is considered an ester of phosphoric acid,making it highly unstable
E)all of the above
Answer: A
Q2) Which of the following would be considered a closed system?
A)a human living alone on a small island
B)the planet Earth
C)a fish living in a fish bowl
D)a bacteria living in the large intestine
E)a bacteria living in a Petri dish
Answer: B
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Q1) Which of the following types of DNA are often supercoiled?
A)extremely long linear DNA,such as seen in human chromosomes
B)very short linear DNA
C)circular DNA
D)DNA molecules that contain both circular and linear regions
E)all of the above
Q2) Which of the following bases is found only in DNA?
A)adenine
B)thymine
C)uracil
D)cytosine
E)guanine
Q3) Which of the following is the most commonly observed nucleic acid form for storing of genomic information?
A)single-stranded DNA
B)double-stranded DNA
C)single-stranded RNA
D)double-stranded RNA
E)hybrid molecules of DNA and RNA
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Q1) Given the following peptide,what pair of protease enzymes would be able to produce three smaller peptides?
Gly-Ser-Ala-His-Phe-Pro-Asn-Ala-Val-Glu-Cys-Ala-Ser
A)chymotrypsin and thrombin
B)trypsin and chymotrypsin
C)thermolysin and chymotrypsin
D)trypsin and thermolysin
E)none of the above
Q2) Which of the following undergoes an oxidation reaction to form a disulfide bond?
A)serine
B)cysteine
C)methionine
D)threonine
E)tyrosine
Q3) What is the pI for the following peptide: Ala-Glu-Val-Asp-Lys-Leu
Q4) Draw each of the structures of aspartic acid that predominate at pH 1,3,7,and 11.
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Q1) Which of the following types of secondary structure has a non-integer value of residues per turn?
A)antiparallel \(\beta\)-sheet
B)parallel \(\beta\)-sheet
C)\(\alpha\)-helix
D)3<sub>10</sub> helix
E)polyproline II helix
Q2) Which of the following is considered a dead-end complex (and therefore dangerous due to its resistance to proteolytic cleavage)in the protein-folding pathway?
A)disordered aggregate
B)molten globule state
C)prefibrillar species
D)amyloid fibril
E)unfolded protein
Q3) Show the most likely interaction that would occur between a serine residue and a glutamine residue.
Q4) Draw a section of antiparallel \(\beta\)-sheet showing two sheets with three residues in each sheet.Clearly show the hydrogen bond pattern between the two sheets.
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Q1) Which of the following is a homotropic effector of hemoglobin-oxygen binding?
A)O<sub>2</sub>
B)H<sup>+</sup>
C)CO<sub>2</sub>
D)Cl<sup>-</sup>
E)2,3-bisphosphoglycerate (2,3-BPG)
Q2) Which of the following occurs when hemoglobin switches from the T (deoxy)state to the R (oxy)state?
A)the heme group goes from a slightly puckered conformation to a flat conformation
B)the ferrous ion is pulled into the plane of the heme group
C)the F8 (proximal)histidine rotates about 8S1U1P1\(\circ\)S1S1P0 to better align with the ferrous ion
D)movement of the F8 histidine causes a shift in the F helix,thus weakening interactions with other subunits
E)all of the above
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Q1) Which portion of the myosin protein found in muscle is responsible for both ATP and actin binding?
A)heavy-chain coiled-coiled tails
B)heavy-chain stalk
C)heavy-chain globular head
D)essential light chain
E)regulatory light chain
Q2) In muscle,thin filaments are made of _______ while thick filaments are made of
A)myosin;actin
B)actin;myosin
C)myofibril;myofiber
D)myofiber;myofibril
E)none of the above
Q3) Which of the following proteins is found in a bacterial flagellum?
A)actin
B)myosin
C)flagellin
D)dynein
E)all of the above
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Q1) Draw a \(\beta\)-disaccharide composed of glucose linked to its C-2 epimer by an \(\alpha\)(1\(\to\)4)glycosidic bond with the anomeric carbon of glucose contributing to the glycosidic bond.
Q2) Oseltamivir,also known as Tamiflu,is effective as an antiviral against the influenza virus due to its ability to block the action of which protein associated with the surface of the viral particle?
A)hemagglutinin
B)neuraminidase
C)M1
D)M2
E)none of the above
Q3) Which of the following explains the importance of sucrose as a disaccharide?
A)the glycosidic bond is much more stable than a typical glycosidic bond
B)the presence of two glucose residues provides a readily available glucose source
C)\(\beta\)-glycosidic bonds are much more stable than \(\alpha\)-glycosidic bonds
D)since both anomeric carbons are involved in the glycosidic bond,oxidation is limited
E)none of the above
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Q1) When comparing the sequences of a peripheral membrane protein with an integral membrane protein,which of the following amino acids would most likely be present in a higher percentage in the integral membrane protein?
A)aspartic acid
B)leucine
C)histidine
D)serine
E)none of the above
Q2) Which of the following would most likely move across a membrane by simple diffusion?
A)potassium ions
B)glucose
C)carbon dioxide
D)sodium ions
E)water
Q3) Draw the following fatty acid: 18:3c\(\Delta\)9,12,15 as it would appear at physiological pH.With reference to the omega carbon,what type of fatty acid is this? Draw the result if this fatty acid underwent partial hydrogenation to produce 18:1t\(\Delta\)11
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Q1) What must be true if K<sub>M</sub> is truly a measure of the affinity of enzyme and substrate?
A)k<sub>c</sub><sub>at</sub> must be larger than K<sub>M</sub>
B)k<sub>cat</sub> must be smaller than K<sub>M</sub>
C)k<sub>cat</sub> must be about equal to k<sub>1</sub>
D)k<sub>cat</sub> must be much smaller than k<sub>-1</sub>
E)k<sub>cat</sub> must be much larger than k<sub>-1</sub>
Q2) Which amino acid most commonly serves as a general acid and general base in an enzyme mechanism?
A)serine
B)arginine
C)aspartic acid
D)histidine
E)cysteine
Q3) In a Lineweaver-Burke plot,what does the slope represent?
A)K<sub>M</sub>
B)V<sub>max</sub>
C)V<sub>max</sub>/K<sub>M</sub>
D)K<sub>M</sub>/V<sub>max</sub>
E)none of the above
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Q1) In stage ____ metabolism,a catabolic pathway might produce ________ while the opposing anabolic pathway might produce _________.
A)2;monosaccharides;polysaccharides
B)3;CO<sub>2</sub>;glucose
C)2;acetyl CoA;lipids
D)1;amino acids;proteins
E)3;NH<sub>3</sub>;nucleotides
Q2) Which of the following would be considered a biosynthetic pathway?
A)glycolysis
B)glycogen synthesis
C)fatty acid \(\beta\)-oxidation
D)citric acid cycle
E)electron transport
Q3) Which of the following functional groups is a commonly seen nucleophile in biochemical reactions?
A)aldehyde
B)deprotonated alcohol
C)amide
D)carbocation
E)iodide ion
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Q1) When glucagon binds to receptors on mammalian liver cells,which of the following occurs due to enzyme phosphorylation?
A)activation of PFK-2 followed by activation of glycolysis
B)activation of FBPase-2 followed by inhibition of gluconeogenesis
C)activation of PFK-2 followed by activation of gluconeogenesis
D)activation of FBPase-2 followed by activation of gluconeogenesis
E)activation of PFK-2 followed by inhibition of glycolysis
Q2) Besides its role in glycogen synthesis,which of the following directly relies on UDP-glucose?
A)glycolysis
B)gluconeogenesis
C)fructose metabolism
D)sucrose metabolism
E)galactose metabolism
Q3) Which isoform of hexokinase is found in the vertebrate liver?
A)hexokinase I
B)hexokinase II
C)hexokinase III
D)hexokinase IV
E)all of the above
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Q1) For each molecule of acetyl-CoA that enters the citric acid cycle,which of the following best represents the net products of the cycle?
A)2 CO<sub>2</sub>,2 NADH,2 FADH<sub>2</sub>,1 GTP,1 oxaloacetate
B)1 CO<sub>2</sub>,3 NADH,1 FADH<sub>2</sub>,2 GTP,1 oxaloacetate
C)2 CO<sub>2</sub>,3 NADH,1 FADH<sub>2</sub>,1 GTP,0 oxaloacetate
D)1 CO<sub>2</sub>,2 NADH,1 FADH<sub>2</sub>,2 GTP,0 oxaloacetate
E)2 CO<sub>2</sub>,3 NADH,1 FADH<sub>2</sub>,1 GTP,1 oxaloacetate
Q2) Which of the following reactions is commonly used to replenish intermediates of the citric acid cycle?
A)citrate \(\to\) oxaloacetate + acetyl CoA
B)oxaloacetate \(\to\) aspartate
C)glutamate \(\to\) \(\alpha\)-ketoglutarate
D)malate \(\to\) pyruvate
E)all of the above
Q3) __________ activates __________,thereby inhibiting pyruvate dehydrogenase.
A)NADH;pyruvate dehydrogenase phosphatase
B)Ca<sup>2+</sup>;pyruvate dehydrogenase phosphatase
C)NAD<sup>+</sup>;pyruvate dehydrogenase kinase
D)ATP;pyruvate dehydrogenase kinase
E)pyruvate;pyruvate dehydrogenase kinase
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Q1) __________ increases oxygen consumption while decreasing ATP synthesis,but ____________ decreases both oxygen consumption and ATP synthesis.
A)rotenone;valinomycin
B)azide;2,4-dinitrophenol
C)antimycin A;nigericin
D)2,4-dinitrophenol;oligomycin
E)cyanide;valinomycin
Q2) Which of the following acts as an uncoupler of the mitochondrial proton gradient due to its action as an ionophore?
A)valinomycin
B)nigericin
C)trifluorocarbonylcyanide phenylhydrazone
D)2,4-dinitrophenol
E)cyanide
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Q1) What specific part of the chloroplast is responsible for the light reactions of photosynthesis?
A)thylakoid lumen
B)thylakoid membrane
C)stroma
D)inner membrane of chloroplast
E)outer membrane of chloroplast
Q2) Which of the following carbohydrates is the most common molecule exported by photosynthetic cells for use in other parts of the plant?
A)amylose
B)amylopectin
C)glucose
D)sucrose
E)fructose
Q3) Which of the following would have an inhibitory effect upon rubisco?
A)Mg<sup>2+</sup>
B)CO<sub>2</sub>
C)H<sup>+</sup>
D)reduced thioredoxin
E)none of the above
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Q1) Which of the following enzymes of fatty acid synthesis is most analogous to thiolase when considering that fatty acid synthesis is analogous to a reversal of \(\beta\)-oxidation?
A)\(\beta\)-ketoacyl-ACP synthase
B)\(\beta\)-ketoacyl-ACP reductase
C)3-hydroxyacyl-ACP dehydratase
D)enoyl-ACP reductase
E)thioesterase
Q2) Which of the following leads to the formation of atherosclerotic plaques?
A)non-specific interactions between LDL particles
B)oxidation of LDL particles resulting in cross linking with proteins
C)uptake of oxidized LDL particles by macrophages
D)excess uptake of LDL particles converting endothelial cells to foam cells
E)none of the above
Q3) Which of the following lipoproteins distributes dietary lipids?
A)chylomicron
B)very low density lipoprotein
C)intermediate density lipoprotein
D)low density lipoprotein
E)high density lipoprotein

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Q1) Which of the following hormones affects the arcuate nucleus of the hypothalamus and ultimately results in an inhibition of nutrient intake?
A)adiponectin
B)leptin
C)ghrelin
D)glucagon
E)none of the above
Q2) Which of the following types of tissue can use glucose,but not fatty acids,as a source of fuel?
A)skeletal muscle
B)cardiac muscle
C)liver
D)brain
E)adipose
Q3) What process in the brain consumes most of the ATP that is produced?
A)movement of actin/myosin
B)maintenance of membrane potentials
C)active transport of glucose and amino acids
D)cellular growth
E)none of the above

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Q1) Which of the following forms of vitamin A is covalently attached to a lysine residue of the protein opsin to form the complex called rhodopsin?
A)all-trans-retinal
B)11-cis-retinal
C)all-trans-retinoic acid
D)all-trans-retinol
E)\(\beta\)-carotene
Q2) How is the activity of HMG-CoA reductase reduced?
A)allosteric inhibition by cholesterol
B)ubiquitination in response to sterol accumulation resulting in proteolysis
C)serine phosphorylation by an insulin-activated protein kinase
D)tyrosine phosphorylation by AMPK
E)none of the above
Q3) Which of the following is accomplished in one enzyme catalyzed reaction?
A)progesterone to androstenedione
B)17-hydroxyprogesterone to cortisol
C)progesterone to aldosterone
D)androstenedione to testosterone
E)androstenedione to estradiol
Q4) Show the reaction catalyzed by 3-hydroxy-3-methylglutrayl-CoA reductase.
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Q1) Which of the following amino acids relies upon the synthesis of carbamoyl phosphate?
A)lysine
B)histidine
C)arginine
D)glutamine
E)asparagine
Q2) In the nitrogen fixation process,which step of the electron transfer process requires ATP hydrolysis?
A)transfer of electron from ferredoxin to the 4Fe-4S complex
B)transfer of electron from 4Fe-4S complex to the P cluster
C)transfer of electron from P cluster to iron-molybdenum cofactor (FeMo-co)
D)transfer of electron from FeMo-co to nitrogen
E)none of the above
Q3) Which of the following amino acids is exclusively ketogenic?
A)phenylalanine
B)tyrosine
C)isoleucine
D)arginine
E)leucine
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Q1) One route for tryptophan degradation leads to the coenzyme _____________.
A)pyridoxal phosphate
B)FAD
C)NAD<sup>+</sup>
D)tetrahydrobiopterin
E)none of the above
Q2) Which amino acid utilizes nitrogen and carbon from adenine in the synthesis of its R-group?
A)histidine
B)arginine
C)lysine
D)asparagine
E)all of the above
Q3) Bilirubin is conjugated with _________ to increase its solubility for excretion.
A)phospholipids
B)glycine
C)glucuronic acid
D)taurine
E)all of the above

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Q1) What molecule(s)is(are)the source of the two nitrogen atoms for pyrimidine synthesis?
A)asparagine
B)glutamine,glutamate
C)aspartate,carbamoyl phosphate
D)carbamoyl phosphate,glutamine
E)aspartate,glutamate
Q2) Which of the following shows the correct and complete flow of electrons for ribonucleotide reductase?
A)NADH \(\to\) FAD \(\to\) thioredoxin \(\to\) ribonucleotide reductase
B)NADPH \(\to\) glutathione \(\to\) glutaredoxin \(\to\) ribonucleotide reductase
C)NADPH \(\to\) thioredoxin \(\to\) cytochrome-b \(\to\) ribonucleotide reductase
D)FADH<sub>2</sub> \(\to\)glutathione \(\to\) glutaredoxin \(\to\) ribonucleotide reductase
E)none of the above
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Q1) Like G proteins,the Ras protein binds _______ when in its active state which is hydrolyzed to ______ to convert the protein to its inactive state.
A)GTP;GDP
B)GTP;GMP
C)GMP;cGMP
D)cGMP;GMP
E)cGMP;GDP
Q2) The principle inhibitory neurotransmitter,__________,works by triggering an influx of ______ causing hyperpolarization of nerve cells.
A)\(\gamma\)-aminobutyric acid;K<sup>+</sup>
B)\(\gamma\)-aminobutyric acid;Cl<sup>-</sup>
C)serotonin;K<sup>+</sup>
D)serotonin;Cl<sup>-</sup>
E)none of the above
Q3) Insulin activates glycogen synthase while glucagon inhibits glycogen synthase.Explain the intracellular mechanisms that are used to bring about this activity.
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Q1) Which of the following represents the correct order of steps usually taken in a Southern analysis?
A)electrophoresis \(\to\) restriction digest \(\to\) nitrocellulose transfer \(\to\) hybridization
B)electrophoresis \(\to\) hybridization \(\to\) restriction digest \(\to\) nitrocellulose transfer
C)hybridization \(\to\) restriction digest \(\to\)electrophoresis \(\to\) nitrocellulose transfer
D)restriction digest \(\to\) electrophoresis \(\to\) hybridization \(\to\) nitrocellulose transfer
E)restriction digest \(\to\) electrophoresis \(\to\) nitrocellulose transfer \(\to\) hybridization
Q2) What proteins,responsible for specific protein kinase activation,are major control elements in the cell cycle?
A)Rb proteins
B)cyclins
C)p53
D)cohesins
E)nonhistone chromosomal proteins
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Q1) Which of the following describes the correct sequence of enzyme activity upon the lagging strand?
A)primase,DNA ligase,DNA polymerase I,DNA polymerase III
B)primase,DNA polymerase I,DNA polymerase III,DNA ligase
C)DNA polymerase III,primase,DNA polymerase I,DNA ligase
D)primase,DNA ligase,DNA polymerase III,DNA polymerase I
E)primase,DNA polymerase III,DNA polymerase I,DNA ligase
Q2) Which of the following exonuclease activities is present in DNA polymerase I?
A)3' exonuclease that degrades double stranded DNA
B)3' exonuclease that degrades hairpin DNA
C)5' exonuclease that degrades single stranded DNA
D)5' exonuclease that removes RNA from a DNA-RNA duplex
E)none of the above
Q3) What is an Okazaki fragment?
A)a small section of DNA bound to the leading strand
B)a small section of DNA bound to the lagging strand
C)a small section of RNA and DNA bound to the leading strand
D)a small section of RNA and DNA bound to the lagging strand
E)none of the above
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Repair,recombination,rearrangement,amplification
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Q1) What role does integration host factor (IHF)play in site-specific recombination during phage \(\lambda\) lysogeny?
A)binds host DNA forcing a 90S1U1P1\(\circ\)S1S1P0bend
B)supercoils phage DNA
C)cleaves host and phage DNA at specific sites to create sticky ends
D)ligates host and phage DNA once recombination occurs
E)all of the above
Q2) The repair of a double-strand break can be accomplished by ______________,which requires the Ku70/80 protein to
A)nonhomologous end joining;catalyze blunt end ligation
B)nonhomologous end joining;bind to both ends of the break
C)homologous recombination;catalyze blunt end ligation
D)homologous recombination;bind to both ends of the break
E)none of the above
Q3) Show the common base pair seen between 8-oxoguanine and adenine.
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Q1) Transcription of the 5S rRNA gene occurs by ________ covering the entire gene so that pol III can ____________.
A)TFIIB;transcribe the gene several times before dissociating B)TFIIIC;transcribe the gene several times before dissociating C)TFIIB;transcribe both strands of DNA before dissociating D)TFIIIC;transcribe both strands of DNA before dissociating E)none of the above
Q2) What is the mechanism by which enhancers,despite the fact that they are often several kilobase pairs away from the promoter,activate transcription?
A)DNA unwinding
B)DNA looping
C)chromatin remodeling
D)DNA hairpin formation
E)none of the above
Q3) Draw a transcription bubble,clearly labeling the proteins and nucleic acids involved in the process.
Q4) Give the mRNA sequence that would result from the following sense strand:
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27 Verified Questions
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Source URL: https://quizplus.com/quiz/73685
Sample Questions
Q1) What site is occupied by the tRNA<sup>fMet</sup> during intitiation?
A)A site
B)P site
C)E site
D)binds first to A site then moves to P site
E)binds first to P site then moves to E site
Q2) A repetitive mRNA of GAG could produce which of the following?
A)polyglutamate
B)polyleucine
C)polyleucine,polyserine,or polyproline
D)polyarginine,polyglycine or polyglutamate
E)none of the above
Q3) Which of the following is a difference between prokaryotic and eukaryotic translation?
A)the genetic code is different
B)prokaryotic ribosomes are free in the cytosol;eukaryotic chromosomes are always membrane bound
C)eukaryotic translation requires more protein factors
D)the ribosomes in prokaryotes are larger
E)none of the above

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Available Study Resources on Quizplus for this Chatper
24 Verified Questions
24 Flashcards
Source URL: https://quizplus.com/quiz/73686
Sample Questions
Q1) The phosphorylation of several RNA polymerase II serine residues has been identified as a key event in eukaryotic translation initiation.Which of the following is one of the enzymes responsible for this phosphorylation?
A)Mediator complex
B)Rap1
C)TFIIH
D)TATA box-binding protein
E)ACT
Q2) If an miRNA is completely complementary to an mRNA,what is the result of the pairing of these two molecules?
A)rapid translation of the mRNA
B)repeated translation as the miRNA prevents destruction of the mRNA
C)slowed translation of the mRNA
D)degradation of the mRNA
E)none of the above
Q3) Show how glutamine interacts with an A-T base pair as seen in the cI and Cro repressors.
Q4) Design an antisense RNA that prevents the start of translation for any mRNA in an E.coli cell.
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