Flowchart Unit 1

UNIT 1 Principles of Biophysical Chemistry pH • •

It is the Negative logarithm of Hydrogen ion concentration.

When weak acids are dissolved in water, they contribute H+ by ionizing; when weak bases consume H+ by becoming protonated. The total hydrogen ion concentration from all sources is experimentally measurable and is expressed as the pH of the solution

The Ionization of water is expressed by an Equilibrium constant

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The pH scales

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pH of some Aqueous fluids

Buffer •

Aqueous systems that tend to resist changes in pH when small amounts of acid (H+) or base (OH-) are added •

consists of:  a weak acid (the proton donor) and  its conjugate base (the proton acceptor).

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At the midpoint of the buffering region, where the concentration of the proton donor (acetic acid) exactly equals that of the proton acceptor (acetate), the buffering power of the system is maximal;

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pH changes least on addition of H+ or OH-.

The pH at this point in the titration curve of acetic acid is equal to its pKa.

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Henderson- Hasselbalch equation

Thermodynamics- Deals with the study of different forms of energy & their relationships

Internal Energy • Sum total of all energies stored in a substance.

• Change in internal energy is denoted by ∆E Enthalpy • Enthalpy is Heat content of the reacting system • Change in enthalpy is denoted by ∆H Entropy • Measure of randomness or disorderness of the system • Change in entropy is denoted by ∆S • If ∆S is +ve, the process is spontaneous • If ∆S is -ve, the process is non-spontaneous • If ∆S is zero, the process is in equilibrium Gibbs free energy • Helps in predicting spontaneity of a process • Change in free energy is denoted by ∆G • If ∆G is +ve, the process is non-spontaneous • If ∆G is -ve, the process is spontaneous • If ∆G is zero, the process is in equilibrium

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Standard free energy (denoted by ∆G’o)

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Enzymes Biocatalysts that increase rate of biochemical reactions.

Chemical nature: 1. Proteins 2. RNA(RIBOZYMES) 3. Abzymes (Ab + enzymes) Cofactors• •

Additional chemical component {inorganic ions & organic molecules (coenzymes)} Undergo structural changes to initiate the reaction/ to enhance the rate of reaction

Coenzymes• • •

Are organic cofactors acts as transient carriers of specific functional gp Derived from vitamins, organic nutrients etc

Holoenzyme- Complete catalytically active enzyme + coenzyme (Prosthetic gp) •

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Apoprotein or apoenzyme- protein part of holoenzyme

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Classification of enzymes

Some important points: Active site- catalytic site of an enzyme Substrate- molecule bound in the active site & acted upon by the enzyme Function of enzyme: ¡ To increase the rate of reaction ¡ Do not disturbs the reaction equilibrium ¡ Ground state- starting point for forward or reverse reaction Reaction intermediate: any species on the reaction pathway that has a finite chemical lifetime [ES and EP complexes] Rate-limiting step- step (or steps) with the highest activation energy Entropy effect : ¡

At equilibrium entropy is maximum.

¡ Also called as proximity effect. ¡ Decrease in entropy contributes to the rate enhancement.

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Enzyme Kinetics

Kinetic Parameters Km: - It is equivalent to the substrate concentration at which V0 is one-half Vmax.

Vmax: - Represents maximum velocity attainable by an enzyme catalyzed reaction Kcat (Turnover no of enzyme): - equivalent to the number of substrate molecules converted to product in a given unit of time on a single enzyme molecule when the enzyme is saturated with substrate Enzyme inhibition: - Three types • • •

Competitive inhibition Uncompetitive inhibition Mixed inhibition

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Carbohydrates •

Most abundant biomolecules on Earth

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Polyhydroxy aldehydes or ketones, or substances that yield such compounds on hydrolysis.

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Carbohydrates have the empirical formula (CH2O)n; some also contain nitrogen, phosphorus, or sulfur

Classes of carbohydrates

Monosaccharides (contain single aldehyde or ketone unit)

Oligosaccharides (contains 2-10 monosaccharide units)

Polysaccharides (contain more than 10 monosaccharide units)

Monosaccharides • • •

Monosaccharides are colorless, crystalline solids that are freely soluble in water but insoluble in non-polar solvents.

Most have a sweet taste Monosaccharides Have Asymmetric (chiral) Centers. Hence, occur in optically active isomeric forms or enantiomers called as D & L isoforms

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Examples of Monosaccharides

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Aldotetroses and all monosaccharides with five or more carbon atoms in the backbone occur in cyclic form in aq. Solutions.

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The formation of these ring structures is the result of a general reaction between alcohols and aldehydes or ketones to form derivatives called hemiacetals or hemiketals.

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Hemiacetals & hemiketals contain an additional asymmetric carbon atom and thus can exist in two stereoisomeric forms designated as α & β

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Oligosaccharides •

Contains 2-10 monosaccharide units.

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Categorised as  Disaccharides  Trisaccharides  Tetrasaccharides  Pentasaccharides

 Hexasaccharides etc

Examples of oligosaccharides Maltose:- a cleavage product of starch, is a disaccharide with an α (1  4) glycosidic linkage between the C1 hydroxyl of one glucose and the C4 hydroxyl of a second glucose.

Lactose, occurs naturally only in milk. The anomeric carbon of the glucose residue is available for oxidation, and thus lactose is a reducing disaccharide. Its abbreviated name is Gal(1-> 4)Glc.

Sucrose (table sugar) is a disaccharide of glucose and fructose. It is formed by plants but not by animals. It contains no free anomeric carbon atom; the anomeric carbons of both monosaccharide units are involved in the glycosidic bond hence it is therefore a non reducing sugar.

Polysaccharides •

Also called as glycans.

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Made up of more than 10 monomer units joined by glycosidic bond.

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2 Types:  Homopolysaccharide - contain only a single type of monomer  Heteropolysaccharide- contain 2 or more different type of monomer

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Can be branched or unbranched

Examples of Polysaccharides Starch: Starch contains two types of glucose polymer, amylose and amylopectin. The amylose consists of long, unbranched chains of D-glucose residues connected by α (1 4) linkages.

Amylopectin is unbranched, the glucose residues are joined by α (14) & α (16) linkages; Note: the branch points (occurring every 24 to 30 residues)

Glycoproteins •

have one or several oligosaccharides of varying complexity joined covalently to a protein.

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Carohydrate moieties are smaller & more structurally diverse than glycosaminoglycans of proteoglycans

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Anomeric C of oligosaccharide attaches to the ser (-OH) or Thr (O-linked) or Asn (Nlinked) residue

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Carbohydrate constitute 1-70% of glycoprotein by mass

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found on the outer face of the plasma membrane, in the extracellular matrix, and in the blood.

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Also found in Golgi complexes, secretory granules, and lysosomes.

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they are rich in information, forming highly specific sites for recognition and highaffinity binding by other proteins

E.g. Glycophorin A of erythrocyte membrane  Contains 60% carbohydrate by mass

 Has 16 oligosaccharide chains each with 60-70 monosaccharide residues  15 oligosaccharide are linked to ser or Thr & 1 is linked to Asn

Generally all proteins secreted by cells are glycoprotein.

E.g. Ab, FSH, TSH, Lactalbumin, Ribonuclease

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UNIT 1 (contd.)

1. Back Bonding

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Backbonding is the sharing of electrons between an atomic orbital on one atom with an antibonding π* orbital on another atom.

The bonding is from the metal to the ligand rather than the usual ligand to metal, and it involves π orbitals. Thus, the phenomenon is also called π backbonding.

This type of bonding is possible between atoms in a compound in which one atom has lone pair of electron and the other has vacant orbital placed adjacent to each other.

Backbonding is mostly observed in CO ligands which is a sigma donor as well as piacceptor. [The typical example given for synergy in chemistry is the synergic bonding seen in transition metal carbonyl complexes.]

2. Cellular Processes

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Cellular processes form a fundamental system that involves complicated cascades of biochemical reactions and signaling pathways.

DNA replication is the process of copying the DNA in a cell so that there are two copies.

Transcription is the process of making an RNA copy of a gene sequence. This copy, called a messenger RNA (mRNA) molecule, leaves the cell nucleus and enters the cytoplasm, where it directs the synthesis of the protein, which it encodes. It simply involves copying DNA into RNA. Translation is the process of translating the sequence of a messenger RNA (mRNA) molecule to a sequence of amino acids during protein synthesis.

3. IMP Synthesis

purine degradation

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Inosine is a purine nucleoside containing the base hypoxanthine and the sugar ribose, which occurs in transfer RNAs and as an intermediate in the degradation of purines and purine nucleosides to uric acid and in pathways of purine salvage.

Inosine monophosphate (IMP) a nucleotide produced by the deamination of adenosine monophosphate (AMP); it is the precursor of AMP and GMP in purine biosynthesis and an intermediate in purine salvage and in purine degradation.

IMP or Inosinic acid is formed by the deamination of adenosine monophosphate, and is hydrolysed to inosine.

Important derivatives of inosinic acid include purine nucleotides found in nucleic acids and adenosine triphosphate, which is used to store chemical energy in muscle and other tissues.

4. Degradation of nucleic acids

Relation of dipole with temperature

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Nucleic acid metabolism is the process by which nucleic acids (DNA and RNA) are synthesized and degraded.

Purine and pyrimidine nucleosides can either be degraded to waste products and excreted or can be salvaged as nucleotide components.

Denaturation (loss of native structure) of the polymer duplex can be promoted by a variety of conditions or agents, including heat, chemical denaturants, and extremes of pH.

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5. Conversion of UDP to dTTP

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Uridine diphosphate, abbreviated UDP, is a nucleotide diphosphate. It is an ester of pyrophosphoric acid with the nucleoside uridine. UDP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase uracil.

Deoxythymidine triphosphate is one of the four nucleoside triphosphates that are used in the in vivo synthesis of DNA.

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6. Galactosemia

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Galactosemia is a hereditary defect in the metabolism of the sugar galactose, a constituent of lactose, the main carbohydrate of milk.

Normally, galactose is metabolized glucose, in case of galactosemia the enzyme responsible for converting galactose-1-phosphate to glucose-1-phosphate, is not active.

Galactosemia is transmitted by an autosomal recessive gene.

Galactose is present in the blood and urine of persons suffering from galactosemia, and there is decreased formation of glucose in the body, which may result in a lowering of the blood glucose level.

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7. H-bonding affects water molecule structure

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The key to understanding water’s chemical behavior is its molecular structure. A water molecule consists of two hydrogen atoms bonded to an oxygen atom, and its overall structure is bent.

The most stable arrangement is the one that puts them farthest apart from each other: a tetrahedron, with the O-H bonds forming two out of the four “legs”.

Due to polarity, water molecules attract each other. They are examples of hydrogen bonds, weak interactions that form between a hydrogen with a partial positive charge and a more electronegative atom, such as oxygen.

Water molecules are also attracted to other polar molecules and to ions. A charged or polar substance that interacts with and dissolves in water is said to be hydrophilic.

8. Hydrophobic interactions

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Hydrophobic molecules are molecules that do not have a charge, meaning they are non-polar. By lacking a charge, these molecules do not have any charge-to-charge interactions that will allow them to interact with water.

The interactions between the non-polar molecules are called hydrophobic interactions.

The mixing of fat and water is a good example of this particular interaction.

Hydrophobic Interactions are important for the folding of proteins. This is important in keeping a protein stable and biologically active, because it allow to the protein to decrease in surface are and reduce the undesirable interactions with water.

9. Conversion of IMP to GMP and AMP

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Inosine 5'-monophosphate (IMP) is a branch point in the process of De Novo synthesis of purines that can lead to either AMP or GMP. Aspartate condenses with IMP in the presence of GTP to produce adenylsuccinate which, on cleavage, forms AMP. IMP undergoes NAD+ dependent dehydrogenation to form xanthosine monophosphate (XMP). Glutamine then transfers amide nitrogen to XMP to produce GMP. The conversion of IMP to either AMP or GMP is highly regulated - AMP feedback inhibits the first step from IMP to AMP and GMP feedback inhibits the first step from IMP to GMP.

10.Micro RNA

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MiRNA are small, evolutionary conserved, single-stranded, non-coding RNA molecules that bind target mRNA to prevent protein production by one of two distinct mechanisms.

MicroRNAs are transcribed by RNA polymerases II and III, generating precursors that undergo a series of cleavage events to form mature microRNA. The conventional biogenesis pathway consists of two cleavage events, one nuclear and one cytoplasmic.

The miRNA functions as a guide by base-pairing with target mRNA to negatively regulate its expression. The regulatory functions of microRNAs are accomplished through the RNA-induced silencing complex (RISC).

The degree and nature of the complementarity between the microRNA and target determine the gene silencing mechanism, slicer-dependent mRNA degradation or slicer-independent translation inhibition.

11.Discovery of Neutron

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In 1930, W. Bothe and H. Becker found an electrically neutral radiation when they bombarded beryllium with alpha particle. They thought it was photons with high energy (gamma rays). In 1932, Irène and Frédéric Joliot-Curie showed that this ray can eject protons when it hits paraffin or H-containing compounds.

• The question arose that how mass less photon could eject protons which are 1836 times heavier than electrons. So the ejected rays in bombardment of beryllium with alpha particles cannot be photon.

• In 1932, James Chadwick performed the same experiment as Irène and Frédéric JoliotCurie but he used many different target of bombardment besides paraffin.

By analyzing the energies of different targets after bombardment he discovered the existence of a new particle which is charge less and has similar mass to proton. This particle is called neutron. Beryllium undergoes the following reaction when it is bombarded with alpha particle.

12.Purine Inhibitors

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Folic acid is essential for the synthesis of purine. Sulfa drugs inhibit the synthesis of folic acid by microorganisms which indirectly reduces the synthesis purines and nucleic acids.

The structural analogues of folic acid (eg, methotrexate) also inhibit synthesis of purines and nucleic acids. This affects proliferation of normal cells.

Azaserine is a glutamine antagonist and inihibits reactions involving glutamine.

Other synthetic nucleotide analogues used as anticancer agents are 6-thio guanine & 8aza guanine.

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13.Pyrimidine Biosynthesis

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Biosynthesis of pyrimidine is simpler than purines and involves six steps.

In contrast to purines, pyrimidines are not synthesized as nucleotide derivatives.

Instead, the pyrimidine ring system is completed before a ribose-5-P moiety is attached. Also, only two precursors, carbamoyl-P and aspartic acid, contribute atoms to the six-membered pyrimidine ring, compared to seven precursors for the 9 purine atoms.

This pathway results in the synthesis of Uridine-5-monophosphate (UMP).

Six enzymes involved- five are present in cytosol and the remaining is present on outer surface of inner mitochondrial membrane. In mammals, this pathway is regulated through two steps.

14. Thomson's Experiment

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In the late 19th century, physicist J.J. Thomson began experimenting with cathode ray tubes. To test the properties of the particles, he placed two oppositely-charged electric plates around the cathode ray.

When the cathode ray was deflected away from the negatively-charged electric plate and towards the positively-charged plate, this indicated that the cathode ray was composed of negatively-charged particles.

J.J. Thomson's experiments with cathode ray tubes showed that all atoms contain tiny negatively charged subatomic particles or electrons.

Thomson's plum pudding model of the atom had negatively-charged electrons embedded within a positively-charged "soup."

15.Rutherford's Scattering Experiment

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Rutherford's gold foil experiment showed that the atom is mostly empty space with a tiny, dense, positively-charged nucleus.

Based on these results, Rutherford proposed the nuclear model of the atom, in which an atom consists of a very small, positively charged nucleus surrounded by the negatively charged electrons.

Based on the number of α particles deflected in his experiment, Rutherford calculated that the nucleus took up a tiny fraction of the volume of the atom.

16. Relationship of Dipole with Temperature

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A dipole usually refers to the separation of charges within a molecule between two covalently bonded atoms or atoms that share an ionic bond. For example, a water molecule (H2O) is a dipole.

Dipole moments are applied to the distribution of electrons between two bonded atoms.

The existence of a dipole moment is the difference between polar and nonpolar bonds.

The dipole moment is dependent on temperature.

Higher potential energy configurations are only able to be populated at elevated temperatures.

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17.The Hydrogen Bond Underlying Water’s Chemical and Biological Properties

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Water – a polar molecule – tends to be slightly positive on the hydrogen side and slight negative on the oxygen side. When ionic compounds such as sodium chloride are added to water, hydrogen bonding will tend to pull those ionic compounds apart. This makes water a natural solvent.

At 32°F (or 0°C) and below, water molecules form hydrogen bonds in a chrystalline lattice structure. This bonding spaces the molecules a bit farther apart than usual, causing water to expand when it freezes. This results in ice being less dense than liquid water, which is why ice floats.

Water has adhesive and cohesive properties, due to H2O being a polar molecule.

Water has a high specific heat capacity, and a high heat of vaporization.

18.Back Bonding In BF3

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Boron has empty p-orbital and p-orbital of fluorine contains lone pair and hence Boron act as Lewis acid and fluorine as Lewis base. Fluorine donates it's lone pair to Boron and this bonding is called back bonding.

BF3 has trigonal plannar structure all the three BF bonds lie in plane and thus porbitals of boron and fluorine become parallel.

Backbonding is effective only when the size of the valence shell matches. In the case of BF3, both boron and fluorine have their valence electrons in 2p. Hence, effectiveness of back bonding with Boron decreases down the halogen group.

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19.Purine Nucleotide Biosynthesis Is Regulated By Feedback Inhibition

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Nucleotide biosynthesis is regulated by feedback inhibition in a manner similar to the regulation of amino acid biosynthesis. Carbamoyl phosphate synthetase is a site of feedback inhibition in both prokaryotes and eukaryotes.

The committed step in purine nucleotide biosynthesis is the conversion of PRPP into phosphoribosylamine by glutamine phosphoribosyl amidotransferase. This important enzyme is feedback-inhibited by many purine ribonucleotides.

Inosinate is the branch point in the synthesis of AMP and GMP. The reactions leading away from inosinate are sites of feedback inhibition.

As already noted, GTP is a substrate in the synthesis of AMP, whereas ATP is a substrate in the synthesis of GMP. This reciprocal substrate relation tends to balance the synthesis of adenine and guanine ribonucleotides.

20.6-MP Nucleotide Is An Analog Of IMP

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6-Mercaptopurine is an antimetabolite antineoplastic agent with immunosuppressant properties.

6-Mercaptopurine and 6-Thioguanine are both purine analogues and must be activated by HGPRT to T-IMP and 6-thioGMP. T-IMP and 6-thioGMP are poor substrates for guanylyl kinase, therefore IMP and GMP accumulate, causing “pseudofeedback inhibition” of purine nucleoside phosphorylase (PNP), PRPP glutamyl amidotransferase and HGPRT. It interferes with nucleic acid synthesis by inhibiting purine metabolism and is used, usually in combination with other drugs, in the treatment of or in remission maintenance programs for leukemia.

21.Degradation Of Purine Nucleotides

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Because nucleic acids are ubiquitous in cellular material, significant amounts are ingested in the diet. Nucleic acids are degraded in the digestive tract to nucleotides by various nucleases and phosphodiesterases.

• Nucleotides are then converted to nucleosides by base-specific nucleotidases and nonspecific phosphatases.

NMP + H2O --->nucleoside + Pi • The various nucleotides are first converted to nucleosides by intracellular nucleotidases.

Nucleosides are then degraded by the enzyme purine nucleoside phosphorylase (PNP) to release the purine base and ribose-l-P. The PNP products are merged into xanthine by guanine deaminase and xanthine oxidase, and xanthine is then oxidized to uric acid by this latter enzyme.

22.Formation of dTMP

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Thymidylate synthase (TS) catalyzes the conversion of deoxyuridine monophosphate (dUMP) to thymidylate (TMP), in a reductive methylation that involves the transfer of a carbon atom from the cofactor 5,10-methylenetetrahydrofolate to the 5 position of the pyrimidine ring. This transformation, that is the only de novo source of thymidylate, is part of the so-called thymidylate cycle.

Once synthesized, dTMP is then metabolized intracellularly to the dTTP triphosphate form, an essential precursor for DNA biosynthesis.

While dTMP is also formed through the salvage pathway using thymidine kinase, the TS-catalyzed reaction provides the sole intracellular de novo source of dTMP.

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23.Degradation Of Pyrimidine Nucleotides

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Like purines, free pyrimidines can be salvaged and recycled to form nucleotides via phosphoribosyltransferase reactions similar to those discussed earlier.

Pyrimidine catabolism results in degradation of the pyrimidine ring to products reminiscent of the original substrates, aspartate, CO2, and ammonia. b-Alanine can be recycled into the synthesis of coenzyme A.

24.Nitrogen Cycle

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Nitrogen exists in the atmosphere as N2 gas. In nitrogen fixation, bacteria convert N2 into ammonia, a form of nitrogen usable by plants. When animals eat the plants, they acquire usable nitrogen compounds.

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Nitrogen is a common limiting nutrient in nature, and agriculture. A limiting nutrient is the nutrient that's in shortest supply and limits growth.When fertilizers containing nitrogen and phosphorous are carried in runoff to lakes and rivers, they can result in blooms of algae—this is called eutrophication.

25.Allosteric Regulation

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An allosteric site does not bind substrate, but instead binds another molecule that affects the enzyme's regulation. Allosteric enzyme regulation is when a molecule binds a site other than the active site and changes the behavior of the enzyme by changing its conformation.

In most cases, the binding of a molecule to the allosteric site acts like a dimmer switch that can turn a light on, making it brighter or dimmer, or turn it off. Just like the switch, allosteric molecules can activate, or turn on, the enzyme, as well as increase, or turn up, the enzyme's activity. They can also lower, or turn down, the activity of the enzyme, as well as inactivate, or turn off, the enzyme.

Allosteric regulation allows for a higher degree of enzyme control than could be achieved through simply inhibiting or activating an enzyme. With this regulation, the activity of an enzyme can be more tightly regulated by concentrations of not only enzymes and substrates, but also other molecules that are not affected by the enzyme.

26.Urea Cycle

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The urea cycle mediates the removal of ammonia as urea in the amount of 10 to 20 g per day in the healthy adult.

The absence of a fully functional urea cycle may result in hyperammonemic encephalopathy and irreversible brain injury in severe cases. A failure of ureagenesis occurs because of acquired disease, such as cirrhosis secondary to alcoholism, or secondary to an inherited defect, usually a congenital enzymopathy.

One turn of the cycle: consumes 2 molecules of ammonia; consumes 1 molecule of carbon dioxide; creates 1 molecule of urea ((NH2)2CO; regenerates a molecule of ornithine for another turn.

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27.Biosynthesis of Amino Acids

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All amino acids are derived from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen enters these pathways by way of glutamate and glutamine.

Ignoring tyrosine, all of the nonessential amino acids are synthesized from intermediates of major metabolic pathways. Furthermore, the carbon skeletons of these amino acids are traceable to their corresponding a-ketoacids.

Therefore, it could be possible to synthesize any one of the nonessential amino acids directly by transaminating its corresponding a-ketoacid, if that ketoacid exists as a common intermediate. A "transamination reaction", in which an amino group is transferred from an amino acid to the a-carbon of a ketoacid, is catalyzed by an aminotransferase.

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28.Gamma Glutamyl Cycle

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GGT catalyzes the transfer of gamma-glutamyl group from peptides or peptide like compounds to an acceptor peptide molecule.

In plants, the gamma-glutamyl cycle is a metabolic route of extra-cytosolic (apoplastic and vacuolar) glutathione degradation by gamma-glutamyl-transferase (GGT) and cysgly dipeptidase, followed by the re-uptake of constituent amino acids, intracellular resynthesis and extrusion.

GGTs are extracytosolic (apoplastic and vacuolar) whereas GGCT and 5OPase activities are restricted in the cytosol. Thus, the gamma-glutamyl cycle involving apoplastic GGTs is functional to the recovery of extracellular glutathione, whereas the alternative GGCT/5OPase pathway participates in controlling cytosolic glutathione homeostasis.

29.Biosynthesis And Assembly Of Collagen

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The hallmark of a collagen is a molecule that is composed of three polypeptide chains, each of which contains one or more regions characterized by the repeating amino acid motif (Gly-X-Y), where X and Y can be any amino acid.

The first event following synthesis of procollagen chains on the ribosome is their import into the rough endoplasmic reticulum.

There they undergo a series of post-translational modifications resulting in the assembly of procollagen molecules. These steps include modification of proline residues to hydroxyprolines, modification of lysines to hydroxylysines, N- and Olinked glycosylation, trimerization, disulphide bonding, prolyl cis–trans isomerization and folding of the triple helix.

Under appropriate conditions collagen molecules will selfassemble into fibers, and conversely fibers can be dissolved to collagen molecules. Fiber formation is an endothermic process and is accompanied by loss of solvated water.

39. Chloride Shift

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Chloride shiftis the exchange of chloride and carbonate between the plasma and the er ythrocytes that takes place whenthe blood gives up oxygen and receives carbon dioxide . It serves to maintain ionic equilibrium between the cell and surrounding fluid.

As a result of the "trapping" of hydrogen ions within the red blood cells by their attachment to hemoglobin and the outward diffusion of bicarbonate, the inside of the red blood cell gains a net positive charge. This attracts chloride ions (Cl-), which move into the red blood cells as HCO3- moves out. This exchange of anions as blood travels through the tissue capillaries is called the chloride shift.

40. Ramachandran Plot

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The Ramachandran plot is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in a peptide.

By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides.

The plot is obtained by plotting the φ values on the x-axis and the ψ values on the yaxis, as for the image at left. Plotting the torsional angles in this way graphically shows which combination of angles are possible.

The torsional angles of each residue in a peptide define the geometry of its attachment to its two adjacent residues by positioning its planar peptide bond relative to the two adjacent planar peptide bonds, thereby the torsional angles determine the conformation of the residues and the peptide.

41. Classification of Lipids

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Simple lipids- esters of fatty acid linked with various alcohols- Fats and Oils, Waxes.

Compound Lipids or Heterolipids- are fatty acid esters with alcohol and additional groups- Phospholipids, Glycolipids.

Derived Lipids- These substances are derived by hydrolysis from compound and simple lipids. These fatty acids include alcohols, mono- and diglycerides, carotenoids, steroids, and terpenes.

Based on biological functions, they are classified under strorage lipids, structural lipids, and precursor lipids.

42. Membrane Lipids

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The three major kinds of membrane lipids are phospho-lipids, glycolipids, and cholesterol.

A phospholipid molecule is constructed from four components: fatty acids, a platform to which the fatty acids are attached, a phosphate, and an alcohol attached to the phosphate. The fatty acid components provide a hydrophobic barrier, whereas the remainder of the molecule has hydrophilic properties to enable interaction with the environment.

Glycolipids are sugar-containing lipids. In Glycolipids one or more sugars (rather than phosphoryl choline) are attached to the primary hydroxyl group. The simplest glycolipid, called a cerebroside, contains a single sugar residue, either glucose or galactose.

Cholestrerol structure- a hydrocarbon tail is linked to the steroid at one end, and a hydroxyl group is attached at the other end. In membranes, the molecule is oriented parallel to the fatty acid chains of the phospholipids, and the hydroxyl group interacts with the nearby phospholipid head groups.

43. Abnormal Accumulation Of Membrane Lipids Can Cause Diseases

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In Gaucher’s disease, glucocerebrosides, which are a product of fat metabolism, accumulate in tissues. Gaucher’s disease is the most common lipidosis.

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In Tay-Sachs disease, gangliosides, which are products of fat metabolism, accumulate in tissues. In Niemann-Pick disease, the deficiency of a specific enzyme results in the accumulation of sphingomyelin (a product of fat metabolism) or cholesterol.

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In Fabry’s disease, glycolipid, which is a product of fat metabolism, accumulates in tissues. The GM1 gangliosidoses (or GM1 gangliosidosis) are caused by a deficiency of beta-galactosidase, with resulting abnormal storage of acidic lipid materials in cells of the central and peripheral nervous systems, but particularly in the nerve cells.

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Sandhoff disease is caused by a deficiency of the enzyme beta-hexosaminidase, which results in the harmful accumulation of certain fats (lipids) in the brain and other organs of the body. It is a severe form of Tay-Sachs disease.

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44. Functions of Cholesterol

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Hormone production. Cholesterol plays a part in producing hormones such as estrogen, testosterone, progesterone, aldosterone and cortisone.

Bile production. Cholesterol produces bile acids which aid in digestion and vitamin absorption.

Cholesterol is a structural component of cells and along with polar lipids makes up the structure of every cell in our body. Cholesterol is there to basically provide a protective barrier.

Cholesterol is essential for our immune system to function properly. Our immune cells rely on cholesterol to fight infections and repair themselves after the fight.

45. Regulation of Cholesterol Biosynthesis

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The amount of cholesterol that is synthesized in the liver is tightly regulated by dietary cholesterol levels. When dietary intake of cholesterol is high, synthesis is decreased and when dietary intake is low, synthesis is increased.

LDL receptors regulate the cellular transport of lipid rich low density lipoprotein (LDL) particles. One mechanism for regulating LDL receptor expression and controlling the expression of all the enzymes in the cholesterol biosynthetic pathway is dependent on Sterol-Sensitive Response Elements (SREs).

Transcription factors important to activating SREs are Sterol Regulating Element Binding Proteins (SREBPs).These transcription regulating proteins are bound by another protein called SREBP cleavage activating proteins (SCAPs). SCAPs bind to SREBPs in the endoplasmic reticulum (ER) where a regulatory domain within SCAP responds to the level of oxysterols present in the cell.

Limiting cholesterol synthesis leads to a homeostatic response in which cells increase the density of LDL receptors on their surfaces. This increases the clearance rate of LDL particles from the plasma and reduces plasma LDL cholesterol and its related health risks. The decrease in cholesterol synthesis also promotes an increase of HDL, thus, clearing even more cholesterol from the plasma.

46. Roles of Cofactors in Enzyme Function

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A cofactor is a non-protein chemical compound that is required for the protein's biological activity. Many enzymes require cofactors to function properly. Cofactors can be considered "helper molecules" that assist enzymes in their action.

Cofactors can be ions or organic molecules (called coenzymes). Organic cofactors are often vitamins or are made from vitamins. Small quantities of these vitamins must be consumed in order for our enzymes to function correctly.

Many cofactors will sit in the enzyme active site and assist the binding of the substrate.

An inactive enzyme without the cofactor is called an apoenzyme, while the complete enzyme with cofactor is called a holoenzyme.

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Triacylglycerol (TAG) in adipose tissue serves as the major energy storage form in higher eukaryotes.

The level of free fatty acids in the blood reflects both the rate of release of fatty acids and the balance between the synthesis and breakdown of triacylglycerols in adipose tissue and liver.

When the mobilization of fatty acids is required to meet energy needs, release from adipose tissue is stimulated by the hormones glucagon and epinephrine, the released fatty acid is taken up by a number of tissues, including muscle, where it is oxidized to provide energy. Much of the fatty acid taken up by liver is not oxidized but is recycled to triacylglycerol and returned to adipose tissue.

YOUR NOTES

39. Acetyl-CoA Transport Across the Membrane

Quick Notes ďƒź Since acetyl-CoA cannot be transported directly across the inner mitochondrial membrane to the cytosol, its carbon atoms are transferred by two transport mechanisms: 1. Transport dependent on carnitine: Carnitine participates in the transport of long-chain acylCoA into the mitochondria and plays a similar role in the transport of acetyl-CoA out of mitochondria. However, carnitine acetyl transferases have a minor role in acetylCoA transport.

2.Cytosolic generation of acetyl-CoA (citrate shuttle): This pathway is shown in Figure 16.8.

Citrate synthesized from oxaloacetate and acetyl-CoA is transported from mitochondria to the cytosol via the tricarboxylate anion carrier system and cleaved to yield acetyl-CoA and oxaloacetate.

40. Regulation of Fatty Acid Synthesis

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The two processes of β-oxidation and FA synthesis are coordinately regulated.

Three hormonal signals determine the state of FA metabolism. Glucagon and epinephrine inhibit FA synthesis and favor oxidation, whereas insulin is antilipolytic and stimulates FA biosynthesis.

The mechanism of hormonal regulation is covalent phosphorylation of acetylCoA carboxylase, the rate-limiting step of FA biosynthesis.

Acetyl CoA carboxylase is inhibited by phosphorylation. Phosphorylated acetylCoA carboxylase can regain partial activity by allosterically binding citrate.

41. Conversion of Palmitate to Higher Unsaturated Fatty Acids

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The 16-carbon fatty acid palmitic acid (palmitate at pH 7) undergoes seven passes through this oxidative sequence, in each pass losing two carbons as acetyl-CoA. At the end of seven cycles the last two carbons of palmitate (originally C-15 and C-16) are left as acetyl-CoA. The overall result is the conversion of the 16-carbon chain of palmitate to eight twocarbon acetyl-CoA molecules. Formation of each molecule of acetyl-CoA requires removal of four hydrogen atoms (two pairs of electrons and four H+) from the fatty acyl moiety by the action of dehydrogenases.

In the second stage of fatty acid oxidation the acetyl residues of acetyl-CoA are oxidized to CO2 via the citric acid cycle, which also takes place in the mitochondrial matrix. Acetyl-CoA derived from fatty acid oxidation thus enters a final common pathway of oxidation along with acetyl-CoA derived from glucose via glycolysis and pyruvate oxidation.

The first two stages of fatty acid oxidation produce the reduced electron carriers NADH and FADH2, which in the third stage donate electrons to the mitochondrial respiratory chain, through which the electrons are carried to oxygen. Coupled to this flow of electrons is the phosphorylation of ADP to ATP, to be described in Chapter 18.

Thus energy released by fatty acid oxidation is conserved as ATP.

YOUR NOTES

42. Phosphatidic Acid Formation

YOUR NOTES

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PtdOH can be synthesized via two different acylation pathways named after their respective precursor, namely (a) the Gro3P (glycerol 3-phosphate) pathway, and (b) the GrnP (dihydroxyacetone phosphate) pathway.

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In the Gro3P pathway, the first step of acylation catalyzed by Gro3P acyltransferase (Gro3P AT) leads to the formation of 1-acylGro3P (also known as lyso-PtdOH).

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In the GrnP pathway, the first intermediate formed by GrnP acyltransferase (GrnP AT) is 1-acyl-GrnP. This compound is converted to lyso-PtdOH in an NADPHdependent reaction catalyzed by 1-acyl-GrnP reductase.

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Lyso-PtdOH either formed through the Gro3P pathway or the GrnP pathway, respectively, is further acylated to PtdOH by 1-acylGro3P acyltransferase (1-acylGro3P AT).

YOUR NOTES

43. Regulation of Triacylglycerol Synthesis

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If carbohydrate, fat, or protein is consumed in amounts exceeding energy needs, the excess is stored in the form of triacylglycerols. The fat stored in this way can be drawn upon for energy and enables the body to withstand periods of fasting.

The biosynthesis and degradation of triacylglycerols are regulated reciprocally, with the favored path depending upon the metabolic resources and requirements of the moment.

The rate of triacylglycerol biosynthesis is profoundly altered by the action of several hormones. Insulin, for example, promotes the conversion of carbohydrate into triacylglycerols.

People with severe diabetes mellitus, due to failure of insulin secretion or action, not only are unable to use glucose properly but also fail to synthesize fatty acids from carbohydrates or amino acids. They show increased rates of fat oxidation and ketone body formation. As a consequence they lose weight. Triacylglycerol metabolism is also influenced by glucagon, and by pituitary growth hormone and adrenal cortical hormones.

44. Conversion to Phospholipids to Anti Inflammatory Agents

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Membrane phospholipids containing the 20-carbon fatty acid arachidonic acid are enzymatically broken apart.

Therapeutic use of glucocorticoids such as cortisone can inhibit this pathway, thus reducing the amount of any of the resulting regulator molecules.

Arachidonic acid is then converted by the COX pathway to either prostaglandins or thromboxanes.

Arachidonic acid may alternatively be converted by the lipoxygenase pathway to a leukotriene.

45. Strategy for Attachment Of Head Group

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In mammals, phosphatidylserine is not synthesized from CDP diacylglycerol; instead, it is derived from phosphatidylethanolamine via the head group exchange reaction.

In mammals, synthesis of all nitrogen-containing phospholipids occurs by strategy 2 phosphorylation and activation of the head group followed by condensation with diacylglycerol. For example, choline is reused ("salvaged") by being phosphorylated then converted into CDP-choline by condensation with CTP. A diacylglycerol displaces CMP from CDP-choline, producing phosphatidylcholine.

An analogous salvage pathway converts ethanolamine obtained in the diet into phosphatidylethanolamine. In the liver, phosphatidylcholine is also produced by methylation of phosphatidylethanolamine using S-adenosylmethionine, as described above.

In all other tissues, however, phosphatidylcholine is produced only by condensation of diacylglycerol and CDP-choline.

46. Plasmalogen Synthesis

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The starting metabolite for plasmalogen biosynthesis is dihydroxyacetone phosphate from glycolysis, which is used to form the glycerol backbone of the plasmalogen.

The biosynthesis of plasmalogens is initiated in peroxisomes and completed in the endoplasmic reticulum. Thus, the first three enzymes of plasmalogen biosynthesis, dihydroxyacetone phosphate acyltransferase, alkyl dihydroxyacetone phosphate synthase, and acyl/ alkyl dihydroxyacetone reductase, are located in peroxisomes.

The endoplasmic reticulum contains the other enzymes, namely 1-alkyl-sn-GroP acyltransferase, 1-alkyl-2-acyl-sn-GroP phosphohydrolase, and 1-alkyl-2-acyl-sn-Gro: CDP-choline (CDP-ethanolamine) choline (ethanolamine) phosphotransferase.

Dihydroxyacetone phosphate acyltransferase may be a crucial enzyme for plasmalogen biosynthesis, but it is not a rate-limiting step for plasmalogen synthesis.

YOUR NOTES

47. Sphingomyelin Synthesis

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The initiation of the synthesis of the sphingoid bases (sphingosine, dihydrosphingosine, and the various ceramides) takes place via the condensation of palmitoyl-CoA and serine. This reaction occurs on the cytoplasmic face of the endoplasmic reticulum (ER) and is catalyzed by the pyridoxal phosphate-dependent enzyme, serine palmitoyltransferase (SPT).

The sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthases (SMS). There are two SMS genes in humans identified as SMS1 and SMS2. SMS1 is found in the trans-Golgi apparatus while SMS2 is predominantly associated with the plasma membrane.

Sphingomyelins are degraded via the action of sphingomyelinases resulting in release of ceramides and phosphocholine. The sphingomyelinase in humans functions at acidic pH and is, therefore, referred to as acid sphingomyelinase (ASMase or aSMase).

48. Feedback Inhibition of Pentose Phosphate Pathway

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A higher activity of the PPP is maintained by feedback inhibition of triosephosphate isomerase (TPI) by the glycolytic intermediate phosphoenolpyruvate (PEP).

PK and its feedback regulatory function on TPI and other metabolic enzymes play a crucial regulatory role. In budding yeast, the activity of PK is reduced when cells respire at high rate, and less active isoforms (i.e. PKM2 in mammals, PYK2 in yeast) are expressed.

The resultant accumulation of PEP causes feedback inhibition of several glycolytic enzymes, including the redox regulator TPI, and flux in the PPP increases.

TPI inhibition by PEP was required to prevent oxidative stress and oxidative damage, and led to protein oxidation and mitochondrial damage in respiring cells when interrupted.

49. Pentose Phosphate Pathway

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While the products of glycolysis are sent through the rest of cellular respiration to produce energy, there is also an alternative branch off glycolysis to produce the sugars that make up DNA and RNA. This pathway, called the Pentose Phosphate Pathway, is special because no energy in the form of ATP, or adenosine triphosphate, is produced or used up in this pathway.

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Two phases of the pentose phosphate pathway: 1) The oxidative phase and 2) The nonoxidative phase.

50. Pathway For Pyruvate To Phosphoenolpyruvate

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Conversion of pyruvate to phosphoenolpyruvate occurs by a combination of two reactions, and requires hydrolysis of two ATP to ADP. In the first reaction, pyruvate is converted to oxaloacetate by pyruvate carboxlyase, which uses biotin as a cofactor.

To be used for gluconeogenesis, the oxaloacetate must be transferred back into the cytoplasm. Therefore, oxaloacetate is reduced to malate, by malate dehydrogenase which converts one molecule of NADH to NAD+. Malate is then transported out and reoxidized to oxaloacetate, regenerating NADH from NAD+ in the cytoplasm.

Phosphoenolpyruvate carboxykinase simultaneously decarboxylates and phosphorylates oxaloacetate to generate phosphoenolpyruvate. GTP is used as the phosphoryl donor. Decarboxylation drives this reaction, which would otherwise be endergonic.

51. Glycolysis Vs. Gluconeogenesis

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Glycolysis -the simple sugar glucose is broken down in the cytosol. Two phases: 1) Investment phase- The NADH electron shuttle delivers high energy electrons to the electron transport chain where they will eventually power the production of ATP. 2) Reward phase- In the reward phase, ATP and NADH are made. This is the payoff of the original molecule of ATP invested in the first phase.

The reversal of glycolysis is called gluconeogenesis. Instead of using carbohydrates to produce glucose, our body converts non-carbohydrate sources (like amino acids) in our liver into glucose. Our body then takes that glucose and uses it to maintain our blood sugar at a constant, healthy level.

YOUR NOTES

52. Metabolism Of Trehalose And Fructose For Entry Into Glycolysis

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Phosphofructokinase-1 (PFK-1) irreversibly catalyzes the phosphorylation of fructose6-phosphate to form fructose-1,6-bisphosphate in the three step of glycolysis. This is the first committed step in glycolysis. After fructose-1,6-bisphosphate has been synthesized, the cell is committed to glycolysis.

Stage 1 of glycolysis ends with the cleavage of fructose-1,6-bisphosphate into two three-carbon molecules: glyceraldehyde-3-phosphate (G-3-P) and dihydroxyacetone phosphate (DHAP).

Certain types of mutant yeast cells are unable to grow anaerobically on glucose despite having a completely functional glycolytic pathway. These mutants die when exposed to large concentrations of glucose and research has revealed that defects in TPS1, the gene that codes for the catalytic subunit of trehalose-6-phosphate synthase, are responsible. Trehalose-6-phosphate is a compatible solute used by yeast and various other organisms to resist several forms of abiotic stress.

There are five pathways for trehalose biosynthesis present in the three domains of the tree of life. The most common and the best studied route among different species involves the enzyme trehalose-6-phosphate synthase (TPS), which catalyses the transfer of glucose by means of UDP-glucose to glucose-6-phosphate, leading to trehalose-6-phosphate (T6P). In a second stage trehalose-6-phosphate phosphatase (TPP) catalyzes the hydrolysis of the phosphate group from the intermediate disaccharide to generate trehalose.

YOUR NOTES

53. Amino Acid Degradation

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The carbon skeletons of amino acids are broken down into metabolites that can either be oxidized into CO2 and H2O to generate ATP, or can be used for gluconeogenesis.

Each of the 20 amino acids has a separate catabolic pathway, yet all 20 pathways converge into 5 intermediates, all of which can enter the citric acid cycle. From the citric acid cycle the carbon skeletons can be completely oxidized into CO2 or diverted into gluconeogensis or ketogenesis.

Glucogenic amino acids are broken down into one of the following metabolites: pyruvate, α- ketoglutarate, succinyl CoA, fumarate or oxaloacetate. Ketogenic amino acids are broken down into acetoacetate or acetyl-CoA. Larger amino acids, tryptophan, phenylalanine, tyrosine, isoleucine and threonine are both glucogenic and ketogenic.

Only 2 amino acids are purely ketogenic they are lysine and leucine. If 2 of the amino acids are purely ketogenic and 5 amino acids are both ketogenic and glucogenic, than that leaves 13 amino acids that are purely glucogenic: Arg, Glu, Gln, His, Pro, Val, Met, Asp, Asn, Ala, Ser, Cys, and Gly.

54. Franz Knoop's Experiment

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Franz Knoop - classic experiment: first use of chemical labels to trace metabolic pathways Fed dogs fatty acids labeled at theirω(last) carbon atom with a benzene ring an disolated phenyl-containing metabolic products. Fatty acids have to be broken down in two carbon units by oxidation of the carbon atom beta to the carboxyl group(otherwise, he would have expected phenylacetic acid to befurther oxidized to benzoic acid.)

Odd-chain fatty acids produced hippuric acid (containing One carbon from fatty acid).

Even-chain fatty acids produced phenylaceturic acid (containing two carbons from fatty acid).

66. Anabolism and catabolism

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Metabolism breaks down large molecules like food into usable energy. But metabolism is a pretty broad term, and it includes all of the chemical activities in your body. We can think of metabolism in two separate forms: catabolism and anabolism. Catabolism involves all of the metabolic processes that tear down biomolecules, while anabolism is all of the metabolic processes that build biomolecules.

There are three basic stages of anabolism. (1) Stage 1 involves production of precursors such as amino acids, monosaccharides, isoprenoids and nucleotides. (2) Stage 2 involves activation of these precursors into reactive forms using energy from ATP. (3) Stage 3 involves the assembly of these precursors into complex molecules such as proteins, polysaccharides, lipids and nucleic acids.

Catabolism can be broken down into 3 main stages. (1) Stage of digestion- The large organic molecules like proteins, lipids and polysaccharides are digested into their smaller components outside cells using digestive enzymes such as glycoside hydrolases. (2) Release of energy- Once broken down these molecules are taken up by cells and converted to yet smaller molecules, usually acetyl coenzyme A (acetyl-CoA), which releases some energy. (3) The acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing the energy that is stored by reducing the coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH.

55. Degradation of Phenylalanine To Acetoacetate

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The degradation of aromatic amino acids requires molecular oxygen to break down the aromatic rings. The degradation of phenylalanine begins with a monooxygenase, phenylalanine hydroxylasewhich adds a hydroxyl group to phenylalanine to form tyrosine.

From there the remaining five catabolic pathways for phenylalanine and tyrosine are the same.

Tyrosine aminotransferase deaminates tyrosine to form p-hydroxyphenylpyruvate which is converted into homogentisate by the enzyme p-hydroxyphenylpyruvate dioxygenase.

The final three steps in the catabolism of tyrosine and phenylalanine are carried out by the enzymes homogentisate 1,2-dioxygenase, maleylacetoacetate isomerase and fumarylacetoacetate hydrolase resulting in the production of fumarate (glucogenic) and acetoacetate (ketogenic).

56. TCA Cycle

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Second stage of cellular respiration. The three-stage process by which living cells break down organic fuel molecules in the presence of oxygen to harvest the energy they need to grow and divide.

The cycle is initiated (1) when acetyl CoA reacts with the compound oxaloacetate to form citrate and to release coenzyme A (CoA-SH). Then, in a succession of reactions, (2) citrate is rearranged to form isocitrate; (3) isocitrate loses a molecule of carbon dioxide and then undergoes oxidation to form alpha-ketoglutarate; (4) alphaketoglutarate loses a molecule of carbon dioxide and is oxidized to form succinyl CoA (5) succinyl CoA is enzymatically converted to succinate; (6) succinate is oxidized to fumarate; (7) fumarate is hydrated to produce malate; and, to end the cycle, (8) malate is oxidized to oxaloacetate. Each complete turn of the cycle results in the regeneration of oxaloacetate and the formation of two molecules of carbon dioxide.

57. Glyoxylate Cycle

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The glyoxylate cycle is a sequence of anaplerotic reactions (reactions that form metabolic intermediates for biosynthesis) that enables an organism to use substrates that enter central carbon metabolism at the level of acetyl-CoA as the sole carbon source. Such substrates include fatty acids, alcohols, and esters (often the products of fermentation), as well as waxes, alkenes, and methylated compounds. The pathway does not occur in vertebrates, but it is found in plants and certain bacteria, fungi, and invertebrates.

The pathway is essentially a modified version of the TCA cycle I (prokaryotic) that bypasses those steps in the cycle that lead to a loss of CO2. Acetyl-CoA enters the cycle at two steps, but no carbon escapes it in the form of CO2.

The glyoxylate cycle uses a two-step bypass. One key enzyme, isocitrate lyase, converts D-threo-isocitrate to form succinate and glyoxylate. A second key enzyme, malate synthase, condenses glyoxylate and a second molecule of acetyl-CoA to form (S)-malate. The subsequent oxidation of malate regenerates the initial acetyl-CoA acceptor molecule of the TCA cycle, oxaloacetate. Thus, the succinate that was formed by isocitrate lyase can be withdrawn from the cycle and used for cell carbon biosynthesis.

58. Flow of Electrons Through Complex 1

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Complex I, also called NADH‐coenzyme Q reductase, accepts electrons from NADH. The NADH releases a proton and two electrons. The electrons flow through a flavoprotein containing FMN and an iron‐sulfur protein.

First, the flavin coenzyme (flavin mononucleotide) and then the iron‐sulfur center undergo cycles of reduction and then oxidation, transferring their electrons to a quinone molecule, coenzyme Q(see Figure 1).

Complex I is capable of transferring protons from the matrix to the intermembrane space while undergoing these redox cycles. One possible source of the protons is the release of a proton from NADH as it is oxidized to NAD, although this is not the only explanation.

Apparently, conformational changes in the proteins of Complex I also are involved in the mechanism of proton translocation during electron transport.

59. Flow of Electrons Through Complex II

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Complex II, also known as succinate‐coenzyme Q reductase, accepts electrons from succinate formed during the TCA cycle. Electrons flow from succinate to FAD (the flavin‐adenine dinucleotide) coenzyme, through an iron‐sulfur protein and a cytochrome b 550 protein (the number refers to the wavelength where the protein absorbs), and to coenzyme Q. No protons are translocated by Complex II. Because translocated protons are the source of the energy for ATP synthesis, this means that the oxidation of a molecule of FADH 2 inherently leads to less ATP synthesized than does the oxidation of a molecule of NADH. This experimental observation also fits with the difference in the standard reduction potentials of the two molecules. The reduction potential of FAD is ‐0.22 V, as opposed to ‐0.32 V for NAD. Coenzyme Q is not bound to a protein; instead it is a mobile electron carrier and can float within the inner membrane, where it can transfer electrons from Complex I and Complex II to Complex III.

60. Inhibition of ETS by Rotenone

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The inhibitors of the Electron Transport Chain are substances that bind to some of the components of the ETC blocking its ability to change in a reversible form from an oxidized state to a reduced state. This inhibition results in the accumulation of reduced forms before the inhibitor point, and oxidized forms of the components of the ETC downstream (ahead) the inhibition point.

Since energy is not released, the synthesis of ATP also stops. The most important known inhibitors of the ETC are Amytal, Rotenone, Antimycin A, CO, Sodium Azide, and Cyanides.

Rotenone causes inhibition of mitochondrial respiratory chain complex I, which can cause oxidative stress and lead to selective degeneration of striatal-nigral dopamine neurons. Rotenone toxicity depended on a direct interaction with complex I, because cells expressing the rotenone‐insensitive, single‐subunit NADH dehydrogenase of yeast, NDI1, were resistant to rotenone toxicity.

In this system, electrons from complex I substrates are shunted through NDI1 into downstream portions of the electron transport chain, thereby allowing mitochondrial respiration.

61. Inhibition of ETS by Antimycin A

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One of the important known inhibitors of the ETC. It is an antibiotic produced by Streptomyces griseous that has been used as a piscicide for the control of some fish species.

Antymicine A interferes with electron flow from cytochrome bH in Complex III (Qcytochrome c oxidoreductase).

In the presence of this substance, cytochrome bHcan be reduced but not oxidized, consequently, in the presence of antimycin A cytochrome c remains oxidized, as do the cytochromes a and a3 that are ahead.

YOUR NOTES

62. Inhibition of ETS By Cyanide And Carbon Monoxide

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Cyanide binds to the Iron(III) in the Heme group of the Cytochrom oxidase C which is associated with Complex IV. The binding of cyanie prevents the oxidation reaction from taking place so no energy is released to allow the Complex to pump the Hydrogen ions out.

Thus, the PMF does not build up and there is not enough energy to allow the H ions to return via ATP synthase and be coupled to the formation of ATP. Carbon monoxide intoxication causes impaired oxygen delivery and utilization at the cellular level. CO binds to one of the Hem groups of Hemoglobin increases the affinity of the other three Hem groups for Oxygen, so the delivery of Oxygen to tissues is very affected. The brain and the heart, that has a high Oxygen consumption, are the most affected.

It left-shifts your oxygen-hemoglobin dissociation curve, causing reduced oxygen unloading at tissues.

63. Abnormalities Related to Urea Cycle

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The urea cycle is made up by six enzymatic reactions that are responsible for the conversion of excess nitrogen into urea. Individual defects in five of these enzymes can lead to life threatening hyperammonemia, severe morbidity and death. People with a urea cycle disorder are missing a gene that makes the enzymes needed to break down ammonia in the body.

Enzymes of the urea cycle are N-acetylglutamate synthetase (NAGS), carbamyl phosphate synthetase I (CPS-1), ornithine transcarbamylase (OTC), argininosuccinate synthetase (ASS, deficiency leading to Citrullinemia Type I ), and argininosuccinate lyase (ASA lyase).

Diseases are Argininosuccinic aciduria, Arginase deficiency, Carbamyl phosphate synthetase (CPS) deficiency, Citrullinemia, N-acetyl glutamate synthetase (NAGS) deficiency, Ornithine transcarbamylase (OTC) deficiency.

64. LDL Receptor Mediated Endocytosis in Mammalian Cells

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In receptor-mediated endocytosis, a specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasmamembrane region containing the receptor-ligand complex then undergoes endocytosis, becoming a transport vesicle.

Cells express LDL receptor on their plasma membrane. The receptor binds to sites on Apoprotein in LDL. Bound receptors cluster in coated pits and are then endocytosed by clathrin. The endocytic vesicles acidify to become endosomes and the low pH causes a conformational change in the LDL receptor which releases LDL. The LDL receptor is sorted into vesicles that return the receptor to the cell membrane.

The remaining endosome fuses with the lysosome where proteases and lipases can digest the lipoprotein. The component parts are then targeted to their appropriate sub cellular location. For cholesterol, it most likely returns to the ER but could also be trafficked to mitochondria for synthesis of steroids.

Cells can efficiently remove LDL from serum if they express and adequate amount of LDL receptor on their cell surface and can endocytose LDL receptor. Several genetic mutations in the receptor reduce its numbers at the cell membrane, leading to excess serum LDL and hypercholesterolemia.

YOUR NOTES

65. Branched Pathway of Isoprenoid Metabolism In Mammals

YOUR NOTES

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Mammalian cells synthesize cholesterol and various nonsterol isoprenoid compounds via a branched pathway in which mevalonate, the product of the reaction catalyzed by HMG'- CoA reductase, occupies a central position as a precursor for all end products.

The mevalonate pathway is an important central metabolic pathway in all higher eukaryotic cells. The key isomers dimethylallyl pyrophosphate (DMAPP) and isopentenyl pyrophosphate (IPP) are produced via the mevalonate pathway from (R)mevalonate and its subsequent phosphorylated metabolites (R)-mevalonate-5phosphate and (R)-mevalonate-pyrophosphate.

DMAPP and IPP are further utilized in condensation reactions for the biosynthesis of isoprenoids. These isoprenoids are transformed to more complex, cyclised structures through steroid and terpenoid biosynthesis and are involved in protein prenylation and protein anchoring.

Mechanisms for feedback regulation of low-density lipoprotein receptors and enzymes involved in mevalonate biosynthesis ensure that sufficient mevalonate is available to generate the required quantity of DMAPP and IPP. The mevalonate pathway is of biomedical interest in certain types of cancer as well as heart disease, and a number of therapeutic drugs target this regulatory system.

YOUR NOTES

66. Control Of Plasma LDL Production And Uptake By Liver LDL Receptors

Uptake by Liver LDL Receptors is called receptor-specific endocytosis- same as concept 75.

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The production of LDL is controlled by the cell's need for cholesterol. Therefore, in essence, the strategy is to deprive the cell of ready sources of cholesterol.

When cholesterol is required, the amount of mRNA for the LDL receptor rises and more receptor is found on the cell surface. This state can be induced by a two-pronged approach.

First, the intestinal reabsorption of bile salts is inhibited. Bile salts are cholesterol derivatives that promote the absorption of dietary cholesterol and dietary fats.

Second, de novo synthesis of cholesterol is blocked.

YOUR NOTES

67. Enzyme Substrate Interaction

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The first step in an enzyme catalyzed reaction is the formation of the enzyme-substrate complex. This is represented by the equation: E + S = ES = E + P This complex lowers the activation energy of the reaction and promotes its rapid progression by providing certain ions or chemical groups that actually form covalent bonds with molecules as a necessary step of the reaction process.

The enzyme will always return to its original state at the completion of the reaction.

One of the important properties of enzymes is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme is done catalyzing a reaction, it releases its products (substrates).

Two models for interaction- induced fit, lock & key model. Factors affecting reaction rates- temperature, pH, enzyme concentration, substrate concentration.

68. Diseases Related to Amino Acid Metabolism

YOUR NOTES

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Amino acids are the building blocks of proteins and have many functions in the body.

Hereditary disorders of amino acid processing can result from defects either in the breakdown of amino acids or in the body’s ability to get amino acids into cells.

Because these disorders cause symptoms early in life, newborns are routinely screened for several common ones.

Phenylketonuria occurs in infants born without the ability to normally break down an amino acid called phenylalanine. Maple syrup urine disease is caused by lack of the enzyme needed to metabolize amino acids. By-products of these amino acids cause the urine to smell like maple syrup.

Homocystinuria is caused by lack of the enzyme needed to metabolize homocysteine. Tyrosinemia is caused by lack of the enzyme needed to metabolize tyrosine. The most common form of this disorder mostly affects the liver and the kidneys.

Alkaptonuria occurs when your body can’t produce enough of an enzyme called homogentisic dioxygenase (HGD). The buildup of homogentisic acid causes your bones and cartilage to become discolored and brittle. Albinism is a disease characterized by lack of skin pigments due to a deficiency in the enzyme tyrosinase which converts tyrosine to melanin-based pigments.

YOUR NOTES

69. Cholesterol Mediated Activation Of SREBP

YOUR NOTES

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Lipid homeostasis in vertebrate cells is regulated by a family of membrane-bound transcription factors designated sterol regulatory element–binding proteins (SREBPs).

Each SREBP precursor of about 1150 amino acids is organized into three domains: (a) an NH2-terminal domain of about 480 amino acids that contains the bHLH-Zip region for binding DNA; (b) two hydrophobic transmembrane–spanning segments interrupted by a short loop of about 30 amino acids that projects into the lumen of the ER; and (c) a COOH-terminal domain of about 590 amino acids that performs the essential regulatory function.

Three proteins required for SREBP processing- SCAP, S1P, and S2P.

YOUR NOTES

70. Hyperammonemia and Hyperinsulinemia

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Hyperammonemia is a metabolic condition characterized by elevated levels of ammonia in the blood.

Increased entry of ammonia to the brain is a primary cause of neurologic disorders, such as congenital deficiencies of urea cycle enzymes, hepatic encephalopathies, Reye syndrome, several other metabolic disorders, and some toxic encephalopathies.

Hyperinsulinemia means that the amount of insulin in the blood is higher than considered normal amongst non-diabetics.

When a person has hyperinsulinemia they have a problem controlling blood sugar, meaning that the pancreas has to secrete larger amounts of insulin to keep blood sugar at a normal level.