A Few Biochemistry points to start with..

Biochemistry: Carbohydrates and Lipids

Bioenergetics: Role of ATP

1. First law of thermodynamics states that the total energy of a system, including its surroundings, remains constant. It implies that within the total system, energy is neither lost nor gained during any change. The second law of thermodynamics states that the total entropy of a system must increase if a process is to occur spontaneously.

2. ATP contains 3 phosphate groups, adenine and ribose, Mg2+

3. E.g. of high energy phosphates:
1. Acetyl-Co-A, 2. SAM 3. PRPP 4. UDPglc, 5. PEP 6.Creatine phosphate, 6.1, 3-BPG.

4. ATP à ADP DG0= -7.3kcal/mol or -30.5kJ/mol.

5. ATP àAMP + Pi, DG0= -7.7 or -32.2 kJ/mol. Highest energy phosphate is PEP.

6. There are three major sources of ~P taking part in energy conservation or energy capture:
· Oxidative phosphorylation: The greatest quantitative source of ~P in aerobic organisms. Free energy comes from respiratory chain oxidation using molecular O2 within mitochondria.
· Glycolysis: A net formation of two ~P results from the formation of lactate from one molecule of glucose, generated in two reactions catalyzed by phosphoglycerate kinase and pyruvate kinase, respectively.
· The citric acid cycle: One ~P is generated directly in the cycle at the succinyl thiokinase step.

7. Phosphagens act as storage forms of high-energy phosphate and include creatine phosphate, occurring in vertebrate skeletal muscle, heart, spermatozoa, and brain; and arginine phosphate, occurring in invertebrate muscle.

8. Cytochrome oxidase is a hemoprotein; the enzyme is poisoned by carbon monoxide, cyanide, and hydrogen sulfide. The cytochrome oxidase enzyme complex is known as cytochrome aa3. It contains two molecules of heme (2Fe) and 2 atoms of Cu.

9. Xanthine Oxidase and Aldehyde Dehydrogenase contains Molybdenum. Glutathione Peroxidase contains Selenium.

10. All cytochromes are classified as Dehydrogenases except Cytochrome Oxidase.

11. Enzymes of Mitochondria, Outer MM- 1. Glycerophosphate acyl transferase, 2.Acyl CoA Synthetase; Matrix 1. TCA Cycle enzymes 2.Beta Oxidation Enzymes 3. Pyruvate Dehydrogenase, Inner MM 1. ATP Synthase 2. ETC 3. Membrane Transporters.

12. The Electron transport Chain
· Complex I or NADH-Q-Oxidoreductase.
· Complex III or Q-cyt c-Oxidoreductase.
· Complex IV or cytochrome oxidase.
· Complex II or Succinate-Q- Reductase.
Q and Cyt-C are the mobile units. Complex I utilize 5H+. In Complex II (succinate -Q reductase), FADH2 is formed during the conversion of succinate to fumarate in the citric acid cycle. The chemiosmotic theory, proposed by Peter Mitchell, postulates that the two processes are coupled by a proton gradient across the inner mitochondrial membrane so that the proton motive force caused by the electrochemical potential difference (negative on the matrix side) drives the mechanism of ATP synthesis. Complexes I, III, and IV act as proton pumps.

13. The ATP Synthase complex consists of 2 subcomplexes F0 and F1. F1 is a fixed one containing 3 alpha and 3 bets subunits. ATP Synthase has a “bent-axle” consisting of Gamma and Epsilon subunits. F0 consists of multiple ‘C’ units arranged as a disc which rotates while protons pass through them, thereby rotating the axle also, resulting in the formation of 3ATPs from the Beta subunit in one turn.

14. When substrates are oxidized via Complexes I, III, and IV in the respiratory chain (i.e., via NADH), 2.5 mol of ATP are formed per half mol of O2 consumed; i.e., the P: O ratio = 2.5. On the other hand, when a substrate (e.g., succinate or 3-phophoglycerate) is oxidized via Complexes II, III, and IV, only 1.5 mol of ATP are formed; i.e., P:O = 1.5. These reactions are known as oxidative phosphorylation at the respiratory chain level. Most cells in the resting state are in state 4 of respiratory control, i.e., Availability of ADP only.

15. Inhibitors of ETC
Complex I: Amobarbital, Rotenone and Piericidin-A.
Complex II: Malonate, Carboxin and TTFA.
Complex III: BAL/Dimercaprol and Antimycin A
Complex IV: H2S, Cyanide and Carbon Monoxide.
Atractyloside inhibits oxidative phosphorylation by inhibiting the transporter of ADP into and ATP out of the mitochondrion.
Uncouplers dissociate oxidation in the respiratory chain from phosphorylation. E.g. ,4-dinitrophenol, Thermogenin, Oligomycin.
Thermogenin (or the uncoupling protein) is a physiological uncoupler found in brown adipose tissue that functions to generate body heat, particularly for the newborn and during hibernation in animals. The antibiotic oligomycin completely blocks oxidation and phosphorylation by blocking the flow of protons through ATP synthase.

16. The condition known as fatal infantile mitochondrial myopathy and renal dysfunction involves severe diminution or absence of most oxidoreductases of the respiratory chain. MELAS (mitochondrial encephalopathy, lactic acidosis, and stroke) is an inherited condition due to NADH:Q oxidoreductase (Complex I) or cytochrome oxidase (Complex IV) deficiency. It is caused by a mutation in mitochondrial DNA and may be involved in Alzheimer's disease and diabetes mellitus.

17. D and L isomerism: The designation of a sugar isomer as the D form or of its mirror image as the L form is determined by its spatial relationship to the parent compound of the carbohydrates, the three-carbon sugar glycerose (glyceraldehyde). Most of the monosaccharides occurring in mammals are D sugars. The presence of asymmetric carbon atoms also confers optical activity on the compound. When a beam of plane-polarized light is passed through a solution of an optical isomer, it rotates either to the right, dextrarotatory (+), or to the left, levorotatory (–). The direction of rotation of polarized light is independent of the stereochemistry of the sugar, so it may be designated D(–), D(+), L(–), or L(+). For example, the naturally occurring form of fructose is the D(–) isomer. For glucose in solution, more than 99% is in the pyranose form.

18. Alpha and beta anomers: The ring structure of an aldose is a hemiacetal, since it is formed by combination of an aldehyde and an alcohol group. Similarly, the ring structure of a ketose is a hemiketal. Crystalline glucose is Alpha-D-glucopyranose. The cyclic structure is retained in solution, but isomerism occurs about position 1, the carbonyl or anomeric carbon atom.

19. Epimers: Isomers differing as a result of variations in configuration of the —OH and —H on carbon atoms 2, 3, and 4 of glucose are known as epimers. Biologically, the most important epimers of glucose are mannose and galactose, formed by epimerization at carbons 2 and 4, respectively.

20. Excreted in the urine in essential pentosuria- L-Xylulose. An intermediate in the uronic acid pathway- L-gulonate. D-galactosamine is also known as chondrosamine.

21. Lactose may be excreted in the urine in pregnancy. Glycophorin is a major integral membrane glycoprotein of human erythrocytes.
Physiologically Important Lipids

22. Eicosapentaenoic Acid- Timnodonic Acid (fish oil), Docosahexaenoic Acid- Cervonic Acid (6 double Bonds).

23. Ergosterol occurs in plants and yeast and is important as a precursor of vitamin D.

24. Glycerol is a substrate for gluconeogenesis. The fatty acids are transported bound
to serum albumin; they are taken up by most tissues (but not brain or erythrocytes). In the liver, triacylglycerol arising from lipogenesis, free fatty acids, and chylomicron remnants is secreted into the circulation in very low density lipoprotein (VLDL).

25. Flux-Generating Reaction: It may be identified as a nonequilibrium reaction in which the Km of the enzyme is considerably lower than the normal substrate concentration. E.g. hexokinase.

26. Muscle preferentially takes up and metabolizes free fatty acids in the fasting state.
TCA Cycle

27. Isocitrate Dehydrogenase The decarboxylation requires Mg++ or Mn++ ions.

28. Succinyl-CoA is converted to succinate by the enzyme succinate thiokinase (succinyl-CoA synthetase). This is the only example in the citric acid cycle of substrate level phosphorylation. Tissues in which gluconeogenesis occurs (the liver and kidney) contain two isoenzymes of succinate thiokinase, one specific for GDP and the other for ADP. The GTP formed is used for the decarboxylation of oxaloacetate to PEP in gluconeogenesis, and provides a regulatory link between TCA activity and the withdrawal of oxaloacetate for gluconeogenesis.

29. Twelve ATP are formed per turn of the Citric Acid Cycle, three molecules of NADH and one of FADH2 are produced for each molecule of acetyl-CoA catabolized in one turn of the cycle.

30. Vitamins Play Key Roles in the Citric Acid Cycle 4: 1. Flavin-FAD for Succinate Dehydrogenase 2. Niacin NAD 3.Thiamine TPP for Isocitrate Dehydrogenase Decarboxylation 4. Pantothenic Acid – CoEnzyme A

31. Serine-Cystine-Threonine-Glycine-Hydroxyproline, Alanine (ßTryptophan): àà
Pyruvate.

32. Valine, Isoleucine and Methionine VIM be converted into Succinyl CoA, similarly
Tyrosine and Phenylalanine can be coverted into Fumarate.

33. Glutamine, Arginine, Proline and Histidine into GLUTAMATE then into alphaketoglutarate.

34. Glucokinase has a Km very much higher than the normal intracellular concentration of glucose.


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