NEET MDS Lessons
Biochemistry
Glycolysis enzymes are located in the cytosol of cells. Pyruvate enters the mitochondrion to be metabolized further
Mitochondrial compartments: The mitochondrial matrix contains Pyruvate Dehydrogenase and enzymes of Krebs Cycle, plus other pathways such as fatty acid oxidation.
Pyruvate Dehydrogenase catalyzes oxidative decarboxylation of pyruvate, to form acetyl-CoA
FAD (Flavin Adenine Dinucleotide) is a derivative of the B-vitamin riboflavin (dimethylisoalloxazine-ribitol). The flavin ring system undergoes oxidation/reduction as shown below. Whereas NAD+ is a coenzyme that reversibly binds to enzymes, FAD is a prosthetic group, that is permanently part of the complex.
FAD accepts and donates 2 electrons with 2 protons (2 H):
Thiamine pyrophosphate (TPP) is a derivative of thiamine (vitamin B1). Nutritional deficiency of thiamine leads to the disease beriberi. Beriberi affects especially the brain, because TPP is required for carbohydrate metabolism, and the brain depends on glucose metabolism for energy
Acetyl CoA, a product of the Pyruvate Dehydrogenase reaction, is a central compound in metabolism. The "high energy" thioester linkage makes it an excellent donor of the acetate moiety
For example, acetyl CoA functions as:
- input to the Krebs Cycle, where the acetate moiety is further degraded to CO2.
- donor of acetate for synthesis of fatty acids, ketone bodies, and cholesterol.
ATPs formed in TCA cycle from one molecule of Pyruvate
1. 3ATP 7. 3ATP 5. 3 ATP
8. 1 ATP 9. 2 ATP 11.3 ATP Total =15 ATP.
ATPS formed from one molecule of Acetyl CoA =12ATP
ATPs formed from one molecule of glucose after complete oxidation
One molecule of glucose -->2 molecules of pyruvate
['By glycolysis] ->8 ATP
2 molecules of pyruvate [By TCA cycle] -> 30 ATP
Total = 38 ATP
FATTY ACIDS
Fatty acids consist of a hydrocarbon chain with a carboxylic acid at one end.
• are usually in esterified form as major components of other lipids
• are often complexed in triacylglycerols (TAGs)
• most have an even number of carbon atoms (usually 14 to 24)
• are synthesized by concatenation of C2 units.
• C16 & C18 FAs are the most common FAs in higher plants and animals
• Are either:
—saturated (all C-C bonds are single bonds) or
—unsaturated (with one or more double bonds in the chain)
—monounsaturated (a single double bond)
1.Example of monounsaturated FA: Oleic acid 18:1(9) (the number in unsaturated FA parentheses indicates that the double bond is between carbons 9 & 10)
2. Double bonds are almost all in the cis conformation
—polyunsaturated (more then one double bond)
Polyunsaturated fatty acids contain 2 or more double bonds. They usually occur at every third carbon atom towards the methyl terminus (-CH3 ) of the molecule. Example of polyunsaturated FA: Linoleic acid 18:2(9,12)
• the number of double bonds in FAs varies from 1 to 4 (usually), but in most bacteria it is rarely more than 1
Saturated FAs are highly flexible molecules that can assume a wide range of conformations because there is relatively free rotation about their C-C bonds.
LIPIDS
The lipids are a heterogeneous group of compounds, including fats, oils, steroids, waxes, and related compounds, which are related more by their physical than by their chemical properties.
Lipids are non-polar (hydrophobic) compounds, soluble in organic solvents.
Most membrane lipids are amphipathic, having a non-polar end and a polar end
Lipids are important in biological systems because they form the cell membrane, a mechanical barrier that divides a cell from the external environment.
Lipids also provide energy for life and several essential vitamins are lipids.
Lipids can be divided in two major classes, nonsaponifiable lipids and saponifiable lipids.
A nonsaponifiable lipid cannot be broken up into smaller molecules by hydrolysis, which includes triglycerides, waxes, phospholipids, and sphingolipids.
A saponifiable lipid contains one or more ester groups allowing it to undergo hydrolysis in the presence of an acid, base, or enzyme.
Nonsaponifiable lipids include steroids, prostaglandins, and terpenes
Nonpolar lipids, such as triglycerides, are used for energy storage and fuel.
Polar lipids, which can form a barrier with an external water environment, are used in membranes.
Polar lipids include glycerophospholipids and sphingolipids.
Fatty acids are important components of all of these lipids.
Acyl-CoA Synthases (Thiokinases), associated with endoplasmic reticulum membranes and the outer mitochondrial membrane, catalyze activation of long chain fatty acids, esterifying them to coenzyme A, as shown at right. This process is ATP-dependent, and occurs in 2 steps. There are different Acyl-CoA Synthases for fatty acids of different chain lengths.
Exergonic hydrolysis of PPi (P~P), catalyzed by Pyrophosphatase, makes the coupled reaction spontaneous. Overall, two ~P bonds of ATP are cleaved during fatty acid activation. The acyl-coenzyme A product includes one "high energy" thioester linkage.
Summary of fatty acid activation:
- fatty acid + ATP → acyl-adenylate + PPi
PPi → Pi - acyladenylate + HS-CoA → acyl-CoA + AMP
Overall: fatty acid + ATP + HS-CoA → acyl-CoA + AMP + 2 Pi
For most steps of the b-Oxidation Pathway, there are multiple enzymes specific for particular fatty acid chain lengths.
Fatty acid b-oxidation is considered to occur in the mitochondrial matrix. Fatty acids must enter the matrix to be oxidized. However enzymes of the pathway specific for very long chain fatty acids are associated with the inner mitochondrial membrane (facing the matrix).
Fatty acyl-CoA formed outside the mitochondria can pass through the outer mitochondrial membrane, which contains large VDAC channels, but cannot penetrate the mitochondrial inner membrane.
Transfer of the fatty acid moiety across the inner mitochondrial membrane involves carnitine.
Carnitine Palmitoyl Transferases catalyze transfer of a fatty acid between the thiol of Coenzyme A and the hydroxyl on carnitine.
Carnitine-mediated transfer of the fatty acyl moiety into the mitochondrial matrix is a 3-step process, as presented below.
- Carnitine Palmitoyl Transferase I, an enzyme associated with the cytosolic surface of the outer mitochondrial membrane, catalyzes transfer of a fatty acid from ester linkage with the thiol of coenzyme A to the hydroxyl on carnitine.
- Carnitine Acyltransferase, an antiporter in the inner mitochondrial membrane, mediates transmembrane exchange of fatty acyl-carnitine for carnitine.
- Within the mitochondrial matrix (or associated with the matrix surface of the inner mitochondrial membrane, Carnitine Palmitoyl Transferase II catalyzes transfer of the fatty acid from carnitine to coenzyme A. (Carnitine exits the matrix in step 2.) The fatty acid is now esterified to coenzyme A within the mitochondrial matrix
Control of fatty acid oxidation is exerted mainly at the step of fatty acid entry into mitochondria.
Malonyl-CoA inhibits Carnitine Palmitoyl Transferase I. (Malonyl-CoA is also a precursor for fatty acid synthesis). Malonyl-CoA is produced from acetyl-CoA by the enzyme Acetyl-CoA Carboxylase
AMP-Activated Kinase, a sensor of cellular energy levels, catalyzes phosphorylation of Acetyl-CoA Carboxylase under conditions of high AMP (when ATP is low). Phosphorylation inhibits Acetyl-CoA Carboxylase, thereby decreasing malonyl-CoA production.
The decrease in malonyl-CoA concentration releases Carnitine Palmitoyl Transferase I from inhibition. The resulting increase in fatty acid oxidation generates acetyl-CoA for entry into Krebs cycle, with associated production of ATP
Positively Charged (Basic)
| Amino Acid | Side Chain Group |
|---|---|
| Lysine (K) | ε-amino group |
| Arginine (R) | Guanidino group |
| Histidine (H) | Imidazole ring (partially charged at pH 7.4) |
Mnemonic: "His Lies Are Basic" (Histidine, Lysine, Arginine)
Negatively Charged (Acidic)
| Amino Acid | Side Chain Group |
|---|---|
| Aspartate (D) | Carboxyl group |
| Glutamate (E) | Carboxyl group |
Mnemonic: "Acidic Dragons Eat" (D = Aspartate, E = Glutamate)
| Enzyme | Clinical Use | Indicates |
|---|---|---|
| Amylase | Acute pancreatitis | Rises quickly, short half-life |
| Lipase | More specific for pancreatic damage | Stays elevated longer than amylase |
Lipase is preferred for diagnosing pancreatitis due to higher specificity.
Enzymes are protein catalyst produced by a cell and responsible ‘for the high rate’ and specificity of one or more intracellular or extracellular biochemical reactions.
Enzymes are biological catalysts responsible for supporting almost all of the chemical reactions that maintain animal homeostasis. Enzyme reactions are always reversible.
The substance, upon which an enzyme acts, is called as substrate. Enzymes are involved in conversion of substrate into product.
Almost all enzymes are globular proteins consisting either of a single polypeptide or of two or more polypeptides held together (in quaternary structure) by non-covalent bonds. Enzymes do nothing but speed up the rates at which the equilibrium positions of reversible reactions are attained.
In terms of thermodynamics, enzymes reduce the activation energies of reactions, enabling them to occur much more readily at low temperatures - essential for biological systems.