NEET MDS Lessons
Biochemistry
Glycolysis Pathway
The reactions of Glycolysis take place in the cytosol of cells.
Glucose enters the Glycolysis pathway by conversion to glucose-6-phosphate. Initially, there is energy input corresponding to cleavage of two ~P bonds of ATP.
1. Hexokinase catalyzes: glucose + ATP → glucose-6-phosphate + ADP
ATP binds to the enzyme as a complex with Mg++.
The reaction catalyzed by Hexokinase is highly spontaneous
2. Phosphoglucose Isomerase catalyzes:
glucose-6-phosphate (aldose) → fructose-6-phosphate (ketose)
The Phosphoglucose Isomerase mechanism involves acid/base catalysis, with ring opening, isomerization via an enediolate intermediate, and then ring closure .
3. Phosphofructokinase catalyzes:
fructose-6-phosphate + ATP → fructose-1,6-bisphosphate + ADP
The Phosphofructokinase reaction is the rate-limiting step of Glycolysis. The enzyme is highly regulated.
4. Aldolase catalyzes:
fructose-1,6-bisphosphate → dihydroxyacetone phosphate + glyceraldehyde-3-phosphate
The Aldolase reaction is an aldol cleavage, the reverse of an aldol condensation.
5. Triose Phosphate Isomerase (TIM) catalyzes
dihydroxyacetone phosphate (ketose) → glyceraldehyde-3-phosphate (aldose)
Glycolysis continues from glyceraldehydes-3-phosphate
The equilibrium constant (Keq) for the TIM reaction favors dihydroxyacetone phosphate, but removal of glyceraldehyde-3-phosphate by a subsequent spontaneous reaction allows throughput.
6. Glyceraldehyde-3-phosphate Dehydrogenase catalyzes:
glyceraldehyde-3-phosphate + NAD+ + Pi → 1,3,bisphosphoglycerate + NADH + H+
This is the only step in Glycolysis in which NAD+ is reduced to NADH
A cysteine thiol at the active site of Glyceraldehyde-3-phosphate Dehydrogenase has a role in catalysis .
7. Phosphoglycerate Kinase catalyzes:
1,3-bisphosphoglycerate + ADP → 3-phosphoglycerate + ATP
This transfer of phosphate to ADP, from the carboxyl group on 1,3-bisphosphoglycerate, is reversible
8. Phosphoglycerate Mutase catalyzes: 3-phosphoglycerate → 2-phosphoglycerate
Phosphate is shifted from the hydroxyl on C3 of 3-phosphoglycerate to the hydroxyl on C2.
9. Enolase catalyzes: 2-phosphoglycerate → phosphoenolpyruvate + H2O
This Mg++-dependent dehydration reaction is inhibited by fluoride. Fluorophosphate forms a complex with Mg++ at the active site .
10. Pyruvate Kinase catalyzes: phosphoenolpyruvate + ADP → pyruvate + ATP
This transfer of phosphate from PEP to ADP is spontaneous.
Balance sheet for high energy bonds of ATP:
- 2 ATP expended
- 4 ATP produced (2 from each of two 3C fragments from glucose)
- Net Production of 2~ P bonds of ATP per glucose
| Enzyme | Clinical Use | Timing |
|---|---|---|
| Troponin I/T | Gold standard for myocardial infarction | Rises in 3–6 hrs, peaks at 12–24 hrs |
| CK-MB | Specific to cardiac muscle damage | Rises in 4–6 hrs, peaks at 24 hrs |
| LDH (Isoenzyme 1) | Used historically for MI diagnosis | Peaks at 48–72 hrs |
Troponins remain elevated for up to 10 days—ideal for late diagnosis.
ESSENTIAL FATTY ACIDS (EFAs) Polyunsaturated FAs,such as Linoleic acid and g(gamma)- Linolenic acid, are ESSENTIAL FATTY ACIDS — we cannot make them, and we need them, so we must get them in our diets mostly from plant sources.
The basic characteristics of enzymes includes
(i) Almost all the enzymes are proteins and they follow the physical and chemical reactions of proteins (ii) Enzymes are sensitive and labile to heat
(iii) Enzymes are water soluble
(iv) Enzymes could be precipitated by protein precipitating agents such as ammonium sulfate and trichloroacetic acid.
Acids and bases can be classified as proton donors and proton acceptors, respectively. This means that the conjugate base of a given acid will carry a net charge that is more negative than the corresponding acid. In biologically relavent compounds various weak acids and bases are encountered, e.g. the acidic and basic amino acids, nucleotides, phospholipids etc.
Weak acids and bases in solution do not fully dissociate and, therefore, there is an equilibrium between the acid and its conjugate base. This equilibrium can be calculated and is termed the equilibrium constant = Ka. This is also referred to as the dissociation constant as it pertains to the dissociation of protons from acids and bases.
In the reaction of a weak acid:
HA <-----> A- + H+
the equlibrium constant can be calculated from the following equation:
Ka = [H+][A-]/[HA]
As in the case of the ion product:
pKa = -logKa
Therefore, in obtaining the -log of both sides of the equation describing the dissociation of a weak acid we arrive at the following equation:
-logKa = -log[H+][A-]/[HA]
Since as indicated above -logKa = pKa and taking into account the laws of logrithms:
pKa = -log[H+] -log[A-]/[HA]
pKa = pH -log[A-]/[HA]
From this equation it can be seen that the smaller the pKa value the stronger is the acid. This is due to the fact that the stronger an acid the more readily it will give up H+ and, therefore, the value of [HA] in the above equation will be relatively small.
Protein folding is essential for proper biological function. When folding goes wrong, it can trigger a cascade of pathological effects. Here are three key examples:
1. Alzheimer’s Disease
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Misfolded Protein: Amyloid-β (Aβ) and tau
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Mechanism:
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Aβ peptides misfold and aggregate into amyloid plaques in the brain.
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Tau proteins form neurofibrillary tangles inside neurons.
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Impact:
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Neuronal death, memory loss, cognitive decline.
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Progressive neurodegeneration.
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Fun Fact: These plaques can be seen in brain imaging and are a hallmark of Alzheimer’s pathology.
2. Prion Diseases (e.g., Mad Cow Disease, Creutzfeldt-Jakob Disease)
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Misfolded Protein: Prion protein (PrP^Sc)
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Mechanism:
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Normal prion protein (PrP^C) misfolds into a pathogenic form (PrP^Sc).
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PrP^Sc induces other prion proteins to misfold, creating a chain reaction.
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Impact:
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Rapid brain degeneration, motor dysfunction, fatal outcomes.
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No immune response—prions are host proteins, not foreign invaders.
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Unique Feature: Prions are infectious proteins—no DNA or RNA involved.
3. Sickle Cell Anemia
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Misfolded Protein: Hemoglobin (HbS mutation)
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Mechanism:
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A single amino acid substitution (valine for glutamic acid) in β-globin.
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Causes hemoglobin to polymerize under low oxygen, distorting red blood cells into a sickle shape.
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Impact:
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Blocked blood flow, pain crises, organ damage.
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Reduced oxygen-carrying capacity.
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Note: Unlike amyloid diseases, this is a structural misfolding due to a genetic mutation.
Enzyme assays measure the activity or concentration of specific enzymes in blood or tissue samples. Elevated or reduced levels often indicate organ dysfunction or cellular damage.
Enzyme Groups & Their Clinical Significance
| Enzyme Group | Function | Clinical Relevance |
|---|---|---|
| Oxidoreductases | Catalyze oxidation-reduction reactions | Liver, cardiac, and muscle injury markers |
| Transferases | Transfer functional groups between molecules | Liver and muscle enzymes (e.g., AST, ALT) |
| Hydrolases | Break chemical bonds using water | Pancreatic enzymes (e.g., amylase, lipase) |
| Lyases | Break bonds without hydrolysis or oxidation | Less commonly used in diagnostics |
| Isomerases | Rearrange molecular structures | Rarely used clinically |
| Ligases | Join molecules using ATP | Mostly research-based, not routine diagnostics |