BDS Biochemistry Syllabus

What is an enzyme, and what is its chemical nature?

An enzyme is a biological catalyst that speeds up biochemical reactions by lowering activation energy without being consumed. Most enzymes are proteins; some are catalytic RNA molecules (ribozymes).

Name the six IUBMB classes of enzymes.

1. Oxidoreductases, 2. Transferases, 3. Hydrolases, 4. Lyases, 5. Isomerases, 6. Ligases (synthetases).

Distinguish between an apoenzyme, cofactor, coenzyme, and holoenzyme.

Apoenzyme: the inactive protein part. Cofactor: a non-protein helper (metal ion or organic). Coenzyme: an organic cofactor (often vitamin-derived, e.g., NAD+). Holoenzyme: apoenzyme + cofactor = the active, complete enzyme.

Explain the 'lock-and-key' vs 'induced-fit' models of enzyme action.

Lock-and-key: the substrate fits a rigid, pre-shaped active site. Induced-fit: the active site is flexible and changes conformation upon substrate binding to achieve optimal fit and catalysis.

State the Michaelis-Menten equation and define $K_m$.

$$v = \frac{V_{max}[S]}{K_m + [S]}$$ where $K_m$ is the substrate concentration at which reaction velocity is half of $V_{max}$; a low $K_m$ indicates high enzyme–substrate affinity.

What does the Lineweaver-Burk (double-reciprocal) plot represent?

A linear transformation of the Michaelis-Menten equation: $$\frac{1}{v} = \frac{K_m}{V_{max}}\cdot\frac{1}{[S]} + \frac{1}{V_{max}}$$ The x-intercept gives $-1/K_m$ and the y-intercept gives $1/V_{max}$.

List the main factors affecting enzyme activity.

Substrate concentration, enzyme concentration, temperature, pH, and the presence of activators or inhibitors (and cofactors/coenzymes).

How do temperature and pH affect enzyme activity?

Activity increases with temperature up to an optimum (~37°C in humans), then falls sharply due to denaturation. Each enzyme has an optimum pH (e.g., pepsin ~2, most enzymes ~7); deviation reduces activity by altering ionization/structure.

Compare competitive and non-competitive enzyme inhibition.

Competitive: inhibitor resembles substrate and binds the active site; increases apparent $K_m$, $V_{max}$ unchanged (overcome by more substrate). Non-competitive: inhibitor binds elsewhere; $V_{max}$ decreases, $K_m$ unchanged.

What is feedback (allosteric) inhibition?

Regulation in which the end product of a metabolic pathway inhibits an earlier enzyme (usually the committed/regulatory step) by binding to an allosteric site, preventing overproduction.

How are carbohydrates classified?

Monosaccharides (e.g., glucose, fructose), disaccharides (e.g., sucrose, lactose, maltose), oligosaccharides, and polysaccharides (e.g., starch, glycogen, cellulose).

Distinguish reducing from non-reducing sugars, with examples.

Reducing sugars have a free anomeric ($\ce{-CHO}$ or ketone) group that can reduce Cu²⁺ (positive Benedict's test), e.g., glucose, maltose, lactose. Non-reducing sugars lack a free group, e.g., sucrose, where both anomeric carbons are linked.

What is glycolysis and its net ATP yield?

Glycolysis is the cytoplasmic breakdown of one glucose into two pyruvate molecules. Net yield: 2 ATP, 2 NADH, and 2 pyruvate per glucose (4 ATP produced − 2 ATP consumed).

Write the overall reaction and location of the citric acid (Krebs) cycle.

Occurs in the mitochondrial matrix. Per acetyl-CoA it yields 3 NADH, 1 $\ce{FADH2}$, 1 GTP, and 2 $\ce{CO2}$. Overall: $\ce{Acetyl-CoA + 3NAD^+ + FAD + GDP + Pi + 2H2O -> 2CO2 + 3NADH + FADH2 + GTP + CoA}$.

What is the total ATP yield from complete oxidation of one glucose molecule?

Approximately 30–32 ATP (modern estimate), via glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation.

How is blood glucose regulated hormonally?

Insulin (from pancreatic $\beta$-cells) lowers blood glucose by promoting uptake, glycogenesis, and glycolysis. Glucagon (from $\alpha$-cells), along with epinephrine and cortisol, raises glucose via glycogenolysis and gluconeogenesis.

What is the clinical significance of the fasting blood glucose level in diagnosing diabetes?

Normal fasting glucose is $70$–$100$ mg/dL. A fasting value $\geq 126$ mg/dL (on two occasions) or HbA1c $\geq 6.5\%$ is diagnostic of diabetes mellitus.

How are lipids classified?

Simple lipids (triacylglycerols, waxes), compound/complex lipids (phospholipids, glycolipids, lipoproteins), and derived lipids (fatty acids, steroids, ketone bodies, fat-soluble vitamins).

What is the difference between saturated and unsaturated fatty acids?

Saturated fatty acids have no C=C double bonds (e.g., palmitic, stearic) and are typically solid at room temperature; unsaturated fatty acids have one or more double bonds (e.g., oleic, linoleic) and are usually liquid (oils).

Describe $\beta$-oxidation of fatty acids and its ATP significance.

$\beta$-oxidation occurs in the mitochondrial matrix, sequentially removing two-carbon units as acetyl-CoA. Each cycle yields 1 $\ce{FADH2}$ and 1 NADH; the acetyl-CoA enters the Krebs cycle, making fat a highly energy-dense fuel.

What are ketone bodies, and when are they formed?

Ketone bodies are acetoacetate, $\beta$-hydroxybutyrate, and acetone, formed in the liver from excess acetyl-CoA during starvation, prolonged fasting, or uncontrolled diabetes. Overproduction causes ketoacidosis.

List the major lipoproteins and their roles.

Chylomicrons (transport dietary lipids), VLDL (endogenous triglycerides from liver), LDL ('bad' cholesterol, delivers cholesterol to tissues), and HDL ('good' cholesterol, reverse transport to liver).

What is the clinical importance of the LDL:HDL cholesterol ratio?

High LDL and low HDL increase the risk of atherosclerosis and coronary heart disease; a higher HDL proportion is protective because HDL removes cholesterol from tissues to the liver for excretion.

Describe the double-helix structure of DNA (Watson-Crick model).

Two antiparallel polynucleotide strands wound in a right-handed double helix; sugar-phosphate backbones outside, bases inside. Complementary base pairing: adenine=thymine (2 H-bonds), guanine≡cytosine (3 H-bonds).

State Chargaff's rules for DNA base composition.

In double-stranded DNA, the amount of adenine equals thymine and guanine equals cytosine: $[A]=[T]$ and $[G]=[C]$; therefore total purines equal total pyrimidines ($A+G = T+C$).

How does RNA differ structurally from DNA?

RNA is usually single-stranded, contains ribose (with a 2'-OH) instead of deoxyribose, and uses uracil instead of thymine. DNA is double-stranded, contains deoxyribose, and uses thymine.

Name the three main types of RNA and their functions.

mRNA (messenger) carries the genetic code from DNA to ribosomes; tRNA (transfer) brings amino acids to the ribosome and reads codons via anticodons; rRNA (ribosomal) forms the structural/catalytic core of ribosomes.

What is the central dogma of molecular biology?

The flow of genetic information: $$\text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}$$ (with DNA replication and, in retroviruses, reverse transcription of RNA to DNA).

Define transcription and translation in gene expression.

Transcription: synthesis of an mRNA copy from a DNA template by RNA polymerase (in the nucleus). Translation: decoding of mRNA codons by ribosomes and tRNA to assemble a polypeptide (in the cytoplasm).

What is a codon, and how many code for amino acids?

A codon is a triplet of mRNA nucleotides specifying one amino acid or a stop signal. Of the 64 possible codons, 61 code for amino acids and 3 (UAA, UAG, UGA) are stop codons; AUG is the start codon (methionine).

Name the four fat-soluble vitamins and one deficiency disease of each.

Vitamin A (deficiency: night blindness/xerophthalmia), vitamin D (rickets/osteomalacia), vitamin E (hemolytic anemia/neuropathy), and vitamin K (bleeding due to impaired clotting). They require dietary fat and bile for absorption.