PGIMER Entrance Biochemistry Syllabus

What is the rate-limiting enzyme of the TCA cycle, and how many ATP equivalents does one turn yield?

Isocitrate dehydrogenase is rate-limiting. One turn yields 3 NADH, 1 FADH2, 1 GTP (≈10 ATP); ~25 ATP per glucose from two turns.

Where does oxidative phosphorylation occur and what drives ATP synthesis?

In the inner mitochondrial membrane; the electron transport chain pumps protons creating an electrochemical gradient (proton-motive force) that drives ATP synthase (chemiosmotic theory).

List the complexes of the electron transport chain and their electron carriers.

Complex I (NADH dehydrogenase), Complex II (succinate dehydrogenase), Complex III (cytochrome bc1), Complex IV (cytochrome c oxidase); mobile carriers: coenzyme Q (ubiquinone) and cytochrome c.

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

Approximately 30-32 ATP (using current consensus: ~2.5 ATP/NADH and ~1.5 ATP/FADH2).

What is the rate-limiting enzyme of gluconeogenesis, and which four enzymes bypass the irreversible glycolytic steps?

Fructose-1,6-bisphosphatase is rate-limiting. The four bypass enzymes: pyruvate carboxylase, PEP carboxykinase, fructose-1,6-bisphosphatase, and glucose-6-phosphatase.

Why can't fatty acids (acetyl-CoA) be used for net glucose synthesis in humans?

The pyruvate dehydrogenase reaction is irreversible, and the two carbons of acetyl-CoA entering the TCA cycle are lost as CO2; there is no pathway to convert acetyl-CoA to pyruvate/oxaloacetate net.

Name the key enzymes of glycogen synthesis and breakdown and their regulation.

Synthesis: glycogen synthase (rate-limiting). Breakdown: glycogen phosphorylase (rate-limiting). Glucagon/epinephrine activate phosphorylase and inhibit synthase via cAMP-PKA phosphorylation; insulin reverses this.

What enzyme deficiency causes von Gierke disease (GSD type I) and McArdle disease (GSD type V)?

Von Gierke (type I): glucose-6-phosphatase deficiency. McArdle (type V): muscle glycogen phosphorylase deficiency.

Where does beta-oxidation occur and how is long-chain fatty acyl-CoA transported into the mitochondria?

In the mitochondrial matrix; transported via the carnitine shuttle, with carnitine palmitoyltransferase I (CPT-I) being the rate-limiting step (inhibited by malonyl-CoA).

What are the products of one cycle of beta-oxidation, and the net ATP from palmitate (C16)?

Each cycle yields 1 acetyl-CoA, 1 FADH2, 1 NADH. Complete oxidation of palmitate yields ~106 ATP (7 cycles → 8 acetyl-CoA, 7 FADH2, 7 NADH).

Name the three ketone bodies and where ketogenesis occurs.

Acetoacetate, beta-hydroxybutyrate, and acetone; ketogenesis occurs in liver mitochondria. (Note: acetone is a non-utilizable byproduct.)

Why can't the liver use ketone bodies it produces, and what enzyme is responsible?

The liver lacks thiophorase (succinyl-CoA:acetoacetate CoA transferase), which is needed to activate acetoacetate for utilization in peripheral tissues.

In which organ and cellular location does the urea cycle occur, and what is its rate-limiting enzyme?

In the liver, partly in mitochondria and partly in cytosol; rate-limiting enzyme is carbamoyl phosphate synthetase I (CPS-I), activated by N-acetylglutamate.

List the intermediates of the urea cycle in order.

Carbamoyl phosphate → Citrulline → Argininosuccinate → Arginine → Ornithine (which is regenerated); urea is released from arginine by arginase.

How are the two nitrogen atoms of urea derived?

One nitrogen comes from free ammonia (via carbamoyl phosphate) and the other from aspartate; the carbon comes from CO2.

Classify amino acids as glucogenic, ketogenic, or both, with examples.

Purely ketogenic: Leucine and Lysine. Both glucogenic and ketogenic: Ile, Phe, Trp, Tyr, Thr. The rest are glucogenic.

What is the enzyme defect and accumulated substance in phenylketonuria (PKU)?

Deficiency of phenylalanine hydroxylase (or BH4 cofactor); phenylalanine accumulates and is converted to phenylketones, causing intellectual disability if untreated.

What enzyme deficiency causes alkaptonuria, and what is its hallmark sign?

Homogentisate oxidase deficiency; homogentisic acid accumulates, causing dark urine on standing and ochronosis (dark connective tissue/cartilage).

What enzyme deficiency causes maple syrup urine disease (MSUD)?

Deficiency of branched-chain alpha-ketoacid dehydrogenase, causing accumulation of branched-chain amino acids (Leu, Ile, Val) and their keto-acids; urine smells like maple syrup.

Distinguish leading and lagging strand synthesis in DNA replication.

The leading strand is synthesized continuously 5'→3' toward the replication fork; the lagging strand is synthesized discontinuously as Okazaki fragments away from the fork, later joined by DNA ligase.

What are the main enzymes of DNA replication and their functions?

Helicase (unwinds DNA), Primase (RNA primers), DNA polymerase (synthesizes 5'→3'), Topoisomerase/gyrase (relieves supercoiling), DNA ligase (seals nicks), Single-strand binding proteins (stabilize).

Name the three RNA polymerases in eukaryotes and what each transcribes.

RNA Pol I → rRNA; RNA Pol II → mRNA (and most snRNA); RNA Pol III → tRNA and 5S rRNA.

What are the key post-transcriptional modifications of eukaryotic mRNA?

5' capping (7-methylguanosine), 3' polyadenylation (poly-A tail), and splicing (removal of introns, joining of exons).

Describe the role of the genetic code's properties: degeneracy and wobble.

Degeneracy: multiple codons encode the same amino acid (64 codons, 20 amino acids). Wobble: the third codon base can pair flexibly with the tRNA anticodon, allowing one tRNA to read multiple codons.

What are the start and stop codons in translation?

Start codon: AUG (methionine). Stop codons: UAA, UAG, UGA (no corresponding tRNA; recognized by release factors).

Explain the lac operon's regulation in E. coli.

It is an inducible operon; in the absence of lactose, a repressor binds the operator blocking transcription. Lactose (allolactose) inactivates the repressor (induction). Low glucose raises cAMP, which with CAP enhances transcription (positive control).

Classify gene mutations: silent, missense, nonsense, and frameshift.

Silent: no amino acid change. Missense: one amino acid changed. Nonsense: codon changed to a stop codon (truncated protein). Frameshift: insertion/deletion not a multiple of 3, altering the reading frame.

Define transition vs transversion point mutations.

Transition: substitution of a purine for a purine or pyrimidine for a pyrimidine (A↔G, C↔T). Transversion: substitution of a purine for a pyrimidine or vice versa.

What are the three steps of each PCR cycle and their approximate temperatures?

Denaturation (~94-95°C, separates strands), Annealing (~50-65°C, primers bind), and Extension (~72°C, Taq polymerase synthesizes new strands).

Match each blotting technique to the molecule it detects: Southern, Northern, Western.

Southern blot → DNA; Northern blot → RNA; Western blot → protein (detected with antibodies).

What are restriction endonucleases and their role in recombinant DNA technology?

Enzymes that cut DNA at specific palindromic recognition sequences, often producing 'sticky ends'; used to cut DNA and vectors for cloning, with DNA ligase joining fragments into recombinant DNA.

List the fat-soluble vitamins and a key deficiency of each.

Vitamin A (night blindness/xerophthalmia), Vitamin D (rickets/osteomalacia), Vitamin E (hemolytic anemia/neuropathy), Vitamin K (bleeding/impaired coagulation).

What deficiencies result from lack of vitamin C, niacin (B3), and thiamine (B1)?

Vitamin C: scurvy (impaired collagen, bleeding gums). Niacin: pellagra (dermatitis, diarrhea, dementia). Thiamine: beriberi and Wernicke-Korsakoff syndrome.

What is the role of vitamin B12 and folate, and what deficiency do they share?

Both are needed for DNA synthesis (one-carbon metabolism); deficiency of either causes megaloblastic anemia. B12 deficiency additionally causes neurological damage (subacute combined degeneration).

Name key functions and deficiency signs of iron, iodine, and zinc.

Iron: hemoglobin/oxygen transport (deficiency → microcytic anemia). Iodine: thyroid hormone synthesis (deficiency → goiter/hypothyroidism). Zinc: cofactor for many enzymes (deficiency → poor wound healing, dermatitis, hypogeusia).

What are reactive oxygen species (ROS), and name three major examples.

Highly reactive oxygen-containing molecules that damage lipids, proteins, and DNA; examples: superoxide anion (O2·-), hydrogen peroxide (H2O2), and hydroxyl radical (·OH).

Name the three major enzymatic antioxidant defenses and the reactions they catalyze.

Superoxide dismutase (SOD): converts O2·- to H2O2; Catalase: converts H2O2 to H2O + O2; Glutathione peroxidase (selenium-dependent): reduces H2O2 and lipid peroxides using glutathione.

Name important non-enzymatic antioxidants.

Vitamin C (ascorbate), Vitamin E (tocopherol, lipid-phase), beta-carotene, glutathione (GSH), and uric acid.

What is the Warburg effect in cell metabolism?

The tendency of cancer cells to preferentially use aerobic glycolysis (converting glucose to lactate even with oxygen present) rather than oxidative phosphorylation.