MBBS Bio Chemistry Syllabus

Bio Chemistry syllabus — full chapter and topic list

Expand any chapter to see its topics and sub-topics. This is the whole examinable outline for Bio Chemistry in MBBS, not a summary of it.

1. 1

   Molecular Biology

   5 topics

   • Structure and function of nucleic acids: DNA and RNA
   • DNA replication
     • Enzymes involved
     • Replication fork
     • Leading and lagging strands
   • Transcription
     • RNA polymerase
     • mRNA synthesis
     • Transcription factors
     • Regulation
   • Translation
     • Ribosomes
     • tRNA
     • Codons
     • Initiation
     • Elongation
     • Termination
     • Regulation
   • Genetic code
     • Codons
     • Amino acids
     • Start and stop codons
     • Wobble hypothesis
2. 2

   Proteins

   5 topics

   • Amino acids
     • Classification
     • Structure
     • Properties
     • Essential vs. non-essential amino acids
   • Protein structure
     • Primary structure
     • Secondary structure
     • Tertiary structure
     • Quaternary structure
   • Protein folding and stability
     • Chaperones
     • Denaturation
     • Refolding
   • Enzymes
     • Classification
     • Mechanism of enzyme action
     • Kinetics
     • Enzyme regulation
   • Enzyme inhibitors
     • Competitive inhibitors
     • Non-competitive inhibitors
     • Mixed inhibitors
3. 3

   Carbohydrate Metabolism

   5 topics

   • Glycolysis
     • Pathway
     • Enzymes
     • Regulation
     • Energetics
   • Gluconeogenesis
     • Pathway
     • Substrates
     • Enzymes
     • Regulation
   • Pentose Phosphate Pathway
     • Functions
     • Significance
   • Glycogen Metabolism
     • Synthesis
     • Degradation
     • Regulation
   • Citric Acid Cycle (Krebs Cycle)
     • Steps
     • Enzymes
     • Regulation
     • Metabolic Significance
4. 4

   Lipid Metabolism

   4 topics

   • Fatty acid metabolism
     • β-oxidation
     • Synthesis
     • Desaturation
     • Elongation
   • Triacylglycerol metabolism
     • Synthesis
     • Breakdown
     • Regulation
   • Lipoprotein metabolism
     • Classification
     • Structure
     • Functions
     • Role in lipid transport
   • Ketone bodies
     • Synthesis
     • Utilization
     • Regulation
5. 5

   Amino Acid Metabolism

   3 topics

   • Overview of amino acid metabolism
     • Transamination
     • Deamination
     • Urea cycle
   • Metabolism of specific amino acids
     • Glucogenic vs. ketogenic amino acids
   • One-carbon metabolism
     • Methylation reactions
     • Folate metabolism
     • Vitamin B12
6. 6

   Bioenergetics and Oxidative Phosphorylation

   3 topics

   • ATP synthesis
     • Chemiosmotic hypothesis and mitochondrial electron transport chain
   • Regulation of oxidative phosphorylation
   • Mitochondrial disorders and their biochemical basis
7. 7

   Intermediary Metabolism

   2 topics

   • Regulation of metabolic pathways
     • Hormonal regulation
     • Allosteric regulation
     • Covalent modification
   • Integration of metabolism
     • Metabolic interconversions
     • Metabolic flux
     • Energy balance
8. 8

   Hormones and Signal Transduction

   2 topics

   • Hormone classification
     • Endocrine vs. exocrine hormones
     • Peptide hormones
     • Steroid hormones
     • Mechanisms of action
   • Signal transduction pathways
     • Second messengers
     • G-proteins
     • Protein kinases
     • Gene regulation
9. 9

   Nutrition and Vitamins

   2 topics

   • Essential Nutrients
     • Macronutrients (carbohydrates, proteins, fats)
     • Micronutrients (vitamins, minerals)
   • Functions, Sources, and Deficiencies of Vitamins
     • Fat-soluble vitamins (A, D, E, K)
     • Water-soluble vitamins (B-complex, C)
10. 10

    Biochemical Techniques

    1 topic

    • Principles and applications of biochemical techniques
      • Spectrophotometry
      • Chromatography
      • Electrophoresis
      • PCR
      • DNA sequencing
      • Recombinant DNA technology

Bio Chemistry flashcards for MBBS

24 of 62 cards from the Bio Chemistry deck — real questions with worked answers.

1. What are the building blocks (monomers) of nucleic acids, and what three components make up each one?

   The monomers are nucleotides. Each nucleotide consists of three components: (1) a nitrogenous base, (2) a pentose sugar (ribose in RNA, deoxyribose in DNA), and (3) one or more phosphate groups.

2. Classify the nitrogenous bases of nucleic acids into purines and pyrimidines.

   Purines (double-ring): Adenine (A) and Guanine (G). Pyrimidines (single-ring): Cytosine (C), Thymine (T, in DNA), and Uracil (U, in RNA).

3. State Chargaff's rules for double-stranded DNA base composition.

   In dsDNA, $[A] = [T]$ and $[G] = [C]$; therefore the total purines equal the total pyrimidines: $[A]+[G] = [T]+[C]$. The ratio $\frac{A+T}{G+C}$ is characteristic of a species.

4. Describe the base-pairing rules and hydrogen bonding in the DNA double helix.

   Adenine pairs with Thymine via 2 hydrogen bonds; Guanine pairs with Cytosine via 3 hydrogen bonds. The strands are antiparallel and complementary, which is why $\ce{G\bond{...}C}$-rich DNA is more thermally stable.

5. What is the structure of B-DNA (Watson–Crick model) including helix sense, diameter, and rise per turn?

   B-DNA is a right-handed double helix about $2\ \text{nm}$ ($20\ \text{\AA}$) in diameter, with $\approx 10.5$ base pairs per turn and a pitch (rise) of $\approx 3.4\ \text{nm}$ per turn ($0.34\ \text{nm}$ per base pair). It has a major and a minor groove.

6. List the key structural differences between DNA and RNA.

   DNA: deoxyribose sugar, base thymine, usually double-stranded, stable. RNA: ribose sugar (2'-OH), base uracil instead of thymine, usually single-stranded, less stable. The 2'-OH makes RNA more susceptible to alkaline hydrolysis.

7. Name the three major types of RNA and their functions in protein synthesis.

   mRNA (messenger) carries the genetic code from DNA to ribosomes; tRNA (transfer) brings amino acids and reads codons via its anticodon; rRNA (ribosomal) is the structural and catalytic component of ribosomes (a ribozyme catalyzing peptide bond formation).

8. In which direction is the DNA daughter strand synthesized, and what does this imply about leading vs lagging strands?

   DNA polymerase synthesizes only in the $5' \to 3'$ direction. The leading strand is synthesized continuously; the lagging strand is synthesized discontinuously as Okazaki fragments, later joined by DNA ligase.

9. What is meant by semiconservative DNA replication (Meselson–Stahl)?

   Each new double helix retains one parental (old) strand and one newly synthesized strand. Thus after one round of replication each daughter molecule is half old and half new.

10. Name the major enzymes/proteins of the DNA replication fork and their roles.

    Helicase unwinds the duplex; single-strand binding proteins stabilize ssDNA; topoisomerase/gyrase relieves supercoiling; primase lays down RNA primers; DNA polymerase extends; DNA ligase seals nicks. In E. coli, Pol III is the main replicase and Pol I removes primers.

11. Why is an RNA primer required in DNA replication, and how is it removed?

    DNA polymerase cannot initiate synthesis de novo; it can only add to a free 3'-OH. Primase makes a short RNA primer providing that 3'-OH. The primer is later removed (by RNase H / DNA Pol I 5'→3' exonuclease in prokaryotes) and replaced with DNA.

12. Define transcription and name the enzyme responsible in eukaryotes for mRNA synthesis.

    Transcription is the synthesis of an RNA copy from a DNA template strand. In eukaryotes, RNA polymerase II synthesizes mRNA (Pol I makes rRNA; Pol III makes tRNA and 5S rRNA).

13. What are the three stages of transcription and the role of the promoter?

    Initiation (RNA polymerase binds the promoter, e.g. TATA box, and opens the duplex), elongation (RNA synthesized $5' \to 3'$ using the template strand), and termination (RNA released). The promoter is the DNA sequence that directs where transcription begins.

14. Describe the three main post-transcriptional modifications of eukaryotic pre-mRNA.

    (1) Addition of a 7-methylguanosine 5' cap, (2) addition of a 3' poly(A) tail, and (3) splicing to remove introns and join exons (carried out by the spliceosome).

15. Define translation and identify where it occurs.

    Translation is the synthesis of a polypeptide from the mRNA codon sequence. It occurs on ribosomes in the cytoplasm (or on rough endoplasmic reticulum for secretory/membrane proteins).

16. What are the three stages of translation and the start/stop signals?

    Initiation (ribosome assembles at the start codon $\text{AUG}$, coding for Met/fMet), elongation (peptide bonds formed in the $\text{N} \to \text{C}$ direction), and termination at a stop codon (UAA, UAG, or UGA) by release factors.

17. What are the A, P, and E sites of the ribosome?

    A (aminoacyl) site accepts the incoming aminoacyl-tRNA; P (peptidyl) site holds the tRNA bearing the growing polypeptide chain; E (exit) site holds the deacylated tRNA before it leaves the ribosome.

18. State the key properties of the genetic code (degeneracy, universality, non-overlapping, commaless).

    The code is triplet (3 bases = 1 codon), degenerate (most amino acids have more than one codon), non-overlapping and commaless (read in continuous triplets), nearly universal across species, and unambiguous (each codon specifies only one amino acid).

19. How many codons exist, how many code for amino acids, and what are the stop codons?

    There are $4^{3} = 64$ codons. 61 specify amino acids and 3 are stop (nonsense) codons: UAA, UAG, UGA. AUG is the start codon and also codes for methionine.

20. What is the wobble hypothesis?

    The wobble hypothesis states that the third base of a codon can form non-standard (loose) pairing with the first base of the tRNA anticodon. This allows a single tRNA to recognize more than one codon, explaining the degeneracy of the genetic code.

21. What is the general structure of an α-amino acid at physiological pH?

    An α-amino acid has a central α-carbon bonded to an amino group, a carboxyl group, a hydrogen, and a variable R side chain. At physiological pH it exists as a zwitterion: the amino group is protonated ($\ce{-NH3+}$) and the carboxyl is deprotonated ($\ce{-COO^-}$).

22. How many standard amino acids are there, and how are they classified by side chain polarity?

    There are 20 standard amino acids. They are classified as nonpolar/hydrophobic (e.g. Gly, Ala, Val, Leu), polar uncharged (e.g. Ser, Thr, Cys, Gln), acidic/negatively charged (Asp, Glu), and basic/positively charged (Lys, Arg, His).

23. Define the isoelectric point (pI) of an amino acid and how it is calculated for a neutral amino acid.

    The pI is the pH at which the amino acid carries no net charge (exists as a zwitterion). For a simple amino acid with two ionizable groups, $\text{pI} = \frac{pK_{1} + pK_{2}}{2}$, averaging the $pK_a$ values flanking the neutral species.

24. Which amino acids are essential in humans?

    The essential amino acids are Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine (conditionally), Leucine, and Lysine. Mnemonic: "PVT TIM HALL."

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