FMGE 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 FMGE, 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 FMGE

24 of 50 cards from the Bio Chemistry deck — real questions with worked answers.

1. What are the structural differences between DNA and RNA?

   DNA uses deoxyribose sugar, RNA uses ribose (with a 2'-OH). DNA bases are A, T, G, C; RNA replaces thymine with uracil. DNA is typically double-stranded; RNA is usually single-stranded. RNA is far less stable due to the reactive 2'-OH.

2. Describe the key features of the Watson-Crick B-DNA double helix.

   Right-handed antiparallel double helix; two strands held by complementary base pairing (A=T with 2 H-bonds, G≡C with 3 H-bonds); sugar-phosphate backbone outside, bases stacked inside; ~10.5 bp per turn, major and minor grooves; diameter ~2 nm.

3. State Chargaff's rules for DNA base composition.

   In double-stranded DNA the amount of adenine equals thymine (A = T) and guanine equals cytosine (G = C); therefore total purines equal total pyrimidines (A+G = T+C). The A+T to G+C ratio is constant for a species but varies between species.

4. Why is DNA replication described as semiconservative and bidirectional?

   Semiconservative: each daughter molecule retains one parental (template) strand and one newly synthesized strand (shown by Meselson-Stahl). Bidirectional: replication proceeds in both directions from each origin, forming two replication forks per origin.

5. Why is one strand synthesized continuously (leading) and the other discontinuously (lagging) during replication?

   DNA polymerase only synthesizes 5'→3'. The leading strand runs 3'→5' as template, allowing continuous synthesis toward the fork. The lagging strand template runs 5'→3', so it is made away from the fork in short Okazaki fragments later joined by DNA ligase.

6. List the major enzymes of the DNA replication fork and their functions.

   Helicase unwinds the duplex; topoisomerase/gyrase relieves supercoiling; single-strand binding proteins stabilize ssDNA; primase lays RNA primers; DNA polymerase extends the strands; ligase seals nicks between Okazaki fragments.

7. What is the central dogma of molecular biology?

   The directional flow of genetic information: DNA → RNA → protein. DNA is replicated, transcribed into RNA, and RNA is translated into protein. Reverse transcription (RNA → DNA) is an exception used by retroviruses.

8. What enzyme carries out transcription and in which direction does it read and synthesize?

   RNA polymerase synthesizes RNA. It reads the template (antisense) strand 3'→5' and synthesizes the mRNA 5'→3', producing a transcript identical to the coding (sense) strand except T is replaced by U. It needs no primer.

9. Name the three main steps of post-transcriptional mRNA processing in eukaryotes.

   (1) 5' capping with 7-methylguanosine; (2) 3' polyadenylation (poly-A tail); (3) splicing—removal of introns and joining of exons by the spliceosome. These protect the mRNA and enable export and translation.

10. What is the role of the genetic code, and what are its key properties?

    The genetic code translates nucleotide triplets (codons) into amino acids. It is a triplet, non-overlapping, commaless code that is degenerate (multiple codons per amino acid), nearly universal, and unambiguous (each codon specifies only one amino acid).

11. Identify the start codon and the three stop codons.

    Start codon: AUG (codes for methionine and sets the reading frame). Stop (nonsense) codons: UAA, UAG, and UGA, which signal termination of translation and code for no amino acid.

12. Describe the three stages of translation (protein synthesis).

    Initiation: small ribosomal subunit, initiator tRNA (Met/fMet) and mRNA assemble at AUG. Elongation: aminoacyl-tRNAs add amino acids via peptide bonds (peptidyl transferase) with translocation. Termination: a release factor recognizes a stop codon and releases the polypeptide.

13. What is the wobble hypothesis?

    The pairing of the third (3') codon base with the first (5') anticodon base is less stringent, allowing a single tRNA to recognize multiple synonymous codons. This explains the degeneracy of the genetic code and reduces the number of tRNAs needed.

14. How are amino acids classified by the chemical nature of their side chains?

    Nonpolar/hydrophobic (e.g., Ala, Val, Leu, Ile, Phe); polar uncharged (e.g., Ser, Thr, Cys, Tyr, Asn, Gln); acidic/negatively charged (Asp, Glu); and basic/positively charged (Lys, Arg, His). Glycine and proline have special structural roles.

15. What is the isoelectric point (pI) of an amino acid?

    The pH at which the amino acid carries no net charge (exists as a zwitterion) and does not migrate in an electric field. For a simple amino acid pI = average of the two relevant pKa values (α-COOH and α-NH3+).

16. Name the essential amino acids in humans.

    Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Leucine, Lysine (mnemonic PVT TIM HALL). Arginine is semi-essential (conditionally essential in children).

17. Distinguish the four levels of protein structure.

    Primary: the linear amino acid sequence (peptide bonds). Secondary: local folding into α-helices and β-sheets (H-bonds in backbone). Tertiary: overall 3D fold of one polypeptide. Quaternary: assembly of multiple polypeptide subunits.

18. What bonds and interactions stabilize tertiary protein structure?

    Hydrophobic interactions (major driving force), hydrogen bonds, ionic/electrostatic (salt bridge) interactions, van der Waals forces, and covalent disulfide bonds between cysteine residues.

19. What is protein denaturation, and which structural level is primarily lost?

    Denaturation is the loss of native 3D structure (secondary, tertiary, quaternary) caused by heat, pH extremes, urea, detergents, or heavy metals, leading to loss of function. The primary structure (peptide bonds) is usually preserved.

20. What is the role of molecular chaperones in protein folding?

    Chaperones (e.g., heat-shock proteins/Hsp70, chaperonins/GroEL-GroES) assist correct folding, prevent inappropriate aggregation of nascent or stressed proteins, and do not become part of the final folded structure.

21. Define an enzyme and the terms substrate, active site, and cofactor.

    An enzyme is a biological catalyst (usually protein) that lowers activation energy without being consumed. The substrate is its reactant; the active site is where catalysis occurs; cofactors are non-protein helpers (metal ions or organic coenzymes) required for activity.

22. What do Km and Vmax represent in Michaelis-Menten kinetics?

    Vmax is the maximal reaction velocity when the enzyme is saturated with substrate. Km (Michaelis constant) is the substrate concentration at half Vmax; a low Km indicates high affinity of the enzyme for its substrate.

23. Compare competitive and noncompetitive enzyme inhibition in terms of Km and Vmax.

    Competitive inhibitor binds the active site: Vmax unchanged, Km increased (overcome by excess substrate). Noncompetitive inhibitor binds elsewhere: Vmax decreased, Km unchanged. Uncompetitive: both Km and Vmax decreased.

24. Give two classic examples of irreversible enzyme inhibitors and their targets.

    Aspirin irreversibly acetylates cyclooxygenase (COX). Organophosphates irreversibly inhibit acetylcholinesterase. Penicillin irreversibly inhibits bacterial transpeptidase. These form covalent bonds, permanently inactivating the enzyme.

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