I have biochem viva tmr,help me get prepared for it
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Biochem Viva Prep 🧬
Topics: Proteins | Enzymes | Nucleic Acids | Genetics
🔴 PROTEINS
Amino Acids
Q: Name the 20 amino acids used in proteins.
Learn them by category:
- Essential (9): His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val (mnemonic: "PVT TIM HaLL")
- Non-essential: Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, Pro, Ser, Tyr
Q: Define an amino acid.
An organic compound with both an amino group (-NH₂) and a carboxyl group (-COOH) attached to the same α-carbon, along with a variable R (side chain) group.
Q: What is a zwitterion?
At physiological pH (~7.4), amino acids exist as dipolar ions — the -NH₂ is protonated to -NH₃⁺ and -COOH is deprotonated to -COO⁻. Net charge = 0. This form is called a zwitterion.
Q: What is isoelectric point (pI)?
The pH at which an amino acid (or protein) carries no net charge (exists entirely as zwitterion). At pI, the molecule does not migrate in an electric field.
Q: Classify amino acids.
| Basis | Types |
|---|---|
| Polarity | Polar (Ser, Thr, Tyr) vs Non-polar (Ala, Val, Leu) |
| Charge at pH 7 | Acidic (Asp, Glu), Basic (Lys, Arg, His), Neutral |
| Structure | Aliphatic, Aromatic (Phe, Tyr, Trp), Sulfur-containing (Cys, Met) |
| Nutritional | Essential vs Non-essential |
Protein Structure
Q: Describe the 4 levels of protein structure.
| Level | Description | Bonds |
|---|---|---|
| Primary | Sequence of amino acids in polypeptide chain | Peptide bonds |
| Secondary | Local folding — α-helix, β-pleated sheet | H-bonds |
| Tertiary | 3D folding of entire polypeptide | H-bonds, disulfide, ionic, hydrophobic |
| Quaternary | Assembly of 2+ polypeptide subunits | Same as tertiary |
Q: Classify proteins on basis of physico-chemical properties.
- Fibrous (structural): collagen, keratin, elastin — insoluble, tough
- Globular (functional): enzymes, hormones, antibodies — soluble, spherical
- Conjugated: protein + non-protein prosthetic group (e.g., glycoproteins, lipoproteins, hemoglobin)
Q: Good vs poor quality protein?
- Good/complete protein: contains ALL essential amino acids in adequate amounts (e.g., egg, milk, meat)
- Poor/incomplete protein: lacks one or more essential amino acids (e.g., gelatin, corn — low in Lys/Trp)
🟠 ENZYMES
Q: Define enzyme.
Biological catalysts (mostly proteins) that speed up chemical reactions without being consumed. They lower the activation energy of a reaction.
Q: Classify enzymes (IUB classification — 6 classes).
- Oxidoreductases — oxidation/reduction (e.g., LDH)
- Transferases — transfer of functional groups (e.g., transaminases/ALT, AST)
- Hydrolases — hydrolysis reactions (e.g., lipase, amylase)
- Lyases — addition/removal without hydrolysis (e.g., aldolase)
- Isomerases — interconvert isomers (e.g., phosphoglucose isomerase)
- Ligases — join molecules using ATP (e.g., DNA ligase)
Q: What are coenzymes and cofactors?
- Cofactor: non-protein component required for enzyme activity — can be metal ions (Zn²⁺, Mg²⁺, Fe²⁺)
- Coenzyme: organic, non-protein cofactor — loosely bound (e.g., NAD⁺, FAD, CoA — derived from B vitamins)
- Prosthetic group: tightly/covalently bound cofactor (e.g., heme in catalase)
- Apoenzyme + Cofactor = Holoenzyme (active form)
Q: Lock and Key vs Induced Fit theory.
| Lock & Key (Fischer) | Induced Fit (Koshland) | |
|---|---|---|
| Concept | Active site is rigid, substrate fits exactly | Active site is flexible, changes shape upon substrate binding |
| Reality | Oversimplified | More accurate model |
| Example | Lysozyme (rigid) | Hexokinase, most enzymes |
Q: What is Km? What is Vmax?
- Km (Michaelis constant): substrate concentration at which reaction velocity = ½ Vmax. Reflects enzyme-substrate affinity — LOW Km = HIGH affinity.
- Vmax: maximum reaction velocity when the enzyme is fully saturated with substrate
- Determined from Michaelis-Menten curve or Lineweaver-Burk plot (double reciprocal)
Q: Factors affecting enzyme activity.
- Temperature (optimum ~37°C; denaturation above)
- pH (each enzyme has optimum pH — pepsin: 2, trypsin: 8, salivary amylase: 6.8)
- Substrate concentration
- Enzyme concentration
- Inhibitors (competitive, non-competitive, uncompetitive)
- Activators/cofactors
🟡 NUCLEIC ACIDS
Q: Define nucleic acid.
Polymers of nucleotides that store and transmit genetic information and play roles in protein synthesis. Two types: DNA and RNA.
Q: Nucleoside vs Nucleotide vs Polynucleotide.
- Nucleoside = Nitrogenous base + Pentose sugar (no phosphate)
- Nucleotide = Nitrogenous base + Pentose sugar + Phosphate group (nucleoside + PO₄)
- Polynucleotide = Chain of nucleotides linked by 3'→5' phosphodiester bonds
Q: Bases in DNA vs RNA.
| DNA | RNA | |
|---|---|---|
| Purines | Adenine, Guanine | Adenine, Guanine |
| Pyrimidines | Cytosine, Thymine | Cytosine, Uracil |
| Sugar | Deoxyribose | Ribose |
| Strands | Double-stranded | Single-stranded |
| Location | Nucleus (mainly) | Nucleus + cytoplasm |
| Function | Genetic storage | Protein synthesis |
Q: DNA base pairing rules (Chargaff's rules).
- A pairs with T (2 H-bonds)
- G pairs with C (3 H-bonds)
- %A = %T; %G = %C
Q: Types and functions of RNA.
| Type | Function |
|---|---|
| mRNA | Carries genetic message from DNA to ribosome |
| tRNA | Brings amino acids to ribosome; has anticodon |
| rRNA | Structural component of ribosome (60% of ribosome) |
Q: Biomedical importance of ATP and cAMP.
- ATP (Adenosine triphosphate): universal energy currency; hydrolysis of terminal phosphate releases ~7.3 kcal/mol; used in biosynthesis, muscle contraction, active transport, signal transduction
- cAMP (Cyclic AMP): second messenger; formed from ATP by adenylyl cyclase (activated by hormones like glucagon, adrenaline); activates Protein Kinase A (PKA) → amplifies hormonal signals; degraded by phosphodiesterase
🟢 GENETICS (Molecular Biology)
DNA Replication
Q: Define DNA replication.
The process by which DNA makes an exact copy of itself — semi-conservative replication (each new DNA has one old strand + one new strand).
Q: Theories of replication — justify each.
| Theory | Description | Status |
|---|---|---|
| Semi-conservative | Each daughter DNA has 1 parental + 1 new strand | ✅ CORRECT (Meselson-Stahl experiment, 1958) |
| Conservative | Original double helix intact; new double helix entirely new | ❌ Disproved |
| Dispersive | Both strands of both daughters have mix of old/new | ❌ Disproved |
Q: Requirements/substrates for DNA replication.
- Template strand (unwound by helicase)
- Primase — lays RNA primer
- DNA polymerase III — main synthesizing enzyme (5'→3' only)
- DNA polymerase I — removes RNA primer, fills gap
- DNA ligase — seals nicks
- dNTPs (dATP, dGTP, dCTP, dTTP) — raw materials
- SSB proteins — stabilize single strands
- Topoisomerase — relieves supercoiling ahead of fork
Transcription
Q: Define transcription.
Synthesis of RNA from a DNA template by RNA polymerase. Direction: 3'→5' on template (RNA synthesized 5'→3').
Q: Steps in transcription.
- Initiation — RNA polymerase binds promoter (TATA box in eukaryotes; -10 and -35 in prokaryotes via sigma factor)
- Elongation — RNA polymerase unwinds DNA and adds ribonucleotides complementary to template
- Termination — RNA polymerase reaches terminator sequence; releases mRNA
Q: Functions of RNA polymerase.
- In prokaryotes: one RNA polymerase does all (core enzyme + sigma factor = holoenzyme)
- Sigma factor (σ) — recognizes promoter
- In eukaryotes, 3 types:
- RNA pol I — rRNA (in nucleolus)
- RNA pol II — mRNA (+ snRNA)
- RNA pol III — tRNA, 5S rRNA
Q: Name inhibitors of transcription.
- Rifampicin — blocks bacterial RNA pol II (used in TB treatment)
- Actinomycin D — intercalates DNA; blocks elongation
- α-Amanitin (mushroom toxin) — inhibits eukaryotic RNA pol II
- Rifabutin — similar to rifampicin
Translation & Genetic Code
Q: Define translation.
Decoding of mRNA sequence into a polypeptide/protein sequence at the ribosome.
Q: Characteristics of the genetic code.
- Triplet code — 3 bases (codon) = 1 amino acid
- Degenerate/redundant — multiple codons for same amino acid (64 codons for 20 amino acids)
- Non-overlapping — each base read only once
- Commaless — no gaps between codons
- Universal — same code in almost all organisms
- Start codon: AUG (Met)
- Stop codons: UAA, UAG, UGA ("amber, ochre, opal")
⚡ QUICK-FIRE LIKELY VIVA QUESTIONS
- What is the peptide bond? (Amide bond between -COOH of one AA and -NH₂ of next; rigid, planar)
- What vitamin is NAD derived from? (Niacin/Vit B3)
- What does FAD come from? (Riboflavin/Vit B2)
- What is the Meselson-Stahl experiment? (Used ¹⁵N/¹⁴N labeling to prove semi-conservative replication)
- What is an Okazaki fragment? (Short DNA fragments on the lagging strand)
- What is a ribozyme? (RNA with catalytic activity — "RNA enzyme")
- Difference between competitive and non-competitive inhibition? (Competitive: Km↑, Vmax same; Non-competitive: Km same, Vmax↓)
- What is the anticodon? (3-base sequence on tRNA complementary to mRNA codon)
- What is post-translational modification? (Processing after translation: glycosylation, phosphorylation, cleavage)
- What is a polysome? (Multiple ribosomes translating one mRNA simultaneously)
Good luck tomorrow — you've got this! Focus especially on the definitions (they often ask to "define" first), the Km/Vmax significance, and the characteristics of the genetic code — those are viva favourites.
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