Mutations & Gene Regulation

Question 1 (12)

(a) Template 3'–TAC GGA TTT ACT ATC–5'. mRNA is complementary and antiparallel, read 5'→3': $\text{5'– AUG\;\;CCU\;\;AAA\;\;UGA\;\;UAG –3'}$ (1 mark correct complementarity; 1 mark antiparallel/5'→3' correct). Amino acids: AUG = Met (Start), CCU = Pro, AAA = Lys, UGA = Stop. (1) Protein = Met–Pro–Lys then translation stops. (1)

(b) Third template base C→T. Template first codon TAC → TAT... wait, third base of TAC is C; changing C→T gives TAT. New mRNA codon = complement of 3'–TAT–5' → 5'–AUA–3'...

Correction using given codons: template TAC pairs to mRNA AUG. Changing template C(3rd)→T gives template TAT, mRNA codon = AUA. AUA is not in start table but is Ile; more directly the point: the start/Met codon is destroyed. Accept: codon changes from AUG(Met) to AUA — a missense change (different amino acid / loss of start). (1 codon, 1 classification, 1 justification — amino acid changed, not a stop, so missense.) (3)

(c) Deletion of one base shifts the reading frame downstream of the deletion. (1) All subsequent codons are regrouped, so every amino acid after the site is likely changed. (1) A premature stop codon often appears, truncating the protein — usually total loss of function, unlike a substitution which changes at most one amino acid. (1) (3)

(d) The genetic code is degenerate/redundant — several codons code for the same amino acid, so a base change (esp. in the 3rd/wobble position) can be silent, giving the same amino acid and unchanged protein. (2) (2)

Question 2 (10)

(a) GAG→GTG changes one codon so one amino acid (Glu→Val) is substituted — a different but sense amino acid = missense. (1) Only one base is replaced, not added/removed, so the number of bases and the reading frame are unchanged → no frameshift. (2) (3)

(b) Three bases = one whole codon removed; because 3 is a multiple of 3, the reading frame downstream stays intact (1). Effect: one amino acid (phenylalanine, F508) is deleted, protein misfolds and CFTR chloride channel is faulty/degraded (2). (3)

(c) Claim is false. (1) A deletion of a number of bases that is a multiple of 3 (e.g. CF's 3 bases) does not frameshift; only deletions of 1, 2, 4... bases (not multiples of 3) cause frameshifts. (1) (2)

(d) Heterozygotes (carriers) survive malaria better, so the allele confers a selective advantage (heterozygote advantage/balanced polymorphism) in malarial regions, maintaining it despite homozygote disadvantage. (2) (2)

Question 3 (12)

(a) (1 mark each)

• A: Glucose present, lactose absent → OFF. No inducer, repressor bound; also low cAMP.
• B: Both present → OFF (very low). Glucose lowers cAMP → CAP inactive → poor transcription (catabolite/glucose repression), even though inducer present.
• C: Both absent → OFF. No lactose = no inducer = repressor bound.
• D: Glucose absent, lactose present → ON (high). Inducer removes repressor; low glucose → high cAMP → CAP active → strong transcription. (4)

(b) In medium A the repressor cannot bind the operator, so RNA polymerase can transcribe — operon is expressed constitutively (ON) even without lactose. (1 prediction) Because operator control is lost, structural genes are made needlessly (2 explanation). (3)

(c) Lac: effector is an inducer (allolactose) — it binds the repressor and inactivates it, switching the operon ON. (1.5) Trp: effector is a corepressor (tryptophan) — it binds the repressor and activates it, switching the operon OFF. (1.5) (3)

(d) A biosynthetic (anabolic) pathway should run only when the product is scarce; when tryptophan is plentiful it acts as corepressor to switch the gene off — repression by the end product avoids wasteful synthesis. (2) (2)

Question 4 (10)

(a) Methylation (usually at CpG in promoters) silences transcription without changing base sequence — methyl groups block transcription-factor/polymerase binding or recruit repressive proteins. (2) Different methylation patterns at the controlling gene switch it on/off, giving different phenotypes from identical DNA. (1) (3)

(b) Histone modification — e.g. histone acetylation loosens chromatin (euchromatin) → increased expression; deacetylation/methylation condenses chromatin (heterochromatin) → reduced expression. (2) (2)

(c) The miRNA is complementary to the target mRNA, so it base-pairs with it (via RISC) (1), leading to mRNA degradation or blocked translation (1) → the "yellow" gene is downregulated/silenced (RNA interference). (1) (3)

(d) Differentiation requires cells to express different subsets of the same genome; epigenetic marks stably switch appropriate genes on/off in each cell type and are heritable through cell division, maintaining cell identity. (2) (2)

Question 5 (6)

(a) Germline mutation occurs in gametes/germ cells and can be passed to offspring; somatic mutation occurs in body cells and is not inherited (only passed to daughter cells of that lineage). (2) The ovary (germ-cell) mutation can be inherited; the skin (somatic) one cannot. (1) (3)

(b) A mutagen is a physical or chemical agent that increases the rate/frequency of mutations. (1) Mechanism: e.g. UV causes thymine dimers/DNA damage, or chemicals alter bases, causing errors during DNA replication/repair, raising the mutation rate above background. (2) (3)

[
  {"claim":"Deletion of 3 bases (multiple of 3) does not cause a frameshift; deletion of 1 does.",
   "code":"result = (3 % 3 == 0) and (1 % 3 != 0)"},
  {"claim":"mRNA Met-Pro-Lys then Stop: start codon AUG then two coded amino acids before UGA stop = 3 codons translated to protein.",
   "code":"codons=['AUG','CCU','AAA','UGA']; stops={'UGA','UAA','UAG'}; aa=0; \nfor c in codons:\n    if c in stops: break\n    aa+=1\nresult = (aa == 3)"},
  {"claim":"Lac operon is ON only in medium D (no glucose, lactose present) among A-D.",
   "code":"media={'A':(1,0),'B':(1,1),'C':(0,0),'D':(0,1)}; on=[m for m,(g,l) in media.items() if g==0 and l==1]; result = (on==['D'])"},
  {"claim":"Number of amino acids changed by a substitution (max 1) is less than by a frameshift affecting all downstream codons.",
   "code":"sub_changes=1; frameshift_changes=5; result = sub_changes < frameshift_changes"}
]