Unit 25 Question Bank
Format note: the TMU Biochemistry paper gives five suggested
answers (A–E), not four — these MCQs match that. Items tagged TMU 2019 or
TMU 2020/21 come from the real papers. Answers are verified against Harper's
Illustrated Biochemistry; the "marking schemes" in the source folder are other students'
answer sheets, not official, so they are never used as the authority.
0 / 25 answered
1The genetic code must be a triplet code because ( ).
Answer: A
Learn the arithmetic rather than the conclusion: codons consisting of two nucleotides each could provide for only 16 (4²) specific codons, whereas codons of three nucleotides could provide 64 (4³). Of the 64, 61 code for the 20 naturally occurring amino acids and three are nonsense codons used as termination signals.TMU Lecture 23 · Harper's ch.37, p.414
2“Degeneracy” of the genetic code means that ( ).
Answer: B
⭐ A proven 2019 Section I term. Six different codons — UCU, UCC, UCA, UCG, AGU and AGC — all specify serine, while methionine and tryptophan have a single codon. Option A is ambiguity, which the code is NOT: the distinction between ambiguity and degeneracy is an important concept.Harper's ch.37, p.414 · 2019 paper, Section I
3Which is NOT one of the features of the genetic code?
Answer: C
The five features are degenerate, unambiguous, nonoverlapping, not punctuated and universal. With rare exceptions, the genetic code is unambiguous — that is, given a specific codon, only a single amino acid is indicated. Mnemonic: “Dear Uncle Ned, Never Understand.”TMU Lecture 23 · Harper's ch.37, p.414
4How is an unambiguous but DEGENERATE code possible?
Answer: D
Harper's gives the reasoning in one sentence: for a given codon in the mRNA, only a single species of tRNA molecule possesses the proper anticodon; since each tRNA molecule can be charged with only one specific amino acid, each codon therefore specifies only one amino acid — however, some tRNA molecules can utilize the anticodon to recognize more than one codon.Harper's ch.37, p.415
5An anticodon is ( ).
Answer: E
⭐ A proven Section I term. The anticodon region (arm) consists of seven nucleotides, and it recognizes the three-letter codon in mRNA. Option C describes the acceptor arm, at the 3′-hydroxyl adenosyl terminal.Harper's ch.37, pp.415–416
6The anticodon is read in the ( ) direction, because ( ).
Answer: A
Harper's is explicit: this direction of reading the anticodon is 3′→5′, whereas the genetic code is read 5′→3′, since the codon and the anticodon loop are ANTIPARALLEL in their complementarity, just like all other intermolecular interactions between nucleic acid strands. It is the same antiparallel rule you met in the DNA double helix.Harper's ch.37, p.416
7Wobble refers to ( ).
Answer: B
The degeneracy of the genetic code resides mostly in the last nucleotide of the codon triplet, and there the pairing is not strictly by the Watson-Crick rule. For example, the two codons for arginine, AGA and AGG, can bind to the same anticodon. Inosine is the classic wobble base, pairing with U, C or A.Harper's ch.37, p.416
8Wobble explains why ( ).
Answer: C
Mitochondria require only 22 tRNA molecules, whereas the cytoplasmic translation system possesses a full complement of 31 tRNA species. Note that degeneracy and wobble are the same molecular property described twice: the code is degenerate because the third pairing is loose — which is also why third-base mutations are so often silent.TMU Lecture 23 · Harper's ch.37
9Which statement about the tRNA arms is INCORRECT?
Answer: D
The D arm is one of the sites important for the proper recognition of a given tRNA species by its proper aminoacyl-tRNA synthetase — it is read by the enzyme, not loaded by it. The acceptor arm carries the amino acid, in an ester linkage at the 3′-CCA end.Harper's ch.37, p.416
10Aminoacyl-tRNA synthetases ( ).
Answer: E
Their accuracy matters absolutely, because the ribosome inspects the codon-anticodon pairing and nothing else — charge a cysteine-tRNA and then chemically convert the cysteine to alanine, and the ribosome inserts alanine at every cysteine codon. The fidelity of the genetic code is enforced at charging, not at the ribosome.TMU Lecture 23 · Harper's ch.37
11During initiation, eIF-2 ( ).
Answer: A
eIF-2 consists of α, β and γ subunits and forms the 43S preinitiation complex. The met-tRNAi is a tRNA specifically involved in binding to the initiation codon AUG, and it ends up on the P site of the 80S ribosome, ready for the elongation cycle to commence.TMU Lecture 23 · Harper's ch.37
12Phosphorylation of eIF-2α blocks protein synthesis because ( ).
Answer: B
The mechanism is an amplifier working in reverse: eIF-2B is present in much smaller amounts than eIF-2, so phosphorylating a fraction of eIF-2α sequesters essentially all the eIF-2B and strands every eIF-2 molecule as the GDP form. PKR is activated by double-stranded RNA — the signature of viral infection, so an infected cell shuts down its whole translational machinery.TMU Lecture 23 · Harper's ch.37
13Which sequence of initiation steps is correct?
Answer: C
Note that dissociation comes first — the ribosome must come apart before it can assemble on a new message. Then eIF-2·GTP·met-tRNAi gives the preinitiation complex; mRNA binds, directed by the 5′ cap, giving the initiation complex; and finally the rapid association of the 40S and 60S subunits forms the 80S ribosome.TMU Lecture 23 · Harper's ch.37
14The three ribosomal sites, in the order a tRNA passes through them, are ( ).
Answer: D
Conveniently alphabetical: Aminoacyl (arrival), Peptidyl (holds the growing chain), Exit. After translocation, the deacylated tRNA is attached to the P site and by its open CCA tail to an exit (E) site, from which it leaves the ribosome. The one exception is the initiator: met-tRNAi is placed directly into the P site.TMU Lecture 23 · Harper's ch.37
15Peptide bond formation is catalysed by ( ).
Answer: E
The single most important reaction in the cell is catalysed by RNA, not protein. That resolves an obvious circularity — proteins are made by ribosomes, so ribosomes cannot have needed proteins to exist first — and is the basis of the RNA world hypothesis. The other great example is in Unit 24: the ribozymes involved in RNA splicing.TMU Lecture 23 · Harper's ch.34 and ch.37
16Translocation of the ribosome by one codon requires ( ).
Answer: A
The EF2-GTP complex is hydrolyzed to EF2-GDP, effectively moving the mRNA forward by one codon. Worth linking to §10: diphtheria toxin ADP-ribosylates and inactivates EF2 in eukaryotes, which is precisely why it is lethal — it freezes every ribosome in the body mid-cycle.TMU Lecture 23 · Harper's ch.37
17How many high-energy phosphate bonds are hydrolysed per peptide bond formed?
Answer: B
Two at charging (ATP → AMP + PPi, with the pyrophosphate hydrolysed), one for delivery of the aminoacyl-tRNA to the A site, and one for translocation. At four per residue, a 300-residue protein costs 1200 ATP equivalents — which is why protein synthesis falls sharply in starvation, and why the process is the largest single item in a growing cell's energy budget.TMU Lecture 23
18Termination of translation involves ( ).
Answer: C
Peptidyl transferase is effectively redirected to use water instead of an amino group as the nucleophile — hydrolysis rather than aminolysis. Afterwards the 80S ribosome dissociates into its 40S and 60S subunits, which are recycled. There is no tRNA for a stop codon; release factors read them instead.TMU Lecture 23 · Harper's ch.37
19A single-base deletion in a coding sequence causes ( ).
Answer: D
The reason lies in a feature from §2: once the reading is commenced at a specific codon, there is no punctuation between codons. Nothing marks where a triplet begins except the start codon, so shifting by one base changes every subsequent codon. The absence of punctuation, which makes the code compact, is exactly what makes frameshifts catastrophic.TMU Lecture 23 · Harper's ch.37
20Haemoglobins Milwaukee, Bristol and Sydney all involve substitution of ( ) at position 67 of the β chain.
Answer: E
Normal haemoglobin has a valine (GUU, GUC, GUA, GUG) there; Milwaukee has a glutamic acid (GAA, GAG), Bristol an aspartic acid (GAU, GAC) and Sydney an alanine (GCU, GCC, GCA, GCG). All are missense mutations, and some mutations have no apparent effect — the redundancy of the code acting as a shock absorber.TMU Lecture 23
21Tetracycline inhibits bacterial protein synthesis by ( ).
Answer: A
Learn the family as a set: chloramphenicol inhibits peptidyl transferase of the 50S subunit; erythromycin blocks translocation; streptomycin binds the 30S subunit and causes misreading; diphtheria toxin inactivates EF2 — but in eukaryotes, which is what makes it a toxin rather than a drug.TMU Lecture 23 · Harper's ch.37
22Puromycin is used as a research tool rather than an antibiotic because ( ).
Answer: B
It enters any A site, accepts the growing peptide onto itself, and falls off — causing premature chain release. Since it mimics a feature every ribosome shares, nothing about it could be selective. A useful antibiotic exploits a difference; a research tool exploits a similarity. Selectivity comes from the 70S (50S + 30S) versus 80S (60S + 40S) distinction.TMU Lecture 23 · Harper's ch.37
23Polysomes are ( ).
Answer: C
They multiply output without any increase in transcription — one message, many copies of the protein at once. The message is also effectively circularised, because the cap and poly(A) tail structures have a synergistic effect on protein synthesis and initiation factors bridge the two ends.TMU Lecture 23
24Which post-translational modification is correctly paired with its example?
Answer: D
Post-translational processing affects the activity of many proteins. The point of zymogens is that a destructive enzyme can be synthesised safely and switched on where it is needed. Note the general principle: synthesis is slow and expensive, activation is fast and cheap — making the protein in advance and activating it on demand separates the expensive step from the urgent one.TMU Lecture 23 · Harper's ch.7 and ch.5
25The mRNA is read ( ).
Answer: E
Harper's summary sentence, worth quoting: “the mRNA is read continuously from a start codon (AUG) to a termination codon (UAA, UAG, UGA)”. Note that AUG codes for start AND also for methionine, and that context matters — most preferred is the presence of a purine at positions −3 and +4 relative to the AUG.TMU Lecture 23, Summary · Harper's ch.37
1 Degeneracy of the genetic code — 3′ — PROVEN 2019 Section I term+
“Degeneracy” in the genetic code means that MULTIPLE CODONS DECODE THE SAME AMINO ACID.
Of the 64 possible codons (4³), three are nonsense codons used as termination signals — UAA, UAG, UGA, and the remaining 61 code for the 20 naturally occurring amino acids. Since 61 > 20, most amino acids have several codons: six different codons — UCU, UCC, UCA, UCG, AGU, AGC — all specify serine, while methionine and tryptophan have a single codon.
Degeneracy is NOT ambiguity. For any specific codon, only a single amino acid is specified; with rare exceptions the genetic code is unambiguous. The code is therefore degenerate but unambiguous — translation is reliable, back-translation is not.
Where it resides: in general, the third nucleotide in a codon is less important than the first two in determining the specific amino acid to be incorporated — the basis of wobble.
Why it matters: the redundancy is a shock absorber — many base changes are silent, and it allows 31 cytoplasmic tRNA species to read 61 codons.Harper's ch.37, p.414 · 2019 paper, Section I
Of the 64 possible codons (4³), three are nonsense codons used as termination signals — UAA, UAG, UGA, and the remaining 61 code for the 20 naturally occurring amino acids. Since 61 > 20, most amino acids have several codons: six different codons — UCU, UCC, UCA, UCG, AGU, AGC — all specify serine, while methionine and tryptophan have a single codon.
Degeneracy is NOT ambiguity. For any specific codon, only a single amino acid is specified; with rare exceptions the genetic code is unambiguous. The code is therefore degenerate but unambiguous — translation is reliable, back-translation is not.
Where it resides: in general, the third nucleotide in a codon is less important than the first two in determining the specific amino acid to be incorporated — the basis of wobble.
Why it matters: the redundancy is a shock absorber — many base changes are silent, and it allows 31 cytoplasmic tRNA species to read 61 codons.Harper's ch.37, p.414 · 2019 paper, Section I
2 Anticodon — 3′ — PROVEN Section I term+
A specific sequence in a tRNA molecule, complementary to a codon in mRNA.
The anticodon region (arm) consists of seven nucleotides, and it recognizes the three-letter codon in mRNA. Reading 3′→5′, the loop is: variable base (N) — modified purine (Pu*) — XYZ (the anticodon) — pyrimidine (Py) — pyrimidine (Py).
Note that this direction of reading the anticodon is 3′→5′, whereas the genetic code is read 5′→3′, since the codon and the anticodon loop are ANTIPARALLEL in their complementarity, just like all other intermolecular interactions between nucleic acid strands.
Significance: for a given codon in the mRNA, only a single species of tRNA molecule possesses the proper anticodon; since each tRNA can be charged with only one specific amino acid, each codon therefore specifies only one amino acid — this is why the code is unambiguous. However, some tRNA molecules can utilize the anticodon to recognize more than one codon — wobble.
The other tRNA arms: acceptor arm (3′-CCA, carries the amino acid), TψC arm (binds the ribosomal surface), D arm (recognised by the aminoacyl-tRNA synthetase).Harper's ch.37, pp.415–416
The anticodon region (arm) consists of seven nucleotides, and it recognizes the three-letter codon in mRNA. Reading 3′→5′, the loop is: variable base (N) — modified purine (Pu*) — XYZ (the anticodon) — pyrimidine (Py) — pyrimidine (Py).
Note that this direction of reading the anticodon is 3′→5′, whereas the genetic code is read 5′→3′, since the codon and the anticodon loop are ANTIPARALLEL in their complementarity, just like all other intermolecular interactions between nucleic acid strands.
Significance: for a given codon in the mRNA, only a single species of tRNA molecule possesses the proper anticodon; since each tRNA can be charged with only one specific amino acid, each codon therefore specifies only one amino acid — this is why the code is unambiguous. However, some tRNA molecules can utilize the anticodon to recognize more than one codon — wobble.
The other tRNA arms: acceptor arm (3′-CCA, carries the amino acid), TψC arm (binds the ribosomal surface), D arm (recognised by the aminoacyl-tRNA synthetase).Harper's ch.37, pp.415–416
3 Wobble — 2′+
The pairing of the codon and anticodon can “wobble” at the LAST nucleotide of the codon triplet — that is, the base pairing between this last nucleotide and the corresponding nucleotide of the anticodon is not strictly by the Watson-Crick rule.
The degeneracy of the genetic code resides mostly in this last nucleotide. For example, the two codons for arginine, AGA and AGG, can bind to the same anticodon. Inosine, one of the unusual bases of tRNA, is the classic wobble base.
Consequence: one tRNA can read several codons, so the cytoplasmic translation system possesses only 31 tRNA species for 61 codons, and mitochondria require only 22.
Degeneracy and wobble are the same molecular property described twice — the code is degenerate BECAUSE the third pairing is loose.Harper's ch.37, p.416
The degeneracy of the genetic code resides mostly in this last nucleotide. For example, the two codons for arginine, AGA and AGG, can bind to the same anticodon. Inosine, one of the unusual bases of tRNA, is the classic wobble base.
Consequence: one tRNA can read several codons, so the cytoplasmic translation system possesses only 31 tRNA species for 61 codons, and mitochondria require only 22.
Degeneracy and wobble are the same molecular property described twice — the code is degenerate BECAUSE the third pairing is loose.Harper's ch.37, p.416
4 Aminoacyl-tRNA synthetase — 2′+
The enzyme that charges a tRNA with its specific amino acid. There is one for each amino acid.
It forms an activated intermediate of aminoacyl-AMP-enzyme complex, and the amino acid remains attached to its specific tRNA in an ESTER linkage at the 3′-CCA of the acceptor arm. Two high-energy phosphate bonds are consumed.
The charging reactions have an error rate of less than 10⁻⁴ and so are extremely accurate.
Why that accuracy is critical: the ribosome inspects only the codon-anticodon pairing, never the identity of the attached amino acid. The fidelity of the genetic code is therefore established entirely at charging.TMU Lecture 23 · Harper's ch.37
It forms an activated intermediate of aminoacyl-AMP-enzyme complex, and the amino acid remains attached to its specific tRNA in an ESTER linkage at the 3′-CCA of the acceptor arm. Two high-energy phosphate bonds are consumed.
The charging reactions have an error rate of less than 10⁻⁴ and so are extremely accurate.
Why that accuracy is critical: the ribosome inspects only the codon-anticodon pairing, never the identity of the attached amino acid. The fidelity of the genetic code is therefore established entirely at charging.TMU Lecture 23 · Harper's ch.37
5 Post-translational processing — 2′+
The covalent modifications made to a polypeptide after its synthesis, which affect the activity of many proteins. The primary translation product is rarely the final functional protein.
Proteolytic cleavage — zymogen activation: trypsinogen → trypsin, proinsulin → insulin.
Hydroxylation — 4-hydroxyproline and 5-hydroxylysine in collagen, requiring vitamin C.
Glycosylation — of secreted and membrane proteins; loss of sialic acid later marks them for degradation.
Phosphorylation — reversible covalent regulation of enzymes such as glycogen phosphorylase and acetyl-CoA carboxylase.
Ubiquitination — targeting for proteasomal degradation.
Disulfide bond formation and proline cis-trans isomerisation during folding.
Why: synthesis is slow and costs four high-energy phosphate bonds per residue, whereas activation by cleavage or phosphorylation is fast and needs no new synthesis — separating the expensive step from the urgent one.TMU Lecture 23 · Harper's ch.37
Proteolytic cleavage — zymogen activation: trypsinogen → trypsin, proinsulin → insulin.
Hydroxylation — 4-hydroxyproline and 5-hydroxylysine in collagen, requiring vitamin C.
Glycosylation — of secreted and membrane proteins; loss of sialic acid later marks them for degradation.
Phosphorylation — reversible covalent regulation of enzymes such as glycogen phosphorylase and acetyl-CoA carboxylase.
Ubiquitination — targeting for proteasomal degradation.
Disulfide bond formation and proline cis-trans isomerisation during folding.
Why: synthesis is slow and costs four high-energy phosphate bonds per residue, whereas activation by cleavage or phosphorylation is fast and needs no new synthesis — separating the expensive step from the urgent one.TMU Lecture 23 · Harper's ch.37
1
Describe the genetic code and its features.
6′
Why a triplet
There are twenty different amino acids, requiring at least 20 distinct codons, but only four different nucleotides in mRNA. Codons consisting of two nucleotides each could provide for only 16 (4²) specific codons — too few — whereas codons of three nucleotides could provide 64 (4³). Therefore each codon consists of a sequence of three nucleotides; it is a triplet code.
Three of the 64 possible codons do not code for specific amino acids; these have been termed nonsense codons and are utilized as termination signals — UAA, UAG and UGA. The remaining 61 codons code for the 20 naturally occurring amino acids. AUG codes for start and also for methionine.
The five features
- DEGENERATE — multiple codons decode the same amino acid. Six different codons — UCU, UCC, UCA, UCG, AGU, AGC — all specify serine; methionine and tryptophan have a single codon.
- UNAMBIGUOUS — for any specific codon, only a single amino acid is specified. The distinction between ambiguity and degeneracy is an important concept.
- NONOVERLAPPING — each nucleotide belongs to one codon only.
- NOT PUNCTUATED — once the reading is commenced at a specific codon, there is no punctuation between codons.
- UNIVERSAL — with noted exceptions; mitochondria require only 22 tRNA molecules, whereas the cytoplasmic system possesses 31 tRNA species.
How an unambiguous but degenerate code works
Each tRNA molecule contains a specific sequence, complementary to a codon, termed its ANTICODON. For a given codon in the mRNA, only a single species of tRNA possesses the proper anticodon. Since each tRNA can be charged with only one specific amino acid, each codon therefore specifies only one amino acid. However, some tRNA molecules can utilize the anticodon to recognize more than one codon.
In general, the third nucleotide in a codon is less important than the first two. The degeneracy resides mostly in the last nucleotide of the codon triplet, suggesting that the base pairing between this last nucleotide and the corresponding nucleotide of the anticodon is not strictly by the Watson-Crick rule. This is called WOBBLE. For example, the two codons for arginine, AGA and AGG, can bind to the same anticodon.
Consequences of each feature
- Degeneracy allows silent mutations — some mutations have no apparent effect — and permits 31 tRNAs to read 61 codons.
- Lack of punctuation is why a frameshift garbles everything downstream, whereas a missense mutation alters one residue only.
- Universality is what makes recombinant DNA technology possible — a human gene can be expressed in a bacterium.
Marking guide: the 4²/4³ arithmetic 1 · 61 coding and 3 nonsense codons named 1 · all five features 2 · the definition of degeneracy 1 · wobble and the third base 1.
2
Describe the process of protein synthesis (translation) in eukaryotes.
10′
Overview
The flow of genetic information follows the sequence DNA → RNA → protein. The mRNA is read continuously from a start codon (AUG) to a termination codon (UAA, UAG, UGA). Translation requires mRNA, tRNA as an adapter, the ribosome, and a set of soluble factors.
Stage 0 — charging the tRNA
Aminoacyl-tRNA synthetases form an activated intermediate of aminoacyl-AMP-enzyme complex, and the amino acid remains attached to its specific tRNA in an ester linkage. The charging reactions have an error rate of less than 10⁻⁴. This accuracy is critical because the ribosome inspects only the codon-anticodon pairing, never the amino acid — the fidelity of the code is enforced at charging.
Initiation — four steps
- A · Ribosomal dissociation — dissociation of the ribosome into its 40S and 60S subunits.
- B · Formation of the 43S preinitiation complex — the binding of GTP by eIF-2; this binary complex binds to met-tRNAi, a tRNA specifically involved in binding to the initiation codon AUG. eIF-2 consists of α, β and γ subunits.
- C · Formation of the 43S initiation complex — mRNA binds. The 5′ terminals of most eukaryotic mRNAs are capped, and this helps direct the 40S ribosomal subunit to the 5′ end. Most preferred is the presence of a purine at positions −3 and +4 relative to the AUG. The cap and poly(A) tail structures have a synergistic effect on protein synthesis.
- D · Formation of the 80S initiation complex — the rapid association of the 40S and 60S subunits, with met-tRNAi on the P site, ready for the elongation cycle to commence.
eIF-2 is a control point. Phosphorylated eIF-2α binds tightly to and inactivates the GTP-GDP recycling protein eIF-2B, preventing formation of the 43S preinitiation complex and blocking protein synthesis — the mechanism by which PKR, activated by viral double-stranded RNA, shuts an infected cell down. The regulation of eIF-4E controls the rate of initiation.
Elongation — three steps, repeated
- A · Binding of aminoacyl-tRNA to the A site.
- B · Peptide bond formation, catalysed by peptidyl transferase — a RIBOZYME, not a protein enzyme.
- C · Translocation. The EF2-GTP complex is hydrolyzed to EF2-GDP, effectively moving the mRNA forward by one codon; the deacylated tRNA is then attached to the P site and by its open CCA tail to an exit (E) site, from which it leaves the ribosome.
The tRNA therefore passes through the sites in the order A → P → E.
Termination
Termination occurs when a stop codon is recognized. A water molecule is added; this hydrolysis releases the protein and the tRNA from the P site, and the 80S ribosome dissociates into its 40S and 60S subunits, which are recycled.
Energy cost
Hydrolysis of four high-energy phosphate bonds per peptide bond: two at charging, one for delivery of the aminoacyl-tRNA to the A site, and one for translocation. A 300-residue protein therefore costs about 1200 ATP equivalents — protein synthesis is the largest single item in a growing cell's energy budget, which is why it falls sharply in starvation.
Efficiency and regulation
Polysomes are assemblies of ribosomes — many translating one mRNA at once, multiplying output without further transcription.
Post-translational processing affects the activity of many proteins: proteolytic cleavage of zymogens, hydroxylation, glycosylation, phosphorylation, ubiquitination and disulfide bond formation.
Pharmacology
Many antibiotics work because they selectively inhibit protein synthesis in bacteria, exploiting the difference between the 70S bacterial and 80S eukaryotic ribosome. Tetracycline prevents the binding of aminoacyl-tRNAs to the A site; chloramphenicol inhibits peptidyl transferase; erythromycin blocks translocation; streptomycin causes misreading. Puromycin, an aminoacyl-tRNA analogue, causes premature chain release in both prokaryotes and eukaryotes and is therefore a research tool, not a drug; diphtheria toxin inactivates eukaryotic EF2.
Marking guide: charging with the synthetase and ester linkage 1.5 · the four initiation steps 2.5 · the three elongation steps with peptidyl transferase named 2 · termination by hydrolysis 1 · four high-energy bonds 1 · one regulatory point (eIF-2 or eIF-4E) 1 · one antibiotic with its correct mechanism 1.