4.5.5 · D5Biomolecules
Question bank — Nucleic acids — DNA, RNA; base pairing, double helix, replication, transcription, translation (overview)
Before you start, lock in these anchor definitions — every question below leans on them:
Keep three more facts in mind:
- The backbone (sugar + phosphate) is identical everywhere; only the bases carry information.
- Direction matters: every strand has a 5′ end and a 3′ end, and enzymes only build toward 3′.
- Notation: "%A", "%G", etc. mean the percentage of that base among all nucleotides in the sample, so %A + %T + %G + %C = 100. Where you see math like , read it as " multiplied by itself times" (). This percentage language is the basis of Chargaff's rules.
The two reference figures
Figure s01 draws the antiparallel helix as a ladder: use it whenever a question mentions strand polarity (5′/3′), backbone-vs-base, or the 2-bond/3-bond difference between A–T and G–C. Figure s02 plots how melting temperature rises with GC content — return to it for every "why is G–C harder to separate" or "high-GC" edge case.
True or false — justify
Every DNA molecule has %A = %G.
False. Only %A = %T and %G = %C are forced by pairing; %A vs %G varies freely between species, so a GC-rich genome can have far less A than G.
In any double-stranded DNA, purines equal pyrimidines in amount.
True. %A = %T and %G = %C, so (A+G) = (T+C); every purine on one strand faces a pyrimidine on the other, keeping the totals equal (see figure s01 for the rung geometry).
The two strands of DNA are identical in sequence.
False. They are complementary, not identical — where one reads A the other reads T. Identical strands could not base-pair.
A single strand of DNA already contains enough information to rebuild its partner.
True. Complementary pairing means each base dictates exactly one partner, which is the whole basis of semi-conservative replication (defined above).
RNA can never form base pairs because it is single-stranded.
False. RNA is usually single-stranded but folds back on itself, forming A–U and G–C pairs (e.g. the anticodon loop of tRNA).
Higher GC content makes DNA melt at a lower temperature.
False. G–C pairs have 3 H-bonds vs 2 for A–T, so more GC means stronger holding and a higher melting temperature — exactly the trend in figure s02.
A nucleoside and a nucleotide differ only by a phosphate group.
True. Nucleoside = base + sugar; adding one or more phosphates converts it into a nucleotide.
Thymine and uracil are interchangeable in living cells.
False. Both pair with A, but DNA uses thymine (stable archive) and RNA uses uracil; swapping them would signal repair machinery or corrupt the message.
Base pairing in RNA follows strict Watson–Crick rules just like DNA.
False. Beyond the Watson–Crick pairs (defined above), RNA also allows the non-Watson–Crick G–U wobble pair, so folding rules are looser than the rigid A–T/G–C scheme of double-stranded DNA.
Spot the error
"DNA replication makes two brand-new DNA molecules, discarding both old strands."
Error: replication is semi-conservative (defined above). Each daughter keeps one old strand as template and one new strand; nothing old is discarded.
"During transcription, both DNA strands are copied into one mRNA."
Error: only the template strand is read; the other (coding) strand stays unread, so the mRNA matches just one strand.
"mRNA is built by copying T wherever the template has A."
Error: in RNA, uracil replaces thymine, so a template A gives U in the mRNA, not T.
"The two strands of the double helix run parallel, both 5′→3′ in the same direction."
Error: they are antiparallel — one runs 5′→3′ while its partner runs 3′→5′, so the chemical ends are opposite (see the opposing arrows in figure s01).
"Adenine pairs with guanine because both are purines."
Error: two purines are too wide to fit the helix. A purine always pairs a pyrimidine, so A pairs T (or U), never G.
"A codon is 2 bases long, which is plenty for 20 amino acids."
Error: , too few. A triplet gives , so codons must be at least 3 bases.
"Phosphodiester bonds connect the bases to each other across the helix."
Error: phosphodiester bonds join sugars along the backbone (3′-OH to 5′-phosphate). The bases across the helix are held by hydrogen bonds, not covalent bonds.
"The ribosome reads DNA directly to build a protein."
Error: the ribosome reads mRNA, not DNA. DNA is transcribed into mRNA first; DNA itself stays in the nucleus.
Why questions
Why must a big purine pair with a small pyrimidine rather than purine–purine?
Purine + pyrimidine gives a rung of constant width (~one big ring + one small ring), keeping the helix uniform; two purines would bulge and two pyrimidines would pinch (figure s01).
Why does the 5′→3′ directionality of a strand matter at all?
Enzymes only add new nucleotides to the free 3′-OH end, so direction sets the order of synthesis in replication and transcription.
Why is G–C harder to separate than A–T?
G–C is held by 3 hydrogen bonds versus 2 for A–T, so more energy (heat) is needed to break it apart — the shifted-right curve in figure s02.
Why does the cell use RNA as a "photocopy" instead of sending DNA out to make proteins?
DNA is the protected master archive kept in the nucleus; a disposable RNA copy can leave, be used, and degraded without risking the original information.
Why is the genetic code called "redundant" or "degenerate"?
There are 64 codons but only 20 amino acids, so several different codons can specify the same amino acid — a built-in safety margin (see Genetic code and mutations).
Why does %A + %G always equal 50% in double-stranded DNA?
Because %A = %T and %G = %C, the four percentages split into two equal halves; purines (A+G) and pyrimidines (T+C) each make up half the bases.
Why is the sugar-phosphate backbone described as "the boring part"?
It repeats identically all along the strand, so it stores no message; the varying bases are what encode information.
Edge cases
If a virus stores single-stranded DNA, must %A = %T?
No. Chargaff's equality holds for double-stranded DNA; a single strand can have any base ratio because it has no complementary partner to balance it.
What base pairs form if RNA folds and one region has adenine?
Adenine pairs with uracil inside folded RNA (2 H-bonds), the RNA analogue of the A–T pair in DNA.
In a folded RNA, can guanine ever pair with something other than cytosine?
Yes — the G–U wobble pair forms (2 weak H-bonds), a non-Watson–Crick pairing common in tRNA and rRNA that DNA does not use.
Can a codon exist that codes for no amino acid?
Yes — the three stop codons end translation and add no amino acid; they signal the ribosome to release the finished protein.
What limits the smallest possible functional codon length given 4 bases and 20 amino acids?
Length 2 gives only 16 combinations (too few), so the minimum whole number that covers 20 is length 3, giving 64.
If a DNA sample were 100% G–C with no A–T at all, is that chemically allowed?
Yes, in theory — Chargaff only requires %G = %C and %A = %T; here %A = %T = 0 satisfies both, and such DNA would have a very high melting temperature (far right on figure s02).
How can a base briefly pair with the "wrong" partner even without any chemical damage?
A rare tautomeric shift (e.g. a keto form flipping to its enol, or amino to imino) transiently rearranges the H-bond donors/acceptors, so a mispair like T–G can slip in and later become a point mutation (see Genetic code and mutations).
What happens to base pairing if a single base is chemically changed (e.g. C loses an amino group)?
Its hydrogen-bond pattern shifts, so it may pair with the wrong base during replication — this is another route to a point mutation (see Genetic code and mutations).
Recall One-line summary to lock in
Watson–Crick pairing (A–T = 2 bonds, G–C = 3 bonds) forces strand complementarity and antiparallel geometry; direction (5′→3′) governs all synthesis; more GC means higher melting temperature; RNA additionally tolerates the non-Watson–Crick G–U wobble; replication is semi-conservative; and the code is triplet because .