Title: InkBiology / Nucleic acids, genomes and protein synthesis
On every note of this deck, unless a note says otherwise:
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Front: DEFINE
Define: Ribosome.
Back: An organelle of ribosomal RNA and protein, in two subunits, which holds mRNA and tRNA in position while a polypeptide is assembled.

Front: DEFINE
Define: Exon.
Back: A section of a gene that is represented in the mature mRNA.

Front: DEFINE
Define: Ribosomal RNA (rRNA).
Back: RNA which, with proteins, forms the two subunits of a ribosome and catalyses the formation of peptide bonds.

Front: DEFINE
Define: Anticodon.
Back: A triplet of bases on tRNA, complementary to a codon on mRNA.

Front: DEFINE
Define: Semi-conservative replication.
Back: Replication in which the two strands of the parent molecule separate and each acts as a template, so every daughter molecule contains one original strand and one newly synthesised strand.

Front: DEFINE
Define: Splicing.
Back: The removal of introns from pre-mRNA and the joining of exons to produce mature mRNA.

Front: SPOT THE ERROR
Say what is wrong with this claim:
The genetic code is degenerate, so it is a wasteful system evolution has not got round to tidying up.
Back: Degeneracy is a safety margin rather than waste. Most amino acids have several triplets, usually differing only in the third base, so a copying error in that position often produces the same amino acid and the same protein.

Front: DEFINE
Define: Post-translational modification.
Back: Changes made to a polypeptide after translation, such as cutting out sections or adding carbohydrate or lipid groups, carried out in the endoplasmic reticulum and the Golgi apparatus. Folding is not one of them: it begins on the ribosome and is finished in the endoplasmic reticulum.

Front: DEFINE
Define: Codon.
Back: A triplet of bases on mRNA specifying one amino acid or a stop signal.

Front: DEFINE
Define: Genome.
Back: The complete set of DNA in a cell, including the DNA that does not code for polypeptides.

Front: CHECK YOURSELF
A biotechnology company wants a human gene expressed in a bacterium. They isolate the gene directly from a human chromosome and insert it into E. coli, but no functional human protein is produced. Suggest why, and what they should have used instead.
Back: A gene taken straight from a human chromosome contains introns. Bacteria do not carry out splicing, because their own genes almost never contain introns and they have no spliceosomes.
The bacterium therefore transcribes the whole inserted sequence, introns included, and translates it as though every base were coding. The introns are read in the reading frame that happens to follow, producing wrong amino acids and almost certainly premature stop codons, so no functional human protein appears.
The fix is to start from mature mRNA rather than from the chromosome. Isolate the mRNA from a human cell that expresses the gene heavily, then use reverse transcriptase to make a DNA copy of it. Because the introns have already been spliced out of that mRNA, the resulting DNA is a continuous coding sequence the bacterium can handle.
Note what this does not challenge: the code is still universal, so the bacterium reads each triplet exactly as a human cell would. The problem was never the code. It was the introns.

Front: DEFINE
Define: Polynucleotide.
Back: A chain of nucleotides joined by phosphodiester bonds between the sugar of one and the phosphate of the next.

Front: DEFINE
Define: Antiparallel.
Back: The two strands of a DNA molecule run in opposite directions: the 5′ end of one lies alongside the 3′ end of the other.

Front: DEFINE
Define: Degenerate.
Back: Describing a code in which most amino acids are specified by more than one triplet.

Front: DEFINE
Define: Transfer RNA (tRNA).
Back: A small folded RNA of about 80 nucleotides with an anticodon at one end and a binding site for a specific amino acid at the other.

Front: DEFINE
Define: Nucleotide.
Back: A phosphate group, a pentose sugar and a nitrogenous base joined together.

Front: DEFINE
Define: Non-overlapping.
Back: Describing a code in which each base is part of one triplet only and triplets are read in sequence.

Front: CHECK YOURSELF
A cell is treated with a drug that prevents tRNA molecules from being loaded with their amino acids, while leaving transcription and the ribosome itself untouched. Predict what happens inside the cell over the next few hours, and explain each part of your prediction.
Back: Transcription carries on, so mRNA continues to be produced and to leave the nucleus. The ribosomes are intact, so they still bind mRNA and still find start codons. What stops is the supply of loaded tRNA.
The machinery that delivers tRNA to the A site only accepts a tRNA carrying its amino acid, so with none being loaded the A site goes unfilled, no peptide bond can form and the ribosome cannot move on. Elongation stalls almost immediately, and the polypeptides being made at the moment the drug arrives are left incomplete.
Existing proteins are not destroyed by the drug, so the cell keeps functioning at first. It degrades over hours rather than seconds, as enzymes and other proteins reach the end of their working lives and are broken down without replacement. Proteins with short lifetimes disappear first.
The mRNA also degrades on its own timescale, since it is unstable and nothing about the drug protects it. So the cell ends up with intact DNA, intact ribosomes, a falling stock of mRNA and a falling stock of protein, which is a good illustration of why the loading step, and not the ribosome, is the point at which the genetic code is physically enforced.

Front: DEFINE
Define: Gene.
Back: A sequence of DNA bases coding for a polypeptide or a functional RNA.

Front: DEFINE
Define: Messenger RNA (mRNA).
Back: A single-stranded copy of one gene, made in the nucleus and carrying codons to a ribosome in the cytoplasm.

Front: DEFINE
Define: Deletion.
Back: A mutation in which a base is lost; within a coding region, losing a number of bases not divisible by three shifts the reading of every triplet that follows.

Front: DEFINE
Define: Substitution.
Back: A mutation in which one base is replaced by another.

Front: DEFINE
Define: Codon.
Back: A sequence of three bases in mRNA that specifies one amino acid or a stop signal.

Front: SPOT THE ERROR
Say what is wrong with this claim:
Replication copies one strand, so you end up with the old molecule and a brand new one beside it.
Back: Replication is semi-conservative. Both strands act as templates at once, so each daughter molecule is one original strand paired with one newly built one. No parent molecule survives intact and none is built entirely from scratch.

Front: DEFINE
Define: Template strand.
Back: A strand of DNA whose base sequence determines the sequence of the new strand built against it.

Front: DEFINE
Define: Intron.
Back: A non-coding section of a gene, transcribed into pre-mRNA and then removed before the mRNA leaves the nucleus.

Front: DEFINE
Define: Mutation.
Back: A change in the base sequence of DNA.

Front: DEFINE
Define: Pre-mRNA.
Back: The immediate product of transcription in a eukaryote, containing both exons and introns.

Front: CHECK YOURSELF
A student claims that after two generations in light medium, a conservative model and a semi-conservative model would give the same result, so the experiment proves nothing. Explain why the student is wrong, using the position and number of the bands.
Back: The two models differ at the first generation, and they differ again at the second, so at no point do they predict the same thing.
After one generation the conservative model predicts two bands: the original heavy molecule intact at the bottom of the gradient and a completely new light molecule at the top, with nothing between them. The semi-conservative model predicts one band only, sitting midway, because every molecule is one heavy strand paired with one light one. A single intermediate band was what appeared, so the conservative model was already dead.
After two generations the conservative model would still show a heavy band, since the original molecule is never taken apart under that model. The semi-conservative model predicts no heavy DNA at all: two intermediate molecules and two light ones, giving two bands, one midway and one at the light position. That is what was seen.
The student has confused 'both models predict some light DNA' with 'both models predict the same bands'. The persistence of a heavy band is the difference, and it was absent.

Front: CHECK YOURSELF
A student writes: 'DNA is a good molecule for storing genetic information because it has a double helix shape.' Rewrite this as an answer that would actually score, referring to at least three features of the molecule.
Back: The helix by itself explains nothing, because the question is about storing information and a spiral is not a store. Each feature has to be tied to something the molecule has to do.
The backbone is held together by covalent phosphodiester bonds, so the molecule is chemically stable and the information is not lost over time. The bases are also positioned on the inside of the helix, shielded from the water and from reactive molecules in the nucleus.
The sequence of the four bases can vary without limit, and the molecule can be extremely long, so an enormous amount of information can be encoded in one molecule. Ten bases alone allow over a million arrangements.
The two strands are complementary, held by hydrogen bonds that are weak enough to break when the sequence has to be read or copied. Because the pairing rule is fixed, either strand acts as a template for rebuilding the other, which is what makes replication accurate and repair possible.
A good answer names the bond in each case: covalent for the backbone, hydrogen for the pairing. That contrast, strong along and weak across, is the whole design.

Front: SPOT THE ERROR
Say what is wrong with this claim:
tRNA carries the codon to the ribosome, where it is matched against the mRNA.
Back: The codon is on the mRNA; the tRNA carries the anticodon, the complementary triplet. Codon CCU is read by the tRNA whose anticodon is GGA, and that tRNA carries proline. Swap the two words and the mechanism described could not work.

Front: DEFINE
Define: Complementary base pairing.
Back: Adenine pairs with thymine by two hydrogen bonds and guanine pairs with cytosine by three, so the sequence of one strand fixes the sequence of the other.

Front: DEFINE
Define: Phosphodiester bond.
Back: The covalent bond joining the phosphate group of one nucleotide to the sugar of the next, formed by condensation.

Front: DEFINE
Define: Double helix.
Back: Two antiparallel polynucleotide strands wound into a spiral, bases inside and backbones outside.

Front: SPOT THE ERROR
Say what is wrong with this claim:
The two strands of a DNA molecule are identical, so either one is a spare copy of the other.
Back: Complementary, not identical. Where one strand reads ATGGC the other reads TACCG, and no base matches the one it faces. That is what makes the spare useful: the fixed pairing rule lets either strand specify the other exactly.