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Flashcards · AP® Biology · Unit 6

Unit 6: Gene Expression and Regulation flashcards

56 cards on topics 6.1 to 6.8. Pick a topic or study the whole unit.

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6.1 DNA and RNA Structure

How do prokaryotic and eukaryotic chromosomes differ?
Prokaryotes: typically one circular chromosome in the nucleoid, packed by supercoiling. Eukaryotes: several linear chromosomes in the nucleus, wrapped around histone proteins (nucleosomes) and folded further.
Why does DNA bind tightly to histones?
Histones are positively charged proteins and the DNA backbone is negatively charged, so they attract.
What are plasmids?
Small, circular, extra-chromosomal DNA molecules, common in bacteria and found in some eukaryotes such as yeasts. They often carry genes such as antibiotic resistance and can pass between cells.
Is all genetic material DNA?
No. Some viruses, such as influenza viruses and HIV, use RNA as their genetic material.
What are purines and pyrimidines?
Purines (A, G) have double rings; pyrimidines (C, T in DNA, U in RNA) have single rings. Each pair is one purine + one pyrimidine, giving a constant helix width. A–G or C–T pairs are wrong.
How do you find base percentages in double-stranded DNA?
Purines = pyrimidines = 50%. If C = 22%, G = 22%, A = 50 − 22 = 28% and T = 28%. A 2 000 bp molecule has 4 000 nucleotides, 2 000 of them purines. Not valid for a single strand.
Why are base-pairing rules evidence of common ancestry?
The same pairing rules apply in all known cellular life.

6.2 DNA Replication

What does semiconservative replication mean?
The parent strands separate, each acts as a template, and each new DNA molecule keeps one parent strand and one new strand.
How did the Meselson–Stahl experiment support semiconservative replication?
After one round in a new isotope all DNA was intermediate (ruling out conservative). After two rounds there were two bands, hybrid and all-new (ruling out dispersive).
What do helicase, topoisomerase and ligase do in replication?
Helicase separates strands at the fork by breaking hydrogen bonds between bases. Topoisomerase works ahead of the fork to relieve supercoiling. Ligase seals the backbone between lagging-strand fragments (covalent bonds).
Why does DNA polymerase need a primer?
It can only add nucleotides to an existing 3′ end and cannot start a chain, so an RNA primer provides the 3′ end. DNA polymerase later replaces primers with DNA.
How do the leading and lagging strands differ?
Both are made 5′ → 3′. The leading strand grows toward the fork, continuously, with one primer. The lagging strand grows away from the fork in fragments, each with its own primer, joined by ligase.
How do you write a new strand from a template?
Pair each base and reverse so it reads 5′ → 3′. Template 5′-ATTGCC-3′ gives new strand 5′-GGCAAT-3′.
What happens if DNA ligase is blocked?
The lagging strand stays as separate fragments; the leading strand is largely unaffected.
Where does replication start?
At an origin, which opens two forks moving apart. Bacteria typically have one origin; each eukaryotic chromosome has many.

6.3 Transcription and RNA Processing

What are the jobs of mRNA, tRNA and rRNA?
mRNA carries a gene's information from DNA to a ribosome. tRNA carries a specific amino acid, and its anticodon pairs with an mRNA codon. rRNA, with proteins, is the structural and working part of the ribosome.
How does RNA polymerase transcribe a gene?
It reads one strand, the template strand, 3′ → 5′ and builds RNA 5′ → 3′ with no primer. Pairing: template A → U, T → A, G → C, C → G.
Which DNA strand does the mRNA match?
The coding strand, with U in place of T. It is complementary to the template strand. Template 3′-TACGTT-5′ gives mRNA 5′-AUGCAA-3′.
How is eukaryotic pre-mRNA processed?
In the nucleus: a 5′ cap (modified G) helps the ribosome recognise the mRNA; a 3′ poly-A tail makes it more stable; splicing removes introns and joins exons. Introns are removed from the RNA, not the DNA.
What is alternative splicing?
Joining different combinations of exons from one pre-mRNA to give several mature mRNA versions. Exons of 200, 150 and 90 nt give 440 nt, or 290 nt if the middle exon is skipped.
What happens to an mRNA without its poly-A tail?
It is broken down sooner, so less protein is made from it.
Is prokaryotic mRNA processed?
Prokaryotic mRNA is generally used without the cap, tail and splicing steps of eukaryotes.

6.4 Translation

Where does translation happen?
On ribosomes free in the cytoplasm (all cells) and on the cytoplasmic surface of the rough ER (eukaryotes). Prokaryotes translate mRNA while it is still being transcribed, because there is no nucleus.
What happens in initiation, elongation and termination of translation?
Initiation: rRNA lines up mRNA at start codon AUG, Met-tRNA pairs, ribosome assembles. Elongation: matching tRNA brings an amino acid, a peptide bond forms, ribosome moves one codon toward 3′. Termination: stop codon, no tRNA pairs, polypeptide released.
What are the features of the genetic code?
mRNA is read in triplet codons; 64 codons, 61 for the 20 amino acids and 3 stop codons. Many amino acids have more than one codon. Nearly all organisms share the same code, evidence of common ancestry.
How do you write the anticodon for a codon?
Pair the bases and write it 3′ → 5′. Codon 5′-UGG-3′ pairs with anticodon 3′-ACC-5′.
How do you count amino acids from coding nucleotides?
Amino acids = (translated nucleotides including stop) ÷ 3 − 1; coding nucleotides = (amino acids + 1) × 3. A 300-amino-acid polypeptide needs 903 nt. Start counting at the A of AUG; the stop codon adds no amino acid.
How do retroviruses use reverse transcriptase?
Reverse transcriptase copies the RNA genome into DNA, which integrates into host DNA and is then expressed. They do not make protein directly from RNA without a DNA step.

6.5 Regulation of Gene Expression

What are constitutive, inducible and repressible genes?
Constitutive genes are always on. Inducible genes switch on when an inducer appears (lac). Repressible genes switch off when a corepressor builds up (trp).
What is an operon?
Promoter + operator + several structural genes transcribed as one mRNA. The repressor gene lies outside it. A repressor bound to the operator blocks RNA polymerase for all the genes at once.
How is the lac operon controlled?
No lactose: active repressor sits on the operator, operon off. Lactose present: allolactose binds the repressor, which leaves the operator, operon on (strongly if glucose is scarce, helped by CAP–cAMP). Allolactose binds the repressor, not the operator.
How is the trp operon controlled?
Little tryptophan: repressor inactive, off the operator, operon on. Much tryptophan: tryptophan binds the repressor, which binds the operator, operon off.
What do lac operon mutations do?
No working repressor, or an operator that cannot bind the repressor: on all the time (constitutive). Promoter that cannot bind RNA polymerase: off all the time.
How do DNA methylation and histone acetylation affect expression?
DNA methylation usually silences genes; histone acetylation loosens chromatin and usually activates them. Both are reversible, can pass to daughter cells, and are not mutations.
How do eukaryotes switch on scattered genes together?
Genes that share the same control sequence are switched on together by one transcription factor. Development uses chains of transcription factors (sequential expression).

6.6 Gene Expression and Cell Specialization

Why do different cell types in one body have different proteins?
Nearly all cells carry the same genome; differential gene expression gives each cell type its own proteins, structure and function. Cell types do not have different genes.
What binds at promoters, enhancers and silencers?
Promoter: general transcription factors and RNA polymerase, needed to start, basal rate. Enhancer: activators, which raise the rate. Silencer: repressors, which lower or block it.
How can an enhancer far from a gene affect it?
Enhancers can be far upstream or downstream, even in introns. The DNA loops so bound activators contact the promoter complex through mediator proteins.
Why does each cell type express its own set of genes?
Each gene needs a combination of activators, and each cell type has its own set. A gene needing A and B is expressed only in cells that have both.
How do miRNAs and siRNAs regulate genes?
These 21–23-nucleotide RNAs base-pair with mRNA, reducing translation, causing mRNA breakdown, or both. They do not change DNA or stop transcription.
How do you interpret deletion experiments with a reporter gene?
Deleting a region that lowers output: it is or contains an enhancer. Deleting a region that raises output: a silencer. 900 units falling to 45 (5.0% remaining) shows an enhancer.
Does unchanged mRNA mean unchanged protein?
No. If blocking a miRNA raises protein more than mRNA, the miRNA also blocks translation.

6.7 Mutations

What is a mutation, and what causes it?
A change in the DNA sequence, caused by replication errors, failed repair, radiation or reactive chemicals. Mutations are random: a mutagen raises the rate, not the direction.
What are silent, missense and nonsense mutations?
Substitutions with the frame kept. Silent: same amino acid. Missense: one different amino acid. Nonsense: an early stop codon, shortening the chain. UGG (Trp) → UGA is nonsense.
What is a frameshift mutation?
Inserting or deleting a number of bases that is not a multiple of 3 shifts the reading frame, changing most later amino acids and usually moving the stop. Deleting 3, 6, 9… bases keeps the frame.
Is a mutation always harmful?
No. It is beneficial, detrimental or neutral depending on its effect and the environment. Mutations are the original source of new alleles; organisms do not mutate "in order to" adapt.
How can a mutation change the amount of protein?
A promoter mutation changes how much protein is made, not its sequence.
What are aneuploidy and polyploidy?
Nondisjunction gives n + 1 or n − 1 gametes, leading to aneuploidy (one extra or missing chromosome). Polyploidy is whole extra chromosome sets.
How do prokaryotes gain genetic variation besides mutation?
Horizontal gene transfer by transformation, transduction and conjugation, and transposition. Related viruses in one host cell can also recombine.

6.8 Biotechnology

How does gel electrophoresis separate DNA?
The phosphate backbone makes DNA negative, so it moves toward the positive electrode. Short fragments move farthest. A ladder of known sizes lets you estimate band sizes.
What happens in each step of PCR?
Denature (hot): strands separate. Anneal (cooler): primers bind. Extend: a heat-stable DNA polymerase adds nucleotides to the primers. Only the region between the primers is copied.
How many copies does PCR make?
N = N₀ × 2ⁿ maximum after n cycles, assuming 100% efficiency. 3 copies after 10 cycles: 3 × 2¹⁰ = 3072. Round the number of cycles needed up, not down.
Why must the PCR polymerase be heat-stable?
Each cycle heats the mixture to separate the strands, which would denature an ordinary polymerase.
How does bacterial transformation select transformed cells?
A plasmid carries the gene of interest and an antibiotic-resistance marker. Only transformed cells grow on antibiotic plates; the plasmid gene, not the antibiotic, gives resistance. Dividing bacteria copy the plasmid (gene cloning).
How do you calculate transformation efficiency?
Colonies ÷ µg of DNA actually spread on the plate (transformants per µg), not the total DNA used.
How is DNA fingerprinting used in a kinship test?
Every band in a child must be in the mother or the biological father. A band in neither the mother nor a tested man, in a reliable test, excludes that man. A match supports identity; it does not prove it.

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