Protein Structure
Which part of the amino acid determines whether it is polar, nonpolar, acidic, or basic?
The R group (side chain). This determines chemical properties.
What is the central dogma of molecular biology?
DNA → RNA → Protein.
In eukaryotes, where does transcription occur?
Nucleus.
What type of mutation changes one nucleotide but does not alter the amino acid sequence?
Silent mutation.
What amino acid substitution causes sickle cell anemia?
Glutamic acid → valine at position 6 in β-globin.
A protein has α-helices and β-sheets stabilized by hydrogen bonds. Which level of protein structure is being described?
Secondary structure.
Which enzyme synthesizes RNA during transcription?
RNA polymerase.
What is the function of tRNA in translation?
tRNA carries amino acids, matches codons with anticodons.
What type of mutation introduces a premature stop codon?
Nonsense mutation.
Why are antibiotics that target prokaryotic ribosomes generally safe for humans?
Prokaryotic ribosomes differ from eukaryotic → antibiotics block bacteria only.
A lab technician accidentally denatures a protein by heating it to 95°C. Which levels of structure are disrupted, which bonds are broken, and why does the primary structure remain intact?
Heat breaks hydrogen, ionic, and hydrophobic interactions
A researcher finds that a mutation deleted the promoter region of a gene. Predict what effect this would have on transcription and protein production.
Without a promoter, RNA polymerase cannot bind → no transcription, no protein.
A ribosome begins translating an mRNA but encounters a mutation that changes AUG → AUA at the start codon. Predict what will happen to translation initiation and the resulting protein.
No proper start codon → ribosome cannot start → protein not made.
A frameshift mutation occurs at the beginning of a gene that codes for hemoglobin. Predict how this will affect the amino acid sequence and protein function compared to a mutation near the end of the gene.
Early frameshift → alters entire protein downstream (severe). Late frameshift → affects only a small region.
A patient lacks LDL receptors on liver cells. Explain why this leads to high blood cholesterol and predict what would happen if this mutation affected only half of their receptors.
Without receptors → LDL cannot enter liver → cholesterol builds in blood. Half receptors → partial uptake → moderately high cholesterol.
A mutation changes a hydrophilic amino acid in an enzyme’s active site to a hydrophobic amino acid. Predict how this substitution could alter folding at the tertiary level and explain how it might affect enzyme activity.
Folding changes → hydrophobic residue disrupts shape → enzyme active site altered, lowering activity.
A virus inserts its genome into a host cell. Unlike the host, it uses reverse transcriptase. Explain how this enzyme changes the typical flow of genetic information.
Reverse transcriptase makes DNA from RNA → opposite direction of central dogma.
In a genetic disorder, a mutation eliminates intron splicing. Explain how this would affect the resulting protein and why splicing normally increases protein diversity.
Intron retention → mRNA includes “junk” sequence → protein nonfunctional. Normally splicing allows different proteins from one gene.
Compare a missense mutation that changes a single amino acid in an enzyme’s active site to a nonsense mutation that truncates the enzyme halfway through. Which would be more severe, and why?
P.S Truncating means another way of saying a nonsense mutation that stops translation early, producing a shorter, nonfunctional protein.
Missense in active site can abolish activity; nonsense truncates → usually more severe.
A patient is given ouabain, which blocks the Na⁺/K⁺ ATPase. Predict what happens to sodium, potassium, and water balance in the cell, and explain why this causes swelling and lysis.
Na⁺ accumulates inside, K⁺ decreases → osmotic water influx → swelling, lysis.
A patient’s enzyme normally functions as a tetramer (4 polypeptide subunits). A mutation disrupts the ability of the subunits to bind together. Which level of structure is disrupted first, and what would be the downstream effect on enzyme function?
Quaternary structure is disrupted first
A scientist discovers a mutation in a plant that prevents addition of a 5′ cap and poly-A tail to mRNA. Predict how this would affect the stability, export, and translation of mRNA in the cell.
Without cap/tail → mRNA degrades quickly, cannot leave nucleus efficiently, poorly translated.
A bacterial ribosome is targeted by an antibiotic that prevents tRNA from binding to the A site. Explain how this would affect translation, and why the drug can harm bacteria but not human cells.
tRNA blocked → peptide can’t grow → translation halts. Prokaryotic ribosomes differ structurally from eukaryotic → antibiotics are selective.
A patient has a mutation in the gene for an ion channel. In one family member it is silent, in another it is missense, and in a third it is nonsense. Explain why the same codon change could have different effects and predict the phenotypic consequences of each.
Silent → no effect; missense → single amino acid change (possibly mild or severe); nonsense → early stop, truncated nonfunctional protein.
A cancer patient is treated with chemotherapy, but their tumor cells evolve pumps that export the drug against its gradient. Later, a new drug is added that blocks these pumps. Explain what type of transport the pumps use, why ATP is required, and how blocking the pump makes the chemotherapy more effective.
active transport (ATP-driven efflux pumps). Blocking them → drug stays in tumor cells → chemo regains effectiveness.