Answers to Self-Assessment Short Answer Questions # 1
- What are the three stop codons that commonly terminate protein
synthesis?
UAG UGA UAA
- What is understood in protein structure by a beta-turn?
A turn where the carbonyl oxygen of residue i is H-bonded to
the
NH of residue i + 3
- Most beta sheets are twisted. What is the direction of twist when
viewed
- perpendicular to the direction of the strands?
left-handed twist
- parallel to the strand direction?
right-handed twist
- Which of the 20 standard amino acid residues have side chains that
- fork at the beta-carbon atom?
Val, Ile, Thr.
- cannot form hydrogen bonds?
Gly, Phe, Ile, Leu, Val, Ala, Pro. Met can only weakly H-bond.
- Most experimentally determined protein structures whose
coordinates are deposited in the Protein Data Bank lack hydrogen
positions. Why is this?
Most protein structures are determined by X-ray diffraction and H
atoms diffract X-rays only weakly. Therefore they are only visible in
electron density maps when high resolution X-ray data is available.
- State very briefly the function of the three types of RNA.
mRNA - transcribed from the DNA, codes protein sequences(s).
rRNA - major component of ribosomes.
tRNA - carries an anticodon and corresponding amino acid for protein
synthesis.
- Why is the pKa value of the carboxylate group in glycine lower
than that in acetic acid?
The proximity of -NH3+ in glycine makes the protonation of the
carboxylate more difficult so the pKa is lower.
- How is transcription of DNA terminated in prokaryotes?
A palindromic sequence of G-C pairs in the DNA chain gives rise to
sequences of G and C in the nascent RNA chain and these base pair to
form a stable self-complementary hairpin. The G-C pairs in the DNA are
followed by A-T pairs which only form weak base pairs. This leads to
dissociation of the RNA transcript from the DNA template strand.
Sometimes termination occurs without a special DNA sequence. In these
cases a protein called rho factor is involved which can unwind DNA-RNA
double helices.
- In the genetic code, which residue is coded for by only one codon? Which
residue is coded for by most codons?
One codon: Met (AUG) and Trp (UGG).
Six codons: Arg (CGU CGC CGA CGG AGA AGG), Leu (CUU CUC CUA CUG UUA UUG)
and Ser (UCU UCC UCA UCG AGU AGC).
- How can variations in the structure of RNA polymerases lead to
different pathways for bacterial growth?
Different RNA polymerases can bind to different promoter sequences
and control gene expression and hence bacterial growth.
- Why are cis-peptide bonds rarely found in protein molecules?
Cis-peptide bonds have a higher energy due to steric repulsion between
neighbouring C-alpha atoms. This extra energy is small in the case of Pro and
hence this is the most common cis-peptide in proteins.
- Which residue is most commonly found at the start of the nascent
protein chain in eukaryotes?
Met
- Given the two-dimensional formula of an organic molecule, how
can you tell which carbon atoms are chiral centres?
Chiral carbon atoms are bonded to four different atomic groups.
- Give three types of post-translational amino acid modification.
Phosphorylation, acetylation, carboxylation, hydroxylation and
methylation. Also addition of lipid and carbodydrate polymers.
- What is a common function of the sequence TATAAT in E.coli DNA?
A promoter sequence that binds to the sigma-subunit of RNA polymerase
and initiates trasnscription. Known as a Pribnow or TATA box.
- What is the direction of twist of an alpha-helix when viewed along
the helix.
- from its N-terminus?
right-handed.
- from its C-terminus?
right-handed.
- What is the role of signal recognition particles?
These protein:RNA complexes assist in the synthesis of both secreted
and membrane proteins. They bind to a signal recognition sequence on
the nascent protein chain and to the ribosome forming a complex that
diffuses to the rough endoplasmic reticulum (RER) surface where they
facilitate the passage of the growing polypeptide chain into the lumen
of the RER.
- Where are D-amino acids found in nature?
They are found in bacterial polypeptides that are commonly components
of bacterial cell walls.
- What is chromatin?
A complex of DNA and protein (mainly histones) that constitues the
chromosome of a eukaryote.
- What commonly happens to the geometry of alpha-helices that are
partially exposed to solvent?
An alpha-helix on the surface of a protein is often curved with the
centre of curvature on the hydrophobic side of the helix.