BCH4024 EXAM 1 QUESTIONS WITH
CERTIFIED ANSWERS
What properties of β-strands forms beta sheets - Answer-hydrogen bond
Where is the hydrogen bonds in a β-sheet? - Answer-between the backbone of C=O of
one chain and the N-H of another chain segment
Where is the hydrogen bonds in a α-helix? - Answer-all hydrogen bonds involve the
same element of polypeptide chain
Where are the R-groups of neighboring residues in a β-strand? - Answer-opposite
directions
The peptide bonds of adjacent residues in a β-strand point in directions,
whereas with α-helices the peptide bonds point in - Answer-opposite; same
direction
How far are the adjacent residues in β-strands from one another? - Answer-3.5
Angstroms, but there are two residues per unit, so the total total distance is 7 A
How far are the adjacent residues in α-helix from one another? - Answer-1.5 A
Why are polypeptides in the β-conformation more extended than those in α-helical -
Answer-because the distance between two adjacent residues in beta strands is 3.5 A,
and there are two residues per repeat unit in beta strands, so total distance is 7A. as
opposed to alpha helix, the distance between adjacent residues along helical axis is
only 1.5 angstroms
In a polypeptide, the main chain torsion angles around and are free to rotate -
Answer-phi and psi
Ramachandran used computer models of small polypeptides to vary φ and ψ, what was
the objective - Answer-finding stable conformations
Ramachandran plot represents: - Answer-torsion angles for each residue in a protein
4 classes of protein motifs (recognizable folding pattern) - Answer-all α, all β, α/β, α+ β
large motifs from small motifs of protein structure example: - Answer-pyruvate kinase
RNA world ---- > (evolution) - Answer-protein world
Protein stability depends on what three factors: - Answer-1) unfavorable conformation
entropy (cause of folding)
2) favorable enthalpy due to intramolecular noncovalent interactions
3) favorable entropy due to burying of hydrophobic residues
,Polar amino acids: hydrgen bond - Answer-S, T, N, Q
Serine, Threonine, Asparagine, Glutamine
Charged Amino acids: ionic interactions - Answer-D, E, R, K, H
Aspartate, Glutamate, Arginine, Lysine, Histidine
Nonpolar amino acids: hydrophobic interactions - Answer-A, V, L, I, M, W, F
Alanine
Valine
Leucine
Isoleucine
Methionine
Tryptophan
Phenylalanine
Transfer RNA (tRNA) secondary structure: - Answer-tRNA "reads" genes information
encoded in mRNA (3 nucleotide codon) copied from DNA
What does tRNA transfer during protein synthesis - Answer-the appropriate amino acid
to a growing polypeptide chain
Transcription creates a: - Answer-complementary RNA copy (mRNA) of a sequence of
DNA
Translation steps: - Answer-mRNA decoded by ribosomes and tRNA is used to produce
a specific amino acid chain, or polypeptide, that will later fold into an active protein
Phenotype of an organism is determined by: - Answer-proteins
What defines function by interaction? - Answer-the three dimensional structure of
proteins
what defines the type of amino acid? - Answer-side chain
what kind of molecule are amino acids - Answer-ampholytic molecule (contains both
acidic and basic groups)
Charge of an amino acid is dependent on: - Answer-the pH of a solution
What happens to the net charge of an amino acid as you increase the pH - Answer-net
charge decreases
Which of the 20 common amino acids is achiral? - Answer-Glycine
Isoelectric point - Answer-pI=pH, average charge equals zero.
two equilibrium dissociation reactions w/ isoelectric points - Answer-HAH+ ---- > HA + H
HA --- > A- + H+
pI formula if no ionizable side chain - Answer-pI = ¹/₂ (pK₁ + pK₂)
, simplest amino acid? - Answer-glycine
Ways to classify amino acids based on properties: - Answer--size/shapes
-charges
CERTIFIED ANSWERS
What properties of β-strands forms beta sheets - Answer-hydrogen bond
Where is the hydrogen bonds in a β-sheet? - Answer-between the backbone of C=O of
one chain and the N-H of another chain segment
Where is the hydrogen bonds in a α-helix? - Answer-all hydrogen bonds involve the
same element of polypeptide chain
Where are the R-groups of neighboring residues in a β-strand? - Answer-opposite
directions
The peptide bonds of adjacent residues in a β-strand point in directions,
whereas with α-helices the peptide bonds point in - Answer-opposite; same
direction
How far are the adjacent residues in β-strands from one another? - Answer-3.5
Angstroms, but there are two residues per unit, so the total total distance is 7 A
How far are the adjacent residues in α-helix from one another? - Answer-1.5 A
Why are polypeptides in the β-conformation more extended than those in α-helical -
Answer-because the distance between two adjacent residues in beta strands is 3.5 A,
and there are two residues per repeat unit in beta strands, so total distance is 7A. as
opposed to alpha helix, the distance between adjacent residues along helical axis is
only 1.5 angstroms
In a polypeptide, the main chain torsion angles around and are free to rotate -
Answer-phi and psi
Ramachandran used computer models of small polypeptides to vary φ and ψ, what was
the objective - Answer-finding stable conformations
Ramachandran plot represents: - Answer-torsion angles for each residue in a protein
4 classes of protein motifs (recognizable folding pattern) - Answer-all α, all β, α/β, α+ β
large motifs from small motifs of protein structure example: - Answer-pyruvate kinase
RNA world ---- > (evolution) - Answer-protein world
Protein stability depends on what three factors: - Answer-1) unfavorable conformation
entropy (cause of folding)
2) favorable enthalpy due to intramolecular noncovalent interactions
3) favorable entropy due to burying of hydrophobic residues
,Polar amino acids: hydrgen bond - Answer-S, T, N, Q
Serine, Threonine, Asparagine, Glutamine
Charged Amino acids: ionic interactions - Answer-D, E, R, K, H
Aspartate, Glutamate, Arginine, Lysine, Histidine
Nonpolar amino acids: hydrophobic interactions - Answer-A, V, L, I, M, W, F
Alanine
Valine
Leucine
Isoleucine
Methionine
Tryptophan
Phenylalanine
Transfer RNA (tRNA) secondary structure: - Answer-tRNA "reads" genes information
encoded in mRNA (3 nucleotide codon) copied from DNA
What does tRNA transfer during protein synthesis - Answer-the appropriate amino acid
to a growing polypeptide chain
Transcription creates a: - Answer-complementary RNA copy (mRNA) of a sequence of
DNA
Translation steps: - Answer-mRNA decoded by ribosomes and tRNA is used to produce
a specific amino acid chain, or polypeptide, that will later fold into an active protein
Phenotype of an organism is determined by: - Answer-proteins
What defines function by interaction? - Answer-the three dimensional structure of
proteins
what defines the type of amino acid? - Answer-side chain
what kind of molecule are amino acids - Answer-ampholytic molecule (contains both
acidic and basic groups)
Charge of an amino acid is dependent on: - Answer-the pH of a solution
What happens to the net charge of an amino acid as you increase the pH - Answer-net
charge decreases
Which of the 20 common amino acids is achiral? - Answer-Glycine
Isoelectric point - Answer-pI=pH, average charge equals zero.
two equilibrium dissociation reactions w/ isoelectric points - Answer-HAH+ ---- > HA + H
HA --- > A- + H+
pI formula if no ionizable side chain - Answer-pI = ¹/₂ (pK₁ + pK₂)
, simplest amino acid? - Answer-glycine
Ways to classify amino acids based on properties: - Answer--size/shapes
-charges
