Lecture 2 Prep for Exam 1 Flashcards
Peptide bond is…
A) planar and flexible
B) planar and rigid
C) nonplanar and rigid
B) planar and rigid
The majority of peptides assume ____ conformation.
trans
What is a dna’s primary structure:
a) linear sequence of amino acids
in a polypeptide chain.
b) local spatial arrangement of a polypeptide’s
backbone atoms without regard to the conformations of its side chains (e.g. α-helix, β-sheet, turns).
c) three- dimensional structure of an entire polypeptide, including its side chains
a…linear sequence of amino acids
in a polypeptide chain.
What is a dna’s secondary structure:
a) linear sequence of amino acids
in a polypeptide chain.
b) local spatial arrangement of a polypeptide’s
backbone atoms without regard to the conformations of its side chains (e.g. α-helix, β-sheet, turns).
c) three- dimensional structure of an entire polypeptide, including its side chains
b) local spatial arrangement of a polypeptide’s
backbone atoms without regard to the conformations of its side chains (e.g. α-helix, β-sheet, turns).
What is a dna’s tertiary structure:
a) linear sequence of amino acids
in a polypeptide chain.
b) local spatial arrangement of a polypeptide’s
backbone atoms without regard to the conformations of its side chains (e.g. α-helix, β-sheet, turns).
c) spatial arrangement of two or more polypeptides
d) three- dimensional structure of an entire polypeptide, including its side chains
d) three- dimensional structure of an entire polypeptide, including its side chains
What is a dna’s quaternary structure:
a) linear sequence of amino acids
in a polypeptide chain.
b) local spatial arrangement of a polypeptide’s
backbone atoms without regard to the conformations of its side chains (e.g. α-helix, β-sheet, turns).
c) noncovalent association of two or more polypeptides
d) three- dimensional structure of an entire polypeptide, including its side chains
c) noncovalent association of two or more polypeptides
How many residues does the alpha helix have per tern?
3.6 residues (amino acids)
What is the distance that the alpha helix rises per turn?
5.4 Angstroms
What is the average length of alpha helices?
12 residues (3 helical turns and a length of 18 angstroms)
How is the alpha helix stabilized?
hydrogen bonds within the backbone
What is the optimum distance for H-bonds?
2.8 angstroms
The peptide C=O bond of the second residue points along the helix axis toward the peptide N-H group of what residue?
(n + 4)th residue= (2+4)th residue= 6th residue
What are three conditions that disrupt an alpha helix?
electrostatic repulsion, steric repulsion and proline (if not at the end of the chain)
Beta sheets contain how many polypeptide strands?
2-22 polypeptide strands (average of 6 strands)
Beta sheets contain up to how many residues?
up to 15 (average is 6 residues)
Why are parallel sheets containing less than 5 strands rare?
Due to the longer distance between these hydrogen bonds which causes them to be weaker (as the hydrogen bonds provide the stability). Therefore, there needs to be more parallel strands than 5 in order to be stronger.
What is the length of each zigzag portion of a beta sheet?
7 Angstroms
What are the two common amino acids that are at the turning points in the reverse turns (beta bends)? Why are they the two common amino acids in Turns?
Gly or Pro are common in Turns due to glycine not having a side-chain (easier to turn) and proline already being bent.
Label the N- and C- terminus in the antiparallel strands
Label the N- and C- terminus in the parallel strands
Will an antiparallel beta sheet or parallel beta sheet have a longer beta turn?
parallel! Look at two images for comparison.
A motif is a combination of ______ structure present in _______ structures.
combination of secondary structures present in tertiary structures
Identify the different motifs…
What are two methods protein structure can be determined by?
x-ray crystallography and twp-dimensional NMR spectroscopy