Lecture 2 - Primary and secondary protein structure Flashcards
The primary structure is
the amino acid sequence of a protein.
The primary structure is encoded by the
nucleotide sequence of DNA.
The primary structure is read from the ______ terminus to the ______ terminus.
amino; carboxyl
The peptide bond is usually in the ______ conformation.
trans
Peptide bonds have approximately what percent double bond character?
40%
Peptide bonds have a length of about ______ nm.
0.133
Due to the double bond character, the six atoms of the peptide bond are always ________!
planar
Phi rotation occurs between the
alpha carbon and nitrogen
Psi rotation occurs between the
alpha carbon and the carbon of the carbonyl group
All protein structure is based on the ______ plane.
amide
Do peptide bonds have rotational freedom?
No
Secondary structures are formed by
hydrogen bonds between the peptide N-H and C=O groups near one another in the linear sequence.
In an alpha helix, the _____ extend outward in a helical array.
side chains
The C=O group of each amino acid forms a hydrogen bond with the N-H group that is ______ residues ahead in the sequence.
four
All the C=O and N-H groups in the amino acid are hydrogen bonded except
the terminal amino acids.
There are ____ amino acids per turn of the alpha helix.
3.6
_____-handed helices are very rare.
Left
What kind of amino acids are unlikely to be found in an alpha helix?
- branched
- ones that form hydrogen bonds on their side chains
- ones without an N-H group
A beta pleated sheet consists of _______ polypeptide chains.
two or more
In beta sheets, can hydrogen bonds form within the same strand?
No, must be between different strands
Beta strands can run _____ or _____.
parallel; anti-parallel
In anti-parallel beta sheets, the N-H group and the C=O group of one amino acid form hydrogen bonds with
the C=O and N-H groups of the partner amino acid on the adjacent chain.
In parallel beta sheets, the N-H group is bonded to the C=O group on an adjacent strand, and the C=O is bonded to the N-H group on an amino acid _____ residues down the chain.
two
Which amino acid is not favored in beta sheets?
proline
Where is proline found?
In turns and loops
In a turn, the C=O group of residue i is hydrogen bonded to the N-H group of residue
i + 3
Type I and type II reverse turns differ by
a 180 degree flip of the peptide unit linking residues 2 and 3
Omega loops are how many amino acids long?
6-16
Are turns or loops more structured?
turns
