Lecture 2 - Primary and secondary protein structure

Question 1

The primary structure is

Answer 1

the amino acid sequence of a protein.

Question 2

The primary structure is encoded by the

Answer 2

nucleotide sequence of DNA.

Question 3

The primary structure is read from the ______ terminus to the ______ terminus.

Answer 3

amino; carboxyl

Question 4

The peptide bond is usually in the ______ conformation.

Answer 4

trans

Question 5

Peptide bonds have approximately what percent double bond character?

Answer 5

40%

Question 6

Peptide bonds have a length of about ______ nm.

Answer 6

0.133

Question 7

Due to the double bond character, the six atoms of the peptide bond are always ________!

Answer 7

planar

Question 8

Phi rotation occurs between the

Answer 8

alpha carbon and nitrogen

Question 9

Psi rotation occurs between the

Answer 9

alpha carbon and the carbon of the carbonyl group

Question 10

All protein structure is based on the ______ plane.

Answer 10

amide

Question 11

Do peptide bonds have rotational freedom?

Answer 11

No

Question 12

Secondary structures are formed by

Answer 12

hydrogen bonds between the peptide N-H and C=O groups near one another in the linear sequence.

Question 13

In an alpha helix, the _____ extend outward in a helical array.

Answer 13

side chains

Question 14

The C=O group of each amino acid forms a hydrogen bond with the N-H group that is ______ residues ahead in the sequence.

Answer 14

four

Question 15

All the C=O and N-H groups in the amino acid are hydrogen bonded except

Answer 15

the terminal amino acids.

Question 16

There are ____ amino acids per turn of the alpha helix.

Answer 16

3.6

Question 17

_____-handed helices are very rare.

Answer 17

Left

Question 18

What kind of amino acids are unlikely to be found in an alpha helix?

Answer 18

• branched
• ones that form hydrogen bonds on their side chains
• ones without an N-H group

Question 19

A beta pleated sheet consists of _______ polypeptide chains.

Answer 19

two or more

Question 20

In beta sheets, can hydrogen bonds form within the same strand?

Answer 20

No, must be between different strands

Question 21

Beta strands can run _____ or _____.

Answer 21

parallel; anti-parallel

Question 22

In anti-parallel beta sheets, the N-H group and the C=O group of one amino acid form hydrogen bonds with

Answer 22

the C=O and N-H groups of the partner amino acid on the adjacent chain.

Question 23

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.

Answer 23

two

Question 24

Which amino acid is not favored in beta sheets?

Answer 24

proline

Question 25

Where is proline found?

Answer 25

In turns and loops

Question 26

In a turn, the C=O group of residue i is hydrogen bonded to the N-H group of residue

Answer 26

i + 3

Question 27

Type I and type II reverse turns differ by

Answer 27

a 180 degree flip of the peptide unit linking residues 2 and 3

Question 28

Omega loops are how many amino acids long?

Answer 28

6-16

Question 29

Are turns or loops more structured?

Answer 29

turns