Chapter 5- Secondary Structure

Question 1

Primary structure definition

Answer 1

amino acid sequence of protein

Question 2

Secondary structure definition

Answer 2

local spatial arrangements of the backbone atoms

Question 3

Tertiary structure definition

Answer 3

3D structure of the entire polypeptide chain

Question 4

Quaternary structure definition

Answer 4

Spatial arrangements of protein subunits

Question 5

Peptide bonds are ____ bonds

Answer 5

amide bonds

Question 6

Proteins result from the formation of covalent peptide bonds by

Answer 6

Condensation

Question 7

A polymer of two amino acids is called

Answer 7

dipeptide

Question 8

A polymer of many amino acids

Answer 8

polypeptide

Question 9

Avg mass of amino acid

Answer 9

110 g/mol

Question 10

Polypeptides are _____ polymers not branched

Answer 10

linear

Question 11

The alpha H bonds and carboxyl groups run in the _____ direction

Answer 11

same

Question 12

Amino acids are always read from the __ terminus to the __ terminus

Answer 12

N (amino terminus), C

Question 13

In a peptide group a C–N bond is ___ than a simple amine, while a C=O bond is ____ than a simple ketone

Answer 13

Shorter, Longer

Question 14

Peptide bond has _____ double bond character

Answer 14

~40%

Question 15

C–N torsion angle is called __ and the C–C torsion angle is called ___

Answer 15

Phi, Psi

Question 15

The trans configuration is more favored than the cis configuration because

Answer 15

the trans configuration has less steric hindrance and is more stable

Question 15

the C–N bond is unable to ____

Answer 15

Rotate

Question 15

Side chains dictate the bond angles because

Answer 15

different bond angles reorient to accommodate other groups around it

Question 16

An alpha helix can be right-handed or left-handed which means it has

Answer 16

Chirality

Question 16

Glycine in a peptide chain provides

Answer 16

• flexibility to proteins
• often found in places where proteins make sharp turns

Question 16

Proline in a protein chain provides

Answer 16

• structure rigidity (due to cyclic side chain)
• may be found in kinks of the protein

Question 17

polypeptide made of L-alpha amino acids will have n=___ and pitch =____

Answer 17

3.6 amino acids per turn, 5.4 A

Question 18

____ and _____ of peptide bond point along the long axis (in the opposite direction)

Answer 18

N-H, C=O

Question 19

The sum of all H bonds contributes to stability which means

Answer 19

more H bonds= more stability

Question 20

side chains in an alpha helix point

Answer 20

outwards (avoids steric interference)

Question 21

How do side chains affect stability?

Answer 21

1. affecting the peptide backbone
2. through side chain- side chain interactions

Question 22

How many degrees between each amino acid in an alpha helix

Answer 22

100

Question 23

interactions between side chains can lead to either the ______ or _______ of the helix

Answer 23

destabilization or stabilization

Question 24

Steric clash means

Answer 24

two large bulky side chains stacked on top of each other is more likely to destabilize the helix

Question 25

ASP and LYS have formed a _____ interaction

Answer 25

salt bridge that stabilizes the helix (different charges)

Question 26

Asp and Glu have a _____ interaction

Answer 26

repulsion interaction that destabilizes the helix (same charges)

Question 27

Aromatic amino acids can ____ which are favorable ______ ________

Answer 27

stack ( pi stacking), hydrophobic interactions

Question 28

amino acids that tend to form an alpha helix

Answer 28

MALEK (met, ala, leu, glu, and lys)

Question 29

Beta-branched amino acids that make them more difficult to adopt an alpha-helical conformation

Answer 29

Val, Ile, Thr

Question 30

Amino acid that is entropically expensive and destabilizes helices

Answer 30

Gly

Question 31

Conformationally rigid with no H bonding possible, known to destabilize helicies and may form a kink

Answer 31

pro

Question 32

All dipoles in an alpha helix point in the ____ direction which results in a ______ ______ between the C terminal and N terminal

Answer 32

same, macro dipole (c end is neg and N end is pos)

Question 33

Dipoles in an alpha helix result in

Answer 33

destabilization through entropic effects

Question 34

the N terminal of an alpha helix is often capped by a _____ side chain while a ____ side chain caps a C terminal

Answer 34

negative, positive

Question 35

Antiparallel beta sheets involve two chains running in ____ directions, the H bonds are ~ ______ to each other

Answer 35

opposite, parallel

Question 36

Parallel beta-sheets involve two side chains running in the _____ directions, the H bonds are formed on ____

Answer 36

same, angles

Question 37

Beta strands exhibit a _____ ______ ______ due to the chirality of the amino acids

Answer 37

right-handed twist

Question 38

Beta turns are commonly formed by

Answer 38

proline and glycine

Question 39

beta turns give proteins _____ and promotes the formation of _______ ______ ____

Answer 39

globularity, anti-parallel beta sheets

Question 40

The coil/loop conformation is completely ______ and is typically found on the _____ _____ of the proteins

Answer 40

unstructured, outer surface

Question 41

Random coils are usually ______ and ______ but do not conform to any ______ ______ ____

Answer 41

organized and stable, frequently recurring pattern

Question 42

The stability of seconds structures is determined by

Answer 42

1. steric repulsion minimized
2. H bonding is maximized

Question 43

Characteristics of Circular Dichroism Spectroscopy

Answer 43

• absorption spectroscopy
• provides information on the secondary structure content of proteins
• signal; originated from the amide group and the phi/ psi angles