Ch 4

Question 1

The spatial arrangement of a 3-D strutcture is known as

Answer 1

conformation

Question 2

True or false: the native (folded) conformation of a 3-D structure has the lowest free energy (G) meaning it is the least stable conformation

Answer 2

False, it is the MOST stable

Question 3

What are the two ways 3-D conformation is stabilized?

Answer 3

‘burying’ hydrophobic groups

maximizing H-bonding

Question 4

A peptide bond can twist. True or false?

Answer 4

False, the nitrogen pulls electrons for partial double bond characteristics, when there is a partial double bond, no twisting

Question 5

How many atoms are there in a plane of a peptide bond?

Answer 5

6 atoms

Question 6

Is 360 degree rotation about the N-C and C-C bonds possible?

Answer 6

yes, it is what makes peptides and proteins more flexible, but certain angles are more stable than others

Question 7

What is the most comon example of a secondary structure

Answer 7

alpha helix

Question 8

how are secondary structures stabilized?

Answer 8

by hydrogen bonds

and by R groups on the outside

Question 9

With what molecule (amino acid) can an alpha helix not be formed?

Answer 9

proline - disrupts any alpha helix “proline kink”

Question 10

What type of structure is a beta sheet?

Answer 10

a secondary structure

Question 11

what is an antiparallel beta sheet?

Answer 11

the beta sheet is where at least to parts of a peptide are linked together, in an antiparallel beta sheet the polypeptides alternate directions they are moving in

Question 12

True or false, parallel beta sheet strands alternate the directions they are moving in?

Answer 12

False, they all go in the same direction

Question 13

In globular proteins how much of the amino acid residues are in turns or loops between beta sheets and/or alpha helices?

Answer 13

1/3 of the aa residues

Question 14

2/3 of the amino acids are part of what?

Answer 14

alpha helices or beta sheets (the other 1/3 are connectors)

Question 15

Secondary structure involves what?

a. the spatial arrangement of adjacent amino acids
b. the 3-d structure involving long-range interactions

Answer 15

A

Question 16

tertiary structure involves what?

a. the spatial arrangement of adjacent amino acids
b. the 3-d structure involving long-range interactions

Answer 16

B

Question 17

What are the two major groups of proteins (tertiary structures)?

Answer 17

fibrous and globular

Question 18

What are the three major types of fibrous proteins?

Answer 18

alpha keratin
collagen
silk fibroin

Question 19

What are the defining characteristics of fibrous proteins?

Answer 19

they are elongated, and structural proteins

long amino acid pieces

Question 20

All are true about alpha keratin, except:

a. strong
b. right handed alpha helix (primary structure)
c. the secondary structure is a left handed alpha helix
d. it is strengthened by cross-links
e. it is in tendons, cartilage and bone

Answer 20

E.

alpha keratin is in hair, nails, hooves, horns, and outer skin layers

Question 21

What stabilizes the structure of keratin?

Answer 21

cross links ***cysteine forms cross links

Question 22

What part of the body does collagen make up?

Answer 22

tendons, cartilage, bone

Question 23

True or false: collagen can be pulled apart.

Answer 23

False, collagen has high tensile strength

Question 24

What is unique/significant about collagen?

Answer 24

it has hypro and hylys cross links which are not part of the normal 20 amino acids

Question 25

True or false: the left handed helix in collagen is an alpha helix.

Answer 25

False, it is a single strand, it is the alpha chain but not an alpha helix

Question 26

What does the right handed form of collagen create?

Answer 26

A superhelix (3 helices)

Question 27

What inactivates the enzyme required to convert Pro to Hypro?

Answer 27

the absence of vitamin C

Question 28

The absence of vitamin c can lead to collagen instability and connective tissue problems, what can this cause?

Answer 28

Scurvy

Question 29

We need vitamin C to make what for collagen?

Answer 29

vitamin C is needed to make hypro for collagen

Question 30

What two amino acids are rich in silk fibroin?

Answer 30

Ala and Gly (small, compact)

Question 31

What structure predominates in silk fibroin?

Answer 31

Beta sheets (antiparallel)

Question 32

True or false: silk fibroin can be stretched.

Answer 32

False, it is fully extended

Question 33

What is important about silk fibroin?

Answer 33

There is extensive hydrogen binding and van der waals interactions between sheets, but no covalent cross links making it flexible (Long sheet, no cross links, very flexible)

Question 34

How are alpha helices cross linked?

Answer 34

by disulfide bonds

Question 35

Match the following a. alpha helix, cross linked by disulfide bonds b. beta conformation c. collagen triple helix 1. collagen of tendons, bone matrix 2. alpha keratin of hair, feathers, nails 3. silk fibroin

Answer 35

a, 2 b, 3 c, 1

Question 36

What is important about intrinsically disordered proteins or protein segments?

Answer 36

They may include up to 1/3 human proteins - flexibility allows interaction with many diff. partner molecules - some wrap around each and inhibit targets