Chapter 5: 3-D Structure of Proteins

Question 1

The rigidity of a peptide group can be attributed to..

Answer 1

the double bond character

Question 2

Is a peptide’s carbonyl-nitrogen bond shorter or longer than a regular carbon-nitrogen single bond?

Answer 2

shorter

Question 3

Peptide groups usually assume the….

Answer 3

trans conformation

Question 4

In the trans conformation of a peptide group the alpha carbons are found on the ___________ side of the amide groups

Answer 4

opposite

Question 5

Why is the trans conformation more stable?

Answer 5

b/c of the steric interference of the R groups or side chains

Question 6

The ________ of a peptide are the atoms that participate in peptide bonds while ignoring the side chains.

Answer 6

backbone

Question 7

The torsion angle about the alpha C-N bond is known as

Answer 7

Phi (Φ)

Question 8

The torsion angle about the alpha C-C bond is known as

Answer 8

Psi (Ψ)

Question 9

The angles that Phi and Psi can adopt in a peptide bond can be depicted in a diagram called a…

Answer 9

Ramachandran Diagram

Question 10

The Ramachandran Diagram is about 75% blank, what does this indicate?

Answer 10

most conformation of Phi and Psi are conformationally inaccessible

Question 11

In a Ramachandran Diagram, heavy clustering on the top right-hand side is indicative of…

Answer 11

left-handed α helix

Question 12

In a Ramachandran Diagram, heavy clustering on the bottom left-hand side is indicative of…

Answer 12

right-handed α helix

Question 13

In a Ramachandran Diagram, heavy clustering on the top left-hand side is indicative of…

Answer 13

β pleated sheets

Question 14

On a Ramachandran Diagram antiparallel β pleated sheets are found…

Answer 14

on the top left-hand side slightly more to the left

Question 15

On a Ramachandran Diagram parallel β pleated sheets are found…

Answer 15

on the top left-hand side slightly more to the right

Question 16

Helical structures can be characterized by

Answer 16

the # of peptide units (n) and pitch (p)

Question 17

define pitch

Answer 17

the distance the helix rises per turn

Question 18

right-handed helices have a _______ “n” value

Answer 18

positive

Question 19

left-handed helices have a _______ “n” value

Answer 19

negative

Question 20

What is a helical polypeptide arrangement that has both allowed conformation angles and favorable hydrogen bonds

Answer 20

α helix

Question 21

Linus Pauling discovered the

Answer 21

α helix

Question 22

The α helix is a common secondary structure found in…

Answer 22

fibrous & globular proteins

Question 23

How are right-handed α helices formed?

Answer 23

from polypeptides made from L-α-amino acid residues

Question 24

How are left-handed α helices formed?

Answer 24

from polypeptides made from D-α-amino acid residues

Question 25

In β pleated sheets hydrogen bonding occurs between

Answer 25

neighboring chains

Question 26

What are common structural motifs of proteins

Answer 26

β sheets

Question 27

What type of β sheet is less stable? Why?

Answer 27

- parallel - b/c they are distorted when compared to antiparallel

Question 28

What were the 2 repetitive structures discussed?

Answer 28

β bends Ω loops

Question 29

β bends normally connect successive strands of

Answer 29

antiparallel β sheets

Question 30

What normally occur at protein surfaces

Answer 30

β bends & Ω sheets

Question 31

In type II β bends, residue 2 is usually ____ while residue 3 is usually ____.

Answer 31

proline glycine

Question 32

What were the fibrous proteins discussed?

Answer 32

keratin & collagen

Question 33

α keratins normally occur in

Answer 33

mammals

Question 34

β keratins occur in

Answer 34

birds and reptiles

Question 35

acidic polypeptides are composed of

Answer 35

type I keratin chains

Question 36

basic polypeptides are composed of

Answer 36

type II keratin chains

Question 37

What is a unique characteristic of keratin?

Answer 37

it has a heptad pseudorepeat

Question 38

the heptad pseudorepeat has *a* and *d* positions that form the

Answer 38

hydrophobic strip

Question 39

Keratin is rich in what type of residues?

Answer 39

cysteine (Cys)

Question 40

Cysteine residues in keratin form disulfide bonds that cross link

Answer 40

adjacent polypeptide chains | makes it resistant to stretching

Question 41

Keratins can be _____ like _____ and _____, or ____ like _____.

Answer 41

hard hair nails soft skin

Question 42

Mutation of the keratin gene leads to

Answer 42

Epidermolysis Bullosa

Question 43

Describe Epidermolysis Bullosa

Answer 43

rupturing of epithelial cells resulting in skin blistering

Question 44

What protein occurs in multicellular animals, is extracellular, and occurs most abundantly in vertebrates.

Answer 44

collagen

Question 45

collagen is organized into....

Answer 45

insoluble fibers w/ incredible tensile strength

Question 46

what is a major stress-bearing component of connective tissue

Answer 46

collagen

Question 47

Collagen has distinct amino acid composition with high levels of

Answer 47

Gly Pro Hyp | Hyp- hydroyproline -OH group @ C3

Question 48

Hydroxylated residues of hydroxyproline result from

Answer 48

synthesis by prolyhydroxylase

Question 49

prolyhydroxylase requires ______ for its activity

Answer 49

ascorbic acid (vitamin c)

Question 50

What disease results from vitamin c deficiency

Answer 50

Scurvy

Question 51

Scurvy results in

Answer 51

skin lesions blood vessel fragility

Question 52

When do collagen residues denature @ 25°C?

Answer 52

when they are synthesized w/o Hyp

Question 53

Collagen consists if repeating triplets of Gly-X-Y amino acids where X is ____ and Y is _____

Answer 53

proline hydroxyproline

Question 54

What heritable disorder results from the mutation of Type I collagen

Answer 54

Osteogenesis Imperfecta

Question 55

All known amino acid changes within the.....results in abnormalities

Answer 55

triple helices region of Type I collagen

Question 56

Examples of globular proteins include

Answer 56

- enzymes - transport & receptor proteins

Question 57

globular proteins contain both

Answer 57

α and β sheets

Question 58

functions of carbonic anhydrase

Answer 58

- converts CO2 to bicarbonate (HCO3-) - maintains acid-base balance - helps transport CO2 out of tissues - metalloenzyme

Question 59

Metalloenzyme means

Answer 59

it requires a metal in its active site for activity

Question 60

What is the metal needed for carbonic anhydrase?

Answer 60

zinc ion

Question 61

The zinc ion is held in place by

Answer 61

imidazole rings of 3 His residues

Question 62

What does NOSEY stand for

Answer 62

Nuclear Overhauser Effect Spectroscopy

Question 63

NOE determines interproton distances through

Answer 63

space