Chapter 4

Question 1

What is the native fold?

Answer 1

-proteins 3-d conformation in aqueous solution that can fulfill a biological function

Question 2

What are the four favorable interactions in proteins?

Answer 2

1. hydrophobic effect
2. Hydrogen bonding (dipole-dipole)
3. Van der Waals ( LDF and steric repulsion)
4. Electrostatic Interactions

Question 3

Peptide bond?

Answer 3

an substituted amide linkage between the alpha-amino group of one amino acid and the alpha-carboxyl of another with the elimination of water

Question 4

what does resonance cause the peptide bond to do?

Answer 4

• less reactive
• quite rigid and planar
• exhibit a large dipole moment in the favored trans configuration

Question 5

Is protein folding favored or unfavored?

Answer 5

Unfavored.

Because it is becoming more ordered so entropy increases and to be favored you want - ΔG

Question 6

what is Phi ϕ

Answer 6

bond angle around the α - carbon and amide nitrogen group

Question 7

What is Psi ψ

Answer 7

bond angle around the α - carbon and amide nitrogen bond

Question 8

Is rotation around the peptide bond permitted or not permitted?

Answer 8

not

Question 9

Is rotation around the bonds connected to the α - carbon permitted or not permitted?

Answer 9

it is permitted

Question 10

ϕ and ψ bonds angles help create what structures

Answer 10

secondary

Question 11

Secondary Structures are

Answer 11

refers to spatial arrangement of polypeptide chain

Question 12

What are the two common arrangements of secondary structures are:

Answer 12

α helix

β sheet (really two β sheet = 1 β strand)

Question 13

α helix more ____, with __ dihedral angles

Answer 13

compact, ψ (bond angle around the α - carbon and amide nitrogen bond)

Question 14

α helix backbone is held together by ____ bonding between the nearby backbone amides

Answer 14

Hydrogen

Question 15

α helix is a right-haded helix with ___ residues per turns

Answer 15

3.6

Question 16

What direction in the α helix is peptide bonds and side chains aligned?

Answer 16

peptide bonds - rough parallel

side chains - point out and perpendicular

Question 17

Can the inner diameter of the α helix fit anything “inside”?

Answer 17

no it can’t fit anything inside

Question 18

Where does the outer diameter of the α helix allow it to fit?

Answer 18

major groove of DNA

Question 19

What small hydrophobic residues are stronger helical formers?

Answer 19

Ala and Leu

Alanine and leucine

Question 20

What residues are helical breakers?

Answer 20

Pro and Gly

Pro (Proline) - rotation around the N- C α bond is impossible

Gly (glycine) - the H can support other conformations

Question 21

β sheet backbone is more ____, with ___ dihedral

Answer 21

extended, ψ

Question 22

The planar peptide bond and tetrahedral of the α-carbon create a ___ of the β sheet

Answer 22

pleated sheet

-held by hydrogen bonds of distal backbone amides

Question 23

β sheet side chains protrude the sheet in alternating __ and ___ direction.

Answer 23

up and down

Question 24

Anti-parallel β sheet the H-bond strands run in ___ direction

Answer 24

opposite

Question 25

Parallel β sheet the H-bond strands run in ___ direction

Answer 25

same

Question 26

In β turns 180 degree turn is accomplished by __ amino acids?

Answer 26

4

Question 27

β turns are stabilized by what?

Answer 27

hydrogen bonding from carbonyl oxygen and amide proton

Question 28

In β turns its common that ___ is in position 2 and ___ is in position 3

Answer 28

Proline is in 2 | Glycine is in 3

Question 29

Motifs?

Answer 29

arrangements of several secondary structure elements

Question 30

Tertiary Structure

Answer 30

big picture, overall spatial arrangement of atoms in chain or protein

Question 31

Collagen is

Answer 31

connective tissue: tendons, cartilage

Question 32

Each collagen chain is a long __, ____, ____, rich left-handed helix

Answer 32

Gly, Pro, hydroxyPro

Question 33

Three collagen chains intertwine into _________

Answer 33

right-handed superhelical triple helix

Question 34

Water soluble globular proteins

Answer 34

fold so hydrophobic groups are on inside and hydrophilic on outside

Question 35

Lipid soluble globular proteins

Answer 35

hydrophobic on surface and hydrophilic on inside

Question 36

Quaternary structure

Answer 36

formed by a spontaneous assembly of individual polypeptides into a larger functional cluster

Question 37

A proteins function is dependent on what?

Answer 37

3d/native form

Question 38

loss of structural integrity with accompanying loss of activity is called

Answer 38

denaturation

Question 39

how can a protein be denatured?

Answer 39

- heat or cold - extreme ph - organic solvents - chaotropic agents

Question 40

The psi bond refers to which bond in the amino acid?

Answer 40

Bond between the alpha carbon and carbonyl carbon | *Phi bond is between alpha carbon and NH3 group

Question 41

What type of intermolecular interactions are predominately responsible for the stabilization of secondary structures?

Answer 41

H-bonding (occurs b/w the carbonyl and amide groups of the amino acid ALSO electrostatic forces play a small role

Question 42

In which peptide secondary structure are you most likely to find Proline residues?

Answer 42

Beta sheet

Question 43

A Ramachandran plot shows you the tendency of amino acids to interact in certain ways compared to others.. What factors influence, both favor and disfavor, the interaction of amino acids in certain configurations?

Answer 43

Prohibit Steric Hindrance of backbone atoms/side chains Repulsive forces between backbone atoms/side chains Promote H-bonding Attractive forces between atoms (either electrostatic or dipole) **Always look at h-bonding first for a Q like this

Question 44

Steric hindrance

Answer 44

- -size of the R-group determines the angle of the bond connecting the back-bone - -If you have opposite charges on two R groups on same side = attractive = stable

Question 45

In Collagen, what makes up the right handed, superhelical triple helices?

Answer 45

3 left handed collagen chains intertwine into a right-handed superhelical triple helix

Question 46

Thermodynamics: Is the folding of a peptide into its native form entropically favorable or unfavorable?

Answer 46

Unfavorable (at level of the peptide) | Folding = decreases entropy

Question 47

What type of secondary structure would you find in this type of epithelium (keratinized stratified squamous) in much greater volumes than in the epithelium of the esophagus (non-keratinized in esophagus)?

Answer 47

Keratin, a protein, is made of several alpha helices that have been cross-linked by disulfide bonds

Question 48

Looking a Beta sheet with many turns.. Asked to identify the 3rd amino acid in a specific beta turn sequence.. What’s your guess?

Answer 48

Glycine (Mneumonic 3G like the internet) | **Know position of gly and pro (2) on beta sheet

Question 49

Fibrous proteins typically consist of how many polypeptide subunits?

Answer 49

Alpha helices only | *side note: beta barrel forms in globular protein

Question 50

You extract a protein from the lipid bilayer of a cancer cell. What category of protein would you label this as?

Answer 50

Globular protein

Question 51

``` The basic building block of a Collagen protein is a helix. Which of these amino acids would you NOT expect to find in this helix? A. Proline B. Hydroxoproline C. Glycine D. Threocine ```

Answer 51

D. Each collagen chain is a long Gly, Pro, hydroxyPro rich left-handed helix Starts with 3 left handed helix Right handed helix, basically opposite of left handed (lecture 2 page 36) *Memorize slide 36

Question 52

Got a new protein.. Wants to figure out what's responsible for the shape this protein takes in its native form.. What would be an underlying determinant of a random proteins tertiary structure?

Answer 52

Its primary structure sequence (polypeptide sequence) If keyword is "drive" then going to be some "effect" like interactions

Question 53

Which is most likely to be found in a right handed alpha helix-- Leucine, Proline, and Glycine?

Answer 53

Leucine

Question 54

The Phi bond refers to which bond in the amino acid?

Answer 54

Bond between alpha carbon and amide nitrogen

Question 55

The structure of a protein is ultimately determined by its ___ sequence and dictates in turn the biological function of the protein

Answer 55

Primary

Question 56

What forces drive the formation of a peptide's secondary structure?

Answer 56

Side chain interactions | Ex. H-bonding, hydrostatic forces, ionic interactions

Question 57

What is most likely the 2nd AA in a specific Beta turn sheet?

Answer 57

Proline (I have 2 PEE)

Question 58

How many AAs are required to complete a Beta turn in a beta sheet?

Answer 58

4