Chapters 5 & 6 Review

Question 1

Roles of proteins

Answer 1

• monitoring extracellular and intracellular conditions
• sending info to other cell components
• important structural components.

Question 2

Primary Structure

Answer 2

The amino acid sequence itself

Question 3

Secondary Structure

Answer 3

α-helix or β-sheet (optimization)

Question 4

Tertiary Structure

Answer 4

One complete protein chain

Question 5

Quaternary Structure

Answer 5

Multiple tertiary structures that make an oligomeric protein (2 or more tertiary structures)

Question 6

Peptide bonds assume _______ conformation.

Answer 6

Trans

Question 7

Peptide bond = ___________

Answer 7

a nitrogen bound to a carbonyl

Question 8

Side chain is always on the _____ carbon.

Answer 8

α ; allowed because single bonds are more flexible.

Question 9

Can rotate along Cα - N bond

Answer 9

Phi (Φ)

Question 10

Can rotate along Cα - C bond

Answer 10

Psi (Ψ)

Question 11

Steric Hinderance

Answer 11

The two groups can rotate until the carbonyl hits the hydrogen bond

Question 12

Which amino acids do not fit in the Ramachadran Diagram?

Answer 12

Proline and Glycine

Question 13

Of a double helix, there are ____ residues per turn (160 degree turn). The pitch (rise) is ______.

Answer 13

3.6 residues ; 5.4 angstroms

Question 14

All carbonyls will ___________.

Answer 14

Hydrogen bond. Utilizes the hydrogen backbone of the helix.

Question 15

With β-sheets, there are _____degrees between carbonyls.

Answer 15

180

Question 16

________ and _______ bonding optimize the hydrogen bonding between the β-sheets. Each pleating of the β-sheet is about _____ angstroms.

Answer 16

Antiparallel and parallel ; 7.8

Question 17

Optimum number of beta sheets

Answer 17

8 beta sheets

Question 18

________ is more conserved than sequence

Answer 18

structure

Question 19

All side chains are ____________.

Answer 19

Always on the outside

Question 20

Bragg’s Law

Answer 20

sin θ = (λ/2d) ; 2d sinθ = λ

Question 21

______ is better for observing protein in solution. Shows the backbone

Answer 21

NMR

Question 22

________ is good for rigid, stationary molecules

Answer 22

Crystallography

Question 23

The protein core is

Answer 23

hydrophobic

Question 24

Supersecondary structures are called

Answer 24

motifs

Question 25

How does something folding (protein structure) increase entropy?

Answer 25

Water is being lost

Question 26

Supersecondary structures make ____, which then make _______.

Answer 26

domains ; proteins

Question 27

Positive hydropathy index

Answer 27

hydrophobic (makeup inside)

Question 28

negative hydropathy index

Answer 28

hydrophilic (makeup outside)

Question 29

_________ is the most dominant force driving protein stability and structure.

Answer 29

Hydrophobic effect

Question 30

What does a metal ion do in the middle of the protein?

Answer 30

It stabilizes the unit.

Question 31

Salt bridge

Answer 31

Occurs between the two charged ions from the amino acids.

Question 32

Four main factors of the Protein Stability

Answer 32

1) Hydrophobic Effect
2) Ionization of side chains (affected by pH)
3) Metal Ions
4) Disulfide Bonds

Question 33

Four ways to denature proteins

Answer 33

1) Temperature (melt)
2) pH ( ionization of the side chains)
3) Detergents
4) Chaotropic agents

Question 34

Chaotropic agents

Answer 34

-Increase the solubility of nonpolar substances in water.
Can be used to denature proteins.
-Ex: Guanidium ions, Urea

Question 35

BME (aka 2-mercaptoethanol)

Answer 35

Cleaves disulfide bonds

Question 36

Define hydropathy

Answer 36

A measure of the combined hydrophobicity and hydrophilicity of an amino acid residue. it is indicative of the likelihood of finding that residue in a protein interior.