Protein Structure and Function 1 (L3)

Question 1

what is the bond between amino acids in a protein?

Answer 1

peptide bond (amide bond)

Question 2

how is a peptide bond formed?

Answer 2

condensation/dehydration reaction

Question 3

hydrophobic amino acids

Answer 3

A, V, I, L, M, F, Y, W (not charged)

Question 4

hydrophilic amino acids

Answer 4

either polar or carry net charge:
Basic - K, R, H (positive charge)
Acidic - D, E (negative charge)
Polar uncharged - S and T (hydroxyl), and N and Q (amide group)

Question 5

what functional group does the side chain of His contain?

Answer 5

imidazole ring (ring w/ 2 N’s)

Question 6

special amino acids

Answer 6

P: structural rigidity
G: neutral, very small
C: sulfhydryl group that can form -S-S- bonds - relatively permanent covalent bond (adds rigidity)

Question 7

what are the 5 amino acid modifications?

Answer 7

1. acetylation
2. phosphorylation
3. hydroxylation
4. methylation
5. carboxylation

Question 8

what two amino acid modifications are important for control of gene expression?

Answer 8

acetylation and methylation

Question 9

what does the hydroxylation of tyrosine initiate?

Answer 9

catecholamine biosynthesis

Question 10

what is one implication of phosphorylation?

Answer 10

activates/inactivates proteins as part of signal transduction - can get uncontrolled growth if a protein is always on (cancer)

Question 11

what is the charge on an amino acid a function of?

Answer 11

pH

Question 12

what is a buffer?

Answer 12

substance that resists changes in pH

Question 13

Ka

Answer 13

acid dissociation constant

Question 14

relationship b/w acid strength and Ka

Answer 14

higher Ka = stronger acid

lower Ka = weaker acid

Question 15

H-H equation

Answer 15

pH = pKa + log ([A-] / [HA])

Question 16

pKa

Answer 16

pH where [HA] = [A-]

Question 17

when do buffers work best?

Answer 17

b/w pKa+1 and pKa-1 (best when pH = pKa)

Question 18

primary structure of a protein

Answer 18

linear sequence of aa’s - N terminal and C terminal

Question 19

how are proteins built?

Answer 19

from N-terminal to C-terminal

Question 20

why do peptide bonds have planar properties and what does this cause in the arrangement of the polypeptide?

Answer 20

partial db character that prevents free rotation -> planar;

causes R groups to come off opposite of one another in an alternating manner

Question 21

secondary structure - 4 types of side chain interactions

Answer 21

1. electrostatic
2. H-bond
3. hydrophobic interactions
4. covalent bond (disulfide)

Question 22

alpha helix

Answer 22

side chain 1 interacts with side chain 4 aa away; side chains point to outside

Question 23

beta sheet

Answer 23

antiparallel manner; side chains point perpendicular to plane of backbone; pleat due to permanent fold b/c of peptide bond rigidity

Question 24

supersecondary structure - 3 motifs

Answer 24

1. coiled-coil motif
2. EFhand/helix-loop-helix motif
3. zinc-finger motif

Question 25

what holds the coiled-coil motif together

Answer 25

side chain interactions b/w the 2 helices forms a hydrophobic stripe that holds coil together

Question 26

Ras and cancer implications

Answer 26

Ras is a protein involved in signal transduction when active - mutations G12V and Q61K stabilize Ras-GTP binding, which keeps the molecular switch in the on state -> can lead to cancer

Question 27

quaternary structure

Answer 27

multiple polypeptide chains

Question 28

examples of quaternary structure

Answer 28

hemagluttinin (HA) - 3 subunits, each w/ 2 polypeptides

hemaglobin (Hb) - 4 subunits, 2 alpha and 2 beta

Question 29

hemagluttinin

Answer 29

surface protein on the flu virus (H_N_: is the H)

Question 30

difference b/w fetal and adult Hb

Answer 30

fetal Hb has higher affinity for O2 than adult Hb so that it can take O2 from the mother

Question 31

Mb vs Hb

Answer 31

Mb binds differently than Hb (one subunit vs. four)

Mb - hyperbolic curve; Hb - sigmoidal curve (cooperativity)

Question 32

Hb mutation can cause what disease?

Answer 32

B-chain mutation at Q6V -> chains of Hb -> changes morphology of RBC -> sickle cell anemia

Question 33

sickle cell anemia and malaria

Answer 33

mutation not always bad -> sickle cell carrier provides malaria resistance: higher turnover of RBC’s, parasite doesn’t finish life cycle -> not infected as easily)