Block 1

Question 1

Non-polar Amino Acids

Answer 1

MILFY GAP VW

Question 2

Polar Amino Acids (non charged)

Answer 2

STNQC

Question 3

Polar Amino Acids (charged)

Answer 3

HERD K

Question 4

Aromatic Amino Acids

Answer 4

Tryptophan
Phenylalanine
Tyrosine

Question 5

pKa

Answer 5

pH at which a group is 50% protonated and 50% unprotonated

Question 6

Raising pH 1 unit from pKa.. what is ratio of unprot. to prot.

Answer 6

10:1

Question 7

isoelectric point

Answer 7

pI

pH where the AA. peptide, or protein will have a net charge of zero

Question 8

buffering region

Answer 8

where the pH of the solution is near the pKa of an ionizable group

Question 9

pI equation

Answer 9

pk1 +pk2 / 2

Question 10

nascent

Answer 10

newly synthesized

Question 11

what AA always on N terminal

Answer 11

Methionine

Question 12

S-H –> S-S

Answer 12

cysteine to cystine bond
common in extracellular proteins b/c increases stability but not intracellular
can have interchain and intrachain

Question 13

Why are there limits to possible conformation states for a polypeptide?
what conformation?

Answer 13

strong electroneg of carbonyl O and amide N in peptide bond
forms partial double bond, delocalizes e- and creates resonance
chooses trans conformation

Question 14

what is largest driving factor to protein folding?

Answer 14

hydrophobic forces

Question 15

Explain funnel analogy

Answer 15

• reversible, local interactions that are both correct and incorrect happen but the correct ones cause alignment that facilitates more correct ones and increases stability.
  as you get closer to the native state, less possible conformations are incorrect (funnel)

Question 16

primary-quat structure

Answer 16

1: AA sequence
2: folding -> a helix vs b sheet
3: create domains/subunits
4: combination of subunits

Question 17

alpha helix (characteristics)

Answer 17

R handed
3.6 residues/turn
stabilized by H bonds between carbonyl carbon of AA i and amide proton of AA i+4
h bonds parallel to helix axis, R groups project outward
a helices on surface of protein are amphipathic

Question 18

B sheet (characteristics)

Answer 18

H bonds run between carbonyl o and amide H of non-contiguous parts of a chain
H bonds coplanar with the B sheet
R groups alternately project above and below the plane of the sheet
often form the hydrophobic core

Question 19

Parallel B sheet

Answer 19

N–C
N–C
N–C

bonds look diagonal

Question 20

Antiparallel B sheet

Answer 20

N–C
C–N
N–C

bonds look straight up and down

Question 21

Can you have mixed B sheets?

Answer 21

yes

Question 22

relative stability of beta sheets?

Answer 22

all equivalent and allow dense packing

Question 23

Reverse/B/hairpin turns

Answer 23

found in antiparallel beta sheets if strands are part of same chain
know type 1 occurs 2x as frequently (just differ on orientation of peptide bonds between 2 and 3)

Question 24

why does 2nd structure matter with hydrophobic cores?

Answer 24

peptides bonds are polar and 2nd structure allows for H bonding between the polar areas of AA instead of those polar areas binding H20

Question 25

what is special about proline and 2ndary structure?

Answer 25

proline cannot form H bonds of a helix or b sheets so often found where they end

Question 26

domain

Answer 26

smallest thermodynamically stable unit of protein | often account for a particular part of an enzyme's active site

Question 27

subunits interacting is what structure?

Answer 27

quaternary

Question 28

metomorphic proteins

Answer 28

2 funnel holes | multiple options for structures that are equal in native state energy

Question 29

alpha keratin what type of helix

Answer 29

2 R handed alpha-helices intertwined in a L handed supercoil (alpha coiled coil)

Question 30

what type of bonding between coils of a-keratin?

Answer 30

non covalent and covalent (disulfide bonds) between coils | moderate # of disulfide bonds to allow stretch and recoil

Question 31

what family does a keratin belong to?

Answer 31

large family of coiled-coil proteins that also include scaffolding for cells and myosin and tropomyosin

Question 32

Collagen general facts

Answer 32

20-25% of protein in your body (most abundant protein in the body) superfamily of molecs. rich in proline (gives rigidity) and glycine (every 3rd position to fit into space where three strands come together)

Question 33

Collagen structure

Answer 33

long rigid structure where 3 polypeptides are wond around each other in a rope-like triple helix

Question 34

individual chains of collagen

Answer 34

alpha chains left handed helices (not left handed alpha helices though) three wound in R handed triple helix

Question 35

other words for coiled coil

Answer 35

super coil or triple helix

Question 36

collagen microfibrils

Answer 36

multiple triple helices

Question 37

what is the Y in Gly-X-Y

Answer 37

hydroxyproline or hydroxylysine formed through post-translational hydroxylation enzymes that catalyze this require Vit C (ascorbate)

Question 38

what is the X in Gly-X-Y

Answer 38

usually proline

Question 39

symptoms of scurvy

Answer 39

corkscrew hair | dental problems

Question 40

pathway of collagen

Answer 40

procollagen -- ecm-- collagen --peptidases cleave terminal propeptides-- tropocollagen (mature collagen triple helix) --self-assemble fibrils with crosslinking-- mature collagen fibers

Question 41

Elastin facts

Answer 41

connective tissue protein w/ rubber-like properties lungs, arterial walls, elastic ligaments composed primarliy of small nonpolar aa rich in proline and lysine but not hydroxylated

Question 42

degradation

Answer 42

alpha1-antitrypsin inhibits elastase which degrades elastin

Question 43

a1-antitrypsin insufficiency what how and why

Answer 43

if nothing inhibits elastase, then it can destroy alveolar epithelium genetic insufficiency and environmental (cig smoke oxidizes met residue.. a1-AT cannot inactivate elastase)

Question 44

what is elastase released by?

Answer 44

neutrophils

Question 45

precursor to elastin and mech

Answer 45

tropoelastin (excreted into ecm) becomes elastin by glycoprotein microfibril interaction