L1 and L2 Amino Acids and pH

Question 1

of proteins in bacterium vs human cell

Answer 1

3000 vs 30000

Question 2

Amino acids made of?

Answer 2

H O N C and occasionally S

Question 3

Amino acids consist of

Answer 3

Common core (a-carbon w H, amino and carboxyls) plus R-group

Question 4

With the exception of ___, aC is chiral

Answer 4

glycine

Question 5

Only ___ amino acids are present in proteins

Answer 5

L

Question 6

With the exception of ___, all amino acids are a-amino acids

Answer 6

proline (secondary amine = imine)

Question 7

R group tree

Answer 7

20 > 9 non-polar and 11 polar > 6 uncharged and 5 charged > 2 acidic and 3 basic

Question 8

nonpolar Amino Acids

Answer 8

GAVLIPTMP

Question 9

nonpolar amino acids have even distribution of charge except

Answer 9

Met and Trp, where polar atom enegativity masked by surrounding hydrocarbons

Question 10

formation of ____ in the inside of proteins is a major force behind the folding of globular proteins

Answer 10

hydrophobic core (hydrophobic effect)

Question 11

uncharged polar

Answer 11

S Th Ty (-OH) Asp Glu (-CONH2) Cysteine (-SH) neutral but have an electronegative group (NOS)

Question 12

though weak individually, strong in large numbers

Answer 12

H bonds

Question 13

strong bonds, oxidation between 2 cysteines

Answer 13

disulfide bonds, covalent

Question 14

only AA to make disulfide bonds

Answer 14

2 cysteines = cystine

Question 15

Negative charged AA (Acidic)

Answer 15

Aspartic Acid, Glutamic Acid, COOH (COO- at physio pH)

Question 16

Basic amino acids

Answer 16

Pos charged at physio pH Lysine, Arg, not His [between 0-1])

Question 17

charged AA’s can form __bonds

Answer 17

H and ionic

Question 18

21st AA

Answer 18

selenocysteine, selenium vs cysteine. Not in genome

Question 19

Aas provide sites for ___

Answer 19

post-translational modification, PhPhates or carbs to OH- groups

Question 20

___ and ____ are hydroxylated in mature collagen

Answer 20

proline and lysine

Question 21

pH remains between

Answer 21

7.35-7.45 vs life pH 6.8-7.8

Question 22

1 mole

Answer 22

6.023 x 10^23

Question 23

pH =

Answer 23

-log[H+]

Question 24

pH vs H

Answer 24

large change in H to get small change in pH

Question 25

____ are weak acids

Answer 25

Carboxy and amino

Question 26

Ka =

Answer 26

H A / HA

Question 27

pow high pka

Answer 27

high/low tendency to dissociate. Acidic/basic

Question 28

HH

Answer 28

pH = pKa + log[A-]/[HA] conj base / weak acid

Question 29

when [A-] = [HA]

Answer 29

acid is 50% dissociated

Question 30

pKa = pH

Answer 30

weak acid is 50% dissociated

Question 31

does pka change

Answer 31

no, intrinsic quality

Question 32

pKa -1 +1

Answer 32

91% HA, 9.1% A- vs vice versa

Question 33

Ph vs Pka

Answer 33

if ph

Question 34

only ____ can pass through membranes via passive diffusion

Answer 34

nonionized (uncharged) form

Question 35

potent anesthetic

Answer 35

sodium pentothal, intravenous, unconsciousness in <1 minute, WA pKa = 7.6

Question 36

buffer

Answer 36

weak acid/Conj base pair

Question 37

3 tier defense system

Answer 37

buffers (HCO3 most important) AA free in soln or part of proteins. Pulmonary ventilation, renal adjustments

Question 38

maximum buffering range

Answer 38

values close to pKa (pKa-1 to pKa +1)

Question 39

peptide bond

Answer 39

covalent bond between aCarboxyl group of one AA and amino group of next AA

Question 40

residue

Answer 40

AA added to part of peptide or protein

Question 41

peptide naming

Answer 41

add prefixes and -yl

Question 42

peptide bond structure

Answer 42

partial double bond (rigid and planar, adjacent bonds rotate phi and psi) trans side chains, uncharged polar, C=O and NH do H bonds

Question 43

written

Answer 43

amino N to carboxy C

Question 44

evolution did what now

Answer 44

conserved AA important to protein structure and function

Question 45

1 2 3 4 structure

Answer 45

sequence, local folding (stabilized by H bonds in the peptide bonds not R) a B loop, folding and packing (globular or fibrous) , association among chains

Question 46

spiral

Answer 46

3.6 AA/turn. H bonds C=O to N-H 4 away, R groups pointing out, polar or nonpolar

Question 47

coiled coil

Answer 47

2 a helices, hphobic inside, 3 collagena chain not a helix

Question 48

b sheets often display

Answer 48

twist

Question 49

loop

Answer 49

not in a regular folding. Connecting region.

Question 50

turns

Answer 50

4-5 residues in a loop, B turns most common in antiparallel B strands

Question 51

motif

Answer 51

recog folding pattern involving 2+ elements of a secondary structure and connection(s) between them, not biological but unstable w/o them

Question 52

hydrophobic core drives

Answer 52

globular

Question 53

hydrophobic effect

Answer 53

hpobes in

Question 54

domains

Answer 54

stable structural elements within a protein, that have a specific function by themselves

Question 55

3d structure imaging

Answer 55

X-ray crystallography any sie but has to be crystal, NMR small (<200 residues) no need crystal, Cryo-electron M (large complexes only)

Question 56

hemoglobin

Answer 56

15-16g/100ml, sickle cell half

Question 57

SCA

Answer 57

caused by a single mutation at the 6th position of the Hb chain from Glu to Val. Hphillic for a hphobic

Question 58

sickeling

Answer 58

HBs polymerizes into fibers that change the shape of the RBC and block the blood capillaries when oxygen levels are low