amino acids and proteins

Question 1

amino acid structure

Answer 1

alpha amino group next to tetrahedral carbon with R group next to alpha carboxyl group

Question 2

acidic amino acids

Answer 2

Aspartic acid (D, Asp) - CH2 attached to COO-
Glutamic acid (E, Glu) - CH2 attached to CH2 attached to COO-

both contain carboxylic acid R groups

Question 3

basic amino acids

Answer 3

lysine (K, lys) - 4 CH2 attached to an amine
arginine (R, arg) - 3 CH2 attached to NH which attaches to a carbon that has two NH2 groups attached to it, one NH2 has a positive charge
histidine (H, his) - CH2 attached to 5 membered aromatic ring including NH and NH+

-histidine can sometimes act as an acid

Question 4

hydrophobic (non polar) amino acids

Answer 4

glycine (G, gly) - R group is hydrogen
alanine (A, ala) - methyl R group
valine (V, val) - R group is CH attached to two methyl groups
leucine (L, leu) - R group is CH2 attached to CH attached to two methyl groups
isoleucine (I, ile) - CH2 attched to a methyl and ethyl group
phenylalanine (F, phe) - methyl attached to phenyl group
tryptophan (W, Trp) - has a CH2 attached to two aromatic rings, one ring contains NH, one is just a 6 membered carbon ring
methionine (M, Met) - CH2 attached to CH2 attached to S attached to methyl
proline (P, Pro) - Nitrogen is part of side chain, three CH2 are part of R group with last one attaching to NH2+

F and W have aromatic side chains, the rest have alkyl side chains (CH)
methionine contains sulfur
proline’s amino group is covalently bound to its non polar side chain, disrupting backbone hydrogen bonding in secondary structure

Question 5

polar amino acids

Answer 5

serine (S, Ser) - CH2 attached to OH
threonine (T, Thr) - CH attached to methyl and OH
tyrosine (Y, Tyr) - methyl attached to phenyl which has a hydroxy group attached to it
asparagine (N, Asp) - CH2 attached to amide functional group
glutamine (Q, Gln) - CH2 attached to CH2 attached to amide functional group
cysteine (C, cys) - CH2 attached to SH

polar enough to form hydrogen bonds with water but don’t act as an acid or a base
cysteine contains sulfur

Question 6

relationship between pH and pKa

Answer 6

when pH of solution is less than pKa of an acidic group, acidic group will mostly be in its protonated form

when pH of solution is greater than pKa of an acidic group, acidic group will mostly be in its deprotonated form

Question 7

isoelectric point

Answer 7

pH at which a molecule is uncharged (zwitterionic)

Question 8

How is pI (isoelectric point) calculated

Answer 8

average of the pKas of the two functional groups

Question 9

two types of covalent bonds between amino acids in proteins

Answer 9

peptide bonds that link amino acids together into polypeptide chains and disulfide bridges between cysteine R groups

disulfide bridges play an important role in stabilizing tertiary protein structure

Question 10

polypeptide backbone

Answer 10

N-C-C-N-C-C pattern formed from amino acids

Question 11

proteolytic cleavage

Answer 11

hydrolysis of a protein by another protein done by protease

Question 12

denaturation

Answer 12

disruption of a protein’s shape without breaking peptide bonds

Question 13

primary structure

Answer 13

linear ordering of amino acid residues in a polypeptide chain

Question 14

secondary structure

Answer 14

initial folding of a polypeptide chain into shapes stabilized by hydrogen bonds between backbone NH and CO groups, include alpha helix and beta pleated sheet

Question 15

tertiary structure

Answer 15

concerns interactions between amino acid residues located more distantly from each other in the polypeptide chain, R groups interact with each other

Question 16

hydrophobic effect

Answer 16

hydrophobic R groups tend to fold into the interior of the protein and hydrophilic R groups tend to be exposed to water on the surface of the protein

Question 17

quaternary structure

Answer 17

interactions between polypeptide subunits

Question 18

reaction coupling

Answer 18

one very favorable reaction is used to drive an unfavorable one

Question 19

active site

Answer 19

region in an enzyme’s three dimensional structure that is directly involved in catalysis

Question 20

substrates

Answer 20

reactants in an enzyme catalyzed reaction

Question 21

enzyme function

Answer 21

accelerate the rate of a given reaction by helping to stabilize the transition state

Question 22

recognition pocket

Answer 22

near active site of enzyme, attract certain residues on substrate polypeptides

Question 23

cofactors

Answer 23

metal ions or small molecules required for activity in many enzymes

Question 24

how are enzymes regulated?

Answer 24

1. covalent modification (ex. addition of a phosphoryl group from a molecule of ATP by a protein kinase to a hydroxyl of serine, threoinine, or tyrosine)
2. proteolytic cleavage
3. association with other polypeptides
4. allosteric regulation

Question 25

allosteric regulation

Answer 25

binding of small molecules to particular sites on enzyme distant from active site, causing regulation of molecule.

Question 26

negative feedback

Answer 26

end product shuts off enzyme early in pathway

Question 27

feedforward stimulation

Answer 27

stimulation of an enzyme by its substrate or by a molecule used in the synthesis of the substrate.

Question 28

saturated enzyme

Answer 28

when there is so much substrate that every active site is continuously occupied and adding more substrate doesn’t increase reaction rate at all

reaction rate = Vmax

Question 29

Km

Answer 29

substrate concentration at which reaction velocity is half its maximum

low Km indicates enzyme has high affinity for particular substrate

Question 30

positive vs negative cooperatively

Answer 30

positive - binding of a substrate to one subunit increases affinity of other subunits for substrate
negative - binding of a substrate to one subunit reduces affinity of other subunits for substrate

cooperative enzymes must have more than one active site

Question 31

competitive inhibitors

Answer 31

compete with substrate for binding at active site, more substrate required to reach Vmax, Km is increases as a result but Vmax isn’t affected

slope of LW burk plot increases

Question 32

noncompetitive inhibitors

Answer 32

bind at an allosteric site, causing Vmax and Vmax1/2 to decrease, while Km stays the same

slope of LW burk plot increases

Question 33

uncompetitive inhibitors

Answer 33

inhibitor is only able to bind to enzyme substrate complex (on allosteric sites), decreasing Vmax by limiting amount of available enzyme substrate complex that can be converted to product

increases affinity of enzyme for substrate causing Km to decrease

works most efficiently when substrate concentration is at its highest.

slope of LW burk plot doesn’t change because both Km and Vmax decrease

Question 34

mixed type inhibition

Answer 34

occurs when an inhibitor can bind to either the unoccupied enzyme or the enzyme substrate complex

Vmax decreases and Km change varies depending on whether enzyme has greater affinity for inhibitor in its free form or as a complex.

slope of LW burk plot will vary

Question 35

line weaver Burk plot

Answer 35

1/V = (Km/Vmax)(1/S) + 1(Vmax)

y axis is inverse of reaction rate (1/V)
X axis is inverse of substrate concentration (1/S)

slope of graph is Km/Vmax
y intercept of graph is 1/Vmax
x intercept of graph is -1/Km

As V increases, y axis value decreases

As substrate conc increases, x value decreases