Chapter 1- Amino Acids, Peptides, and Proteins

Question 1

proteinogenic amino acids

Answer 1

20 amino acids that are encoded by the human genetic code

Question 2

only amino acid that is not optically active

Answer 2

glycine, its also achiral

Question 3

only amino acid with an R configuration

Answer 3

cysteine

Question 4

amino acids that are nonpolar and have nonaromatic side chains

Answer 4

GAPVLIM

glycine (only an H)

ALKYL SIDE CHAIN W/ 1-4 CARBONS
alanine
valine
leucine
isoleucine

methionine (sulfur and methyl group)

proline (cyclic)

Question 5

amino acids that are uncharged and have aromatic side chains

Answer 5

FYW

tryptophan (largest), phenylalanine (relatively nonpolar), tyrosine (relatively polar)

Question 6

amino acids that are polar and NOT aromatic

Answer 6

STCNQ

OH groups in side chains (highly polar/ participate in H bonding)
serine
threonine

AMIDE SIDE CHAINS (dont gain/lose protons with pH change and do not become charged)
asparagine
glutamine

cystine [thiol (SH)]

Question 7

amino acids that are negatively charged (acidic)

Answer 7

DE

INSTEAD OF AMIDES THESE HAVE CARBOXYLATE (COO-)
aspartic acid (aspartate)
glutamic acid (glutamate)

Question 8

amino acids that are positively charged (basic)

Answer 8

KRH

ALL HAVE POSITIVELY CHARGED NITROGENS
lysine (terminal primary amino group)
arginine (3 nitrogen atoms)
histidine (aromatic ring with 2 nitrogens, called imidazole)

Question 9

what happens to ionizable groups in acidic and basic conditions?

Answer 9

acidic- gain protons (protonated at low pH)

basic- lose protons (deprotonated at high pH)

Question 10

pKa

Answer 10

pH at which half molecules of the species are deprotonated

Question 11

what happens to majority species if pH is less than pKa

Answer 11

protonation

Question 12

what happens to majority species if pH is more than pKa

Answer 12

deprotonation

Question 13

pKa for carboxyl and amino group

Answer 13

c- 2

a- 9-10

Question 14

Ionization under acidic, intermediate, and basic conditions

Answer 14

A- positively charged
I- zwitterionic (carboxylic acid deprotonates)
B- negatively charged

Question 15

Alkaline

Answer 15

Basic

Question 16

is a carboxyl group or amino group more acidic

Answer 16

carboxyl is more acidic so it will deprotonate first

Question 17

how to pH and pKa relate in buffer regions

Answer 17

pKa and pH have similar values

Question 18

isoelectric point (pI)

Answer 18

pH at which every molecule in a solution is electrically neutral

Question 19

typical pI for amino acids with nonionizable side chains

Answer 19

around 6

Question 20

pH trend for amino acids with acidic or basic side chains

Answer 20

acidic- low isoelectric point (pI below 6)

basic- high isoelectric point (pI above 6)

Question 21

oligopeptide vs. polypeptide

Answer 21

o- relatively small peptides (up to 20)

p- longer chains (over 20)

Question 22

what functional group forms when a peptide bond forms

Answer 22

COO- and NH3+ form the functional group -C(O)NH-

Question 23

what type of reaction is a peptide bond formation

Answer 23

condensation (dehydration) b/c it involves the removal of a water molecule

Question 24

how do enzymes catalyze hydrolysis

Answer 24

adding a hydrogen atom to the amid nitrogen and an OH group to the carbonyl carbon

Question 25

primary structure

Answer 25

linear arrangement of amino acids coded in an organisms DNA. stabilized by the formation of covalent peptide bonds between adjacent amino acids. encodes all the info needed for folding at all higher structural levels.

Question 26

secondary structure

Answer 26

primarily a result of hydrogen bonding b/w nearby amino acids. (2 most common structures are a-helices and B-pleated sheets)

Question 27

a-helices

Answer 27

rodlike structure, coils around (important in keratin structure- fibrous structural protein found in skin, hair, and fingernails)

Question 28

B-pleated sheet

Answer 28

either parallel or anitiparallel. peptide chains lie alongside on another forming rows or strands held together by intramolecular h-bonds b/w carbonyl oxygen of one chain and amide hydrogen of an adjacent chain (fibroin- primary protein of silk fibers is composed of B-sheets)

Question 29

what does proline to in a peptide chains secondary structure?

Answer 29

put a kink in the chain (usually found in turns of B-sheet and at the start of an a-helix chain)

Question 30

tertiary structure

Answer 30

primarily due to moving hydrophobic amino acid side chains to interior of protein. important structure- disulfide bonds.

Question 31

example of fibrous protein

Answer 31

collagen, resemble sheets or long strands

Question 32

example of globular protein

Answer 32

myoglobin, tend to be spherical

Question 33

disulfide bonds

Answer 33

form when 2 cysteine molecules become oxidized to form cystine (requires loss of 2 protons and 2 electrons). create loops in protein chain. determine how wavy or curly hair is (more bonds = curlier)

Question 34

molten globules

Answer 34

intermediate state in between when hydrophobic interactions and hydrogen bonds cause protein to collapse into its proper 3D structure. (very rapid process)

Question 35

denaturation

Answer 35

protein loses its tertiary structure

Question 36

quaternary structure

Answer 36

interactions b/w separate subunits of a multisubunit protein. for proteins with more than 1 polypeptide chain. (ex: hemoglobin w/ 4 distinct subunits)

Question 37

4 potential roles of quaternary structures?

Answer 37

1. more stable
2. reduce amount of DNA needed to encode protein complex
3. bring catalytic sites close together so 1 reaction can quickly shuttle to the next one
4. allosteric effects (cooperativity)- one subunit can undergo conformational/structural changes to enhance or reduce activity of other subunits

Question 38

prosthetic groups

Answer 38

major role in determining function of proteins (ex: prosthetic group in hemoglobin is called heme- contains iron which binds to/carries oxygen)

Question 39

why are proteins denatured by heat/solutes?

Answer 39

heat- increased KE of molecules thus disrupting hydrophobic interactions
solutes- directly interfering with forces that hold proteins together