Chapter 1- Amino Acids, Peptides, and Proteins Flashcards Preview

MCAT Biochemisty > Chapter 1- Amino Acids, Peptides, and Proteins > Flashcards

Flashcards in Chapter 1- Amino Acids, Peptides, and Proteins Deck (39)
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1

proteinogenic amino acids

20 amino acids that are encoded by the human genetic code

2

only amino acid that is not optically active

glycine, its also achiral

3

only amino acid with an R configuration

cysteine

4

amino acids that are nonpolar and have nonaromatic side chains

GAPVLIM

glycine (only an H)

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

methionine (sulfur and methyl group)

proline (cyclic)

5

amino acids that are uncharged and have aromatic side chains

FYW

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

6

amino acids that are polar and NOT aromatic

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)]

7

amino acids that are negatively charged (acidic)

DE

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

8

amino acids that are positively charged (basic)

KRH

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

9

what happens to ionizable groups in acidic and basic conditions?

acidic- gain protons (protonated at low pH)
basic- lose protons (deprotonated at high pH)

10

pKa

pH at which half molecules of the species are deprotonated

11

what happens to majority species if pH is less than pKa

protonation

12

what happens to majority species if pH is more than pKa

deprotonation

13

pKa for carboxyl and amino group

c- 2
a- 9-10

14

Ionization under acidic, intermediate, and basic conditions

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

15

Alkaline

Basic

16

is a carboxyl group or amino group more acidic

carboxyl is more acidic so it will deprotonate first

17

how to pH and pKa relate in buffer regions

pKa and pH have similar values

18

isoelectric point (pI)

pH at which every molecule in a solution is electrically neutral

19

typical pI for amino acids with nonionizable side chains

around 6

20

pH trend for amino acids with acidic or basic side chains

acidic- low isoelectric point (pI below 6)
basic- high isoelectric point (pI above 6)

21

oligopeptide vs. polypeptide

o- relatively small peptides (up to 20)
p- longer chains (over 20)

22

what functional group forms when a peptide bond forms

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

23

what type of reaction is a peptide bond formation

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

24

how do enzymes catalyze hydrolysis

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

25

primary structure

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.

26

secondary structure

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

27

a-helices

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

28

B-pleated sheet

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)

29

what does proline to in a peptide chains secondary structure?

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

30

tertiary structure

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