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MCAT biochem > amino acids and proteins > Flashcards

amino acids and proteins Flashcards

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MCAT flashcards
1
Q

basic structure of amino acids

A

nh3 group
central carbon
cooh group
hydrogen

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2
Q

all amino acids are

A

L- amino acids

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3
Q

what kind of organisms have d amino acids

A

bacteria

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4
Q

which orientation are most amino acids? R/s?

A

most are S with the exception of cystine

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5
Q

what is the R/S configuration of cysteine

A

R

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6
Q

aliphatic amino acids

A

G, A, V, L, I, P

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7
Q

is methionine polar or nonpolar

A

nonpolar

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8
Q

what is unique about proline?

A

it disrupts secondary protein stucture and causes proline kinks

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9
Q

which amino acids can be phosphorylated

A

serine, threonine, tyrosine on their -OH residues

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10
Q

what is unique about histidine?

A

pka of 6.0 so it acts as a buffer at physiological pH

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11
Q

amide amino acids

A

glutamine (Q) asparagine (N)

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12
Q

sulfur containing amino acids

A

cysteine and methionine

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13
Q

which amino acids are achiral

A

glycine only

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14
Q

peptide bond

A

hydrolysis reaction that takes the OH group from a COOH and the next H from an NH3 group

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15
Q

proteases

A

hydration reaction that breaks up primary structure/ breaks the peptide bonds

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16
Q

average protein size

A

50 kDa

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17
Q

how are proteins assembled in the ribosome

A

from the N to C terminus

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18
Q

terciary structure

A

interactions are typically non-covalent and charge driven.
- salt bridges
- disulfide bridges

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19
Q

2- mercatoethanol

A

a reducing agent that breaks up disulfide bonds

20
Q

what kind of bond are disulfide bridges

A

COVALENT
- very strong compared to most tericiary interactions

21
Q

where does hydrogen bonding occur in secondary structure of proteins

A

between the COOH anf NH3 residues of the protein backbone

22
Q

what structure do proteases cleave

A

primary

23
Q

what structure do denaturing agents cleave?

A

2, 3, 4
- not permenent

24
Q

taq polymerase

A

a protein that is challenging to denature at high temp and is used in PCR technique

25
Q

entropy relationship with protein folding

A

proteins will fold in a way that encourages entropy, so it is considered favorable
- example: why hydrophobic tail is on side of lipid bilayer

26
Q

zwitterion

A

ion where one group of amino acid is negative (coo-) and 1 is positive (nh3+)
- so for normal amino acid at physiological ph charge is 0

27
Q

henderson - hasselbach eqn

A

pH = pKa + log [A-/HA]

28
Q

pKa

A

pH= -log[H+]

29
Q

pka

A

point where half of a functional group is positive and half is 0

30
Q

when pka> pH

A

not abundant amounts of h+ in solution so functional group is deprotinated

31
Q

when pka<pH

A

plentiful h+ in solution and species is protinated

32
Q

pka1

A

cooh, around 2.3

33
Q

pka2

A

nh3 around 9.5

34
Q

isoelectric point pI

A

pH where average charge is 0

35
Q

isoelectric point for diprotic amino acids

A

average pka1 and pka2

36
Q

isolelectric point for triprotic amino acids that are acidic

A

pka1 + pkar / 2 (two acidic)

37
Q

isolelectric point for triprotic basic amino acids

A

pka2 + pkar / 2 (2 basic

38
Q

flat region of a titration curve

A

pka and half of species is prot/ deprot
-buffer zone

39
Q

vertical region of a titration curve

A

isoelectric point

40
Q

ph = pka

A

half equivalence point

41
Q

equivalence point

A

isoelectric point = pH
- the middle of the vertical region
where charge is 0

42
Q

what stabilizes a peptide bond

A

resonance between c=o bond and makes the bond unable to rotate bc of planar

43
Q

stecker synthesis

A

making amino acids from aldehydes via
1. imine
2. add cyanide (form nitrile)
3. hydrolysis to form cooh

44
Q

imine group

A

C=N where n has 1 or 2 R groups

45
Q

nitrile group

A

c triple bond N

46
Q

precursor to gabriel synthesis

A

N-pththalidicmalonic ester “THAD”
- use nitrogen for amine group
- central c and cooh

MCAT biochem (11 decks)

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