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Biochemistry (Class) > module 2: amino acids > Flashcards

module 2: amino acids Flashcards

1
Q

four levels of protein structure

A

primary - amino acid sequence
secondary - local structures such alpha helix
tertiary - 3D structure
quarternary - polypeptide 3D structure

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2
Q

anatomy of amino acid

A

composed of protonated amine (NH3+), an acid (COO-), and a central alpha carbon which all groups are bonded to

alpha carbon is also bound to a side chain and an H atom

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3
Q

enantiomer

A

two mirror images of a chiral molecule

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4
Q

how are amino acids categorized?

A

based on size and shape, types of interactions, and conformational flexibility

distinguished between non polar and polar

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5
Q

types of polar amino acids

A

neutral, acidic, basic

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6
Q

non polar amino acids

A

glycine (G, gly) -
alanine (A, ala) -
valine (V, val)
leucine (L, leu) -
isoleucine (I, ile) -
phenylalanine (F, phe) -
methionine (M, Met) -
proline (P, Pro) -
tryptophan (W, trp)

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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

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7
Q

polar amino acids

A

serine (S, Ser) -
threonine (T, Thr) -

tyrosine (Y, Tyr) -
asparagine (N, Asp) -
glutamine (Q, Gln) -
cysteine (C, cys) -

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

tyrosine may be non polar

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8
Q

acidic amino acids

A

Aspartic acid (D, Asp) -
Glutamic acid (E, Glu) -

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both contain carboxylic acid R groups

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9
Q

basic amino acids

A

lysine (K, lys) -
arginine (R, arg) -

histidine (H, his) -

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-histidine can sometimes act as an acid

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10
Q

characteristics of non polar amino acids

A

glycine - R group is hydrogen
alanine - methyl R group
valine - two methyl groups
leucine - CH attached to two methyl groups
isoleucine - methyl and ethyl group
phenylalanine - methyl attached to phenyl group
tryptophan - two aromatic rings, one ring contains NH, one is just a 6 membered carbon ring
methionine - S attached to methyl
proline - Nitrogen is part of side chain, three CH2 are part of R group with last one attaching to NH2+

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11
Q

characteristics of polar amino acids

A

serine - OH
threonine - methyl and OH

tyrosine - phenyl which has a hydroxy group attached to it
asparagine - amide functional group
glutamine - CH2 attached to amide functional group
cysteine - SH

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12
Q

characteristics of acidic amino acids

A

Aspartic acid - CH2 attached to COO-
Glutamic acid - CH2 attached to CH2 attached to COO-

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13
Q

characteristics of basic amino acids

A

lysine - 3 CH2 attached to an amine
arginine - 2CH2 attached to NH which attaches to a carbon that has two NH2 groups attached to it, one NH2 has a positive charge

histidine - 5 membered aromatic ring including NH and NH+

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14
Q

zwitterion

A

ionic form containing no net charge

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15
Q

equivalence point

A

when moles of acid = moles of base

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16
Q

relation of ph and pKa to deprotonation and protonation

A

when ph>pKa, there is more deprotonation

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17
Q

pKa values of carboxyl and amine groups

A

carboxyl - around 2

amine - around 9

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18
Q

tyrosine side chain pKa

A

10.07

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19
Q

cysteine side chain pKa

A

8.33

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20
Q

side chain pKas of acids

A

aspartic - 3.86

glutamic - 4.25

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21
Q

side chain pKas of bases

A

arginine - 12.48
histidine - 6
lysine - 10.53

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22
Q

isoelectric point

A

when pH is equal to pI, amino acid is electrically neutral and zwitterion concentration is at its max

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23
Q

pI formula

A

1/2(pka1 +pka2)

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24
Q

what happens to amino acids at physiological pH?

A

acids are deprotonated and bases are protonated

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25
Q

essential amino acids

A

not produced by our body

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26
Q

function of disulfide bonds

A

provide stability between and within polypeptides

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27
Q

proline rotation

A

N is connected to side chain, so freedom of rotation is restricted

28
Q

half equivalence point

A

inflection, contains equal amounts of acid we’re trying to neutralize and base

29
Q

primary structure

A

how amino acids are connected to each other through peptide bonds

30
Q

peptide bond

A

bond between carbonyl group and NH

31
Q

protein definition

A

polypeptide of 50 or more amino acids with biological activity

32
Q

oxytocin vs vasopressin

A

oxytocin has Arginine and Leucine at positions 3 and 8, while Vasopressin has phenylalanine and arginine at positions 3 and 8. The structures are the same otherwise, but they both have very different structures.

33
Q

peptide bond characteristic

A

exhibits resonance between carbonyl and nitrogen, causing all amino acids except proline to be found in the cis or trans configuration

34
Q

proline exception

A

Proline doesn’t have a free amine/carboxyl group causing it to have less steric hindrance in the cis configuration

35
Q

alpha helix

A

all side chains outside of helix, right handed structure

36
Q

how many residues per turn of an alpha helix

A

3.6

37
Q

do side chains stabilize secondary structure in alpha helices?

A

No!

38
Q

pattern in which alpha carbon forms H-bond with backbone NH group

A

I+4 pattern

39
Q

strong alpha helix formers

A

Alanine, Leucine, Methionine, Glutamic acid

40
Q

alpha helix breakers

A

proline and glycine (they add too much flexibility to the structure)

41
Q

Beta sheet characteristics

A

fully extended chains, stabilization by H bonds
can be parallel or anti parallel

42
Q

parallel vs anti parallel B sheets

A

parallel- both chains in same direction

antiparallel - chains in opposite direction

43
Q

strong b sheet formers

A

isoleucine, valine, phenylalanine

44
Q

amphiphatic polypeptides

A

alternating polar/nonpolar residues

45
Q

tertiary structure

A

combinations of secondary structure, found in all proteins , stabilized by noncovalent interactions and disulfide bridges between cysteines

highest protein structure order for monomeric proteins
( one polypeptide)

46
Q

types of tertiary structures

A

BaB unit - two parallel strands of beta sheet connected by stretch of alpha helix,
aa unit - contains two antiparallel a-helices,
B-meander - antiparallel sheet is formed by a series of tight reverse turns connecting stretches of the polypeptide chain,
greek key - formed when a polypeptide chain doubles back on itself

47
Q

where are hydrophobic bonds found in tertiary structure

A

on the interior

48
Q

types of non covalent interactions

A

salt brides between basic and acidic amino acids and hydrogen bonds between H of polar R group and N or O of amino acid

49
Q

protein denaturation

A

affects secondary, tertiary, and quaternary structure causing loss of biological activity

50
Q

how does denaturation happen?

A

heat breaks apart H bonds and disrupts hydrophobic interactions,
acids/bases break H bonds between polar R groups and disrupt ionic bonds,
heavy metal bonds react with S-S bonds to form solids, and agitation that stretches peptide chains until bonds break

51
Q

guanadine hydrochloride and urea function in tertiary structure

A

break H bonds

52
Q

b mercaptoethanol function

A

breaks apart S-S bonds through reduction

53
Q

fibrous vs globular proteins

A

fibrous proteins are elongated, have strong IMFs, and are insoluble in water
globular proteins are spherical, have weak IMFs, and are soluble in water

54
Q

isoforms

A

related proteins created by same gene

55
Q

collagen properties

A

several isoforms of collagen found in body, consist of a helix include glycine. proline, and hydroxyproline, which form into a triple helix

56
Q

myoglobin

A

globular protein that only has tertiary structure and only consists of alpha helices, stores O2 and consists of a heme group

lacks quaternary structure, composed of a single polypeptide chain

57
Q

heme group

A

cofactor/prosthetic group that contains iron, required for myoglobin and hemoglobin to function.

turns apoenzyme to holoenzyme

58
Q

protoporphyrin IX

A

organic part formed by pyrrole structure, heme has Fe in coordination site

penetrates into human red blood cells and releases oxygen from them, interacts with haemoglobin and myoglobin forming ground state complexes.

59
Q

how is heme formed

A

iron forms four bonds with pyrrole rings and the fifth coordination site is bound by N atoms

60
Q

function of histidine residues globular proteins

A

pulls heme in specific orientation

61
Q

hemoglobin

A

has a quarternary structure, can bind up to four molecules of O2
consists of two alpha chains (141 residues) and two beta chains (146 residues)

62
Q

affinities for oxygen of hemoglobin and myoglobin

A

hemoglobin - sigmoidal due to quaternary structure, displays positive cooperatively, making it easier for O2 to bind when another O2 is already bound
myoglobin - hyperbolic curve, meaning that its saturated with O2 quickly.

63
Q

what causes sickle cell anemia

A

a single amino acid substitution, where a mutation occurs in the beta chain, changing glutamic acid (negative) to valine (hydrophobic).

64
Q

Effect of sickle cell substitution

A

valine faces exterior of hemoglobin, leading to crystallization of a beta chain causing insoluble fibers of sickle cell hemoglobin to form.

65
Q

urea effect on sickle cell anemia

A

enhances gene that forms gamma chain in adults, causing the sickle trait to become somewhat improved.

Biochemistry (Class) (7 decks)

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