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MCG > LEC2: Amino Acids and Proteins > Flashcards

LEC2: Amino Acids and Proteins Flashcards

1
Q

explain the naming of carbons in amino acid side chains

A

named using Greek letters

alpha-carbon is carbon bound to amino and carboxyl groups of amino acid

beta-carbon is next, etc

lysine here

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2
Q

which conformation of optical isomer of proteins are mostly seen in humans?

A

L-conformation, not D

D mostly found in bacteria

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3
Q

how are amino acids classified?

A

by their R groups (aka side chains)

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4
Q

name the nonpolar/hydrophobic amino acids

A

Glycine

Alanine

Valine

Leucine

Isoleucine

Phenylalanine

Troptophan

Methionine

Proline

Cysteine (can be nonpolar or polar)

(9 or 10)

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5
Q

name the uncharged polar amino acids

which are alcohols? which are amides?

A

Alcohols: Serine, Threonine, Tyrosine

Amides: Asparagine, Glutamine

Cysteine (can be nonpolar or uncharged polar)

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6
Q

Which amino acids can be phosphorylated? How?

A

serine, threonine, tyrosine

contain a hydroxyl group, can be replaced by a phosphoryl group

phosphorylation of an amino acid in a protein > alters protein’s activity or transmits a signal

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7
Q

do non-polar amino acids react w/ water?

A

no

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8
Q

do polar side chain amino acids react w/ water? how?

A

yes

side chain can form H-bond w/ water or other groups

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9
Q

where are polar side chain amino acids often found?

A

the surface of proteins

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10
Q

what happens in a H-bond?

A

2 electronegative atoms share an e-

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11
Q

what is unique about cysteine?

A

can be described as either hydrophobic or polar

has an SH group

in environment of an oxidant, cysteine interacts w/ other cysteines, forms **disulfide bridge, **a covalent interaction

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12
Q
A

glycine

G

Gly

non-polar

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13
Q
A

Alanine

Ala

A

non-polar

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14
Q
A

Valine

Val

V

non-polar

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15
Q
A

Leucine

Leu

L

non-polar

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16
Q
A

Isoleucine

Ile

I

non-polar

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17
Q
A

Phenylalanine

Phe

F

non-polar

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18
Q
A

Tryptophan

Trp

W

non-polar

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19
Q
A

Methionine

Met

M

non-polar

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20
Q
A

Proline

Pro

P

non-polar

side chain is covalently attached to amine group, forming a rigid, not aromatic, ring > limits conformaitons proline can adopt in nature

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21
Q
A

Serine

Ser

S

polar, alcohol

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22
Q
A

Tyrosine

Tyr

Y

polar, alcohol

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23
Q
A

Threonine

Thr

T

polar, alcohol

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24
Q
A

Asparagine

Asn

N

polar, amide

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25
Q
A

Glutamine

Gln

Q

polar, amide

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26
Q

which amino acids can be glycosylated?

what does this mean?

what is it an example of?

what is the purpose?

A

**addition of chains of sugar or oligosaccharide to side chain of amino acid **

serine, threonine, asparagine

is a post-translational modification

can mark proteins to go to the membrane & be involved w/ signaling pathways

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27
Q

2 types of glycosylation? where does each occur?

A

_1) N-linked glycosylation _

sugar attaches to amide group

only Asparagine (Asp)

_2) O-linked glycosylation _

sugar attaches to **O of OH **

Serine or Threonine

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28
Q

what is fatty acylation?

A

a post-translational modification of Cysteine

hydrocarbon chain, ie farnesyl group is added to sulhydryl group of cysteine

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29
Q

what catylyzes phosphorylation?

A

enzyme kinases

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30
Q

name the acidic amino acids

A

aspartic acid

glutamic acid

have negative charges at physiologic pH

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31
Q
A

Aspartic acid

Asp

D

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32
Q
A

Glutamic acid

Glu

E

has 3 ionizable groups, so there are 4 forms of the amino acid

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33
Q

overall charge of glutamic acid, and protonation state, at:

  • acidic environment?
  • physiologic pH?
  • basic environment?
A

acidic: all groups are protonated; +1 overall charge

physiologic pH: -1

basic environment: -2

34
Q

name the basic amino acids

A

Histitide, Lysine, Arginine

35
Q
A

Histidine

His

H

basic

36
Q
A

Lysine

Lys

K

basic

37
Q
A

Arginine

Arg

R

basic

38
Q

what is unique about His and its pKa?

A

its side chain pKa = 6.0

therefore very close to physiologic pH

therefore can be both charged and uncharged, depending on conditions

if charged, can be an **active site for enzymes **

39
Q

explain this

A

titration curve of histidine

shows side chain pKa = 6.0

40
Q

what is this, what does it show?

A

titration curve of glutamic acid

has 3 groups that can be ionized

41
Q

what are peptide bonds? how are they formed?

A

bonds that join amino acids

rxn that connects amino and carboxyl groups of amino acids, releases H2O

polar structures, participate in hydrogen bonding

42
Q

what is a peptide? a protein?

A

peptide: < 50 amino acid chain
protein: > 50 amino acid chain

43
Q

how are small peptides named?

A

for their constituent amino acids

start at amino terminus, add “yl” to name of each amino acid except for the one at the carboxyl terminus

44
Q

name this molecule

A

glutaminyl-arginyl-methionine

45
Q

what steric constraints are there on proteins re: primary structure?

A

1) peptide bond is **planar **bond, so limits interactions a protein can have
2) side chains provide a steric constraint - not all atoms can go anywhere

46
Q

how is protein weight measured? unit?

what is avg size of a protein?

A

sum of the weights of all atoms in the protein molecule

molecular weight = in kDa, kiloDalton

avg size of a protein = 50 kDa

47
Q

what is the primary structure of a protein?

A

its amino acid sequence - the linear order of amino acids in the chain

48
Q

what is the secondary structure of a protein?

motifs?

how are they formed?

A

local three-dimensional conformation

alpha-helix and beta-sheet

formed from hydrogen bonds btwn hydrgoen of amino group and oxygen of carbonyl group in a peptide bond

49
Q

how does an alpha helix form?

A

by hydrogen bonds btwn atoms in peptide bonds of a single linear chain of amino acids

50
Q

what specifically bonds to form an alpha-helix?

A

hydrogen bond btwn:

oxygen in carbonyl gorup of amino acid R1 (C=O) and

hydrogen in amino group of amino acid (N-H) R5

therefore a 3.6 (~4) amino acid turn

51
Q

which amino acid won’t appear in an alpha helix?

why?

A

proline

its side chain is covalently attached to the amine group, which limits the conformations it can adopt - it’s kinky

52
Q

how are B-sheets formed?

A

hydrogen bonds formed btwn atoms in peptide bonds of same or different linear chains

can be antiparallel, where protein folds upon itself, or parallel, where N-terminus of each strand is oriented same direction

strands are connected by loops

53
Q

what is protein tertiary structure?

A

protein’s overall 3D conformation - determined yb its amino acid sequence

peptide bond backbone and amino acid side chains both contribute to tertiary structure

54
Q

what kinds of non-covalent interactions can proteins have? their effect?

A

form proteins’ tertiary structure

1) ionic bonds
2) hydrogen bonds
3) van der waals interactions

55
Q

what are ionic bonds? where do they occur in proteins?

A

cohesion btwn 2 atoms of opposite (+ and -) charges

electrostatic attraction

occurs btwn a charged and a polar amino acid, i.e. glutamate and lysine

56
Q

what is hydrogen bonding? where does it occur in proteins?

A

when electropositive hydrogen atom is partially shared by 2 electronegative atoms

occurs btwn side chains of 2 amino acids but also back bone of all amino acids in peptide chain

57
Q

what are hydrophobic interactions? where do they occur, what is their effect?

A

weakest type of non-covalent interaction

found at close range btwn nonpolar atoms

drive protein folding

58
Q

what drives protien folding?

A

the “hydrophobic effect”

nonpolar side chains cluster together in middle of structure; polar side chains on outside, where form H-bonds w/ H2O

59
Q

what kind of bond forms btwn 2 cysteines?

what causes their formation?

where do they occur?

A

S-S of cysteines form **covalent **disulfide bond, **aka a cystine residue

formed by the oxidation of 2 cysteines

can be inter- or intra-molecular

common in antibodies

60
Q

what is this visualization called?

what can you see?

A

ribbon or cartoon

shows backbone atoms, highlights secondary structure elements

arrows indicate parallel/antiparallel sheets

61
Q

what is this visualization called?

what can you see?

A

lines or sticks

see amino acid side chains

can analyze particular residues of the protein

62
Q

what is this visualization called?

what can you see?

A

surface

see approximated, functionally important regions that interact w/ the solvent

use to design small molecule potential drugs against proteins

63
Q

are all proteins the same size/shape?

A

no, they come in many sizes/shapes

64
Q

what is this? properties?

A

four-helix bundle

hydrophobic core stabilized by ionic interactions

65
Q

what is this? properties?

A

Tim Barrel

8 alpha helicies + 8 parallel beta strands

most common fold in nature

gut of protein includes some irregular structural elements which bind to specific molecules (ligands, ions)

66
Q

what is this? structure? where is it found?

A

immunoglobulin

7-9 beta strands

found in antibodies & signaling molecules

67
Q

what is a domain

A

a region of a protein w/ a particular fxn

usually physically distinct from other parts of the protein

pt of the polypeptide that folds independently into a compact, stable structure

68
Q

antibody structure?

function of each part?

A

immunoglobulin

2 identical heavy chains, 2 identical light chains

each subunit contains variable & constant domains

variable domains: bind antigen (what ab targets)

constant domains: interact w/ other immune system components

69
Q

what gives an antibody specificity?

A

antigen binding site

70
Q

what is this?

explain components

explain how structure > function

A

src protein kinase

has 3 domains:

kinase domain: responsible for catalytic activity

SH3, SH2 domains: important for regulation of interaction w/ other proteins

loops in btwn domains allows protein to be modular, which helps w/ interactions and turning on/off

71
Q

what is quarternary structure of a protein?

A

non-covalent joining of more than 1 polypeptide

stabilized by noncovalent interctions, as explained (ionic, H-bonds, van der waals)

72
Q

describe the structure of hemoglobin

A

quarternary structure made of 4 polypeptides:

2 identical alpha-globin chains; 2 identical beta-globin chains

each subunit contains a heme group, which binds to oxygen

73
Q

what is this? fxn?

A

respiratory complex I

transports electrons in mitochondria

74
Q

what are fibrous proteins?

A

coiled coil proteins - 2 helices, connected by long hydrophobic interaction

provide structural framework for many elongated proteins, form fibers

highly stable, highly flexible

75
Q

what type of protein is keratin

A

fibrous

76
Q

what are intrinsically disordered proteins (IDPs)?

A

do not adopt stable structure under physiological conditions

have low hydrophobicity, high net charge - so don’t just fold on their own

in some conditions, can fold

77
Q

which amino acids can participate in hydrogen bond formation?

A
78
Q

which amino acid side chains are likely to be found w/in a region of a protein that spans a lipid membrane?

A
79
Q

what types of modifications are found on proteins that are excreted from cells?

A
80
Q

why are regions of an a-helix and B-sheet found in most proteins, including those that have very different amino acid compositions?

A
81
Q

what determines overall 3D conformation of a protein?

A
82
Q

what interacitons stabilize the tertiary structure of proteins and multi-subunit complexes?

A

MCG (77 decks)

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