LEC2: Amino Acids and Proteins Flashcards Preview

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Flashcards in LEC2: Amino Acids and Proteins Deck (82):
1

explain the naming of carbons in amino acid side chains

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

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

L-conformation, not D

D mostly found in bacteria

3

how are amino acids classified?

by their R groups (aka side chains)

4

name the nonpolar/hydrophobic amino acids

Glycine

Alanine

Valine

Leucine

Isoleucine

Phenylalanine

Troptophan

Methionine

Proline

Cysteine (can be nonpolar or polar) 

(9 or 10)

5

name the uncharged polar amino acids

which are alcohols? which are amides?

Alcohols: Serine, Threonine, Tyrosine

Amides: Asparagine, Glutamine

Cysteine (can be nonpolar or uncharged polar)

6

Which amino acids can be phosphorylated? How?

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

7

do non-polar amino acids react w/ water?

no

8

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

yes

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

9

where are polar side chain amino acids often found?

the surface of proteins

10

what happens in a H-bond?

2 electronegative atoms share an e-

11

what is unique about cysteine?

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, covalent interaction 

12

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glycine

G

Gly

non-polar

13

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Alanine

Ala

A

non-polar

14

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Valine

Val

V

non-polar

15

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Leucine

Leu

L

non-polar

16

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Isoleucine

Ile

I

non-polar

17

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Phenylalanine

Phe

F

non-polar

18

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Tryptophan

Trp

W

non-polar

19

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Methionine

Met

M

non-polar

 

20

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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

21

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Serine

Ser

S

polar, alcohol

22

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Tyrosine

Tyr

Y

polar, alcohol

23

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Threonine

Thr

T

polar, alcohol

24

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Asparagine

Asn

N

polar, amide

25

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Glutamine

Gln

Q

polar, amide

26

which amino acids can be glycosylated?

what does this mean?

what is it an example of?

what is the purpose?

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

27

2 types of glycosylation? where does each occur?

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

28

what is fatty acylation? 

a post-translational modification of Cysteine 

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

 

 

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29

what catylyzes phosphorylation?

enzyme kinases

30

name the acidic amino acids 

aspartic acid 

glutamic acid 

have negative charges at physiologic pH

31

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Aspartic acid 

Asp

D

 

32

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Glutamic acid 

Glu

E

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

 

33

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

- acidic environment?

- physiologic pH? 

- basic environment?

acidic: all groups are protonated; +1 overall charge 

physiologic pH: -1 

basic environment: -2

34

name the basic amino acids

Histitide, Lysine, Arginine

35

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Histidine

His

H

basic

36

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Lysine

Lys

K

basic

37

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Arginine

Arg

R

basic

38

what is unique about His and its pKa?

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

explain this

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titration curve of histidine

shows side chain pKa = 6.0 

40

what is this, what does it show?

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titration curve of glutamic acid 

has 3 groups that can be ionized

41

what are peptide bonds? how are they formed?

bonds that join amino acids 

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

polar structures, participate in hydrogen bonding

42

what is a peptide? a protein?

peptide: < 50 amino acid chain 

protein: > 50 amino acid chain

43

how are small peptides named?

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

name this molecule 

 

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glutaminyl-arginyl-methionine

45

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

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

how is protein weight measured? unit?

what is avg size of a protein?

sum of the weights of all atoms in the protein molecule 

molecular weight = in kDa, kiloDalton

avg size of a protein = 50 kDa

47

what is the primary structure of a protein?

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

48

what is the secondary structure of a protein?

motifs?

how are they formed?

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

how does an alpha helix form?

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

50

what specifically bonds to form an alpha-helix?

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

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

why?

proline

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

52

how are B-sheets formed?

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

what is protein tertiary structure?

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

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

form proteins' tertiary structure

1) ionic bonds

2) hydrogen bonds

3) van der waals interactions

55

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

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

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

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

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

weakest type of non-covalent interaction 

found at close range btwn nonpolar atoms

drive protein folding 

58

what drives protien folding?

the "hydrophobic effect" 

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

 

 

59

what kind of bond forms btwn 2 cysteines? 

what causes their formation? 

where do they occur? 

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

what is this visualization called? 

what can you see?

 

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ribbon or cartoon 

shows backbone atoms, highlights secondary structure elements 

arrows indicate parallel/antiparallel sheets

61

what is this visualization called? 

what can you see?

 

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lines or sticks 

see amino acid side chains

can analyze particular residues of the protein

62

what is this visualization called? 

what can you see?

 

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surface 

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

use to design small molecule potential drugs against proteins

63

are all proteins the same size/shape?

no, they come in many sizes/shapes

64

what is this? properties? 

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four-helix bundle 

hydrophobic core stabilized by ionic interactions

 

65

what is this? properties?

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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

what is this? structure? where is it found?

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immunoglobulin 

7-9 beta strands

found in antibodies & signaling molecules 

 

67

what is a domain

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

antibody structure?

function of each part?

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

what gives an antibody specificity?

antigen binding site

 

70

what is this?

explain components

explain how structure > function 

 

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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

what is quarternary structure of a protein?

non-covalent joining of more than 1 polypeptide 

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

72

describe the structure of hemoglobin

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

what is this? fxn?

 

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respiratory complex I

transports electrons in mitochondria

 

74

what are fibrous proteins?

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

provide structural framework for many elongated proteins, form fibers 

highly stable, highly flexible

75

what type of protein is keratin

fibrous

76

what are intrinsically disordered proteins (IDPs)?

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

which amino acids can participate in hydrogen bond formation?

78

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

79

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

80

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

81

what determines overall 3D conformation of a protein?

82

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

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