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Biochemistry > new protein structure -LEARN > Flashcards

new protein structure -LEARN Flashcards

1
Q

GLYCINE

A

R group= H -adds flexibility to protein chain since other side chains are too bulky -alpha carbon shows no chirality

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2
Q

ALANINE

A

R group-CH3 -biosynthesis -non-polar

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3
Q

PROLINE

A

side chain bonds to the amine (CH2CH2CH2) group –> imposes tight restraints on the conformation of a protein -both CIS and TRANS bonds -found in rigid proteins e.g. collagen

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4
Q

HISTIDINE

A

-only aa with a pKa of a side chain of near neutral pH -found in AS -side chain can alter its charge at physiological pH -chaegre modulated by other amino acids surrounding it

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5
Q

CYSTEINE

A

R group -SH (free thiol group) -can form disulphide bridges -only covalent bond found to hold protein in tis correct for -side chain has pKa of 8.4 -found in AS

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6
Q

hierarchy of protein structure

A

primary- amino acid sequence secondary: beta and alpha and turn and loops tertiary- overall fold of protein quaternary: when several proteins fold together

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7
Q

peptide bond

A

partial double bond character

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8
Q

length of peptide bond

A

1.32A

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9
Q

Phi

A

angle of rotation about the bond between the nitrogen and carbon

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10
Q

Psi

A

angle of rotation about the bond between alpha carbon and carbonyl carbon

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11
Q

both Phi and Psi determine

A

the path of the polypeptide chain

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12
Q

why are many combinations of Phi and Psi

A

STERIC collisions between atoms

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13
Q

allowed values of Phi and Psi can be visualised on a

A

Ramachandron Plot

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14
Q

Phi and Psi restrict

A

angles therefore limit the number of structures available to the unfolded form

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15
Q

secondary structures

A

alpha helix beta sheet turns and loops

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16
Q

who discovered Alpha helices and Beta sheets and when

A

Linus Paul and Robert Corey 1951

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17
Q

why do alpha helices arise

A

due to H bonding capacity of NH backbone and CO groups

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18
Q

properties of alpha helices

A

right handed, 3.6 residues

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19
Q

R groups of alpha helices always point

A

outwards

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20
Q

how hydrogen bonds form in aloha helices

A

the Co group of residue n forms a hydrogen bond with the NH group of residue n+4

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21
Q

helical wheel

A

amino acid residues facing outwards are ion contact with water- hydrophilic -those inside are hydrophobic

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22
Q

alpha helical content can range from

A

0-100%

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23
Q

ferritin

A

75% of residues are in alpha helices

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24
Q

25% of all soluble proteins are composed of

A

alpha helices connected by loops and turns

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25
Q

Beta sheet found by

A

linus Pauling and Robert Corey in 1951

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26
Q

Beta sheets are mad cup of

A

at least two polypeptide chains (typically 4/5, but can be up to 10)

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27
Q

Beta sheets are

A

parallel or antiparallel

28
Q

parallel

29
Q

antiparallel

30
Q

Bonding in Beta sheets

A

H bonding b/w c=o of one chain to N-H of another chain

31
Q

in globule proteins beta sheets are … residues long

A

15 residues long

32
Q

beta proteins can be

A

purely parallel, purely antiparallel or mixed

33
Q

reverse turn also known as

A

hairpin turn

34
Q

what do reverse turns do

A

interaction stabilised abrupt changes in direction of the poly-peptide chain

35
Q

loops don’t have

A

a regular structure like alpha and beta

36
Q

loops are

A

right and well defined

37
Q

loops lie

A

on the surface of proteins and interact with other proteins or olecules

38
Q

loops are present in

A

antibodies

39
Q

super secondary structure

A

elements of secondary structure link together into combination that are very common

40
Q

what to super secondary structures form

A

mini-domains -formed early in the process of making the whole protein structure

41
Q

tertiary

A

overall fold of the protein

42
Q

tertiary structures are any

A

combination of alpha-helices, B-sheets or loops

43
Q

myoglobin

A

all alpha helix protein -binds heme, a prostethic group -

44
Q

how much of myoglobin is alpha helices

A

70% folded into 8 alpha helices, the rest are turns and loops

45
Q

Dimensions of myoglobin

A

45 x 35 x 25 a

46
Q

first protein sturcutr to be determined

A

myoglobin by watson and Kindred in 1950

47
Q

myoglobin is made up of

A

1 polypeptide chain and 153 amino acids

48
Q

all B sheet protein

A

concavalin A

49
Q

concavalin a

A

all beta sheet -14 beta strands

50
Q

concavalin a is a

A

lectin (carbohydrate binding protein)

51
Q

most proteins have a mixture of

A

alpha and beta

52
Q

B barrel

A

alpha on outside -beta on inside

53
Q

Domains

A

section which can fold independently -each protein has at least on domain but can be more than 10

54
Q

quaternary structure

A

many proteins form in a group of 2 or more protein chains

55
Q

homomultimers

A

same protein, 2 or more copies

56
Q

heteromultimers

A

several diff proteins come together to make a mature protein

57
Q

haemoglobin is made up of

A

2 alpha subunits 2 beta subunits and 4 heme groups

58
Q

fibrous proteins are either

A

alpha or B

59
Q

examples of alpha helix fibrous protein

60
Q

examples of B sheet protein

A

insect silk

61
Q

hair

A

2 helices -non-polar -cys residues cross link adjacent chains (broken and reformed when you have permanent wave)

62
Q

B-silk

A

made up of repeating hexapeptide -antiparallel B sheets -Gly extents from one surface and Ala from the other

63
Q

collagen

A

-200A lon and 15 A wide -fibrous component of skin, bone, tendon, cartilage and teeth -has a hydroxyl group in place of H atom -2 helices and 1000 residues long -no H bonding -eveyr 3rd residue is glycine -made up of three helix (wound around each other) -polypropine helix

64
Q

in collagen H group is replaced by

65
Q

residues in collagen

A

1000 residues long and every 3rd residue is glycine

Biochemistry (18 decks)

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