Biochemistry - Chemistry of Amino Acids, Peptides and Protein

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1

3-d structure of a protein

tertiary structure

2

3-d structure is related to ___

function

3

tertiary structure determines function, what is an example?

the enzyme catalytic site which forms a pocket for a specific substrate

4

4 examples of tertiary structures

H-bonds
ionic bonds
hydrophobic interactions
disulfide bonds

5

quaternary structure involves more than 1 ___ subunit (aka monomer)

polypeptide

6

3 examples of quaternary structure

H-bonds
ionic bonds
hydrophobic interactions

7

in quaternary structure, the degree of subunit ___ affects function

association

8

found in RBCs; hemoprotein

hemoglobin

9

hemoglobin: ___ polypeptides of 2 classes; each subunit has a ___
adult HbA: alpha2beta2
fetal HbF: alpha2___2

4; heme; gamma

10

8 ___-handed alpha-helices in each alpha subunit

right

11

___ right-handed alpha-helices in each beta subunit

7

12

functions of hemoglobin

O2 and CO2 transport, buffer

13

what binds O2 as it relates to hemoglobin function?

Fe2+
His (F8)
His (E7) --> specifically hinders CO binding

14

hemoglobin contains 4 subunits held by ___ bonds --> ___ structure

non-covalent; quaternary

15

___ and ___ hemoglobin structures are flexible

secondary; tertiary

16

___-form of hemoglobin binds O2, ___-form cannot

R; T

17

binding of first O2 takes the longest time...the rest get progressively faster. this is b/c binding O2 changes conformation of other subunits, facilitating further O2 binding

cooperative allosterism

18

T-conformation has a ___ O2 affinity; R-conformation has a ___ O2 affinity

low; high

19

sickle-cell anemia = ?

reduced O-carrying capacity of blood

20

myoglobin found in ___; hemo___; 1 polypeptide of ___ amino acids; ___ right-handed alpha-helices (A-H) with heme b/t helices ___ and ___

muscle; protein; 153; E; F

21

O2 bound to ___ is a reserve for when pO2 of tissues is low...it is then released for ___ synthesis

myoglobin; ATP

22

most abundant protein in the body

collagen

23

mature ___ composed of 3 alpha-chain subunits

tropocollagen

24

collagen consists of ___ subunits held together by ___-bonds

3; H

25

re: collagen, different tissues have different ___ ___ compositions, e.g. type I collagen is ___ alpha-1 and ___ alpha-2 chain

amino acid; 2; 1

26

___ is the most abundant amino acid in collagen, with lots of proline and ___

glycine; lysine

27

amino acids definition

monomeric unit of peptides and proteins

28

most amino acids occur as?

L-alpha amino acids

29

ideal formula of amino acid has ___ charges and practical formula has ___ and ___ charges and the ___ from the carboxyl group shifts

zero; +; -; hydrogen

30

acronym to describe the essential amino acids is?

Phenylalanine
Valine
Threonine

Tryptophan
Isoleucine (Ile)
Methionine

Histidine
Arginine
Leucine
Lysine

31

essential amino acids ___ be synthesized by the body

cannot

32

adults can synthesize which 2 essential amino acids (children cannot)?

histidine and arginine

33

amino acid classification by nutritional criteria includes the ___ amino acids

non-essential

34

what are the 12 non-essential AAs?

glycine
alanine
serine
aspartic acid
tyrosine
asparagine
cysteine
proline
hydroxyproline
hydroxylysine
glutamic acid
glutamine

35

which 2 AAs are not required for protein synthesis since they are formed after protein is synthesized?

hydroxyproline & hydroxylysine

36

amino acid classification by chemical criteria incorporates the use of ___ ___ properties (R-group)

side chain

37

AA classification by chemical criteria includes which 7 groups of amino acids?

aliphatic
hydroxyl
sulfur
carboxyl/amide
basic
aromatic
pyrrolidine

38

5 aliphatic AAs

Gly, Ala, Val, Leu, Ile

39

5 hydroxyl AAs

Ser, Thr, Tyr, Hyl, Hyp

40

2 sulfur AAs

Cys, Met

41

3 carboxyl/amide AAs

Asp, Glu/Asn, Gln

42

4 basic AAs

Lys, Arg, His, Hyl

43

4 aromatic AAs

His, Phe, Tyr, Trp

44

2 pyrrolidine AAs

Pro, Hyp

45

which 4 AAs DON'T occur in proteins?

homocysteine
ornithine
citruline
arginosuccinic acid

46

req'd for Met synthesis
functions with Vit B12
high levels associated with atherosclerosis

homocysteine

47

intermediates in biosynthesis of urea

ornithine, citrulline, arginosuccinic acid

48

precursor for biosynthesis of catecholamines

L-DOPA (3,4-dihydroxyphenylalanine)

49

what are the 3 most abundant catecholamines?

epinephrine (adrenaline)
norepinephrine (noradrenaline)
dopamine

50

the most abundant catecholamines are all produced by which 2 AAs?

phenylalanine & tyrosine

51

when the 4 groups on a carbon are different

chiral carbon

52

3 non-alpha amino acids

beta-alanine
taurine (2-aminoethylsulfonate)
GABA (gamma-aminobutryic acid)

53

part of pantothenic acid (Vit B5)

beta-alanine

54

resp. for integrity and function of retina
part of a bile acid (taurocholic acid)

taurine

55

inhibitory neurotransmitter from glutamate

GABA

56

when the 4 groups on a carbon are different

chiral carbon

57

there is more ___ charge at low pH and more ___ charge at high pH

+; -

58

a pH with lots of protons would favor the ___ form at the bottom of the ratio and would be ___ 1 and for a higher pH it would be the opposite

uncharged; less than

59

if R-groups are hydrocarbons then they are ___ and can form ___ bonds

hydrophobic; hydrophobic

60

if R-groups are polar (COOH, NH3, OH) then they are ___ and can form ___ bonds (salt bridge) or ___ bonds

hydrophilic; ionic; hydrogen

61

if r-groups are aromatic then they possess strong ___ absorption; this is used for quantitation of ___ in solution

UV; protein

62

if r-groups are -OH then they become esterified by ___

PO4

63

phosphorylation alters ___ function; major role is in phosphorylation ___

protein; cascade

64

if r-groups are -SH (usually Cys) then they are oxidized to form ___ bonds

disulfide

65

if a compound has hydrogen it's in ___ form and w/o hydrogen it's ___

reduced; oxidized

66

b/t COOH and NH3
in vivo, catalyzed by enzymes
aka peptide bond

amide bond

67

usually formed b/t 2 cysteines
involved in redox reactions
antioxidants
general 3D protein structure

disulfide bond

68

if r-groups are -OH or -NH2 they can form ___ by covalently bonding carbohydrates via ___ bonds

glycoproteins; glycosidic

69

HbA1c stands for?

hemoglobin
adult
1 carbohydrate attached

70

glycohemoglobin is ___ or ___ hemoglobin

glycosylated; glycated

71

less than/equal to 10 amino acids

peptide

72

more than 10 AAs

polypeptide

73

many AAs
may be comprised of multiple polypeptides

protein

74

N-terminal aka? C-terminal aka?

amino terminal
carboxy terminal

75

intracellular antioxidant; will prevent oxidation of other compounds, thus it must reduce other compounds while it is being oxidized

glutathione (GSH)

76

tripeptide of glutathione

Glu Cys Gly; Cys contains S so can possibly form disulfide bond

77

tripeptide form hypothalamus, stimulates pituitary

thyrotropin-releasing hormone (TRH)

78

pain neurotransmitter; 11 AA peptide in gut, SC and brain

substance P

79

vasodilating; derived form proteolytic cleavage

kinins (bradykinin and kallidin)

80

analgesic action like opiates

opiopeptides

81

3 types of opiopeptides are?

enkaphalins
beta-endorphin
dynorphin

82

Leu and Met are part of which sub-group?

enkaphalins

83

30 AA polypeptide derived from lipotropin about 60x stronger than opium

beta-endorphin

84

an opiopeptide in the SC

dynorphin

85

specific amino acid sequence

primary structure

86

in primary structure:
connected by ___ bond (covalent amide bond) which can be hydrolyzed by ___ or boiling
dictated by ___ in genes
dictates subsequent ___

peptide; proteases; codons; organization

87

4 types of secondary structure

alpha helix
beta pleated sheet
beta bending
random coil

88

alpha helix and beta pleated sheet are examples of ___ bonding

hydrogen

89

3 steps of collagen synthesis

1.translation of mRNA into pro-alpha chain in fibroblasts
2.hydroxylation of pro-alpha chains
proline by prolyl hydroxyls
lysine by lysyl hydroxylase
3.three hydroxylated pro-alpha-chains H-bond to form pro-collagen (hydroxyproline, hydroxylysine, glycine)
4. secretion of pro collagen out of cell by exocytosis
5. cleavage of N and C-terminal segments by procollagne peptidases -->tropocollagens
6. oxidation of some lysine's to lysyl aldehydes by lysyl oxidase

90

both reactions in the collagen synthesis 2nd step require which 3 components?

vit C, iron, O2

91

genetic mutation where Gly is replaced by Cys; easy bone bending and fracture, humpback (twisted spine); delayed wound healing

osteogenesis imperfecta

92

step 6 of collagen synthesis requires which 3 components?

Cu, vit B6, O2

93

re: step 6 of collagen synthesis, the ___ functional group leads to cross linking of tropocollagen-->collagen fibrils (the ___ structure)

aldehyde; quaternary

94

due to deficiency of lysyl oxidase; deformed spine; bone demineralization; joint dislocation; aortic aneurysms

lathyrism

95

protein classification based on which 4 factors?

function
conjugation
shape
solubility

96

which 4 contractile proteins are resp. for contraction & relaxation?

actin, myosin, tropomyosin, troponins

97

globular actin polymerizes into actin ___

filaments

98

G-actin =? F-actin=?

globular actin; actin filaments

99

f-actin is wrapped with a dimer of rope-shaped ___ and is attached by ___ troponins-->thin filament of the ___

tropomyosin; 3; sarcomere

100

___ is the thick filament

myosin

101

found in lung, large aa., skin and other CT
many random coils (2 degree structure) --> elasticity and extensibility
pralines are hydroxylated (as in collagen)
some lysine's oxidized to aldehydes (as in collagen)

elastin

102

___ formed from condensation of ___ lysine aldehydes plus ___ unmodified lysine-->marker of elastin metabolism/turnover (i.e. emphysema); comes out of ___

desmosine; 3; 1; urine

103

due to lack of ATP; actin cannot be released; the actin-myosin complex remains contractd

rigor mortis

104

whenever you see ATP there's going to be ___ involved

Mg2+

105

albumins are ___, e.g. serum albumin
globulins are ___ ___ solutions with low water solubility, e.g. antibodies
glutelins are ___ or ___ soluble, e.g. gluten
basic proteins are ___ or ___ soluble, e.g. histones

water-soluble; dilute salt; acid or base; acid or salt

106

most proteins, when classified according to shape, belong to this class

globular

107

elongated proteins, generally structural e.g. actin, myosin, collagen, elastin, keratin, etc.

fibrous

108

no attachment of non-protein component

simple proteins

109

apoprotein + prosthetic group

conjugated (complex) proteins

110

5 conjugated proteins

hemo Hb, cytochromes
glyco antibodies, glycophorin
lipo chylomicrons, LDL, HDL, VLDL
phospho casein
metallo some hemoproteins (Fe), IGFBP-5 protease

111

9 types of proteins based on function

enzymes; structural proteins; contraction; transport; hormones; protection; storage; receptor; cross-membrane transporter

112

2 protein sub-classifications based on conjugation

simple & conjugated

113

2 sub-classes of protein based on shape

globular & fibrous