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mcat biochem textbook > ch 4 > Flashcards

ch 4 Flashcards

1
Q

what are polymers

A

strings of repeated units called monomers

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2
Q

what does an amino acid back bone consist of

A

the alpha amino group (NH2), the tetrahedral alpha carbon, the alpha carboxyl group (OH), and the variable R side chain

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3
Q

what is special about the side chain of an amino acid

A

it gives it the physical and chemical properties that make it different from the other nineteen amino acids

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4
Q

what are the acidic amino acids

A

aspartic acid and glutamic acid

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5
Q

what are the basic amino acids

A

lysine, arginine, and histidine

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6
Q

what is so special about histidine

A

its pka is close to the ph of the blood so it may be deprotonated or protonated. it can be either a proton acceptor or donor.

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7
Q

what are the hydrophobic amino acids

A

glycine, alanine, valine, leucine, isoleucine, phenylalanine, tryptophan, methionine, and proline

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8
Q

what does aliphatic mean

A

compounds that are not aromatic

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9
Q

what are the hydrophilic AA’s

A

serine, threonine, tyrosine, asparagine, cysteine and glutamine, lysine, histidine, arg

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10
Q

hydrophobic amino acids mean what about its polarity

A

hydrophobic means non polar

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11
Q

hydrophilic amino acids mean what about its polarity

A

polar

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12
Q

what AA’s work often with kinases

A

the ones with OH’s in side chain, serine, threonine, and tyrosine

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13
Q

what AA’s have sulfur in them

A

cysteine and methionine

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14
Q

what AA(s) make disulfide bonds

A

cysteine

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15
Q

what is special about proline

A

its very small due to the ring structure it has

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16
Q

what is an essential AA

A

those that cannot be made by the body and must be eaten

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17
Q

what are the essential AA’s

A

lysine. histidine, threonine, valine, leucine, isoleucine, phenylalanine, tryptophan, methionine

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18
Q

are AA’s amphoteric?

A

yes, they can act as bases or acids

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19
Q

when the PH of the solution is less than the pKa of an acidic group,

A

the acidic group will mostly be in its protonated form

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20
Q

when the PH of the solution is greater than the pKa of an acidic group,

A

the acidic group will mostly be in its deprotonated form

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21
Q

what is a zwitterion

A

an amino acid that after removing certain protons, they have an overall neutral charge

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22
Q

what is a protonated amine called

A

its acidic and its called the ammonium group

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23
Q

what is the isoelectric point

A

the ph in which a molecule is uncharged (zwitterion)

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24
Q

what are the two covalent bonds between AA’s

A

peptide bonds and disulfide bonds

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25
Q

how are polypeptides formed

A

linking two AA’s together by the carboxyl group of one AA, and the amine group of the other

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26
Q

what is the backbone of a polypeptide chain

A

N-C-C-N-C-C

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27
Q

an individual AA is called what when in a polypeptide chain

A

residue

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28
Q

hydrolysis of a protein is called

A

proteolysis or proteolytic cleavage

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29
Q

the protein that hydrolyzes another protein is called

A

proteolytic enzyme or a protease

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30
Q

trypsin cleaves what

A

Arg and lys

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31
Q

chymotrypsin cleaves what

A

aromatic AA’s

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32
Q

once a cystine residue becomes disulfide bonded to other Cys what is it called

A

cysteine

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33
Q

denatured proteins

A

non functional

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34
Q

what denaturation

A

the disruption of a proteins shape without breaking the peptide bonds

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35
Q

what are things that can denature a protein

A

salt conc, ph change, acidity, urea (reducing agent)

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36
Q

what is a primary structure

A

the linear ordering of a polypeptide chain or the sequence of AA’s

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37
Q

what is a secondary structure

A

the initial folding of the AA chain stabilized by the hydrogen bonding, youll see some alpha helices and beta pleaded sheets

38
Q

alpha helices of proteins are always what direction

A

right handed

39
Q

what AA will never be in beta sheets

A

proline because of kink creation

40
Q

why is alpha helices favorable in hydrophobic membranes

A

because all polar NH and Co groups are on the inside of the helix while the non polar are on the outside

41
Q

what are parallel beta sheets? antiparallel?

A

parallel are beta sheets that same in the same direction of N terminus to c terminus while anti parallel run in the opposite direction

42
Q

what is a tertiary structure

A

the next level of protein folding where it can be active and interactions between AA like van der waals or disulfide bonds

43
Q

what does the hydrophobic effect cause in AA’s

A

nonpolar AA’s tend to fold into the protein and polar AA’s ten to fold towards the outside of the protein to interact with water

44
Q

what is a quaternary structure

A

the highest level where there are interactions between protein subunits

45
Q

what is a subunit

A

a single polypeptide chain that is part of a large complex containing many subunits

46
Q

enzymes are what

A

catalysts

47
Q

how do enzymes work to make reactions more favorable

A

they lower the activation energy and DO NOT affect delta G

48
Q

enzymes have what kind of role

A

kinetic NOT a thermodynamic one

49
Q

hydrolase

A

hydrolyzes chemical bonds

50
Q

isomerase

A

rearranges bonds within a molecule to form an isomer

51
Q

ligase

A

forms a chemical bond

52
Q

lyase

A

breaks down bonds by means other than oxidation or hydrolysis

53
Q

kinase

A

transfers phosphate groups from a high energy carrier like ATP

54
Q

oxidoreductase

A

runs redox rxns

55
Q

polymerase

A

polymerization like addition of nucleotides to leading strand of DNA

56
Q

phosphatase

A

removes a phosphate group

57
Q

phosphorylase

A

transfers a phosphate group to a molecule from inorganic phosphate

58
Q

protease

A

hydrolyzes peptide bonds

59
Q

how can unfavorable rxns take place

A

reaction coupling

60
Q

rxn coupling

A

one very favorable rxn is used to drive an unfavorable one

61
Q

active site

A

the region in an enzymes 3d structure that is directly involved in catalysis.

62
Q

substrate

A

reactants in a enzyme catalyzed rxn

63
Q

induced fit model

A

the substrate and active site differ slightly in structure and that the binding of the substrate induces a conformational change in the enzyme

64
Q

cofactor/coenzymes

A

metal ions or small molecules (organic origin if coenzyme) that help enzymes in their rxns

65
Q

what are the four ways you can regulate enzyme activity

A

covalent modification, proteolytic cleavage, association with other polypeptides, allosteric regulation

66
Q

covalent modification

A

proteins can have several different groups covalently attached to then and this like regulate their activity like GP and kinase to make it active

67
Q

proteolytic cleavage

A

zymogens are inactive but once cleaved become active

68
Q

what is the association of enzymes with other polypeptides

A

subunits within the protein can start or stop the enzyme from working

69
Q

allosteric regulation

A

modification of NOT the active site by turning it on or off with activators or inhibitors

70
Q

negative feedback

A

the product of a metabolic pathway can act as an inhibitor for a step of the metabolic pathway to allow the body to either absorb the product or allow it to catch up

71
Q

enzyme kinetics

A

study of the rate of formation of products from substrates in the presence of an enzyme

72
Q

the reaction rate

A

known as V, and is the amount of product formed per unit time

73
Q

rxn rate depends on what

A

conc of substrate and enzyme

74
Q

what is vmax

A

the rate when the enzyme is saturate with substrate

75
Q

what is km

A

the sub conc at half of vmax

76
Q

low km? high km?

A

high affinity, low affinity

77
Q

positive cooperativity

A

the binding of a substrate to one subunit increases the affinity of the other subunits for substrate

78
Q

competitive inhibitor? how to overcome it? km and vmax?

A

competes for the active site of enzyme, you can overcome by increasing substrate, vmax stays the same but km increases

79
Q

non competitive inhibitor? km and vmax?

A

binds at an allosteric site NOT at the active site, vmax decreases but km stays the same

80
Q

uncompetitive inhibitor? km and vmax?

A

can only bind to the E/S complex but trapping substrate and both vmax and km are lowered

81
Q

mixed type inhibition

A

when an inhibitor can bind either the unoccupied enzyme or the E/S complex. the vmax decreases and km varies

82
Q

slope of LWB plot

A

km over vmax

83
Q

y intercept of lWB plot

A

1/vmax

84
Q

x intercept of IWB plot

A

-1/km

85
Q

where does a new amino acid add to a chain

A

carboxyl

86
Q

alpha helices are favorable for what

A

for its hydrophobic membrane

87
Q

irreversible inhibition is similar to

A

noncompetitive

88
Q

competitive in. graph meets

A

at y axis

89
Q

uncomp in graph meets

A

at no point because its parallel

90
Q

noncomp meets where on the LWB plot

A

at x axis

91
Q
A

mcat biochem textbook (6 decks)

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