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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
how are polypeptides formed
linking two AA's together by the carboxyl group of one AA, and the amine group of the other
26
what is the backbone of a polypeptide chain
N-C-C-N-C-C
27
an individual AA is called what when in a polypeptide chain
residue
28
hydrolysis of a protein is called
proteolysis or proteolytic cleavage
29
the protein that hydrolyzes another protein is called
proteolytic enzyme or a protease
30
trypsin cleaves what
Arg and lys
31
chymotrypsin cleaves what
aromatic AA's
32
once a cystine residue becomes disulfide bonded to other Cys what is it called
cysteine
33
denatured proteins
non functional
34
what denaturation
the disruption of a proteins shape without breaking the peptide bonds
35
what are things that can denature a protein
salt conc, ph change, acidity, urea (reducing agent)
36
what is a primary structure
the linear ordering of a polypeptide chain or the sequence of AA's
37
what is a secondary structure
the initial folding of the AA chain stabilized by the hydrogen bonding, youll see some alpha helices and beta pleaded sheets
38
alpha helices of proteins are always what direction
right handed
39
what AA will never be in beta sheets
proline because of kink creation
40
why is alpha helices favorable in hydrophobic membranes
because all polar NH and Co groups are on the inside of the helix while the non polar are on the outside
41
what are parallel beta sheets? antiparallel?
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
what is a tertiary structure
the next level of protein folding where it can be active and interactions between AA like van der waals or disulfide bonds
43
what does the hydrophobic effect cause in AA's
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
what is a quaternary structure
the highest level where there are interactions between protein subunits
45
what is a subunit
a single polypeptide chain that is part of a large complex containing many subunits
46
enzymes are what
catalysts
47
how do enzymes work to make reactions more favorable
they lower the activation energy and DO NOT affect delta G
48
enzymes have what kind of role
kinetic NOT a thermodynamic one
49
hydrolase
hydrolyzes chemical bonds
50
isomerase
rearranges bonds within a molecule to form an isomer
51
ligase
forms a chemical bond
52
lyase
breaks down bonds by means other than oxidation or hydrolysis
53
kinase
transfers phosphate groups from a high energy carrier like ATP
54
oxidoreductase
runs redox rxns
55
polymerase
polymerization like addition of nucleotides to leading strand of DNA
56
phosphatase
removes a phosphate group
57
phosphorylase
transfers a phosphate group to a molecule from inorganic phosphate
58
protease
hydrolyzes peptide bonds
59
how can unfavorable rxns take place
reaction coupling
60
rxn coupling
one very favorable rxn is used to drive an unfavorable one
61
active site
the region in an enzymes 3d structure that is directly involved in catalysis.
62
substrate
reactants in a enzyme catalyzed rxn
63
induced fit model
the substrate and active site differ slightly in structure and that the binding of the substrate induces a conformational change in the enzyme
64
cofactor/coenzymes
metal ions or small molecules (organic origin if coenzyme) that help enzymes in their rxns
65
what are the four ways you can regulate enzyme activity
covalent modification, proteolytic cleavage, association with other polypeptides, allosteric regulation
66
covalent modification
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
proteolytic cleavage
zymogens are inactive but once cleaved become active
68
what is the association of enzymes with other polypeptides
subunits within the protein can start or stop the enzyme from working
69
allosteric regulation
modification of NOT the active site by turning it on or off with activators or inhibitors
70
negative feedback
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
enzyme kinetics
study of the rate of formation of products from substrates in the presence of an enzyme
72
the reaction rate
known as V, and is the amount of product formed per unit time
73
rxn rate depends on what
conc of substrate and enzyme
74
what is vmax
the rate when the enzyme is saturate with substrate
75
what is km
the sub conc at half of vmax
76
low km? high km?
high affinity, low affinity
77
positive cooperativity
the binding of a substrate to one subunit increases the affinity of the other subunits for substrate
78
competitive inhibitor? how to overcome it? km and vmax?
competes for the active site of enzyme, you can overcome by increasing substrate, vmax stays the same but km increases
79
non competitive inhibitor? km and vmax?
binds at an allosteric site NOT at the active site, vmax decreases but km stays the same
80
uncompetitive inhibitor? km and vmax?
can only bind to the E/S complex but trapping substrate and both vmax and km are lowered
81
mixed type inhibition
when an inhibitor can bind either the unoccupied enzyme or the E/S complex. the vmax decreases and km varies
82
slope of LWB plot
km over vmax
83
y intercept of lWB plot
1/vmax
84
x intercept of IWB plot
-1/km
85
where does a new amino acid add to a chain
carboxyl
86
alpha helices are favorable for what
for its hydrophobic membrane
87
irreversible inhibition is similar to
noncompetitive
88
competitive in. graph meets
at y axis
89
uncomp in graph meets
at no point because its parallel
90
noncomp meets where on the LWB plot
at x axis
91

mcat biochem textbook (6 decks)

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