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ABS > Biochem 2: Enzymes > Flashcards

Biochem 2: Enzymes Flashcards

1
Q

an enzyme is a

A

biological catalyst

-proteins (with the exception of some RNAs that catalyze their own splicing, all enzymes are proteins)

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2
Q

enzymes can increase the

A

rate of a reaction by a factor of up to 10^20 over an uncatalyzed reaction

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3
Q

the rate of a reaction depends on its

A

activation energy (delta G)

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4
Q

enzymes do what to activation energy

A

an enzyme provides an alternative pathway with a lower activation energy

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5
Q

substrate

A

reactant binds to active site of an enzyme

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6
Q

active site

A

the small portion of the enzyme surface where the substrate(s) is bound

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7
Q

enzyme substrate complex (ES) is held together by

A

hydrogen bonding, electrostatic attractions, van der Waals attractions

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8
Q

what two models have been developed to describe formation of the enzyme-substrate complex

A
  1. lock and key model

2. induced fit model (most enzymes follow this model)

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9
Q

in the lock and key model, the

A

substrate binds to that portion of the enzyme with a complementary shape

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10
Q

in the induced fit model, the

A

binding of the substrate induces a change in the conformation of the enzyme that results in a complementary fit

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11
Q

the rate of a catalyzed reaction depends on

A

substrate concentration

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12
Q

concentration of an enzyme is usually much _____ than the concentration of substrate

A

lower

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13
Q

what occurs at saturation

A

all enzyme is bound to substrate, it is working at maximum rate

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14
Q

list of things that can affect the rate of a reaction

A
  • temperature
  • pH
  • enzyme concentration
  • substrate concentration
  • presence of controlling molecules
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15
Q

pH influences ______ of the functional groups

A

ionization

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16
Q

example of how pH affects enzyme function

A

at low pH (high H+), COO- may react with H+ to form COOH which is no longer charged
-this affects folding and thus enzyme function

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17
Q

increasing temperature will _____ reaction rate

A

increase

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18
Q

at high temperature what bonds begin to break?

A

non-covalent

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19
Q

what happens with denaturation and around what temperature

A

enzymes can lose tertiary structure and become denatured, usually occurs around 50-55 degrees C

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20
Q

what occurs when the enzyme is saturated

A

the rate of the reaction is maximal and cannot increase

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21
Q

the rate of the reaction is _____ proportional to the enzyme concentration

A

directly

as long as substrate does not run out

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22
Q

the rate and observed kinetics of an enzymatic reaction depends on

A

substrate concentration

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23
Q

at low substrate concentration, adding more substrate will

A

increase the rate of reaction

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24
Q

a constant rate Vmax is reached when

A

the enzyme is completely saturated with substrate

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25
Q

Km is the

A

michaelis constant

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26
Q

the higher the value for Km, the ____ the affinity for substrate

A

lower

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27
Q

the lower the Km value, the ____ the affinity for substrate

A

higher

28
Q

how can you liberalize the michaelis-menten equation

A

with the lineweaver-burke plot (y=mx + b) form

29
Q

lineweaver-burke plot is of ___ versus ____
slope=
y intercept=

A

1/V versus 1/[S] which gives a straight line
slope: Km/Vmax
y intercept: 1/Vmax

30
Q

what is a reversible inhibitor and what types are there

A

a substance that binds to an enzyme to inhibit it, but can be released
-competitive and noncompetitive

31
Q

reversible inhibitor:

competitive

A

binds to the active (catalytic) site and blocks access to it by substrate

32
Q

reversible inhibitor:

noncompetitive

A

binds to a site other than the active site

-inhibits the enzyme by changing its conformation

33
Q

irreversible inhibitor

A

a substance that causes inhibition that cannot be reversed

-usually involves formation or breaking of covalent bonds to or on the enzyme

34
Q

list of things important to enzyme regulation

A 
-feedback inhibition 
allosteric regulation 
-covalent modification: phosphorylation 
-proteolytic activation 
-regulatory proteins
35
Q

feedback inhibition

A

formation of product inhibits its continued production

36
Q

allosteric enzyme

A

an oligomer whose biological activity is affected by other substances binding to it

37
Q

how do allosteric enzymes work

A

these substances change the enzyme’s activity by altering the conformation(s) of its 4 quaternary structure

38
Q

allosteric effector

A

a substance that modifies the behavior of an allosteric enzyme
-may be an allosteric inhibitor or allosteric activator

39
Q

a _____ shape of curve describes allosteric behavior

A

sigmoidal

40
Q

the side chains -OH groups of ___, ___, an d___ can form phosphate esters

A

Ser, Thr, Tyr

41
Q

what changes can phosphorylation by ATP cause

A

can convert an inactive precursor into an active enzyme

42
Q

what is a zymogen

A

an inactive precursor of an enzyme where proteolytic cleavage of one or more covalent bonds transforms it into the active enzyme

43
Q

common examples of zymogens

A

digestive enzymes, complement proteins, blood clotting factors and capsizes in apoptosis

44
Q

chymotrypsinogen

A
  • synthesized and stored in the pancreas
  • a single polypeptide chain of 245 amino acid residues cross linked by 5 disulfide bonds
  • when secreted into the small intestine, the digestive enzyme trypsin cleaves a 15 unit polypeptide from the N-terminal end to give pi-chymotrypsin
45
Q

apoptosis is a

A

programmed form of cellular suicide in which the cell participates actively in its own death

46
Q

what is a prearranged signaling pathway of cell death triggered by a variety of special extracellular and intracellular signals

A

apoptosis

47
Q

why is apoptosis useful

A

it is a self-defense mechanism to destroy cells infected with pathogens or those with genomic alterations

48
Q

events of apoptosis

A
  • cell detaches from its neighbors
  • chromatin is digested by enzymes that cut DNA between nucleosomes
  • forms membraneous lobes called “blebs” that break into fragments
  • surrounding living cells ingest remains of the dead cell and recycle the contents
49
Q

signals that initiate apoptosis:

A
  • hormones
  • growth factors
  • viral infections
  • toxins
  • extensive DNA damage
50
Q

apoptotic signals: what do the pathways affect?

A

some affect: mitochondria, increasing permeability of the membranes, ATP production stops and the cell dies

51
Q

proteases called _____ may be activated in apoptosis

A

caspases

52
Q

what do capsases do

A

they hydrolyze membrane proteins in nuclear and cell membranes and nucleosomes

53
Q

G proteins are activated during

A

signal transduction once a hormone binds its receptor and the receptor activates the G-protein (found in cAMP cascade)

54
Q

what is transducer and what is it involved in?

A

transducin is a G-protein in retinal rods and cones that is involved in transduction of the visual signal

55
Q

what is an isozyme?

A

isozymes are enzymes that catalyze the same reaction but have different properties, such as optimal temperatures

56
Q

enzyme differences in humans vs. bacteria

A

enzymes in humans have higher optimal temperature than enzymes in most bacteria- a fever can denature the bacterial enzymes

57
Q

types of non protein “partners” of enzymes

A
  • prosthetic groups
  • inorganic cofactors
  • coenzymes
58
Q

prosthetic groups

A

non-amino acid groups bound to enzymes

59
Q

inorganic cofactors

A

ions permanently bound to enzymes

60
Q

coenzymes

A

small carbon-containing molecules, not permanently bound

61
Q

NAD is a type of

A

coenzyme- carries electrons/protons

62
Q

NAD+ facts

A

nicotinamide adenine dinucleotide, used in many redox reactions in biology
contains: nicotinamide ring, adenine ring, 2 sugar-phosphate groups

63
Q

NAD+ is a ___ ___ ____ ____ and reduced to what?

A

two-electron oxidizing agent

-reduced to NADH

64
Q

where on NAD does the reduction-oxidation occur

A

nicotinamide ring

65
Q

B6 vitamins are

A

coenzymes involved in amino group transfer from one molecule to another
-important in amino acid biosynthesis

ABS (31 decks)

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