MCAT > Biochem Chapter 2 > Flashcards

Biochem Chapter 2 Flashcards

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1
Q

Do catalysts affect thermodynamics and kinetics

A

Not thermodynamics like delta H or equilibrium position doesn’t change

Kinetics is in the sense it makes reaction go faster

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2
Q

What is enzyme specificity

A

Enzymes will only catalyze a single reaction with a specific substrate

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3
Q

What is oxidoreductases, what it do

A

Catalyzes oxidation and reduction reactions

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4
Q

Electron donor vs electron acceptor

And match with reductant or oxidant

A

Electron donor is reductant

Electron acceptor is oxidant

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5
Q

What is the usual cofactor for oxidoreductases enzymes

A

Nadp or nad +

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6
Q

Oxidoreductases usually have what suffix (2)

A

Dehydrogenase or reductase

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7
Q

What do transferases do

A

Catalyze movement of a functional group from one molecule to another

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8
Q

What type of enzymes are kinases

A

Transferases

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9
Q

What do kinases do

A

Transfer phosphate group from ATP to other molecules

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10
Q

What is usually transferases suffix (2)

A

Kinase and transferase

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11
Q

What do hydrolases do

A

Catalyze the breakdown of a compound into 2 molecules by adding water

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12
Q

What are some common hydrolases (4)

A

Lipases nucleases peptidases phosphotases

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13
Q

What do lyases dow

A

Cleave single molecule into 2

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14
Q

What suffixes fo lyases ususlaly have

A

Synthases

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15
Q

What do isomerases do

A

Catalyzes rearrangement of bonds within a molecule

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16
Q

Do isomerases catalyze reactions between stereoisomers or constitutional isomers

A

Both

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17
Q

Isomerases suffix

A

Isomerases

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18
Q

What do ligases do

Where are they mostly found

A

Catalyze addition or synthesis reactions between large molecules

Usually needing ATP

Nucleic acid synthesis and repiar

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19
Q

Major enzymes classifications (6)

A

Lyases
Isomerases
Ligaments
Hydrolases
Oxidoreductases
Transferases

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20
Q

Does endergonic or exergonic reaction require energy input

What is G for both , positive or negative

A

Endergonic need energy, G is positive

Exergonic release energy , G is negative

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21
Q

Is there an activation barrier when there is catalyst

What does it do to it

A

Yes there are still energy barrier needed to be pushed through

Lowering activation energy

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22
Q

What are enzymes

A

They are a catalyst

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23
Q

The physical interaction between enzyme and substrate is called

A

Enzyme substrate complex

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24
Q

Where the enzyme binds to substrate, what is that area called

A

Active site

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25
The two models for how substrate and enzyme interact What are they difference
Lock and key theory: only the right substrate cuz the exact shape is already carved out Induced fit model: enzymes have a little bit of shape changing after bindings to make it a more precise fit
26
According to induced fit theory, when the substrate binds to it and leaves Whcih part is endergonic and exergonic
Starts with endergonic because energy is needed for inducing the fit. Then exergonic .
27
What are cofactors
Inorganic molecules or metal ions that are often ingested as dietary minerals
28
What are coenzymes
Small organic groups. Such as vitamins, cozneyme A, FAD and NAD+ Whcih are vitamin derivatives
29
If enzymes have cofactors what are they called And without what are they called
With they are called holy enzymes Without they are called apoenzymes
30
What are prosthetic groups when it comes to coenzymes and cofactors
If they are tightly bound because they are necessary for enzyme functioning , then they are called prosthetic groups
31
Another name for b1
Thiamine
32
Another name for b2
Riboflavin
33
Another name for b3
Niacin
34
B5 another name
Pantothenic acid
35
B6 other name
Pyridoxal phosphate
36
B7 another name
Biotin
37
B9 another name
Folic acid
38
B12 anaother name
Cyanocobalamin
39
What is V max when it comes to enzymes
When saturation has occured, and the enzyme is working at maximum velocity
40
What is the only way to increase Vmax
Increasing enzyme concentration
41
What is the equation that relates velocity of enzyme to substrate concentration
Rate of reaction = Vmax [S] / Km + [S]
42
HOW does substrate concentration affect reaction rate Low and high
When substrate concentration is low, rate increases sharply with small increases in substrate When substrate concentration is high, rate levele off and approaches Vmax.
43
What is Km in Michaelis-Menten
Substrate concentration at which reaction rate is equal to half of Vmax w
44
what does Km tells us about the enzyme
Reflects affinity of enzyme
45
What does Kcat tell us
Turnover number Tells us how many substrate molecules one enzyme molecule can convert into product per second when the enzyme is fully saturated
46
Vmax and Kcat relationship equation
Vmax = [ concentration of enzyme ] x Kcat
47
High Km meaning for enzyme affinity for substrate What does high Km mean
High Km means low enzyme affinity for substrate High Km means larger amount of substrate is needed is to reach half maximum rate
48
Low Km meaning for enzyme affinity for substrate What does low Km mean
Low Km means high enzyme affinity for substrate Needs less to get going
49
When substrate is limited and at low concentrations, and Km >>>>S , what formula should you use between Kcat and Km
V= Kcat/Km. [E][S]
50
A more efficient enzyme with higher catalytic efficiency Has high or low Kcat values Has high or low Km values
Large Kcat ( high turnover ) Low Km ( high substrate affinity )
51
Ratio of Kcat/Km is called
Catalytic efficiency
52
What is the line weaver plot , what does it look like
Is double reciprocal graph of MM equation It shud be straight line , we take inverse as 1/v and 1/s as the x and y axis
53
What does Kcat tell us
How efficient each enzyme is when its fully active
54
Slope of line weaver plot is what divided by what
Km/Vmax
55
Cooperative enzymes show what type of curve
Sigmoidal
56
What are the two states that the enzymes exist in for cooperative enzymes
T - low affinity tense state R - high affinity relaxed state
57
When substrate binding happens, from what state to what state do enzymes convert
T to R
58
Cooperativity can be quantified using what
Hill’s coefficient
59
If hills coefficient is positive what does that mean
Postitively cooperative binding is happening After one ligand is bound the affinity of the enzyme for further ligand increases
60
If hills coefficient is negative , what does it mean
Negative cooperative binding is happening After on ligand is bound,the affinity of the enzyme for further ligand binding is decreased
61
If hills coefficient is 1, what it mean
The enzyme does not exhibit cooperative binding
62
What does cooperativity mean in enzyme binding
That means that when if binding of one ligand increases the affinity for more ligand
63
How deos temperature affect enzyme Catalyzes reactions in terms of velocity
These enzyme catalyzed reactions tend to double in velocity for every 10 degrees increase in temperature until optimum is reached
64
How does pH affect enzyme functioning (2)
PH affects ionization of active site PH can lead to enzyme denaturation
65
How does salinity affect enzyme activity
Changing salt concentrations can disrupt ionic hydrogen and ionic bonds within enzyme or within enzyme and substrate Alter shape - decrease activity - denaturation
66
Ideal tempature of body
37 degrees 310K
67
Ideal pH for most enzymes
7.4
68
Idea ph for gastric enzymes
2
69
Ideal ph for pancreatic enzymes
8.5
70
What is feed forward regulation
Enzymes being regulated by intermediates that precede hte enzyme in the pathway
71
What is negative feedback w
If too much product it’ll signal back things to slow down or stop producing , energy efficien t
72
What are the 4 types of reversible inhibition
Competitive Non competitive Mixed Uncompetitive
73
What is competitive inhibition
An inhibitor binds directly to active site to block substrate from entering
74
How do you overcome competitive inhibition What happens do vmax and Km
Adding more substrate Vmax is the same because higher concentration is needed Km increases
75
How doles competitive inhibition graph intersect, like where
With inhibitor and without inhibitor present, they intersect at the y axis
76
What is non competitive inhibition
Inhibitor binds to allosteric site, different site on enzyme and not active site. This binding changes the shape or function of enzyme so it can’t perform catalyses.
77
What happens to Vmax and Km in non competitive inhibition
Vmax lowers because less enzymes are available to react Km stays the same because substrate binding affinity hasn’t changed.
78
Where doles line intersect for non competitive inhibition
X axis
79
What is uncompetitive inhibition
The inhibitor only binds to the enzyme substrate complex, locking the substrate in place , so it can’t be released
80
What doles uncompetitive inhibition do to Vmax and Km
Lowers both
81
How does uncompetitive inhibition graph intersect
They do not they are just parallel lines
82
What is mixed inhibition
When the inhibitor can bind to the enzyme or the enzyme substrate complex, but has a different affinity for each of them
83
Where do mixed inhibitors bind to
Not active site, allosteric site
84
If in mixed inhibition - the inhibitor binds to enzyme , what happens to Km value - the inhibitor binds to substrate complex, what happens to Km value
If enzyme , increases Km value so lower affinity If complex, decreases Km value so higher affinity
85
What doles mixed inhibition do to Vmax
Decrease in either situations of binding to enzyme or complex
86
What does mixed inhibition graph look like
Intersect at a point that is not on either axis
87
For all 4 types of reversible inhibitions, which ones bind to active site, and which to allosteric site
Competitive - active Non competitive, uncompetitive, mixed - allosteric
88
Vmax always decreases with inhibitions except What is it in that
Competitive inhibition where its unchanged
89
What happens to active site for irreversible forms of inhibition What are the 2 ways it occurs
The active site is made unavailable for a long time or the enzyme is permananetly altered
90
How does regulated enzymes like allosteric enzymes work
1. Allosteric enzymes are in active and inactive form. The allosteric activators or inhibitors cause conformational shift in protein , they can also alter the activity of the enzyme
91
What are graphs of MM plots of cooperative allosteric enzymes like
Sigmoidal S shape
92
Are allosteric enzymes transient or convalent enzyme modifications
Transient
93
What are covalently modified enzymes As in what can they be activated or deactivated by (3)
Covalently modified enzymes can be activated or deactivated through phophosphorylation and dephosphorylation Another modification is glycosylaiton. It can tag an enzyme for transport in cell, or can modify protein activity and selectivity
94
What are zymogens - what are they activated by - how are they secreted
Some enzymes are released as zymogens Their inactive zymogens form is ones that are secreted They are activated by cleavage
95
Zymogens suffix
-Ogen
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