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MCB 301 > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

What constitutes a nucleotide?

A

Phosphate, Sugar, and Base

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2
Q

What are the Pyrimidines? Are they DNA or RNA?

A

Uracil (RNA), Thymine (DNA), and Cytosine (Both)

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3
Q

Draw: Uracil

A

Get it?

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4
Q

Draw: Thymine

A

Get it?

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5
Q

Draw: Cytosine

A

Get it?

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6
Q

How are Pyrimidines numbered?

A

Starting at the bottom N as 1, goes counterclockwise around

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7
Q

What are the Purines?

A

Adenine and Guanine

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8
Q

Draw: Adenine

A

Get it?

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9
Q

Draw: Guanine

A

Get it?

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10
Q

How are Purines labeled?

A

Look at notes lol

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11
Q

What are the two sugars and are they DNA or RNA?

A

Ribose= RNA
DeoxyRibose= DNA

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12
Q

Draw: Ribose and Deoxyribose

A

Get it?

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13
Q

How are sugars numbered?

A

1prime end starts on carbon that is attached to the base and goes clockwise

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14
Q

Draw: Phosphate

A

Get it?

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15
Q

Where are nucleotides synthesized on a sugar?

A

The 5 prime end

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16
Q

Where do phosphates link a sugar and base?

A

On the 3 prime end

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17
Q

What is the Major and minor groove?

A

Areas in a dsDNA where there are large spaces are small spaces in the helix

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18
Q

What is the Tm

A

Melting point of DNA, where half of the DNA is denatured

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19
Q

What are the enthalpic and entropic factors that favor ssDNA?

A

Enthalpic:
-H-bonding with water
- Relief of ionic repulsion in the phosphate groups

Entropic:
- Strands have more rotation

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20
Q

What are the enthalpic and entropic factors that favor dsDNA?

A

Enthalpic:
- H-bonding between bases
- Stacking interactions

Entropic:
- Some release of water

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21
Q

What is stacking?

A

A bases interaction with a base under or above it.

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22
Q

Explain nucleation and propagation in DNA denaturation?

A

Nucleation is an input of energy (heat) that breaks H-bonding between bases, making pockets within the dsDNA.
- AT rich regions will go first
Propagation is the spontaneous breaking of the rest of the bonds forming a ssDNA.

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23
Q

What impacts DNA’s Tm?

A
  1. Length of sequence: The larger the more energy needed
  2. Composition of bases: GC is stronger than AT
24
Q

How do enzymes work?

A

They lower the energy of activation and speeds up chemical reactions

25
Q

What are the roles of an active site?

A
  1. Brings the substrate into proximity
  2. Orients groups for catalysis
  3. Provides catalytic groups
  4. Binds transition state molecule more tightly than the reactants or products
    - this lower the deltaG
26
Q

What is induced fit?

A

Upon binding to a substrate, an enzyme changes conformation to fit the substrate more tightly, rather than just lock and key.

27
Q

Describe how a DNA nick is repaired?

A
  1. ATP binds to the amine group on the lysine residue within the DNA ligase.
  2. A enzyme-AMP intermediate is formed, releasing two phosphates. Then the nicked part of the DNA molecule is transferred inside of the Ligase
  3. The phosphate on the nicked DNA attacks the phosphate in the Ligase, and causes the dissociation of the phosphate from the Lysine residue
  4. The 3’ OH on the deoxyribose will then attack one of the phosphates, causing the phosphates to dissociate from one another
  5. A new phosphodiester bond is made and the DNA is fixed
  6. AMP is released, and more ATP will join to restart the cycle
28
Q

What is a nucleophile? What is an electrophile?

A

Nucleophiles: Electron rich and want to donate their electrons
Electrophiles: Electron poor and want to accept electrons

29
Q

What is Vmax?

A

The maximum velocity for a particular enzyme, (speed)

30
Q

What happens to Vmax if the enzyme concentration changes?

A

The vmax will change by the same amount

31
Q

What is Km? What does it mean if it is small or large?

A

Measure of the affinity of the substrate to an enzyme. A small Km=better affinity while a large km= weaker affinity

32
Q

What is the equation of a substrate meeting an enzyme?

A

E+s–K1–> ES–K2–> E+P

33
Q

What is Vo?

A

The initial velocity in uM/min

34
Q

What does a time vs [P] graph look like?

A

Get it ?

35
Q

What does a Vo vs. [S] look like?

A

Get it?

36
Q

What is the equation for vmax? How about kcat?

A

Vmax=Kcat*[ET] (total enzyme concentration)
kcat= vmax/[et]

37
Q

What is kcat?

A

The turn over number, the rate of how efficient an enzyme is. How many times per second that enzyme can convert a substrate into product
- Also the k2

38
Q

What is the specificity constant ?

A

kcat/ Km, MEASURE OF HOW GOOD A CATALYST IT IS

39
Q

Draw: The graph of 1/vo vs 1/[s], what is y and x?

A

Get it? Y=1/vmax and X= -1/km

39
Q

What is the equation for V

A

V= (kcat/Km)[ET][S]

39
Q

What is competitive inhibition? How does Vmax and Km change?

A

When an inhibitor has more affinity to the active site than the ligand, competed for same spot
Vmax=does not change
Km=does change

40
Q

Draw the graph of competitive inhibition. How does vmax and Km change? Why?

A

Vmax will stay the same, because the substrate acting with the enzyme still goes at the same speed. The functionality of the enzyme has not changed

Km increases because the affinity of the ligand to the active site is competing with the inhibitor

41
Q

What is uncompetitive inhibition? How does vmax and Km change?

A

Inhibitor binds to something that is not the active site and only binds to the enzyme substrate complex. Both the vmax and Km change

42
Q

Draw the graph for uncompetitive inhibition. How does vmax and Km change? Why?

A

Both Km and Vmax will decrease. Vmax decreases because there is less functional enzyme, Km decreases because. The Km decreases too because the inhibitor only binds to the enzyme when substrate is bound, meaning that it shifts equilibrium to ES complex making the affinity appear better.

43
Q

What is mixed inhibition? How does Km and vmax change?

A

Mixed inhibition is when inhibitor binds to substrate and ES complex.Km and vmax change

44
Q

Draw the graph for mixed inhibition. How does vmax and Km change? Why?

A

Km will increase or decrease depending on the inhibitor. Km will increase if the inhibitor binds to E tighter than ES. Km will decrease if inhibitor binds to ES more than E.

V max will decrease because the amount of active enzyme is reduced.

45
Q

What is irreversible inhibition ? How does it effect km and Vmax?

A

Inhibitor inactivates enzyme, vmax decreases but KM changes

46
Q

Draw the graph for irreversable inhibition. How does vmax and Km change? Why?

A

Vmax will decrease, because there is less functional enzyme

Km will stay the same. because the inhibitor is not attacking the substrates affinity to the enzyme.

47
Q

Where are regulatory enzymes located?

A

At the beginning of reactions

48
Q

Typically, how are enzymes regulated?

A

The end product will usually modulate the regulated enzyme

49
Q

Draw a Vo vs [s] plot with positive and negative modulators? not k1/2

A

Get it?

50
Q

How can you tell if there is a positive modulator?

A

The curve is more hyperbolic

51
Q

How can you tell if there is a negative modulator?

A

The curve is more sigmoidal (flatter)

52
Q

What are some post transtitoinal modifications to enzymes?

A

covalent modifications, proteolytic cleavage

53
Q

What is the equation for Vo that also has the hill coefficient?

A

Vo=Vmax*[S]^n / K0.5^n + [S]^n

MCB 301 (3 decks)

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