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CHEM 472 Biochem > Final: Chapter 11 - Transcription and Translation > Flashcards

Final: Chapter 11 - Transcription and Translation Flashcards

1
Q

How are major and minor grooves with DNA determined?

A

sugar phosphate back bone spacing between strands

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2
Q

What are four sources of DNA movement?

A

1) rotation around sugar phosphate backbone
2) rotation around glycosidic bond
3) syn and anti confirmations of glycosidic bond
4) puckering of carbons in sugar five membered ring

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3
Q

What are two ways bairs pairs can be oriented with one another?

A

1) helical twist creates 32 degree angle between stacked pairs
2) propeller twist paired bases are not in the same plane

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4
Q

What are the three double helical forms that DNA can adopt?

A

A, B, and Z

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5
Q

When does DNA take on B confirmation? Why?

A

In solution, major and minor grooves are heavily stabilized by H-bonds to water

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6
Q

Describe 5 features of B-DNA structure

A

1) right-handed helix
2) around 10 bp per turn
3) intermediate shape between A and Z
4) antiglycosidic bonds
5) form containing major and minor grooves

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7
Q

When does DNA take on A confirmation? Why?

A

When it is dehydrated, lack of stabilizing H-bonds from water

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8
Q

What are 4 key feature of A-DNA structue?

A

1) right-handed helix
2) around 11 bp per turn
3) broad shape
4) anti glycosidic bonds

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9
Q

What are three instances that DNA favors Z confirmation?

A

1) alternating purine and pyrimidine sequences
2) high salt concentrations neutralize phosphates
3) methylation of cytosine to 5- methylcytosine

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10
Q

What are 5 key features of ZDNA structure?

A

1) left-handed helix
2) zig-zag pattern
3) 12 bp per turn
4) narrow, elongated shape
5) purine residues adopt syn glycosidic bond which gives DNA the zigzag pattern

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11
Q

Does DNA helix formation have a negative or positive delta G value? Is this favorable?

A

negative

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12
Q

Does DNA helix formation have a negative or positive delta H value?

A

depends on the conditions the DNA exists in

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13
Q

Does DNA helix formation have a negative or positive delta S value? Why? is this favorable?

A

Negative; 2 strands form one; no

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14
Q

What energetically drives formation of the DNA double helix?

A

a negative delta H (enthalpy) caused by bond formation

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15
Q

How do electrostatic forces influence DNA helix formation?

A

decreases favorability because negative charge of phosphate backbones repels the strands

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16
Q

How can electrostatic influence on DNA helix formation be minimized?

A

Neutralizing negative charge of phosphate backbone using cations (typically from salts)

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17
Q

How do Vanderwaals forces influence DNA helix formation?

A

decreases delta H; stacking of nitrogenous bases increases pi-pi stacking interactions by further delocalizing the pi electrons in the aromatic ring

18
Q

How much energy does a pi-pi stacking interaction release?

A

51 kJ/mol`

19
Q

How does h-bond formation influence DNA formation?

A

Decreases delta H because energy is released by bond formation

20
Q

How do hydrophobic effects influence DNA formation?

A

Increase favorability by making delta S less negative; nitrogenous bases are hydrophobic and cluster in center of helix

21
Q

What are intercalating agents?

A

molecules that distort the DNA double helix

22
Q

What are two key components of intercalating agents?

A

1) flat
2) made of fused aromatic rings

23
Q

Why does the structure of intercalating agents allow them to insert into the DNA double helix?

A

Their own aromatic electrons can participate in pi-pi stacking interactions between base pairs

24
Q

What is an additional structural component that some intercalating agents have to help their insertion into the DNA double helix? Why?

A

A positively charged nitrogen because it can interact with the negative phosphate backbone

25
Q

What wavelength does DNA fluoresce at?

A

260 nm

26
Q

How does DNA absorbance change with denaturaton?

A

Increases with denaturation

27
Q

Why does DNA absorbance increase with denaturation?

A

pi-pi stacking is broken which frees electrons to absorb light

28
Q

What 4 methods of DNA denaturation?

A

1) temperature
2) salt concentration
3) pH
4) H-bonding organic compounds

29
Q

Why does temperature increase cause denaturation?

A

thermal energy overcomes the non-covalent interactions

30
Q

Why does melting point differ between DNA strands?

A

different concentrations of G/C and A/T result in different amounts of H-bonds

31
Q

How does salt concentration affect DNA denaturation?

A

increasing salt concentration increases melting point

32
Q

Why does increasing salt concentration increase DNA melting point?

A

decreases electrostatic repulsion between strands by neutralizing negative phosphate backbone with cations

33
Q

What does DNA melting point describe? Is it an actual melting point?

A

temperature describing midpoint of DNA denaturation; No

34
Q

How does pH impact DNA denaturation?

A

disrupts the H-bonds between bases that hold strands together reducing the # of H-bonds to over come

35
Q

How does pH impact number of H-bonds present in a DNA molecule?

A

1) pH < 2.3; nitrogenous bases become extensively protonated
2) pH > 10; nitrogenous bases become extensively deprotonated

36
Q

How do the speeds of denaturation and renaturing/reannealing differ?

A

Denaturation is must faster than reannealing

37
Q

Why is annealing slow? What makes it faster?

A

Slowly because correct bases must be repaired; once first base pair is made it is must easier anneal the others

38
Q

What are two examples of higher order DNA structures?

A

1) Supercoiled DNA
2) Chromosomes

39
Q

When does supercoiling occur?

A

overwinding or underwinding creates tension that condenses DNA in circular DNA molecules or linear DNA molecules with fixed ends

40
Q

What kind of AAs make up histones? Why?

A

Lys and Arginine; positively charged so they interact favorably with DNA’s negatively charged phosphate backbone

CHEM 472 Biochem (12 decks)

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