Final: Chapter 11 - Transcription and Translation Flashcards
How are major and minor grooves with DNA determined?
sugar phosphate back bone spacing between strands
What are four sources of DNA movement?
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
What are two ways bairs pairs can be oriented with one another?
1) helical twist creates 32 degree angle between stacked pairs
2) propeller twist paired bases are not in the same plane
What are the three double helical forms that DNA can adopt?
A, B, and Z
When does DNA take on B confirmation? Why?
In solution, major and minor grooves are heavily stabilized by H-bonds to water
Describe 5 features of B-DNA structure
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
When does DNA take on A confirmation? Why?
When it is dehydrated, lack of stabilizing H-bonds from water
What are 4 key feature of A-DNA structue?
1) right-handed helix
2) around 11 bp per turn
3) broad shape
4) anti glycosidic bonds
What are three instances that DNA favors Z confirmation?
1) alternating purine and pyrimidine sequences
2) high salt concentrations neutralize phosphates
3) methylation of cytosine to 5- methylcytosine
What are 5 key features of ZDNA structure?
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
Does DNA helix formation have a negative or positive delta G value? Is this favorable?
negative
Does DNA helix formation have a negative or positive delta H value?
depends on the conditions the DNA exists in
Does DNA helix formation have a negative or positive delta S value? Why? is this favorable?
Negative; 2 strands form one; no
What energetically drives formation of the DNA double helix?
a negative delta H (enthalpy) caused by bond formation
How do electrostatic forces influence DNA helix formation?
decreases favorability because negative charge of phosphate backbones repels the strands
How can electrostatic influence on DNA helix formation be minimized?
Neutralizing negative charge of phosphate backbone using cations (typically from salts)
How do Vanderwaals forces influence DNA helix formation?
decreases delta H; stacking of nitrogenous bases increases pi-pi stacking interactions by further delocalizing the pi electrons in the aromatic ring
How much energy does a pi-pi stacking interaction release?
51 kJ/mol`
How does h-bond formation influence DNA formation?
Decreases delta H because energy is released by bond formation
How do hydrophobic effects influence DNA formation?
Increase favorability by making delta S less negative; nitrogenous bases are hydrophobic and cluster in center of helix
What are intercalating agents?
molecules that distort the DNA double helix
What are two key components of intercalating agents?
1) flat
2) made of fused aromatic rings
Why does the structure of intercalating agents allow them to insert into the DNA double helix?
Their own aromatic electrons can participate in pi-pi stacking interactions between base pairs
What is an additional structural component that some intercalating agents have to help their insertion into the DNA double helix? Why?
A positively charged nitrogen because it can interact with the negative phosphate backbone
What wavelength does DNA fluoresce at?
260 nm
How does DNA absorbance change with denaturaton?
Increases with denaturation
Why does DNA absorbance increase with denaturation?
pi-pi stacking is broken which frees electrons to absorb light
What 4 methods of DNA denaturation?
1) temperature
2) salt concentration
3) pH
4) H-bonding organic compounds
Why does temperature increase cause denaturation?
thermal energy overcomes the non-covalent interactions
Why does melting point differ between DNA strands?
different concentrations of G/C and A/T result in different amounts of H-bonds
How does salt concentration affect DNA denaturation?
increasing salt concentration increases melting point
Why does increasing salt concentration increase DNA melting point?
decreases electrostatic repulsion between strands by neutralizing negative phosphate backbone with cations
What does DNA melting point describe? Is it an actual melting point?
temperature describing midpoint of DNA denaturation; No
How does pH impact DNA denaturation?
disrupts the H-bonds between bases that hold strands together reducing the # of H-bonds to over come
How does pH impact number of H-bonds present in a DNA molecule?
1) pH < 2.3; nitrogenous bases become extensively protonated
2) pH > 10; nitrogenous bases become extensively deprotonated
How do the speeds of denaturation and renaturing/reannealing differ?
Denaturation is must faster than reannealing
Why is annealing slow? What makes it faster?
Slowly because correct bases must be repaired; once first base pair is made it is must easier anneal the others
What are two examples of higher order DNA structures?
1) Supercoiled DNA
2) Chromosomes
When does supercoiling occur?
overwinding or underwinding creates tension that condenses DNA in circular DNA molecules or linear DNA molecules with fixed ends
What kind of AAs make up histones? Why?
Lys and Arginine; positively charged so they interact favorably with DNA’s negatively charged phosphate backbone
