Biochem Exam 5--Chap 2

Front 1

DNA---?--->RNA

RNA---?--->protein

Back 1

transcription

translation

Front 2

What are the purine bases?

a) adenine
b) guanine
c) cytosine
d) thymine
e) uracil

Back 2

a) adenine
b) guanine

Front 3

What are the pyrimidine bases?

a) adenine
b) guanine
c) cytosine
d) thymine
e) uracil

Back 3

c) cytosine
d) thymine
e) uracil

Front 4

ribonucleosides = ? + ?

Back 4

ribose + base

Front 5

What's the difference btwn a ribose molecule and a 2-deoxyribose molecule?

Back 5

ribose has an -OH on 2' carbon

2-deoxyribose just has a -H

Front 6

deoxyribonucleosides = ? + ?

Back 6

2-deoxyribose + base

Front 7

Name some ribonucleosides.

Back 7

adenosine
guanosine
cytidine
uridine

Front 8

Name some deoxyribonucleosides.

Back 8

deoxyadenosine
deoxyguanosine
deoxycytidine
deoxythymidine

Front 9

nucleotide = ? + ? + ?

Back 9

phosphate + pentose + base

Front 10

Name some nucleotides.

Back 10

deoxycytidine 5'-monophosphate (dCMP)

guanosine 5'-triphosphate (GTP)

adenosine 3',5'-cyclic monophosphate (cAMP)

Front 11

What are polymers of nucleotides called?

which direction does it go?

Back 11

polynucleotides

5' ----> 3'

Front 12

In an RNA polynucleotide, at what carbon is there an extra -OH attached?

Back 12

2' carbon

Front 13

In both DNA & RNA polynucleotides, where do phosphates connect?

Back 13

3'C on one down to the 5' on the next

Front 14

Describe the Watson-Crick model of DNA.

Back 14

2 antiparallel and complimentary strands are paired in right-handed double helix

Front 15

What's the difference between C-G and A-T bonding?

Back 15

C-G forms 3 H-bonds
A-T forms 2 H-bonds

more energy req'd to seperate C-G

Front 16

What are the 2 forces that help DNA stay together?

Back 16

1) stacking of bases (helps stabilize molecule)
2) H-bonds

Front 17

How bp's are there per turn of a DNA twist?

Back 17

10bp/turn

Front 18

Describe the core of the stacked bases.

Back 18

hydrophobic force + van der Waals = 4-15kcal/mol

hydrogen bonds=2-3 kcal/mol ("glue," "zipper")

directional, accumulative

The destabilizing effect of a reagent is determined by the solubility of the free bases in the reagent.

Front 19

The destabilizing effect of a reagent is determined by what?

Back 19

the solubility of the free bases in the reagent

Front 20

Describe the exterior of the charged sugar-phosphate groups.

Back 20

hydrophilic!
highly solvated by water

high concentration of cations, especially some divalent ions such as Mg2+, stabilize the helical conformation of polynucleotides by shielding the charges of the phosphodiester groups in the backbone

Front 21

When looking at the hydrophilic exterior of the double helix DNA, high concentration of ___a____, especially some ____b____ ions such as Mg2+, stabilize the helical conformation of polynucleotides by shielding the charges of the _____C______ groups in the backbone

Back 21

a) cations

b) divalent

c) phosphodiester

Front 22

When describing denaturation, the double helix is disrupted during almost every important biological process in which DNA participates, including what?

Back 22

DNA replication
transcription
repair
recombination

Front 23

Denaturation is accompanied by several physical changes, including what?

Back 23

-buoyant density increase
-reduction in viscosity
-change in ability to rotate polarized light
-changes in absorbance of UV light

Front 24

__________ increase can split DNA.

Back 24

temperature

Front 25

DNA can be denatured at pH values >__a__ as the N-H groups on the bases become ____b_____, preventing them from participating in H-bonding.

Back 25

a) 11.3

b) deprotonated

Front 26

What prevents N-H groups on bases from participating in H-bonding when pH values >11.3 during denaturation?

Back 26

deprotonation of the N-H groups on the bases

Front 27

_________ denaturation is often used in preference to heat denaturation to prevent breakage of phosphoester bonds that can occur at a high temperature or low pH.

Back 27

alkaline

Front 28

Because of the strong absorbance of the purine and pyrimidine bases, DNA absorbs strongly in the UV region with a maximum near ____nm.

Back 28

260nm

Front 29

The absorbance of individual bases is reduced by ________ interactions that arise from base stacking.

Back 29

electronic

Front 30

The total absorbance of the stacked bases may be reduced by as much as ___% compared to an unstacked state.

Back 30

40%

Front 31

As the ordered structure of the double helix is disrupted as temperature increases, stacking interactions _______ gradually.

Back 31

decrease

Front 32

When looking at a curve of UV absorbance vs temp, complete strand seperation occurs at a critical temperature corresponding to what part of the curve?

Back 32

upper plateau of the curve

Front 33

More C-G base pairs req's more energy to denature, so the curve shifts to the ____.

A-T base pairs req less energy, so curve shifts to the ____.

Back 33

right

left

Front 34

What is the "midpoint temperature"?

Back 34

the temp at which 1/2 of the max optical density is reached
Tm

Front 35

Tm (midpoint temp) is characteristic of what?

Back 35

of the base content of DNA under standard conditions of concentration and ionic strength.

Front 36

The higher the C-G content, the ______ the transition temp btwn double-stranded helix and single strands, and Tm.

Back 36

higher

Front 37

T/F? During renaturation (reannealing), formation of the 1st base pair is really fast?

Back 37

false (its very slow)

Front 38

Annealing of neighboring pairs is ___________, especially after what?

Back 38

facilitated

after formation of a 3--5 bp "nucleation site"

note: denaturation follows a similar course, but order of steps is reversed

Front 39

T/F?
In renaturation, after the slow 1st bp formation, there's formation of nucleation site, and then the helix propagation is fast.

Back 39

true

Front 40

What has provided the bases for development of hybridization?

Back 40

self-association of complementary polynucleotide strands

Front 41

A number of tachniques have been developed for detecting and quantitating DNA & RNA, including...

Back 41

Southern blot (DNA-DNA)
Northern blot (detect RNA by DNA probe)
Western blot (uses antibx to detect probe)

(micro-array analysis is more efficient)

Front 42

When dealing with hydridization, _____________ _____ have shown great promise for applications.

Back 42

oligonucleotide arrays

Front 43

Oligonucleotide arrays consist of what?

Back 43

of a number of gene-specific oligonucleotide probes immobilized at specific sites on a solid matrix (chip).

Front 44

Oligonucleotides contain thousands of what?

Back 44

thousands of unique probe molecules, each fixed within an "address"

Front 45

Gene chips can be treated with what?

Back 45

labeled target nucleic acids (DNA or RNA) derived from cells of an organism

Front 46

What kind of DNA conformation can be found under conditions of low humidity and high salt concentatration, is shorter and thicker, and have about 11 bps/turn?

Back 46

A-DNA

Front 47

What kind of DNA conformation has a left-handed helix with a zigzagging backbone?

What else can you say about this type of DNA?

Back 47

Z-DNA

The conformation of Z-DNA may be viewed as the result of the major groove of B-DNA having "popped out" in order to form the outer surface of Z-DNA (not stable...not common!)

Front 48

What kind of DNA conformation appeared under conditions of high humidity and low salt concentration and was the basis of the Watson-Crick structure?

Back 48

B-DNA

note: DNA in living organisms is generally B-DNA-like

Front 49

T/F? DNA forms unusual structures such as cruciforms ot triple-stranded arrangements and bends as it interacts with certain proteins.

Back 49

true

Front 50

What do you call a sequence that goes like this:
5' --------> 3'
3' <--------5'

Back 50

inverted repeat

Front 51

What do you call a sequence that goes like this:
5'-------> <--------3'
3' 5'

Back 51

mirror repeat

Front 52

What do you call a sequence that goes like this:
5' --------> --------> 3'
3' 5'

Back 52

direct repeat

Front 53

Cruciform structures have ________ repeats.

Back 53

inverted

Front 54

What kind of helix is not very stable and is very salt-dependent to hold its structure?

Back 54

Hoogsteen triple helix

TAT base triplet
CGC base triplet

Front 55

A reversed Hoogsteen triple helix includes what?

Back 55

GCG
AAT
TAT

Front 56

What's H-DNA?

Back 56

intermolecular triple helices
(w/in 1 DNA molecule)