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BCH Final > DNA structure > Flashcards

DNA structure Flashcards

1
Q

what is the central dogma

A

dna (transcription) rna (translation) protein

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2
Q

what are the differences between the DNA and RNA primary structure

A

the DNA structure has deoxyribose & uses T as a base

the RNA has ribose (so every C accompanied by O unlike DNA) & uses U as a base

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3
Q

what is indicative of the 5’ end vs 3’

A

5’ has unreacted phosphate

3’ has unreacted hydroxyl

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4
Q

what are the 2 characteristics of primary structures

A
  1. each strand has direction & enzymes recognize that direction
  2. the sequences of bases determine the info
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5
Q

what are the complementary base pairs in DNA and how would it be different in RNA

A

DNA: A=T G=C
RNA: A=U G=C

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6
Q

what forms can adenine and cytosine exist in

A

amino or imino forms

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7
Q

what forms can thymine and guanine exist in

A

keto or enol forms

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8
Q

bases primarily exist in what forms

A

amino and keto

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9
Q

what are the purines and what are the pyrimidines

A

purine: adenine, Hypoxanthine, Guanine, Xanthine
pyrimidine: cytosine, uracil, thymine

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10
Q

what does the major groove allow

A

it allows proteins to gain access to the bases

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11
Q

during transcription which form (B, A, or Z) predominates

A

A form bc of DNA/RNA associations

-A form is also the structure for double stranded RNA and RNA-DNA hybrids

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12
Q

Why is there no B form RNA

A

because there’s an extra hydroxyl group on RNA

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13
Q

which form of DNA is left handed (B, A, or Z)

A

Z form

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14
Q

which form of DNA has a zigzag path due to alternating purine and pyrimidine sequences

A

Z form

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15
Q

which form of DNA has major and minor grooves

A

B form

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16
Q

which form of DNA has the bases tilted WITH respect to the helical axis

A

A form

-while B form is perpendicular to helical axis

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17
Q

a GC repeating sequence is characteristic of what form of DNA

A

Z form

-GC makes it very stable

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18
Q

which form is wet and which is low humidity

A 
B = wet
A = low humidity
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19
Q

what is the least stable form of DNA and why

A

P form bc it puts the negatives in the middle so they repel a lot

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20
Q

which base pair is more stable A=T or G=C? why?

A

G=C bc it has more hydrogen bonds

and adjacent GC pairs have stronger van der waals intxn than AT

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21
Q

what are the three stabilizing factors of secondary dna

A

hydrogen bonds
van der waals interactions
ions in cells (K, Na, Mg)

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22
Q

which has the largest melting poitn, A=T or G=C?

A

G=C

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23
Q

what is the destabilizing factor of secondary dna

A

electrostatic repulsion aka if there was a negative charge on a phosphate group at pH=7 bc the negative charges would repel

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24
Q

which absorbs more light? single stranded or double stranded

A

single stranded bc the bases absorb UV light and SS bases are more exposed

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25
Q

hybridization is when

A

complementary nucleic acids are combined

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26
Q

the more percent of GC you have then the higher the…

A

melting point at which it can be denatured is

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27
Q

nucleotides and nucleic acids absorb light at how many nm

A

260

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28
Q

what is the problem with the HIV virus in relation to the central dogma

A

it causes reverse transcriptase so from RNA –> DNA

-the reverse has poor proof reading abilities

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29
Q

what inhibitor is used to treat HIV and how does it do so

A

NRTIs (nucleoside reverse transcriptase inhibitors)

they block HIV RNA from being reverse transcribed into DNA

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30
Q

what molc is an example of an NRTI and what structures is it made of

A

AZT

-Nucleoside and Thymine

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31
Q

how does the AZT work to block HIV (hint has to do w it’s structure)

A

the thymidine is incorporated into the growing DNA strand

the lack of an unreacted hydroxyl group in its 3’ position prevents addition of the next nucleotide

32
Q

how does acyclovir help treat HIV

A

acyclovir converted into dGTP (a nucleoside analog)

it inhibits viral DNA polymerase by acting as an analog to dGTP

dGTP–> DNA results in chain termination bc of the absence of a 3’ hydroxyl group to attach more nucleosides

33
Q

what type of drug is ciprofloxacin

A

topoisomerase inhibitor

34
Q

denaturing is also called…

A

melting bc heat is usually used to separate the double stranded DNA into single stranded

35
Q

hyperchromicity

A

increased absorption as the strands of the double helix separate

36
Q

the Tm or melting point is the temperature where

A

half the DNA has denatured

37
Q

T/F

once dna is denatured it can never return to it’s last state

A

false

dna can renature or reanneal under specific conditions

38
Q

enxymes that break one or both strands of DNA

A

topoisomerase

39
Q

increasing or decreasing the number of helical turns in the DNA causes it to be

A

strained

40
Q

to reduce the strain, the DNA

A

forms supercoils

41
Q

why is DNA negatively supercoiled in nature

A

causes opennes to the structure while is needed for it to be utilized

if it were positively supercoiled, the dna would be less accessible for info retrieval

42
Q

T/F

type 1 topoisomerase found in prokaryotes while type 2 is found in eukaryotes

A

false

both types are present in both pro and eu

43
Q

type 1 topoisomerase acts on DNA that is strained. so when it cuts the DNA..

A

the strain in the supercoiled DNA forces it towards a more relaxed state

44
Q

if the DNA is negatively supercoiled when cutting w a type 1 topoisomerase

A

it removes one negative supercoil –> more relaxed state

45
Q

if the dna is positively supercoiled when cutting with a type one topoisomerase will

A

remove one positive supercoil

46
Q

T/F

no ATP is involved in the topoisomerase type 1 process

A

true

47
Q

describe the steps of topoisomerase type 1A

A

cuts one strand of the double helix
enzyme bridges the break by covalent attachment to one end and noncovalent binding to the other
the unbroken strand is passed through the break
then rejoined

48
Q

describe the steps of topoisomerase type 1B

A

binds to the dna
cuts one strand
stays covalently attached to one cut strand
other end of cut strand free to rotate about the intact strand
cut ends then rejoin

49
Q

type 2 topoisomerases introduce negative supercoils into newly synthesized dna in… (pro or eu)

A

prokaryotes

50
Q

in eukaryotes

which topoisomerases relax negatively supercoiled DNA and which relax positively supercoiled

A

Type 1A relaxes negative

type 1B and type 2 relax positive or negative

51
Q

how do eukaryotes relax their supercoils

A

by dna wrapping around histones in the formation of nucleosomes

52
Q

how do topoisomerase inhibitors (used on rapidly dividing cells like cancer and bacterial cells) work

A

they introduce breaks into the DNA by inhibiting the rejoining step
this blocks DNA replication

53
Q

compacted form of the tertiary structure of the bacterial chromosone that is associated with a RNA-protein scaffold is known as

A

nucleoid

54
Q

T/F

all prokaryotic dna is linear

A

falso

all eukaryotic

55
Q

tight wrapping of DNA around the nucleosome pore causes

A

the removal of 1 helical –> creates negative supercoil

56
Q

what is linker dna

A

area bn nucleosomes thats not packed as tightly

57
Q

H1 histone is positively charged at both ends and does what

A

binds to linker regions to keep nucleosomes tightly associated

*H5 replaces H1 in some vertebrae

58
Q

what does nucleosome packing do to DNA

A

shortens the DNA length by 6-7 fold

59
Q

what does the solenoid folding do to DNA

A

shortens it by 35-40 fold

60
Q

which is the most dispersed form of chromatin the cell

A

euchromatin

61
Q

which chromatin is more condensed

A

heterochromatin

62
Q

ehich chromatin results in higher order folding of the solenoid structure

A

heterochromatin

63
Q

what is the most compact chromatin structure and how much does it shorten by

A

mitotic chromosomes - shorten by 10,000 fold

64
Q

loops of solenoid may be held together by what

A

H1 which bind to linker DNA in two adjacent loops of the solenoid

65
Q

what are the three advantages to nucleosome folding

A
  1. pack large amounts of DNA into small nucleus
  2. negative supercoiling opens DNA for utilization
  3. chromatin structure brings sequences closer together so regulatory proteins can bind to sequences that aren’t next to each other
66
Q

In prokaryotes

DNA/protein sequences are

A

colinear

67
Q

the size of the genome corresponds to the number of genes in pro or eu

A

PROKARYOTES

68
Q

dna is not unique in pro or eu

A

eukaryotes

69
Q

in eukaryotes, what does 10% of the genome code for

A

proteins

70
Q

tandem repears are usually short and rich in

A

AT

71
Q

in highly repetitive eukaryotes, each repeat is present how many times

A

> 300,000

72
Q

tandem repeats make up how much of genome

A

10% or less

73
Q

what is the difference (using values) between unique, moderately repetitive, and highly repetitive sequences

A

1= unique
2-300,000= moderately repetitive
>300,000=highly repetitive

74
Q

what are transposons & which type of sequence is derived from them

A

segments of DNA that can move from one location to another

moderately repetitive sequences are derived from transposons

75
Q

in a prokaryote, what is the relationship bn the DNA and the mRNA

A

sequence identical besides U in RNA and T in DNA

76
Q

which frequency of sequences is interspersed with single copy DNA (LINES and SINES)

A

moderately repetitive sequences

BCH Final (5 decks)

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