DNA structure Flashcards by Erica Camacho

what is the central dogma

dna (transcription) rna (translation) protein

How well did you know this?

Not at all

Perfectly

what are the differences between the DNA and RNA primary structure

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

How well did you know this?

Not at all

Perfectly

what is indicative of the 5’ end vs 3’

5’ has unreacted phosphate

3’ has unreacted hydroxyl

How well did you know this?

Not at all

Perfectly

what are the 2 characteristics of primary structures

each strand has direction & enzymes recognize that direction
the sequences of bases determine the info

How well did you know this?

Not at all

Perfectly

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

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

How well did you know this?

Not at all

Perfectly

what forms can adenine and cytosine exist in

amino or imino forms

How well did you know this?

Not at all

Perfectly

what forms can thymine and guanine exist in

keto or enol forms

How well did you know this?

Not at all

Perfectly

bases primarily exist in what forms

amino and keto

How well did you know this?

Not at all

Perfectly

what are the purines and what are the pyrimidines

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

How well did you know this?

Not at all

Perfectly

what does the major groove allow

it allows proteins to gain access to the bases

How well did you know this?

Not at all

Perfectly

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

A form bc of DNA/RNA associations

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

How well did you know this?

Not at all

Perfectly

Why is there no B form RNA

because there’s an extra hydroxyl group on RNA

How well did you know this?

Not at all

Perfectly

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

Z form

How well did you know this?

Not at all

Perfectly

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

Z form

How well did you know this?

Not at all

Perfectly

which form of DNA has major and minor grooves

B form

How well did you know this?

Not at all

Perfectly

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

A form

-while B form is perpendicular to helical axis

How well did you know this?

Not at all

Perfectly

a GC repeating sequence is characteristic of what form of DNA

Z form

-GC makes it very stable

How well did you know this?

Not at all

Perfectly

which form is wet and which is low humidity

B = wet
A = low humidity

How well did you know this?

Not at all

Perfectly

what is the least stable form of DNA and why

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

How well did you know this?

Not at all

Perfectly

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

G=C bc it has more hydrogen bonds

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

How well did you know this?

Not at all

Perfectly

what are the three stabilizing factors of secondary dna

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

How well did you know this?

Not at all

Perfectly

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

G=C

How well did you know this?

Not at all

Perfectly

what is the destabilizing factor of secondary dna

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

How well did you know this?

Not at all

Perfectly

which absorbs more light? single stranded or double stranded

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

How well did you know this?

Not at all

Perfectly

hybridization is when

complementary nucleic acids are combined

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

melting point at which it can be denatured is

nucleotides and nucleic acids absorb light at how many nm

260

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

it causes reverse transcriptase so from RNA --> DNA | -the reverse has poor proof reading abilities

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

NRTIs (nucleoside reverse transcriptase inhibitors) they block HIV RNA from being reverse transcribed into DNA

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

AZT | -Nucleoside and Thymine

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

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

how does acyclovir help treat HIV

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

what type of drug is ciprofloxacin

topoisomerase inhibitor

denaturing is also called...

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

hyperchromicity

increased absorption as the strands of the double helix separate

the Tm or melting point is the temperature where

half the DNA has denatured

T/F | once dna is denatured it can never return to it's last state

false | dna can renature or reanneal under specific conditions

enxymes that break one or both strands of DNA

topoisomerase

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

strained

to reduce the strain, the DNA

forms supercoils

why is DNA negatively supercoiled in nature

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

T/F | type 1 topoisomerase found in prokaryotes while type 2 is found in eukaryotes

false | both types are present in both pro and eu

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

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

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

it removes one negative supercoil --> more relaxed state

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

remove one positive supercoil

T/F | no ATP is involved in the topoisomerase type 1 process

true

describe the steps of topoisomerase type 1A

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

describe the steps of topoisomerase type 1B

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

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

prokaryotes

in eukaryotes | which topoisomerases relax negatively supercoiled DNA and which relax positively supercoiled

Type 1A relaxes negative | type 1B and type 2 relax positive or negative

how do eukaryotes relax their supercoils

by dna wrapping around histones in the formation of nucleosomes

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

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

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

nucleoid

T/F | all prokaryotic dna is linear

falso | all eukaryotic

tight wrapping of DNA around the nucleosome pore causes

the removal of 1 helical --> creates negative supercoil

what is linker dna

area bn nucleosomes thats not packed as tightly

H1 histone is positively charged at both ends and does what

binds to linker regions to keep nucleosomes tightly associated *H5 replaces H1 in some vertebrae

what does nucleosome packing do to DNA

shortens the DNA length by 6-7 fold

what does the solenoid folding do to DNA

shortens it by 35-40 fold

which is the most dispersed form of chromatin the cell

euchromatin

which chromatin is more condensed

heterochromatin

ehich chromatin results in higher order folding of the solenoid structure

heterochromatin

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

mitotic chromosomes - shorten by 10,000 fold

loops of solenoid may be held together by what

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

what are the three advantages to nucleosome folding

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

In prokaryotes | DNA/protein sequences are

colinear

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

PROKARYOTES

dna is not unique in pro or eu

eukaryotes

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

proteins

tandem repears are usually short and rich in

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

>300,000

tandem repeats make up how much of genome

10% or less

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

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

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

segments of DNA that can move from one location to another moderately repetitive sequences are derived from transposons

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

sequence identical besides U in RNA and T in DNA

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

moderately repetitive sequences