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MoMF > DNA Structure And Function > Flashcards

DNA Structure And Function Flashcards

1
Q

Central Dogma

A

DNA –> RNA –> Protein

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2
Q

Ribose

A

RNA sugar- has an OH on the C2

C4 is the carbon attached to the phosphate group
(C1 has base attached to it)

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3
Q

Deoxyribose

A

DNA sugar

Only an H on the C2 carbon

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4
Q

What form of the bases are most common?

A

Amino-keto form

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5
Q

Pauling and Corey Model (P Form)

A

Proposed the thin model because that way the base pairs are readily accessible –> not possible though because the DNA backbone is negative and this would be unstable (bases too close to one another)

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6
Q

Width of DNA

A

2 nm

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7
Q

Length of one turn of DNA

A

0.34 nm

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8
Q

Major groove

A

Transcription acts thru this groove

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9
Q

B-Form of DNA

A

-in wet conditions (found in vivo)
^but not necessarily b/c proteins associated with DNA can induce local hydrophobic environments

  • helices are right handed
  • dimensions: 10.4 bp/turn
  • diameter: 2nm
  • 0.34 nm helical rise
  • base pairs formed across the double helix are flat, perpendicular to the helix axis and are internal to the sugar phosphate backbone
  • A and C present in amino form
  • G and T present in keto form
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10
Q

A-form of DNA

A
  • found in low humidity environments
  • dehydrated form of DNA
  • bases are on the outside
  • slightly wider
  • grooves more equal in size
  • bases are tilted with respect to the helical axis
  • base pairs are closer to one another
  • helix is broad

-i.e.: double stranded RNA and RNA-DNA hybrid

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11
Q

Z Form of DNA

A

Doesn’t code for anything –> used as space

Separates actively

it is the transcribing parts of the DNA

GCGCGCGC –> guarantees Z-form with this sequence

Helices are left handed due to a change in the purine: deoxyribose conformation

Helix is narrow and bases further apart

Some solvents and the presence of a methyl group on the 5 position of C favor the formation of Z form

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12
Q

Why is the B form impossible for RNA?

A

The extra hydroxyl on the RNA makes the B form impossible

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13
Q

Helix Handedness for 3 forms

A

A- right
B-right
Z-left

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14
Q

Base pairs per turn for 3 forms DNA

A

A- 11
B- 10
Z- 12

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15
Q

When do forms of DNA with 3-4 strands appear?

A

Appear at sites important for initiation or regulation of DNA metabolism such as replication and transcription –> candidates for drug design

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16
Q

Stabilizing factors for DNA structure

A

Due to hydrophobic interactions between adjacent stacked base pairs

Hydrogen bonds between base pairs –> plays major role in complementarity

More G/C base pairing

Van Der Waals interactions

Ions in the cells: K, Na, Mg, etc

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17
Q

Destabilizing factors for DNA

A

Electrostatic repulsion

–>negative charge on phosphate group at pH 7

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18
Q

Hyperchromicity

A

Increase in the absorption of UV light as more bases are exposed from denaturation

19
Q

Difference between ssDNA and dsDNA in absorption?

A

ssDNA > dsDNA

20
Q

Denaturation curve for dsDNA

A

Sample of ds DNA at specific salt concentration heated

1) absorption constant until DNA starts to melt
2) denatures cooperatively over a narrow temperature range

21
Q

Tm

A

50% denaturation

Depends on % of AT and GC base pairs

I.e.: ^GC raises Tm because of increased stability

22
Q

PCR and FISH

A

DNA can reanneal under specific conditions

Hybridization can also be achieved

23
Q

Stopping HIV life cycle

A

1) Nucleoside reverse transcriptase inhibitors (i.e.: AZT) –> block HIV RNA being reverse transcribed into DNA
2) Non-nucleoside reverse transcriptase inhibitors (NNRTIs) –> block HIV RNA being reverse transcribed into DNA using different mechanism to NRTIs –> some also target other processes
3) Protease inhibitors- the proteins needed to create new HIV virus are cut into specific pieces
4) Entry inhibitors- Prevent HIV from entering the cell
5) HIV integrase inhibitors- prevent HIV from inserting its genetic code into the human cell’s genome

24
Q

Type I topoisomerase

A

Act on DNA that is strained by coiling

They catalyze single strand breaks and change the supercoiling by one turn of the double helix

Helps DNA reach a more relaxed state

It DNA (-) supercoil: type 1 topo will remove one negative supercoil 
If DNA (+) supercoil: type 1 topo will remove one positive supercoil

No ATP used

25
Q

Type IB Topoisomerase

A
  • binds to DNA and cut one strand
  • only act on strained DNA b/c trying to release energy
  • remains covalently attached to one end of the cut strand
  • other end of the cut strand is then free to rotate about the intact strand
  • the cut ends are then relighted and the enzyme dissociates from the DNA
  • works to get rid of strain*
26
Q

Type IB on (-) and (+) supercoiling

A

(-) = remove one negative supercoil to make less loops and more relaxed

(+) = will remove one positive supercoil

27
Q

Type II topoisomerase

A
  • requires ATP
  • works with relaxed DNA to get to its natural negative super coil (but can also introduce positive super coils)
  • cuts both strands
28
Q

What’s the difference between eukaroytic and prokaroytic Type II topoisomerase?

A

Eukaroytic type II does not introduce negative super coils into newly synthesized DNA –> this is accomplished by wrapping the DNA around histones

Just relax negatively supercoiled DNA (or positively)

29
Q

Topoisomerase inhibitors

A

Used to introduce breaks into the DNA and then inhibit the religation step –>

Blocks processes such as DNA replication –>

Cell can possibly die

30
Q

Nucleoid

A

Compacted form of bacterial DNA

31
Q

Chromatin

A

DNA + histones

Histones introduce super coiling in eukaryotic DNA (negative super coiling)

32
Q

Nucleosome Structure

A

Two tetramer core histones associate to form histone octamer

Histones associate by electrostatic interactions with the positive charges from the basic amino acids on the outside of the octamer that interact with (-) backbone of DNA

Tight wrapping of DNA around nucleosome requires the removal of approximately 1 helical turn

33
Q

What is the result of nucleosome packing?

A

6-7 fold shortening of the DNA length

34
Q

Linker DNA

A

Region between adjacent nucleosome a that is not packed as tightly

H1 is positively charged at both ends (carboxyl and amino) and binds to linker regions to keep nucleosome a tightly associated

35
Q

Solenoid

A
  • results in 35-40 fold shortening of the DNA
  • supercoil of 6 nucleosomes per turn forming a 30 nm fiber

I.e.: euchromatin, heterochromatin, and mitotic chromosomes

-loops helps together by H1

36
Q

Packing Hierarchy

A

Double helix –> nucleosome –> solenoid –> loops –> condensed section of mitotic chromosome –> mitotic chromosome

37
Q

Prokaryote- nucleotide sequence organization

A

1) DNA/protein sequences are co-linear with a DNA sequence corresponding directly to a protein sequence
2) Gene sequences are mostly single copy (except rRNA)
3) size of genome reflects gene number
4) regulatory and integrative sequences may be repetitive

38
Q

Eukaryotes- nucleotide sequence organization

A
  • size of genome does not correspond to number of genes
  • most eukaryotic DNA is non functional or not unique
  • about 10% genome codes for protein
  • single copy genes are often transcribed in a tissue specific or developmentally specific fashion
39
Q

Gene Families

A

Genes that are duplicated genes that have diverged in sequence but encode proteins with related function

I.e.: globins, tubulins, actions

Make up 40-60% genome (coding and noncoding)

All are unique sequences

40
Q

Basic transcription

A
  • mRNA identical sequence to non-template strand

* colinear sequences: protein –> RNA –> DNA *

41
Q

Highly Repetitive sequences

A

300,000 copy

42
Q

Pseudogenes

A

Certain non-functional unique sequences that arise by gene duplication

Loose activity over time

43
Q

Moderately Repetitive Sequences

A

25-45% of genome

Usually transcribed but not translated (except those that code for functional genes)

Derived from transposons

Some are functional genes that code for certain proteins in high demand, others unclear

2-300,000 copies/genome

I.e.: histones, rRNA, tRNA, SINES, and LINES

44
Q

Single Copy Sequences

A

40-60% of genome

All are unique sequences

Exons, Introns, genes clustered and dispersed

Some translated and transcribed others not

Functional genes, pseudo genes

Most proteins are these!!

MoMF (25 decks)

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