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Flashcards in DNA Structure And Function Deck (44):
1

Central Dogma

DNA --> RNA --> Protein

2

Ribose

RNA sugar- has an OH on the C2

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

3

Deoxyribose

DNA sugar
Only an H on the C2 carbon

4

What form of the bases are most common?

Amino-keto form

5

Pauling and Corey Model (P Form)

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)

6

Width of DNA

2 nm

7

Length of one turn of DNA

0.34 nm

8

Major groove

Transcription acts thru this groove

9

B-Form of DNA

-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

10

A-form of DNA

-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

11

Z Form of DNA

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

12

Why is the B form impossible for RNA?

The extra hydroxyl on the RNA makes the B form impossible

13

Helix Handedness for 3 forms

A- right
B-right
Z-left

14

Base pairs per turn for 3 forms DNA

A- 11
B- 10
Z- 12

15

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

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

16

Stabilizing factors for DNA structure

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

17

Destabilizing factors for DNA

Electrostatic repulsion
-->negative charge on phosphate group at pH 7

18

Hyperchromicity

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

19

Difference between ssDNA and dsDNA in absorption?

ssDNA > dsDNA

20

Denaturation curve for dsDNA

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

Tm

50% denaturation

Depends on % of AT and GC base pairs

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

22

PCR and FISH

DNA can reanneal under specific conditions

Hybridization can also be achieved

23

Stopping HIV life cycle

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

Type I topoisomerase

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

Type IB Topoisomerase

-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

Type IB on (-) and (+) supercoiling

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

(+) = will remove one positive supercoil

27

Type II topoisomerase

-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

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

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

Topoisomerase inhibitors

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

Blocks processes such as DNA replication -->

Cell can possibly die

30

Nucleoid

Compacted form of bacterial DNA

31

Chromatin

DNA + histones

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

32

Nucleosome Structure

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

What is the result of nucleosome packing?

6-7 fold shortening of the DNA length

34

Linker DNA

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

Solenoid

-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

Packing Hierarchy

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

37

Prokaryote- nucleotide sequence organization

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

Eukaryotes- nucleotide sequence organization

-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

Gene Families

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

Basic transcription

- mRNA identical sequence to non-template strand

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

41

Highly Repetitive sequences

300,000 copy

42

Pseudogenes

Certain non-functional unique sequences that arise by gene duplication

Loose activity over time

43

Moderately Repetitive Sequences

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

Single Copy Sequences

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!!