DNA Structure And Function Flashcards
Central Dogma
DNA –> RNA –> Protein
Ribose
RNA sugar- has an OH on the C2
C4 is the carbon attached to the phosphate group
(C1 has base attached to it)
Deoxyribose
DNA sugar
Only an H on the C2 carbon
What form of the bases are most common?
Amino-keto form
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)
Width of DNA
2 nm
Length of one turn of DNA
0.34 nm
Major groove
Transcription acts thru this groove
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
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
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
Why is the B form impossible for RNA?
The extra hydroxyl on the RNA makes the B form impossible
Helix Handedness for 3 forms
A- right
B-right
Z-left
Base pairs per turn for 3 forms DNA
A- 11
B- 10
Z- 12
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
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
Destabilizing factors for DNA
Electrostatic repulsion
–>negative charge on phosphate group at pH 7
Hyperchromicity
Increase in the absorption of UV light as more bases are exposed from denaturation
Difference between ssDNA and dsDNA in absorption?
ssDNA > dsDNA
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
Tm
50% denaturation
Depends on % of AT and GC base pairs
I.e.: ^GC raises Tm because of increased stability
PCR and FISH
DNA can reanneal under specific conditions
Hybridization can also be achieved
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
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
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*
Type IB on (-) and (+) supercoiling
(-) = remove one negative supercoil to make less loops and more relaxed
(+) = will remove one positive supercoil
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
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)
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
Nucleoid
Compacted form of bacterial DNA
Chromatin
DNA + histones
Histones introduce super coiling in eukaryotic DNA (negative super coiling)
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
What is the result of nucleosome packing?
6-7 fold shortening of the DNA length
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
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
Packing Hierarchy
Double helix –> nucleosome –> solenoid –> loops –> condensed section of mitotic chromosome –> mitotic chromosome
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
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
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
Basic transcription
- mRNA identical sequence to non-template strand
* colinear sequences: protein –> RNA –> DNA *
Highly Repetitive sequences
300,000 copy
Pseudogenes
Certain non-functional unique sequences that arise by gene duplication
Loose activity over time
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
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!!
