DNA Flashcards
Composition of nucleotides
- Cyclic nitrogenous bases
- Pentose sugars
- Phosphate groups
Structural difference between Uracil and Thymine
CH3 on C3 of Thymine
Structural differences between Thymine and Cytosine
- Cytosine has NH2 instead of O on C4
- 2 double bonds 1 between C4 and C5 in Cytosine
- C5 has N instead of HN on cytosine
Structural differences between Adenine and Guanine
- Adenine has double bond between C7 and C8
- Adenine has NH2 instead of O on C7
- Guanine has NH2 instead of H on C = CN across from O/ NH2 group
Structural differences between ribose and deoxy ribose sugar
Ribose - OH OH
Deoxyribose - OH H
Bases are connected to sugars by
Beta - N glycosidic bonds
How are successive deoxyribose resides joined?
By phosphate group between 3’ of one sugar and 5’ of next -> one end (left) free 5’ end and the other is 3’ end
B-form DNA characteristics
- Wide + deep major groove, narrow + less deep minor groove
- bp/ turn : 10.4
- av. rise/ bp : 0.34 nm
- helical diameter: 2.4nm
- pitch: 3.5 nm
Nucleases cleave ______ which contribute to _____ with products X and Y
Phosphodiester bond , 5’ and 3’C polarity
X = 5’phosphate + 3’hydroxyl group
Y = 3’ Phosphate + 5’ hydroxyl group
Types of nucleases:
- DNAses + RNAses
- Endo + exonucleases
- Specific for ds DNA/ ssDNA
- Restriction endonucleases cleave both strands of dsDNA at specific sequences
type 2 : palindromic
Ligase
catalyse formation of ppd between 5’ and 3’ end
Chargraff principle
purine : pyrimidine 1:1
Packing ratio
Length B-form DNA / actual length
Nucleosome characteristics
30nm fiber : DNA xomplexed with histones
-> 8 histones each wrapped by DNA 1.65 times
Histone
Basic repeating unit of 11nm chromatic fibre
Chromatosome
Nucleosome + H1
Chromatid is produced by
Tight coiling of 250 nm fiber
Core Histones are :
H2A, H2B, H3 and H4
Which is the linker histone and how does it differ to the core histones?
H1 , Much higher Mr and higher Lys/arg percentage
A histone octamer consists of
2 H2A-H2B dimers and a H3-H4 tetramer
In a histone octamer DNA wraps around how many times?
Twice
Functions of H1
Fastens DNA to nucleosome core
Length and configuration of DNA in metaphase chromosome
1400 nm with condensed scaffold - associated chromatin at 700 nm
Length and configuration of DNA in interphase chromosome
Extended scaffold associated chromosome - 300 nm whole beads on a string form chromatin -> DNA double helix -> condensed
How does the packing ratio differ between interphase and mitotic chromosome?
1K to 10K
Histone tails are generally…
Methylated and acetylated
Stacking is when
Induced dipole interactions between bases
-> electrostatic repulsion of anionic phosphate bonds are counteracted by cations
What does hydrophobic effect cause in conformation of DNA?
Purine and pyrimidine rings are burried in interior which increases stability
Microarray overview
cDNA of known identified sequenced genes printed on glass -> spot with DNA fragments of interest -> appearance of single genes of interest
FISH overview
- Cells in metaphase treated to swell
- Fixed onto slide
- Treated so Chr DNA SS + proes hybridise with comp. sequence
- Excess probes washed
- Fluorescent microscope
