FINAL - CH3 Flashcards
purines
Adenine Gaunine
pyrimidines
Cytosine Thymine Uracil
Nomenclature for nucleosides and nucleotides
2 different structures if DNA
Primary: SIngle strand of DNA
Secondary: 2 strands pair in an antiparallel fashion
1 turn in B DNA =
10.5 bp
36 Å
1 bp =
3.4 Å
Chargaffs rule
A-T
C-G
Base stacking
base pairs are stacked upon each other within van der Waals distance
DNA stability:
Base stacking: hydrophobic effect and van der Waals interactions
Different Helix forms
A-DNA- Short and wide, right handed
B-DNA- most stable DNA
Z-DNA- Long and narrow, Left handed
Hyperchromic shift
Occurs when DNA is denatured (2 strands to 1 strand), It allows the aromatic rings of the base pairs to interact with light increasing absorbance
Renature
“Annealing”
two DNA strands reform a helix.
C-G binds with _____ H bonds
A-T binds with _____ H bonds
3
2
Tm
Melting temperature
Affected by: GC content
DNA length
Ionic strength
How does ionic strength afftect Tm
If you add NaCl to DNA the Na+ ions will interact with the negatively charged DNA backbone, therefore stabilizing the sturcture. This stabillity will require more heat to cause denaturing, so Tm goes up
Supercoiling is found in _______and________
prokaryotes
eukaryotes
Nucleosome
Circular DNA wrapped around histone proteins
(not sequence specific)
Right handed supercoils
Negative
Left handed supercoils
Positive
DNA has _____ supercoils
Negative
Topoisomerase
Breaks and removes positive supercoil, assists in DNA wrapping around histone
Histone protein
Made up of 2 each:H2A, H2B, H3 and H4
and 1 H1
Histone binding with DNA:
Positively charged surface of the protein binds to the negatively charged backbone of the DNA
Autocleavage
Can occur in RNA which is more reactive because of extra O
Does NOT occur in DNA
Spontaneous deamination
Cytosine –> Uracil
Ribozymes
RNA molecules with catalytic activity
Heterochromatin vs Euchromatin
Euchromatin - coding DNA
Heterochromatim - Non-coding DNA
How chromosomes condense:
DNA, Nucleosomes, Chromatin, looped chromatin, Coiled chromatin, chromosome
Telomere
G rich DNA forms loop structures that protect ends
________and ________ promote genetic diversity
Exon shuffling
alternative splicing
The field used in biochemistry to discover the function of an unknown gene, such as a human disease gene, that can be targeted with pharmaceutical drugs
Bioinformatics
Hutchinson-Gilford progeria
LMNA mutation
C –> T substitution
STR
Short tandem repeats
Deletions and insertions in the genome
VNTR
Variable number tandem repeats
Repeats of a core sequence
Can be used in forensic applications
Plasmids are found in _________ organisms
both prokaryotic and eukaryotic
3 modes of transfering genentic information in plasmids
Conjugation
Transformation: when a cell dies it realeases its contents to be taken up by other cells
Transduction: Visures infect bacteria through this process
Enzymes that protect bacteria
DNA methylases: methylates DNA in bacteria
Restriction nuclease: Cleaves non-mehtylated DNA, so attakcs viral DNA
Restriction endonucleases
Type I and III:
Require ATP
Type II:
Cleave DNA at specific recognition sequences
Useful in gene cloning
Lac Z gene
Codes for ß-galactosidase
Helps break down lactose
X-gal is a substrate for ß-galactosidase (blue color)
Blue colonies will have functional enzyme
White colonies will not (mutants)
Type II REs:
Blunt end
5’ over hang
3’ over hang
PCR three temperature phases:
Phase I – DNA denaturation
Phase II – Annealing
Phase III – Primer extension and DNA synthesis
DNA polymerase
DNA replication
DNA plyerization ocurs in a _______ direction
5’ –> 3’
ATP bonds
Phosphoanhydride
How does ATP transfer energy
It is an energy carrier that has high energy phosphoanhydride bonds
