DNA Structure Flashcards
Chargaff’s First Rule
A-T, G-C
Chargaff’s Second Rule
Composition of DNA varies from one species to another but not within an organism
What’s on the 5’ end?
Phosphate group
What’s on the 3’ end?
Hydroxyl group
B-DNA
Hydrophillic backbone of each strand is on the outside. Ten base pairs per turn.
Z-DNA
Rare left-handed double helix occuring in G-C rich regions.
A-DNA
produced by dehydration of B form. 11 base pairs per turn. Conformation found with DNA-RNA hybrids or RNA-RNA double stranded regions.
Disruption of non-covalent interactions which hold the DNA duplex together.
Denaturation
What can cause DNA denaturation?
Heat, pH extremes, urea, and other denaturation agents.
Hyperchromic effect in DNA
Denatured DNA become less viscous and absorb (more) ultraviolet light
Melting Temperature
50% of double-stranded DNA, 50% single-stranded
Which are weaker, A-T hydrogen bonds or G-C?
A-T
What is the single circular chromosome of bacteria called?
nucleoid
What are the additional, small circular DNA that bacteria have called?
Plasmids
Chromatin
DNA/RNA and proteins (incl. histones)
What sorts of amino acid residues do histones have?
Basic / positively charged. (DNA is negative)
Nucleosome
Structural unit for chromatin packaging. DNA wound around a histone core.
What are the components of a histone core?
Two copies of: H2A, H2B, H3, H4
What, alongside linker DNA, is found between nucleosomes
Histone H1
Nucleosomes make up…
Chromatin
Euchromatin
Loosely packaged and transcriptionally active
Heterochromatin
Tightly packaged and transcriptionally inactive
Positive Supercoiling
Winding in the same direction of the double helix turns
Negative Supercoiling
Winding in the opposite direction of the double helix turns
What maintains underwinding and relaxes supercoiling effects?
Topoisomerases
Group of antibiotics targeting topoisomerase
Quinolones (specifically, ciprofloxacin)
Chemotherapy drug blocking topoisomerase
Doxorubicin
Specialized repeat DNA sequence with specialized proteins, found at the end of eukaryotic chromosomes
Telomere
Ori site
Origin of replication; nucleotide squence at which DNA synthesis begins
What is the chromosomal complement of a cell, individual or species called?
Karyotype
Two functions of DNA methylation
1) inhibiting the binding of transacting factors (usually promoters but can also block repressive factors)
2) recognition motif for binding of specific factors
Enzyme that catalyze DNA methylation
DNA Methyltransferases (DNMTs)
What serves as the donor for DNA methylation?
S-adenosyl Methionine
Removal of DNA methylation
Ten-Eleven Translocation (TET) enzymes followed by base-excision repair using Thymine-DNA Glycosylase (TDG)
Possible modifications of histones
acetylation, phosphorylation, methylation, ADP-ribosylation, glycosylation, ubiquination, amino-terminal modifications.
Histone Code
Histone covalent modifications (collectively)
Catalyze the transfer of an acetyl group from acetyl-CoA to epsilon-amino group of histone lysine residue
Histone Acetyltransferases (HATs)
Responsible for removing acetyl groups from histones.
Histone Deacetylases (HDACs)
