DNA and Chromatin Structure Flashcards
Pyrimidines
Purines
Describe the structure of a nucleotide
Difference between deoxyribose and ribose
Deoxyribose has a “H” at the 2’ carbon Ribose has a “OH” at the 2’ carbon
What is a nucleotide comprised of
Sugar, nitrogenous base, phosphate group
In which direction is DNA written
5’ to 3’ direction
How are the two strands in DNA configured
Antiparallel
What are the major and minor grooves of DNA and why are they important
Major grooves (12 angstroms wide) Minor grooves (6 angstroms wide) Both can hydrogen bond with foreign molecules - DNA binding proteins will typically target major grooves (because of larger surface area) and affect DNA or RNA synthesis
How tall is each turn of B DNA
10.5 residues, 36 angstroms = 2 major + 2 minor turns
What forces help to hold together DNA
Resonance of aromatic rings from nitrogenous bases on top of one another (orbital overlap) Hydrogen base pairing between nitrogenous bases
Explain why Adenine pairs with Thymine and why Guanine pairs with Cytosine, which pairing is stronger
These pairings maximize the number of hydrogen bonds between nitrogenous bases A:T form 2 hydrogen bonds, G:C form 3 hydrogen bonds G:C are thus stronger
What are a-form and z-form DNA
B-form DNA is the most stable and commonly witnessed biological state of DNA
a-form and z-form DNA are mutagenic variants and are less stable
a-form is more compact - 28A per turn (vs 36A of B DNA)
How does base pairing affect DNA hybridization
DNA strands will spontaneously hybridize in the most complementary form possible (most A:T and G:C overlap) so as to optimize thermodynamic stability DNA form keeps relatively hydrophobic nitrogenous bases on the inside
How can DNA denaturation be observed
Nitrogenous bases absorb UV light at 260nm (this only occurs when they are not hydrogen bound to other bases) Relative UV absorbance will increase as temperature is increased (thus increasingly denaturing the DNA)
What is the Tm (melting temperature), what does it depend on
The temperature at which DNA is 50% denatured G:C content of the DNA (more G:C = higher Tm) and ionic strength of solution (cations neutralize the repulsive force of the negatively charged phosphate backbone = more stabile DNA = higher Tm)
What are the different types of supercoiling, what categories of DNA can supercoil
There is positive and negative supercoiling - circular DNA and long strands of linear DNA can both supercoil - must be of B-form DNA
How is supercoiling relieved, why must this be done
Supercoiling can make DNA inaccessible to transcription, topoisomerases cleave the DNA, relieve tension, and repair the DNA Type 1 topoisomerases snip single strands of DNA and do not require energy Type 2 topoisomerases snip double strands of DNA but require energy to do so
How are topoisomerases clinically relevant
Certain antibacterials and cancer treatments target topoisomerase function to either (1) prevent target cell relief of supercoiling OR (2) prevent the repair of DNA after unwinding
What comprises a nucleosome
An octamer of histone proteins wrapped in 140 bp of DNA with 60 bp of linking DNA on either side
What are the different families of histones and their functions
H1 - linker histone H2A, H2B, H3, H4 - histones forming the nucleosome core. 2 of each
What is the function of histones
Providing scaffolding for chromosomes and inhibiting DNA transcription
How are histone modifications characterized
Rapid short-term changes that regulate gene expression
What histone modifications inhibit transcription, how is this accomplished
Hyper phosphorylation of histones condenses the chromatin Methylation of H3 (carried out by histone methyltransferase (HMT)) Deacetylation by histone deacetylase (HDAC) Encourages the condensation of chromatin
What histone modification activates transcription, what carries out this process
Acetylation of lysine residues on H3 and H4 histones carried out by Histone acetyl transferase (HAT) - inhibits ability of histones to interact with DNA
Where does histone modification occur
On the exposed amino terminal tails of the core histones
What is an epigenetic modification
A modification that produces a heritable change in gene function WITHOUT actually changing the DNA sequences
What is DNA methylation an example of, what does it do
DNA methylation is a form of epigenetic modification Attaches a methyl group to the 5’ of cytosine in CGCG sequences (CpG’s) Blocks transcription factors, resulting in repression of the gene
How does DNA methylation work with histone modification to condense chromatin
Methyl CpG can be targeted by methyl-CpG binding protein (MBP) MBP then recruits histone deacetylase (HDAC) to remove acetyl groups MBP also recruits histone methyltransferase (HMT) to methylate histones - methylated histones are recognized and bound by the HP-1 protein which silence gene expression
What is the clinical significance of epigenetic modifications
epigenetic modifications that suppress gene expression can suppress tumor suppressor genes thus leading to cancer - medications will either protect the DNA from processes such as methylation or inhibit enzymes that would promote gene repression
Describe a transcriptionally active segment of chromatin
Known as euchromatin Linking strands are free of H1 histone, the first two nucleosomes are missing to allow for polymerase binding Nuclease (DNA cutters) can access the chromatin Core histones H3 and H4 are acetylated on lysine residues (by HAT)
How are histone acetyl transferases (HAT) activated to acetylate histones 3 and 4?
Expression of various combinations of growth factors (LIF and BMP) causes transcription factors A and B to be imported into the nucleus A and B attach to the DNA - HAT anchors to A and B and proceeds to acetylate the histones on lysine residues - inhibits histone’s ability to interact with DNA
What is a 30nm fiber? How is it formed
Fiber formed by 6 nucleosomes coiling together H1 binds to the linking strands on euchromatin which promotes the condensation of euchromatin into hetero-chromatin
What happens during the formation of a chromatin loop
Fifty sequential chromatin fibers form loops that are anchored to the nuclear matrix (the attachment points are highly active for transcription because they contain proteins such as RNA polymerase and transcription factors)
What is a miniband
A ring of 18 chromatin loops
What are the orders of chromatin structure? number of base pairs in each?
nucleosome - beads on a string - 200 bp total - 140 bp wrapped around the histone octamer - 60 bp in between each ‘bead’ 30nm fiber - 1200 bp - H1 attaches to ‘string’, causes 6 nucleosomes to coil together chromatin loop - 50x 30nm fibers form a loop - 60,000 bp - each loop can potentially contain several genes miniband - 18x chromatin loops - 1 million base pairs chromosomes - 75 minibands - 75 million base pairs - formation is mediated by hyper-phosphorylation
