Protein & DNA
What is a protein domain?
A functional and structural unit within a protein, often responsible for a specific function.
List the names of the 5 histones
H2A, H2B, H3, H4 (nucleosome core)
H1 (required for 30 nm fiber packing level)
What happens in depurination?
loss of purine base (A or G) from DNA
results in empty site
What is the role of disulfide bonds?
They form between cysteine residues and stabilize tertiary (and sometimes quaternary) structure.
The histone H3 tail has both trimethylation at K4 and acetylation at K9.
Predict the effect on gene expression and explain why.
K4 trimethylation = active chromatin
Ac reduces positive charge on histones -> loosens DNA histone interaction
opens chromatin structure (euchromatin) --> gene expression activated
What happens in deamination? What does cytosine turn into?
removal of an amino group (–NH₂) from a base
uracil - mismatch
Where are new nucleotides added on the DNA strand?
to the free hydroxyl at 3' end. the free phosphate at the 5' end is the beginning.
What does trimethylation on the histone H3 tail (K9) result in?
binding site for proteins that promote compaction --> heterochromatin formation --> gene silencing
What causes thymine dimers & what is it?
caused by UV radiation
2 adj T bases on same DNA strand form covalent bond --> dimers & bulge in helix (distortion)
What are the four levels of protein structure, and what stabilizes each?
Primary: Amino acid sequence (peptide bonds)
Secondary: α-helices & β-sheets (hydrogen bonds between backbone atoms)
Tertiary: 3D folding (hydrophobic interactions, ionic bonds, H-bonds, disulfide bonds)
Quaternary: Multiple polypeptides (noncovalent interactions between subunits)
One of the two X chromosomes is inactivated in the cells of mammalian females by heterochromatin formation (random)
same X chromosome is inactivated in all descendants of the original cell
all mammalian females are "mosaics" of cells with either inactivated maternal or paternal X
A researcher observes that DNA replication is stalling at a specific site, and sequencing reveals two adjacent thymine bases are covalently linked on the same strand.
Which repair pathway is activated, and why?
nucleotide excision repair (NER)
thymine dimer is a structural distortion - NER removes entire stretches of damaged DNA, not just a single base
List the multiple levels of DNA structure in packaging in order
2 nm DNA --> 11 nm nucleosomes --> 30 nm chromatine --> 300 nm chromatine loops --> 700 nm condensed chromatine loops --> 1400 nm chromosome
List the levels of chromosomal organization in order
short region of DNA double helix --> "beads on a string" chromatin --> 30 nm chromatin fiber of packed nucleosomes --> section of chromosome in extended form --> condensed section of chromosome --> entire mitotic chromosome
Immediately after DNA replication, a cell detects a G paired with T.
Which repair pathway will be used & why?
base pairing error - removes mismatched base