biochem 7A - DNA structure, replication, and repair Flashcards
what bond links polymers of deoxyribonucleoside monophosphates
covalent 3-5 phosphodiester bonds
3-5 phosphodiester bonds are cleaved by what
nucleases
(deoxyribonuelases for DNA)
(ribonucleases for RNA)
strands of DNA are held together by what type of bonds
H-bonds
AT how many H bonds
2H bonds
GC how many H bonds
3H bonds
when would a DNA strand have higher melting temp
more GC base pairs
hands of DNA
A (right handed)
B (right handed)
Z (left handed)
in prokaryotic DNA syntehsis, what base pairing is it almost exclusively that faciliate melting
AT base pairs
DnaA protein
binds to origina and causes the AT rich regions to melt
DNA helicase
undwinds the double helix
ssDNA-binding proteins
keeps the strands apart and protect DNA from nucleases that degrade ssDNA
topoisomerase 1
cut and rejoin one strand of double helix to remove supercoils
topoisomerase II
cuts and rejoins both
what direction does DNA polymerase read
3’ -> 5’
what direction does syntehsis occur
5’->3’
RNA primer catalzyed by what
primase
RNA primer charactieristics
~10 nucleotide w free OH on 3’ end
chain elongation in prokaryotic DNA synthesis is catalzyed by what
DNA polymerase III
how does DNA pol III correct mismatch
has 3’-5’ exonuclease
RNA is excised and the gap is filled by
DNA pol I
how does eukaryotic DNA replication differ from prokaryotic
-has multple origins of replication
-RNA primers are removed by RNase rather than DNA polymerase
G1 phase
cell prepares to initiate DNA synthesis, biosynthesis occurs (growth)
S phase
DNA content doubled (DNA synthesis)
G2 phase
biosynthesis for mitosis to occur (growth and preparation for mitosis)
DNA pol alpha
-contains primase
-initiates DNA synthesis
DNA pol gamma
replicates michondria DNA
DNA pol delta
elongates okazaki fragments of the lagging strand
DNA pol epsilon
elongates the leading strand
telomeres
-consist of several thousand tandem repeats of noncoding AGGGTT
-GT strand longer than its complement leaving a few hundred nucleotides in length at the 3’ end
-complexes of noncoding DNA plus proteins located at the end of linear chromosomes
-maintain structural integrity of the chromosome, preventing attack by nucleases
-allow repair enzymes to distinguish between a true end from a break in dsDNA
-in normal somatic cells, telomeres shorten with each successive division (once they shortened beyond a critical length, cell no longe table to divide and is said to be senescent
what cells has telomerase and what does it do
stem and cancer cells
maintains telomeric length in the cells
reverse transcriptase function
enzyme that syntehsizses DNA from RNA
are histones basic or acidic
basic
nucleosomes
order DNA in structural units
nucleosomes further arranged into what
chromosomes
DNA damage
-hydrolysis
-oxidation
-methylation
-UV light
-ionizing radiation
UV light leads to the formation of what
pyrimidine dimers (thymine dimers)
Base Excision Repair (BER)
removes and replaces individual damaged bases
Nucleotide excision repair (NER)
-removes and replaces damaged bulky lesions (2-30 nu)
-recognizes physical distortion rather than specific base sequences
(larger area)
mismatch repair
removes nu that do not form correct base pairs
Xeroderma pigmentosum (DNA repair disease)
-pyrimidine dimers formed in skin cells exposed to UV light
-defects in excision repair due to a mutant UV-specific endonuclease
ataxia telangiectasia
-defects in excision repair
-neurodegenerative disease
-poor coordination
