unit 2 exam Flashcards
where are bases located in DNA?
on the inside of the helix
B-form DNA
asymmetric, major and minor grooves, major groove accessible to proteins
Z-form
left handed helix, Hoogstein base pairs, one base in syn formation and one in anti
A-form
RNA-RNA or RNA-DNA interactions
difference between RNA and DNA sugar
RNA has a 2’ OH and DNA does not
what affects melting points of DNA?
longer DNA fragment = higher Tm
more A-T pairs, less C-G pairs = lower Tm
what does topoisomerase do?
cuts DNA to decrease Lk
key points of topology
Lk = Tw + Wr
natural twist = #bp/10.4
Tw = -Wr is most favorable
highly supercoiled DNA moves faster in gel electrophoresis
key points of acetylation
added by enzymes called Histone Acetyl Transferases (HATs)
makes DNA more accessible
stimulates transcription
reversible!
process for compacting DNA
DNA –wound around histone–> nucleosome –compressed to 30nm fiber–> chromosome
heterochromatin
inaccessible
histone methylation
euchromatin
accessible
histone acetylation
purpose of S-methylcytosine
silences gene expression
how is the STOP codon different from other codons
it is recognized by a protein rather than W-C-F base pairing with tRNA
what catalyzes peptide bond formation in rRNA
the protein component
what is being copied in RNA translation?
The coding strand
what is necessary for group 1 introns to carry out splicing functions
a free guanosine nucleotide cofactor to perform first step of splicing
function of DNA pol III
workhorse polymerase
function of DNA pol I
handyperson polymerase
what is the opening enzyme?
helicase
what is the primer?
primase
what happens in deamination?
H-bond donor switched to H-bond acceptor
what happens in depurination?
the entire base is removed
what happens in dimerization (UV-induced)?
glues stacked pyrimidines
how to repair alkylation
alkyl group moved to alkyl transferase enzyme
- transferase cannot be used again!
how to repair deamination
depurinate problem nucleotide, recognize abasic and repair
how to repair dimerization
cut both sides, pol 1 and ligase patch up hole
characteristics of homologous recombination
can be used to repair double strand breaks
uses 3’ overhangs on DNA to sample for base pairing interactions
can occur between ANY two homologous species
requires 5’ –> 3’ exonuclease
characteristics of sequence specific recombination
only occurs at defined sites
more predictable and controllable
viruses use it to bind to hosts
has tyrosine and serine mechanisms
how does tyrosine recombinase work?
-OH attacks phosphate backbone, forms a junction, and then reseals
how does serine recombinase work?
double strand break, swap strands, reseal
characteristics of transposons
mobile genetic element
can insert themselves into a gene to inactivate it
what is a class I transposon?
retrotransposons
copy/paste from one region to another
what is a class II transposon?
DNA transposons
cut/paste from one region to another
characteristics of DNA polymerase
DNA template
RNA/DNA primer needed
3’–>5’ exonuclease proof reader
produces DNA
replicates entire genome
characteristics of RNA polymerase
DNA template
no primer needed
no exonuclease to proof read
produces RNA
only replicates part of genome
transcription begins by melting the DNA
RNA holds on to coding and template strand during transcription
how do gene promoters work?
10 or 35 nucleotides back from start site
tell the polymerase to start transcription
recognized in prokaryotes by sigma factor of RNA polymerase
specify which strand of DNA will be used as template
how does rho dependent termination work?
the polymerase transcribes a binding site for rho factor
the rho factor is a helicase that translates from binding site to 3’ end
the helicase unwinds the DNA/RNA hybrid and RNA peels off
how does rho independent termination work?
polymerase transcribes through a G/C rich region to produce a hairpin structure
the hairpin causes a stall
a U rich segment downstream has weaker base pairing with the template strand and the RNA falls off
characteristics of the spliceosome
made up of protein AND RNA components
an RNA lariat structure is excised during splicing
splicing is a process thought to be evolutionarily related to splicing by group II introns
which way does polymerase synthesize?
5’—>3’
what happens when primase is halted?
lagging strand stops synthesizing
base excision repair
damaged bases removed by glycosylase
nucleotide excised by AP endonuclease
characteristics of DNA binding proteins
sequences read through H-bonding between protein side chains and nucleobases
part of protein that binds DNA can often be separated from part that activates transcription
typically involve interaction with major groove of B-form DNA
requirement for pre-mRNA to undergo splicing by spliceosome
“branch point A” RNA nucleotide
eukaryotic translation
occurs outside nucleus and separate from transcription
involves assembly of initiation complex mediated by 5’m7G cap and 3’ poly A tail of mRNA
can be regulated to control when and where mRNAs are translated into protein inside the cell
CRISPR cas-9
locates specific locations in genome using guide RNA molecule
induces double strand breaks at sequences it is programmed to recognize
discovered as part of bacterial immune system to fight against phage
telomerase
responsible for synthesis of telomeres on chromosomes
carries own RNA primer to template DNA synthesis at ends of telomeres
prevents shortening of lagging strand of DNA after replication
RNA characteristics
can base pair with DNA to form A-form double stranded structures
can fold into 3D shapes to perform basic function in cell
not typically double-stranded in cells
group 2 introns
splicing reaction initiated by internal adenosine
produce RNA lariat structure that is excised during splicing
group 1 introns
splicing reaction initiated by guanosine cofactor
Shine-Delgarno sequence
ribosomal binding site in bacterial mRNA
