exam 1 & 2 practice test Flashcards
how many rings do purines have
2 rings
how many rings do pyrimidines have
1 ring
how many H bonds are in the A-T bond
2
how many bonds are in the C-G bond
3
what is a palindrome in a DNA sequence
the nucleotides pair with each other to form a loop
what secondary structure can ssDNA or RNA with a palindrome adopt
hairpin
what is one function of a hairpin loop in transcription in bacteria
termination of transcription
fill in the blank:
DAM methylation ensures that replication _____ by recruiting ____ on the hemimethylated DNA
is initiated only once per cell division
seqA
fill in the blank: during \_\_\_\_\_(a type of repair pathway), DAM methylation enables recognition of the strand to be repaired which is the \_\_\_\_\_\_ ((un) (hemi) methylated)
mismatch repair
unmethylated strand
what type of point mutation is purine –> purine or pyr –> pyr
transition
how can a transition mutation happen
modification of a base leading to incorrect base-pairing during replication
incorporation of the wrong dNTP during replication
what do you need for a knock in crispr/cas
cas 9, gRNA, donor sequence
which DNA repair pathway is required to do knock in for crispr/cas
homologous recombination
what are the functions of the beta sliding clamp in bacteria
increases the processivity of DNA polymerase
recruits the ligase at the end of replication of an okazaki fragment
recruits pol I at the end of replication of an okazaki fragment
what additional step is required to measure RNA by RT-PCR compared to DNA
reverse transcription of RNA to DNA
can you determine information about the amount of copies of a gene by an RT-PCR graph
no
what is the function of sigma factors in bacteria
helps the RNA pol bind to specific promoter
what are the classes of sigma factors in bacteria
sigma 70
sigma 54
what is the difference during transcription between sigma 70 and other sigma factors
sigma 70: spontaneous isomerization can occur
sigma 54: needs ATP
what would be the result of a footprinting experiment that used a different sigma factor
it would attach at a different location on the DNA
what would be the result if the footprinting experiment was done without DNAase
the strand would not be cut so there would not be a blank spot that could be visualized and we could not see where the sigma factor was bound
what is the mechanism in which the RNA chain reaches ~10rNTPs, the sigma factor is released from the exit channel. enabling transcription elongation
promoter clearance
what is abortive initiation
when the RNA pol is assembling the first rNTPs and the chain is unstable, the RNA will fall off the polymerase
if the RNA pol stalls on a mismatched nucleotide, it leaves time for pyrophosphorolysis (last rNTP is spontaneously lost). what is this mechanism called?
kinetic proofreading
at the end of transcription, a helicase is activated and moves along the RNA until it collides against the RNAP. what is this mechanism called?
rho-dependent termination
which pol is involved in transcription (in regards to RNA processing (capping))
pol II
where is the capped mRNA attached
the c terminal domain
provide the enzyme:
a bacterial DNA pol that has both 3’–>5’ and 5’–>3’ exonuclease activity
pol I
provide the enzyme:
a bacterial DNA endonuclease that uses an RNA as a target guide
cas9`
provide the enzyme:
a eukaryotic RNA pol that does not need a template
poly A polymerase
provide the enzyme:
a eukaryotic DNA polymerase that uses a specific RNA as a template
reverse transcriptase
