Block 1 Flashcards
the 2 outermost phosphates of ATP are cleaves to release energy for what
formation of a phosphodiester bond
how is a nucleoside different from a nucleotide
nucleoside= base+sugar
nucleotide= base+sugar+phosphate
in a nucleotide, the base is connected to what number carbon
1
phosphodiester bonds are made between carbons __ and __ on adjacent molecules
3 and 5
new nucleotides are always added in the __’ to __’ direction
5’-3’
AT has __ H bonds
CG has __ H bonds
AT= 2
CG= 3
DNA helix is a hydrophobic or hydrophilic molecule
hydrophilic
if a DNA sequence is not marker either 5’-3’ or 3’-5’, it is assumed to be __’ to __’
5’-3’
what does Chargaff’s rule tell us
% of A= % of T
% of C= % of G
what is an exception to Chargaff’s rule
single stranded DNA viruses
is DNA a right or left handed helix
right
how many bases are in one complete rotation of a DNA helix
10
what form of DNA (A, B, or Z) is most predominant and stable under physiological conditions
B
what do prokaryotes and mitochondria do to reduce the size of their genome
supercoil
histone proteins are rich in what 2 amino acids
arginine
lysine
what histones make up a nucleosome
2 each of:
H2A
H2B
H3
H4
what is the function of H1
caps nucleosome and joins nucleosomes together
heterochromatin vs euchromatin appearance under microscope
heterochromatin- dark
euchromatin- light
in histone proteins, which amino acid is most often methylated
lysine
does acetylation or methylation cause genes to be turned on
acetylation
“acetylation= active”
origins of replication are rich in what DNA sequences, AT or CG
AT
how many origins of replication do prokaryotes have
1
how many origins or replication do eukaryotes have
many
new DNA is always made ‘-’
5’ to 3’
what enzyme separates double stranded DNA at the replication fork
DNA helicase
what is the function of single stranded DNA binding proteins
keeps the 2 strands of DNA separate
what is the difference between positive and negative supercoiling
positive supercoiling occurs ahead of the replication form
negative supercoiling occurs behind the replication fork
what is the function of DNA gyrase (topoisomerase II)
releases mechanical stress and tension
what is the function of DNA ligase
joins Okazaki fragments on lagging strand
what is the function of RNA primase
adds a primer to initiate new strand synthesis
what is the function of DNA polymerase I
replace RNA primer with DNA
what is the function of DNA polymerase III
main replicating enzyme
what enzyme removes RNA primers in eukaryotes
RNAase H
in prokaryotes, what DNA polymerase can proofread
I, II, and III
in eukaryotes, what DNA polymerase can proofread
delta
epsilon
with DNA proofreading, there needs to be what type of activity
3’-5’ exonuclease
what prokaryotic DNA polymerase can also remove bases in front of it since it has 5’-3’ exonuclease activity
DNA polymerase I
what is the function of telomerase
extends the 3’ end using an internal RNA guide
what type of enzyme is telomerase (DNA dependent DNA polymerase or RNA dependent DNA polymerase)
RNA dependent DNA polymerase
what amino acids can form dimers as a result of UV light
cysteine
thymine
how are thymine/cysteine dimers corrected
nucleotide excision repair
when in the cell cycle does nucleotide excision repair occur
G1
what class of enzyme performs nucleotide excision repair
endonuclease
a common example of base excision repair is due to cysteine spontaneously becoming ___
uracil
when in the cell cycle does base excision repair occur
G1
how does base excision repair work
base is removed, not deoxyribose or sugar, leaving an AP site
AP endonuclease recognizes this and removes the deoxyribose and sugar
missing base is replaced by DNA poly I (prokaryotes) or DNA poly beta (eukaryotes)
DNA ligase creates new phosphodiester bond
when in the cell cycle does mismatch repair occur
G2
what are microsatellite DNA sequences
short repeated sequences of 2, 3, or 4 bases
how are microsatellite DNA sequences used in cancer
mismatch repair has failed, microsatellite sequences have different lengths compared to nearby noncancerous tissue (microsatellite instability)
where in the cell cycle does DNA proofreading occur
S
are catabolic or anabolic genes normally on
anabolic
what does it mean to say catabolic genes are inducible
they’re normally off
in codons, each coding region has an individual __ and __ codon
start
stop
the lactose operon metabolizes __ into __ and __
lactose into glucose and galactose
what genes must be expressed in the prokaryotic lactose operon
lacA, lacY, lacZ
when are the lacA, lacY, and lacZ genes expressed in prokaryotes
presence of lactose, absence of glucose
what genes are involved in E.coli lac operon
LacI, LacZ, LacY, LacA
what does LacI do
make repressor protein that binds to operator, keeping operon off
always on
what does LacZ do
cleaves lactose by producing beta-galactosidase
what does LacY do
transports lactose into cell
what happens with the lac operon when lactose is present
lactose bind repressor protein causing a conformational change, removing it from the operator
what is a mechanism of lac operon control that involves RNA polymerase
if there is a change in sequence at -10 and -35 where RNA polymerase normally binds, RNA polymerase binds with more difficulty, reducing gene expression
what is diauxic growth
preferred way of bacteria to metabolize glucose rather than lactose
what must e.coli do to achieve diauxic growth
turn off lac operon if glucose is present in the cell
do e.coli prefer to use glucose or lactose
glucose
why do e.coli prefer to use glucose before lactose
glucose is an simple molecule, lactose is disaccharide that must be broken down
what gene must be turned off by bacteria in high glucose environment in order to metabolize glucose rather than lactose
ZYA (lacZ+Y+A)
low glucose= __(high/low) ATP= __(high/low) cAMP=__(stabilize/destabilize) RNA polymerase= ZYA (lacZ+Y+A genes) __(on/off)
low
high
stabilize
on
Low glucose= break down lactose
with the lac operon, under low glucose conditions, cAMP is __ and binds __ protein
high
CRP
*CRP is added under low glucose conditions
low glucose=low ATP=high cAMP
does cAMP with CRP in bacteria allow or inhibit transcription
allow
in low glucose environment, is ZYA turned on or off
on
is the trp operon on or off with no tryptophan present
on
what do the ZYA genes make proteins to do
degrade lactose
if tryptophan is present, it will bind to the trp repressor, enabling it to bind to trp operator, preventing or allowing transcription
preventing
what does the attenuator in the trp operon do
detects whether trp is available and working in the cell
what is located between the operator and the 1st structural gene in the trp operon
leader sequence (trpL) of mRNA
under high trp concentration, ribosome translates through trp codons and covers sections __ and __ of leader sequence
1 and 2
as a result of ribosome covering sections 1 and 2, sections __ and __ fold with rho-__ (dependent or independent) transcription. no new trp is synthesized
3 and 4
independent
if there is a fold in sections 2 and 3 of trp operon leader sequence, trp levels are __ (high or low), causing an __(increase/decrease) in trp transcription
low
increase
what are the 3 types of mRNA that participate in protein synthesis
mRNA
rRNA
tRNA
what RNA polymerase produces rRNA
I
what RNA polymerase produces mRNA
II
what RNA polymerase produces tRNA
III
is the top strand of DNA non-template (coding/sense) or template (non-coding/antisense)
non-template
is the bottom strand of DNA non-template (coding/sense) or template (non-coding/antisense)
template
in what direction is non-template/coding/sense strand, 3’-5’ or 5’-3’
5’-3’
in what direction is template/non-coding/antisense strand, 3’-5’ or 5’-3’
3’-5’
the mRNA and ___ (template or nontemplate) strand are complimentary to each other
non-template coding (5’-3’ strand)
what binds to the promoter DNA sequence
RNA polymerase
what sequence is the promoter DNA sequence
TATA
where is the promoter sequence (TATA box) located
5’ (upstream) at -10
at what location is the first base to be transcribed
+1
what are the 3 stages of transcription of DNA to RNA by RNA polymerase
initiation
elongation
termination
in prokaryotes, what binds TATA at -10 and -35
sigma protein
in eukaryotes, what binds TATA at -25 and -70
TFIID (TBP)
where are the RNA polymerase binding sites in prokaryotes
-10
-35
where are the RNA polymerase binding sites in eukaryotes
-25
-70
what are the subunits of prokaryotic RNA polymerase (sigma)
alpha, alpha, beta, beta prime, wo, sigma
once transcribing, does sigma remain or dissociate from RNA polymerase
dissociate
once transcribing, does TBP remain or dissociate from RNA polymerase
remain
does RNA polymerase use the top or bottom strand as a template
bottom
what provides energy for the formation of a new phosphodiester bond during elongation of transcription
release of terminal 2 phosphates from ATP