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161 Cards in this Set

  • Front
  • Back
how may carbons are in nucleotides? why?
5 carbon pentose.
b/c 6 carbon is metabolized.
what are the 3 parts of the nucleotide?
sugar 5C
phosphate group, forms P bond
Nitrogen containing Base
diff b/w purine & pyrimidine?
A & G purine (hetracycles)
T & C pyrimidines
purines larger w 3 H bonds
pyrimidines w 2 H bonds
in dna molecule adenine and thymine bases appeared in equal number, & CG too, who discovered this?
Chargaff.
how is the double helix oriented?
antiparallel.
how many bases per sweep of major groove?
about 10 bases per sweep - top of the major groove
distance b/w adjacent bases is how many angstroms?
about 3.4 angstoms b/w bases. 34 angstroms from the top of the major groove to the bottom of the major groove.. that means 10 bases per sweep of major groove
what is the function of DNA?
replication
protein synthesis &
regulation
what kind of replication goes down?
semi-conservative
___ Angrums is the radius of the DNA
10 angstroms.
proposals for dna relication?
dna molecule dissasembled by breaking backbone. Dispersive model. NOT TRUE.
what did Griffith, Hershey & chase, Roselyn Fraklyn, Chargaff, Messelsyn & stahl, and watson & crick.
M & S did semi-conservative repro.
light nitrogen given during to replication in order for what?
M&S : to prove semi-conservative - heavy nitrogen & light dna nitrogen, not dispersive but semi-conservative. half & half
what 4 things are unique about prokaryotes?
1. singular circular DNA molecule
2. specific DNA structure
3. Naked
4. associated plasmids
blue green algae (archeabacteria) and bacteria are what?
prokaryotes
eukaryotes 3 things unique
1. more dna (46 chromosomes in humans) it's linear
2. milticellular
3. true organelles
4. nucleus
single circular molecule with associated proteins is all together called?
whats in place of nucleus?
chromosome for prokaryotes. no nucleus.
tethering protein instead, the region is called the nucleoid (b/c no nucleus).
free associates are circular, small & outside the nucleoid. separate but can become associated, these are called what?
plasmids
Yes / No
can plasmids be used between different prokaryotic individuals?
YES
can be very useful
b/c few assoicated proteins w/ DNA prokarotic chromosome called ...?
naked
what is polytene? where are they found?
found in saliva.
Failure in spindle apparatus pulling dna apart, every time gets wider with each reproduction… b/c wider, you can see it under light magnification
where does replication begin for prokaryotes?
what is used - proteins?
at the at AT rich origin
. they're recognized by dna-a, which recruit helicases & dna-b's, which melt at origin. making 2 forks. replisomes attach at forks & mediated via dna polymerase 3 & ssbp & clamps and other associated proteins help
about __ different proteins that make up the replisome of prok. __ for euk. why so many more
13
30
1. many are part of unwinding of dna off of nucleosomes.
2. Also role in nucleosome formation
how do euk make up the slower speed of replication?
1000 base pairs/sec prok
50-100 base paris/sec euk
they begin replicating at multiple replicating forks. maybe over 1000 origins per chromosome. over 2000 replicating forks... this still takes hours.
difference of origin b/w prok and euk. both are AT rich, on euk, they're called ____ sites.
annonymous with ____ on prok
ORC (eukaryotes)
stands for origin recognizing complex proteins.

same as dna-a with prok's.
after orc, comes ___ protein. this coats the now unwound dna strand.
ncm proteins
ncm does what?
this preps the site for replication by the replisome and enzymatic proteins
when do you want ncm to work?
when you want to replicate.
geminin?
this protects the newly synthesized strand against re-replication & replisome & enzymatic proteins

inactivates ncm protein.
what are the polymerases in proks?

what are polymerases in euks?
poly 1 & poly 3

poly alpha & poly delta

poly gamma (mitochondria)
& poly epsilon
what does CAF-1 do?
it is an accessory protein responsible for the remodeling of the histone proteins
the nucleosome is an _____.
octomer, consisting of 2 h2a's 2h2b's h3's & ... .
all individual proteins.
CAF -1 fxn mainly consists of working with what proteins?
the nucleosome which is an octomer. it models the octomer and the dna will then wrap around this.
what is the CLAMP on a eukaryote?
PCNA is another accessory protein. it's used by polymerizing enzmye making it processive. (proliferating cell nuclear antigen)
open replicating fork and first on the scene is ___ with euks.
polymerase alpha
what's polymerase alpha do?
it can synthesize 2 diff rxns.

dna strand synthesizing
rna strand synthesizing

it synthesizes rna primer for replication.
the primer with euk's are uinque b/c
have an rna tag attached to dna section. it's a chimera (part rna, part dna, this is synthesized by polymerase alpha).
what is the same as primase, but for euks?
dna polymerase alpha
distributive
not clamped
most dna polymerases are also exonucleases, what does that mean?

is poly alpha an exonuclease?
it means that it can proof read itself.

no (although poly 1 & 3 are)
after primer added w euks, via poly 1, what comes in ...
pcna. b/c this works as the clamp.
pcna recruits & poly alpha gets kicked off by poly delta and poly delta synthesizing from 5' --> 3'
is poly delta an exonucelase?
yes. it clips out primer, adds appropriate bases where primer set.
processive
means clamped. once bases added, it goes until termination signal.
what are part of the replisome?
just a few of the 27 proteins, mcm's caf1, pcna's, polymerases, helicases, etc
all pat of replisome.
what do MCM's do?
they are proteins that either activate or inhibit the creation of attachment for replication.

inhibit via protein Geminin.
when replicating end of euk, you don't need a primer, you have leading strand. only needed at origin. on lagging strand add primer, go backwards replicating fork opens and go back. problem?
poly delta fills the pimer gaps, but there's no poly delta addition after the last primer.
these nucleotides therefore are not replicated.
telomere


who makes telomeres?
non-code-ing, highly repetetive, at the end of chromosomes. okay if chopped off every time.

only germ cells can make telomeres
how do germ cells add telomeres?
they are a reverse transcriptase

they have telomerase
somatic cells that can't regenerate telomerase, cells therefore have life spans before genetic material is lost. true/false?
true.
a type of cell programmed death
what's the difference b/w rna and dna?
ribose vs. deoxyribose. C #2 has a hydroxyl group where dna only has H. U replaces T. rna act as ribozymes.
transcription involves what 3 steps?
initiation
elongation
termination
what sites are significant for the promotor in prokaryotes?
-35 region and -10 region (-10 called pribnow box)
what protein (peptide) attaches loosely to -35 region?
the Signma
what binds to the pribnow box?
rna polymerase w 2 peptides, the 2a,2b & 2b'.
what are the 5 types of rna?
mRNA, tRNA, rRNA, snRNA (euk only) does processing, HnRNA becomes mRNA
what's the sigma protein do?
the sigma binds to the pribnow box and melts the dna, unwinding it.
operons
s.t coding region is going to be a gene, sometimes multiple genes. (true of proK's) operon is coding sequence that makes mRNA that'll be translated into multiple peptides.
how many untwisting parts occur per polymerase. why this many?
the polymerase unwinds about 2 twists or 20 base pairs. no ssb's so we don't want to expose all the nucleotides.
when does sigma leave
after 10 - 20 base pairs are paired after polymerase
what makes up an rna polymerase?
4 proteins: 2 aplha's, beta and beta prime.
at start of transcrition, polymerase core attaches another peptide called what?
sigma peptide
when sigma attaches to polymerase core, it forms
functional enzyme that first attaches to 35 region loosely. now sigma attaches to pribnow box and opens dna strand.
if polymerase core wants to go, but no sigma availible?
will not melt, can attach, but not melt without sigma.
no ssbs? so what does replication do?
only exposes ~20 bases at a time.
what is the name of the -35 and -10 regions
consensus sequences. these are the binding sites for the polymerases.
how do you get different regions transcribed?
all cores are the same, but not all sigmas are not equal. the sigma factor attached to polymerase decides which is transcribed
in transcription, name the region that is the first translated part of the strand.
the 5' end. it takes about 10 bases before the first translation occurs, this is called the 5' UTR (un-translated region)
do rna polymerases have exonuclease activity
no rna polymerases do not have proof reading exonuclease activity
in what state are the nucleotides coming in?
coming in as triphosphates to help form phosphodiester bonds
what causes speed to be checked during transcription?
AT rich regions slow down the polymerase to help stabilize.
how fast can rna polymerases work?
30-50 bases/second
there are 2 strands, sense and nonsense. what region is read?
the sense region is read. the nonsence strand is a template only.
what are the 2 possible mechanisms for termination?
RHO independent and dependent
at the end of the rho independent what is found?
40 base pairs that are AT rich followed by AAAA's . it would go slow here making UUUU's.
what helps pinch off the end at termination?
a hairpin loop caused by CG's. a hairpin loop is formed and when polymerase looks back it's kicked off. although cant proof read, it can survey.
what finally kicks the polymerase?
it becomes distributive and when surveying the look kicks it off.
rho independent AKA
intrinsic mechanism
rho independent region terminates how?
the CG base pairs form a loop and polyerase drops after stalling
the rho dependent region terminates how?
40 to 50 GGG's make CCC's and afterwards comes a region: "rut site". this "rut site" binds RHO. conformational change causes the popping off of the polymerase
RHO binds to What?
RUT. by acting rho to rut (rut is on rna strand) it pulls polymerase off

rho is an independent protein
what're rna poly's in eukaryotes? jobs of each?
poly I - makes rRNA (ss)
poly II - hmRNA (pre mRNA's), sometimes makes snRNA (rhomozymes)
poly III - tRNA, 5s rRNA, snRNA's
what allows for fast, slow or medium rate of transcription in euK's?
these are analogus to what in the prok?
the GTF's (general transcrition factors). there's GTF II, IIa, IIb, etc. these are ACCESSORY PROTEINS, or similar b/c they're like prok's sigma
an _______ increases the binding affinity for polymerase, speeds it up
enhancer
what part do we need to cut out of a gene
cut out introns, need to use exxons.
what's the general regulation of proK's
operon control. on or off.
what's general regulation of euK's
on/off high rate/slow rate ... this is seen b/c of the GTF's (Transcription Factors)
GTF's play a role in removing DNA from protein so it can be transcribed. T/F
True. helps get off of histones some TF's help find right start code
in proK's what helps find pribnow box?
sigma.

series of GTF's do a similar fxn in euK's
what's a major difference b/w proK & euK & transcription
location. translation in nucleus. transcription outside nucleus. separated by Time & Space
- in proK's happen simultaneously
at ~ - 30 is a consensus sequence called ____. this site is significant for what?
TATA
this is promotor region of the gene. polymerase attaches here
for TATA to work. we take a TF (transcription factor) called ____ and this protein binds to TATA box.
TF is called the 2 TF II D.
After TF II D bound. what happens?
other TGF's called to promotor. IIA, IIF ... others come in and act as enhancers (better binding for polymerase) NOW CALLED PRE INitiation COMPLEX
what's included in pre initiation complex?
function?
the sense strand of dna. GTF's IIA & IID, other regulatory proteins. this calls polymerase to site
After pre complex ready, what happens?
polymerase attaches and elongation occurs. in the 5' to 3' direction
is rna polymerase an exonuclease?
no. not even in euK's
the initiation coplex is there, and starts what are the options now?
to be re-copied, or to be disposed of. depends on what signals it receives.
signaling usually to phosphorylate or dephosphorylate via kinases.
what happens if signalling is messed up?
cancer maybe
what's the role & name of the polymerase tail?
the tail is called the CDT (carboxyl tail domain) tail
helps to break from initiation complex and helps to break away at termination
if signal required dephosphorylation then not a kinase, but a ....
phosphatase
post transcriptional processsing, what happens?
introns removed. after transcription. before termination however.

happens during elongation
post transcriptional processing requires a ______. this is put in the wrong orientation, why?
the 5' CAP is a 7 methyl guanosine. ints in incorrect orientation. reason is to protect from degredation and to find the right orientation on ribosome
what are enzymes that help attach/splice the exons?
splice-o-zymes
what's the major difference in transcription b/w prok's & euk's?
the structure, ie. histones.
also, multiple polymerases in eukaryotes (we study poly 2 mostly)
also, transcript must be processed
where's the initiaion in prok's vs. euks?
think about it, look it up
what one is -30 tata box?
the tata box binds proteins to TBP & is part of the TF II D
what is TF II D?
it's a general transcription factor. these proteins locate, assist with binding, recuriting and regulating transcrition. some bind, some melt, some recruit others regulate
other promotor sites besides TaTa box?
yes, try the CaaT box. this one is big on regulation.
what's the fxn of the pre-initiation complex?
for recruitment of poly & opens dna (uses sense strand) from 3' to 5'. poly goes, complex stays
what's with the poly's tail?

CTD is name of tail. means what?
this is 5-7 AA's long & can be phosphorylated or dephosphorlated. this action allows attachment of poly. called CTD or carboxyl tail domain
what causes the termination of euk?
a terminator sequence. AAUAAA or AUUAAA. it ends ~ 20 bases furhter down stream. the 5' end is given CAP, a modified guanosine
how does splicing occur? where does it cut exactly?
from a splice-o-zome.
cuts at the GU and AG. includes the GU and AG
What's trans splicing?
the exon is spliced out and tagged onto the 5' end of a new strand. when transcribed a whole new protein is made
what was discovered with splicing and the human genome project?
thought some 100 k genes, but discovered only ~30K. b/c trans splicing.
why 1.7 million bases, 1.7 megabases long but widdled to only 10K?
b/c they believe lots of transposons left around.
some are thought to be evolutionary past, grandmas closet.
when reacing termination sequence like _ _ _ _ _ _ go 20 and cut. the following AAA's are considered what/why?
are the poly A tail. they are registers for the # of times used and tells cell machinery how many times this has been used.
that are the 4 phases of a polypeptide chain?
1' (straight)
2' (beta sheet, alpha helix)
3' (folded & often fxnal)
4' (multiple 3's, ie. hemoglobin)
when is a gene considered "on"?
when the info is made into a FUNCTIONAL protein
are "-ogens" on?
no, not until a part is clipped off
ie. pepsinogen --> pepsin
pepsin would be an active protease
where does AA bind on the tRNA?
on the 3' end
what enzyme holds the AA on the tRNA?

how many enzymes are there?
aminoacetyl-t-RNA-synthase

like 20 of these. look @ proline, think proline-aminoacetyl-trna-synthase
what 's with the 3 loops on tRNA?
the 2 sides play regulatory and placement roles
the 3rd middle one has the anti-codon that's read 3' to 5'
what's with the subunits of ribosomes of euk's vs prok's?
2 subunits. ProK have 50 s & 30 s to make 70 s ribosome.
euK's made up of 60 s & 40 s to make 80 S ribosome. S - svedburg units (centrifuge)
what's with the "rosetta stone" of coding AA's?
its degenerate.
the 3rd base is the wobble base so it's a wobble code.
what're the stop codons?
UAA & UAG
what're the stop codons?
codes for what?
UAG is the major one.
codes for MET. when at beginning, called the N-Formyl MET (i). met often cut out when folded
what's significant about the 5' UTR?
this is the "un-translated region"
5-10 bases up from this is location of the Shine delgarno region.
what's shine delgarno do?
pairs w/ initation complex, so initation codon put in correct location relative to complex forming. on the P site.
where/how does shine delgarno attach?
5-10 bases up from utr. it attaches in the 30s subunit plasing P site just right.
what do IF factors 1,2 & 3 do?
1 & 2 do alignment
3 plays a role in keeping 30 S and 50S apart
First real step w/ translation is what?
the IF3, IF1 & 30S unit all come together binding to mRNA by the shine delgardo region.
who comes first with initation, trna w AA, or the large subunit?
the initaiton, AUG, with IF 2 help in alignment.
how fast does the average molecule move?
3200 ft/sec
what are the 3 sites on the ribosome?
the E (exit)
P (peptidyl) &
A (amino) sites
T/F
the sine delgarno was attached to 30S unit so it would align with P
T
what direction is peptide synthesized
in the 5' to 3' direction
what's the name for the shift in the RNA when reading an mRNA?
translocation
what's the name of the enzyme that helps with translocation?
peptidyl transferase
where does the 30 S subunit initially bind with prok's?
10 bases upstream in the shine delgarno region. this region is in the 5' UTR.
the 16 S ribosomal unit has compliment bases to shin delgarno region
what else bids during prok initiation of translation? what do they do?
you have IF3 & IF1 binding here too. they basically work to ensure alignment. they make sure that 30S fits just right so E & I sites are aligned.
what site is availible after the 50 S sits down?
the P site is open, the E & A are covered.
anything unique about the first tRNA?
yes. the first tRNA is i tRNA. It carries the AA : met.
it binds to AUG.
IF 2 is helpful relative to the initation complex because why?
b/c the IF2 is a gtp-ase. there is energy required to recruit the 50S subunit.
how doe's IF 1 and others get kicked off?
what's the last IF factor kicked?
when initiation complex attached at P site the anticodon - codon makes a conformational change on the 30S ribosome. happens before 50S binds.
last kicked is IF2 (b'c it's a gtpase)
elongation. what's a charged tRNA?
one that has an AA on the 3' end.
what protein helps with the binding of the complimentary anti-codon?
EF-TU
this EF-TU is also a GTP-ase.
what 2 rxn's must occur after the tRNA bring in the 2nd AA?
first hydrolysis and then formation of Peptide bond (met w/ 2nd AA)
what enzymes help prok's with this rxn?
ribozyme and peptidyltransferase.
to put it into steps. with elongation what is step 1?
(is a gtp-ase that helps match up the anticodon)
the EF-TU protein
it's
what is located in the 23S region of 50S?
the peptidyl transferase
what would step 2 be?
(related to last question)
the formation of a peptide bond
step 3
translocation. everything shifted 1 reading frame.
what protein aids in reading frame shifting?
elongation factor G

EFG (an associated protein)
step 4
(final step)
termination.
occurs when termination codon falls in the A site.
w/ termination, we don't bind the tRNA anticodon, instead we bind what?
we bind 1 of 2 releasing factors.
either
RF1 or
RF2
RF 1 is called in with ____ or ____

RF 2 is called in with ____
RF 1 with UAA or UAG

RF 2 with UGA
so, what exactly happens when an RF factor binds?
hydrolysis of ester bond. breaks las AA from tRNA.
1. RF binds A site. 2. bond breaks, untethers peptide. 3. exits via E site (tunnel)
who get s the RF off?
RF1 & RF 2 released from RF 3
polysomes
multiple ribosomes re transcribing at the same time. they are at least 100 bp's apart.
polycistronic
systron is a more specific name for a gene. you can have 3 cistrons lined up with 1 promotor
when would you want to make a polycistronic line-up?
usually with metabolism, or some kind of pathway
true/false
operons are polycistronic.
true. 1 promotor
ie. lac operon or trp operon

again operons only in prok's
what's the poly A tail have to do with any function?
just basically tells how many times a transcript has been read.