exam 1 fr Flashcards
first to isolate DNA
Miescher
identified DNA as the transforming principle
Avery, McCarty, McLeod
determined that DNA for yeast consisted of an equal amount of purines and pyrimides
Chargaff
discovered the helical structure of DNA
Franklin
published the structure of DNA
Watson and Crick
demonstrated the phenomenon of transformation but did not identify the transforming principle
Griffeth
identified DNA as the genetic material in bacteriophages
Hershey and Chase
determined that DNA replication is semiconservative
Meselson and Stahl
main force stabilizing DNA
hydrophobic interactions
characteristics of histones
- bind to negatively charged DNA
- highly conserved
- eight histones and 147 bp of DNA are required to form the nucleosome core particle
characteristics of heterochromatin
- usually contains condensed chromatin
- seen in barr bodies
- contains few genes
in EUK DNA replication what is the role of licensing factor
to ensure all DNA is replicated only once
in DNA replication, what is the function of primase
to create a short RNA primer for the DNA polymerase
RNA is different than DNA in that
it has a 2’ OH
what is sometimes required for proper termination or transcription in prokaryotes
rho
what component is present in the holoenzyme but is not present in the core in enzyme in prokaryotes
sigma
in EUK cells, where does the basal transcription apparatus bind
core promoter
component of ribosomes
rRNA
brings amino acids to ribosomes
tRNA
processing of mRNA (splicing)
snRNA
used in degrading mRNA
siRNA
contains codons
mRNA
processing of pre-mRNA to produce mature mRNA includes
- splicing of exons, along with removal of introns
- addition of the 5’ 7-methyl-guanylate cap
- addition of the 3’ poly-A tail
what is not typically found in an mRNA molecule
promoter
how many reading frames possible for a sequence of mRNA
3
during translation, the peptide bond formation is catalyzed by
rRNA
what enzyme is responsible for joining the tRNA molecule with its amino acid
aminoacyl synthetase
the 5’ cap on an mRNA is important for
- stability of the mRNA molecule
- ribosomal interaction
- intron splicing efficiency
- initiation of translation
what class of RNA is most abundant in cells
rRNA
which part of the tRNA does the amino acid bind to
3’ end
on which molecule is the shine-dalgarno sequence found
mRNA
what connects the sugar-phosphate backbone
phosphodiester bonds
hyperchromic effect
an increased UV absorption due to denaturation
which pair of bases is harder to pull apart
G and C
Tm=
69 + (.41)(%GC)
chromatin
the complex of DNA, chromosomal proteins and RNA within the nucleus
Euchromatin (lighter)
- actively transcribed genes
- condenses and relaxes
11nm fiber
tandem nucleosomes
nucleosome
nucleosome core + 53bp linker DNA
nucleosome core
core histones + 147 bp DNA
nuclear matrix
fibrous network throughout the nucleus that anchors a series of DNA loops
supercoiling
occurs when DNA coils back on itself when it is overwound or underwound
positive supercoiling
same direction as DNA coil so left handed compensates
negative supercoiling
DNA is underwound so right handed compensates
topoisomerase
alter torsional stress in DNA by cutting the DNA backbone
what is the most compacted chromatin
mitotic chromosomes
what are bands
characteristic for a strain of organism and can be used to identify specific chromosomes
endopolyploidy
several rounds of DNA replication without separation of replicated chromosomes
what are puffs
areas where the DNA is loosely coiled so that transcription can occur
telomeres
- provide stability to ends of chromosomes so they aren’t degraded by exonucleases
- prevent chromosomes from joining together
- provide proper replication of end of chromosomes
t-loop
when the 3’ overhang of extra copies in the telomeric sequences loop and pair with another chromosome
theta replication
common in bacteria and other circular DNA
rolling circular replication
the F factor and some viruses
linear eukaryotic replication
for euk chromosomes which have multiple origins for replication
how does theta replication work?
bidirectional replication that results in 2 circular molecules
how does rolling circle replication work?
the replication fork continues around many times producing many strands that can be used as templates to synthesize many double stranded circular DNA
how does linear euk replication work?
- many origins and start at different times
- bidirectionally
DNA polymerase 1
removes primers and replaces with DNA
DNA polymerase 3 simple
DNA synthesis and elongates DNA
phosphodiester bond formation requires
nucleoside triphosphate
initiator protein
binds to origin of replication causing local unwinding and a short stretch of single stranded DNA
helicase
attaches to replication fork and break H-bonds as the replication fork moves along DNA
single stranded binding proteins
coat single stranded DNA to protect and stabilize it to prevent hairpins
gyrase
a topoisomerase that relieves supercoiling ahead of replication fork
DNA polymerases must have what
a 3’OH that they can add nucleotides to
primosome=
helicase and primase
elongation steps
- DNA pol 1 removes primer and fills in the gap
- a nick is missing a sugar phosphate
- DNA ligase seals nick
objective of replication licensing
to make sure each piece of each chromosome is replicated once and only once per cell division in euk cells
replication licensing factor attaches to
each origin of replication early in the replication cycle
replication will only start at
licensed origins
* as replication proceeds from origin the licensing factor is removed
licensing factors are only activated
after mitosis and before replication starts in ell cycle
telomerase extends
the telomere
telomerase
contains RNA which it uses to make several repeats of DNA to extend the 3’ end of the telomere
telomerase is only activated in
gametes
no primers needed for
synthesis of RNA
rNTP
building blocks of RNA
- U instead of T
transcription unit
a segment of DNA that codes for an RNA molecule and the sequences necessary for its transcription
stages of transcription in prokaryotes
- template binding
- chain initiation
- chain elongation
- chain termination
consensus sequence
a sequence that describes the nucleotides most often present in a segment of interest
(in prokaryotes) RNA binds to DNA at
consensus sequence found in promotor
template binding and initiation in bacteria
- core enzyme and sigma associate and bind to promotor
- DNA strands separate making transcription bubble
- sigma dissociates after about 9-12 nucleotides are joined from RNA
- elongation occurs 5’ to 3’ using only core enzyme
Direct repeats
exact copies of sequence
inverted repeats
leads to hairpin formation in the RNA during transcription
inverted repeats are pesent
on the DNA sequence near termination and are transcribed
termination in bacteria using Rho
- Rho binds to the RNA and moves toward the 3’ end and RNA polymerase
- RNA polymerase pauses at termination pin
- Rho has helicase activity that causes the DNA-RNA hybrid to unwind and transcription ends
what is needed at the end in a transcription termination sequence in prokaryotes?
A bunch of U’s at the 3’ end
transcription in Euk happens in
nucleus
mRNA processing occurs in
Euk not Pro
RNA polymerase 1
transcribes rRNA genes
cis elements
- close to coding region
- help cell determine when the gene should be transcribed
- binding sites for proteins
trans-acting elements
- proteins or RNA from other genes
- attach to cis elements
- recruit RNA polymerase to
core basal promotor
- immediately upstream of gene
- where basal transcription apparatus binds
- has TATA box
regulatory promotor
- immediately upstream of core promotor
- variety of consensus sequences
Euk elongations steps
- after ~30 bp are synthesized, RNA polymerase leaves the promotor and begins elongation
- many transcription factors stay bound at the promotor
- transcription bubble contains about 8bp of DNA-RNA hybrid
- structure of the RNA polymerase causes separation of the newly formed RNA strand from the DNA template strand
structure of RNA polymerase II
has its own helicase
what is required for termination of RNA polymerase II
RatI
- it binds and degrades the trailing RNA
processing of pre-mRNA to form mRNA
- capping 5’ end
- PolyA tail added to 3’ end
- removal of introns
promotors can be located
in the coding region
RNA polymerase III
transcribes tRNA, 5S rRNA, and snRNA
RNA primase
lays down the RNA primer since DNA polymerase requires a free 3’OH
Primer
small piece of RNA required for DNA polymerase to begin replication
single stranded binding proteins
binds to single strands of DNA to keep them separated
DNA polymerase 3 (complicated)
attaches to the primer and adds nucleotides
phosphodiester bonds
bonds joinging nucleotides
ligase
seals the new strand by repairing the remaining nicks in the DNA
wobble only happens on
3’ end of codon
R1/2 formula
recombinant + DCO / total times 100
RNAi
in EUK shuts off gene expression using double stranded RNAs
tRNA
transfer RNA
I is only found in
tRNA
importance of capping
- gives mRNA stability
- aids in RNA splicing deficiency
- aids in translation efficiency
capping mRNA
- 1 phosphate is removed from 5’ end
- guanine nucleoside tri-P is added with a 5’-5’ linkage
importance of 3’ poly-A tail
- protects mRNA
- helps initiate translation
- involved in termination of transcription (due to RAT1)
the longer mRNA lives
the more protein made
Rat 1
binds and degrades the trailing RNA
spliceosome
structure at which introns are removed and exons are joined together
snRNPs
small nuclear ribonucleoproteins
snRNAs
have regions complementary to ends of exons, sites in introns, or sites on other snRNAs
a single gene can by spliced multiple times to result in
multiple different proteins
a single pre-mRNA molecule can undergo alternative splicing methods resulting in
different functional mRNAs
viruses have what kind of RNA
double stranded RNA
RNAi does not change …
DNA
amino acids are joined together by
peptide bonds
how many reading frames in DNA
6
due to wobble, a single tRNA can pair with …
more than 1 codon
translation steps
- charging the tRNA
- initiation
- elongation
- termination
shine-dalgarno sequence is found in and important for …
5’ untranslated region and ribosome binding
polycistronic mRNA
1 RNA molecule is produced but contains the info for more than 1 gene then translated into more than 1 gene product
peptidyl transferase activity
when 23S rRNA acts as ribozyme to form the peptide bond between amino acids
translocation of ribosome requires
GTP (energy) and elongation factor
prokaryotic termination
- stop codon at A site
- release factor binds at stop codon
- protein is released from P site
- GTP hydrolysized to GDP
polysomes
multiple ribosomes translating the same mRNA simultaneously
in Pro, transcription and translation can happen same time because
there is no nucleus
ribosome in EUK binds to
cap
ribosome in PRO binds to
shine-delgarno
DNA to mRNA switches
A -> U instead of A -> T
