quiz 6 Flashcards
which contains the genetic material in organisms, DNA, protein, or RNA? Which is the transforming principle in most experiments?
DNA and DNA
Describe the Hammerling experiment (what happened in it and what did it determine)
cut cells of A.crenulata and A.mediterranea and put them together (both alga) and found out the head is still the same regardless of the graft. Discovered that hereditary information is stored in the cell’s nucleus (in the base for alga)
What were the results of Frederick Griffith’s experiment
you could genetically transform bacteria. From Rough strain of streptococcus pneumonia to smooth strain
What is the difference between the S and R strain in strep
S strain has a capsule and is virulent while R does not have capsule and is not virulent
What happened to mice when injected with Live S cells and what happened when injected with Live R cells
Live S cells caused mice death while R cells did not
What happened to mice when injected with heat killed S cells and when injected with Heat killed S cells and Live R cells
With just heat killed S cells had no effect, heat killed S cells+ live R cells cause cell death indicating there is a factor that can convert R cells to S cells found in dead S cells
Describe Avery’s experiments
Avery broke down heat killed S bacteria and destroyed protein, DNA, and RNA one by one and found out that when DNA is destroyed, no transformation occurred therefore DNA was the transforming principle. When Protein or RNA was destroyed, R bacteria still turned into S bacteria
in Avery’s experiements, what enzyme destroyed DNA
DNase
Hershey-Chase experiement labeled DNA and protein with what?
radioactive isotope tracer
what did the Hershey-Chase experiment determine?
determined DNA contained hereditary information and not protein
what are the parts of a virus and what is its role of a virus
Viruses have a protein head and DNA core and its goal is to infect other cells and inject them with their DNA so the cell can make more viruses
what is another name for virus
bacteriophages
What radioactive isotope tracer was used to trace protein and DNA
32P (phosphorus) for DNA and 35S (sulfur) for protein
What happened after infecting E.coli with the viruses that had protein tracers or DNA tracers
For the protein labeled virus, we didn’t see protein enter the E.coli nor did we see progeny with any radioactive tracers
For the DNA labeled virus, we saw the E.coli had radioactive tracers and the progeny viruses had radioactive tracers as well
For Hershey and Chase experiment, when centrifuging viruses mixed with bacteria, what was in the supernatant and what was in the pellet? Which one had the radioactive tracer if we put 32P? how about 35S?
the pellet was bacteria and supernatant was viral protein coats. If 32P then it was pellet showed bacteria with viral DNA (radioactive). If 35S then we saw radioactive viral protein coats in supernatant
Maurice Wilkins and Rosalind Franklin used what method/technique to study DNA structure? What did the technique show?
Used X-ray diffraction and showed an X shaped distribution of spots which meant its Helical structure
Describe X-ray diffraction
X ray beam is directed at a solid molecule and positions of atoms are deduced by the pattern produced on photographic film
Using Maurice Wilkins’ DNA fibers, what did Franklin discover about the helix
the molecule was 2nm in diameter and its a complete turn every 3.4 nm
how many nucleotides per turn? And how many nm is between each nucleotide
10 nucleotides per turn to .34nm between each nucleotide
Did Watson and Crick person a single experiment related to DNA
no
What did Watson and Crick propose?
Double helix structure
Why did Franklin not receive a nobel prize unlike watson and crick
She already passed away at the time of the award
DNA is what kind of macromolecule
nucleic acid
what is a nucleotide composed of (and to which carbon are the groups attached to)
5 carbon sugar called deoxyribose
Phosphate (PO4) at 5’
Nitrogenous base (Adenine, thymine, cytosine, guanine)
Free Hydroxyl group (OH) at 3’
which nitrogenous bases are purines. How are purines structurally different than pyrimidines? How do you tell the difference between the 2 purines
Adenine and Guanine and purines are 2 ring structures. Guanine has a ketone while adenine does not
which nitrogenous bases are pyrimidines? How are pyrimidines structurally different than purines? How do you tell the difference between the 2 pyrimidines that we need to know?
Cytosine, thymine, and Uracil, and pyrimidines are 1 ring structures. Uracil have 2 double bond O’s and Cytosine has an amine group (NH2)
A phosphodiester bonds connects 2 _____
It is formed between a _____ group at the 5’ and a ____ at the 3’
connects 2 adjacent nucleotides and is formed between a phosphate group at the 5’ and a OH group at the 3’
how many hydrogen bonds between Adenine and thymine
2
how many hydrogen bonds between Cytosine and guanine
3
Pairs are made up of
A)purine-purine and pyr-pyr
B)purine-pyr
and why?
purine and pyr so the DNA molecule can be uniformly 2nm in diameter
how do you know which end of the double helix is which
5’ will be the phosphate end and 3’ will be the OH end
DNA strands are (parallel or antiparallel) with each other
anti parallel
What is the complimentary strand to this
5’ AAGTCTA 3’
3’ TTCAGAT 5’
why can’t C pair with A nor G pair with T
hydrogen bonding requirements
What are Chargaff’s rules
Amount of adenine = amount of thymine
amount of cytosine = amount of guanine
always an equal proportion of purines and pyrimidines
is this true
A+C=T+G and it will always end up 50%=50%
yes
How many hydrogen bonds in 5’ AATTGGCC 3”
how about 5” TAGCAT 3’
which strand would be easier to denature?
20 bonds and 14 bonds therefore the 2 strand will be easier to denature
Does a polynucleotide chain of DNA have polarity? If so then why?
Yes, because one end is phosphate (5’) and the other is hydroxyl (3’)
what is the difference between a major groove and minor groove
major groove is one full turn (3.4nm) and minor groove is just the a half turn? not sure
Watson and Crick recognized genetic information is coded into what?
DNA by the linear sequence of the 4 nucleotides, and there were a infinite number of different sequences to be written
which dna replication model requires the most energy
dispersive model
what determines the sequence of bases in the new strand (daughter)
the template (parental) strand
what are the 3 DNA replication models and describe each of them
conservative: 2 strands unwind and serve as templates but then rewind to a old molecule.
semiconservative: 2 strands unwind and the new dna molecules wind with the templates
dispersive: neither parental strand is conserved and both chains of each replicated model contain old and new segments
Describe Meselson and Stahl experiment
bacterial cells were grown in N15 then switched to N14 then DNA was extracted at 0,20,40mins, then centrifuged. We found 1 band (N15/N15) at 0, 1 bands(N14/N15) at 20, 2 bands (N14/N14 and N14/N15) which shows the semiconservative model is true
When we centrifuge in Meselson and Stahl’s experiment, which DNA components (N15/N15, N14/N15, N14/N14) will be at the top of the tube and which will be at the bottom
from top to bottom, its 14/14, 14/15, 15/15
why did Meselson and Stahl take out dna samples at 20min intervals
thats the amount of time for bacteria to go through cell cycle
in each interval of meselson and stahl’s experiment, what would we expect to see if it was conservative model? how about dispersive?
for conservative we would see 15/15 at 0, 15/15 and 14/14 at 20 and 40
for dispersive we would see 15/15 at 0, and 14/15 at 20 and 40
what is the job of DNA polymerase
to assemble complementary polynucleotide chains from individual deoxyribose nucleotides
what are the 4 different deoxyribose nucleotide triphosphates
dATP dGTP dCTP dTTP
DNA polymerase adds nucleotides to which end of the nucleotide chain
an existing 3’ end, hydroxyl group
DNA polymerase assembles nucleotide chains in what direction
5’ –> 3’
how is the new strand read? and why
because its antiparallel, its read from 5’ to 3’
where do we get energy to make nucleotide chains
hydrolysis of pyrophosphate to 2Pi
how can we imagine DNA polymerase’s structure
its hand shapped with cupping our hand where the template and DNA lies over the palm in a groove formed by finger and thumb
What meets at the active site of DNA polymerase
the template strand and the 3’OH of the new strand
Where is the relative location of the sliding DNA clamp?
behind the DNA polymerase relative to forward movement of DNA synthesis
what is the role of sliding DNA clamp. Also what does it look like
to ensure the DNA polymerase doesn’t fall off and to increase rate of DNA synthesis. It looks like a ring around the DNA strand
What is the research question and the conclusion for the DNA sliding clamp
how is the sliding clamp loaded and unloaded onto replicating DNA?
The efficient unloading of sliding clamps by clamp loaders once DNA polymerase has dissociated from DNA is important efficiency of DNA replication
what loads and unloads DNA sliding clamps?
clamp loaders
Does DNA polymerase add nucleotides to a new strand? (for example a strand with no complementary nucleotides on it)
no
What is the role of an RNA primer
its a short chain of RNA to jumpstart DNA polymerase, and later the RNA primers are replaced with DNA
what enzyme makes the RNA primer and what does it resemble
RNA primase and it resembles DNA polymerase
what is the ori
origin of replication of DNA unwinding in bacterial chromosome
what is the role of DNA helicase and what does it produce
to unwind DNA strands producing a y shaped replication fork
what is the role of single stranded binding proteins (ssb)
coats the exposed single stranded DNA segments preventing them from pairing again
What is the role of topoisomerase
cuts and rejoins DNA to prevent twisting in circular bacterial chromosomes
does helicase require ATP hydrolysis
yes to fuel its energy
What is the difference between leading and lagging strand
leading strand is making a new DNA strand in the direction of unwinding (towards the fork) and is one long chain
lagging strand requires multiple primers and is discontinuous and is synthesized in the opposite direction of the unwinding
is the 3’ end of the template the leading or lagging strand
leading
what are okazaki fragments
fragments of DNA on the lagging strand that are 100-200 base pairs long
what causes the negative charge on DNA
the phosphate group
describe electrophoresis
use agarose gel to put in DNA and use an electric field to move DNA from - end to + end. This way we can see the size of dna or number of nucleotides since larger numbers of Base pairs wont move as much as smaller segments
how do we see the dna in electrophoresis
we add ethidium bromide so it intercalates between the base pairs and shine a UV light
how do we estimate the size or number of pairs of an unknown dna strand
we use molecular weight marker as a control and estimate from that
what 3 things do we need for dna replication
something to copy (parental dna molecule)
something to do the copying (dna polymerase)
building blocks to make the copy (nucleotide triphosphates)
what is a density gradient and what experiement used it
a gradient with varying densities, used in meselson’s and stahls experiement
if you have 22% adenine, what are the other percentages of the other nucleotides
22 thymine, 28 cytosine and 28guanine
describe the lytic life cycle
bacteriophage injects DNA to bacteria, then bacteria makes copies of that DNA and virus proteins capsules, then packs the DNA in the virus, then lysis releasing the viruses. Injection then expression/replication then packaging then lysis
what did Rosalind Franklin not know about the DNA structure
if the phosphate group was inside or outside the DNA molecule
what are the 3 models of DNA replication and explain all 3.
Conservative: DNA unwinds and act as template strand for new strands but then rewind to have the old parent strands together
semi conservative: parent unwinds and both new strands have a parent and daughter strand
dispersive: daughter strands have parts of parent strands
which model of dna replication did watson and crick propose
semi conservative
Describe Meselson and Stahl’s experiment
Bacteria were grown in N15 and then switched to N14 and samples were taken every 20mins to see the new daughter bands of Bacterial cell DNA (E.coli)
how long was each interval in meselson and stahl’s experiment and why was it that long?
20 mins because it took 20mins to go through dna replication in E.coli
what were the results of Meselson and Stahl’s experiment and which mode of replication matches it
in round 0, we found 15/15 heavy bottom band, then round 1 was 15/14 hybrid middle band, then round 2 was 15/14 and 14/14 2 bands so it was semi conservative
which modes of replication show a hybrid band after the first round of replication
dispersive and semi-conservative
what enzyme adds complementary deoxyribosenucleotides and makes polynucleotide chains
DNA polymerase
How do we get the energy for DNA chain elongation reaction
hydrolysis of pyrophosphate
what are the 3 rules of dna replication
Must be added to an exisitng 3’ OH end, so its made 5’ to 3’
a 3’ OH group is the “newest” end of the new DNA strand while the “oldest” end is the exposed 5’ triphosphate
DNA strands run antiparallel so the template is read 3’ to 5’
what bactiera do we use for the prokaryotic replication model
E.coli
is prokaryote dna circular or linear
circular
is prokaryotic dna replication bi directionally or uni
bidirectional or bilateral
what is a replicon
DNA controlled by an origin, a complex that actually does dna replication at the origin and stops at the termination
Eukaryotes usually have ___, ____ chromosomes with ____ origins of replication
eukaryotes usually have multiple, large chromosomes with multiple origins of replication
is eukaryotic DNA linear or circular
linear
the basic enzymology of eukaryotic replication and prokaryotic replication are similar, except….
in eukaryotic replication, it requires new enzymatic activity for dealing with the ends only (telomerase)
what is a replisome and what are the main components of it (and the subcomponents of those components)
enzymes involved in DNA replication form a macromolecular assembly
2 main components: Primosome (made of primase, helicase, ssb, topoisomerase)
complex of 2 DNA polymerase 3 (one for each strand)
which enzyme initiates all new strands
primase
What are the 3 different DNA polymerases and what are the roles of them
DNA pol 1: acts on lagging strand to remove primers and replace them with DNA
DNA pol 2: involved in DNA repair processes
DNA pol 3: main replication enzyme
All 3 DNA polymerases have what in common and what unique thing does pol 1 have
they all have 3’ to 5’ exonuclease activity - proofreading
DNA pol 1 has 5’ to 3’ exonuclease activity
Primase synthesizes RNA primer in what direction
5’ to 3’
what is DNA ligase
seals nicks left between adjacent fragments after RNA primers replaced with DNA
what is dna gyrase
relieves torque, just like dna topoisomerase
why is there shortening of chromosomes after cell division
you can’t duplicate the last section of the lagging strand because when the terminal primer is removed, it leaves a gap at the 3’ end on the lagging strand and the 5’ end of the new strand on the lagging strand
what solves the problem of shortening of chromosomes
telomeres which protect ends of chromosomes from nucleases and maintain integrity of linear chromosome
what are telomeres
a noncoding DNA buffer consisting of short repeating sequences (telomere repeats)
what is telomerase
adds telomere repeats to chromosomes ends
how does telomerase work?
an RNA section/template binds to DNA and is the template for addition of telomere repeats
when do we see telomerase being acitve
in rapidly dividing embryonic cells, germ cells, and in cancerous somatic cells
what does it mean for telomerase to be developmentally regulated
theres a relationship between senescence (aging) and telomere length
what are mutagens
any agent that increases the number of mutations above background level
what is the proofreading mechanism
allows DNA polymerase to back up and remove mispaired nucleotides
if a newly added nucleotide is mismatched, dna polymerases reverses using which nuclease activity
3’ to 5’ exonuclease activity
what dna repair mechanisms correct base pair mismatches even after proofreading
mismatch repair
can there still be errors after proofreading?
yes
what happens in mismatch repairs
repair enzymes cut the new DNA strand on each side of the mismatch, then removes it and DNA polymerase fills the gap and DNA ligase seals it up
what is base excision repair
mechanisms repair nonbulky damage by removing the erroneous base and replacing it with the correct one based on complementary pairing rules
what is nucleotide exicison repair
repairs bulky distortions in dna (such as thymine dimers) by removing an entire segment of DNA
what is a primary source of mutations
errors that remain after proofreading and DNA repair
what is the ultimate source of variability acted on by natural selection
mutations
how did we connect genes to proteins
Garrod connected alkaptonuria to a recessive allele correlating to a lacking of an enzyme so we connected genes to enzymes which are proteins
What is the central dogma francis crick proposed
flow of information is from DNA to RNA to protein
what is the difference between transcription and translation
transcription is information on DNA strand is copied into complementary RNA strand
Translation is RNA copy being used to assemble amino acids into a polypeptide
does transcription and translation happen at the same time in eukaryotes? How about prokaryotes?
not in eukaryotes, but yes in prokaryotes, called translation transcription coupling
Describe transcription and translation in eukaryotes
in the nucleus, DNA produces precursor mRNA then altered to make functional mRNA then exits nucleus for translation by ribosomes to make polypeptide
how does pre mRNA turn into functional mRNA
pre mRNA ends are modified and extra segments are removed by RNA processing
is pre mRNA produced in prokaryotes
no
there are 6 types of RNA, name them and their function
messenger (mRNA) information to make polypeptide
Ribosomal (rRNA) information made of ribosomes
transfer (tRNA) read nucleotides and translate it into amino acids
small nuclear RNA (snRNA) process pre mRNA by splicing
signal recognition particle RNA binds ribosomes to RNA
micro RNA (miRNA)
how many different amino acids can be made from mRNA
20
what is genetic code
nucleotide information that specifies the amino acid sequence
what is a codon
three letter word (triplet)
3 letter codons in DNA are transcribed into complementary three letter RNA codons T/F
true
how does dna pol 3 move in the same direction in the leading and lagging strand
lagging strand loops
what does the DNA alphabet consist of ? What does the RNA alphabet consist of
ATCG and AUCG
What is the DNA template and the RNA code for the start codon/initiator codon and which amino acid does it code for
The DNA template is TAC while the RNA code is AUG and codes for Met
what are the 3 RNA stop codons
UAA UAG and UGA
is the stop codon an amino acid?
no
how many difference combinations are there in mRNA
4^3 so 64
how many sense codons are there and what are sense codons
61 sense codons and sense codons are codons that specify amino acids
what is degeneracy
many amino acids (except Met and Trp) are represented by more than one codon
what does it mean for genetic code to be commaless
no indicator to mark the end of one codon and beginning of the next
what does it mean for genetic code to be universla
essentially the same in all living organisms and viruses
what are the two main parts of the gene
promoter (control sequence for transcription) transcription unit (section of the gene that is copied into an RNA molecule)
what are the 3 stages of transcription
initiation
elongation
termination
How many types of RNA polymerase in prokaryotic transcription
one type
does initiation of mRNA synthesis require a primer? What else does it require?
no, it requires a promoter, start site, termination site
what is needed for initiation in eukaryotic
RNA polymerase 2 needs to get to a promoter to form initiation complex at promoter to initiate gene expression
What are the 3 different RNA polymerases and what are their roles in eukaryotic transcription
RNA pol 1 transcribes rRNAs
RNA pol 2 transcribes mRNA
RNA pol 3 transcribes tRNA
what is the difference in prokaryotic and eukaryotic transcription
prokaryotes have single factor but eukaryotes require a host of transcription factors
how is RNA pol 2 difference in eukaryotes and prokaryotes
eukaryotes, RNA pol 2 can’t bind directly to DNA (transcription factors must bind to promoter), in bacteria RNA pol binds directly to DNA
how is there termination in prokaryotic transcription
formation of hairpin loop in AU base pairing
how is there termination in transcription for eukaryotes
capping of 5’ end and addition of poly A tail at 3’ end
give the RNA complementary strand to this DNA strand
3’ AAATTTCCCGGG 5”
5’ UUUAAAGGGCCC 3’
Does adenyl cyclase convert ATP to cAMP or AMP to cAMP
ATP to cAMP
