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BIOL 2325 > quiz 6 > Flashcards

quiz 6 Flashcards

1
Q

which contains the genetic material in organisms, DNA, protein, or RNA? Which is the transforming principle in most experiments?

A

DNA and DNA

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2
Q

Describe the Hammerling experiment (what happened in it and what did it determine)

A

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)

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3
Q

What were the results of Frederick Griffith’s experiment

A

you could genetically transform bacteria. From Rough strain of streptococcus pneumonia to smooth strain

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4
Q

What is the difference between the S and R strain in strep

A

S strain has a capsule and is virulent while R does not have capsule and is not virulent

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5
Q

What happened to mice when injected with Live S cells and what happened when injected with Live R cells

A

Live S cells caused mice death while R cells did not

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6
Q

What happened to mice when injected with heat killed S cells and when injected with Heat killed S cells and Live R cells

A

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

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7
Q

Describe Avery’s experiments

A

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

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8
Q

in Avery’s experiements, what enzyme destroyed DNA

A

DNase

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9
Q

Hershey-Chase experiement labeled DNA and protein with what?

A

radioactive isotope tracer

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10
Q

what did the Hershey-Chase experiment determine?

A

determined DNA contained hereditary information and not protein

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11
Q

what are the parts of a virus and what is its role of a virus

A

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

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12
Q

what is another name for virus

A

bacteriophages

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13
Q

What radioactive isotope tracer was used to trace protein and DNA

A

32P (phosphorus) for DNA and 35S (sulfur) for protein

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14
Q

What happened after infecting E.coli with the viruses that had protein tracers or DNA tracers

A

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

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15
Q

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?

A

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

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16
Q

Maurice Wilkins and Rosalind Franklin used what method/technique to study DNA structure? What did the technique show?

A

Used X-ray diffraction and showed an X shaped distribution of spots which meant its Helical structure

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17
Q

Describe X-ray diffraction

A

X ray beam is directed at a solid molecule and positions of atoms are deduced by the pattern produced on photographic film

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18
Q

Using Maurice Wilkins’ DNA fibers, what did Franklin discover about the helix

A

the molecule was 2nm in diameter and its a complete turn every 3.4 nm

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19
Q

how many nucleotides per turn? And how many nm is between each nucleotide

A

10 nucleotides per turn to .34nm between each nucleotide

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20
Q

Did Watson and Crick person a single experiment related to DNA

A

no

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21
Q

What did Watson and Crick propose?

A

Double helix structure

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22
Q

Why did Franklin not receive a nobel prize unlike watson and crick

A

She already passed away at the time of the award

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23
Q

DNA is what kind of macromolecule

A

nucleic acid

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24
Q

what is a nucleotide composed of (and to which carbon are the groups attached to)

A

5 carbon sugar called deoxyribose
Phosphate (PO4) at 5’
Nitrogenous base (Adenine, thymine, cytosine, guanine)
Free Hydroxyl group (OH) at 3’

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25
Q

which nitrogenous bases are purines. How are purines structurally different than pyrimidines? How do you tell the difference between the 2 purines

A

Adenine and Guanine and purines are 2 ring structures. Guanine has a ketone while adenine does not

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26
Q

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?

A

Cytosine, thymine, and Uracil, and pyrimidines are 1 ring structures. Uracil have 2 double bond O’s and Cytosine has an amine group (NH2)

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27
Q

A phosphodiester bonds connects 2 _____

It is formed between a _____ group at the 5’ and a ____ at the 3’

A

connects 2 adjacent nucleotides and is formed between a phosphate group at the 5’ and a OH group at the 3’

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28
Q

how many hydrogen bonds between Adenine and thymine

A

2

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29
Q

how many hydrogen bonds between Cytosine and guanine

A

3

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30
Q

Pairs are made up of
A)purine-purine and pyr-pyr
B)purine-pyr
and why?

A

purine and pyr so the DNA molecule can be uniformly 2nm in diameter

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31
Q

how do you know which end of the double helix is which

A

5’ will be the phosphate end and 3’ will be the OH end

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32
Q

DNA strands are (parallel or antiparallel) with each other

A

anti parallel

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33
Q

What is the complimentary strand to this

5’ AAGTCTA 3’

A

3’ TTCAGAT 5’

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34
Q

why can’t C pair with A nor G pair with T

A

hydrogen bonding requirements

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35
Q

What are Chargaff’s rules

A

Amount of adenine = amount of thymine
amount of cytosine = amount of guanine
always an equal proportion of purines and pyrimidines

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36
Q

is this true

A+C=T+G and it will always end up 50%=50%

A

yes

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37
Q

How many hydrogen bonds in 5’ AATTGGCC 3”
how about 5” TAGCAT 3’
which strand would be easier to denature?

A

20 bonds and 14 bonds therefore the 2 strand will be easier to denature

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38
Q

Does a polynucleotide chain of DNA have polarity? If so then why?

A

Yes, because one end is phosphate (5’) and the other is hydroxyl (3’)

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39
Q

what is the difference between a major groove and minor groove

A

major groove is one full turn (3.4nm) and minor groove is just the a half turn? not sure

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40
Q

Watson and Crick recognized genetic information is coded into what?

A

DNA by the linear sequence of the 4 nucleotides, and there were a infinite number of different sequences to be written

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41
Q

which dna replication model requires the most energy

A

dispersive model

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42
Q

what determines the sequence of bases in the new strand (daughter)

A

the template (parental) strand

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43
Q

what are the 3 DNA replication models and describe each of them

A

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

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44
Q

Describe Meselson and Stahl experiment

A

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

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45
Q

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

A

from top to bottom, its 14/14, 14/15, 15/15

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46
Q

why did Meselson and Stahl take out dna samples at 20min intervals

A

thats the amount of time for bacteria to go through cell cycle

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47
Q

in each interval of meselson and stahl’s experiment, what would we expect to see if it was conservative model? how about dispersive?

A

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

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48
Q

what is the job of DNA polymerase

A

to assemble complementary polynucleotide chains from individual deoxyribose nucleotides

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49
Q

what are the 4 different deoxyribose nucleotide triphosphates

A

dATP dGTP dCTP dTTP

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50
Q

DNA polymerase adds nucleotides to which end of the nucleotide chain

A

an existing 3’ end, hydroxyl group

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51
Q

DNA polymerase assembles nucleotide chains in what direction

A

5’ –> 3’

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52
Q

how is the new strand read? and why

A

because its antiparallel, its read from 5’ to 3’

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53
Q

where do we get energy to make nucleotide chains

A

hydrolysis of pyrophosphate to 2Pi

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54
Q

how can we imagine DNA polymerase’s structure

A

its hand shapped with cupping our hand where the template and DNA lies over the palm in a groove formed by finger and thumb

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55
Q

What meets at the active site of DNA polymerase

A

the template strand and the 3’OH of the new strand

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56
Q

Where is the relative location of the sliding DNA clamp?

A

behind the DNA polymerase relative to forward movement of DNA synthesis

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57
Q

what is the role of sliding DNA clamp. Also what does it look like

A

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

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58
Q

What is the research question and the conclusion for the DNA sliding clamp

A

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

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59
Q

what loads and unloads DNA sliding clamps?

A

clamp loaders

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60
Q

Does DNA polymerase add nucleotides to a new strand? (for example a strand with no complementary nucleotides on it)

A

no

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61
Q

What is the role of an RNA primer

A

its a short chain of RNA to jumpstart DNA polymerase, and later the RNA primers are replaced with DNA

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62
Q

what enzyme makes the RNA primer and what does it resemble

A

RNA primase and it resembles DNA polymerase

63
Q

what is the ori

A

origin of replication of DNA unwinding in bacterial chromosome

64
Q

what is the role of DNA helicase and what does it produce

A

to unwind DNA strands producing a y shaped replication fork

65
Q

what is the role of single stranded binding proteins (ssb)

A

coats the exposed single stranded DNA segments preventing them from pairing again

66
Q

What is the role of topoisomerase

A

cuts and rejoins DNA to prevent twisting in circular bacterial chromosomes

67
Q

does helicase require ATP hydrolysis

A

yes to fuel its energy

68
Q

What is the difference between leading and lagging strand

A

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

69
Q

is the 3’ end of the template the leading or lagging strand

A

leading

70
Q

what are okazaki fragments

A

fragments of DNA on the lagging strand that are 100-200 base pairs long

71
Q

what causes the negative charge on DNA

A

the phosphate group

72
Q

describe electrophoresis

A

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

73
Q

how do we see the dna in electrophoresis

A

we add ethidium bromide so it intercalates between the base pairs and shine a UV light

74
Q

how do we estimate the size or number of pairs of an unknown dna strand

A

we use molecular weight marker as a control and estimate from that

75
Q

what 3 things do we need for dna replication

A

something to copy (parental dna molecule)
something to do the copying (dna polymerase)
building blocks to make the copy (nucleotide triphosphates)

76
Q

what is a density gradient and what experiement used it

A

a gradient with varying densities, used in meselson’s and stahls experiement

77
Q

if you have 22% adenine, what are the other percentages of the other nucleotides

A

22 thymine, 28 cytosine and 28guanine

78
Q

describe the lytic life cycle

A

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

79
Q

what did Rosalind Franklin not know about the DNA structure

A

if the phosphate group was inside or outside the DNA molecule

80
Q

what are the 3 models of DNA replication and explain all 3.

A

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

81
Q

which model of dna replication did watson and crick propose

A

semi conservative

82
Q

Describe Meselson and Stahl’s experiment

A

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)

83
Q

how long was each interval in meselson and stahl’s experiment and why was it that long?

A

20 mins because it took 20mins to go through dna replication in E.coli

84
Q

what were the results of Meselson and Stahl’s experiment and which mode of replication matches it

A

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

85
Q

which modes of replication show a hybrid band after the first round of replication

A

dispersive and semi-conservative

86
Q

what enzyme adds complementary deoxyribosenucleotides and makes polynucleotide chains

A

DNA polymerase

87
Q

How do we get the energy for DNA chain elongation reaction

A

hydrolysis of pyrophosphate

88
Q

what are the 3 rules of dna replication

A

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’

89
Q

what bactiera do we use for the prokaryotic replication model

A

E.coli

90
Q

is prokaryote dna circular or linear

A

circular

91
Q

is prokaryotic dna replication bi directionally or uni

A

bidirectional or bilateral

92
Q

what is a replicon

A

DNA controlled by an origin, a complex that actually does dna replication at the origin and stops at the termination

93
Q

Eukaryotes usually have ___, ____ chromosomes with ____ origins of replication

A

eukaryotes usually have multiple, large chromosomes with multiple origins of replication

94
Q

is eukaryotic DNA linear or circular

A

linear

95
Q

the basic enzymology of eukaryotic replication and prokaryotic replication are similar, except….

A

in eukaryotic replication, it requires new enzymatic activity for dealing with the ends only (telomerase)

96
Q

what is a replisome and what are the main components of it (and the subcomponents of those components)

A

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)

97
Q

which enzyme initiates all new strands

A

primase

98
Q

What are the 3 different DNA polymerases and what are the roles of them

A

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

99
Q

All 3 DNA polymerases have what in common and what unique thing does pol 1 have

A

they all have 3’ to 5’ exonuclease activity - proofreading

DNA pol 1 has 5’ to 3’ exonuclease activity

100
Q

Primase synthesizes RNA primer in what direction

A

5’ to 3’

101
Q

what is DNA ligase

A

seals nicks left between adjacent fragments after RNA primers replaced with DNA

102
Q

what is dna gyrase

A

relieves torque, just like dna topoisomerase

103
Q

why is there shortening of chromosomes after cell division

A

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

104
Q

what solves the problem of shortening of chromosomes

A

telomeres which protect ends of chromosomes from nucleases and maintain integrity of linear chromosome

105
Q

what are telomeres

A

a noncoding DNA buffer consisting of short repeating sequences (telomere repeats)

106
Q

what is telomerase

A

adds telomere repeats to chromosomes ends

107
Q

how does telomerase work?

A

an RNA section/template binds to DNA and is the template for addition of telomere repeats

108
Q

when do we see telomerase being acitve

A

in rapidly dividing embryonic cells, germ cells, and in cancerous somatic cells

109
Q

what does it mean for telomerase to be developmentally regulated

A

theres a relationship between senescence (aging) and telomere length

110
Q

what are mutagens

A

any agent that increases the number of mutations above background level

111
Q

what is the proofreading mechanism

A

allows DNA polymerase to back up and remove mispaired nucleotides

112
Q

if a newly added nucleotide is mismatched, dna polymerases reverses using which nuclease activity

A

3’ to 5’ exonuclease activity

113
Q

what dna repair mechanisms correct base pair mismatches even after proofreading

A

mismatch repair

114
Q

can there still be errors after proofreading?

A

yes

115
Q

what happens in mismatch repairs

A

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

116
Q

what is base excision repair

A

mechanisms repair nonbulky damage by removing the erroneous base and replacing it with the correct one based on complementary pairing rules

117
Q

what is nucleotide exicison repair

A

repairs bulky distortions in dna (such as thymine dimers) by removing an entire segment of DNA

118
Q

what is a primary source of mutations

A

errors that remain after proofreading and DNA repair

119
Q

what is the ultimate source of variability acted on by natural selection

A

mutations

120
Q

how did we connect genes to proteins

A

Garrod connected alkaptonuria to a recessive allele correlating to a lacking of an enzyme so we connected genes to enzymes which are proteins

121
Q

What is the central dogma francis crick proposed

A

flow of information is from DNA to RNA to protein

122
Q

what is the difference between transcription and translation

A

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

123
Q

does transcription and translation happen at the same time in eukaryotes? How about prokaryotes?

A

not in eukaryotes, but yes in prokaryotes, called translation transcription coupling

124
Q

Describe transcription and translation in eukaryotes

A

in the nucleus, DNA produces precursor mRNA then altered to make functional mRNA then exits nucleus for translation by ribosomes to make polypeptide

125
Q

how does pre mRNA turn into functional mRNA

A

pre mRNA ends are modified and extra segments are removed by RNA processing

126
Q

is pre mRNA produced in prokaryotes

A

no

127
Q

there are 6 types of RNA, name them and their function

A

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)

128
Q

how many different amino acids can be made from mRNA

A

20

129
Q

what is genetic code

A

nucleotide information that specifies the amino acid sequence

130
Q

what is a codon

A

three letter word (triplet)

131
Q

3 letter codons in DNA are transcribed into complementary three letter RNA codons T/F

A

true

132
Q

how does dna pol 3 move in the same direction in the leading and lagging strand

A

lagging strand loops

133
Q

what does the DNA alphabet consist of ? What does the RNA alphabet consist of

A

ATCG and AUCG

134
Q

What is the DNA template and the RNA code for the start codon/initiator codon and which amino acid does it code for

A

The DNA template is TAC while the RNA code is AUG and codes for Met

135
Q

what are the 3 RNA stop codons

A

UAA UAG and UGA

136
Q

is the stop codon an amino acid?

A

no

137
Q

how many difference combinations are there in mRNA

A

4^3 so 64

138
Q

how many sense codons are there and what are sense codons

A

61 sense codons and sense codons are codons that specify amino acids

139
Q

what is degeneracy

A

many amino acids (except Met and Trp) are represented by more than one codon

140
Q

what does it mean for genetic code to be commaless

A

no indicator to mark the end of one codon and beginning of the next

141
Q

what does it mean for genetic code to be universla

A

essentially the same in all living organisms and viruses

142
Q

what are the two main parts of the gene

A 
promoter (control sequence for transcription) 
transcription unit (section of the gene that is copied into an RNA molecule)
143
Q

what are the 3 stages of transcription

A

initiation
elongation
termination

144
Q

How many types of RNA polymerase in prokaryotic transcription

A

one type

145
Q

does initiation of mRNA synthesis require a primer? What else does it require?

A

no, it requires a promoter, start site, termination site

146
Q

what is needed for initiation in eukaryotic

A

RNA polymerase 2 needs to get to a promoter to form initiation complex at promoter to initiate gene expression

147
Q

What are the 3 different RNA polymerases and what are their roles in eukaryotic transcription

A

RNA pol 1 transcribes rRNAs
RNA pol 2 transcribes mRNA
RNA pol 3 transcribes tRNA

148
Q

what is the difference in prokaryotic and eukaryotic transcription

A

prokaryotes have single factor but eukaryotes require a host of transcription factors

149
Q

how is RNA pol 2 difference in eukaryotes and prokaryotes

A

eukaryotes, RNA pol 2 can’t bind directly to DNA (transcription factors must bind to promoter), in bacteria RNA pol binds directly to DNA

150
Q

how is there termination in prokaryotic transcription

A

formation of hairpin loop in AU base pairing

151
Q

how is there termination in transcription for eukaryotes

A

capping of 5’ end and addition of poly A tail at 3’ end

152
Q

give the RNA complementary strand to this DNA strand

3’ AAATTTCCCGGG 5”

A

5’ UUUAAAGGGCCC 3’

153
Q

Does adenyl cyclase convert ATP to cAMP or AMP to cAMP

A

ATP to cAMP

BIOL 2325 (9 decks)

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