Genetic Lecture 4 Flashcards

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1
Q

Order of experiments for the discovery of DNA?

A

Isolation of nucleic, transformation of bacteria, purification of DNA: the transforming principle, radioactive DNA, X-ray diffraction, DNA model, semi-conservative DNA replication, and molecular components of DNA replication

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2
Q

Freidrich Miescher

A

Wanted to become a doctor but had troubles hearing so he became a scientist (1869). Scientists at this time were still debating the concept of the cell.

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3
Q

What was Freidrich Miescher Question?

A

What’s in the nucleus?

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4
Q

What was Freidrich Miescher experiment?

A

His supervisor told him to study nuclein and told him he could find it in white blood cells. So he collected bandages and scraped pus off of it. Then he put it in a tube and purified the nuclein by using alcohol and detergent (a method still used today).

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5
Q

What was Freidrich Miescher results?

A

Isolated a new molecule from the nucleus – nuclein (now known as DNA). He came up with the chemical composition of nuclear acids. Made up of hydrogen, oxygen, nitrogen and
phosphorus. Unique ratio of phosphorus to nitrogen. He also found that salmon sperm was a fish source of nuclein. However, he didn’t know the importance of nuclein.

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6
Q

Fred Griffith

A

Griffith wanted to make a vaccine against Diplococcus pneumoniae, the causative agent of pneumonia. He wished to kill the deadly bacterium by heating to make a safe vaccine. By doing this he wanted to kill pathogens by heat and put in the vaccine so when the actual thing comes you already have antibodies for it (1928).

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7
Q

What are the two strains of bacteria that Griffith used?

A

A harmless R-strain of D. pneumoniae produced rough shaped colonies on a petri plate. R stands for rough and it doesn’t have a sugar coat. A virulent S-strain of the bacterium produced smooth shaped colonies on a petri plate. S stands for the sugar coat it forms.

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8
Q

What was Griffith’s experiment?

A

Griffith injects live and heat- killed
Diplococcus pneumoniae into mice. #1 Living S cells = mouse dies. #2 Living R cells= mouse healthy. #3 Heat-killed S cells= mouse health. #4 mixture of heat killed S cells and living R cells=mouse dies but living S cells are present.

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9
Q

Interpretation of Griffith’s Experiment?

A

Q. Perhaps, the heat-killed S-cells in the mixture in Expt. #4 were not really dead?
A. Not true, because in Expt. #3, the mice injected with heat killed S-cells did not die.
Q. Perhaps, the R-cells in the mixture in Expt. #4 had mutated into the killer form?
A. Not true; Expt. #2 serves as a “control”.

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10
Q

Conclusion from Griffith’s Experiment?

A

The ability to cause infection has been transferred from the dead S-cells to the harmless R-cells. The R-cells had been “Transformed”, i.e., a permanent change in the hereditary system of the R-strain of the
bacterium. Something transferred from the dead S cells to harmless R cells that makes them pathogenic/virulent. But he didn’t know if the transforming principle was protein or DNA.

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11
Q

Transformation?

A

The transfer of exogenous DNA into a host cell, thereby causing a permanent change in the hereditary system of the bacteria.

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12
Q

What was Oswald Avery’s experiment?

A

He repeated Griffith’s 4th experiment. However, instead he did his experiment in vitro. He added detergent to heated s cells and isolated the lysate (centerfige) then mixed lysate with the R cells, and it transformed the R cells into S cells.

In lysate we have many different things: protein, DNA, RNA, and the sugar coat. To figure out the principle you just eliminate things one by one. First enzyme chews up the coat sugars, then mix with the R cells again. Repeat until it’s just the DNA and RNA. Then purify them with alcohol, then put into water. Then destroyed RNA by RNase. DNA still results in S cells, then remove it and get R cells.

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13
Q

In Vitro

A

In glass. It’s easier to control the variables and isolate the parts needed.

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14
Q

In Vito

A

In animal/ living thing.

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15
Q

Avery’s Results (1944)?

A

Figured out it was DNA bringing the info from one generation to the next. However, some people still thought the DNA was doing something to the R cells turning them on and off. Because it’s not complex enough to be doing all of that. Thought it was protein that was the principle.

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16
Q

What strain of DNA is infectious?

A

The S strain because it has the sugar coat to protect it from the host’s immune system.

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17
Q

What did Avery mix with the R cells?

A

Lysate

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18
Q

What are viruses composed of?

A

Nucleic Acid (DNA OR RNA) and Protein

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19
Q

What did Hershey and Chase use in their Experiment?

A

Using a virus called bacteriophage that attacks bacteria. It’s made of a capsule and they land on bacteria and inject their DNA into the bacteria. Then it starts to make more of the virus and then the bacteria bursts open, freeing a whole bunch of phage. It’s a chain reaction.

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20
Q

How did they differentiate protein and DNA?

A

Proteins have suppler from the dicysteine bonds which have cystene which have sulphur. They used an isotope of sulphur that’s radioactive. Incubated phage with bacteria and grew them with S35, felt is phage where all of its proteins had some of this isotope. Did the same thing with DNA and phosphate.

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21
Q

Hershey-Chase Experiment (1952):
The Theoretical Basis?

A

Protein contains sulphur, but lacks phosphorous. Protein can be specifically labelled with radioactive sulphur (35S), can then be detected with a machine (scintillation counters). DNA contains phosphorous, but lacks sulphur. DNA can be specifically labelled with
radioactive phosphorous ( 32P). By this method, either DNA or protein can be detected in cells.

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22
Q

Hershey-Chase Experiment?

A

Phages were grown with radioactive sulphur, which was incorporated into phage protein (pink). Mixed radioactively labelled phages with bacteria. The phages inflected the bacterial cells. Agitated the mixture in a blender to free phage parts outside the bacteria from the cells. Centrifuged the mixture so that bacteria formed a pellet at the bottom of the test tube; free phages and phage parts, which are lighter, remained suspended in the liquid. Measured the radioactivity in the pellet and liquid. No radioactivity in the bacteria (bottom). Repeated with phages grown with radioactive phosphorus which was incorporated into phage DNA (blue). The pellet was found to be radioactive.

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23
Q

Hershey-Chase Results?

A

That it is DNA that is transferring the information, not protein.

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24
Q

After the 4 experiments people knew what?

A

That it’s DNA that carried to info, so now they wanted to know its structure.

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25
Q

What’s a nucleotide?

A

The building block of DNA. Has five carbon deoxyribose sugar group. A phosphate group, and a nitrogenous base. They are joined together to form a polymer of a DNA strand.

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26
Q

The backbone of DNA consists of what?

A

A succession of sugars and phosphates.

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27
Q

Why is it important where the carbons in DNA are?

A

It gives directionality to DNA.

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28
Q

What is on the important carbons of DNA?

A

1’C has the nitrogenous base
3’C has the OH group
5’C has the phosphate group on it

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29
Q

What are the base pairs?

A

A and T/U
G and C

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30
Q

Strands of the DNA molecular are what?

A

Anti-parallel:
5’»»»»»»>3’
3’««««««<5’

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31
Q

Why is it called nitrogenous bases?

A

Because there is a lot of nitrogen in the bases.

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32
Q

What’s the difference between Thymine and Uracil?

A

Thymine has a methyl group attached and uracil doesn’t.

33
Q

Purines

A

Have 2 rings. A and G

34
Q

Pyrimidines

A

Have 1 ring. C, T, and U

35
Q

The differences between DNA and RNA?

A

DNA: double stranded, has thymine (methyl group), and doesn’t have an OH group in 2’C.
RNA: Single Stranded, has uracil (no methyl group), and has an OH group on 2’C.

36
Q

Nucleotides are joined together by what?

A

Covalent phosphodiester bonds

37
Q

What joins the bases together?

A

Hydrogen bonds

38
Q

Chargaff’s experiment?

A

He isolated DNA from different organisms and measured the levels of each of the 4 nitrogenous bases. This was many experiments.

39
Q

Chargaff’s results?

A

The base pairs produce roughly the same amount. It gives as a way of determining the composition of DNA just by knowing the amount of DNA just going from one of the bases. If 10% A then 10% T, so 40% C and 40% G.

40
Q

What’s the distance between two bp rows/rungs?

A

0.34 nm

41
Q

How many bp are needed to make a complete turn of the DNA helix?

A

10 bp, it’s about 3.34nm.

42
Q

Rosalind Franklin’s experiment?

A

Got pure crystal of DNA (just A form). X ray of DNA through the crystal. She modified her x-ray to beam at the right place, amplitude and strength through the crystal. Produced picture 51 from which the stricture of DNA was established.

43
Q

Rosalind Franklin’s results?

A

Her X-ray crystallography diffraction photo showed the helical structure of the of DNA molecule. Using math and distance picture could figure out the structure.

44
Q

Watson and Crick’s experiment?

A

Used Rosalind Franklin’s photo to determine the structure of DNA. They had to fit the base pairing within the diameter specified by Franklin’s x-ray.

45
Q

Watson and Crick’s results?

A

Purine + Purine = too wide
Pyrimidine + Pyrimidine = too narrow
Purine + Pyrimidine = width consistent with x-ray data.
They also figured out it was a helix with bases pointing inside.

46
Q

Structure of DNA?

A

Double-stranded molecule made of
polymers of nucleotides. DNA strands are complementary (A = T, G = C).
Nucleotides in one strand of the
DNA determines the nucleotides in
the complementary strand.

47
Q

The three models proposed of how DNA is replicated?

A

Conservative model, Semi-conservative model,
Dispersive model

48
Q

Conservative model

A

The parent DNA is a template for another DNA. The double helix is conserved through every generation and doesn’t unwind.

49
Q

Semi-conservative model

A

Each strand is a template for another strand. The helix separates.

50
Q

Dispersive model

A

DNA is blasted into pieces and then goes back together is the correct order.

51
Q

What is the density of the parent DNA

A

Heavy

52
Q

Meselson & Stahl’s question?

A

They needed to figure out how to differentiate the old and new DNA. DNA contains a lot of nitrogen, and there are many different isotopes of nitrogen that all weigh differently. They used nitrogen 15.

53
Q

Meselson & Stahl’s Experiment (1958)?

A

Bacteria cultured in medium with heavy nitrogen isotope (so all the DNA had the isotope). Then bacteria is transferred to medium with the lighter isotope. They used cesium chloride (CsCl) density-gradient centrifugation, it causes the CsCl to change into two densities. They mix DNA and CsCl in the tube. DNA sample is centrifuged after first replication (intermediate line). DNA sample centrifuged after second replication (fainter intermediate line and light line). Top is less dense, bottom is more dense. In the centrifuge the DNA will go down to its density and stop there.

54
Q

What happens to the bands from each generation?

A

The intermediate band gets lighter and lighter until it disappears because there is a lot of DNA so it gets diluted.

55
Q

Meselson & Stahl’s results?

A

Conservative model had a heavy and light band twice. Semiconservative model has an intermediate band then a lighter intermediate band and a light bad. Dispersive Model had an intermediate band, then a light band. So the semiconservative model is the correct way for DNA replication.

56
Q

Where are new nucleotides added to?

A

At the 3’ end of the new strand bring synthesized.

57
Q

When the nucleotide is being at, how many phosphates does it have?

A

Three and two get removed afterwards (pyrophosphate).

58
Q

What was Arthur Kornberg (1960’s) two requirements for DNA synthesis?

A

DNA replication by any DNA polymerase needs to be initiated (started) from a double- stranded segment of nucleic acid, either a DNA:DNA, or DNA:RNA hybrid. This is needed to make the complementary strand.
Synthesis of newly replicated DNA can only
proceed in the 5ʹ to 3ʹ direction.

59
Q

Hybrid

A

When you have two complementary strands

60
Q

Start of DNA replication?

A

In the beginning of s phase a lot of bubbles open up then fuse together to create one big bubble.

61
Q

Steps of DNA replication?

A

The helix unwinds, bubbles, primase starts the process by making a small section of RNA called a primer then DNA polymerase binds to it. The leading strand is synthesized continuously from 5’ to 3’. Then the primase begins the synthesis of the Okazaki fragments of lagging strand. Then DNA pol 3 completes the synthesis from the fragments. DNA pol 1 removes the primers and the space is filled in with DNA by DNA pol 1. Then DNA ligase joins the 3’ end of the fragment with the 5’ end of fragment 1, so they are stitched together to make one smooth lagging strand.

62
Q

Leading strand

A

The side that can be synthesized continuously.

63
Q

Lagging strand

A

The strand the has to be synthesized in pieces. The older strands are in the middle and newer strands are near the helicase.

64
Q

Helicase

A

It unwinds parental double helix at replication forks (like a zipper).

65
Q

Single-stranded binding protein

A

Binds to and stabilizes single-stranded DNA until it is as a template. It makes sure the DNA doesn’t come back together.

66
Q

Primase

A

Synthesizes an RNA primer at the 5’ end of the leading strand and at the 5’ end of each Okazaki fragment of lagging strand.

67
Q

DNA pol 3

A

Using parental DNA as a template, synthesizes new DNA strand by adding nucleotides to an RNA primer or preexisting DNA strand.

68
Q

DNA ligase

A

Joins Okazaki fragments of lagging strand; on leading strand, joins 3’ end of DNA that replaces primer to rest of leading strand DNA.

69
Q

DNA pol 1

A

DNA repair by removing the short RNA primer required for DNA synthesis during replication and filling in gaps in single-stranded DNA.

70
Q

Replication Fork

A

It’s a very active area where DNA replication takes place. It’s bidirectional and can go both ways and starts at the middle. The two sides are mirrors of each other.

71
Q

Why can’t DNA be synthesized continuously?

A

Because the DNA pol 3 can only synthesize in the direction of the replication fork. DNA polymerase cannot make a new strand in the 3’ to 5’ direction.

72
Q

A replication bubble has how many replication forks?

A

Two

73
Q

Exonuclease

A

An enzyme that removes all RNA primers from both strands of DNA

74
Q

Okazaki Fragments

A

Small sections of DNA that are formed during discontinuous synthesis of the lagging strand during DNA replication.

75
Q

The primer is made of what?

A

RNA

76
Q

Nucleoside

A

A five carbon sugar and the base

77
Q

Nucleotide

A

A five carbon sugar and the base, and one phosphate group

78
Q

Nucleoside diphosphate

A

A five carbon sugar and the base, and two phosphate groups

79
Q

Nucleoside triphosphate

A

A five carbon sugar and the base, and three phosphate groups