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BIO 2 > DISCOVERY OF DNA AND DNA REPLICATION (LECTURE 6) > Flashcards

DISCOVERY OF DNA AND DNA REPLICATION (LECTURE 6) Flashcards

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1
Q

What are the monomers of nucleic acids?

A

Nucleotides.

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2
Q

What are the polymers of nucleic acids? (3)

A

DNA and RNA (polynucleotides).

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3
Q

How are nucleic acid monomers linked?

A

Nucleotides are linked by phosphodiester bonds.

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4
Q

What are the functions of nucleic acids?

A

Information storage (DNA) and information transport (RNA).

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5
Q

What does DNA stand for? What does it contain? How is it structurally unique?

A

Deoxyribonucleic acid (DNA) contains genes which code for protein synthesis. They are double stranded.

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6
Q

What does RNA stand for? What does it do? How many types are there? What is particular about its structure?

A

Ribonucleic acid (RNA) functions in the synthesis of proteins. There are 3 types : ribosomal RNA (rRNA), transfer RNA (tRNA) and messenger RNA (mRNA). They are single stranded.

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7
Q

What are the 3 structural components of a nucleotide?

A

The nitrogen containing base, the pentose sugar and the phosphate group.

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8
Q

What are the 2 types of nitrogen containing bases?

A

The pyrimidines and the purines.

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9
Q

Describe the pyrimidines.

A

These are 6-membered rings made of carbon and nitrogen. There are 3 pyrimidines: cytosine, uracil (RNA) and thymine (DNA).

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10
Q

Describe the purines.

A

These are 5-membered rings fused to a 6-membered ring (both rings made of carbon and nitrogen). There are 2 purines: guanine and adenine.

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11
Q

Describe the pentose sugar found in a nucleotide. What role does it play?

A

This is a 5-carbon backbone of the nucleotide.

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12
Q

Which pentose sugar is found in DNA? What is particular about this pentose sugar?

A

Deoxyribose, which lacks an oxygen on carbon 2.

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13
Q

Which pentose sugar is found in RNA?

A

Ribose.

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14
Q

To what is the phosphate group of a nucleotide attached to? (Which atom?)

A

To carbon 5 of pentose (5’C).

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15
Q

How are the 2 DNA strands held together?

A

They are held together by hydrogen bonds between nitrogenous bases.

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16
Q

DNA strands are complementary, meaning what?

A

Complementary meaning purines bind with pyrimidines (A-T, G-C in DNA and A-U, G-C in RNA).

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17
Q

How many hydrogen bonds are there between adenine and thymine (A-T)?

A

2 bonds.

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18
Q

How many hydrogen bonds are there between guanine and cytosine (G-C)?

A

3 bonds.

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19
Q

Double stranded DNA is anti_____, meaning what?

A

Double stranded DNA is antiparallel, meaning one strand runs 5’–>3’ and the other 3’–>5’.

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20
Q

What is a phosphodiester bond?

A

The link between a phosphate group of one nucleotide to the pentose of the next nucleotide.

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21
Q

How many nitrogenous bases are there per full turn of the helix?

A

10 bases per full turn of the helix.

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22
Q

Describe the relative positions of nitrogenous bases and the sugar-phosphate backbone in DNA.

A

The sugar-phosphate backbone is on the outside of the DNA helix while the nitrogenous base-pairs are on the inside of the helix.

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23
Q

What is the “packaged” form of DNA called?

A

Chromatin.

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24
Q

Describe chromatin.

A

It is DNA wrapped around histones (DNA + histones = chromatin).

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25
Q

What are histones? What is significant about their composition?

A

These are small proteins rich in the positively charged (basic) amino acids arginine and lysine.

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26
Q

Why does DNA bind tightly to histones?

A

DNA is negatively charged and thus binds tightly to the positively charged histones.

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27
Q

Why is DNA negatively charged?

A

It is negatively charged because of its phosphate groups (which themselves are negatively charged). DNA is thus negatively charged due to the abundance of phosphate in DNA.

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28
Q

Describe prokaryotic DNA. (4)

A

It is circular, less complex, located in the cytosol, double stranded.

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29
Q

Describe eukaryotic DNA. (7)

A

It is linear, structured, complex, associated with large amounts of proteins (forms chromatin), located in the nucleus and double stranded.

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30
Q

What DNA related discovery was made in 1928? By who?

A

Frederick Griffith discovered in 1928 that information is stored in a molecule that can be transferred between organisms.

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31
Q

In 1928, Frederick Griffith studied 2 strains of what? Name both strains.

A

He studied 2 strains of Streptococcus pneumonia: the smooth (S) and rough (R) strains.

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32
Q

Describe both strains of streptococcus pneumonia studied by Frederick Griffith in 1928.

A

S cells (smooth strain) are encapsulated in a polysaccharide coat, making them pathogenic (disease causing). R cells (rough strain) lack this coat, making them harmless.

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33
Q

Describe the experiment performed by Frederick Griffith in 1928 and the results obtained.

A

Griffith mixed heat-killed S cells with R cells and injected mice. These mice died and living S cells were found in its body. Thus something in the dead S-cells transformed the harmless R-cells.

34
Q

What DNA related discovery was made in 1944? By who?

A

In 1944, Oswald Avery, Maclyn McCarty and Colin Macleod discovered that the information molecule is DNA.

35
Q

Describe the experiment performed by Avery, McCarty and Macleod in 1944. What were the results?

A

They opened up heat-killed S cells and treated them with enzymes that destroy either proteins, RNA or DNA. Only Dnase treated samples could not transform R cells (samples where the DNA was destroyed).

36
Q

What DNA related discovery was made in 1950?

A

Erwin Chargaff discovered that the percentage of cytosine in DNA matched the percentage of guanine, while the percentage of adenine in DNA matched the percentage of thymine.

37
Q

What DNA related discovery was made in 1952?

A

Alfred Hershey and Martha Chase discovered that information to make new bacteriophages is stored in DNA, and that DNA is transferred into bacteria.

38
Q

What is a bacteriophage? (3)

A

It is a virus that infects bacteria. It consists of protein and DNA. The infected cell will “manufacture” viruses.

39
Q

Describe the experiment performed by Hershey and Chase in 1952.

A

E. coli (bacteria) were infected with T2 bacteriophage which contained either radiolabeled proteins (35S) or radiolabeled DNA (32P). Cells were placed in a blender to separate the phage from the bacteria and the mixture was centrifuged.

40
Q

Describe the results of the experiment performed by Hershey and Chase in 1952.

A

Radiolabeled proteins (35S) were found in the supernatant (outside of cells) and radiolabeled DNA (32P) was found in the pellet (inside of cells). Thus it is the DNA that contains the information to make new viruses.

41
Q

Name the three models for DNA replication.

A

Conservative, semi-conservative and the dispersive model.

42
Q

Describe the conservative model for DNA replication.

A

The 2 original strands remain together following replication.

43
Q

Describe the semi-conservative model for DNA replication.

A

The 2 original strands separate and each is copied.

44
Q

Describe the dispersive model for DNA replication.

A

The DNA molecule breaks into pieces and is copied.

45
Q

What DNA related discovery was made in 1953? By who?

A

Rosalind Franklin, James Watson and Francis Crick discovered the structure of DNA in 1953.

46
Q

What DNA related discovery was made in 1958? By who?

A

Matthew Meselson and Franklin Stahl discovered that DNA replication is semi-conservative in 1958.

47
Q

Describe the experiment performed by Meselson and Stahl in 1958.

A

E.coli were grown in heavy nitrogen (15N) and switched to media with lighter nitrogen (14N). At this point, all newly synthesized DNA will incorporate 14N. DNA was isolated at 20 min and 40 min and separated by density centrifugation.

48
Q

Describe the results of the experiment performed by Meselson and Stahl in 1958.

A

The first replication (20 mins) resulted in 1 band at (14N/15N). The second replication (40 mins) resulted in 2 bands; 1 at (14N/15N) and another at (14N). These results were only supported by the semiconservative model.

49
Q

If we repeated the experiment performed by Meselson and Stahl in 1958, what results would you obtain after 3 rounds of CONSERVATIVE DNA replication?

A

2 bands would be obtained after centrifugation. One at 14N and the other at 15N.

50
Q

When is DNA replication happening in the cell cycle?

A

In the S phase (DNA synthesis).

51
Q

What are the 5 primary enzymes that participate in DNA replication?

A

Helicase, DNA polymerase, primase, ligase and single-stranded binding proteins.

52
Q

Describe the role of helicase in DNA replication. What bonds are breaking?

A

Helicase unwinds DNA strands (breaks hydrogen bonds between nitrogenous bases).

53
Q

Describe the role of DNA polymerase in DNA replication.

A

DNA polymerase synthesizes DNA by catalyzing the formation of phosphodiester bonds between nucleotides. It uses the parental strand as a template and adds complementary nucleotides

54
Q

In what “direction” does DNA polymerase build DNA. In what direction does it “read” the template strand?

A

DNA polymerase makes DNA in the 5’–>3’ direction (links 5’ phosphate group of new nucleotide to 3’-OH group of growing strand). It reads the template strand from 3’–>5’.

55
Q

Describe the role of primase in DNA replication.

A

It is an RNA polymerase that synthesizes an RNA primer on the template strand. This is required because DNA polymerase can only add a nucleotide to a free 3’-OH group.

56
Q

Describe the role of ligase in DNA replication.

A

Ligase glues together nicks in DNA sugar-phosphate backbone (it forms phosphodiester bonds). This is needed after RNA primers are replaced by DNA and for Okazaki fragments.

57
Q

Describe the role of single-stranded binding proteins in DNA replication.

A

These stabilize single stranded DNA.

58
Q

Where does DNA polymerase get energy from?

A

To catalyze phosphodiester bond formation between 5’-phosphate group of incoming nucleotide and the free 3’-OH end of the growing stand, DNA polymerase uses energy from hydrolyzing the bond between 2 phosphates and the rest of a nucleotide.

59
Q

DNA replication can be split into two steps. What are they?

A

Initiation and elongation.

60
Q

Describe the initiation of DNA replication.

A

Helicases bind to origins of replication and begin unwinding DNA to form a replication bubble (2 replication forks). Single stranded binding proteins bind to the now single stranded DNA.

61
Q

Describe the elongation step of DNA replication.

A

Primase makes a complementary RNA primer (around 5-10 nucleotides long). DNA polymerase synthesizes a new strand of DNA using the parental strand as a template.

62
Q

Each replication fork in DNA replication has 2 of what?

A

Each replication fork has 2 strands.

63
Q

Name the 2 strands of each replication fork in DNA replication.

A

There is the leading strand and the lagging strand.

64
Q

Describe the leading strand of DNA replication. (3)

A

The leading strand is characterized by continuous DNA synthesis, DNA polymerase is synthesizing DNA in the same direction as the DNA unwinding and only necessitates 1 RNA primer.

65
Q

Describe the lagging strand of DNA replication. (3)

A

There is discontinuous DNA synthesis (Okazaki fragments), DNA polymerase must synthesize DNA in the opposite direction of DNA unwinding and this necessitates many RNA primers.

66
Q

Describe DNA replication as it occurs on the leading strands (5’ –> 3’). (5 steps)

A

Helicase unwinds DNA, primase makes an RNA primer, DNA polymerase extends from primer, DNA polymerase replaces RNA primer with DNA, DNA ligase repairs nick in backbone between replaced primer and rest of new strand.

67
Q

Describe DNA replication as it occurs on the lagging strands (3’ – > 5’).

A

Helicase unwinds DNA, primase makes RNA primer 1, DNA polymerase extends from primer 1, primase makes primer 2, DNA polymerase extends from primer 2 (etc). DNA polymerase replaces RNA primers with DNA. DNA ligase repairs nicks in backbone between replaced primers and rest of strand and between Okazaki fragments.

68
Q

DNA polymerase has a very low what?

A

DNA polymerase has a very low error rate.

69
Q

For what reasons does DNA polymerase have a very low error rate?

A

DNA polymerase proofreads each added nucleotide. If there is an incorrect match, DNA polymerase will fix it by removing incorrect nucleotide and resuming synthesis. Errors not caught by DNA polymerase can be repaired by mismatch repair.

70
Q

What is nucleotide excision repair?

A

When errors/changes in already synthesized DNA are corrected.

71
Q

Describe the process of nucleotide excision repair. (3)

A

A nuclease removes changed nucleotides. DNA polymerase fills in the gap and DNA ligase glues together the backbone.

72
Q

Changes to DNA can be caused by what? (4)

A

Chemicals, radioactivity, x-rays and UV light.

73
Q

Provide an example of an error in already synthesized DNA (other than mismatched nitrogenous bases).

A

A thymine dimer, which occurs when two adjacent thymines are covalently bonded to one another.

74
Q

Describe the end replication problem.

A

The removal of RNA primer from the beginning of a lagging strand leaves a gap and a free 5’-phosphate end. This gap cannot be filled by DNA polymerase because it can only add DNA to 3’-OH end. Each replication results in shorter DNA.

75
Q

What does the end replication problem entail?

A

Since each replication results in shorter DNA, this can result in the depletion of genes and is a limiting factor in the life span of a cell.

76
Q

Why do prokaryotes not have the end replication problem?

A

Because prokaryotic DNA is circular.

77
Q

What is the solution to the end replication problem for eukaryotic cells?

A

Eukaryotic DNA is flanked by telomeres.

78
Q

What are telomeres?

A

Telomeres are repeats of noncoding nucleotide sequences.

79
Q

How are telomeres created?

A

Telomeres are synthesized by the enzyme telomerase (RNA and protein).

80
Q

Where is telomerase active?

A

Telomerase is only active in germ cells and stem cells (not in somatic cells).

81
Q

Telomerase isn’t active in somatic cells. What does this entail?

A

Telomeres shorten as cells age.

82
Q

How can we visualize telomeres?

A

Telomeres can be visualized by fluorescence microscopy.

BIO 2 (14 decks)

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