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Biology > DNA: Regulation of Gene Expression > Flashcards

DNA: Regulation of Gene Expression Flashcards

1
Q

Who discovered the structure of DNA?

A

Crystallography - Rosaline Franklin
Double Helix - James Watson and Francis Crick

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2
Q

Who discovered nucleic acid?

A

Friedrich Miescher

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3
Q

What did Kossel and Levene show about DNA?

A

DNA consist of repeating molecule containing sugar, nitrogenous base, and phosphate

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4
Q

Why was it believed that protein were the genetic material of DNA back then?

A

Protein were more complex than to DNA. Protein had 20 amino acids while DNA had 4 bases

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5
Q

What was the first key experiment that led to the identification of DNA as genetic material?

A

Frederick Griffith Experiment

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6
Q

How did the Griffith Experiment work?

A

There were two strains of bacteria:
R Stand (non lethal) and S Strain (lethal)

Griffith injected R strand into the mice and the mice live. He also injected the S strain which cause the mice to die.

Then Griffith killed all the S cell and injected the cell into the mouse and the mouse live

He then mix the R strain with the dead S strain and injected into the mouse. The mouse died

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7
Q

What was the conclusion of the griffith experiment?

A

The experiment sowed that material could be transferred from a heat-killed virulent strain to a non-virulent strain, making the non-virulent strain virulent; transformation

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8
Q

Who support that DNA was the genetic material after the Griffith Experiment?

A

Avery, MacLeod and McCarty

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9
Q

What did Avery MacLeod and
McCarty demonstrate?

A

DNA component in S Strain cell caused the appearance of S Strain, while all other components such as RNA, protein, lipid, and carbohydrate result in R Strain

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10
Q

Who validated that DNA was the genetic material?

A

Hershey Chase

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11
Q

What happened during the Hershey Chase experiment?

A

T2 Virus were used because it’s only made of protein and DNA. The virus inject its genetic material into a bacterium so that its viral cap will be empty. Two batches of bacteria were made

To determine whether the genetic material of the virus is made of protein or DNA, radioactive phosphorus was used as a label on one batch and radioactive sulfur on the other batch.

Result: P label DNA entered the bacteria while S label protein remained in the solution.

Conclusion: Phosphorus fused with the bacteria, proving that DNA was the genetic material because DNA lacks sulfur and protein lacks phosphorus

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12
Q

Why was phosphorus and sulfur used in the Hershey Chase experiment?

A

DNA lacks sulfur and protein lacks phosphorus

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13
Q

Conclusion of Hershey Chase experiment?

A

Conclusion: Phosphorus fused with the bacteria, proving that DNA was the genetic material because DNA lacks sulfur and protein lacks phosphorus

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14
Q

What makes up a nucleotide?

A

Base + Pentose + Phosphate

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15
Q

What bases are purines?

A

Adenine and Guanine

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16
Q

What bases are pyrimidines?

A

Cytosine and Thymine

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17
Q

What is Chargaff’s Rule?

A
  1. base composition varied
    significantly from species to species
  2. Base composition was constant
    within the species, no matter if DNA came from tissue or organ.
  3. Most importantly, A=T and G=C, that is A and T were present in equimolar amounts as were G and C, and A+T
    did not equal G+C
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18
Q

What are the three rules of structure of DNA

A
  1. 5’ to 3’
  2. Antiparallel
  3. DNA Double Helix
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19
Q

How are nucleotides held together?

A

Phosphodiester Bond

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20
Q

Why is DNA strand polar?

A

Because the ester linkages to the sugar molecules on either side of the bond are different. 5’ start with phosphate while 3’ ends with hydroxyl

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21
Q

What holds the two polynucleotide chains of DNA double helix together?

A

Hydrogen bonding between the bases of different strands

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22
Q

Why is the base pairing of G-C more stable than A-T

A

G-C has three hydrogen bonding and A-T only has two.

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23
Q

What helps stack the bases on top of each other in DNA

A

Hydrophobic Interaction and Van der waals

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24
Q

What are the major and minor grooves on DNA?

A

Spaces between the turns of the helix forms

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25
Q

Why are grooves important in DNA?

A

important sites for DNA/protein interactions

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26
Q

What’s the direction of the central dogma?

A

DNA -> RNA -> Protein

the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible, but transfer from protein to protein, or from protein to nucleic acid is impossible

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27
Q

What are chromosomes?

A

very long, single DNA molecules associated with proteins that fold and pack the DNA into a compact structure

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28
Q

What does DNA package itself into?

A

Chromosomes

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29
Q

What helps DNA in eukaryotic cells package into chromosomes?

A

Specialized protein called histones

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30
Q

How is DNA stored in prokaryotes?

A

It’s store as a single circular molecule - bacterial chromosomes

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31
Q

What are chromatin?

A

mixture of DNA and proteins that form the chromosomes in eukaryotes

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32
Q

What are genes?

A

a segment of DNA that contains the instructions for making a particular protein or RNA

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33
Q

What are genome?

A

The total DNA complement of an organism

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34
Q

What are karyotypes?

A

an ordered display of chromosomes in the nucleus of a
eukaryotic cell

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35
Q

Rank the order from smallest to largest:

Genome, Gene, Chromosome, Chromatin

A

Gene -> Chromatin -> Chromosome -> Genome

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36
Q

Does more complex organism result in larger genome?

A

Not always, Genome size does not always correlate with organism complexity

Human have a genome pool 200x larger than yeast but 30 smaller times than that of some plant

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37
Q

What happens to chromosomes in the interphase?

A

Chromosomes get duplicated

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38
Q

What happens to chromosomes in the mitotic phase?

A

Chromosomes are segregation

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39
Q

Why would chromosomes contain multiple replication origin?

A

To allow the long DNA molecules to be replicated rapidly

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40
Q

What are telomeres?

A

A DNA sequence that marks the end of a chromosome

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41
Q

What does telomeres do?

A

Allow the end of the chromosome to be replicated and protect the chromosome tips from being mistaken by the cell as broken DNA in need of repair

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42
Q

What are centromere?

A

DNA sequence that allow duplicated chromosome to be separated during the M phase

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43
Q

Why is it important that chromosomes are dynamic?

A

For DNA packaging to be more accessible. Chromatin can exposed localized region of DNA to allow proteins access to modify the DNA (repair or replication)

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44
Q

What enables DNA packing?

A

Nucleosome

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45
Q

What are nucleosomes?

A

Basic units of eukaryotic chromatin structure

DNA + 8 Histones

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46
Q

What does nucleosomes do?

A

convert
the DNA molecules in an interphase nucleus into a chromatin fiber

47
Q

What are histones?

A

Protein that helps with DNA packaging

The most fundamental level of chromatin packing

48
Q

How many histones are present?

A

5 types of histones.

4 of the 5 type is used to make a nucleosome
- 2 molecule each of H2A, H2B, H3 and H4
- 8 total histone in one nucleosome

H1 is used for 30 nm fiber packing level

49
Q

Why would histones be positively charged?

A

The positive charges help the histones bind tightly to the negatively charged sugar–phosphate backbone of DNA.

50
Q

Why might a histone tail be important during DNA packaging?

A

These histone tails are subjected to modification that control aspect of chromatin structure

51
Q

What does histone being highly conserved indicate?

A

Histones are vital in controlling eukaryotic chromosome structures

52
Q

Do bacteria have nucleosomes?

A

No. Instead they have a big piece of circular DNA that is compacted by various protein

53
Q

Considering how histones are highly conserved between all eukaryotic organism, how would a change in the amino acid sequence be deleterious?

A

Changing amino acids may disrupt the charged which may disrupt the efficiency of packaging.

Small problem may cause DNA to die because its DNA cannot be efficiently wrapped

54
Q

How can cells use ATP to alter their chromatin structure?

A

To locally alter the arrangement of the nucleosome, making DNA more accessible to other protein.

55
Q

What is an ATP-dependent chromatin remodeling complexes?

A

Proteins that use the energy of ATP hydrolysis to change the position of the DNA wrapped around nucleosomes

56
Q

How can histone tail alter chromatin structure?

A

Since the tails the histones can undergo covalent modification, their affinity for adjacent nucleosome can be reduced by the acetylation of lysine, neutralizing the positive charge and loosening chromatin structure, allowing access to nuclear protein

57
Q

What is the most important aspect of histone modification enzyme?

A

Modifications can serve as docking sites on the histone tail for other protein that influence chromatin structure.

58
Q

What are the two types interphase chromatin

A

Euchromatin and Heterochromatin

59
Q

What are heterochromatin?

A

The most highly condensed form of interphase chromatin that is concentrated around the centromere and telomere region.

60
Q

What are euchromatin?

A

The rest of the interphase chromatin that is not heterochromatin. They are looser and less condensed

61
Q

What is the impact of heterochromatin attracting heterochromatin specific protein?

A

The heterochromatin specific protein can modify nearby histone which heterochromatin can spread until it encounters a barrier DNA sequence.

62
Q

Why doesn’t heterochromatin contain gene?

A

Heterochromatin is so compact so that the genes that is accidentally packaged usually fail to be expressed. This can be bad or good

Bad: Anemia in human from deactivation of B-globin gene

63
Q

When can heterochromatin silencing gene be good?

A

In female mammals. In some case, a double dose of chromosome product could be lethal so the second X-chromosome is silenced

64
Q

What is DNA replication?

A

Process of producing two identical replicas from one original DNA made; each strand of the original DNA can be served as a template strand

65
Q

How is DNA replicated?

A

Semi Conservative

66
Q

What does it mean for DNA to be semi conservative?

A

Every daughter cell will have half of the old and half of the new DNA

67
Q

Describe the process of Meselson and Stahl’s experiment that proved that DNA replication is semi conservative

A

Grew bacteria in two different environment: heavy nitrogen and light nitrogen

  1. They took the bacteria cultured in the heavy medium and transferred into the light medium
  2. After 20 minutes, they examined the mixed medium and found that the DNA is semi conservative
68
Q

What must happen to the DNA strand to being replication?

A

The strands must be pried apart.

69
Q

How are DNA strands pried apart?

A

Inhibitor proteins pull apart the two strands, causing replication forks on each side

70
Q

What protein catalyze DNA synthesis?

A

DNA polymerase

71
Q

How does DNA polymerase catalyze protein synthesis?

A

DNA polymerase catalyze the addition of nucleotides to the 3’ end of a growing DNA strand

72
Q

What direction is DNA being synthesized?

A

5’ to 3’

Nucleotides are being added to the 3’ end

73
Q

How is DNA polymerase so accurate?

A
  1. Mismatch Repair
  2. Proofreading
74
Q

How does DNA polymerase proofread?

A

It checks if the previously added nucleotide is correctly based-pair to the template strand. If it is correct, the polymerase adds the next nucleotide and if not, it clips the mispaired nucleotide and tries again.

Proofreading is only possible from 5’ to 3’

75
Q

What does RNA primer do?

A

Providing the starting point for DNA polymerase to work

76
Q

How are replication fork asymmetrical?

A

Lagging strands are discontinous

77
Q

Why are Okazaki fragment formed in the synthesis of the lagging strand?

A

So DNA can be synthesized in the essential 5’ to 3’ manner on the lagging strand.

78
Q

Which way does lagging strand run?

A

3’ to 5’

79
Q

Which way does leading strand run?

A

5’ to 3’

80
Q

What does primase do?

A

Synthesize RNA primer

81
Q

What does DNA ligase do?

A

Join the Okazaki fragment together

82
Q

What does ribonuclease do?

A

Degrade RNA primer

83
Q

What does repair polymerase do?

A

replace RNA with DNA after ribonuclease degrade RNA primer

84
Q

What does DNA helicase do?

A

Unzips DNA helix prior to replication

85
Q

What does single strand DNA binding protein do?

A

Prevent the DNA strands from realligning

86
Q

What does the sliding clamp do?

A

keeps DNA polymerase attached to template
and on lagging strand, releases when Okazaki fragment is
completed

87
Q

What does initiator protein do?

A

Initiate DNA replication by creating a replication origin

88
Q

Describe the steps of DNA replication

A
  1. Initiator protein create a replication origin
  2. DNA helicase forms replication fork
  3. Primase makes RNA primer
  4. RNA primer bind to DNA
  5. DNA polymerase bind to primer and synthesize from 5’ to 3’, adding nucleotide to the 3’ end
89
Q

Why is the absence of telomere so devastating to DNA replication?

A

Without telomeres, the lagging strands will become shorter after each DNA replication round, shrinking the chromosome and genetic material can be loss

90
Q

What does telomeres do?

A

Attract telomerase which carries its own RNA template to add multiple copies of the same repetitive DNA sequence to the lagging strands.

91
Q

What are the common chemical reactions that cause DNA damage?

A
  1. Depurination
  2. Deamination
  3. Thymine Dimerization
92
Q

What is depurination?

A

Removal of purines (A and G) from the sugar

93
Q

What is deamination?

A

removal of NH2 group from cytosine,
converting it to uracil.

DNA does not uracil

94
Q

What is thymine dimerization?

A

Covalent link between two
adjacent Thymines instead of their compliment base pair

95
Q

Describe the process on how DNA is repair

A
  1. Excision
    - nuclease removes the damaged DNA by cleaving the covalent bond that joins the damaged DNA to the rest of the DNA.
  2. Replacement
    - a repair DNA polymerase binds to the 3’- hydroxyl end of the cut DNA strand and fills in the gap by making a complementary copy of the information present in the undamaged strand.
  3. Ligation
    - ligase will connect the newly synthesized nucleotide with the next one
96
Q

Describe mismatch repair in DNA replication

A

Mismatch repair protein can detect DNA mismatch, remove the DNA mismatch and then synthesized the missing DNA

97
Q

What are the two ways cells can repair double stranded break?

A
  1. Non homologous end joining
  2. Homologous Recombination
98
Q

What is non homologous end joining?

A

When an accidental double strand break, which is hurriedly fixed by DNA polymerase

99
Q

What are the cons of non homologous end joining?

A

If this imperfect repair disrupts the activity of a gene, the cell could suffer serious consequences. Moreover, there is a loss of nucleotide, losing genetic information

100
Q

Describe homologous recombination

A
  1. Recombination nuclease chew back the 5’ end of the two broken strands at the break
  2. One of the broken 3’ ends invade the unbroken homologous DNA duplex and search for a complementary sequence through base pairing
  3. Once a match is made, the invading strand is elongated by a repair DNA polymerase, using the complimentary strand as a template
  4. Newly elongated strand rejoin its original partner
  5. DNA ligase, combines the synthesized DNA with the broken strand
101
Q

What are transposons?

A

Mobile genetic elements that move from one place to another as DNA rather

102
Q

What is responsible for transposon movement?

A

Transposase

103
Q

What are the two mechanism of transposition in bacteria

A
  1. Cut and paste
  2. Replicative Transposition
104
Q

How can transposition make bacteria resistant to antibodies?

A

Transposon can carry antibiotic resistant gene that can be absorbed by bacteria as it is moving

105
Q

How does cut and paste transposition work?

A

The element is cut out of the donor DNA and inserted into the target DNA, leaving behind a broken DNA which will be repaired

106
Q

How does replicative transposition work?

A

The mobile genetic element is copied by DNA replication. Donor molecule remain unchanged and the target molecule receive a copy of the mobile genetic element.

107
Q

What are retrotransposon?

A

Type of genetic component that copy and paste themselves into different genomic locations by converting RNA back into DNA

108
Q

How can mobile genetic element move exon from one gene to another?

A

When two mobile genetic material of the same type happen to insert near each other, the chromosomal DNA that lies between the mobile genetic elements gets
excised and moved to a new site.

109
Q

What is a virus?

A

small genomes enclosed by a protective protein coat

110
Q

How does a virus replicate?

A

By hijacking the host cell’s molecular machinery to reproduce; the virus use the DNA polymerase in a cell to replicate

111
Q

Why must virus need a host cell?

A

Viruses do not possess the genes
needed for replication. Instead they hijack the cell’s replication machinery and infect other cell through the lytic effect

112
Q

What are retrovirus?

A

An RNA virus exclusive to eukaryotes that converts its genetic material to DNA before injecting it into a host cell

113
Q

How are retrotransposon and retrovirus similar?

A

Both use enzyme reverse transcriptase to convert RNA into DNA

Biology (20 decks)

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