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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
Why are grooves important in DNA?
important sites for DNA/protein interactions
26
What's the direction of the central dogma?
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
27
What are chromosomes?
very long, single DNA molecules associated with proteins that fold and pack the DNA into a compact structure
28
What does DNA package itself into?
Chromosomes
29
What helps DNA in eukaryotic cells package into chromosomes?
Specialized protein called histones
30
How is DNA stored in prokaryotes?
It's store as a single circular molecule - bacterial chromosomes
31
What are chromatin?
mixture of DNA and proteins that form the chromosomes in eukaryotes
32
What are genes?
a segment of DNA that contains the instructions for making a particular protein or RNA
33
What are genome?
The total DNA complement of an organism
34
What are karyotypes?
an ordered display of chromosomes in the nucleus of a eukaryotic cell
35
Rank the order from smallest to largest: Genome, Gene, Chromosome, Chromatin
Gene -> Chromatin -> Chromosome -> Genome
36
Does more complex organism result in larger genome?
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
37
What happens to chromosomes in the interphase?
Chromosomes get duplicated
38
What happens to chromosomes in the mitotic phase?
Chromosomes are segregation
39
Why would chromosomes contain multiple replication origin?
To allow the long DNA molecules to be replicated rapidly
40
What are telomeres?
A DNA sequence that marks the end of a chromosome
41
What does telomeres do?
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
42
What are centromere?
DNA sequence that allow duplicated chromosome to be separated during the M phase
43
Why is it important that chromosomes are dynamic?
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)
44
What enables DNA packing?
Nucleosome
45
What are nucleosomes?
Basic units of eukaryotic chromatin structure DNA + 8 Histones
46
What does nucleosomes do?
convert the DNA molecules in an interphase nucleus into a chromatin fiber
47
What are histones?
Protein that helps with DNA packaging The most fundamental level of chromatin packing
48
How many histones are present?
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
Why would histones be positively charged?
The positive charges help the histones bind tightly to the negatively charged sugar–phosphate backbone of DNA.
50
Why might a histone tail be important during DNA packaging?
These histone tails are subjected to modification that control aspect of chromatin structure
51
What does histone being highly conserved indicate?
Histones are vital in controlling eukaryotic chromosome structures
52
Do bacteria have nucleosomes?
No. Instead they have a big piece of circular DNA that is compacted by various protein
53
Considering how histones are highly conserved between all eukaryotic organism, how would a change in the amino acid sequence be deleterious?
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
How can cells use ATP to alter their chromatin structure?
To locally alter the arrangement of the nucleosome, making DNA more accessible to other protein.
55
What is an ATP-dependent chromatin remodeling complexes?
Proteins that use the energy of ATP hydrolysis to change the position of the DNA wrapped around nucleosomes
56
How can histone tail alter chromatin structure?
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
What is the most important aspect of histone modification enzyme?
Modifications can serve as docking sites on the histone tail for other protein that influence chromatin structure.
58
What are the two types interphase chromatin
Euchromatin and Heterochromatin
59
What are heterochromatin?
The most highly condensed form of interphase chromatin that is concentrated around the centromere and telomere region.
60
What are euchromatin?
The rest of the interphase chromatin that is not heterochromatin. They are looser and less condensed
61
What is the impact of heterochromatin attracting heterochromatin specific protein?
The heterochromatin specific protein can modify nearby histone which heterochromatin can spread until it encounters a barrier DNA sequence.
62
Why doesn't heterochromatin contain gene?
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
When can heterochromatin silencing gene be good?
In female mammals. In some case, a double dose of chromosome product could be lethal so the second X-chromosome is silenced
64
What is DNA replication?
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
How is DNA replicated?
Semi Conservative
66
What does it mean for DNA to be semi conservative?
Every daughter cell will have half of the old and half of the new DNA
67
Describe the process of Meselson and Stahl's experiment that proved that DNA replication is semi conservative
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
What must happen to the DNA strand to being replication?
The strands must be pried apart.
69
How are DNA strands pried apart?
Inhibitor proteins pull apart the two strands, causing replication forks on each side
70
What protein catalyze DNA synthesis?
DNA polymerase
71
How does DNA polymerase catalyze protein synthesis?
DNA polymerase catalyze the addition of nucleotides to the 3' end of a growing DNA strand
72
What direction is DNA being synthesized?
5' to 3' Nucleotides are being added to the 3' end
73
How is DNA polymerase so accurate?
1. Mismatch Repair 2. Proofreading
74
How does DNA polymerase proofread?
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
What does RNA primer do?
Providing the starting point for DNA polymerase to work
76
How are replication fork asymmetrical?
Lagging strands are discontinous
77
Why are Okazaki fragment formed in the synthesis of the lagging strand?
So DNA can be synthesized in the essential 5' to 3' manner on the lagging strand.
78
Which way does lagging strand run?
3' to 5'
79
Which way does leading strand run?
5' to 3'
80
What does primase do?
Synthesize RNA primer
81
What does DNA ligase do?
Join the Okazaki fragment together
82
What does ribonuclease do?
Degrade RNA primer
83
What does repair polymerase do?
replace RNA with DNA after ribonuclease degrade RNA primer
84
What does DNA helicase do?
Unzips DNA helix prior to replication
85
What does single strand DNA binding protein do?
Prevent the DNA strands from realligning
86
What does the sliding clamp do?
keeps DNA polymerase attached to template and on lagging strand, releases when Okazaki fragment is completed
87
What does initiator protein do?
Initiate DNA replication by creating a replication origin
88
Describe the steps of DNA replication
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
Why is the absence of telomere so devastating to DNA replication?
Without telomeres, the lagging strands will become shorter after each DNA replication round, shrinking the chromosome and genetic material can be loss
90
What does telomeres do?
Attract telomerase which carries its own RNA template to add multiple copies of the same repetitive DNA sequence to the lagging strands.
91
What are the common chemical reactions that cause DNA damage?
1. Depurination 2. Deamination 3. Thymine Dimerization
92
What is depurination?
Removal of purines (A and G) from the sugar
93
What is deamination?
removal of NH2 group from cytosine, converting it to uracil. DNA does not uracil
94
What is thymine dimerization?
Covalent link between two adjacent Thymines instead of their compliment base pair
95
Describe the process on how DNA is repair
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
Describe mismatch repair in DNA replication
Mismatch repair protein can detect DNA mismatch, remove the DNA mismatch and then synthesized the missing DNA
97
What are the two ways cells can repair double stranded break?
1. Non homologous end joining 2. Homologous Recombination
98
What is non homologous end joining?
When an accidental double strand break, which is hurriedly fixed by DNA polymerase
99
What are the cons of non homologous end joining?
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
Describe homologous recombination
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
What are transposons?
Mobile genetic elements that move from one place to another as DNA rather
102
What is responsible for transposon movement?
Transposase
103
What are the two mechanism of transposition in bacteria
1. Cut and paste 2. Replicative Transposition
104
How can transposition make bacteria resistant to antibodies?
Transposon can carry antibiotic resistant gene that can be absorbed by bacteria as it is moving
105
How does cut and paste transposition work?
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
How does replicative transposition work?
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
What are retrotransposon?
Type of genetic component that copy and paste themselves into different genomic locations by converting RNA back into DNA
108
How can mobile genetic element move exon from one gene to another?
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
What is a virus?
small genomes enclosed by a protective protein coat
110
How does a virus replicate?
By hijacking the host cell's molecular machinery to reproduce; the virus use the DNA polymerase in a cell to replicate
111
Why must virus need a host cell?
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
What are retrovirus?
An RNA virus exclusive to eukaryotes that converts its genetic material to DNA before injecting it into a host cell
113
How are retrotransposon and retrovirus similar?
Both use enzyme reverse transcriptase to convert RNA into DNA

Biology (20 decks)

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