Lecture 2: DNA, Chromatin, Epigenetics and Replication Flashcards
1
Q
How many genes in human genome? Is this number increasing or decreasing?
A
20-25K
Increasing with the discovery of new genes
2
Q
2 purines?
A
Adenine and guanine
3
Q
3 pyrimidines?
A
Cytosine, thymine, and uracil
4
Q
Ring structure of purines?
A
6 member ring + 5 member ring
5
Q
Ring structure of pyrimidines?
A
6 member ring
6
Q
Difference between cytosine and thymine?
A
Carboxyl (thymine) vs amine (cytosine) at C4
Methyl (thymine) at C5 instead of H (cytosine)
7
Q
Difference between uracil and thymine?
A
Methyl (thymine) at C5 instead of H (uracil)
8
Q
What kind of sugars are riboses and deoxyriboses?
A
Pentoses
9
Q
What’s the difference between a ribose and a deoxyribose?
A
OH at C2
10
Q
At which carbons on the ribose/deoxyribose are bases and phosphoric acids attached?
A
Phosphoric acids at C3 and C5
Base at C1
11
Q
What is a nucleoside?
A
P base + sugar
12
Q
Difference between nucleoside and nucleotide?
A
Phosphoric acid in the nucleotide
13
Q
What are nucleic acids?
A
Nucleotides linked together via the phosphate groups
14
Q
Nucleic acid sequence convention direction?
A
5’ –> 3’
15
Q
What group is free at the 5’ end of a nucleic acid?
A
Phosphate group
16
Q
What group is free at the 3’ end of a nucleic acid?
A
Hydroxyl at C3
17
Q
What kind of bonds link sugars in nucleic acids?
A
Phosphodiester bonds
18
Q
What is Chargaff’s rule?
A
The amount of adenine equals the amount of thymine, and that the amount of guanine equals the amount of cytosine in any double stranded DNA molecule
19
Q
Number of H bonds between C and G bases?
A
3
20
Q
Number of H bonds between A and T bases?
A
2
21
Q
Distance between base pairs?
A
3.4 angstroms
22
Q
How many bases per B DNA turn?
A
10
23
Q
Distance in a turn of DNA?
A
34 angstroms
24
Q
What causes the helix structure of DNA?
A
Hydrophobic and electrostatic interactions between bases
25
What holds the 2 DNA strands together?
H bonds and hydrophobic interactions
26
What is DNA transformation?
Ability to deliver foreign DNA to cells, both prokaryotic and eukaryotic
27
What is a plasmid?
Autonomously replicating DNA molecule
28
What are restriction endonucleases?
Molecular scissors to selectively cut DNA
29
What is DNA ligation?
The ability to join different pieces of DNA
30
What is DNA selection?
Methods to rapidly select those host cells that contain recombinant DNA
31
What is PCR? What does it stand for?
Amplifies DNA millions of fold, by repeated replication of a template
Polymerase Chain Reaction
32
How many BPs in human DNA?
3.3 B
33
How many BPs in plasmids?
3-10 K
34
How many BPs in bacteria?
3 M
35
What is personal genomics?
Branch of genomics where the genotyping stage employs single-nucleotide polymorphism (SNP) analysis (0.02% of genome) or partial/full genome sequencing
36
What is personalized medicine?
The tailoring of medical treatment to the genomic characteristics of each patient
37
Why is whole genome sequencing actually not sequencing someone's whole genome?
Because the human genome has repeat sequences that we are unable to sequence
38
What is an obstacle of treating cancer with personalized medicine?
A single biopsy of a tumor is not representative of the mutational landscape of the entire tumor
39
What is the purpose of a centromere on a chromosome?
It's required for chromosome segregation during cell division during which one copy of each sister chromatid is segregated to each daughter cell
40
What forms the kinetochore?
A repeated sequence in centromeres known as α-satellite DNA
41
How is telomere activity controlled? 2 mechanisms
1. Erosion: where part of the telomere is lost after each cell division leading to apoptosis.
2. Addition: of telomere sequence during active cell division is determined by the activity of telomerase
42
How do cancer cells become immortal?
Addition of telomere sequence by telomerase
43
What are the 2 main cells in the body that replicate?
Enterocytes and blood cells
44
What causes telomere erosion?
Their repeat sequences sometimes confuse the DNA polymerase and they get skipped during replication
45
How long is naked human DNA?
2 m
46
What are the 2 classes of DNA binding proteins?
1. Histones
| 2. Non-histone proteins
47
What are the 5 histones that bind DNA?
1. H1
2. H2A
3. H2B
4. H3
5. H4
48
Charge of histones? Why?
+
Because they contain basic AAs
49
How does chromatin form with histones?
1. H3 and H4 OR H2A and H2B form a dimer
2. 2 dimers form a tetramer, which binds DNA
3. A tetramer (different pairs than in step 1) bind to form an octamer of histone proteins ==> a nucleosome
4. Beads on a string then wraps itself into a helix
50
What is the role of H1?
It connects to the linker between adjacent nucleosomes
51
How thick is chromatin fiber?
300 angstroms
52
What DNA structure interacts with the nuclear matrix during DNA replication?
Chromatin fiber
53
What causes chromosome translocation? What can happen after the translocation? When is this common?
Caused by a rearrangement between nonhomologous chromosomes. A gene fusion may be created when the translocation joins two otherwise separated genes, the occurrence of which is common in cancer
54
What are the 2 main types of chromosome translocation?
1. Reciprocal (an exchange)
2. Robertsonian (transfer from one to the other, no exchange, where the participating acrocentric chromosomes break at their centromeres and the long arms fuse to form a single, large chromosome with a single centromere)
55
Other name for reciprocal translocation?
Non-Robertsonian
56
What does it mean for a translocation to be balanced or not?
Balanced: even exchange of material with no extra or missing genetic information
Unbalanced: unequal exchange of chromosome material resulting in extra or missing genes
57
What are acrocentric chromosomes?
Chromosomes with centromeres that aren't centered
58
Mechanism of Chronic Myeloid Leukemia (CML)?
Reciprocal translocation between chromosomes 9 and 22 creating the Philadelphia chromosome where the BCR from 22 and the ABL1 from 9 are joined causing the ABL1 to code for an out of control tyrosine kinase and abnormal cellular growth
59
What are epigenetics?
Heritable alterations in gene expression, which are not due to structural changes in the DNA. These changes are induced spontaneously, in response to environmental factors, or in response to the presence of a particular allele
60
5 types of epigenetic processes? What do they modify?
1. Methylation
2. Acetylation
3. Phosphorylation
4. Ubiquitylation
5. Sumolyation
Modify DNA and the histone proteins involved in packaging DNA
61
Example of environment epigenetics?
BPA in plastic bottles and in cans
62
4 functions of DNA methylation in mammals?
1. Transcriptional gene silencing
2. Chromatin compaction
3. Genome stability
4. X chromosome inactivation (females)
63
Which cytosines get methylated?
CPG dinucleotides
64
What is a Barr body?
Inactive X in females in the nucleus
65
What is dosage compensation?
X-inactivation in females for equal expression in males and females to normalize expression of X-linked genes
66
What is parental allele-specific imprinting?
Either the maternal or paternal allele is methylated significantly such that only one copy produces protein
67
What are imprint genes critical for?
For early brain development and the lack of proper methylation leads to diseases such as Prader-Willi syndrome, Beckwith-Wiedermann syndrome, Silver-Russell syndrome, and Angelman syndrome
68
What is an example of transgenerational epigenetic inheritance with a non imprinted gene? Explain.
The agouti viable yellow (Avy) gene.
The Avy locus is a jumping gene or retrotransposon present in thousands of copies in the mouse genome with one upstream of the agouti gene. The Avy elements are normally methylated, thus, shut off. However, in the Agouti mouse, they are unmethylated and active, leading to a yellow coat and very pronounced obesity
69
What is an example of environmental epigenetics with obesity?
Ancestral dichlorodiphenyltrichloroethane (DDT) exposure promotes epigenetic transgenerational inheritance of obesity
70
What are the consequences of the 5 histone modifications?
1. Methylation: turns gene off
2. Acetylation: turns gene on
3. Phosphorylation: both positive and negative consequences
4. Ubiquitylation: targets histones for degradation
5. Sumolyation: promotes gene silencing
71
How does histone acetylation turn genes on? What enzyme does this?
Histone acetylation by histone acetyltransferase (HAT) reduces the positive charge of the histone N-terminal tails that protrude from each nucleosome ==> tails make less contact with negatively charged patches on neighboring nucleosomes or the negatively charged DNA phosphate backbone ==> open chromatin structure accessible to the transcription machinery
72
Consequence of histone deacetylation? What enzyme does this?
The activity of histone deacetylase (HDAC) reestablishs the positive charge on lysines residues leading to a tighter packing of the DNA which is less accessible for regulatory factors
73
Role of DNA polymerase?
DNA synthesis
74
Role of DNA ligase?
Phosphodiester bond formation
75
Role of helicase?
Unwinds DNA helix
76
Role of single strand binding proteins?
Keep DNA single stranded during replication
77
Role of DNA primase?
Makes RNA primer that initiates DNA synthesis
78
Role of topoisomerase?
Removes torsional stress in DNA
79
What are Okazaki fragments?
Small segments of newly synthesized DNA on the lagging strand
80
Direction of DNA synthesis?
5' ==> 3'
81
Are the 2 antiparallel DNA strands replicated simultaneously?
Yes
82
What happens to the RNA primers used in DNA replication?
They are removed and the DNA fragments are joined by DNA ligase
83
Which parental strand produces the leading strand?
The strand at the 3' end
84
Which parental strand produces the lagging strand?
The strand at the 5' end
85
What are topoisomerase inhibitors? What are these used for?
They inhibit the religation of strands after ligation resulting in the accumulation of irreversible double strand breaks lethal to cells
These are chemotherapy agents
86
Original use for Viagra?
Blood flow to lungs in premature babies
