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Mcb1 > Genes And Chromosomes > Flashcards

Genes And Chromosomes Flashcards

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1
Q

What accounts for the non coding sequence in humans?

A

Regulatory sequences]

Unknown function

  • repetitive DNA (not in bacteria)
  • unique sequence
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2
Q

What are regulatory sequences?

A

Signal defining the start or end of a gene
Influence transcription and translation
Introns (not in bacteria)
Invitation points for replication

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3
Q

What percent human DNA codes for protein?

A

~1.5%

59% is repetitive DNA
24% regulatory gens
15% unknown

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4
Q

What kind of genes have introns?

A

Eukaryotic genes have introns

Prokaryotic genes do not

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5
Q

Eukaryotic genes are monoistronic, what does it mean?

A

One gene/mRNA

Alternative splicing may result in multiple mRNAs per gene

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6
Q

Prokaryotic genes may be polycistronic, what does this mean?

A

Multiple genes/mRNA

Usually with related function

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7
Q

What is a plasmid in bacteria?

A

Independent circular DNA
Replicate autonomously
Have horizontal gene transfer in bacteria

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8
Q

DNA in a bacteria (in the nucleoid) is attached to what?

A

A core protein and RNA

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9
Q

What protein core is seen in bacterial DNA?

A

HU: a histone-like protein that bends DNA in a tight circle

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10
Q

What is RNAse?

A

An enzyme that degrades RNA

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11
Q

What are some examples of genes that are repeated in the human genome?

A

Histone genes

rRN genes

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12
Q

What are the characteristics of highly repeated sequences?

A 
Almost always the same
Short repeated units
Repeated in Tandem in clusters
>100k repeats
3% of the human genome
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13
Q

What are the characteristics of moderately repeated genes?

A

Diverge considerably
Larger repeated units
Dispersed throughout our genome
42% of the human genome

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14
Q

What is highly repeated DNA referred as? Why?

A

Satellite DNA because it separates from the bulk of the genomic DNA in ultracentrifugation
-like a satellite of a larger body

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15
Q

What are the 3 classes of satellites?

A

Satellite
Minisatellite
Micro satellite

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16
Q

Where are satellites usually found?

A

Centromeres where spindles attach (kinetochore)

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17
Q

Where are mimisatellites found?

A

Telomeric repeats

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18
Q

What are minisatellites used for?

A

DNA markers in DNA fingerprinting and allele tracking

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19
Q

Which of the satellites are polymorphic?

A

Minisatellite

Micro satellite

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20
Q

What are microsatellites also known as?

A

Short tandem repeats (STR)

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21
Q

What satellites can be used for DNA markers in DNA fingerprinting and allele tracking?

A

Mini and micro satellites

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22
Q

What is a telomere?

A 
A special class of minisatellites
Repeat ~1500 times at the end of all chromosomes

Vertebrate telomeres repeat sequence:TTAGGG

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23
Q

What are the 2 clases of interspersed repeats? (Moderately repeated DNA)s

A

SINEs

LINEs

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24
Q

What are SINEs?

A

Short interpersed nuclear elements

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25
What are some characteristics of SINEs?
~300 bp, with > a million copies throughout the genome ~13% of the genome All elements re most common
26
What are Alu elements?
Most abundant sequence in the human genome | Often play a role in unequal crossing over, leading to chromosomal deletions and duplications, or inversions
27
What are LINEs?
Long interspersed nuclear elements
28
What are some characteristics of LINEs?
L1 elements: ~6000bp long | ~21% of the nuclear genome
29
What are SINEs and LINEs evolutionary remnants of?
Retrotransposons
30
What are retrotransposons?
"Jumping genes" DNA fragments that can copy themselves to new locations 99.9% are inactive. A small number remain active and can cause gene mutations after transposition
31
What do class 1 transposons do?
Use a "copy and paste" mechanism Transcription to RNA reverse transcription to DNA
32
LINEs carry genes for what?
Reverse transcriptase and an endonuclease (for reintegration)
33
What do class II transposons do?
Use a "cut and paste" mechanism | Require an enzyme called a transposase
34
How do prokaryote package their DNA?
Use supercoiling | Coating with positively charged polyamines (spearmint or spermidine)
35
How do Eukaryotes package their DNA?
Wrapping around small, positively charged proteins called histones Compaction into chromatin
36
How many base pairs are there in the double helix per turn?
10.5 by per turn
37
When DNA is overwound what develops?
Positive supercoils
38
When DNA is under wound what develops?
Negative supercoils This restores the normal Watson and crick structure
39
What increases the tendency toward strand separation?
Negative supercoils Under winding typically precedes strand separation
40
What occurs in front of strand separation such re replication and transcription?
Positive supercoils
41
What occurs in front of eukaryotic replication forks?
Positive supercoils
42
What typed of DNA is easier to separate?
It takes less energy to separate underwound DNA than to separate normal relaxed DNA
43
What is linking number?
The number of times one strand crosses the other Is a method for quantitatively describing supercoiling In DNA Lk= length of DNA in bp/ Number of bp per turn
44
If you have 2100 bp in a DNA circle and you have relaxed DNA (10.5 be per turn), what is the linking number?
Lk=2100/10.5=200
45
How is Lk increased or decreased?
Negative supercoiling decreases Lk Positive supercoiling increases Lk
46
What are topoisomerases?
Enzymes that alter supercoiling -relieves torsional stress by removing or creating supercoils
47
What do type I topoisomerases do?
Nick DNA (cut one strand) Don't require energy
48
What do type 2 Topoisomerase do?
Cut both strands of DNA Require ATP
49
How many topoisomerase do bacteria have?
4 | 2 of each type I and type 2
50
What is gyrase?
A special topoisomerase found in bacteria with unique properties
51
By how much does type 1 topoisomerase change Lk by?
They change Lk by 1
52
What is the reaction mechanism of type 1 of topoisomerase?
1. A hydroxyl in a tyrosine (Y) in the enzyme attacks a phosphodiester bond on one strand 2. The cleaved strand rotates around the other strand 3. The cleaved strand is religated
53
How many super oils do type 2 topoisomerase remove and by how much do they change Lk?
Removes 2 supercoils at a time and change Lk by 2
54
Where is type 2 topoisomerase activated at?
Regions where 2 double strands cross over each other
55
What is the reaction mechanism for type 2 topoisomerase?
1. The enzyme binds to one double-strand (called G segment, for gate) 2. It then binds 2 ATP molecules, undergoes a structural transition, and cleaves both strands of the G segment 3. The second double-strand (T segment, for transport) moves through the break 4. The G segment is re-ligated and ATP hydrolysis resets the enzyme
56
What does gyrase introduce to DNA?
Introduces negative supercoils using energy from ATP hydrolysis
57
What is the function of DNA gyrase?
The negative supercoils introduced neutralize the positive supercoils introduced by strand unwinding during DNA replication
58
What are some examples of type 2 topoisomerase (gyrase) inhibitors (antibiotics).
Quinolones: -1. Fluoroquinolones, -2. Nalidixic Acid, -3. Ciprofloxacin
59
What is the major for of chromatic during interphase?
Euchromatin
60
What is the major form of chromatin during mitosis and meiosis?
Heterochromatin
61
Where is heterochromatin found during interphase?
Nuclear periphery -Genes are unavailable for transcription and silent
62
What is the basic unit of a chromatin?
Nucleosomes ~1.8 turns of DNA (146bp) about a histone octamer
63
What is a histone octamer found in a nucleosome?
``` 2 of each: H2A H2B H3 H4 ```
64
What does Histone H1 bind to?
Binds the linker DNA DNA facilitates higher level of packaging (30nm fiber or solenoid fiber)
65
What does a nucleosome look like?
"Beads-on-a-string" or the 10nm Fiber
66
How does Nuclease break down chromatin and naked DNA?
Chromatin produces DNA fragments 146 by in length Naked DNA is completely broken down into nucleotides
67
What are the four core proteins found in the same protein family?
H2A H2B H3 H4
68
What kind of charge do histones carry?
They are positively charged because they are rich in Lysine and Arginine
69
How do core histones attach to DNA?
They behind very strongly to the negatively charged phosphate groups of DNA through ionic interactions (mainly in minor groove)
70
What are the parts of a nucleosome?
Hydrophobic core (C-terminal alpha-helical domains) N-terminal tails (flexible, rich in Lys and Arg)
71
How can the tails of nucleosome be modified?
The basic residues in the tail can be modified by acetylation or methylation (Example of epigenetics)
72
How can you neutralize histones ?
Acetylation of Lys or Arg neutralizes their positive charge
73
What is histone acetylation associated with?
Euchromatin | Active gene expression
74
What is Histone deacetylation associated with?
Heterochromatin | Gene silencing
75
What are the enzymes involved in Histone acetylation?
Histone acetyltransferase (HATS) add acetylation groups Histone Deacetylases (HDACs) remove acetylation groups
76
Where can methylation occur in a histone?
Methyl groups can be added to Lys and Arg residues in their tails
77
What are the effects of histone methylation?
W/ Eu/heterochromatin Depends on which specific reside in the various histones is methylated Mediated by other proteins that bind these methylation
78
What are some examples of histone methylation?
H3K9-trimethylation is associated with heterochromatin and gene silencing H3K4-trimethylation is associated with euchromatin and gene expression
79
What kind of supercoil do histones introduce?
Negative supercoiling
80
What are some examples of Eukaryotic topoisomerase inhibitors (chemotherapeutics)?
Type I topoisomerse inhibitors : Irinotecan, topotecan Type II topoisomerase inhibitors: amsacrine, etoposide, doxorubicin*, daunorubicin

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