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Mcb1 > Genes And Chromosomes > Flashcards

Genes And Chromosomes Flashcards

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
Q

What are some characteristics of SINEs?

A

~300 bp, with > a million copies throughout the genome
~13% of the genome
All elements re most common

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26
Q

What are Alu elements?

A

Most abundant sequence in the human genome

Often play a role in unequal crossing over, leading to chromosomal deletions and duplications, or inversions

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27
Q

What are LINEs?

A

Long interspersed nuclear elements

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28
Q

What are some characteristics of LINEs?

A

L1 elements: ~6000bp long

~21% of the nuclear genome

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29
Q

What are SINEs and LINEs evolutionary remnants of?

A

Retrotransposons

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30
Q

What are retrotransposons?

A

“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

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31
Q

What do class 1 transposons do?

A

Use a “copy and paste” mechanism
Transcription to RNA
reverse transcription to DNA

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32
Q

LINEs carry genes for what?

A

Reverse transcriptase and an endonuclease (for reintegration)

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33
Q

What do class II transposons do?

A

Use a “cut and paste” mechanism

Require an enzyme called a transposase

34
Q

How do prokaryote package their DNA?

A

Use supercoiling

Coating with positively charged polyamines (spearmint or spermidine)

35
Q

How do Eukaryotes package their DNA?

A

Wrapping around small, positively charged proteins called histones

Compaction into chromatin

36
Q

How many base pairs are there in the double helix per turn?

A

10.5 by per turn

37
Q

When DNA is overwound what develops?

A

Positive supercoils

38
Q

When DNA is under wound what develops?

A

Negative supercoils

This restores the normal Watson and crick structure

39
Q

What increases the tendency toward strand separation?

A

Negative supercoils

Under winding typically precedes strand separation

40
Q

What occurs in front of strand separation such re replication and transcription?

A

Positive supercoils

41
Q

What occurs in front of eukaryotic replication forks?

A

Positive supercoils

42
Q

What typed of DNA is easier to separate?

A

It takes less energy to separate underwound DNA than to separate normal relaxed DNA

43
Q

What is linking number?

A

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
Q

If you have 2100 bp in a DNA circle and you have relaxed DNA (10.5 be per turn), what is the linking number?

A

Lk=2100/10.5=200

45
Q

How is Lk increased or decreased?

A

Negative supercoiling decreases Lk

Positive supercoiling increases Lk

46
Q

What are topoisomerases?

A

Enzymes that alter supercoiling

-relieves torsional stress by removing or creating supercoils

47
Q

What do type I topoisomerases do?

A

Nick DNA (cut one strand)

Don’t require energy

48
Q

What do type 2 Topoisomerase do?

A

Cut both strands of DNA

Require ATP

49
Q

How many topoisomerase do bacteria have?

A

4

2 of each type I and type 2

50
Q

What is gyrase?

A

A special topoisomerase found in bacteria with unique properties

51
Q

By how much does type 1 topoisomerase change Lk by?

A

They change Lk by 1

52
Q

What is the reaction mechanism of type 1 of topoisomerase?

A
  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
Q

How many super oils do type 2 topoisomerase remove and by how much do they change Lk?

A

Removes 2 supercoils at a time and change Lk by 2

54
Q

Where is type 2 topoisomerase activated at?

A

Regions where 2 double strands cross over each other

55
Q

What is the reaction mechanism for type 2 topoisomerase?

A
  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
Q

What does gyrase introduce to DNA?

A

Introduces negative supercoils using energy from ATP hydrolysis

57
Q

What is the function of DNA gyrase?

A

The negative supercoils introduced neutralize the positive supercoils introduced by strand unwinding during DNA replication

58
Q

What are some examples of type 2 topoisomerase (gyrase) inhibitors (antibiotics).

A

Quinolones: -1. Fluoroquinolones, -2. Nalidixic Acid, -3. Ciprofloxacin

59
Q

What is the major for of chromatic during interphase?

A

Euchromatin

60
Q

What is the major form of chromatin during mitosis and meiosis?

A

Heterochromatin

61
Q

Where is heterochromatin found during interphase?

A

Nuclear periphery

-Genes are unavailable for transcription and silent

62
Q

What is the basic unit of a chromatin?

A

Nucleosomes

~1.8 turns of DNA (146bp) about a histone octamer

63
Q

What is a histone octamer found in a nucleosome?

A 
2 of each:
H2A
H2B
H3
H4
64
Q

What does Histone H1 bind to?

A

Binds the linker DNA DNA facilitates higher level of packaging (30nm fiber or solenoid fiber)

65
Q

What does a nucleosome look like?

A

“Beads-on-a-string” or the 10nm Fiber

66
Q

How does Nuclease break down chromatin and naked DNA?

A

Chromatin produces DNA fragments 146 by in length

Naked DNA is completely broken down into nucleotides

67
Q

What are the four core proteins found in the same protein family?

A

H2A
H2B
H3
H4

68
Q

What kind of charge do histones carry?

A

They are positively charged because they are rich in Lysine and Arginine

69
Q

How do core histones attach to DNA?

A

They behind very strongly to the negatively charged phosphate groups of DNA through ionic interactions (mainly in minor groove)

70
Q

What are the parts of a nucleosome?

A

Hydrophobic core (C-terminal alpha-helical domains)

N-terminal tails (flexible, rich in Lys and Arg)

71
Q

How can the tails of nucleosome be modified?

A

The basic residues in the tail can be modified by acetylation or methylation

(Example of epigenetics)

72
Q

How can you neutralize histones ?

A

Acetylation of Lys or Arg neutralizes their positive charge

73
Q

What is histone acetylation associated with?

A

Euchromatin

Active gene expression

74
Q

What is Histone deacetylation associated with?

A

Heterochromatin

Gene silencing

75
Q

What are the enzymes involved in Histone acetylation?

A

Histone acetyltransferase (HATS) add acetylation groups

Histone Deacetylases (HDACs) remove acetylation groups

76
Q

Where can methylation occur in a histone?

A

Methyl groups can be added to Lys and Arg residues in their tails

77
Q

What are the effects of histone methylation?

A

W/ Eu/heterochromatin
Depends on which specific reside in the various histones is methylated
Mediated by other proteins that bind these methylation

78
Q

What are some examples of histone methylation?

A

H3K9-trimethylation is associated with heterochromatin and gene silencing

H3K4-trimethylation is associated with euchromatin and gene expression

79
Q

What kind of supercoil do histones introduce?

A

Negative supercoiling

80
Q

What are some examples of Eukaryotic topoisomerase inhibitors (chemotherapeutics)?

A

Type I topoisomerse inhibitors : Irinotecan, topotecan

Type II topoisomerase inhibitors: amsacrine, etoposide, doxorubicin*, daunorubicin

Mcb1 (13 decks)

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