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GENES & CHROMOSOMES > ALL THE THINGS > Flashcards

ALL THE THINGS Flashcards

1
Q

Do prokaryotic genes have introns?

A

NO

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2
Q

Do eukaryotic genes have introns?

A

YES

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3
Q

Eukaryotic genes are monocistronic. What does this mean?

A

one gene per mRNA; alternative splicing may result in multiple mRNA’s per gene

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4
Q

Prokaryotic genes may be polycistronic. What does this mean?

A

multiple genes per mRNA; usually with related function

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5
Q

What is the shape of plasmid DNA in Bacteria?

A

circular

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6
Q

How does a plasmid replicate?

A

autonomously

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7
Q

What kind of gene transfer occurs in bacteria?

A

horizontal gene transfer through the plasmids

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8
Q

Plasmids are used frequently in what type of DNA technology?

A

recombinant DNA tech

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9
Q

The circular bacterial DNA is ___ longer than the cell diameter

A

80X

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10
Q

In the bacterial nucleoid, how is the DNA stored?

A

attached to a core protein and RNA; supercoiled with 40 loops

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11
Q

What are two examples of coding repeats in the genome?

A

Histone genes (116 genes for 5 classes of histones)

rRNA genes in the p-arms of acrocentric chromosomes

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12
Q

What fraction of the repetitive DNA do coding/non-coding repeats comprise?

A

very small fraction

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13
Q

Describe Highly Repeated DNA

A

repeated sequence is almost always the same

short repeated units ( < few hundred bp )

repeated in tandem in clusters (tandem repeats)

make up 3% of the human genome

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14
Q

Describe Moderately Repeated DNA

A

repeated sequence may diverge considerably

large repeated units (few thousand bp)

dispersed throughout our genomes (interspersed repeats)

make up 42% of the human genome

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15
Q

Why are tandem repeats referred to as “satellite DNA”?

A

because it separates from the bulk of the genomic DNA in ultracentrifugation

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16
Q

What are the 3 classes of tandem repeats?

A

Satellite, Minisatellite, Microsatellite

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17
Q

Describe satellite DNA

A

171 or 68 bp repeats extending over millions of bp

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18
Q

Where can you find satellite DNA?

A

found in centromeres where spindles attach (kinetochore)

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19
Q

Describe minisatellite DNA

A

6-64 bp repeats, highly variable total repeat size (polymorphic)

Used as DNA markers in DNA fingerprinting and allele tracking

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20
Q

Where can you find minisatellite DNA?

A

telomeric repeats

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21
Q

Describe microsatellite DNA

A

aka Short Tandem Repeats (STRs)

Di-, tri-, tetranucleotide units, highly variable total repeat size (polymorphic)

Use as DNA markers in DNA fingerprinting and allele tracking

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22
Q

Where can you find microsatellite DNA?

A

CA-repeats

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23
Q

What are variable number tandem repeats (VNTRs)?

A

either mini- or microsatellite repeats

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24
Q

Telomeres are a special class of what?

A

minisatellites

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25
Q

What is the vertebrate telomere repeat sequence?

A

TTAGGG

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26
Q

What are the 2 classes of interspersed repeats?

A

SINEs (Short interspersed nuclear elements)

LINEs (Long INEs)

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27
Q

Describe SINEs

A

~300 bp with > a million copies throughout the genome

13% of the genome

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28
Q

What is the most common type of SINE?

A

Alu Elements; most abundant in the human genome; plays a role in unequal crossing over

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29
Q

Describe LINEs

A

L1 elements: ~6000 bp long, 21% of the nuclear genome

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30
Q

SINEs and LINEs are evolutionary remnants of what?

A

retrotransposons

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31
Q

What are retrotransposons?

A

“jumping genes”; DNA fragments that can copy themselves to new locations;

99.9% inactive, but a small number remain active and can cause gene mutations after transposition

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32
Q

What are Class I transposons?

A

use a copy and paste mechanism; transcription to RNA; reverse transcription to DNA

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33
Q

LINEs carry genes for what two things?

A

reverse transcriptase and an endonuclease (for reintegration), hence their large size

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34
Q

~3% of the human genome also contains what class of transposons?

A

Class II

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35
Q

What are Class II transposons?

A

use a cut and paste mechanism

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36
Q

What enzyme is required by Class II transposons?

A

transposase

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37
Q

Packaging DNA takes into account what characteristics of DNA?

A

Size and charge of the DNA

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38
Q

How do prokaryotes package DNA?

A

supercoiling; coating with positively charged polyamines (spermine or spermidine)

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39
Q

How do eukaryotes package DNA?

A

wrapping around postively charged Histone proteins; compacts the DNA into chromatin

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40
Q

How would you describe supercoiling in simple terms?

A

supercoiling is coiling of a coil

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41
Q

Why does supercoiled DNA migrate more quickly in Gel Electrophoresis?

A

because it is more compact

42
Q

When DNA is ‘overwound,’ what does it develop?

A

positive supercoils

43
Q

Where do positive supercoils occur?

A

occurs in front of strand separation (during replication and transcription)

44
Q

When DNA is ‘underwound,’ what does it develop?

A

negative supercoils

45
Q

What do negative supercoils increase the chance of?

A

strand separation

46
Q

Supercoiled DNA is in a ____ energy state

A

higher

47
Q

What are the two functions of supercoiling?

A

compact the DNA (both positive and negative)

facilitate strand separation (only negative)

48
Q

In bacterial chromosome replication, strand separation causes what and results in what?

A

causes overwinding and results in positive supercoils

49
Q

Where in Eukaryotic replication do we see strand separation that results in positive supercoils?

A

eukaryotic replication forks

50
Q

What is the linking number?

A

the number of times one strand crosses the other

51
Q

Determining the linking number allows us to —

A

quantitatively describe supercoiling

52
Q

What is the equation used to find the linking number?

A

In DNA:

Lk = Length of DNA in bp / Number of bp per turn

53
Q

All DNA molecules will have a Lk above —

A

0

54
Q

How is the Lk number affected by positive and negative supercoiling?

A

Negative: decreases Lk
Positive: increases Lk

55
Q

Enzymes that alter supercoiling are —

A

called Topoisomerases

56
Q

What do topoisomerases do?

A

relieve torsional stress by removing or creating supercoils

57
Q

What are the two families of topoisomerases?

A

Type I and Type II

58
Q

What do Type I topoisomerases do?

A

Nick DNA (cut one strand)

don’t require energy

59
Q

What do Type II topoisomerases do?

A

cut both strands

require ATP

60
Q

How many topoisomerases do Bacteria have?

A

4

2 of each type

One of the Type II’s is Gyrase with unique properties

61
Q

How many supercoils are removed by Type I topoisomerases?

A

1 supercoil at a time

Changes the Lk by 1

62
Q

What is the reaction mechanism for Topoisomerase I?

A
  1. hydroxyl from a tyrosine in the enzyme attacks the phosphodiester bond on one side.
  2. The cleaved strand rotates around the other strand
  3. The cleaved strand is re-ligated

THE REACTION IS A TRANSESTERIFICATION RXN

63
Q

In the first step of the topoisomerase 1 reaction, what transient bond is generated?

A

tyrosine-phosphate bond

64
Q

How many supercoils are removed at a time by Type II topoisomerases?

A

2 supercoils

Change Lk by 2

65
Q

At what regions are type II topoisomerases activated?

A

where 2 double-strands cross over each other

66
Q

What is the reaction mechanism for type II topoisomerases?

A
  1. enzyme binds to one double strand (G-segment)
  2. theN binds 2 ATP molecules, undergoes structural transition, and cleaves both strands of the G segment
  3. The second double strand (T-segment) moves through the break
  4. The G-segment is religated and ATP hydrolysis resets the enzyme
67
Q

What is DNA Gyrase and what does it do?

A

a type II topoisomerase

Introduces negative supercoils using energy from ATP hydrolysis

Acts like a swivel ahead of the replication fork

68
Q

What are some common bacterial type II topoisomerase (Gyrase) inhibitors?

A

Quinolones like Nalidixic acid and ciprofloxacin

the inhibitors are often antibiotics

69
Q

Are the bacterial topoisomerase type II inhibitors effective against eukaryotic ones?

A

NO. They have a low affinity for the eukaryotic counterparts

70
Q

Eukaryotic chromosomes are packaged into what?

A

Chromatin: complex assembly of DNA, histones and non histone chromatin proteins

71
Q

What is Euchromatin?

A

dispersed, open structure; major form of chromatin during interphase; has genes available for transcription

72
Q

What is Heterochromatin?

A

condensed, closed structure; major form of chromatin during mitosis and meiosis; found at the nuclear periphery during interphase; genes are unavailable for transcription and silent

73
Q

What is a nucleosome?

A

the basic unit of chromatin; ~1.8 turns of DNA about a histone octamer

74
Q

What are 4 core histones that make up the histone octamer?

A

H2A, H2B, H3, H4

75
Q

Each nucleosome is separated by a variable amount of DNA called —

A

Linker DNA

76
Q

Nucleosomes assemble on what kind of DNA and are separated by what kind of DNA?

A

naked DNA; linker DNA

77
Q

Where does Histone H1 bind to facilitate higher level packaging that creates the 30 nm fiber (Solenoid)?

A

binds the linker DNA

78
Q

What is another name for the nucleosome?

A

10 nm fiber

79
Q

When chromatin is treated with nuclease what happens?

A

146 bp in length DNA fragments are created

Naked DNA is completely broken down into nucleotides

80
Q

Can nuclease still do its job when DNA is bound by a protein?

A

No. The DNA is protected from digestion

81
Q

The core histones belong to the same —

A

protein family; well conserved evolutionarily

82
Q

What are some characteristics of the core histones?

A

small proteins encoded by small genes (no introns)

positively charged (rich in K and R)

83
Q

How and where do the core histones bind DNA?q

A

bind very strongly to the negatively charged phosphate groups of DNA through ionic interactions mainly in the minor groove

84
Q

Describe the hydrophobic core of the nucleosome

A

C-terminal alpha-helical domains

85
Q

Describe the N-terminal tails of the nucleosome

A

flexible, relatively unstructured; rich in K and R, interact with phosphates in DNA backbone

86
Q

How can the basic residues in the tails of the nucleosome be modified?

A

acetylation or methylation

87
Q

What does Histone acetylation do?

A

neutralizes positive charge of K and R; weakens binding of histones; leads to more open chromatin structures

88
Q

Histone acetylation/deactylation is associated with —

A

Euchromatin —- active gene expression

Heterochromatin —- gene silencing

89
Q

What do the enzymes Histone acetyltransferase and histone deacetylase do respectively?

A

HATs add acetyl groups

HDACs remove acetyl groups

90
Q

Histone methylation has what kinds of effects?

A

variable; gene silencing/expression

91
Q

What is important about Histone methylation?

A

associate with either eu- or heterochromatin; depends on which specific histone residues are metylated; effects mediated by other proteins that bind to methylation

92
Q

What is the Histone Code?

A

hypothesis that specific combinations of histone modifications provide information (or a language) that specifies the structural state of chromatin, and thus the degree of gene expression

93
Q

How many methylations can K have?

A

lysine can be trimethylated

94
Q

Are acetylation and methylation the only ways histones can be modified?

A

NO! many many more ways!

95
Q

Histones induce what kind of supercoling in eukaryotic DNA?

A

negative suprcoling

96
Q

What are eukaryotic topoisomerase inhibitors called?

A

chemotherapeutics

97
Q

Eukaryotic type I topoisomerase inhibitors include —

A

Irinotecan, topotecan

98
Q

Eukaryotic type II topoisomeras inhibitors include —

A

doxorubicin, amsacrine, etoposide, daunorubicin

99
Q

Histone H1 facilitates coiling of the 10 nm fiber into what?

A

30 nm fiber or solenoid

6 nucleosomes per rotation

100
Q

The 30 nm fiber forms loops which anchor to what?

A

a scaffold protein

topoisomerases are components of the scaffold

GENES & CHROMOSOMES (1 decks)

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