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ALL THE THINGS Flashcards

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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
What is the vertebrate telomere repeat sequence?
TTAGGG
26
What are the 2 classes of interspersed repeats?
SINEs (Short interspersed nuclear elements) LINEs (Long INEs)
27
Describe SINEs
~300 bp with > a million copies throughout the genome 13% of the genome
28
What is the most common type of SINE?
Alu Elements; most abundant in the human genome; plays a role in unequal crossing over
29
Describe LINEs
L1 elements: ~6000 bp long, 21% of the nuclear genome
30
SINEs and LINEs are evolutionary remnants of what?
retrotransposons
31
What are retrotransposons?
"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
32
What are Class I transposons?
use a copy and paste mechanism; transcription to RNA; reverse transcription to DNA
33
LINEs carry genes for what two things?
reverse transcriptase and an endonuclease (for reintegration), hence their large size
34
~3% of the human genome also contains what class of transposons?
Class II
35
What are Class II transposons?
use a cut and paste mechanism
36
What enzyme is required by Class II transposons?
transposase
37
Packaging DNA takes into account what characteristics of DNA?
Size and charge of the DNA
38
How do prokaryotes package DNA?
supercoiling; coating with positively charged polyamines (spermine or spermidine)
39
How do eukaryotes package DNA?
wrapping around postively charged Histone proteins; compacts the DNA into chromatin
40
How would you describe supercoiling in simple terms?
supercoiling is coiling of a coil
41
Why does supercoiled DNA migrate more quickly in Gel Electrophoresis?
because it is more compact
42
When DNA is 'overwound,' what does it develop?
positive supercoils
43
Where do positive supercoils occur?
occurs in front of strand separation (during replication and transcription)
44
When DNA is 'underwound,' what does it develop?
negative supercoils
45
What do negative supercoils increase the chance of?
strand separation
46
Supercoiled DNA is in a ____ energy state
higher
47
What are the two functions of supercoiling?
compact the DNA (both positive and negative) facilitate strand separation (only negative)
48
In bacterial chromosome replication, strand separation causes what and results in what?
causes overwinding and results in positive supercoils
49
Where in Eukaryotic replication do we see strand separation that results in positive supercoils?
eukaryotic replication forks
50
What is the linking number?
the number of times one strand crosses the other
51
Determining the linking number allows us to ---
quantitatively describe supercoiling
52
What is the equation used to find the linking number?
In DNA: Lk = Length of DNA in bp / Number of bp per turn
53
All DNA molecules will have a Lk above ---
0
54
How is the Lk number affected by positive and negative supercoiling?
Negative: decreases Lk Positive: increases Lk
55
Enzymes that alter supercoiling are ---
called Topoisomerases
56
What do topoisomerases do?
relieve torsional stress by removing or creating supercoils
57
What are the two families of topoisomerases?
Type I and Type II
58
What do Type I topoisomerases do?
Nick DNA (cut one strand) don't require energy
59
What do Type II topoisomerases do?
cut both strands require ATP
60
How many topoisomerases do Bacteria have?
4 2 of each type One of the Type II's is Gyrase with unique properties
61
How many supercoils are removed by Type I topoisomerases?
1 supercoil at a time | Changes the Lk by 1
62
What is the reaction mechanism for Topoisomerase I?
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
In the first step of the topoisomerase 1 reaction, what transient bond is generated?
tyrosine-phosphate bond
64
How many supercoils are removed at a time by Type II topoisomerases?
2 supercoils Change Lk by 2
65
At what regions are type II topoisomerases activated?
where 2 double-strands cross over each other
66
What is the reaction mechanism for type II topoisomerases?
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
What is DNA Gyrase and what does it do?
a type II topoisomerase Introduces negative supercoils using energy from ATP hydrolysis Acts like a swivel ahead of the replication fork
68
What are some common bacterial type II topoisomerase (Gyrase) inhibitors?
Quinolones like Nalidixic acid and ciprofloxacin the inhibitors are often antibiotics
69
Are the bacterial topoisomerase type II inhibitors effective against eukaryotic ones?
NO. They have a low affinity for the eukaryotic counterparts
70
Eukaryotic chromosomes are packaged into what?
Chromatin: complex assembly of DNA, histones and non histone chromatin proteins
71
What is Euchromatin?
dispersed, open structure; major form of chromatin during interphase; has genes available for transcription
72
What is Heterochromatin?
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
What is a nucleosome?
the basic unit of chromatin; ~1.8 turns of DNA about a histone octamer
74
What are 4 core histones that make up the histone octamer?
H2A, H2B, H3, H4
75
Each nucleosome is separated by a variable amount of DNA called ---
Linker DNA
76
Nucleosomes assemble on what kind of DNA and are separated by what kind of DNA?
naked DNA; linker DNA
77
Where does Histone H1 bind to facilitate higher level packaging that creates the 30 nm fiber (Solenoid)?
binds the linker DNA
78
What is another name for the nucleosome?
10 nm fiber
79
When chromatin is treated with nuclease what happens?
146 bp in length DNA fragments are created Naked DNA is completely broken down into nucleotides
80
Can nuclease still do its job when DNA is bound by a protein?
No. The DNA is protected from digestion
81
The core histones belong to the same ---
protein family; well conserved evolutionarily
82
What are some characteristics of the core histones?
small proteins encoded by small genes (no introns) positively charged (rich in K and R)
83
How and where do the core histones bind DNA?q
bind very strongly to the negatively charged phosphate groups of DNA through ionic interactions mainly in the minor groove
84
Describe the hydrophobic core of the nucleosome
C-terminal alpha-helical domains
85
Describe the N-terminal tails of the nucleosome
flexible, relatively unstructured; rich in K and R, interact with phosphates in DNA backbone
86
How can the basic residues in the tails of the nucleosome be modified?
acetylation or methylation
87
What does Histone acetylation do?
neutralizes positive charge of K and R; weakens binding of histones; leads to more open chromatin structures
88
Histone acetylation/deactylation is associated with ---
Euchromatin ---- active gene expression Heterochromatin ---- gene silencing
89
What do the enzymes Histone acetyltransferase and histone deacetylase do respectively?
HATs add acetyl groups HDACs remove acetyl groups
90
Histone methylation has what kinds of effects?
variable; gene silencing/expression
91
What is important about Histone methylation?
associate with either eu- or heterochromatin; depends on which specific histone residues are metylated; effects mediated by other proteins that bind to methylation
92
What is the Histone Code?
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
How many methylations can K have?
lysine can be trimethylated
94
Are acetylation and methylation the only ways histones can be modified?
NO! many many more ways!
95
Histones induce what kind of supercoling in eukaryotic DNA?
negative suprcoling
96
What are eukaryotic topoisomerase inhibitors called?
chemotherapeutics
97
Eukaryotic type I topoisomerase inhibitors include ---
Irinotecan, topotecan
98
Eukaryotic type II topoisomeras inhibitors include ---
doxorubicin, amsacrine, etoposide, daunorubicin
99
Histone H1 facilitates coiling of the 10 nm fiber into what?
30 nm fiber or solenoid 6 nucleosomes per rotation
100
The 30 nm fiber forms loops which anchor to what?
a scaffold protein topoisomerases are components of the scaffold

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