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Bioc 406 03 > L 16 > Flashcards

L 16 Flashcards

(46 cards)

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1
Q

What are some uses of DNA sequencing?

A
  • Research: unjerstand genomes, phylogeny
  • Research tool to manipulate DNA: forsensic science
  • Medicine: genetic testing, personalized medicine.
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2
Q

What is an essential tool for DNA sequencing? (that’s not normally found in nature)

A

ddNTPs

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3
Q

What are ddNTPs?

A

DideoxyNTP.

-synthetic nucleotides that lack 3’-OH

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4
Q

What is the reaction mixture for sanger method?

A
  1. Template
  2. Primer
  3. dNTPs
  4. ddNTPs
  5. Polymerase (taq Pol)
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5
Q

What happens during DNA sequencing if you have too much ddNTP?

A

Short terminated primers, and not very good coverage over the template

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6
Q

What happens during DNA sequencing if you have a polymerase that makes too much errors?

A

Errors are incorporated into the product

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7
Q

What does ACV stand for?

A

Acyclovir, nucleoside analogue

- an antiviral (pro)drug

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8
Q

ACV is a key drug against what?

A

Against herpes viruses, cytomegalovirus

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9
Q

How is ACV activated in infected cells? What does it mimic?

A

activated by phosphorylation, making it a dGTP mimic

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10
Q

ACV-TP is an active form, what does it lack and what is it called?

A

lacks a 3’-OH and is a chain terminator

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11
Q

Why is ACV very effective and has low toxicity?

A

it’s because it has a much better substrate for viral TK and viral DNA polymerase than for human TK or polymerases

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12
Q

What are sources of DNA sequence errors?

A
  1. base misincorporation (dU instead of dT)
  2. chemical mutagenesis
  3. ionizing radiation (UV, x rays, cosmic rayrs)
  4. genetic mutagenesis (retrovirus integration)
  5. spontaneous lesions (backbone hydrolysis)
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13
Q

What is mutagenesis?

A

genetic information of an organism is changed in a stable manner

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14
Q

What kind of mutations are there?

A
  1. base substitution: transitions and transversions
  2. insertions and deletions
  3. breaks in the backbone
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15
Q

What are Darwin’s three ideas that provide an explanation of biological diversity

A
  1. variation
  2. heritable
  3. differential survival (fitness)
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16
Q

As genomes get larger, what happens with the mutation rate?

A

It increases and is poorly tolerated as there are more critical parts to higher eukaryotes.

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17
Q

How many bases does the human genome have?

A

~3billion bases

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18
Q

What percentage of the human genome is repeating?

A

Fifty

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19
Q

What percentage of the human genome transcribes to RNA

20
Q

What percentage of the human genome encodes proteins?

21
Q

RNA is the intermediate in the central dogma, state the process.

Study These Flashcards
A

DNA–Transcription–> mRNA to which it utilizes tRNA –Translation–>protein

22
Q

What is the RNA world hypothesis?

Study These Flashcards
A
  1. Genetic continuity via RNA replication
  2. Watson Crick base paring was the key to replication
  3. Genetically encoded proteins were not catalysts
23
Q

RNA is catalytic, what could it function as? (two things)

Study These Flashcards
A

both genome and replicase

24
Q

RNA is the only currently used macromolecule that is both what?

Study These Flashcards
A

carrier of genetic info and an enzyme

25
Why have DNA when we have RNA?
DNA is more stable while | RNA is susceptible to base catalyzed hydrolysis
26
Why are proteins used instead of ribozymes?
Amino acids provide more catalytic diversity than ribozymes b/c of functional groups
27
How does reverse transcriptase for viral enzyme work?
1. Retrovirus uses RNA template 2. 5 to 3 synthesis 3. antithetical to central dogma 4. makes cDNA so there's no proof reading
28
Overall the quantity of DNA roughly correlates with what?
an organism's complexity
29
What is heterochromatin?
portions of chromatin that are relatively tightly condensed. Not much transcription occurs
30
What is euchromatin?
portions of chromatin that are loosely packed These are regions of active transcription
31
What does chromatin influence?
influences gene expression, nuclesomes, remodeling complex
32
What are two types of histones?
HATs- histone acetlytransferases (increases gene expression by loosing up DNA) HDACs- histone deacetylases (decreases gene expression by condensing DNA)
33
What does histone methylation do?
silence or activate genes
34
What are the names of transciprtional activators?
activators (enhancers) | repressors (silencers)
35
How is transcription initiation regulated by DNA accessibility?
by changing chromatin structure
36
During transcription, motors use energy of ATP hydrolysis to do what?
shove nucleosomes back and forth on DNA. The enzymes resemble helicases and helps expose promoter sequence. Although it lacks the ability to directly unwind DNA.
37
how do proteins gain access to chromatin?
Remodeling complexes. remodeling complex binds to DNA and translocate the DNA so that it is untwisted ahead of the remodeler and overtwisted behind it.
38
phosphorylation adds what kind of charge?
negative
39
acetylation and methylation has what kind of charge?
neutralize and positive charges
40
What does the charge from phosphorylation and acetylation and methylation do?
modifies how DNA backbone winds around nucleosomes.
41
N terminal tails of histone proteins are what?
Major targets of regulatory post translational modification
42
Active genes have heavily what?
acetylated histones
43
Primed genes (inactive genes in an activatable state) have
less heavily acetylated histonse
44
Silenced genes are not very heavily acetylated but what?
heavily methylated on DNA and on histones
45
what's interesting about methylation of DNA?
not modified genes but inherited. epigenetics
46
If chromatin state controls transcription, how do DNA bindingg proteins control transcription?
An example is signal transduction pathways relay signals to nucleus: JAK STAT

Bioc 406 03 (7 decks)

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