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Biol 311 > Final > Flashcards

Final Flashcards

1
Q

Three properties of DNA

A
  1. Accurate replication
  2. Have info with instructions to encode for proteins
  3. Be able to change (rarely) so that it results in hereditary changes/mutations
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2
Q

What is purines made of

A

Adenine and Guanine
(Pure as gold)

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3
Q

What is Pyrimidines made of

A

Cytosine and Thymine
(C(U)T) the py (pie)

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4
Q

Phosphate of DNA binds to what?

A

5’ position of CH2 deoxyribose sugar

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5
Q

Where is the OH located on the deoxyribose sugar?

A

3’ position

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6
Q

Base pairing

A

A+G = T+C
A=T; G=C

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7
Q

Base pairing practice

If G+C of a double-stranded DNA is 48%, what is the percentage of ‘A’ in this DNA molecule

A

Since G+C= 48% we can find A+T
A+T= 100% - 48% = 52%
Since we know A=T we divide 52% by 2 to find A and T individually
52%/2 = 26%

Therefore A is 26%

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8
Q

Complementary base pairs (Chargaff’s Rule)

A

A-T and G-C

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9
Q

the sugar of DNA binds to what?

A

3’ end

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10
Q

the phosphate of DNA binds to what?

A

5’ end

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11
Q

How is DNA replicated?

A

Semi-conservative replication

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12
Q

What is semi-conservative replication?

A

when parental DNA strands unwind and combine for synthesis of new complementary strand

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13
Q

What produces energy to help DNA synthesis?

A

cleaving of pyrophosphate

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14
Q

what makes up dNTP (Deoxyribonucleoside triphosphate)?

A

3 phosphates, sugar group, one nucleotide

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15
Q

What is the first step of DNA replication?

A

DNA gyros relaxes DNA helices and rejoins strands
(makes sure DNA is not coiled)

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16
Q

What is the second step of DNA replication?

A

Helices distrupts H bonds thus unwinding helices
(ssB= ssDNA binding proteins that stabilizes unwound DNA)

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17
Q

What is the third step of DNA replication?

A

RNA polymerase synthesizes primers. Primers synthesize (in 5-3) RNA primers using DNA as template.

(Creates binding site for DNA Pol III)

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18
Q

What is the fourth step of DNA replication?

A

DNA Polymerase III catalyzes synthesis of DNA (starts at 3’ end of primer)

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19
Q

What is the fifth step of DNA replication

A

DNA polymerase I removes RNA primers and fills in gaps

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20
Q

What is the sixth step of DNA replication?

A

DNA ligase connects adjacent DNA fragments

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21
Q

why is DNA replication semi-discontinuous?

A

The lagging strand needs to be synthesized in small sections.

(DNA Pol III bind to RNA primers and synthesizes Okazaki strands. DNA ligase needs to connect adjacent DNA fragments)

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22
Q

what does the OH on the sugar do to the triphosphate?

A

a nucleophilic attack on an incoming nucleotide so that it can bind to it

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23
Q

what are PCRs? (Polymerase chain reaction)

A

a method of amplifying DNA
(ex. forensics)

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24
Q

What is the first component for PCRs?

A

Isolated genomic DNA (like from hair) to act as template DNA

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25
Q

What is the second component for PCRs?

A

Multiple copies of DNA primers.
- approx 20 nucleotides long WITH FREE OH GROUP
- reverse and forward primers always written in 5-3

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26
Q

what is the third component for PCRs?

A

dNTPS (dATP, dGTP, dCTP, dTTP)
- provides single bases (A, G, C, T)

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27
Q

What is the fourth component for PCRs

A

Taq polymerase (special DNA polymerase
- acts as DNA POL III
- Synthesis in 5-3 direction
- active at high temps over multiple cycles of heating and cooling

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28
Q

PCR step one

A

Denaturation of DNA via heating

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29
Q

PCR step two

A

Annealing of primers onto appropriate locations on template via cooling

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30
Q

PCR step three

A

Tax polymerase binds to primers for synthesis of DNA via heating (adds to 3’ end)

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31
Q

what determines annealing temperature?

A

depends on melting point (mp) of primers. temp should be lower than mp

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32
Q

What determines melting point of PCRs?

A
  • melting point is when 50% of primers are bound and 50% of primers aren’t bound
  • more GC = higher temp
  • longer dna = higher temp
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33
Q

what is the difference between DNA Pol I and DNA Pol III?

A

DNA Pol I removes RNA primers and fills in gaps
DNA Pol III synthesizes DNA

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34
Q

designing forward and reverse primers

A
  • Forward primers is always the same as the top strand (from 5’ end)
  • the reverse primers is the compliment of the top strands (from 3’ end and backwards)
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35
Q

what is gel electrophoresis

A

method used to separate DNA (or RNA and proteins) molecules based on their sizes by using electrical field to move molecules through gel matrix

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36
Q

what is agarose primers?

A

used to make ‘gel’ to separate DNA

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37
Q

what DNA molecules will travel quickly through the gel matrix?

A

small DNA molecules because they have lower molecular weight

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38
Q

what DNA molecules will travel slower through the gel matrix?

A

larger DNA molecules bc it has higher molecular weight

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39
Q

why do we stain DNA in gel electrophoresis?

A
  • to see DNA under UV light bc DNA is colourless
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40
Q

what are molecular ladders?

A

DNA pieces with known sizes to help determine size of DNA samples

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41
Q

What are SNPs?

A

single base pair difference between DNA sequences (can be transition or transvehrsion)

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42
Q

what is transition?

A

replaces pyrimidine with pyrimidine
replaced purine with purine

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43
Q

what is transversion

A

replaces purine with a pyrimidine or vice versa

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44
Q

what is spontaneous DNA replication error?

A
  • a cause of SNPs
  • mismatching
  • can be caused by tautomerization
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45
Q

what is tautomerization?

A

changes in position of a base’s atoms and bonds between atoms

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46
Q

how are mismatched errors repaired?

A
  • by the DNA Pol III or I
  • remove mis-paired bases by working backwards (3-5) (3-5 exonuclease activity)
  • if mistake is still there, its usually repaired by other DNA repair mechanism
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47
Q

what is “other chemical changes to nucleotide?”

A
  • a cause of SNPs
  • can be caused by depurination or deamination
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48
Q

what is depurination?

A
  • loss of purine base
  • can cause polymerase to stop or add random base
    (phosphate and sugar backbone still intact)
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49
Q

what is deamination?

A

removal of amine groups (cytosine, adenine, and guanine)

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50
Q

what are insertion-deletions (Indels)?

A
  • insertion or deletion of bases
    (Deletion of bases results in no frameshift)
  • can result in non-repetitive indels (point mutations) or STRs (short tandem repeats of 2-9 nucleotide)
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51
Q

what is point mutation?

A

single base pair being added, deleted, or changed (SNPs)

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52
Q

More info about STRs?

A
  • also called micro satellites- repeated region could be exon, intron, regulatory regions, nonfunctional DNA sequences
  • high mutation rates
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53
Q

what is slippage?

A

when a CAG repeat folds in and causes right side (of CAG) to be repeated since it fell backwards

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54
Q

what os the sufferance between dideoxynucleoside and deoxynuclooside?

A

Dideoxy has H on the 3’ position while Deoxy has OH on 3’ position

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55
Q

How is PCR different from Sanger Sequencing?

A
  • PCR results in exponential amplification (sequencing does not)
  • one primer is needed in Sanger
    (PCR needs 2)
  • Sanger needs ddNTPS and dNTPs
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56
Q

In Sanger sequencing, which base is always causes the termination of synthesis?

A

In T tube: T
In C tube: C
In G tube: G
In A tube: A

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57
Q

how are RNA and DNA different (structurally?)

A
  • RNA sugar has OH on the 2’ carbon while DNA has H on the 2’
  • RNA has U (no CH3 group) and DNA has T
    (thymine is more stable)
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58
Q

what direction does RNA synthesize in?

A

5’ to 3’ direction

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59
Q

what direction does the RNA polymerase reads the template strand? (in RNA transcription elongation)

A

3’-5’ direction

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60
Q

Newly synthesized RNA is made in what direction?

A

5’-3’ direction

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61
Q

What does the RNA polymerase do

A
  • unwinds about 17bp of DNA
  • catalyzes RNA synthesis
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62
Q

what does upstream mean

A

The region that is closer to the 5’

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63
Q

what does downstream mean

A

the region towards the 3’ end

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64
Q

what happens in RNA transcription?

A
  • The DNA has regulatory sequences (enhancer/silencer, promoter), UTRs, exons, and introns
  • Splicing splices off all regulatory proteins leaving only start/stop codons, exons, introns, UTRs and terminator. (Turns into pre-mRNA)
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65
Q

What happens during RNA translation?

A
  • introns gets splices out leaving only exons, UTRs, and terminator
  • then gets turned into protein
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66
Q

How does the RNA know where the introns are to splice them off?

A
  • the spliceosome recognizes specific nucleotide sequence at exon and intron junctions
  • Introns begins with GU and end with AG
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67
Q

at what position/site does transcription start?

A

+1 site

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68
Q

what is the non-template strand?

A
  • sense or coding strand
  • 5’-3’
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69
Q

what is the template strand?

A
  • antisense or noncoding strand
  • 3’-5’
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70
Q

Where is the TATA box and what does it do?

A
  • positions -25 to -35
  • positions the RNA polymerase for initiation of transcription
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71
Q

what is quantitative PCR?

A
  • method of PCR allowing us to quantify the amount of DNA in sample (by using fluorescent dye)
  • used for COVID19 testing
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72
Q

what is CT?

A

amount of cycles needed to pass the threshold

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73
Q

what does low CT value mean?

A

More DNA is present bc it takes less cycles

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74
Q

what does high CT value mean?

A

Less DNA is present bc it takes more cycles

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75
Q

what forms between amino acids?

A

peptide bonds

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76
Q

(genetic code) what does it mean when codes are degenerate?

A
  • multiple codons encode the same amino acid
  • helps buffer against transition SNPs
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77
Q

N terminal on a protein does what?

A
  • amino group
  • synthesize first
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78
Q

C terminal of a protein does what?

A
  • carboxyl group
  • synthesize last
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79
Q

what are tRNAs?

A
  • act as adaptors (or links) between mRNA and amino acids
  • has anticodon loop (3’-5’)
  • animo acid attached to 3’ end
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80
Q

what does aminoacyl-tRNA synthetase do?

A

its an enzyme that attaches amino acids to tRNAs

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81
Q

what does ribosomes do?

A
  • bring together the charged tRNA and mRNA
  • move along mRNA in 5-3
82
Q

what does the peptide-transferase centre do?

A

catalyze the formation of peptide bonds between amino acids

83
Q

what is the shine-dalgarno sequence and kozak sequence and how are they different?

A
  • both are sequences in mRNA that the rRNA recognizes (helps position the ribosome)
  • kozak sequence is found in eukaryotes
  • shine-dalgarno sequence is found in prokaryotes
84
Q

what are the 4 outcomes of SNPs in exons?

A
  1. silent mutations
  2. missense mutation (conservative)
  3. missense mutation (non-conservative)
  4. nonsense mutation
85
Q

what is silent mutation?

A
  • synonymous (same)
  • encodes same amino acid
86
Q

what is missense mutation (conservative)

A

encodes a chemically similar amino acid
ex. AAG (Lys) –> AGG (Arg)

87
Q

what is missense mutation (non-conservative)?

A

encodes a chemically different amino acid
ex. AAG (Lys) –> ACG (The)

88
Q

what is nonsense mutation?

A

encodes a stop codon

89
Q

how can insertions and deletions in exons impact amino acids?

A

can cause frame shift mutation

90
Q

where is the shine-dalgarno and kozak sequence usually placed?

A

after +1 poisition

91
Q

what is a Western Blot?

A
  • it is used to detect particular proteins in a mixture of proteins
  • can determine size of proteins and lvl of expression
92
Q

what does a probe (in Western Blot) do?

A

they are antibodies that bind to protein of interest

  • secondary antibody binds to primary antibody and has fluorescent body
  • primary antibody binds to protein of interest
93
Q

in terms of western blot, “expansion” means

A

more bp = bigger = towards the top

94
Q

in terms of western blot, “increased expression” means

A

bigger protein spot (bigger circle) bc there is more protein for antibody to bind to

95
Q

where is the promoter positioned?

A

upstream and before position 1+

96
Q

RNA polymerase in prokaryotes (E.coli)

A
  • made of 5 subunit core and a subunit of sigma factor
  • sigma factor leaves after initiation
97
Q

what is the role of the sigma factor?

A

to position enzyme correctly at promoters

98
Q

what are the two transcription termination in E. coli?

A
  1. factor-independent termination
  2. Rho-dependent termination
99
Q

what is factor-independent termination?

A

A G-C rich DNA followed w/A-rich stretch causing RNA polymerase to release from DNA template

100
Q

what is Rho-dependent termination?

A

Rho-factor (protein) recognizing c-rich sequence and releases RNA polymerase from DNA template

101
Q

Regulation of gene expression in bacteria

A
  • needs to breakdown sugar from enviro (uses sugar as carbon source)
  • conserve energy by making enzymes required for import + metabolism when sugar is present
102
Q

what is the role of the activator protein?

A

brings RNA polymerase closer to promotor for transcription

103
Q

what is the role of the repressor protein

A

it blocks RNA polymerase from binding to promoter or blocks it from moving along DNA

104
Q

what does removing the activator protein do?

A

causes no transcription or basal/low transcription

105
Q

what is the role of allosteric effectors?

A

they bind to allosteric sites on regulatory proteins and changes the conformation of those proteins.

  • activator effectors allow protein to bind to promoter therefore have transcription
  • repressor effectors changes conformation of repressor protein making it unable to bind to operator (allowing transcription)
106
Q

What is permease (Y)?

A
  • type of lactose operon, structural gene (protein coding gene)
  • transports lactose into the cell
107
Q

what is Beta-galactosidase (Z)?

A
  • type of lactose operon, structural gene (protein coding gene)
  • modifies lactose into allolactose + cleaves lactose
108
Q

what is an “I” gene?

A

encodes a repressor

109
Q

What is trans-acting regulator elements?

A

affects gene expression of distant genes (can be on other DNA)

110
Q

what is cis-acting regulator elements?

A

affects gene expression of nearby genes (on same DNA)

ex. promotor/operator both only affect things its physically attached to

111
Q

what does negative regulation require?

A

always involves a repressor

112
Q

what is allolactose?

A

an allosteric effector causing repressor to be unable to bin to operator

113
Q

what is activator effector?

A

a type of allosteric effector that allows regulatory protein too be able to bind to promoter

114
Q

what is repressor effector?

A

type of allosteric effector that binds to the repressor and makes it unable to bind to the operon

115
Q

In negative regulation, what happens if there is NO lactose?

A

lac operon = off = no expression bc a repressor is encoded

116
Q

in negative regulator, what happens if there IS lactose present?

A

lac operon = on = transcription bc allolactose is made (repressor effector)

117
Q

what is a constitutive mutation?

A

gene is expressed (no control over its expression)

operon is an example

118
Q

what is Oc?

A

repressor cannot bind to operator.

119
Q

what is an inducer?

A

it allows stuff to be turned on

120
Q

Oc is epistatic (masks effect) of what?

A

Is

121
Q

if glucose is present, what is the expression from the lac operon?

A

minimal expression

122
Q

if glucose is NOT present, what is the expression from the lac operon?

A

enhanced expression (bc cell needs to work harder to break down lactose)

123
Q

What is cAMP?

A

An allosteric effector for CAP

124
Q

What is CAP?

A

(catabolite activator protein)
- cap-cAMP complex enhances transcription

125
Q

define attenuation

A

level of regulation that occurs after transcription has been initiated

  • high levels of Trp = low mRNA production

(In Trp operon)

126
Q

In tryptophan operon level 1 regulation, what happens if there is tryptophan?

A

Trp will bind to TrpR repressor to bind to TrpO (opressor) and inhibit transcription

127
Q

In tryptophan operon level 1 regulation, what happens if there is NO tryptophan?

A

no Trp will bind to TrpR therefore transcription will happen

128
Q

In tryptophan operon level 2 attenuation, what happens if there is A LOT of trp?

A

there is a 3+4 pairing seen in the loop. It signals for termination (also has a string of U after region 4)

(transcription and translation are happening at the same time bc it is prokaryote)

129
Q

In tryptophan operon level 2 attenuation, what happens if there is LOW trp?

A

regions 2 +3 pair continuing transcription

ribosome stalls at TRP codons in the leader peptide bc leader peptide is incomplete

130
Q

what does general transcription factors in transcription initiation in eukaryotes do?

A

binds to specific sequences (ex. TATA box, +1 site, etc) in the promoter to help RNA Pol II bind to correct site

131
Q

what does the preinitiation complex (PIC) in transcription initiation in eukaryotes do?

A
  • it is a complex made of RNA Pol II and general transcriptional factors
  • when RNA Pol II bind to general transcription factor, the C-terminal domain (CTD) of the pol is phosphorylated to facilitate processing of 5’ end of mRNA
  • caps the m7G (at 5’ to decrease degradation)
132
Q

why do we cap the m7G?

A
  • protects mRNA from decay from exonuclease
  • addition of methylated G signals start of transcription
  • assists in splicing and translation
133
Q

what is polyadenylation?

A

conserved sequences in 3’UTR signalling for termination of transcription with addition of poly-A-tail

134
Q

what does the poly-a-tail do?

A

protects from decay and assists in translation

135
Q

how do you get a variety of proteins?

A

Variety of proteins can be achieved by splicing the exons and introns out in different ways

136
Q

what is the polyadenylation signal?

A
  • part of the 3’UTR
  • processes sequence for poly-A-tail (tells transcription to stop)
137
Q

what is the landing site for ribosomes in mature eukaryotic mRNA?

A

5’-UTR

138
Q

regulatory protein factors like transcription factors bind to what part?

A

DNA

139
Q

regulatory protein factors like co-regulators bind to what part?

A

they bind to general transcriptional factors and NOT directly on DNA

140
Q

what is the core promoter?

A
  • in the +1 region where the general transcription factor (GTC) binds to to start transcription
141
Q

since the enhancer is more upstream than the promoter, how is it able to influence the core promoter?

A

it bends so that it is close to the co-regulator

142
Q

what are the enzymes involved in the import and metabolism of galactose in yeast?

A

Gal 2, 1, 7, 10

143
Q

what happens if there is no galactose?

A

enzyme coding genes are not expressed

144
Q

what happens if there is galactose

A

enzyme coding genes are expressed

145
Q

where does GAL4 bind to?

A

the UAS (enhancer sequence) to activate transcription

146
Q

which GAL proteins are always expressed?

A

GAL 3 and GAL 80

147
Q

what represses GAL 4?

A

GAL 80

148
Q

What are regulatory proteins in the yeast GAL system?

A

GAL 4, 3, 80

(regulate transcription of enzyme coding genes)

149
Q

what goes under conformational change in presence of galactose?

A

GAL 3

150
Q

what is a chromatin?

A

complex of DNA + protein that make up eukaryotic chromosomes

151
Q

what is a nucleosome

A

DNA is packed around histone proteins (each nucleosome has 8 histone proteins)

152
Q

what is the charge of histones? and what’s the function of its folded core and flexible tails?

A
  • positive
  • folded core controls how compact histones are
  • flexible tails interact with adjacent nucleosomes and other proteins
153
Q

what is heterochromatin

A

more compact

154
Q

what is euchromatin

A

less compact (transcriptionally active)

155
Q

what is constitutive heterochromatin

A

DNA that is always compact

(in regions that arent transcribed like telomeres and centromeres)

156
Q

facultative heterochromatin

A

varies between being compact (heterochromatin) and open (euchromatin)

157
Q

Chromatin modification: Histone modification

A
  • primarily affects tails
  • example: Histone acetylation
158
Q

what is histone acetylation?

A

addition of acetyl group to lysine amino sic

159
Q

what are the effects of histone acetylation?

A
  1. reduces chromatin compaction (loosening interaction between histones and DNA)
  2. creates binding site for protein domain )transcriptional activators) called bromodomain
160
Q

what is bromodomain?

A

found in many transcriptional activators and it turns on genes (reads it)

(coregulator bc it binds to histone and not DNA)

161
Q

what is the protein code hypothesis?

A

different combos of histone modification specify different transcription outcomes

162
Q

what is HAT (histone acetyltransferase)?

A

writes genes

163
Q

what is HDAC (histone deacetylase)?

A

gene eraser

164
Q

Chromatin modification: DNA Modification Histones

A

methyl group gets added to cytosine (making every C be methylated)

165
Q

what is unmethylated CpG

A
  • in expressed genes
  • acts as transcription controller
  • associated with open chromatin and active transcription
166
Q

methylated CpG

A
  • in unexpressed genes
  • acts as transcription controller
  • is not recognized by RNA
  • associated with closed chromatin and repressed transcription
167
Q

what does methylation do?

A
  • prevents transcription factor from binding
  • creates binding sites for HDACs (histone deacetylase)
168
Q

If a parent strand has a methylated C (cytosine), would the new strand have the methylated C or no?

A

The new strand will have the methylated C. The new strand will see its parent strand having it so it will change its C to have it

169
Q

what does imprinting mean?

A

gene is silenced through methylation (so other parent trait will be expressed)

170
Q

what are the steps when cloning insulin?

A
  1. obtain an expression plasmid (vector)
  2. obtain human insulin gene (cDNA) (cut with restriction enzymes)
  3. insert cDNA into expression plasmic (perform restriction map to confirm)
  4. introduce recombinant plasmid to bacteria (bacteria will produce insulin protein which will be extracted and purified)
171
Q

what are restriction enzymes?

A

they are endonuclease that cleave phosphodiester bonds between nucleotides at specific DNA

172
Q

why is ligating with sticky ends more compatible?

A

pieces of DNA cut with same restriction enzyme can be ligated together

(newly ligated DNA recreates original restriction site)

173
Q

why is ligating with blunt ends less compatible?

A

any piece of DNA can be ligated together but the efficiency is lower

174
Q

single enzyme cloning

A
  • insertion can happen in either orientation
175
Q

double enzyme cloning

A
  • insertion only occurs in one orientation
176
Q

what are some essential features for cloning?

A
  • origin or replication (ori)
  • antibiotic resistance gene
  • Polylinker (multiple cloning sites)
177
Q

what is the origin of replication (ori)

A

allows plasmids to replicate in bacteria host cell

178
Q

what does the antibiotic resistance gene do?

A

allows only cells with plasmids to grow

179
Q

what does the polylinker (multiple cloning site) do?

A

region containing many unique restriction enzyme sites

180
Q

what are some optional features for cloning?

A
  • promoter (required for expression plasmids)
    (found upstream of polylinker)
  • (if you want an expression plasmid) 3’UTR, 5’UTR, shine-dalgarno, terminator
181
Q

inherited means what?

A

DNA replication

182
Q

what is morphogen?

A
  • molecule whose effects are concentration-dependent (established a pattern of tissue development and body plan formation)
  • determines hox gene expression
183
Q

what are hox genes?

A
  • genes responsible for regulation of animal development
  • controls identity of segments and appendages
  • encodes transcriptional factors
184
Q

classes of toolkit genes

A
  1. Maternal effect genes (bicoid and nanos)
  2. gap genes
  3. pair-rule genes
  4. segment-polarity genes
  5. Hox genes

(2-3 and zygotic ally expressed)

185
Q

Class of toolkit gene 1: Maternal effects gene

A
  • established AP axis
  • bicoid and nanos (codes transcription factors to regulate next genes) mRNA tethered to anterior and posterior
  • proteins express gradient after fertilization
  • if mom is mutant, all offspring is mutant
186
Q

Class of toolkit gene 2: gap genes

A
  • segmentation genes
  • divide embryo into broad regions
  • define regional sections
187
Q

Class of toolkit gene 3: Pair-rule genes

A
  • segmentation gene
  • affects development of pairs of segments
  • acts in more narrow regions than gap genes
  • define individual segments
188
Q

Class of toolkit gene 4: segment-polarity genes

A
  • segmentation gene
  • affects organization of segments (some segments may be facing opposite directions if there was a mutation)
  • define organization of individual segments
189
Q

Class of toolkit gene 5: hox genes

A
  • determine identity of structure or segment
  • 8 hox genes in flies
  • order of genes in chromosome corresponds to order of body regions
  • regulate expression of networks of other genes

IMPORTANT
- sequence specific DNA binding proteins
- bind to cis-acting regulatory elements of other genes to regulate or repress

190
Q

what are gap genes activated by?

A
  • maternal-effect proteins
  • bicoid protein (transcription factor) localized in anterior
  • ## bicoid only binds when there is high concentration
191
Q

what is the hunchback gene?

A
  • it is a gap gene that is expressed by high bicoid lvls
192
Q

toolkit gene expression is regulated by what?

A
  • transcription factor binding to cis-acting regulatory genes
  • earlier transcription factors regulate genes expressed later
  • results in genes being expressed at discrete regions
193
Q

expression of pair rule gene: even skipped (eve)

A
  • cis acting regulatory elements (enhancers) controlling eve gene bound by precise combos of transcription factors
194
Q

how are genes expressed in precise patterns at different times?

A
  • most toolkit genes function at more than one time and space
  • function are context dependent
    ( some expression can repress/promote other genes)
195
Q

what is CRISPR

A

a gene editing tool

196
Q

Step 1 and 2 of CRISPR

A

acquire spacers (foreign or viral DNA) and incorporate it into genomic CRISPR region

197
Q

Step 3 and 4 of CRISPR

A

CRISPR region gets transcribed to generate guide RNA (gRNA)

gRNA will assemble with Cas9 gene to guide it to cleave (introduce double stranded break) the invading DNA with precision

198
Q

where must the target sequence be in CRISPR for the Cas9 to cleave it?

A

3 nucleotides upstream of PAM (5’NGG)

199
Q

What is Cas9?

A
  • inherited enzyme that makes cut in invading enzymes so that it wont infect
200
Q

what’s the first way to fix a doublestranded break?

A

homologous recombination (HR)

  • Introduces donor DNA that will be used as template to repair double stranded break
201
Q

what is the second (and less efficient) way to fix a double stranded break?

A

Nonhomologous ending joining (NHEJ)

  • Introduces deletions/mutations that can inactivate genes

Biol 311 (1 decks)

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