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Genetics > Week 6 > Flashcards

Week 6 Flashcards

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Biology 101 flashcards
1
Q

What is the central question in the regulation of gene expression?

A

How does a cell or organism with the same initial DNA sequence/genotype exhibit different phenotypes?

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2
Q

How does a cell or organism with identical initial DNA sequence/genotype exhibit different phenotypes?

A

Different environmental conditions

Different cell types

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3
Q

How does a cell or organism with identical initial DNA sequence/genotype exhibit different phenotypes?

A

Different environmental conditions

Different cell types

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4
Q

Differences between bacteria and eukaryotes

A

Compartmented;Uncompartmented

Polycistronic mRNA/monocistronic

Coupled transcription and translation/Uncoupled

mRNA primary transcripts not spliced/spliced and modified

One RNA polymerase/multiple RNA polymerases

Bare DNA/Chromatin

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5
Q

Polycistronic mRNA

A

A single mRNA encodes multiple polypeptides (in viruses the DNA is expressed as polycistronic in a eukaryote)

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6
Q

RNA polymerase eukaryotes

A

RNAP I (rRNA)

RNAP II (mRNA)

RNAP III (tRNA)

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7
Q

Regulation at the level of transcription (bacteria)

A

Is the gene the same structure

Is the gene transcribed

Where is the transcript initiaited/terminated (Polycistronic)

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8
Q

Regulation at the level of the transcript (bacteria)

A

Stability of the transcript

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9
Q

Regulation at the level of translation (bacteria)

A

Is the transcript translated

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10
Q

Regulation at the level of the protein (bacteria)

A

Is the protien active?

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11
Q

Regulation at the level of transcription (eukaryotes)

A

Is the gene the same structure

is the transcript initiated

where is the transcript initiated

where does the transcript end

how was the transcript spliced

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12
Q

Regulation at the level of the transcript (eukaryote)

A

How stable?

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13
Q

Regulation at the level of translation (eukaryotes)

A

Is the trancript translated

Where is the transcript

Is the transcript exported from the nucleus

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14
Q

Regulation at the level of the protein (eukaryote)

A

is the protein active?

where is the protein?

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15
Q

Determining at what level gene expression is regulated?

A

Is the transcript present or not?

What is the structure of the transcript?

Is the protein expressed?

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16
Q

Is the transcript present or not?

A

Transcript detection/accumulation

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17
Q

What is the structure of the transcript

A

transcript analysis/sequencing

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18
Q

Is the protien expressed

A

Protein detection/antibody or activity

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19
Q

Transformer gene and female development

A

In Males: OFF

In Females: ON

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20
Q

Is tra transcribed in females only?

A

Nope tra transcription occurs in both males and females

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21
Q

Is TRA mRNA translated in females

A

YES TRA protein is only detected in females

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22
Q

Difference in tra mRNA in males and females

A

Male transcript has extra RNA sequence information that introduces a stop codon in the mRNA.

In females the splicing of the mRNA results in mRNA that lacks this sequence that is present in the male transcript resulting in no premature truncation.

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23
Q

RNAP Role in Transcription

A

RNAP binds forming a closed complex.

Regulates the rate at which the gene is transcribed/amount of transcript produced.

conformational change to form a bubble.

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24
Q

DNA elements: promoter

A

RNA polymerase in bacteria recognize the -35/-10 sequence directly by binding

In eukaryotes the TATA box is 30bp upstream of the start of transcription

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25
Q

DNA elements: regulatory sequence role

A

Rate of transcription are regulated by the regulatory sequence (positive/negative sequences).

26
Q

Bacteria regulatory sequences

A

Activator sequence (positive)

Operator (negative)

27
Q

Yeast regulatory sequences

A

upstream activation sequence (UAS)

Operator/silencer

28
Q

Eukaryote regulatory sequence

A

Enhancer/Silencer

29
Q

A major difference between prokaryotic and eukaryotic promoters

A

A transcription unit with a promoter is generally going to be transcribed in prokaryotes.

Promoter is not sufficient for transcription in eukaryotes

30
Q

Effects of silencer/operators and enhancers/activaters

A

P: transcription (pro), no transcription (euk)

O/Sil and P: no transcription (pro), no transcription (euk)

A/enh and P: increased transcription (pro) and transcription (euk)

A/enh, O/sil and P: no transcription (pro) and transcription (euk)

31
Q

Transcription factors

A

DNA-binding proteins that recognize specific DNA sequences.

When bound to DNA they affect the rate of initiation of transcription

32
Q

Transcription factors (2)

A

DNA binding can be influenced by the binding of small molecules.

When allolactose binds to the Lac repressor it can not bind the operator DNA regulatory sequence.

33
Q

Lac Operon

A

Transcribed from one promoter and the transcript encodes three proteins.

Beta galactosidase (LacZ)
Permease (LacY)
Galactosidase acetyltransferease (LacA)

Promotor and Operator part of a gene

34
Q

laci and lacZ

A

two seperate genes

35
Q

LacZ-

A

Recessive

No betagalatosidase

36
Q

Oc

A

Dominant

Betagalactosidase always present

37
Q

laci-

A

recessive

Betagalactosidase

38
Q

laci sr

A

dominant

no betagalactosiadase

gf

39
Q

laci encodes a ______ ______that regulates beta galactosidase. the conclusion comes from laci being _____-_____ to lacZ

A

Diffusable factor

trans acting

40
Q

The _______ of lacZ is the sequence recognized by the diffusable factor encoded by laci and is required on the _____ ______ as the lacZ coding region. Operator alleles are ____-_______.

A

operator
same molecule
cis-acting

41
Q

Genetic analysis of mutant alleles

A

The experiments showing trans-acting and cis-acting are distinct.

Trans-acting is the conclusion of an intergenic complementation analysis.

Cis-acting is the conclusion of an intragenic analysis of gf and lf lacZ alleles.

42
Q

Basic Complementation analysis (cis-trans test); LacZ(lf) and Laci(lf)

A

trans: different molecules
cis: same molecules

Wild type expression occurs in both cis and trans arrangement of the DNA molecules.

laci encodes for a diffusable factor that can bind to operators in either WT gene

43
Q

cis-acting does not come from a complementation analysis; refers to __-_______

A

cis-acting refers to cis-dominance which is the interaction between two mutant alleles in the same locus/gene.

To observe cis-dominance, one allele is a dominant gain of function and the other is a recessive loss of function; they have opposite phenotypes.

regulatory sequences are genetic elements within a gene.

44
Q

Oc allele is _____ to lacZ (lf) allele when trans.

A

dominant

45
Q

Wt allele are dominant when Oc and lacZ (lf) are ____.

A

cis

46
Q

When we observe cis-dominance does that mean we are dealing with just the same DNA molecule ie. do the elements have to be just on the same DNA molecule?

A

NO. The elements could be on the same RNA molecule or the same protein molecule.

47
Q

How can transcription occurring in a cell?

A

Take advantage of splicing. Place a block of DNA that encodes the MS2 binding site, bound by an RNA binding protein.

The MS2 binding site is places in the intron of the ftz gene such that when a nascent primary transcript is formed it contains the MS2 binding site. After splicing the MS2 binding site is rapidly degraded. The presence of a MS2 binding protein fused to a red fluorescence protein detects the nascent transcripts.

48
Q

delay between transcription and translation

A

13 minute delay

49
Q

Reporter Genes

A

Reporter expression is easy to assay (green fluorescence)

Reporter genes can reproduce the expression of a gene.

Use of reporter genes requires that you use an organism where it is possible to reintroduce DNA (transform)

50
Q

Translational fusion to a reporter gene

A

fuse the regulatory region of a gene to a reporter gene any protein that is easy to assay

51
Q

Reporter genes can reproduce the expression of a gene

A

the reporter gene construct has recapitulated the gene expression pattern.

51
Q

Reporter genes can reproduce the expression of a gene

A

the reporter gene construct has recapitulated the gene expression pattern.

52
Q

Protein that regulates splicing of tra mRNA

A

Sex lethal protein

SXL found in females but not males

53
Q

Method of splicing used in the tra transcript

A

Alternative 3’ splice sites used

SXL binds to a specific sequence in RNA (GUUGUUUUUU)

SXL binds to the intron of tra pre-mRNA in females, pushing U2AF to bind the later female 3’ splice site

54
Q

SXL is a

A

negative regulator of splicing

if the male 3’ splice site is removed SXL is not required to block its use.

The transcript is spliced in the female manner in both males (SXL -) and females (SXL +)

55
Q

A mature mrna of the same structure is present, but in one condition it is translated and in another it is not translated

A

regulation at the level of translation

56
Q

Hunchback mRNA and Hunchback protein expresison

A

there is no protein at the posterior end of the cell but mRNA is present in the entire cell.

57
Q

_____ is required to suppress HB protein expression

A

Nanos.

LF in the nanos allele results in a difference in how GB mRNA is translated, we see HB protein present at the posterior end

58
Q

HB expression in the posterior ______ _______ of the _____.

A

supresses
development
abdomen

59
Q

What does nanos recognize in HB mRNA to suppress translation

A

NRE: nanos regulatory element

60
Q

Pumilio

A

binds NRE both at the anterior and posterior end of the embryo

no nanos at the anteiror end results in HB mRNA being translated and we get HB protein

61
Q

How does nanos supress HB mRNA translation

A

nanos binds to pumilio and recruits 4EHP that binds the cap forming a ring structure that is unable to be translated by ribosomes.

Genetics (16 decks)

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