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Biol 207 > Lecture 7 > Flashcards

Lecture 7 Flashcards

1
Q

What is a Gene?

A

The sum of all transcribed and non-transcribed regions that are necessary to properly express a gene

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2
Q

What is the Transcription unit?

A

The transcribed region of a gene

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3
Q

What is the Open Reading Frame (ORF) of the transcription unit?

A

The Coding Region, the part that has a start codon and the stop codon

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4
Q

What have more than one ORF?

A

Operon-derived mRNAs have more than one ORF

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5
Q

What are examples of RNA that are not translated?

A

rRNA, tRNA, microRNA and long non-coding RNAs

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6
Q

What are Untranslated Regions (UTR) and introns?

A

Parts of a gene that are transcribed but not necessarily coding

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7
Q

Where are regulatory sequences commonly located?

A

In the non-transcribed regions of a gene, but sequences with important regulatory functions may reside in the transcription unit and coding region

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8
Q

What does Transcription occur in?

A

The transcription bubble

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9
Q

What is Transcription carried out by?

A

RNA polymerase

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10
Q

What is the reason for the Transcription bubble?

A

Closing the DNA right away will prevent accidental transcription by other factors

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11
Q

What is the Non-template Strand of the DNA known as?

A

The Coding strand and the Sense strand. It is equivalent to the mRNA

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12
Q

What is the Template Strand of DNA known as?

A

The Noncoding strand and the antisense strand

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13
Q

What is the Key difference between Bacterial and Eukaryotic gene regulation?

A

The ground state of bacteria is on and the ground state of eukaryotes is off

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14
Q

Why is the Ground state of genes in Eukaryotic organisms off?

A

Because they are tightly wound around nucleosomes and are inaccessible from DNA binding proteins

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15
Q

Why is the Ground state of genes in Bacteria on?

A

Because the same nucleosomes and histones are not present in bacteria as they are in Eukaryotes so the DNA is naked and accessible

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16
Q

How do Bacteria turn off a gene?

A

They must actively deploy a repressor protein

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17
Q

How many gene products are needed for the core enzyme of bacterial RNA polymerase?

A

4

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18
Q

What are the 5 parts of Bacterial RNA polymerase?

A

2 alpha subunits, omega, beta and prime

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19
Q

What are the two alpha subunits encoded by for Bacterial RNA polymerase?

A

The same gene

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20
Q

What is the Sigma actor needed for?

A

Specific binding of the RNA polymerase to the promoter

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21
Q

What is Holoenzyme?

A

The Core enzyme of bacteria RNA polymerase plus Sigma factor

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22
Q

Where are Promoters found?

A

In eukaryotes and prokaryotes

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23
Q

What is the Promoter?

A

A region of a gene containing regulatory sequences that are close to (or contain) the transcription start site

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24
Q

What is the Promoter required for?

A

Transcription initiation via RNA Polymerase

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25
Q

What does the Promoter region have?

A

Binding sites for the RNA Polymerase and helper factors like sigma factor

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26
Q

What is the function of the terminator region?

A

It terminates bacterial transcription

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27
Q

Which organisms is the Terminator region found?

A

In bacteria only

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28
Q

What occurs in Positive Regulation?

A

An activator protein involved that recruits RNA polymerase

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29
Q

What occurs in negative regulation?

A

An Repressor protein that binds to the operator sequence and interferes with transcription by blocking RNA polymerase

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30
Q

What is Basal Transcription?

A

When RNA polymerase hasn’t been recruited specifically but there is no repressor to stop it. It is unregulated

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31
Q

What are Ligands?

A

Small molecules that bind to activators and change the confirmation of the protein which promote the binding of DNA

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32
Q

What are Activators and Repressors regulated by?

A

Ligands (hormones, small peptides or metabolites etc)

33
Q

What is an Allosteric site?

A

A region in a protein to which a small molecule can bind (the ligand) resulting in a conformational change of the protein that modifies the activity of the protein

34
Q

How is Glucose formed in E. coli?

A

Lactose is brought into the cell the by b-Galactosidase and then breaks the lactose into allolactose or then to Galactose + Glucose

35
Q

How many Genes is the Lac operon composed of?

A

3

36
Q

What are the Genes of the lac operon?

A

LacZ
LacY
LacA

37
Q

What does the lacI encode for?

A

The repressor protein which is the regulatory portion

38
Q

What does the lacZ encode for?

A

B-galactosidase

39
Q

What does the LacY encode for?

A

Permease that transports lactose into the cell

40
Q

What is an Operon?

A

A group of genes that are adjacent to each other and transcribed together because they are controlled by a single regulatory region

41
Q

What is the product of the operon?

A

A polycistronic mRNA

42
Q

What is polycistronic mRNA?

A

An mRNA that encodes multiple proteins

43
Q

What is an Operator?

A

A sequence of DNA that is the binding site for a repressor protein which prevents transcription by preventing RNA polymerase from binding or blocking it

44
Q

Where are operators found?

A

In bacteria

45
Q

What does CAP stand for?

A

Catabolite activator protein

46
Q

What is the Lac Operon regulated by?

A

Ligands b-1,6-allolactose (which blocks the activity of the lac repressor) and cAMP activates CAP

47
Q

What conditions must be met for the lac operon to be induced?

A

Lactose is present and glucose is absent

48
Q

What occurs in the Lac operon when glucose and Lactose are both present?

A

Basal Transcription

49
Q

What occurs when glucose is present and lactose is absent?

A

The operon is repressed

50
Q

What occurs when glucose is absent and lactose is absent?

A

The operon is repressed

51
Q

What is Basal Transcription?

A

When RNA polymerase binds to DNA in the absence of activators and repressors

52
Q

How does the lac repressor work?

A

A homotetramer and binds to two lac operators at the same time

53
Q

Why is there no Transcription in the absence of Lactose?

A

Because allolactose is a product of B-galactosidase working on Lactose and allolactose is a ligand of the repressor protein which causes it to be inactive

54
Q

Why does the lac operon not work in the presence of glucose?

A

Glucose inhibits the synthesis of cAMP by inhibiting the enzyme that produces it

55
Q

What is cAMP?

A

A ligand that activates the CAP protein which recruits the RNA polymerase

56
Q

How does cAMP work?

A

It changes the shape of CAP by rotating the DNA-recognition helices

57
Q

What is CAP?

A

An activator that binds to the CAP site of the lac promoter

58
Q

Why can basal transcription occur when there is a low presence of glucose?

A

Because the repressor protein is only bound to the operator 96% of the time which gives opportunity for basal transcription to occur

59
Q

What was the approach by Jacob and Monod in figuring out the function of the different portion of the Lac Operon?

A

They used a plasmid called F-factor to make a partially diploid E. coli since E. coli is haploid. Then they cause mutations of these parts and saw the outcome

60
Q

What does the Cis-Regulatory element refer to?

A

A small section of DNA important for regulation of a gene. Cis indicated that is is located on the same piece of DNA as the gene that it regulates, usually in the vicinity of the gene

61
Q

What does the Trans-acting factor refer to?

A

A regulatory protein that binds to cis-regulatory elements or contributes to the regulation of a gene is some other fashion. The gene encoding the trans-acting factor does not need to be on the same piece of DNA

62
Q

What are Trans Acting factors of the Lac Operon

A

The proteins of Cap and the Lac Repressor

63
Q

What are the Cis-regulatory elements of the Lac Operon

A

Cap binding site and the Operator

64
Q

What is Constitutive activity?

A

A situation where a gene/enzyme is continuously active regardless of the biological condition. Even it is on it should be off

65
Q

What are the Structural genes of the Lac Operon?

A

LacZ, LacY, LacA

66
Q

Why are LacZ, LacY, LacA structural genes?

A

Because they do not directly affect the regulation of the operon

67
Q

What are the Regulatory elements of the Lac Operon?

A

Lac Repressor, lac operator, CAP site, promoter elements

68
Q

What are Inducers?

A

Small ligands that bind to proteins and increase gene activity

69
Q

What are the Inducers for the Lac Operon?

A

Allolactose for the lac repressor and cAMP for the CAP

70
Q

What is the opposite of an inducer?

A

Co-repressor which are small ligands promoting repression

71
Q

Where is the term inducer used?

A

Only in bacteria

72
Q

What happens when B-galactosidase digests X-gal?

A

It turns blue

73
Q

What occurs in the lacI-, type I mutation?

A

No lac repressor is made

74
Q

What occurs in the lacI-, type III mutation?

A

Lac repressor is made but is not capable of binding to the operator (so the DNA binding domain is effected)

75
Q

What occurs in the lacIs mutation?

A

The Lac repressor is made but cannot bind to allolactose or IPTG (mutation affecting allosteric site)

76
Q

What is the acting of the Operon?

A

Cis-Regulatory

77
Q

What is the acting of the Lac repressor?

A

It is Trans acting

78
Q

What does the Is mutation result in?

A

A non inducible operon because Is is dominant to I+

79
Q

What kind of Morph is the Is mutation?

A

An anti morph

Biol 207 (14 decks)

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