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DMD 5243 > Gene Expression and Biotech (complete) > Flashcards

Gene Expression and Biotech (complete) Flashcards

1
Q

where are the two levels where regulation of gene expression can occur

A
  1. Transcription

2. Translation

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2
Q

What is the difference between cis-acting and trans-acting regulation

A

cis-acting regulation is transcriptional regulation based on the DNA sequence alone
trans-acting regulation is transcriptional regulation based on something outside of the DNA sequence

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3
Q

Trans-acting regulation factors are usually _______

A

proteins which bind to the DNA

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4
Q

do trans anc cis-acting regulation factors usually work together? if so how?

A

trans-acting regulation factors usually bind to the cis-acting factors

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5
Q

Of these, which are cis-acting

  1. RNA polymerase
  2. Helicase
  3. Transcription factors
  4. promoter
  5. gene
  6. enhancer
  7. repressor
A

Promotor
Gene
Enhancer
repressor

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6
Q

Of these, which are trans-acting

  1. RNA polymerase
  2. Helicase
  3. Transcription factors
  4. promoter
  5. gene
  6. enhancer
  7. repressor
A

RNA polymerase
Helicase
Transcription factors

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7
Q

Is most regulation of gene expression done at translation or transcription

A

transcription

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8
Q

Where is gene expression regulation done in prokaryotes

A

only transcription, no translation

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9
Q

What is an operon

A

a cluster of genes with related functions, acting as a coordinated unit and controlled by a regulatory sequence

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10
Q

What are the components of an operon

A
  1. Structural genes
  2. Promoter
  3. Repressor
  4. Activator
  5. Operator
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11
Q

What are the structural genes of an operon

A

the genes that code for proteins

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12
Q

what is the difference between the structural genes of an operon in prokaryotes vs. eukaryotes

A

the structural genes in eukaryotes only codes for one protein, where as in prokaryotes it can code for multiple proteins

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13
Q

Is operon usually used in association with prokaryotes or eukaryotes

A

prokaryotes

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14
Q

What is the promoter of an operon

A
  1. it is the location where the RNA polymerase will bind
  2. It has the TATA box
  3. it increases the efficiency of gene transcription
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15
Q

What is the repressor of an operon

A
  1. a gene that codes for an inhibitor protein of the gene

2. it inhibits the transcription of the protein

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16
Q

What is an activator of an operon

A
  1. it increase the transcription of a protein

2. a gene that codes for an activator protein of the gene

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17
Q

What is an operator of an operon

A

the sequence of DNA that binds repressor or activator proteins

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18
Q

How many promoters per gene is there in eukaryotes

A

one promoter per gene

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19
Q

How many promoters per gene are there in prokaryotes

A

multiple promoters per gene

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20
Q

Genes can be either:
1. Constantly activated and turned off when you have too much of the protein
2. Constantly inactivated and turned on when more of the protein is needed
True or False? if only one, which is it?

A

True,

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21
Q

In prokaryote transcription, what is the concensus sequence

A
  1. the preferred binding sequence for transctiption factors.
  2. it is about 35 bases prior to the location where transcription begins
  3. TTGACA is the sequence
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22
Q

in prokaryote transcription, what is the pribnow box

A

a portion of the promoter that is about 10 bases prior to transcription start point
TATAAT is the sequence

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23
Q

What are the proteins that are a created and regulated by the LAC operon

A

They are three catabolic enzymes that break down lactose

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24
Q

Which prokaryotic operon is known as the catabolic operon

A

the LAC operon

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25
Q

Is the Lac operon normally on, or off

A

the lac operon is normally OFF

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26
Q

When is the lac operon turned on

A

when lactose needs to be used for energy

When there is high lactose and allolactose

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27
Q

What is the lac operon like in its normal state

A
  1. It is off

2. it has a repressor protein (from the repressor gene)that is bound to its operator

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28
Q

How does the lac operon get turned on

A
  1. Lactose enters the scene and binds to the repressor protein that is on the operon, this pulls the repressor protein off and allows transcription to begin
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29
Q

What is an inducer

A

a substance that binds to a repressor, causing it to be inactive

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30
Q

in the LAC operon what is the inducer

A

lactose

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31
Q

in prokaryotes what is also known as the Anabolic operon

A

the TRP operon

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32
Q

What are the two main important prokaryotic operons

A

LAC operon

TRP operon

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33
Q

Is the TRP operon normally on or off

A

normally on

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34
Q

What causes the TRP operon to get shut off

A

high levels of Tryptophan

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35
Q

in the TRP operon, tryptophan will bind to an inactive repressor on the operon, causing it to become active, and stop transcription. What is tryptophan acting as

A

a corepressor

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36
Q

what is a corepressor

A

something that binds to a repressor, causing the repressor to be activated

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37
Q

What is the product protein of the TRP operon

A

proteins that are used in the biosynthesis of tryptophan

38
Q

how many proteins are coded for in the TRP operon

A

5

39
Q

Can prokaryotes do translational regulation

A

yes, but not very often. sometimes the protein made from an mRNA will bind to that mRNA causing it to become inactive

40
Q

What is the very first method of transcription regulation in eukaryotes

A

The DNA being bound to histones, making the genes impossible to access until they are removed from the histones

41
Q

What enzyme will pull the DNA off of histones, allowing the DNA to unwind from the chromatin structure, allowing the genes to be transcribed.

A

HAT

Histone Acetyltransferase

42
Q

What does HAT (histone Acetyltransferase) do to pull the DNA off of histones

A

it acetylates the histone

43
Q

What enzyme will allow the histones to rebind DNA, form the chromatin structure, and stop any transcription

A

HDAC

HIstone Deacetylase

44
Q

What does HDAC do to allow histones to bind to DNA

A

it deacetylates the histones

45
Q

Do Eukaryotes require initiation factors and promoter sequences for transcription

A

yes

46
Q

what are the different promoter sequences in eukaryotes used to help RNA polymerase begin transcription

A
  1. TATA box (25 Base pairs upstream)
  2. CAAT box (75 Base pairs upstream)
  3. GC-rich sequence
47
Q

do most eukaryotic genes have all three of the promoter sequences?

A

No, most have the TATA box, and EITHER the CAAT box, or the GC-rich sequence.

48
Q

in Eukaryotes, do hormones help regulate transcription

A

yes

49
Q

Do hormones usually enhance transcription, or inhibit it

A

they usually enhance transcription, but rarely can inhibit it

50
Q

How do lipid soluble hormones affect gene transcription

A

the hormone-receptor complex binds to the DNA and directly enhances transcription by assisting RNA polymerase 2 attachement

51
Q

how else can hormones and other substances (that aren’t able to cross the cell-membrane into the cell) affect transcription

A

they bind to surface receptors, then they change the cellular chemistry and that can affect transcription

52
Q

What are the two main molecules in a cell that have their levels either raised or decreased by activated surface receptors

A

cAMP

Ca++

53
Q

What are the steps involved in transcription regulation via cell surface receptors

A
  1. Molecule binds to the cell surface receptor
  2. This causes an increase in cAMP (or Ca++)
  3. This activates CBP (cAMP binding protein)
  4. CBP phosphorylates CREB (cAMP response element protein)
  5. CREB then binds to CRE (cAMP response elements) on the DNA, and
54
Q

What are 4 types of translational control in eukaryotes

A
  1. Alternative splicing
  2. mRNA editing
  3. mRNA stability
  4. RNA interference (RNAi)
55
Q

What is Alternative splicing

A

in eukaryotes there are multiple introns and exons on a single gene. introns are cut out and exons are left in the mRNA and lead to the resulting protein. Alternative splicing is the ability in eukaryotes to selectively cut out some of the exons along with the introns. This allows multiple different proteins that can be made from one gene

56
Q

What is mRNA editing

A

translational control that only happens in eukaryotes. Usually it is enzymes changing out bases

57
Q

in mRNA editing what is a C usually converted to, and what enzyme does it?

A

C is converted to U

Cytidine deaminase

58
Q

in mRNA editing what is an A usually converted into, and what enzyme does it?

A

A is converted to I (inosine)

Adenosine deaminase

59
Q

A ribosome reads an I (inosine) as a ______ when translating mRNA

A

Guanine.

so in effect A–> I = A –>G

60
Q

What is the purpose of the shine delgarno sequence

AKA the cozac sequence

A

it is a sequence on the mRNA that recruits the ribosome to the mRNA

61
Q

What are the three sites of ribosomes, and what happens at each

A

A site - where the tRNA/amino acid combo enter the ribosome
P site - the 2nd site the tRNA moves to, where the bond between adjacent amino acids is formed
E site - the last site, from where the tRNA leaves the ribosome

62
Q

what are the subunits of the ribosome, how many are there?

A

there are two subunits. a large and a small one

63
Q

does mRNA eventually “expire” or get too worn out to use?

A

yes

64
Q

what does mRNA stability do for mRNA

A

it increases the life of the mRNA

65
Q

What is RNAi (RNA interference)

A

a method of silencing the translation of certain genes by controlling the RNA for those genes

66
Q

What is the thought as to how RNAi developped

A

it is thought to have developped as an intracellular “immune system” to defend against viral infection

67
Q

What is the effect that RNAi has on endogenous genes

A

it controls their expression. keeps them from making proteins

68
Q

What does RNAi target

A

double stranded DNA

69
Q

double stranded DNA is rare in cells, where do we often find it

A

in RNA viruses

endogenous mRNA

70
Q

what is the mechanism by which RNAi degrades mRNA

A
  1. Dicer protein recognizes double stranded RNA and cuts them into short segments (small interfering RNA, (siRNA))
  2. RNA-induced silencing complex (RISC) binds one of these siRNA and uses it as a template to hunt its complimentary strands
  3. RISC then degrades the complimentary strands that it finds
71
Q

Do eukaryotes also do post-translational modifications

A

yes

72
Q

what are the types of post translational modifications that eukaryotes do

A
  1. Protein stability
  2. Additional functional groups
  3. Propeptide
73
Q

What are the two classes of biotechnically-derived products

A
  1. Proteins produced from recombinant DNA

2. Monoclonal antibodies

74
Q

What is a common use of recombinant proteins

A

they are used as therapeutics (rDNA drugs)

75
Q

what is a common use of monoclonal antibodies

A

diagnostics tests (pregnancy tests)

76
Q

What are the 4 different recombinant DNA technologies

A
  1. DNA cloning
  2. Restriction enzymes
  3. DNA plasmids (Vectors)
  4. PCR technique
77
Q

What are the steps in producing recombinant DNA proteins

A
  1. Identify the gene of interest from the genome
  2. Isolate the gene using restriction endonucleases
  3. Amplify (copy) the gene using PCR technology
  4. place the gene in a vector
  5. insert the plasmid into a host cell (transfection)
  6. Allow host to express protein
  7. collect protein
78
Q

What are restriction endonucleases

A

enzymes that cut DNA in the middle of a strand

79
Q

What are the two types of cuts that restriction endonucleases can do

A 
Flush ends (cuts straight through both strands)
Sticky ends (cuts strands in an offset manner, leaving a few nucleotides open so they can base pair)
80
Q

Do restriction enzymes cut at random places, or do they cut at certain sequences

A

they cut at specific sequences

81
Q

What is the purpose of using PCR technology

A

to amplify/copy the gene

82
Q

What does PCR stand for

A

polymerase chain reaction

83
Q

What are the steps of PCR technology (used to amplify the gene)

A
  1. add initial DNA, primers, and DNA polymerase
  2. heat DNA to denature the DNA strands
  3. cool DNA partially so that the primers pair with the DNA (annealing)
  4. Heat slightly to activate the DNA polymerase.
  5. Keep repeating steps 2 through 5
84
Q

What is a plasmid/Vector

A

a circular ring of DNA containing a specific gene or a set of genes

85
Q

what are the three things you need to make a plasmid/vector

A
  1. DNA
  2. restriction enzymes
  3. DNA ligase
86
Q

once you have made a plasmid with your gene of interest what do you do with it

A

insert it into a host organism

87
Q

What happens once you enter your plasmid into a host cell

A

the host uses it machinery to make your protein of interest

88
Q

What is transfection

A

the insertion of a DNA sequence into an organism

89
Q

What are the different types of transfection

A 
Chemical methods
liposomes
electroporation/sonoporation
magnetofection
optical transfection
impalefection
Gene gun
viral tranduction
90
Q

what is the most common recomdinant DNA drug

A

insulin

91
Q

besides the proteins themselves, what things can be the desired products of recombinant DNA

A
  1. enzymes

2. antibodies

DMD 5243 (17 decks)

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