Bio 214 #3 Flashcards

Front 1

Genes reside on _______ in the nucleus and carry the information that encodes _________

Back 1

*DNA
*Proteins

Front 2

Where are proteins syntheized?

Back 2

In the cytoplasm

Front 3

What is the enzyme that catalyzes the linking of rNTPs?

Back 3

RNA Polymerase

Front 4

Where are RNA polymerase found?

Back 4

In both prokaryotes and eukaryotes

Front 5

RNA polymerase uses _______ as substrates

Back 5

rNTPs

Front 6

RNA polymerase uses a ________ as a template to synthesize the polymer of RNA

Back 6

double stranded DNA

Front 7

What direction does RNA synthesis occur in?

Back 7

The 5' -> 3' direction

Front 8

What is transcription

Back 8

Copying of DNA into RNA

Front 9

Is the RNA molecule a copy of the template or non-template strand?

Back 9

Non-template

Front 10

Is the non-template strand called the coding or non coding strand?

Back 10

Coding

Front 11

Is the template strand called the coding or non coding strand?

Back 11

non-coding

Front 12

Why is the non-template strand called the coding strand

Back 12

Because one can read the amino acid codons directly from it

Front 13

Is the copying of RNA on a per gene basis?

Back 13

Yes

Front 14

What does a per gene basis mean?

Back 14

Some genes are transcribed with the bottom strand as the template and some are transcribed as the top strand as the template

Front 15

A gene is a region encoding a _________, the sequences that are ______ and the sequences that carry signals for _________

Back 15

*Protein
*transcribed
*the initiation and termination of transcription and translation

Front 16

Are initiation signals in the moelcule that is made?

Back 16

No

Front 17

What are initiation signals/

Back 17

Controlling elements that are "upstream" of the transcribed or translated sequence

Front 18

RNA is identical in sequence to the ________ strand of DNA except for what?

Back 18

*Non-template
*Uridine nucleotides replace thymidine nucleotides

Front 19

Transcription of a gene must begin at a nonfixed position. True or false?

Back 19

False

Needs to bein at a fixed position

Front 20

Transcription proceeds in _____ direction

Back 20

One

Front 21

What are the two short regions upstream to the start of transcrition that are centered at 10 nucleotides and 35 nucleotides before transcrioton starts called?

Back 21

Consensus sequences

Front 22

What is the +1 position for?

Back 22

First nucleotide transbribed into RNA

Front 23

Is there a 0 in the numbering convention for RNA?

Back 23

No

Front 24

What is the -35 consensus region look like?

Back 24

TTGACA

Front 25

What is the -10 Consensus region nucleotides

Back 25

TATAAT

Front 26

What are the attachment points for RNA polymerase?

Back 26

The two consensus regions

-35 (TTGACA)

-10 (TATAAT)

Front 27

What is the promotor

Back 27

The region that the RNA polymerase "covers" which is about 70 nucleotides long, but it only binds to the -10 and -35 region.

Front 28

Is the specific sequences that surround and are between the -10 and -35 regions important?

Back 28

Not really, they are variable

Front 29

Is the length of the sections that surround and are between the -10 and -35 sequences improtant?

Back 29

Yes

Front 30

Why must the length of neucleotides between the -10 to -35 region have to be important?

Back 30

Because the -10 and -35 seuqences must match with the speicific contact of RNA polymerase

Front 31

About how many nucleotides need to be between the -10 and -35 sequences

Back 31

18 nuclotides (give or take two)

Front 32

After it is in position, RNA polymerase begins synthesizing RNA about how many nucleotides downstream? At what position?

Back 32

* about 10 nucleotides downstream
*Position +1

Front 33

What are the two types of promotor mutations?

Back 33

1) Down mutations
2) Up mutations

Front 34

"Down" mutations result so that _____ rNA is being made

Back 34

Less

Front 35

Why is less RNA being made in the "down" mutation of the sequence alignment

Back 35

Because the RNA polymerase binds less well to these mutant promotors and that will initiate transcription less frequently.

Front 36

How is the promotor mutated in a "down" mutation

Back 36

Less similar to the consensus

Front 37

Does an "up" mutation cause an increase or decrease in the rate of transcription initiation?

Back 37

Increase

Front 38

Does the "up" mutation make the promotor more or less like the consensus sequence?

Back 38

More

Front 39

Does the "up" mutation cause the RNA polymerase bind better or worse to the promotors

Back 39

Better

Front 40

Does the up mutation make a stronger promoter?

Back 40

Yes

Front 41

In addition to a signal for a transcription initiation (the promoter), a signal to begin ______ is also present

Back 41

Translation

(Protein synthesis)

Front 42

In prokaryotes there exists in the RNA / DNA, a sequence that serves as a binding site for the ribosome what is its consensus sequence?

Back 42

5'-AGGAGG-3'

Front 43

Is the poostion relative to the strat of transcription variable?

Back 43

Yes

Front 44

The position relative to the start of transcription is located within _____ nucleotides of the translation initiation codon (the first AUG codon)

Back 44

10

Front 45

What are the two classes of enzymes?

Back 45

1) Inducible
2) Constitutive

Front 46

What are inducible enzymes?

Back 46

Adaptable such as β-galactosidase

Front 47

What are constitutive enzymes?

Back 47

Always present such as ribosomal rpoteins

Front 48

What is the function of β-galactosidase?

Back 48

Cleave the disaccharide lactose into the monosaccharides glucose and galactose

Front 49

What induces the synthesis of β-galactosidase

Back 49

Lactose

Front 50

Lactose is said to be an ________

Back 50

Inducer

Front 51

What are the two toher proteins that are coordinately regulated with β-galactosidase? (that is, they're induced with lactose):

Back 51

1) Lactose permease
2) Lactose transacetylase

Front 52

What does lactose permease do?

Back 52

Required for the absorption of lactose

Front 53

Waht does lactose transacetylase do?

Back 53

Acetylates other β-galactoside sugars so that β-galactosidase won't cleave them

Front 54

Why does the coordinated induction of the three enzymes, permease, β-galactosidase and transacetylase occur?

Back 54

Because they are all made from the same RNA (co-transcribed)

Front 55

What forms the operon?

Back 55

A group of coordinately regulated bacterial gene

Front 56

What is lacZ for?

Back 56

β-galactosidase

Front 57

What is lacY for?

Back 57

Permease

Front 58

What is lacA for?

Back 58

Transacetylase

Front 59

LacZ, lacY and lacA are called _______ genes

Back 59

Structural genes

Front 60

What are structural genes

Back 60

They encode enzymes

Front 61

Mutations in structural genes are dominant or recessive?

Back 61

Recessive

Front 62

What kind of expression does the lacI- give to the expression of lacZ, Y and A?

Back 62

Constitutive

Front 63

For a lacI- mutation is there need for an inducer to stimulate transcription of the operon?

Back 63

No

Front 64

LacI is a _______ gene

Back 64

Regulatory

Front 65

Mutations in a regulatory gene will do what?

Back 65

Simultaneously affect the transcription of several other genes

Front 66

What is the noraml function for lacI+?

Back 66

Keep lacZ, Y and A shut off in the absence of lactose

Front 67

Is lacI a negative or positive regulator?

Back 67

Negative

Front 68

The lacI gene encodes a _________

Back 68

Repressor

Front 69

What does the repressor do?

Back 69

Functions to repress transcription of the lac operon

Front 70

What is an episome?

Back 70

A large, self-transmissible circular DNA molecule (a plasmid) that can be transferred from a donor cell (F+)to a recipient cell (F-)

Front 71

A recipient of an episome will be a _______

Back 71

Partial diploid

Front 72

Does the product of the lacI+ gene work in trans or cis?

Back 72

Trans (it is diffusible)

Front 73

What is the role of lactose?

Back 73

To de-repress the operon; neutralize the repressor so that the repressor's inhibitory effect is lifted

Front 74

What is the phenotype of the lacIS mutation

Back 74

Uninducible

Front 75

Is the operator a site?

Back 75

Yes

Front 76

Does the operatuor encode a diffusible protein?

Back 76

No

Front 77

Does the operator work in cis or trans?

Back 77

Cis

Front 78

What does the lacI- mutant do?

Back 78

It makes a repressor that ca't bind the operator

Front 79

What does a lacIs mutant do?

Back 79

Makes a repressor that has a defect in the domain in which the inducer binds

If inducer can't bind, then the pressor can't be removed from the operator

Front 80

What does the Oc mutation do?

Back 80

It changes the recognition sequence, or target, of the repssor

The repressor won't bind because it no longer has a site for binding

Front 81

What is the positive regulation of the lac operon?

Back 81

through the glucose and cAMP of the CAP protein

Front 82

What does the presence of glucose do for lac operon expression?

Back 82

Shuts down lac operon expression

Front 83

What mediates the positive regulation of the lac operon?

Back 83

cAMP

Front 84

What does positive regulatio nof the lac operon mean?

Back 84

It activates the operon

Front 85

How is cAMP made?

Back 85

Made from ATP through the action of the enzyme adenylate cyclase

Front 86

Why is glucose catabolized preferenitally over other sugars?

Back 86

It is the most efficient carbon and energy source for most non-photosynthetic organisms. Its presence causes the shutdown of toehr sugar catbolic operons to prevent wasteful synthesis of enzymes that are not needed

Front 87

What is catabolite repression?

Back 87

Glucose is catabolized preferentially over other sugars so its presence causes the shutdown of other sugar catbolic operons to prevent wasteful synthesis of enzymes that are not needed

Front 88

What serves as a glucose level signal to these operons?

Back 88

cAMP

Front 89

High levels of glucose (indirectly) results in _____ levels of cAMP

Back 89

Low

Front 90

The CA{ is the activator of all ______

Back 90

Catabolic sugar operons

Front 91

The cAMP and CAP form a compelx that does what?

Back 91

Activates transcription of sugar catabolic operons by aiding the binding of RNA polymerase

Front 92

How does cAMP aid in CAP binding?

Back 92

It induces a conformational change in CAP that enables the bindign of CAP to its site

Front 93

Do CAP activated operons have poor or strong promotors?

Back 93

Poor

Front 94

The does the cAMP-CAP complex bind on the DNA?

Back 94

Around nucleotides -50 to -70

Front 95

Does protein synthesis occur in a different location than the gene?

Back 95

Yes

Front 96

What is needed to synthesizze RNA?

Back 96

*Double stranded DNA
*rNTPs
*RNA polymerase

Front 97

What has to occur for the synthesis of RNA?

Back 97

Local unwinding of the region, acitively transcribed (transcribing from one form to another)

Front 98

What direction is RNA synthesized from?

Back 98

5' to 3'

Front 99

The transcript (RNA molecule) is a copy of the template or the nontemplate strand

Back 99

Non-template

[Except the uracil replaces the thyamines]

Front 100

Is the transcription of each gene independent or dependent of the trascription of the other gene on the same dNA

Back 100

Is independent, as long as there is the correct polarity

Front 101

What genes control?

Back 101

Synthesis of protein

Front 102

The open reading frame is the _______ encoding region

Back 102

Protein

(Codons)

Front 103

What are the sequences for regulation of transcription

Back 103

The sequences for regulation of translation (protein synthesis)

Front 104

What is special about the +1 location for the transcription

Back 104

Start of the transcription

Front 105

Is there a 0 on the gene?

Back 105

No

Front 106

For the DNA, everything with a negative charge is part of transcription. True or false.

Back 106

False,

Everything with negative charge is before the transcription (and is important for the regulation of RNA)

Front 107

What is the RNA polymerase contact site within a gene called?

Back 107

The promotor

Front 108

Why can each promotor differ?

Back 108

Because of the amount of protein that needs to be made

(IE if need less made can have less contact)

Front 109

Promotor includes _______ and ______

Back 109

-35 and -10

Front 110

What are "down" mutations?

Back 110

*Affects levels of transcriotion (negative)
*Lower rate of transcription
*Make the native promotor of the traget gene less similar to the consensus

Front 111

What are "up" mutations?

Back 111

*Higher rate of transcription
*Make native promotor more similar to the consensus

Front 112

Does the RNA polymerase need 1 or 2 strands?

Back 112

2

Front 113

If you mess with the promotor, the RNA polymerase binds with _______ affinity. What sort of mutation is this?

Back 113

*Decreased
*Down

Front 114

Does the promotor get transcribed?

Back 114

No

Front 115

What is the promotor for ribosomoes

Back 115

Ribosome binding site

5'-AGGAGG-3'

Front 116

How are genes turned ON and OFF?

Back 116

"Adaptive" enzymes

Front 117

What are inducible genes?

Back 117

Enzymes made under "inducing" conditions

Front 118

What are constitutive genes?

Back 118

Made regardless of conditions (always made)

Levels don't change

Front 119

How big of a shadow does the RNA polymerase cast?

Back 119

By ~70 nucleotides

Front 120

The repressor binding site, binds the enzyme next to _____

Back 120

The promotor

Front 121

How does the negative reulation work?

Back 121

By way of a repressor

Front 122

What does the negative regulation do for the transcription rates

Back 122

Helps to regulate rates of transcritions

Front 123

How does negative regulation work by its steps?

Back 123

*RNA polymerase can't bind
*So don't make RNA
*Is a way to turn down transcription when it is not needed

Front 124

Positiive regulation is by way of an ______

Back 124

Activator

Front 125

Genes regulators are sensitive to what?

Back 125

Environmental conditions

Front 126

What is an operon

Back 126

A group of coordinately regulated bacterial genes and their regulatory sequences

Front 127

Is an operon found within prokaryotes, eukaryotes or both

Back 127

Prokaryotes ONLY

Front 128

The regulatory sequence, is that found within prokaryotes, eukaryotes or both?

Back 128

Prokaryotes

Front 129

What does coordinately regulated mean?

Back 129

β-galactosidase, permease, transacetylase all response identically to the presence and absence of lactose

Front 130

What are the structural genes in the lac operon?

Back 130

Lac Z, lac Y and lac A

Front 131

What are structural genes?

Back 131

Encode enzymes/proteins that do work

Front 132

What does co-transcribed mean?

Back 132

All genes transcribed

Front 133

What are the two categories for genes?

Back 133

1) Regulatory
2) Structural

Front 134

A plasmid is called what?

Back 134

Episome

Front 135

Lac Z- mutation is _____ to lac Z +

Back 135

Recessive

Front 136

For the lac I- mutation, what sort of synthesize do you see of the three enzymes?

Back 136

Constitutive

There is no lactose needed to induce the synthesis

Front 137

Does lac I work in trans or cis?

Back 137

Trans to repress lac enzymes

Front 138

What does the lac I gene make?

Back 138

Makes diffusible product that affects genes in different parts of all

Front 139

Operator works in cis and trans

Back 139

Cis (same location)

Front 140

Lac A+ gene is controlled by ________

Back 140

O ^ c

Front 141

Lac Z+ gene is controlled by ______

Back 141

O+

Front 142

Is the lactose a negative or positive allosteric effector of the repressor

Back 142

Negative

Front 143

If the binding site for the lactose is defective does the lactose bind?

Back 143

No

Front 144

Is the repressor a homotetramer?

Back 144

Yes

Front 145

How does the Oc mutation come about?

Back 145

Operator has change within the base pairs

So, polymerase can still keep going through with high transcription

Front 146

Does lactose cause a high or low β-galactosidase activity?

Back 146

High

Front 147

Does glucose cause a high or low β-galactosidase acitivity

Back 147

Low (Baseline level)

Front 148

Does lactose and glucose cause a high or low β-galactosidase activty?

Back 148

Low/none

Front 149

Is glucose preferentially catabolized over lactose or is lactose preferentially catabolized over glucose?

Back 149

Glucose is preferentially catabolized over lactose

Front 150

What is cAMP derived from?

Back 150

ATP

Front 151

What enzyme catalyzes the production of ATP to cAMP?

Back 151

Adenylate cyclase

Front 152

What is the signaler is eukaryote and prokaryote cells about the availablility of carbon sources?

Back 152

cAMP

Front 153

If there is glucose, lactose and cAMP what is the β-galactosidase activity?

Back 153

High

(The cAMP is counteracting the negative effect by glucose)

Front 154

Is [cAMP] inversely related to [glucose]?

Back 154

Yes

Front 155

High [glucose] = _______ cAMP = _____ lac operon transcription

Back 155

*Low
*Low

Front 156

Low [glucose] = ____ cAMP = _____ lac operon transcription

Back 156

*High
*High

Front 157

Does cAMP help to activate or deactivate the lac operon?

Back 157

Activate

Front 158

What are other sugar operons that are subject to catabolite repression?

Back 158

*Arabinose operon
*Maltose operon
*Raffinose operon


They all ahve a systemic (global) response to glucose

Front 159

Does cAMP have a negative or positive effect on the lac operon?

Back 159

Positive

Front 160

Activation requires two components, CAMP and ______

Back 160

CAP protein

(Binding site for CAP too)

Front 161

IS cAMP a positive or negative effector?

Back 161

Positive