Chapter 16 Facts - Genetics, A Conceptual Approach, V.3 By Benjamin A. Pierce

Front 1

What is a gene?

Back 1

A gene is any DNA sequence that is transcribed into an RNA molecule. There are two basic types, structural genes and regulatory genes.

Front 2

Describe a structural gene.

Back 2

Structural genes code for proteins that are used in metabolism or biosynthesis, or that help with the structure of the cell.

Front 3

Describe a regulatory gene.

Back 3

Regulatory genes are genes whose products (either RNA or proteins) interact with other sequences and affect the transcription or translation of the sequences.

Front 4

Describe a constitutive gene.

Back 4

Constitutive genes code for essential cell functions and they are expressed all the time in the cell.

Front 5

What are regulatory elements?

Back 5

Regulatory elements affect the expression of the sequences that they are linked to. They are common in bacterial and eukaryotic cells.

Front 6

How does gene regulation happen?

Back 6

Gene regulation mostly happens through proteins that regulatory genes produce, which recognize and bind to regulatory elements.

Front 7

What are the five ways that gene regulation can occur?

Back 7

Altering gene structure, during transcription, during mRNA processing, in RNA stability, and during translation.

Front 8

Describe domains.

Back 8

Domains are the regulatory proteins that bind to DNA sequences and affect their expression have different parts.

Front 9

What is the basic structure of a domain?

Back 9

Each domain is normally 60-90 amino acids that bind to DNA.

Front 10

What do the domains do with DNA?

Back 10

These amino acid domains often form hydrogen bonds with the bases or interact with the sugar-phosphate backbone of the DNA.

Front 11

What are motifs?

Back 11

Motifs are the groups of DNA-binding proteins, based on their characteristic structures.

Front 12

What is the basic structure of a motif?

Back 12

Motifs are simple structures like alpha helices that can fit into the major groove of the DNA.

Front 13

What are operons?

Back 13

Operons are a group of bacterial structural genes that are transcribed together (with their promoters and extra sequences that control transcription, too).

Front 14

What is the basic structure and function of an operon?

Back 14

At one end of the operon is a set of structural genes (gene a, gene b, gene c). These genes are transcribed into one mRNA, which gets translated to make enzymes A, B, and C. These enzymes carry out biochemical reaction series that convert the precursor molecule X into the product Y.

Front 15

What is a regulator gene?

Back 15

A regulator gene helps control the transcription of the structural genes of the operon.

Front 16

What is the regulator gene a part of?

Back 16

The regulator gene is not part of the operon; it has its own promoter and it is transcribed into a short mRNA, which is translated into a small protein.

Front 17

What is a regulator protein?

Back 17

A regulator protein is the small protein made from the regulator gene. It can bind to a region of DNA called the operator and affect whether transcription can happen.

Front 18

What are the two types of transcriptional control?

Back 18

There are two kinds of transcriptional control: negative control and positive control. Operons can also be either inducible or repressible.

Front 19

What is negative control?

Back 19

Negative control is when a regulatory protein is a repressor that binds to DNA and inhibits transcription.

Front 20

What is positive control?

Back 20

Positive control is when a regulatory protein is an activator that stimulates transcription.

Front 21

What are inducible operons?

Back 21

Inducible operons are operons where transcription is normally not taking place, and something has to happen to turn transcription on.

Front 22

What are repressible operons?

Back 22

Repressible operons are operons where transcription is normally happening, and something has to happen to turn transcription off.

Front 23

Describe negative inducible operons.

Back 23

Negative inducible operons have a negative control at the operator site, and the regulatory protein is a repressor.

Front 24

In negative inducible operons, what does transcription and translation of the gene produce?

Back 24

In negative inducible operons, transcription and translation of the regulator gene produce an active repressor that binds to the operator (the substrate makes the repressor inactive).

Front 25

What happens when the protein binds to the promoter site of the negative inducible operon?

Back 25

When the protein binds to the promoter site of the negative inducible operon, the protein physically blocks the binding of RNA polymerase to the promoter, so it prevents transcription.

Front 26

How is transcription turned on in a negative inducible operon?

Back 26

Transcription gets turned on in a negative inducible operon when an inducer (a small molecule) binds to the repressor. This alters the shape of the repressor and keeps it from binding to DNA with its other binding site (that makes this an allosteric protein, since it can change its shape when it binds to another molecule).

Front 27

What do inducible operons normally control?

Back 27

Inducible operons normally control proteins that carry out degradative processes (proteins that break down molecules).

Front 28

What are negative repressible operons, and how are they turned off?

Back 28

Negative repressible operons have negative control, and they turn off transcription that is normally taking place. To turn off transcription, a corepressor molecule must bind to the repressor to make it active and turn off transcription.

Front 29

What does a corepressor molecule do?

Back 29

In negative repressible operons, a corepressor molecule must bind to the repressor to make it active and turn off transcription.

Front 30

What do repressible operons normally control?

Back 30

Repressible operons normally control proteins that biosynthesize molecules that are needed in the cell, like amino acids.

Front 31

What is positive control?

Back 31

Positive control uses a regulatory protein as an activator: it binds to DNA (normally not at the operator site) and stimulates transcription. It can be inducible or repressible.

Front 32

Describe a positive inducible operon.

Back 32

In a positive inducible operon, transcription is normally off because the regulator protein (an activator) is produced in an inactive form.

Front 33

Describe a positive repressible operon.

Back 33

In a positive repressible operon, transcription is normally taking place and the regulatory protein has to be made in a form that readily binds to DNA and stimulates transcription.

Front 34

What is lactose?

Back 34

Lactose is a carbohydrate that is found in milk, and it can be metabolized by E. coli bacteria in the mammalian gut.

Front 35

What is the issue with lactose and E. coli?

Back 35

Lactose doesn’t diffuse easily across the E. coli membrane and it has to be actively transported across by permease.

Front 36

How does E. coli use lactose for energy?

Back 36

To use lactose for energy, it must be broken into glucose and galactose first through ß-galactosidase.

Front 37

Describe coordinate induction in the negative inducible lac operon.

Back 37

The lac operon is a negative inducible operon. The boost in enzyme synthesis when lactose is added to a medium instead of glucose is from the transcription of lacZ, lacY and lacA, and shows coordinate induction.

Front 38

What is coordinate induction?

Back 38

Coordinate induction is the simultaneous synthesis of several enzymes and it is stimulated by a specific molecule, the inducer. Allolactose (ß-galactosidase can convert lactose to allolactose) is the inducer.

Front 39

What is the inducer in coordinate induction?

Back 39

Allolactose (ß-galactosidase can convert lactose to allolactose) is the inducer.

Front 40

What happens when lactose is absent?

Back 40

When lactose is absent (and therefore allolactose is too), the regulator protein (a repressor) binds to the operator and inhibits transcription.

Front 41

What happens when lactose is present?

Back 41

When lactose is present, some of it is made into allolactose, which then binds to the regulator protein and makes the protein active. The regulator protein cannot bind to the operator, and the structural genes are transcribed and translated.

Front 42

Describe the structure of partial diploid E. coli cells.

Back 42

The cells of the partial diploid strains of E. coli have two different DNA molecules: the full bacterial chromosome and an extra piece of DNA.

Front 43

What are the two different parts of the partial diploid lac operon of E. coli, and how are they different?

Back 43

It was found that some parts of the lac operon are cis acting (they can control the expression of genes only when they are on the same piece of DNA), and other parts are trans acting (they can control the expression of genes when they are on other DNA molecules).

Front 44

Describe a structural mutation at the lacZ and lacY genes.

Back 44

A structural mutation at the lacZ and lacY genes was independent, and normally only affected the product of the gene where they occurred.

Front 45

When do mutated partial diploids on the lacZ and lacY genes function normally?

Back 45

Partial diploids with lacZ+ lacY- on the bacterial chromosome and lacZ- lacY+ on the plasmid functioned normally, producing ß-galactosidase and permease when lactose was there.

Front 46

Describe the regulator gene in the lacI gene, and how it affects the production of enzymes.

Back 46

A regulator-gene in the lacI gene affects the production of both ß-galactosidase and permease, because genes for both the enzymes are in the same operon and are regulated together.

Front 47

Describe the mutations caused by the regulator gene in lacI, and their effects on the lac enzymes.

Back 47

The mutations were constitutive, and caused the lac enzymes to be made all the time whether lactose was there or not. These mutations were called lacI-. The lacI+ gene is dominant over the lacI- gene.

Front 48

Describe the operator mutations that occurred at the lac operator site.

Back 48

Operator mutations occurred at the operator site and are called lacOc. The lacOc mutations alter the sequence of DNA at the operator so that the repressor protein couldn’t bind anymore: lacOc is dominant over LacO+.

Front 49

Describe the promoter mutations and what they affect.

Back 49

Promoter mutations affect lactose metabolism, and they have been isolated at the promoter site: lacP- interferes with the binding of RNA polymerase to the promoter.

Front 50

Are the promoter mutations cis or trans acting?

Back 50

The promoter mutations are cis acting.

Front 51

Describe the dominant super repressor.

Back 51

The dominant super repressor (lacIs) produces defective repressors that can’t be inactivated by an inducer. They produce a repressor with an altered inducer-binding site, so the inducer can’t bind to the repressor anymore.

Front 52

What can the repressor do in the case of the dominant super repressor? What does the inducer do?

Back 52

The repressor can always attach to the operator site and prevent transcription of the lac genes, because the inducer isn't there to stop it.

Front 53

Do bacteria choose to use glucose or lactose and other sugars? Why?

Back 53

Many bacteria metabolize glucose when they can, instead of lactose or other sugars. This is because glucose enters glycolysis without needing any modifications, and uses up less metabolization energy.

Front 54

What is catabolite repression?

Back 54

Catabolite repression is when genes that participate in metabolizing other sugars are repressed when glucose is available. It results from positive control in response to glucose.

Front 55

When is positive control accomplished?

Back 55

Positive control is accomplished when a dimeric catabolite activator protein (CAP) binds to a site that is about 22 nucleotides long, located within or slightly upstream of the lac gene promoter.

Front 56

What does CAP do before it binds to DNA?

Back 56

Before CAP binds to DNA, it forms a complex with adenosine-3’,5’-cyclic monophosphate (cyclic AMP, or cAMP) a modified nucleotide.

Front 57

What is CAP?

Back 57

A dimeric catabolite activator protein that accomplishes positive control by binding to a specific site upstream of the lac promoter.

Front 58

What happens to cAMP when there is a lot of glucose in the cell?

Back 58

A lot of glucose in the cell lowers the amount of cAMP, so there aren’t many cAMP-CAP complexes to bind to DNA.

Front 59

What happens to cAMP when there is very little glucose in the cell?

Back 59

Little glucose in the cell stimulates high cAMP levels, which increases the amount of cAMP-CAP that binds to the DNA. This increase enhances the RNA polymerase binding to the promoter and it increases the transcription of the lac genes 50-fold.