Bio 131 Regulation of Gene Expression Weeks 10/11 Lecture 1

Figure 15.4

(a) Lactose absent, repressor active, operon off. The lac repressor is innately active, and in the absence of lactose it switches off the operon by binding to the operator. The enzymes for using lactose are not made.

Figure 15.5 B

(b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized. When glucose is present, cAMP is scarce, and CRP is unable to stimulate transcription at a significant rate, even though no repressor is bound. RNA polymerase has high affinity for the lac promoter only when CRP is bound to a DNA site at the upstream end of the promoter. CRP, in turn, attaches to its DNA site only when associated with cyclic AMP (cAMP), whose concentration in the cell rises when the glucose concentration falls. Thus, when glucose is present, even if lactose also is available, the cell preferentially catabolizes glucose and makes very low levels of the enzymes for using lactose.

Figure 15.24 b

(b) Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, binds to the repressor, inactivating it and "derepressing" the operon. The inactive repressor cannot bind to the operator, and so the genes of the lac operon are transcribed, and the enzymes for using lactose are made. E. coli uses three enzymes to take up and metabolize lactose, the genes for which are clustered in the lac operon. The first gene, lacZ, codes for β-galactosidase, which hydrolyzes lactose to glucose and galactose. The second gene, lacY, codes for a permease, a membrane protein that transports lactose into the cell. The third gene, lacA, codes for an enzyme that detoxifies other molecules entering the cell via the permease. Unusually, the gene for the lac repressor, lacI, is adjacent to the lac operon. The function of the teal region within the promoter will be revealed in Figure 15.5

A Trp Operon is a Negative Blank System, and is one of the many operons in the E. coli genome. A Lac Operon is a Negative Blank System***

A Trp Operon is a Negative Repressible System, and is one of the many operons in the E. coli genome. A Lac Operon is a Negative Inducible System***

A key advantage of grouping genes of related function into one transcription unit is that a single "blank-blank switch" can control the whole cluster of functionally related genes

A key advantage of grouping genes of related function into one transcription unit is that a single "on-off switch" can control the whole cluster of functionally related genes

A metabolic pathway can be controlled on two levels: Second, cells can adjust the production of certain enzymes; that is, they can regulate the expression of the blanks encoding the blanks.

A metabolic pathway can be controlled on two levels: Second, cells can adjust the production of certain enzymes; that is, they can regulate the expression of the genes encoding the enzymes.

A repressor protein is encoded by a regulatory gene, a gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes. Are Regulatory genes part or NOT part of the operon?

A repressor protein is encoded by a regulatory gene, a gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes. Regulatory Genes are NOT part of the operon!

A small molecule, a blank, inactivates the repressor, binding to a bacterial repressor protein and changing the repressor's shape so that it cannot bind to an operator, thus switching an operon on.

A small molecule, a inducer, inactivates the repressor, binding to a bacterial repressor protein and changing the repressor's shape so that it cannot bind to an operator, thus switching an operon on.

As tryptophan accumulates, more tryptophan molecules associate with trp blank molecules, which can then bind to the trp blank and shut down production of the tryptophan pathway enzymes. If the cell's tryptophan level drops, many fewer trp blank proteins would have tryptophan bound, rendering them active or inactive; they would dissociate from the operator, allowing transcription of the operon's genes to resume.

As tryptophan accumulates, more tryptophan molecules associate with trp repressor molecules, which can then bind to the trp operator and shut down production of the tryptophan pathway enzymes. If the cell's tryptophan level drops, many fewer trp repressor proteins would have tryptophan bound, rendering them active or inactive; they would dissociate from the operator, allowing transcription of the operon's genes to resume.

The number of β-galactosidase molecules in the cell increases 1,000-fold within about 15 minutes. How can a cell ramp up enzyme production this quickly?

Because it is part of the Lac Operon. (Explanation will take place in #20).

Why are the regulation of both trp and lac operons involve the negative control of genes?

Because the operons are switched off by the active form of their respective repressor protein.

Concept Check 15.1 How does binding of the trp corepressor to the trp repressor alter repressor function and transcription? How does binding of the lac inducer alter the function of the lac repressor?

Binding by the trp corepressor (tryptophan) activates the trp repressor, allowing it to bind to the trp operator, shutting off transcriptions of the trp operon. Binding by the lac inducer (allolactose) inactivates the lac repressor so it can no longer bind to the lac operator.

By facilitating the binding of RNA polymerase to the promoter and thereby increasing the rate of transcription of the lac operon, the attachment of CRP to the promoter directly stimulates gene expression. Therefore, this mechanism qualifies as positive/negative regulation.

By facilitating the binding of RNA polymerase to the promoter and thereby increasing the rate of transcription of the lac operon, the attachment of CRP to the promoter directly stimulates gene expression. Therefore, this mechanism qualifies as positive regulation.

Figure 15.5 A

By facilitating the binding of RNA polymerase to the promoter and thereby increasing the rate of transcription of the lac operon, the attachment of CRP to the promoter directly stimulates gene expression. Therefore, this mechanism qualifies as positive regulation.

E. coli synthesizes the amino acid tryptophan from a precursor molecule in the blank-step pathway shown in Figure 15.2. Each reaction in the pathway is catalyzed by a specific blank, and the five genes that code for the subunits of these enzymes are clustered together on the bacterial blank. A single blank serves all five genes, which together constitute a blank unit.

E. coli synthesizes the amino acid tryptophan from a precursor molecule in the 3-step pathway shown in Figure 15.2. Each reaction in the pathway is catalyzed by a specific enzyme, and the five genes that code for the subunits of these enzymes are clustered together on the bacterial chromosome. A single promoter serves all five genes, which together constitute a transcription unit.

Do only eukaryotes or both eukaryotes and prokaryotes alter gene expression in response to different environmental conditions?

Eukaryotes and prokaryotes both alter gene expression in response to different environmental conditions. (Understanding bio gene expression is regulated in different cells is crucial to our understanding of living systems.

True or False CRP is an Catabolite Receptor Protein?

FALSE CRP - Catabolite Activator Protein or aka (CAP)

A metabolic pathway can be controlled on two levels: First, cells can adjust the activity of blanks already present. This is a fairly rapid physiological response, which relies on the sensitivity of many blanks to chemical cues that increase or decrease their catalytic activity (see Concept 6.5). Ultimately, it allows a cell to adapt to blank-term fluctuations in the supply of a substance it needs.

First, cells can adjust the activity of enzymes already present. This is a fairly rapid physiological response, which relies on the sensitivity of many enzymes to chemical cues that increase or decrease their catalytic activity (see Concept 6.5). Ultimately, it allows a cell to adapt to short-term fluctuations in the supply of a substance it needs.

For the lac operon, the inducer is blank, an isomer of lactose formed in small amounts from lactose that enters the cell. In the absence of lactose (and hence blank), the lac repressor is in its active shape and binds to the operator; thus, the genes of the lac operon are silenced.

For the lac operon, the inducer is allolactose, an isomer of lactose formed in small amounts from lactose that enters the cell. In the absence of lactose (and hence allolactose), the lac repressor is in its active shape and binds to the operator; thus, the genes of the lac operon are silenced.

If lactose is added to the cell's surroundings, blank binds to the lac blank and alters its shape so the blank can no longer bind to the operator. Without the lac blank bound, the lac operon is transcribed into (what type of RNA), and the enzymes for using lactose are made.

If lactose is added to the cell's surroundings, allolactose binds to the lac repressor and alters its shape so the repressor can no longer bind to the operator. Without the lac repressor bound, the lac operon is transcribed into mRNA and the enzymes for using lactose are made.

If the amount of glucose in the cell increases, the cAMP concentration rises/falls, and without cAMP, what? detaches from the operon. Because what? is inactive, RNA polymerase binds less efficiently to the promoter, and transcription of the lac operon proceeds at only a low level, even when lactose is present

If the amount of glucose in the cell increases, the cAMP concentration falls, and without cAMP, what? detaches from the operon. Because what? is inactive, RNA polymerase binds less efficiently to the promoter, and transcription of the lac operon proceeds at only a low level, even when lactose is present

Example of 2nd Level of Metabolic Pathway If, in outerm-4r example, the environment provides all the tryptophan the cell needs, the cell stops making the blanks that catalyze the synthesis of tryptophan (Figure 15.2b). In this case, the control of blank production occurs at the level of transcription, the synthesis of blank RNA from the genes that code for these blank..

If, in our example, the environment provides all the tryptophan the cell needs, the cell stops making the enzymes that catalyze the synthesis of tryptophan (Figure 15.2b). In this case, the control of enzyme production occurs at the level of transcription, the synthesis of blank RNA from the genes that code for these enzymes.

In the case of the lac operon, allolactose induces/represses etc; enzyme synthesis not by directly activating the lac operon, but by freeing it from the negative effect of the inducer/repressor (see Figure 15.4b). Gene regulation is said to be positive only when a blank protein interacts directly with the genome to switch transcription on.

In the case of the lac operon, allolactose induces enzyme synthesis not by directly activating the lac operon, but by freeing it from the negative effect of the repressor (see Figure 15.4b). Gene regulation is said to be positive only when a regulatory protein interacts directly with the genome to switch transcription on.

Inducible/Repressible etc; enzymes usually function in catabolic pathways, which break down a nutrient to simpler molecules. By producing the appropriate enzymes only when the nutrient is available, the cell avoids wasting energy and precursors making proteins that are not needed.

Inducible enzymes usually function in catabolic pathways, which break down a nutrient to simpler molecules. By producing the appropriate enzymes only when the nutrient is available, the cell avoids wasting energy and precursors making proteins that are not needed.

Note that the lac operon is under dual control: negative/positive control by the lac repressor and negative/positive control by CRP. Whether or not transcription occurs is controlled by allolactose: Without allolactose, the lac repressor is inactive/active and the operon is on/off (transcription does not occur; see Figure 15.4a); with allolactose, the lac repressor is inactive/active and the operon is on/off (transcription occurs; see Figure 15.4b).

Note that the lac operon is under dual control: negative control by the lac repressor and positive control by CRP. Whether or not transcription occurs is controlled by allolactose: Without allolactose, the lac repressor is active and the operon is off (transcription does not occur; see Figure 15.4a); with allolactose, the lac repressor is inactive and the operon is on (transcription occurs; see Figure 15.4b).

Based on #20, o far, this sounds just like regulation of the trp operon, but there is one important difference. What is the difference between the trp repressor protein and the lac repressor protein?

Recall that the trp repressor protein is inactive by itself and requires tryptophan as a corepressor in order to bind to the operator. The lac repressor, in contrast, is active by itself, binding to the operator and switching the lac operon off.

Example of 1st Level of Metabolic Pathway The activity of the first enzyme in the pathway is inhibited by the pathway's end product—tryptophan, in this case (Figure 15.2a). Thus, if tryptophan accumulates in a cell, it shuts down the synthesis of more blank by inhibiting blank activity. Such feedback inhibition, typical of anabolic (biosynthetic) pathways, allows a cell to adapt to blank-term fluctuations in the supply of a substance it needs

The activity of the first enzyme in the pathway is inhibited by the pathway's end product—tryptophan, in this case (Figure 15.2a). Thus, if tryptophan accumulates in a cell, it shuts down the synthesis of more tryptophan by inhibiting enzyme activity. Such feedback inhibition, typical of anabolic (biosynthetic) pathways, allows a cell to adapt to short-term fluctuations in the supply of a substance it needs

WHAT IF? A certain mutation in E. coli changes the lac operator so that the active repressor cannot bind. How would this affect the cell's production of β-galactosidase

The cell would continuously produce B- galactosidase and the two other enzymes for using lactose, even in the absence of lactose, thus wasting cell resources.

The enzymes for tryptophan synthesis are said to be Inducible/Repressible etc; Inducible, Repressible etc; enzymes generally function in anabolic pathways, which synthesize essential end products from raw materials (precursors). By suspending production of an end product when it is already present in sufficient quantity, the cell can allocate its organic precursors and energy for (other or SOLELY one) use.

The enzymes for tryptophan synthesis are said to be repressible. Repressible enzymes generally function in anabolic pathways, which synthesize essential end products from raw materials (precursors). By suspending production of an end product when it is already present in sufficient quantity, the cell can allocate its organic precursors and energy for other uses.

The enzymes of the lactose pathway are referred to as blank (could be inducible/repressible etc) enzymes because their synthesis is induced by a chemical signal (allolactose, in this case).

The enzymes of the lactose pathway are referred to as inducible enzymes because their synthesis is induced by a chemical signal (allolactose, in this case).

The gene for β-galactosidase (lacZ) is part of the lac operon, which includes two other genes coding for enzymes that function in the use of lactose (Figure 15.4). The entire transcription unit is under the command of one main operator and promoter. The regulatory gene, lacI, located within or outside the lac operon, codes for an allosteric repressor protein that can switch off the lac operon by binding to the lac operator.

The gene for β-galactosidase (lacZ) is part of the lac operon, which includes two other genes coding for enzymes that function in the use of lactose (Figure 15.4). The entire transcription unit is under the command of one main operator and promoter. The regulatory gene, lacI, located within or outside the lac operon, codes for an allosteric repressor protein that can switch off the lac operon by binding to the lac operator.

The on-off switch (regulatory switch) is a segment of DNA called a blank, usually positioned within the promoter. Positioned within the promoter or, in some cases, between the promoter and the enzyme-coding genes, the blank controls the access of blank polymerase to the genes.

The on-off switch (regulatory switch) is a segment of DNA called an operator, usually positioned within the promoter. Positioned within the promoter or, in some cases, between the promoter and the enzyme-coding genes, the operator controls the access of RNA polymerase to the genes.

The regulatory protein, called cAMP receptor protein (CRP/catabolite activator protein), is a blank, a protein that binds to DNA and stimulates transcription of a gene. In prokaryotes, they bind in or near the promoter; in eukaryotes, activators generally bind to control elements in enhancers.

The regulatory protein, called cAMP receptor protein (CRP), is an activator, a protein that binds to DNA and stimulates transcription of a gene.

The trp operon is said to be a blank operon because its transcription is usually on but can be inhibited (blanked) when a specific small molecule (in this case, tryptophan) binds allosterically to a regulatory protein. In contrast, an blank operon is usually off but can be stimulated (blanked) to be on when a specific small molecule interacts with a different regulatory protein. This is a classic example of the (xxx operon, stands for lactose)

The trp operon is said to be a repressible operon because its transcription is usually on but can be inhibited (repressed) when a specific small molecule (in this case, tryptophan) binds allosterically to a regulatory protein. In contrast, an inducible operon is usually off but can be stimulated (induced) to be on when a specific small molecule interacts with a different regulatory protein. This is a classic example of the (lac operon, stands for lactose)

Continuation from #6 Thus, transcription gives rise to one long blank molecule that codes for the five polypeptides making up the enzymes in the tryptophan pathway (Figure 15.3a). The cell can translate this one blank into blank separate polypeptides because the mRNA is punctuated with blank and blank codons that signal where the coding sequence for each polypeptide begins and ends.

Thus, transcription gives rise to one long mRNA molecule that codes for the five polypeptides making up the enzymes in the tryptophan pathway (Figure 15.3a). The cell can translate this one mRNA into 5 separate polypeptides because the mRNA is punctuated with start and stop codons that signal where the coding sequence for each polypeptide begins and ends.

Tryptophan functions in this system as a Corepressor, a small molecule that cooperates with a repressor protein to switch an operon off. (changes the protein's shape, allowing it to bind to the operator and switch an operon off)

Tryptophan functions in this system as a corepressor, a small molecule that cooperates with a repressor protein to switch an operon off.(changes the protein's shape, allowing it to bind to the operator and switch an operon off)

Figure 15.3 Explanation: Tryptophan is an blank acid, produced by an anabolic pathway catalyzed by three enzymes (see Figure 15.2). (a) The five genes encoding the polypeptide subunits of the enzymes in this pathway are grouped, along with a promoter, into the trp operon. The trp blank (the repressor binding site) is located within the trp blank (the RNA polymerase binding site). (b) Accumulation of tryptophan, the end product of the pathway, represses blank of the trp blank, thus blocking synthesis of all the enzymes in the pathway and shutting down tryptophan production.

Tryptophan is an amino acid, produced by an anabolic pathway catalyzed by three enzymes (see Figure 15.2). (a) The five genes encoding the polypeptide subunits of the enzymes in this pathway are grouped, along with a promoter, into the trp operon. The trp operator (the repressor binding site) is located within the trp promoter (the RNA polymerase binding site). (b) Accumulation of tryptophan, the end product of the pathway, represses transcription of the trp operon, thus blocking synthesis of all the enzymes in the pathway and shutting down tryptophan production.

A protein that inhibits gene transcription. In prokaryotes, blanks bind to the DNA in or near the promoter. In eukaryotes, blanks may bind to control elements within enhancers, to activators, or to other proteins in a way that blocks activators from binding to DNA. Are blank proteins specific for the operator of a particular operon?

What is a Repressor? Are Repressor proteins specific for the operator of a particular operon? And yes, they are! For example, the trp repressor, which switches off the trp operon by binding to the trp operator, has no effect on other operons in the E. coli genome.

A unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway.

What is an Operon?

When cAMP binds to this regulatory protein, CRP assumes its active/inactive shape and can attach to a specific site at the upstream end of the lac promoter

When cAMP binds to this regulatory protein, CRP assumes its active shape and can attach to a specific site at the upstream end of the lac promoter

When glucose and lactose are both present in its environment, E. coli preferentially uses blank. The enzymes for blank breakdown in glycolysis (see Figure 7.9) are continually present. Only when blank is present and blank is in short supply does E. coli use blank as an energy source, and only then does it synthesize appreciable quantities of the enzymes for lactose breakdown.

When glucose and lactose are both present in its environment, E. coli preferentially uses glucose. The enzymes for glucose breakdown in glycolysis (see Figure 7.9) are continually present. Only when lactose is present and glucose is in short supply does E. coli use lactose as an energy source, and only then does it synthesize appreciable quantities of the enzymes for lactose breakdown.

When glucose is plentiful and CRP is inactive, the synthesis of enzymes that catabolize compounds other than glucose generally excels/slows down. The ability to catabolize other compounds, such as lactose, enables a cell deprived of glucose to survive.

When glucose is plentiful and CRP is inactive, the synthesis of enzymes that catabolize compounds other than glucose generally excels/slows down. The ability to Rundown: The compounds present in any given cell at the moment determine which operons are switched on—the result of simple interactions of activator and repressor proteins with the promoters of the genes in question.

Describe the binding of RNA polymerase, repressors, and activators to the lac operon when both lactose and glucose are scarce. What is the effect of these scarcities on transcription of the lac operon?

When glucose is scarce, cAMP is bound to CRP and CRP is bound to the lac promoter, favoring the binding of RNA Polymerase. However, in the absence of lactose, the lac repressor is bound to the lac operator, blocking RNA polymerase binding to the lac promoter. Therefore, the lac operon genes are not transcribed.

Why, then, is the trp operon not switched off permanently? First, the binding of repressors to operators is non or reversible. An operator alternates between two states: one with the repressor bound and one without. The relative duration of the repressor-bound state is higher when more or less active repressor molecules are present. Second, the trp repressor, like most regulatory proteins, is an allosteric protein, with two alternative shapes: blank and blank (see Figure 6.18). The trp repressor is synthesized in the blank form, which has little affinity for the trp operator. Only when tryptophan binds to the trp repressor at an allosteric site does the repressor protein change to the blank form that can attach to the operator, turning the operon off (see Figure 15.3b).

Why, then, is the trp operon not switched off permanently? First, the binding of repressors to operators is non or reversible. An operator alternates between two states: one with the repressor bound and one without. The relative duration of the repressor-bound state is higher when more or less active repressor molecules are present. Second, the trp repressor, like most regulatory proteins, is an allosteric protein, with two alternative shapes: active and inactive (see Figure 6.18). The trp repressor is synthesized in the inactive form, which has little affinity for the trp operator. Only when tryptophan binds to the trp repressor at an allosteric site does the repressor protein change to the active form that can attach to the operator, turning the operon off (see Figure 15.3b).