Chapter 18 (1)

Cells intricately and precisely regulate their __.

Both prokaryotes and eukaryotes must alter their patterns of __in response to changes in environmental conditions. Multicellular eukaryotes must also develop and maintain multiple cell types.
· Each cell type contains the same __ but expresses a different subset of genes, a significant challenge in __.

Gene expression in eukaryotes, as in bacteria, is often regulated at the stage of __, but control at other levels of gene expression is also important.
In recent years, researchers have been surprised to discover the many roles played by __ molecules in regulating eukaryotic gene expression.

Bacterial cells that conserve resources and energy have a selective advantage over cells that are unable to do so.
· Thus __has favored bacteria that express only the genes whose products are needed by the cell.

Metabolic control occurs on two levels. What are they?

· First, cells can adjust the activity of enzymes already present.

The first form of metabolic control is a fairly fast response, which relies on the sensitivity of many enzymes to chemical cues that increase or decrease their __activity.
§ The activity of the first enzyme in the __synthesis pathway is inhibited by the pathway’s end product (__)
· It allows a cell to adapt to short-term fluctuations in the supply of a substance it needs.

The second form of molecular control:

o If the environment, for example, provides all the tryptophan the cell needs, the cell stops making the enzymes that catalyze the synthesis of tryptophan
§ In this case, the control of enzyme production occurs at the level of __, the synthesis of mRNA coding for these enzymes.
§ More generally, many genes of the bacterial genome are switched on or off by changes in the metabolic status of the cell.
§ The basic mechanism for this control of __in bacteria, described as the __, was discovered in 1961 by François Jacob and Jacques Monod at the Pasteur Institute in Paris.

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; in other words, these genes are under __.

The switch is a segment of DNA called an __, in bacterial DNA, a sequence of nucleotides near the start of __to which an active __can attach. The binding of the __prevents RNA pol from attaching to the promoter and transcribing the genes of the __.

Note the ___location and name suit its function: Positioned within the promoter or, in some cases, between the promoter and the enzyme-coding genes, the __controls the access of RNA polymerase to the genes.

· All together, the operator, the promoter, and the genes they control- the entire stretch of DNA required for enzyme production for the tryptophan pathway- constitute an __.

If the operator is the switch for controlling transcription, how does this switch work?
· By itself, the __is turned on (RNA pol can bind to the promoter and transcribe the genes of the __.) The __ can be switched off by a protein called the __.
o The __binds to the __and blocks attachment of RNA polymerase to the promoter, preventing transcription of the genes.
o A __protein is specific for the operator of particular operons.

The trp repressor is the product of a regulatory gene, called trpR, which is located some distance from the operons it controls and has its own promoter.
__ are expressed continuously, although at a low rate, and a few trp repressor molecules are always present in E. coli cells.

Why is the trp operons not switched off permanently?
- First reason: __

Why is the trp operons not switched off permanently?
Second reason: __

The __ is synthesized in an inactive form with little affinity for the trp operator. Only if tryptophan binds to the __ at an allosteric site does the repressor protein change to the active form that can attach to the operator, turning the __ off.

Tryptophan functions in this system as a __, a small molecule that cooperates with a repressor protein to switch an operon off.

As tryptophan accumulates, more tryptophan molecules associate with trp __molecules, which can then bind to the trp __and shut down production of the tryptophan pathway enzymes.
§ If the cell’s tryptophan level drops, transcription of the operon’s genes resumes.
· One example of how __can respond to changes in the cell’s internal and external environment.

The trp operons is said to be a __because its transcription is usually on but can be inhibited (repressed) when a specific small molecule binds allosterically to a regulatory protein.

In contrast, an __is usually off but can be stimulated (induced) when a specific small molecule interacts with a regulatory protein. (Lac operons)

Lactose is available to E coli in the human colon if the host drinks milk. Lactose metabolism begins with hydrolysis of the disaccharide into its component monosaccharides, glucose and galactose, a reaction catalyzed by the enzyme __.
· Only a few are available in an E. coli cell, but if added to the environment, the number of __ molecule sin the cell increases a thousandfold within about 15 minutes.

The gene for __is part of the lac operons, which includes two other genes coding for enzymes that function in lactose utilization.

The entire __is under the command of a single operator and promoter. The __, lacl, located outside the operons, codes for an allosteric __protein that can switch off the lac operons by binding to the operator.

The difference between this and regulation of a trp operons is that while the trp repressor is __by itself and requires tryptophan as a __in order to bind to the operator, the lac repressor is __by itself, binding to the operator and switching the lac operons off.
· In this case, a specific small molecule, called an __, inactivates the repressor.

For the lac operons, the __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 configuration, and the genes of the lac operons are silenced. If lactose is added to the cell’s surroundings, allolactose binds to the lac repressor and alters its conformation, nullifying the repressor’s ability to attach to the operator. Without bound repressor, the lac operon is transcribed into __for the lactose-utilizing enzymes.

In the context of gene regulation, the enzymes of the lactose pathway are referred to as __because their synthesis is induced by a chemical signal. (Allolactose)
__(tryptophan synthesis enzymes) generally function in __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.
In contrast, __usually function in __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.

Regulation of both the trp and lac operons involves the __control of genes, because the operons are switched off by the active form of the repressor protein.
Allolactose induces enzyme synthesis not by acting directly on the genome, but by freeing the lac operons from the negative effect of the repressor.
Gene regulation is said to be __only when a regulatory protein interacts directly with the genome to switch transcription on.

When glucose and lactose are both present in its environment, E. coli preferentially uses __. The enzymes for glucose breakdown in glycolysis 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.

How does the E. coli cell sense the glucose concentration and relay this information to the genome?
The mechanism depends on the interaction of an allosteric regulatory protein with a small organic molecule, called __, which accumulates when glucose is scarce.

The regulatory protein, called __ is an activator, a protein that binds to DNA and stimulates transcription of a gene.

When __binds to this regulatory protein, __assumes its active shape and can attach to a specific site at the upstream end of the lac promoter.
· This attachment increases the affinity of RNA pol for the promoter, which is actually rather low even when no repressor is bound to the operator. By facilitating the binding of RNA pol to the promoter and thereby increasing the rate of transcription, the attachment of __to the promoter directly stimulates gene expression.
o Therefore, this mechanism qualifies as __regulation.

If the amount of glucose in the cell increases, the __concentration falls and without __, __ detaches from the operon.
Because __is inactive, RNA pol binds less efficiently to the promoter, and transcription of the lac operon proceeds at only a low level, even in the presence of lactose.

Thus, the lac operon is under dual control:
· _+_

The state of the lac repressor determines whether or not transcription of the lac operon’s genes occurs at all; the state of __(w/ or w/o bound __) controls the rate of transcription if the operon is __.

In addition to the lac operon, __regulates other operons that encode enzymes used in __pathways.
It may affect expression of more than 100 genes in E. coli.
When glucose is plentiful and __is inactive, the synthesis of enzymes that catabolize compounds other than glucose generally slows down.

The ability to catabolize other compounds, such as lactose, enables a cell deprived of glucose to survive. The compounds present in the cell at the moment determine which __are switched on- the result of simple interactions of activator and repressor proteins with the promoters of the genes in question.