Chapter 11

The overall process by which genetic information flows from genes to proteins, that is from genotype to phenotype, is called-

genen expression

Genes within highly compacted chromatin, as seen in mitotic chromosomes and in varying regions of interphase chromosomes are generally-

not expressed at all

The genes that a cancer-causing virus inserts into a host ell can make the cell cancerous. Such a gene, which can cause cancer when present in a single copy in the cell, is called an ___________________

oncogene

What is a reason that bacteria can change their protein production so quickly in response to environmental changes?

prokaryotic mRNAs have very short lifetimes; they are typically degraded by enzymes within a few minutes after their synthesis. These are called short-lived mRNAs

Once an X chromosome is inactivated, all descendant cells have the same copy turned off. This is an example of ______________________

epigenetic inheritance

Inheritance of traits transmitted by mechanisms not directly involving nucleotide sequence, like the passing on of modifications to DNA and histones to future generations, is called -

epigenetic inheritence

A _____________________ is a series of molecular changes that converts a signal on a target cell's surface to a specific response inside the cell. Describe how it works

signal transduction pathway. The cell sending a message secretes a signaling molecule. This molecule binds to a specific receptor protein embedded in the target cell's plasma membrane. The binding activates the first in a series of relay proteins within the target cell. Each relay molecule activates another. The last relay molecule in the series activates a transcription factor that triggers transcription of a specific gene. Translation of the mRNA produces a protein that performs the function originally called for by the signal.

What is the "default" state for most genes of multicellular eukaryotes and why? exceptions?

"off" because a typical animal or plant cell only need to turn on (transcribe) a small percentage of its genes, those required for the cell's specialized structure and function. Exceptions include housekeeping genes, those continually active in virtually all cells for routine activities such as glycolysis, which may be in an "on" state by default.

In contrast to operators found within prokaryotic operons, enhancer are usually located -

far away on the chromosome from the gene they help regulate

How can a cell acquire an oncogene?

from a virus or from the mutation of one of its own proto-oncogenes

Give examples two different ways in which chromosomes can be chemically modified in ways that help regulate gene expression-

1) the addition of methyl groups to some of the amino acids in histone proteins can cause the chromosomes to become more compact, leading to reduced transcription. 2) Adding acetyl groups opens up the chromatin structure, promoting transcription.

Where does the repressor come from ?

A gene called a regulatory gene, located outside the operon, codes for the repressor.

A cluster of genes with related functions, in this instance, the entire stretch of DNA required for enzyme production--is called a(n) ________________. What is the key advantage to the grouping of related genes?

An operon. that a single "on-off switch" can control the whole cluster.

The inactive X in each cell of a female condenses into a compact object called a _______________

Barr body

Describe the gradual progression from somatic mutation to cancer using colon cancer as an example-

Colon cancer begins when an oncogene arises or is activated through mutation, causing unusually frequent division of apperently normal cells in the colon lining. Later, additional DNA mutations, such as the inactivation of a tumor-suppressor gene, cause the growth of a small benign tumor (a polyp) in the colon wall. Still more mutations eventually lead to formation of a malignant tumor, a tumor that has the potential to metastasize (spread).

Multiple changes must occur at the ______________ level for a cell to become fully cancerous.

DNA

Describe how the trp operon works?

E coli can make tryptophan from scratch, using enzymes encoded in the trp operon. But E coli will stop making tryptophan and simply absorb it from the surroundings whenever possible. When E coli is bathed in tryptophan in the intestines the tryptophan binds to the repressor of the trp operon. This activates the trp repressor, enabling it to switch off the operon. Thus, this type of operon allows bacteria to stop making certain essential molecules when the molecules are already present tin the environment saving materials and energy for the cells.

Describe a key communication mechanism in the coordination of cellular activities

cell-to-cell signaling via proteins or other kinds of molecules carrying messages from signaling cells to receiving (target) cells

In the body, a nerve cell has a very different structure and performs very different functions than a skin cell. Because the two cell types have the same genes, how can the cells be so different?

Each cell type must be expressing certain genes that are present in, but not expressed in, the other cell type.

Describe how miRNA regulates genes

Each miRNA, typically about 22 nucleotides long, forms a complex with one or more proteins. The miRNA-protein complex can bind to any mRNA molecule with 7 to 8 nucleotides of complementary sequence. Then the complex either degrades the target mRNA or blocks ins translation. It has been estimated that miRNAs may regulate the expression of at least one-half of all human genes.

How are microrays used?

First mRNA is isolated, the it is mixed with reverse transcriptase (a viral enzyme that produces DNA form an RNA template) to produce a mixture of single-stranded DNA fragments. These fragments are called cDNA (complementary DNAs) because each on is complementary to one of the mRNAs. The cDNAs are produced in the presence of nucleotides that have been modified to fluoresce. The fluorescent cNDA collection thus represent all of the genes that are being actively transcribed in that particular cell at that particular time. A small amount of fluorescently labeled cDNA mixture is added to each of the wells in the microarray. If a molecule in the cDNA mixture is complementary to a DNA fragment at a particular location on the grid, the cDNA molecule bids to it, becoming fixed there. After the unbound cDNA is rinsed away, the remaining cDNA produces a flow and the pattern of glowing spots enable researchers to determine which genes are being transcribed in the starting cells.

What are the three ways a proto-oncogene--a gene that has an essential function in normal cells--become a cancer-causing oncogene?

In general, an oncogene arises from a genetic change that leads to an increase either in the amount of proto-oncogene's protein product or in the activity of each protein molecule 1) a mutation in the proto-oncogene creates an oncogene that codes for a hyperactive protein, one whose stimulating effect is stronger than normal. 2) An error in DNA replication or recombination can generate multiple copies of the gene, which are all transcribed and translated; the result is an excess of the normal stimulatory protein. 3) the proto-oncogene is moved from its normal location in the cell's DNA to another location. At its new site, the gene is under the control of a different promoter, one that cause it to be transcribed more often than normal; the normal protein is again made in excess.

What happens to a gene that is on?

It is being transcribed into mRNA and that message is being translated into specific protein molecules

What does E. coli do when lactose is plentiful in the digestive system?

It makes the enzymes necessary to absorb the sugar and use it as an energy source.

The regulatory gene is expressed continually so the cell always has a small supply of repressor molecules. But how can an operon be turned on if its repressor is always present?

Lactose interferes with the attachment of the lac repressor to the operator by binding to the repressor and changing its shape. With its new shape, the repressor cannot bind to the operator, and the operator switch remains on.

How is gene regulation in prokaryotes and eukaryotes similar and yet different?

Like prokaryotes, use regulatory proteins--activators and repressors--that bind to specific segments of DNA and either promote or block the binding of RNA polymerase, turning the transcription of genes on or off. However, most eukaryotic genes have individual promoters and other control sequences and are not clustered together as in operons.

Are modifications to the chromatin permanent? why?

No, because unlike mutations to the DNA which are permanent, they do not affect the sequence of DNA itself and can therefore be reversed by processes not fully understood.

How are methylation patterns passed on?

Once methylated, genes usually stay the way through successive cell divisions in a given individual. During replication, when a methylated stretch of DNA is duplicated, enzymes methylate the corresponding daughter strands to match. This allows cells that form specialized tissues to keep a chemical record fo what occurred during embryonic development.

Why don't females, with two X chromosomes, make twice as much of the proteins encoded by genes on the X chromosome compared to the amounts in males?

One X chromosome in each somatic cell is chemically modified and highly compacted, rendering it almost entirely inactive. Inactivation of an X chromosome involves modification of the DNA (by, for example, methylation) and the histone proteins that help compact it. A specific gene on the X chromosomes ensure that only one of them will be inactivated. This X chromosome inactivation occurs early in embryonic development when one of the two X chromosomes in each cell is inactivated at random.

Once lactose interferes with the attachment of the lac repressor, how does transcription proceed?

RNA polymerase is then able to bind to the promoter (because it is no longer being blocked) and from there transcribes the genes for the operon. The resulting mRNA carries coding sequences for all three enzymes needed for lactose metabolism.

A certain mutation in E. coli impairs the ability of the lac repressor to bind to the lac operator. How would this affect the cell?

The cell would wastefully produce the enzymes for lactose metabolism continually, even when lactose is not present.

If a gene has the sequence AATTCGCG, what would be the sequence of an miRNA that turns off the gene?

The gene will be transcribed as the mRNA sequence UUAAGCGC; an miRNA of sequence AAUUCGCG would bind to and disable this mRNA

How are the genes that code for the enzymes that take up and start metabolizing lactose regulated?

The genes that code for these three enzymes are regulated as a single unit. Adjacent to the group of lactose enzyme genes are two control sequences, short sections of DNA that help control the expression of these genes. One control sequence is a promoter, a site where the transcription enzyme, RNA polymerase, attaches and initiates transcription--in this case, transcription of all three lactose enzyme genes. Between the promoter and the enzyme genes, a DNA control sequence called an operator acts as a switch. The operator determines whether RNA polymerase can attach to the promoter and start transcribing the genes.

Among the molecules involved in translation are a great many proteins that control the start of polypeptide synthesis. By controlling the start of protein synthesis, cells can-

avoid wasting energy if the needed components are currently unavailable

When and how is the lac operon in "off" mode?

When there is no lactose in the cell's environment. Transcription is turned off because a protein called a repressor binds to the operator and physically blocks the attachment of RNA polymerase to the promoter.

What can be learned from a DNA microray?

Which genes are active (transcribed) in a particular sample of cells

Why can the single mRNA be translated into three separate polypeptides?

because the mRNA has multiple codons signaling the start and stop of translation.

Any mutation that decreases the normal activity of a tumor-repressor protein may contribute to the onset of __________________

cancer

Unlike the lac operon which is usually turned off and produces the digestive enzymes only when the nutrient is available, what is another kind of repressor that is normally turned on but can be inhibited when a specific molecule is present in abundance?

a repressible operon like the trp operon

What determines which end of a developing fruit fly will become the head?

a specific kind of mRNA localizes at the end of the unfertilized egg that will become the head.

In eukaryotes, the __________________ seem to be more important than ________________

activator proteins, repressors

Another type of operon control involves ___________________, proteins that turn operons on by binding to DNA and stimulating gene transcription.

activators

The lifetime of many proteins are closely regulated. Some of the proteins that trigger metabolic changes in cells are broken down within a few minutes or hours. This regulation allows a cell to-

adjust the kinds and amounts of its proteins in response to changes in its environment

How can an organism produce more than one type of polypeptide form a single gene?

alternative RNA splicing because different mRNA molecules form the same RNA transcript

What is an example of DNA being chemically modified?

certain enzymes add a methyl group to DNA bases, usually cytosine, without changing the actual sequence of the bases. Individual genes are usually more heavily methylated in cells in which they are not expressed, and removing the extra methyl groups can turn on some of these genes. Thus, DNA methylation appears to play a role in turning genes off.

Post-transitional control mechanisms in eukaryotes often involve the _________________ of a polypeptide to yield- ,able to carry out a specific function in the organism.

cleavage, a smaller final product that is the active protein

An organism produced through asexual reproduction from a single parent, is called a ___________

clone

How does the cloning of plants from differentiated cells support the view that differentiation is based on the control of gene expression rather than on irreversible changes in the genome?

cloning sows that all of the genes of a fully differentiated plant cell are still present.

Only 1.5% of the human genome-

codes for proteins

Which regulatory "valves" can operate in a prokaryotic cell?

control of transcription, control of mRNA breakdown, control of translation, control of protein activation, and control of protein breakdown

What accounts for the differences between cell types?

differences between cell types are not due to different genes being present but instead due to selective gene expression.

All multicellular eukaryotes also require an additional level of gene control: during the repeated cell divisions that lead from a zygote to an adult in a multicellular organism, individual cells must undergo __________________, that is they must-

differentiation--that is they must become specialized in structure and function, with each type of cell fulfilling a distinct role.

A crucial aspect of DNA packing is the association of the DNA with small proteins called ________________ which account for about _______________ the mass of eukaryotic chromosomes

histones. half

a ___________________ is a master control gene that regulates the "batteries" of other genes that determine the anatomy of the body.

homeotic genes.

What must a cell do in order to perform its specialized role?

it must maintain a specific program of gene expression in which some genes are expressed and others are not.

How does DNA packing block gene expression?

it prevents RNA polymerase and other transcription proteins from contacting the DNA. Higher levels of packing can therefore inactivate genes for the long term.

In most species of vertebrates, the mRNAs for hemoglobin are unusually stable and probably last as long as the red blood cells that contain them--about a month--and are translated again and again. What kind of mRNA is found in vertebrate red blood cells?

long-lived mRNA

Enzymes in the cytoplasm eventually break down mRNA and the timing is important for regulating the amount of various proteins that are produced in the cell. ________________ can be translated into many more protein molecules than __________________

long-lived mRNA, short mRNA

describe the structure of a nucleosome-

looks like a bead, consists of DNA wound around a protein core of eight histone molecules.

After eukaryotic mRNA is fully processed and transported to the cytoplasm, there are several additional opportunities for regulation:

mRNA breakdown, initiation of translation, protein activation, and protein breakdown.

RNA interference is when-

miRNA is injected into a cell and turns off expression of a gene with a sequence that matches the miRNA.

In 1993, researchers discovered small RNA molecules called _________________ that can -

micro RNAs (miRNAs) that can bind to complementary sequences on mRNA molecules.

A normal gene that has the potential to become an oncogene is called a _____________________

proto-oncogene

reproductive cloning is so named because it

results in the birth of a new living individual

________________ may help control the flow of mRNA form nucleus to cytoplasm

splicing

The key to coordinated gene expression in eukaryotes is often-

the association of a specific combination of control sequences with every gene of a particular metabolic pathway. Copies of the activators that recognize these control sequences bind to them all at once, promoting simultaneous transcription of the genes, no matter where they are in the genome.

What demonstrates that differentiation does not necessarily involve irreversible changes in the plant's DNA?

the fact that a mature plant cell can dedifferentiate or reverse its differentiation and then give rise to al the different kinds of specialized cells of a new plant

If the enzyme responsible for cleaving inactive insulin is deactivated, what effect will this have on the form and function of insulin?

the final molecule will have a shape different form that of active insulin and therefore will not be able to function as a hormone.

When an E coli bacterium encounters lactose, all the enzymes needed for its metabolism are made at once because-

the operon's genes are all controlled by a single switch, the operator.

In what sense is the joining of yeast mating types "sex"

the process results in the creation of a diploid cell that is a genetic blend of two parental haploid cells

_____________________________ are genes that encode for proteins that help prevent uncontrolled cell growth

tumor-suppressor genes

Multiple enhancers and activators may be involved in -

turning on a single gene

What does E. coli do when lactose is not plentiful in the digestive system?

Most enzymes are proteins and their production is an outcome of gene expression. E coli can make lactose-utilization enzymes because it has genes that code for these enzymes. An E. coli cell can turn genes coding for lactose-utilization enzymes off or on, depending on whether lactose is available.

Contrast the action of an oncogene with that of a cancer-causing mutation in a tumor-suppressor gene

an oncogene encodes an abnormal protein that stimulates cell division via a signal transduction pathway; a mutant tumor-supressor gene encodes a defective protein unable to function in a pathway that normally inhibits cell division.

In multicellular eukaryotes, when i cellular differentiation by selective expression most vital?

during the development of an embryo form a zygote.

In nature, how do embryonic stem cells differ from adult stem cells?

embryonic cells give rise to all the different kinds of cells in the body. Adult stem cells generate only a few related types of cells.

Describe the process of gene transcription in prokaryotes

the first step in initiating gene transcription is the binding of activator proteins to DNA control sequences called enhancers. Next, a DNA-bending protein brings the bound activators closer to the promoter. Once the DNA is bent, the bound activators interact with other transcription factor proteins, which then bind as a complex at the gene's promoter. This large assembly of proteins facilitates the correct attachment of RNA polymerase to the promoter and the initiation of transcription. Only when the complete complex of proteins has assembled can the polymerase begin to move along the gnee, producing an RNA strand.

Almost all the cells in an organism contain an identical genome, but -

the subset of genes expressed in each cell type is unique, reflecting its specific function. Each adult human cell expresses only a small fraction of its total genes at any given time.

Gene regulation-

the turning on and off of genes can help orgonasms respond to environmental changes

When the goal is to produce ES cells to used in therapeutic treatments, this process is called

therapeutic cloning

What do activators do>

they act by making it easier for RNA polymerase to bind to the promoter, rather than by blocking RNA polymerase, as repressors do. Activators help control a wide variety of operons.

To function, eukaryotic RNA polymerase requires the assistance of proteins called _____________________

transcription factors