Ch 11 - How Genes are Controlled

Themes: Changing the shape of the lac repressor affects how the repressor acts.

The relationship of structure to function: The ability of any protein (such as the repressor) to act (function) depends upon its precise shape (form).

RNA Processing and Breakdown: * Within a eukaryotic cell, transcription occurs in the nucleus, where ....? * RNA processing includes: - - -

*RNA transcripts are processed into mRNA before moving to the cytoplasm for translation by the ribosomes. - the addition of a cap and a tail, - the removal of introns (the noncoding DNA segments that interrupt the genetic message), and - RNA splicing (the splicing together of exons).

Oncogenes and Tumor-Suppressor Genes: * A gene that causes cancer is called an _____. - A normal gene with the potential to become an oncogene is called a ....? - A cell can acquire an oncogene from ...?

*oncogene - proto-oncogene. - a virus or the mutation of one of its own proto-oncogenes.

Cancer Risk and Prevention: * Some food choices significantly reduce a person's cancer risk. For instance, eating -___-____ g of plant fiber daily, less animal fat, - Vitamins __ and ___ and certain compounds related to vitamin A, and - _____ and its relatives, such as broccoli and cauliflower.

- 20-30g - C and E -cabbage

Gene Regulation in Bacteria: * Natural selection has favored bacteria that express only the genes whose products are needed by the cell. Imagine an Escherichia coli bacterium living in your intestines. - If you drink a milk shake, there will be a sudden rush of the sugar lactose. In response, ...? - After the lactose is gone, ...? - Such regulation is at the heart of _______, the chemical reactions that transform energy and matter within all cells.

- E. coli will express three genes for enzymes that enable the bacterium to absorb and digest this sugar. - these genes are turned off. - metabolism

Master control genes regulate other genes that determine what body parts will develop in which locations. Which major theme is illustrated by this action? - The relationship of structure to function - Information flow - Pathways that transform energy and matter - Interactions within biological systems - Evolution

- Information flow

Changing the shape of the lac repressor affects how the repressor acts. Which major theme is illustrated by this action? - The relationship of structure to function - Information flow - Pathways that transform energy and matter - Interactions within biological systems - Evolution

- The relationship of structure to function

Gene Regulation in Bacteria: * How does the presence or absence of lactose influence the activity of the genes that code for the lactose enzymes? - The key is the way the three lactose-digesting genes are organized: They are adjacent in the DNA and turned on and off as a single unit. -? -?

- This regulation is achieved through short stretches of DNA that help turn all three genes on and off at once, coordinating their expression. - Such a cluster of related genes and sequences that control them is called an operon. The operon considered here is the lac (short for lactose) operon.

Umbilical Cord Blood Banking: * Another source of stem cells is blood collected from the umbilical cord and placenta at birth. - Cord blood stem cells appeared to cure some babies of Krabbe's disease, ...? - To date, however, most attempts at umbilical cord blood therapy have not been successful. - At present, the American Academy of Pediatrics recommends cord blood banking only for babies born into families with a ...?

- a fatal inherited disorder of the nervous system, and have been used as a treatment for leukemia. - known genetic risk.

Visualizing Gene Expression: * A DNA microarray is a- ?? - Often, the cDNAs from two samples (for example, two tissues) are labeled with molecules that ...?

- a glass slide with many tiny wells, each containing a different fragment of single-stranded DNA that derives from a particular gene. - emit different colors and tested on the same microarray.

Cell Signaling: * Within a multicellular organism, information must be communicated between cells. For example, a cell can produce and secrete chemicals, such as hormones, that affect gene regulation in other cells. - A signal molecule can act by binding to a receptor protein and initiating a signal transduction pathway - ??

- a series of molecular changes that converts a signal received outside a cell to a specific response inside the target cell.

Gene Regulation in Bacteria: * Many operons have been identified in bacteria. Some are quite similar to the lac operon, whereas others have different mechanisms of control. - For example, operons that control amino acid synthesis cause ...? Checkpoint: A mutation in E. coli makes the lac operator unable to bind the active repressor. How would this mutation affect the cell? Why would this effect be a disadvantage?

- bacteria to stop making these molecules when they are already present in the environment, saving materials and energy. In these cases, the amino acid activates the repressor. Checkpoint response: The cell would wastefully produce the enzymes for lactose metabolism continuously, even in the absence of lactose.

microRNAs: * A significant amount of the genome is transcribed into functioning but nonprotein coding RNAs. - Small single-stranded RNA molecules, called microRNAs (miRNAs), can ...? - In addition to microRNAs, there is another class of small RNA molecules called .....? -. The blocking of gene expression by ....? is called ....?

- bind to complementary sequences on mRNA molecules. - small interfering RNAs (siRNAs) - siRNAs / RNA interference (RNAi).

The Initiation of Translation and Protein Activation and Breakdown: * The process of translation—in which an mRNA is used to make a protein—offers additional opportunities for control by regulatory molecules. * The final opportunities for regulating gene expression occur after translation. - For example, the hormone insulin must be ...? - Other proteins require ...? before they become active. - Finally, the selective breakdown of proteins allows cells to ...?

- chopped into pieces before it comes active. - chemical modification - adjust the kinds and amounts of its proteins.

The Progression of a Cancer: * The development of a malignant tumor is accompanied by a gradual accumulation of mutations that - -

- convert proto-oncogenes to oncogenes and - knock out tumor-suppressor genes.

Adult Stem Cells: * Adult stem cells - are further along the road to ...? - can therefore give rise to ....?, and - can also generate ...? * Because no embryonic tissue is involved in their harvest, adult stem cells are...?

- differentiation than ES cells, - only a few related types of specialized cells - replacements for some of the body's cells. * less ethically problematic than ES cells.

The Genetic Basis of Cancer: Genes That Cause Cancer: * Cancer occurs when cells...? - One of the earliest clues to the role of genes in cancer was the discovery in 1911 of a virus that causes cancer in chickens. - Viruses that cause cancer can become permanent residents in host cells by ...?

- escape from the control mechanisms that normally limit their growth and division. This escape involves changes in gene expression. - inserting their nucleic acid into the DNA of host chromosomes.

The Regulation of DNA Packing: * Cells may use DNA packing for long-term inactivation of genes. - X chromosome inactivation occurs in ...? --> After one X chromosome is inactivated in each embryonic cell, ...? --> If a female has different versions of a gene on each of her X chromosomes, ...?

- female mammals, takes place early in embryonic development, and happens when one of the two X chromosomes in each cell is inactivated at random. - all of that cell's descendants will have the same X chromosome turned off. - about half of her cells will express one version, while the other half will express the alternate version.

Cloning Plants and Animals: The Genetic Potential of Cells: * Gene regulation affects cloning and cancer. * All body cells contain a complete complement of genes, even if they are not expressing all of them. - A single differentiated plant cell can undergo cell division and ...?

- give rise to a complete adult plant, a task that requires a complete set of genes.

The Progression of a Cancer: * Nearly 150,000 Americans will be stricken by cancer of the colon this year. *Colon cancer, like many cancers, - -

- is a gradual process and - is produced by more than one mutation.

How and Why Genes Are Regulated: * However, the cells in your body are specialized in structure and function. So, how do cells develop differently from one another? - Cells with the same genetic information can develop into different types of cells through gene regulation, which is? - Regulating gene activity allows...?

- mechanisms that turn on certain genes while other genes remain turned off. - for specialization of cells within the body.

Therapeutic Cloning and Stem Cells: Embryonic Stem Cells: *The purpose of therapeutic cloning is ...? - In mammals, embryonic stem (ES) cells are obtained by...? - Embryonic stem cells can divide indefinitely and, under the right conditions, can (hypothetically) ...? - If scientists can discover the right conditions, they may be able to...?

- not to produce a living organism but rather to produce embryonic stem cells. - removing cells from a several day-old embryo and growing them in laboratory culture. - develop into a wide variety of specialized cells. - grow cells for the repair of injuredor diseased organs.

Inherited Cancer: * Multiple genetic changes are required to produce a full-fledged cancer cell. - This helps explain the observation that cancers can run in families. - An individual inheriting an ....? is a step closer to accumulating the necessary mutations for cancer. - Geneticists are devoting much effort to identifying inherited cancer mutations so that predisposition to certain cancers can be detected early in life.

- oncogene or a mutant version of a tumor-suppressor gene

Practical Applications of Reproductive Cloning: * Since the first success in 1996, researchers have cloned many species of mammals. * Why is reproductive cloning used? - In agriculture, animals with specific sets of desirable traits might be cloned to ...? - In research, genetically identical animals can provide perfect "_______ animals" for experiments. - The pharmaceutical industry is experimenting with cloning animals for ...? - Reproductive cloning is used to ...?

- produce identical herds. - control - potential medical use. - restock populations of endangered animals.

Oncogenes and Tumor-Suppressor Genes: * Many proto-oncogenes code for growth factors - ?? - When they malfunction, _____ (uncontrolled cell growth) may result. - For a proto-oncogene to become an oncogene,...?

- proteins that stimulate cell division, or for other proteins that affect the cell cycle. - cancer - a mutation must occur in the cell's DNA.

Reproductive Cloning of Animals: * Nuclear transplantation involves ...? - If the animal to be cloned is a mammal, further development requires ...? - This type of cloning is called reproductive cloning because ....? - In 1996, researchers used reproductive cloning to produce the first mammal cloned from an adult cell, ....?

- replacing the nucleus of an egg cell or a zygote with a nucleus removed from an adult body cell. - implanting the early embryo into the uterus of a surrogate mother. - it results in the birth of a new animal. - a sheep named Dolly.

Cancer Risk and Prevention: * Cancer is the ________ leading cause of death (after ...? ) in most industrialized countries. * Most cancers arise from mutations that are caused by carcinogens - ? * Tobacco use, the consumption of alcohol, and excessive time spent in the sun are all avoidable behaviors that affect cancer risk.

- second / heart disease -cancer-causing agents found in the environment, including ultraviolet (UV) radiation and tobacco products.

The Initiation of Transcription: * The initiation of transcription is...? - In prokaryotes and eukaryotes, regulatory proteins bind to DNA and ...? - Transcriptional regulation in eukaryotes is complex, typically involving ...? - The DNA-protein assembly promotes the binding of...?

- the most important stage for regulating gene expression. - turn the transcription of genes on and off. - many proteins, collectively called transcription factors, acting together to bind to DNA sequences called enhancers and the promoter. - RNA polymerase to the promoter.

How and Why Genes Are Regulated: * Every cell in your body was produced through successive rounds of mitosis starting from the zygote,...? * Therefore, ...?

- the original cell that formed after fusion of sperm and egg. - every cell in your body has the same DNA as the zygote and every somatic (body) cell contains every gene.

The Genetic Potential of Cells: * Regeneration is ...? - When a salamander loses a tail, certain cells in the tail stump reverse their differentiated state, divide, and then differentiate again to give rise to a new tail. - Many other animals, especially among the invertebrates, can regenerate lost parts. - Isolated pieces of a few relatively simple animals can ________ and then develop into an entirely new organism.

- the regrowth of lost body parts. - dedifferentiate

How and Why Genes Are Regulated: * What does it mean that genes are turned on or off? - Genes determine the nucleotide sequence of specific mRNA molecules, and mRNA in turn determines ...? - A gene that is turned on is being ...? - The overall process by which genetic information flows from genes to proteins is called ...?

- the sequence of amino acids in proteins. - transcribed and translated into specific proteins. - gene expression.

Biology and Society: Breast Cancer and Chemotherapy: * How can doctors tell which cases are risky enough to warrant chemotherapy? - Many cancer-associated genes encode proteins that ...? - When these genes are mutated,...? - Scientists can now tell which genes are mutated in a given tumor. - Soon, the genes of all cancer patients may be evaluated in this way, allowing therapy to be optimized for each patient.

- turn other genes on or off. - the proteins malfunction and the cell may become cancerous. -

Homeotic Genes: * Cell-to-cell signaling and the control of gene expression are particularly important during early embryonic development- ??? - Interactions between the cells of an embryo through chemical signals coordinate development. - Master control genes called homeotic genes - ?? - Similar homeotic genes direct early development in nearly every eukaryotic organism examined. Mutations in homeotic genes can produce bizarre effects.

- when a single-celled zygote develops into a multicellular organism. - regulate groups of other genes that determine what body parts will develop in which locations.

Gene Regulation in Bacteria: - In the lac operon, ....? - Transcription is turned off because ...?

- when the operator switch is turned on, all the enzymes needed to metabolize lactose are made at once. - a protein called a repressor binds to the operator and physically blocks the attachment of RNA polymerase to the promoter.

Checkpoint response: black, the color of the nucleus donor: * Cloning may also create new problems. - Conservationists argue that cloning: - - - * An increasing body of evidence suggests that cloned animals are _____ healthy than animals produced via fertilization.

--> may detract from efforts to preserve natural habitats, --> does not increase genetic diversity, and --> is therefore not as beneficial to endangered species as natural reproduction. - less

Inherited Cancer - About _____% of colorectal cancers involve inherited mutations. - There is also evidence that inheritance plays a role in __-____% of patients with breast cancer, a disease that strikes one out of every ten American women. - Mutations in either or both of two genes—called .......? —are found in at least half of inherited breast cancers. Checkpoint: How can a mutation in a tumor-suppressor gene contribute to the development of cancer?

-15% -5-10% - BRCA1 (pronounced "braca-1") and BRCA2 Checkpoint response: A mutated tumor suppressor gene may produce a defective protein unable to function in a pathway that normally inhibits cell division and therefore normally suppresses tumors.

The Genetic Potential of Cells: * Plant cloning is now used extensively in agriculture. - For some plants, such as ____, cloning is the only commercially practical means of reproducing plants. - In other cases, cloning has been used to reproduce a plant with specific desirable traits, such as ...? - Seedless plants (such as seedless grapes, watermelons, and oranges) cannot.....?, leaving cloning as the sole means of mass-producing these common foods.

-orchids - high fruit yield or resistance to disease. - reproduce sexually

RNA Processing and Breakdown: * Within a cell, exon splicing can occur in more than one way, generating different mRNA molecules from the same starting RNA molecule. With this sort of alternative RNA splicing, an organism can ....? * After an mRNA is produced in its final form, its "lifetime" can be highly variable, from hours to weeks to months. Controlling the timing of mRNA breakdown provides ...?

-produce more than one type of polypeptide from a single gene. - another opportunity for regulation. But all mRNAs are eventually broken down and their parts recycled.

Three ways that a proto-oncogene canbecome an oncogene:

1. Mutation with the gene --> oncogene --> hyperactive growth-stimulation protein 2. Multiple copies of the gene --> Normal growth stimulating protein in excess 3. mutation within a Control region of DNA --> mutated promoter --> normal growth-stimulation protein in excess

Evolution Connection: The Evolution of Cancer in the Body; 1. First, all evolving populations have the potential to produce more offspring than can be supported by the environment. Cancer cells, with their uncontrolled growth, clearly demonstrate such overproduction. 2 ? 3 ? * Mutations that enhance survival of malignant cancer cells are passed on to that cell's descendants. In short, a tumor evolves.

2. there must be variation among individuals of the population. 3. variations in the population must affect survival and reproductive success. Indeed, the accumulation of mutations in cancer cells renders them less susceptible to normal mechanisms of reproductive control.

Biology and Society: Breast Cancer and Chemotherapy: * About one out of every ____ women will develop breast cancer. - But if a woman's breast cancer is treated in its earliest stages, her chance of surviving ___ years or more is nearly 100%. - If her breast cancer is not treated until it has spread throughout her body,....? - Treatment typically involves ...?

8 - 5 - the five-year survival rate is less than 25%. - surgery, followed by hormone therapy and radiation to kill cancer cells. Chemotherapy may serve as a final step.

Checkpoint: If your blood cells and skin cells have the same genes, how can they be so different?

Checkpoint response: Each cell type expresses different genes than the other cell type.

Checkpoint: Imagine that mouse coat color is always passed down from parent to offspring. Suppose a nucleus from an adult body cell of a black mouse is injected into an egg removed from a white mouse, and then the embryo is implanted into a brown mouse. What would be the color of the resulting cloned mice?

Checkpoint response: black, the color of the nucleus donor

How does DNA packing in chromosomes prevent gene expression?

DNA polymerase and other proteins required for transcription do not have access to tightly packed DNA.

Themes: Master control genes regulate other genes that determine what body parts will develop in which locations.

Information flow: The proteins produced by master control genes communicate information to other cells about their developmental fate.

A cell can produce and secrete chemicals, such as hormones, that affect gene regulation in another cell. Which major theme is illustrated by this action? - The relationship of structure to function - Information flow - Pathways that transform energy and matter - Interactions within biological systems - Evolution

Interactions within biological systems:

Themes: A cell can produce and secrete chemicals, such as hormones, that affect gene regulation in another cell.

Interactions within biological systems: The endocrine system secretes hormones that interact with nearly every cell in the body.

A mutation in one gene may cause a major change in the body of a fruit fly. Yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big change? What are such genes called?

Master control genes, called homeotic genes, regulate many other genes during development.

Human Cloning: - The cloning of various mammals has heightened speculation that humans could be cloned. - Critics point out the many practical and ethical objections to human cloning. - Practically, cloning of mammals is extremely difficult and inefficient. How ?

Only a small percentage (usually less than 10%) of cloned embryos develop normally and they appear less healthy than naturally born kin.

What is the difference between oncogenes and proto-oncogenes? How can one turn into the other? What function do proto-oncogenes serve?

Proto-oncogenes are normal genes involved in the control of the cell cycle. Mutation or viruses can cause them to be converted to oncogenes, or cancer-causing genes. Proto-oncogenes are necessary for normal control of cell division.

A eukaryotic gene was inserted into the DNA of a bacterium. The bacterium then transcribed this gene into mRNA and translated the mRNA into protein. The protein produced was useless and contained many more amino acids than the protein made by the eukaryotic cell. Why? a. The mRNA was not spliced as it is in eukaryotes. b. Eukaryotes and prokaryotes use different genetic codes. c. Repressor proteins interfered with transcription and translation. d. Ribosomes were not able to bind to tRNA.

a

Gene Regulation in Bacteria: * How do DNA control sequences turn genes on or off? One control sequence, called a promoter, is the site where the enzyme RNA polymerase attaches and initiates transcription. - Between the promoter and the enzyme genes, ...?

a DNA segment called an operator acts as a switch that is turned on or off, depending on whether a specific protein is bound there. - The operator and protein together determine whether RNA polymerase can attach to the promoter and start transcribing the genes.

Gene Regulation in Eukaryotic Cells: * Eukaryotes, especially multicellular ones, have more sophisticated mechanisms than bacteria for regulating the expression of their genes. - The pathway from gene to protein in eukaryotic cells is a long one, providing .....?

a number of points where the process can be turned on or off, speeded up or slowed down.

Which of the following is a substantial difference between embryonic stem cells and the stem cells found in adult tissues? a. In laboratory culture, only adult stem cells are immortal. b. In nature, only embryonic stem cells give rise to all the different types of cells in the organism. c. Only adult stem cells can be made to differentiate in the laboratory. d. Only embryonic stem cells are in every tissue of the adult body.

b

The regulation of gene expression must be more complex in multicellular eukaryotes than in prokaryotes because a. eukaryotic cells are much larger. b. in a multicellular eukaryote, different cells are specialized. c. prokaryotes are restricted to stable environments. d. eukaryotes have fewer genes, so each gene must do several jobs.

b.

Your bone cells, muscle cells, and skin cells look different because a. different kinds of genes are present in each kind of cell. b. they are present in different organs. c. different genes are active in each kind of cell. d. different mutations have occurred in each kind of cell.

c

Name three potential sources of stem cells.

embryonic tissue (embryonic stem cells), umbilical cord blood, and bone marrow (adult stem cells)

The most common procedure for cloning an animal is _______ .

nuclear transplantation

A group of prokaryotic genes with related functions that are regulated as a single unit, along with the control sequences that perform this regulation, is called a(n) _______ .

operon

The Initiation of Transcription: * Repressor proteins, which may bind to DNA sequences called ______, inhibit the start of transcription. - Repressor proteins that turn genes off are less common in eukaryotes than activators, which are...? - The "default" state for most genes in multicellular eukaryotes seems to be off, with the exception of "__________" genes for routine activities such as ...?

silencers - proteins that turn genes on by binding to DNA. Activators act by making it easier for RNA polymerase to bind to the promoter. - housekeeping / the digestion of glucose.

What evidence demonstrates that differentiated cells in a plant or animal retain their full genetic potential?

the ability of these cells to produce entire organisms through cloning

Oncogenes and Tumor-Suppressor Genes: * Changes in genes whose products inhibit cell division are also involved in cancer. - These genes are called.....? because the proteins they encode normally help prevent uncontrolled cell growth. - Any mutation that .....? may contribute to the development of cancer.

tumor-suppressor genes - keeps a growth-inhibiting protein from being made or from functioning

What is learned from a DNA microarray?

which genes are active in a particular sample of cells