How Genes Are Controlled Chapter 11 How Genes Are Controlled Normally a cell has the ability to properly control which genes are active at any given time which is crucial to normal cell function. The cell looses its control if the mutation occurs in the gene. In this chapter we are going to learn how the genes are controlled and how the regulation of genes affects cells and organisms.

HOW AND WHY GENES ARE REGULATED Every somatic cell in an organism contains identical genetic instructions: they all share the same genome, so what makes them different? If every cell contains identical genetic instructions, How do cells become different from one another? Individual cell must undergo cellular differentiation, where cells become specialized in Structure and Function Every cell must have its own structure and function which differentiates them from others Control mechanism must turn on certain genes while other genes remain turned of in a particular cell. This is called gene regulation, the turning on and off of genes. If Every somatic cell in an organism contains identical genetic instructions, how do cells become different from one another? Control mechanism must turn on certain genes while other genes remain turned of in a particular cell. This is called gene regulation, the turning on and off of genes.

Patterns of Gene Expression in Differentiated Cells The whole process of the genetic information flowing from gene to protein (genotype to phenotype) is called gene expression. What does it mean to  say that genes are active or inactive, turned on or off? In gene expression a gene that is turned on is transcribed into mRNA and that message is being translated into specific proteins Information flows from DNA to RNA to proteins. All the different cells that contain the same genes differentiate themselves by the selective expression of genes that is, from the pattern of genes turned on in a given cell at a given time. Therefore, the great differences among cells in an organism must result from the selective expression of genes. When you say that a gene is turned on, the information is being transcribed into mRNA and that message is being translated into specific proteins. Information flows from Genes to proteins, Genotype to phenotype. Because all the differentiated cells in the organism has the same gene, the differences among the cells must come from the selective expression of genes. Such a regulation of gene expression plays a major role in the development of single-celled zygote into a multicellular organism with different cells having different function. See here the patterns of gene expression in three types of human cells

Patterns of gene expression in three types of human cells Colorized TEM Colorized SEM Colorized TEM Pancreas cell White blood cell Nerve cell Gene for a glycolysis enzyme Antibody gene Insulin gene Hemoglobin gene Figure 11.1 Figure 11.1 Patterns of gene expression in three types of human cells

Practice At one point, you were just an undifferentiated, single cell. You are now made of many cells; some of these cells function as liver cells, some as muscle cells, some as red blood cells, while others play different roles. What name is given to the process that is responsible for this? A) gene expression B) regeneration C) carcinogenesis D) cellular differentiation The process by which genotype becomes expressed as phenotype is ______. A) phenogenesis B) transcription C) gene expression D) recombination

Gene Regulation in Bacteria Natural selection has favored bacteria that express only certain genes whose products are needed by the cell at specific times So how do bacteria selectively turn their genes on and off? An example of this would be a bacteria called E-coli, a living bacteria in your intestines If you drink a milkshake, there will be a sudden rush of the sugar lactose. E-coli will express three genes for enzymes that enable it to absorb and digest this sugar The Lac Operon, is a gene system characterized in E-coli for the regulation of the gene of utilization of lactose.

Gene Regulation in Bacteria An operon includes a cluster of genes with related functions the control sequences that turn the genes on or off The bacterium E. coli used the lac operon to coordinate the expression of genes that produce enzymes used to break down lactose in the bacterium’s environment. If lactose is absent the gene is turned off. If lactose is present, the gene is turned on.

The Lac Operon The lac operon uses How do DNA control sequence turn genes on or off? The lac operon uses A promoter, a control sequence where the RNA polymerase attaches and initiates transcription Between promoter and genes is an operator, a DNA segment that acts as a switch that is turned on or off A repressor, which binds to the operator and physically blocks the attachment of RNA polymerase is synthetize by the Regulatory gene Operon turned on (lactose inactivates repressor) Lactose Protein mRNA Lactose enzymes DNA Operon turned off (lactose absent) Translation Inactive repressor RNA polymerase bound to promoter Transcription Active cannot attach to promoter Regulatory gene Promoter Operator Operon Genes for lactose enzymes

Practice In bacteria, what name is given to a cluster of genes with related functions, along with their DNA control sequences? A) operon B) activator C) promoter D) Exon Bacterial RNA polymerase binds to the ______. A) operator B) proto-oncogene C) regulatory gene D) Promoter

Practice Which of the following turns off transcription by binding to the operator? A) RNA polymerase B) repressor C) promoter D) Lactose What would you assume if you found RNA transcripts of lactose-utilizing genes within E. coli? A) the binding of lactose to the lac operon activator B) the presence of lactose C) the presence of lac operon activator protein D) the absence of lac operon repressor protein

Gene Regulation in Eukaryotic Cells Eukaryotic cells have more complex gene regulating mechanisms with many points where the process can be regulated,. The flow of genetic information from a eukaryotic chromosome to an active protein can be illustrated by this analogy to a water supply system with many control valves along the way. Starting with the water from the reservoir of genetic information (chromosome) to the faucets at our kitchen sink (active protein)

DNA Flow of mRNA through nuclear envelope Processing of RNA Transcription of gene Unpacking of DNA Chromosome Gene RNA transcript Intron Exon mRNA in nucleus Tail Cap mRNA in cytoplasm Nucleus Cytoplasm Breakdown of mRNA Translation of protein Various changes to polypeptide Active protein Polypeptide

The Regulation of DNA Packing DNA packing tends to prevent gene expression by preventing RNA polymerase and other transcription proteins from binding to DNA Cells may use DNA packing for long-term inactivation of genes. X chromosome inactivation Occurs in female mammals first takes place early in embryonic development, when one of the two X chromosomes in each cell is inactivated at random All of the descendants will have the same X chromosome turned off.

If a female cat is heterozygous for a gene on the X chromosome X chromosome inactivation: the tortoiseshell pattern on a cat If a female cat is heterozygous for a gene on the X chromosome About half her cells will express one allele The others will express the alternate allele Cell division and X chromosome inactivation Allele for orange fur Early embryo: X chromosomes black fur Inactive X Active X Orange fur Two cell populations in adult cat: Black Figure 11.4X chromosome inactivation: the tortoiseshell pattern on a cat

The Initiation of Transcription The initiation of transcription is the most important stage for regulating gene expression. In prokaryotes and eukaryotes, regulatory proteins Bind to DNA Turn the transcription of genes on and off

The Initiation of Transcription Unlike prokaryotic genes, transcriptional regulation in eukaryotes is complex typically involving many proteins, called transcription factors, that bind to DNA sequences called enhancers and promoter Bend in the DNA Enhancers (DNA control sequences) Transcription factor Promoter Gene RNA polymerase

The Initiation of Transcription The DNA protein assembly promotes the binding of RNA polymerase to promoters. Repressor proteins called silencers Bind to DNA Inhibit the start of transcription Activators are More typically used by eukaryotes Turn genes on by binding to DNA They make it easier for RNA polymerase to bind to the promoters

RNA Processing and Breakdown The eukaryotic cell localizes transcription in the nucleus where RNA transcripts are processed into mRNA before moving into the cytoplasm for translation by the ribosomes. RNA processing includes the Addition of a cap and tail to the RNA Removal of any introns Splicing together of the remaining exons Alternative RNA splicing: an organism can produce more than one type of polypeptide from a single gene

RNA Processing and Breakdown In alternative RNA splicing, exons may be spliced together in different combinations, producing more than one type of polypeptide from a single gene. Eukaryotic mRNAs can last for hours to weeks to months and are all eventually broken down and their parts recycled RNA transcript Exons RNA splicing mRNA DNA or 1 2 3 5 4 Figure 11.6 Alternative RNA splicing: producting two different mRNAs from the same gene (Step 3)

Practice What is the first level of control of eukaryotic gene transcription? A) RNA splicing B) attachment of RNA polymerase to the promoter C) DNA packing and unpacking D) the binding and unbinding of transcription factors to enhancer sequences In eukaryotic cells, repressor proteins inhibit transcription by binding to ______. A) silencers B) enhancers C) regulators D) operators

Introns are ______. A) noncoding DNA sequences B) DNA sequences to which activators bind C) expressed DNA sequences D) the product of RNA splicing How can a single RNA transcript be translated into different polypeptides? A) There is more than one way to splice an RNA transcript. B) There is more than one way to modify the coded polypeptide. C) The length of its tail can vary. D) Two different genes can produce the same RNA transcript, which will then be translated differently.

microRNAs Small single-stranded RNA molecules, called microRNAs (miRNAs), bind to complementary sequences on mRNA molecules in the cytoplasm, and some trigger the breakdown of their target mRNA Some trigger the breakdown of their target mRNA, and others block translation It has been estimated that miRNAs may regulate the expression of up to one-third of all human genes, a striking figure given that miRNA were unknown 20 years ago Figure 11.6 Alternative RNA splicing: producting two different mRNAs from the same gene (Step 3)

Protein Activation and Breakdown Post-translational control mechanisms is the final opportunity for regulating gene expression after translation after translation, the protein is cut into smaller, active final products (molecules) and will be sent to where they're needed The selective breakdown of proteins is another control mechanism operating after translation. The formation of an active insulin molecule Initial polypeptide Cutting Insulin (active hormone)

In this picture, the right side is an initial polypeptide (inactive) after it's cut it become an insulin (active hormone)

Cell Signaling A cell-signaling pathway SIGNALING CELL mRNA Plasma membrane Signal molecule Secretion Receptor protein Transcription factor (activated) Reception Signal transduction pathway TARGET CELL Nucleus Transcription Response Translation New protein In a multicellular organism, gene regulation can cross cell boundaries. A cell can produce and secrete chemicals, such as hormones, that affect gene regulation in another cell. Signal transduction pathway, a series of molecular changes that converts a signal received outside a cell to a specific response inside the target  cell Figure 11.8 A cell-signaling pathway that turns on a gene (Step 6)

Homeotic genes Master control genes called homeotic genes regulate groups of other genes that determine what body parts will develop in which locations. Mutations in homeotic genes can produce bizarre effects. Similar homeotic genes help direct embryonic development in nearly every eukaryotic organism. Normal fruit fly Mutant fly with extra wings Normal head Mutant fly with extra legs growing from head

Homeotic genes in two different animals Fruit fly chromosome Fruit fly embryo (10 hours) Mouse chromosomes Mouse embryo (12 days) Adult fruit fly Adult mouse

Cells communicate with one another via ______. A) cascades of gene activation B) the diffusion of RNA transcripts through adhesion junctions C) signal transduction pathways D) RNA splicing The "master control genes" that regulate other genes, which determine what body parts will develop in which locations, are called ______. A) enhancers B) homeotic genes C) oncogenes D) operons

DNA Microarrays: Visualizing Gene Expression A DNA microarray is a glass slide with thousands of different kinds of single-stranded DNA fragments attached to wells  in a tightly spaced array (grid) to allows visualization of gene expression. Complementary DNA (cDNA) is synthesized using nucleotides that have been modified to fluoresce (glow)  The pattern of glowing spots enables the researcher to determine which genes were being transcribed in the starting cells. Researchers can thus learn which genes are active in different tissues or in tissues from individuals in different states of health

Visualizing gene expression using a DNA microarray mRNA isolated DNA of an expressed gene cDNA made from mRNA cDNA mixture added to wells Unbound cDNA rinsed away Fluorescent spot cDNA unexpressed gene DNA microarray (6,400 genes) Nonfluorescent Reverse transcriptase and fluorescently labeled DNA nucleotides Fluorescent cDNA Figure 11.11 Visualizing gene expression using a DNA microarray (Step 4)

CLONING PLANTS AND ANIMALS The Genetic Potential of Cells Differentiated cells All contain a complete genome Have the potential to express all of an organism’s genes Differentiated plant cells can develop into a whole new organism. Adult plant Young Cell division in culture Root cells in growth medium Root of carrot plant Single cell © 2010 Pearson Education, Inc.

The Genetic Potential of Cells The somatic cells of a single plant can be used to produce hundreds of thousands of clones. Plant cloning Demonstrates that cell differentiation in plants does not cause irreversible changes in the DNA Is now used extensively in agriculture Regeneration is the regrowth of lost body parts Occurs for example when a salamander loses a leg and certain cells in the leg stump reverse their differentiated state, divide, and then differentiate again to rise to a new leg 

Reproductive Cloning of Animals Nuclear transplantation Involves replacing nuclei of egg cells with nuclei from differentiated cells Has been used to clone a variety of animals In 1997, Scottish researchers produced Dolly, a sheep, by replacing the nucleus of an egg cell with the nucleus of an adult somatic cell in a procedure called reproductive cloning, because it results in the birth of a new animal.

Cloning by nuclear transplantation Reproductive cloning Donor cell Nucleus from donor cell Implant embryo in surrogate mother Clone of donor is born Therapeutic cloning Remove nucleus from egg cell Add somatic cell from adult donor Grow in culture to produce an early embryo Figure 11.13 Cloning by nuclear transplantation (Step 5) Remove embryonic stem cells from embryo and grow in culture Induce stem cells to form specialized cells for therapeutic use

Practical Applications of Reproductive Cloning Other mammals have since been produced using this technique including Farm animals Control animals for experiments Rare animals in danger of extinction (a) The first cloned cat (right) (c) Clones of endangered animals (b) Cloning for medical use Gray wolf Gaur Banteng Mouflon calf with mother

Therapeutic Cloning and Stem Cells The purpose of therapeutic cloning is not to produce a viable organism but to produce embryonic stem cells. Embryonic stem cells (ES cells) Are derived from blastocysts Can give rise to specific types of differentiated cells Unlike embryonic ES cells, Adult stem cells are cells in adult tissues, represent partway along the road to differentiation generate replacements for non-dividing differentiated cells Umbilical cord blood Can be collected at birth Contains partially differentiated stem cells Has had limited success in the treatment of a few diseases Unlike embryonic ES cells, adult stem cells Are partway along the road to differentiation Usually give rise to only a few related types of specialized cells

Differentiation of embryonic stem cells in culture Adult stem cells in bone marrow Cultured embryonic stem cells Different culture conditions Different types of differentiated cells Heart muscle cells Nerve cells Blood cells Figure 11.15 Differentiation of embryonic stem cells in culture

Reproductive cloning involves A) reacquire the genes it lost during the course of development B) come from an early stage of embryonic development C) be dedifferentiated D) be implanted in the egg of an organism that is capable of regenerating lost body parts What is a difference between embryonic and adult stem cells? A) The use of embryonic stem cells raises fewer ethical issues than the use of adult stem cells. B) Embryonic stem cells are undifferentiated; adult stem cells are partially differentiated. C) It is easier to enucleate embryonic stem cells. D) Adult stem cells are easier to grow in culture.

Genetic Basis of Cancer: Genes that Cause Cancer Oncogenes versus Tumor-Suppressor Genes As early as 1911, certain viruses were known to cause cancer. Oncogenes are genes that cause cancer Found in viruses Proto-oncogenes are normal genes with the potential to become oncogenes Found in many animals Often genes that code for growth factors, proteins that stimulate cell division For a proto-oncogene to become an oncogene, a mutation must occur in the cell’s DNA.

(for protein that stimulates cell division) How a proto-oncogene can become an oncogene New promoter Normal growth- stimulating protein in excess Hyperactive growth- Gene moved to new DNA position, under new controls Multiple copies of the gene DNA Mutation within the gene Proto-oncogene (for protein that stimulates cell division) Oncogene Figure 11.17 How a proto-oncogene can become an oncogene

Tumor-suppressor genes Inhibit cell division Prevent uncontrolled cell growth May be mutated and contribute to cancer Defective, nonfunctioning protein Cell division under control (b) Uncontrolled cell growth (cancer) Normal growth- inhibiting protein Cell division not (a) Normal cell growth Tumor-suppressor gene Mutated tumor-suppressor gene

The Progression of a Cancer Over 150,000 Americans will be stricken by cancer of the colon or rectum this year. Colon cancer Spreads gradually Is produced by more than one mutation Second tumor-suppressor gene inactivated Tumor-suppressor Oncogene activated DNA changes: Cellular Increased cell division Growth of benign tumor malignant tumor Colon wall

The development of a malignant tumor is accompanied by a gradual accumulation of mutations that Convert proto-oncogenes to oncogenes Knock out tumor-suppressor genes 1 mutation Normal cell Malignant cell 4 mutations 3 2 Chromosomes Student Misconceptions and Concerns 1. Students typically have little background knowledge of cancer at the cellular level. Consider creating your own pre-test to inquire about your students entering knowledge of cancer. For example, ask students if all cancers are genetic (Yes, all cancers are based upon genetic errors and are the main subject of this chapter). In addition, ask students if exposure to a virus can lead to cancer (Yes, as noted in the text.) 2. Students often conclude falsely that most breast cancer is associated with known mutations in the breast cancer genes BRCA1 and BRCA2. However, the vast majority of breast cancer has no known inherited association. 3. Many students do not appreciate the increased risk of skin cancer and premature aging associated with the use of tanning beds. Teaching Tips 1. Tumor-suppressor genes function like the repressor in the E. coli lactose operon. The lac operon is expressed and cancers appear when their respective repressors do not function. 2. The production of a vaccine (Gardasil) against a virus known to contribute to cervical cancer has helped students become aware of the risks of HPV exposure. The following website of the National Cancer Institute describes the risks of HPV infection. (www.cancer.gov/cancertopics/factsheet/Risk/HPV) 3. Students who have had a leg, hip, or back X-rayed may recall a lead apron placed over their abdominal and pelvic region. The lead apron is to prevent the irradiation of the patient’s gonads, which could cause mutations that would be inherited. 4. Students may not realize the possible consequences of testing positive for a predisposition to cancer. Health insurance companies could use that information to deny insurance to people who are more likely to get ill. Further, people may feel obliged or be obligated to share this information with a potential mate or employer. 5. Exposure to carcinogens early in life generally carries greater risks than the same exposure later in life. This is because damage in early life has more time to accumulate additional mutations potentially leading to disease. 6. Nearly one in five deaths in the United States results from the use of tobacco. Additional information on the risks of tobacco can be found at the following web site. (www.cancer.org/docroot/PED/content/PED_10_2X_Cigarette_Smoking_and_Cancer.asp).

“Inherited” Cancer Breast cancer Most mutations that lead to cancer arise in the organ where the cancer starts. In familial or inherited cancer - A cancer-causing mutation occurs in a cell that gives rise to gametes - The mutation is passed on from generation to generation Breast cancer Is usually not associated with inherited mutations In some families can be caused by inherited, BRCA1 cancer genes

Cancer Risk and Prevention Is one of the leading causes of death in the United States Can be caused by carcinogens, cancer-causing agents found in the environment, including Tobacco products Alcohol Exposure to ultraviolet light from the sun Exposure to carcinogens Is often an individual choice Can be avoided Some studies suggest that certain substances in fruits and vegetables may help protect against a variety of cancers.

Table 11.2 Cancer in the United States (Ranked by Number of Cases)

What name is given to a gene that causes cancer? A) pathogene B) cancogene C) homeotic gene D) Oncogene

Summary: gene regulation in bacteria Regulatory gene A typical operon Promoter Operator Gene 3 Gene 2 Gene 1 Switches operon on or off RNA polymerase binding site Produces repressor that in active form attaches to operator DNA Figure 11.UN05 Summary: gene regulation in bacteria

Summary: gene regulation in eukaryotic cells Protein breakdown Protein activation mRNA breakdown RNA transport Translation Transcription DNA unpacking RNA processing Figure 11.UN06 Summary: gene regulation in eukaryotic cells

Summary: genes that cause cancer Proto-oncogene (normal) Oncogene Mutation Normal protein Mutant Defective Normal regulation of cell cycle growth-inhibiting Out-of-control growth (leading to cancer) Mutated tumor-suppressor gene Tumor-suppressor gene (normal) Figure 11.UN09 Summary: genes that cause cancer

C. pancreas beta cells (and alpha) Practice Which of the following cells would likely express the genes that code for glycolysis enzymes? muscle cell white blood cell pancreas beta cells all of these cells none of these cells A. muscle cell B. white blood cell C. pancreas beta cells (and alpha) Correct Answer: d

Practice Nuclear transplantation experiments provide strong evidence for which of the following? Differentiated vertebrate cells still maintain their full complement of DNA. Differentiated vertebrate cells do not maintain their full complement of DNA. Vertebrate cloning is not feasible. Cell differentiation is an irreversible process. Correct Answer: a

Practice Which of the following development events triggers the definition of the head and tail regions in a fruit fly? activation of the homeotic genes in the developing embryo accumulation of “head” mRNA in one end of the unfertilized egg gravitational response in the developing embryo Correct Answer: b