How Genes Are Controlled

How Genes Are Controlled
Chapter 11 How Genes Are Controlled

11.1 Proteins interacting with DNA turn prokaryotic genes on or off in response to environmental changes Gene regulation is the turning on and off of genes. Gene expression is the overall process of information flow from genes to proteins. The control of gene expression allows cells to produce specific kinds of proteins when and where they are needed. Our earlier understanding of gene control came from the study of E. coli. Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. The lactose operon is turned on by removing the repressor a sort of double negative. Students might enjoy various analogies to other situations, including the familiar refrain “When the cat's away, the mice will play.” Like a cat watching mice, if a mom keeps her kids away from cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. Thus, the person occupying Mom’s attention functions most like lactose binding to the repressor. 2. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch. 3. The control of gene expression is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type. © 2012 Pearson Education, Inc. 2

Transcriptional regulation : important Posttranscriptional regulation
Gene expression Gene on DNA mRNA Protein phenotype Transcriptional regulation : important Posttranscriptional regulation

Figure 11.1A Figure 11.1A Cells of E. coli bacteria E. coli 4

11.1 Proteins interacting with DNA turn prokaryotic genes on or off in response to environmental changes A cluster of genes with related functions, along with the control sequences, is called an operon. With few exceptions, operons only exist in prokaryotes. Operon = Gene cluster + promoter + regulatory sequence operator activator-binding site Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. The lactose operon is turned on by removing the repressor a sort of double negative. Students might enjoy various analogies to other situations, including the familiar refrain “When the cat's away, the mice will play.” Like a cat watching mice, if a mom keeps her kids away from cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. Thus, the person occupying Mom’s attention functions most like lactose binding to the repressor. 2. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch. 3. The control of gene expression is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type. © 2012 Pearson Education, Inc. 5

11.1 Proteins interacting with DNA turn prokaryotic genes on or off in response to environmental changes When an E. coli encounters lactose, all the enzymes needed for its metabolism are made at once using the lactose operon. The lactose (lac) operon includes three adjacent lactose-utilization genes, a promoter sequence where RNA polymerase binds and initiates transcription of all three lactose genes, and an operator sequence where a repressor can bind and block RNA polymerase action. Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. The lactose operon is turned on by removing the repressor a sort of double negative. Students might enjoy various analogies to other situations, including the familiar refrain “When the cat's away, the mice will play.” Like a cat watching mice, if a mom keeps her kids away from cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. Thus, the person occupying Mom’s attention functions most like lactose binding to the repressor. 2. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch. 3. The control of gene expression is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type. © 2012 Pearson Education, Inc. 6

Lactose b-galactoside permease (LacY) Lactose b-galactosidase (LacZ) Glucose + Galactose E. coli

11.1 Proteins interacting with DNA turn prokaryotic genes on or off in response to environmental changes Regulation of the lac operon A regulatory gene, located outside the operon, codes for a repressor protein. In the absence of lactose, the repressor binds to the operator and prevents RNA polymerase action. Lactose inactivates the repressor, so the operator is unblocked, RNA polymerase can bind to the promoter, and all three genes of the operon are transcribed. Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. The lactose operon is turned on by removing the repressor a sort of double negative. Students might enjoy various analogies to other situations, including the familiar refrain “When the cat's away, the mice will play.” Like a cat watching mice, if a mom keeps her kids away from cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. Thus, the person occupying Mom’s attention functions most like lactose binding to the repressor. 2. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch. 3. The control of gene expression is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type. © 2012 Pearson Education, Inc. 8

https://www.youtube.com/watch?v=oBwtxdI1zvk Regulator
Repressor: a regulatory protein that inhibits the transcription Activator: a regulatory protein that enhances the transcription Regulation of gene expression Negative regulation (repression) : regulation by a repressor Positive regulation (activation) : regulation by an activator

Operon turned off (lactose is absent): OPERON Regulatory gene
Figure 11.1B Operon turned off (lactose is absent): OPERON Regulatory gene Promoter Operator Lactose-utilization genes DNA mRNA RNA polymerase cannot attach to the promoter Protein Active repressor Operon turned on (lactose inactivates the repressor): Figure 11.1B The lac operon DNA RNA polymerase is bound to the promoter mRNA Translation Protein Inactive repressor Lactose Enzymes for lactose utilization 10

11.1 Proteins interacting with DNA turn prokaryotic genes on or off in response to environmental changes There are two types of repressor-controlled operons. In the lac operon, the repressor is active when alone and inactive when bound to lactose. In the trp bacterial operon, the repressor is inactive when alone and active when bound to the amino acid tryptophan (Trp). Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. The lactose operon is turned on by removing the repressor a sort of double negative. Students might enjoy various analogies to other situations, including the familiar refrain “When the cat's away, the mice will play.” Like a cat watching mice, if a mom keeps her kids away from cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. Thus, the person occupying Mom’s attention functions most like lactose binding to the repressor. 2. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch. 3. The control of gene expression is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type. © 2012 Pearson Education, Inc. 11

The trp operon in Escherichia coli
trpR Enzymes involved in tryptophan biosynthesis

lac operon trp operon DNA Active repressor Active repressor Tryptophan
Figure 11.1C lac operon trp operon Promoter Operator Gene DNA Active repressor Active repressor Tryptophan Figure 11.1C Two types of repressor-controlled operons Inactive repressor Inactive repressor Lactose 13

11.1 Proteins interacting with DNA turn prokaryotic genes on or off in response to environmental changes Another type of operon control involves activators, proteins that turn operons on by binding to DNA and making it easier for RNA polymerase to bind to the promoter. Activators help control a wide variety of operons. Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. The lactose operon is turned on by removing the repressor a sort of double negative. Students might enjoy various analogies to other situations, including the familiar refrain “When the cat's away, the mice will play.” Like a cat watching mice, if a mom keeps her kids away from cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. Thus, the person occupying Mom’s attention functions most like lactose binding to the repressor. 2. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch. 3. The control of gene expression is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type. © 2012 Pearson Education, Inc. 14

Positive regulation Catabolite repression of the lac operon
In the presence of glucose, the lac operon is not expressed High [glucose]  inhibition of adenylyl cyclase  low [cAMP] CRP (cAMP receptor protein)-cAMP complex serves as an activator Positive regulation

11.2 Chromosome structure and chemical modifications can affect gene expression
Differentiation The specialization in the structure and function of cells that occurs during the development of an organism Differentiation results from differential gene expression Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. The control of gene expression is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type. 2. Just as boxes of things that you rarely use are packed into a closet, attic, or basement, chromatin that is not expressed is highly compacted, and stored deeply packed away. 3. Just as a folded map is difficult to read, DNA packaging tends to prevent gene reading or expression. 4. Students might wonder why a patch of color is all the same on a cat’s skin if every cell has an equal chance of being one of the two color forms. The answer is that X chromosome inactivation occurs early in development. Thus, the patch of one color represents the progeny of one embryonic cell after X chromosome inactivation. © 2012 Pearson Education, Inc. 16

Eukaryotic chromosomes undergo multiple levels of folding and coiling, called DNA packing. Nucleosomes are formed when DNA is wrapped around histone proteins. This packaging gives a “beads on a string” appearance. Each nucleosome bead includes DNA plus eight histones. Stretches of DNA, called linkers, join consecutive nucleosomes. At the next level of packing, the beaded string is wrapped into a tight helical fiber. This fiber coils further into a thick supercoil. Looping and folding can further compact the DNA. Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. The control of gene expression is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type. 2. Just as boxes of things that you rarely use are packed into a closet, attic, or basement, chromatin that is not expressed is highly compacted, and stored deeply packed away. 3. Just as a folded map is difficult to read, DNA packaging tends to prevent gene reading or expression. 4. Students might wonder why a patch of color is all the same on a cat’s skin if every cell has an equal chance of being one of the two color forms. The answer is that X chromosome inactivation occurs early in development. Thus, the patch of one color represents the progeny of one embryonic cell after X chromosome inactivation. © 2012 Pearson Education, Inc. 18

DNA packing can prevent gene expression by preventing RNA polymerase and other transcription proteins from contacting the DNA. Cells seem to use higher levels of packing for long-term inactivation of genes. Highly compacted chromatin, found in varying regions of interphase chromosomes, is generally not expressed at all. Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. The control of gene expression is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type. 2. Just as boxes of things that you rarely use are packed into a closet, attic, or basement, chromatin that is not expressed is highly compacted, and stored deeply packed away. 3. Just as a folded map is difficult to read, DNA packaging tends to prevent gene reading or expression. 4. Students might wonder why a patch of color is all the same on a cat’s skin if every cell has an equal chance of being one of the two color forms. The answer is that X chromosome inactivation occurs early in development. Thus, the patch of one color represents the progeny of one embryonic cell after X chromosome inactivation. © 2012 Pearson Education, Inc. 19

chromatin DNA double helix (2-nm diameter) Histones
“Beads on a string” Nucleosome (10-nm diameter) chromatin Tight helical fiber (30-nm diameter) Supercoil (200-nm diameter) 700 nm Metaphase chromosome

Chromatin remodelling 1. Modification of the core histones Methylation of Lys or Arg residues (repression or activation) Phosphorylation of Ser or Thr residues (repression) Acetylation (Lys, activation), ubiquitination (Lys, activation), sumoylation 2. Reposition of nucleosomes on the DNA remodel chromatin so that nucleosomes become more irregularly placed and stimulate the binding of transcription factors 3. Changes in the histone composition of the nucleosome Chemical modification of DNA bases: methylation Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. The control of gene expression is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type. 2. Just as boxes of things that you rarely use are packed into a closet, attic, or basement, chromatin that is not expressed is highly compacted, and stored deeply packed away. 3. Just as a folded map is difficult to read, DNA packaging tends to prevent gene reading or expression. 4. Students might wonder why a patch of color is all the same on a cat’s skin if every cell has an equal chance of being one of the two color forms. The answer is that X chromosome inactivation occurs early in development. Thus, the patch of one color represents the progeny of one embryonic cell after X chromosome inactivation. © 2012 Pearson Education, Inc. 21

O + Lys-NH3 Lys-NH-C-CH3 Histones
Acetylation by histone acetyltransferase Deacetylation by histone deacetylase Histones

Chromatin remodeling

X-chromosome inactivation In female mammals, one of the two X chromosomes is highly compacted and transcriptionally inactive. Either the maternal or paternal chromosome is randomly inactivated. An inactivated X chromosome is called a Barr body. Tortoiseshell fur coloration is due to inactivation of X chromosomes in heterozygous female cats. Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. The control of gene expression is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type. 2. Just as boxes of things that you rarely use are packed into a closet, attic, or basement, chromatin that is not expressed is highly compacted, and stored deeply packed away. 3. Just as a folded map is difficult to read, DNA packaging tends to prevent gene reading or expression. 4. Students might wonder why a patch of color is all the same on a cat’s skin if every cell has an equal chance of being one of the two color forms. The answer is that X chromosome inactivation occurs early in development. Thus, the patch of one color represents the progeny of one embryonic cell after X chromosome inactivation. © 2012 Pearson Education, Inc. 24

DNA double helix (2-nm diameter)
Figure 11.2A DNA double helix (2-nm diameter) Metaphase chromosome Nucleosome (10-nm diameter) Tight helical fiber (30-nm diameter) Linker “Beads on a string” Figure 11.2A DNA packing in a eukaryotic chromosome Supercoil (300-nm diameter) Histones 700 nm 25

Cell division and random X chromosome inactivation
Figure 11.2B Early Embryo Adult Two cell populations Cell division and random X chromosome inactivation X chromosomes Active X Orange fur Inactive X Allele for orange fur Allele for black fur Inactive X Figure 11.2B A tortoiseshell pattern on a female cat, a result of X chromosome inactivation Active X Black fur 26

11.3 Complex assemblies of proteins control eukaryotic transcription
Prokaryotes and eukaryotes employ 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 and off. In eukaryotes, activator proteins seem to be more important than repressors. Thus, the default state for most genes seems to be off. A typical plant or animal cell needs to turn on and transcribe only a small percentage of its genes. Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips The authors note that the selective unpackaging of chromosomes is the “coarse adjustment” of eukaryotic gene expression. The initiation of RNA synthesis is the fine-tuning of the regulation. If you have recently asked your students to use microscopes in lab, you might relate these degrees of adjustment to the coarse and fine control knobs of a microscope. © 2012 Pearson Education, Inc. 27

Eukaryotic RNA polymerase requires the assistance of proteins called transcription factors. Transcription factors include activator proteins, which bind to DNA sequences called enhancers and initiate gene transcription. The binding of the activators leads to bending of the DNA. Other transcription factor proteins interact with the bound activators, which then collectively bind as a complex at the gene’s promoter. RNA polymerase then attaches to the promoter and transcription begins. Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips The authors note that the selective unpackaging of chromosomes is the “coarse adjustment” of eukaryotic gene expression. The initiation of RNA synthesis is the fine-tuning of the regulation. If you have recently asked your students to use microscopes in lab, you might relate these degrees of adjustment to the coarse and fine control knobs of a microscope. © 2012 Pearson Education, Inc. 28

Transcription factors
Figure 11.3 Enhancers Promoter Gene DNA Activator proteins Transcription factors Other proteins RNA polymerase Figure 11.3 A model for the turning on of a eukaryotic gene Bending of DNA Transcription 29

Transcription of eukaryotic genes
The basal transcription factors are required for RNA polymerase II to bind a promoter and to initiate transcription Basal transcription factor TFIID, A, B, F, E, H mRNA is synthesized by RNA pol II rRNA (RNA pol I) tRNA and small nuclear RNA (RNA pol III)

Most eukaryotic genes are regulated by activators Activator binding site = enhancer Some eukaryotic genes are regulated by repressors Repressor binding site = silencer Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips The authors note that the selective unpackaging of chromosomes is the “coarse adjustment” of eukaryotic gene expression. The initiation of RNA synthesis is the fine-tuning of the regulation. If you have recently asked your students to use microscopes in lab, you might relate these degrees of adjustment to the coarse and fine control knobs of a microscope. © 2012 Pearson Education, Inc. 31

11.4 Eukaryotic RNA may be spliced in more than one way
Alternative RNA splicing produces different mRNAs from the same transcript, results in the production of more than one polypeptide from the same gene, and Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips Alternative RNA splicing is like remixing music to produce a new song or re-editing a movie for a different effect. © 2012 Pearson Education, Inc. 32

Exons DNA 1 2 3 4 5 Introns Introns Cap Tail RNA transcript 1 2 3 4 5
Figure 11.4 Exons DNA 1 2 3 4 5 Introns Introns Cap Tail RNA transcript 1 2 3 4 5 RNA splicing Figure 11.4 The production of two different mRNAs from the same gene or mRNA 1 2 3 5 1 2 4 5 33

11.5 Small RNAs play multiple roles in controlling gene expression
microRNAs (miRNAs) can bind to complementary sequences on mRNA molecules either degrading the target mRNA or blocking its translation. RNA interference (RNAi) is the use of miRNA to artificially control gene expression by injecting miRNAs into a cell to turn off a specific gene sequence. Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. References in older books and outdated websites may characterize DNA that does not code for rRNA, tRNA, or mRNA as junk DNA. The relatively recent discovery of miRNA and its significant roles in gene regulation reveals the danger of concluding that the absence of evidence is evidence of absence! 2. Describing the discovery of miRNAs and their potential in research and medicine helps to illustrate the promise of gene regulation research. Students early in their science careers may appreciate knowing about scientific fields with great potential as they consider the direction of their developing careers. © 2012 Pearson Education, Inc. 34

miRNA- protein complex
Figure 11.5 Protein miRNA 1 miRNA- protein complex 2 Target mRNA Figure 11.5 Mechanisms of RNA interference 3 or 4 Translation blocked mRNA degraded 35

11.7 Review: Multiple mechanisms regulate gene expression in eukaryotes
These controls points include: chromosome changes and DNA unpacking, control of transcription, control of RNA processing including the addition of a cap and tail and splicing, flow through the nuclear envelope, breakdown of mRNA, Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips The authors develop an analogy between the regulation of transcription and the series of water pipes that carry water from a local water supply, perhaps a reservoir, to a faucet. At various points, valves control the flow of water. Similarly, the expression of genes is controlled at many points along the process. Figure 11.7 illustrates the flow of genetic information from a chromosome—a reservoir of genetic information—to an active protein that has been made in the cell’s cytoplasm. The multiple mechanisms that control gene expression are analogous to the control valves in water pipes. In the figure, a possible control knob indicates each gene expression “valve.” The larger size of the transcription control knob highlights its crucial role. © 2012 Pearson Education, Inc. 36

11.7 Review: Multiple mechanisms regulate gene expression in eukaryotes
control of translation, and control after translation including cleavage/modification/activation of proteins and breakdown of protein. Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips The authors develop an analogy between the regulation of transcription and the series of water pipes that carry water from a local water supply, perhaps a reservoir, to a faucet. At various points, valves control the flow of water. Similarly, the expression of genes is controlled at many points along the process. Figure 11.7 illustrates the flow of genetic information from a chromosome—a reservoir of genetic information—to an active protein that has been made in the cell’s cytoplasm. The multiple mechanisms that control gene expression are analogous to the control valves in water pipes. In the figure, a possible control knob indicates each gene expression “valve.” The larger size of the transcription control knob highlights its crucial role. © 2012 Pearson Education, Inc. 37

Initial polypeptide (inactive) Folded polypeptide (inactive)
Figure 11.6 SH SH Folding of the polypeptide and the formation of S—S linkages S S S S SH S Cleavage S SH SH S S SH S S S S Initial polypeptide (inactive) Folded polypeptide (inactive) Active form of insulin Figure 11.6 Protein activation: the role of polypeptide cleavage 38

11.8 Cell signaling and cascades of gene expression direct animal development
Regulation of embryonic development Development (발생) Progressive changes in structure or metabolism of an organism Growth: increase in size resulting from a combination of cell division and cell expansion Differentiation Morphogenesis: creation of the overall form of a multicellular organism Embryo (배아): young animal or plant while it is still contained within a protective structure such as a seed, egg, or uterus Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips Homeotic genes are often called master control genes. The relationship between homeotic genes and structural genes is like the relationship between a construction supervisor and the workers. Major rearrangements can result from a few simple changes in the directions for construction. © 2012 Pearson Education, Inc. 39

Pattern formation Determination of the body polarity Segmentation of the larval body Formation of organs and appendages in appropriate segments

Morphogen: Regulatory proteins that lead to pattern formation
Products of pattern-regulating genes Pattern regulating genes Maternal genes: head-tail axis와 dorsal-ventral axis 결정. e.g., bicoid (head-determining gene), nanos (tail-determining gene) Segmentation genes Homeotic genes The products of pattern regulating genes serve as transcriptional or translational regulators

Mutation in a homeotic gene
Figure 11.8A Mutation in a homeotic gene Eye Antenna Figure 11.8A A normal fruit fly (left) compared with a mutant fruit fly (right) with legs coming out of its head Extra pair of legs 42

Egg cell within ovarian follicle
Figure 11.8B Egg cell within ovarian follicle Egg cell Egg cell and follicle cells signaling each other 1 Follicle cells Gene expression Growth of egg cell Localization of “head” mRNA 2 Egg cell “Head” mRNA Cascades of gene expression Fertilization and mitosis Embryo Body segments Figure 11.8B Key steps in the early development of head-tail axis in a fruit fly 3 Expression of homeotic genes and cascades of gene expression Adult fly 4 43

11.10 Signal transduction pathways convert messages received at the cell surface to responses within the cell A signal transduction pathway is a series of molecular changes that convert a signal on the target cell’s surface to a specific response within the cell. Signal transduction pathways are crucial to many cellular functions. Student Misconceptions and Concerns 1. The broad concept of selective reading of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of software manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation. 2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.7 can be a helpful reference to organize the potential sites of regulation. Teaching Tips 1. The authors note that signal transduction pathways were addressed in Module 8.8 and will again be addressed as these pathways are involved in controlling hormone functions in animals in Chapter 26 and in plants in Chapter 33. If your course does not include these other chapters, consider investing some of these aspects into the Chapter 11 materials. 2. The action of an extracellular signal reaching a cell’s surface in a signal transduction pathway is like pushing the doorbell at a home. The signal is converted to another form (pushing a button rings a bell), and activities change within the house as someone comes to answer the door. 3. Some of the stages of a signal transduction pathway can be compared to a human reaction. Consider someone calling your name. (1) Reception—The sound waves of someone’s voice hitting and changing the shape of your eardrum. (2) Transduction—Your ear converts sound waves to nerve impulses and sends a signal to your brain that your name has been called. (3) Response—You look around to see who is calling. © 2012 Pearson Education, Inc. 44

Signal transduction pathway
Signaling cell EXTRACELLULAR FLUID Signal transduction pathway Reception of a signal by a receptor protein Signal transduction Response Signaling molecule 1 Receptor protein Plasma membrane 2 Target cell 3 Relay proteins Signal transduction pathway 4 Transcription factor (activated) NUCLEUS Figure A signal transduction pathway that turns on a gene DNA 5 Transcription mRNA New protein 6 CYTOPLASM Translation 45

Receptor A receptor protein binds to a signal in the same way as an enzyme binds to a substrate (specificity for the ligand) Signaling molecule  ligand Ion channel receptor Protein kinase receptor Membrane-bound receptor G-protein-linked receptor Cytoplasmic receptor (ligands are hydrophobic)

Ion channel receptor e.g., acetylcholine receptor in the skeletal muscle cell Muscle contraction (Response)

Kinase receptor e.g., Insulin receptor Kinase: an enzyme that transfers phosphoryl groups (인산기) to a molecule (-Transport of glucose across the membrane -Glycogen synthesis from glucose)

G protein-linked receptor
e.g., epinephrine (adrenaline) receptor a Response

Cytoplasmic receptor e.g., steroid hormone receptor The signal molecule is hydrophobic Transcriptional activator

Signal transduction은 관련된 단백질들의 순차적인 activation 과정을 통하여 이루어진다

Response를 일으키는 3가지 기작 Membrane channels are opened Enzyme activities are changed Gene expression is regulated

Signal Autocrine signal Paracrine signal Endocrine signal

CLONING OF PLANTS AND ANIMALS
© 2012 Pearson Education, Inc. 55

11.12 Plant cloning shows that differentiated cells may retain all of their genetic potential
Most differentiated cells retain a full set of genes, even though only a subset may be expressed. Evidence is available from plant cloning, in which a root cell can divide to form an adult plant and salamander limb regeneration, in which the cells in the leg stump dedifferentiate, divide, and then redifferentiate, giving rise to a new leg. Student Misconceptions and Concerns 1. Students often fail to see the similarities between identical twins and cloning. Each process produces multiple individuals with identical nuclear genetic material. 2. Students often assume that clones will appear and act identically. This misunderstanding provides an opportunity to discuss the important influence of the environment in shaping the final phenotype. Teaching Tips 1. The basic question asked in Module is whether a cell becomes differentiated by selectively reading the genome or by retaining only the needed sections. In your course, you are unlikely to assign the entire Concepts textbook. Instead, you will likely ask your students to selectively read chapters in the book. Students could remove all of the pages that they do not need, leaving only those assigned. Alternately, students could keep their textbooks intact, reading only the assigned and relevant passages. These latter students, with intact textbooks, behave like cells undergoing differentiation. 2. An even more remarkable aspect of salamander limb regeneration is that only the missing limb segments are regenerated. If an arm is amputated at the elbow, only the forearm, wrist, and hand are regenerated. Somehow, the cells can detect what is missing and replace only those parts! © 2012 Pearson Education, Inc. 56

Root cells cultured in growth medium Cell division in culture
Figure 11.12 Root of carrot plant Single cell Figure Growth of a carrot plant from a differentiated root cell Root cells cultured in growth medium Cell division in culture Plantlet Adult plant 57

11.13 Nuclear transplantation can be used to clone animals
Animal cloning can be achieved using nuclear transplantation, in which the nucleus of an egg cell or zygote is replaced with a nucleus from an adult somatic cell. Using nuclear transplantation to produce new organisms is called reproductive cloning. It was first used in mammals in 1997 to produce the sheep Dolly. Student Misconceptions and Concerns 1. Students often fail to see the similarities between identical twins and cloning. Each process produces multiple individuals with identical nuclear genetic material. 2. Students often assume that clones will appear and act identically. This misunderstanding provides an opportunity to discuss the important influence of the environment in shaping the final phenotype. Teaching Tips 1. The researchers who cloned Dolly the sheep from a mammary gland cell named Dolly after the celebrity country singer Dolly Parton. 2. Preimplantation genetic diagnosis (PGD) is a genetic screening technique that removes one or two cells from an embryo at about the 6 to 10 cell stage. The cells that are removed are genetically analyzed while the remaining embryonic cell mass retains the potential to develop. This technique permits embryos to be genetically screened before implanting them into a woman. However, PGD has another potential use. Researchers can use PGD to obtain embryonic stem cells without destroying a human embryo. This procedure might be more acceptable than methods that destroy the embryo to obtain embryonic stem cells. © 2012 Pearson Education, Inc. 58

11.13 Nuclear transplantation can be used to clone animals
Another way to clone uses embryonic stem (ES) cells harvested from a blastocyst. This procedure can be used to produce cell cultures for research or stem cells for therapeutic treatments. Student Misconceptions and Concerns 1. Students often fail to see the similarities between identical twins and cloning. Each process produces multiple individuals with identical nuclear genetic material. 2. Students often assume that clones will appear and act identically. This misunderstanding provides an opportunity to discuss the important influence of the environment in shaping the final phenotype. Teaching Tips 1. The researchers who cloned Dolly the sheep from a mammary gland cell named Dolly after the celebrity country singer Dolly Parton. 2. Preimplantation genetic diagnosis (PGD) is a genetic screening technique that removes one or two cells from an embryo at about the 6 to 10 cell stage. The cells that are removed are genetically analyzed while the remaining embryonic cell mass retains the potential to develop. This technique permits embryos to be genetically screened before implanting them into a woman. However, PGD has another potential use. Researchers can use PGD to obtain embryonic stem cells without destroying a human embryo. This procedure might be more acceptable than methods that destroy the embryo to obtain embryonic stem cells. © 2012 Pearson Education, Inc. 59

Figure 11.13 Nuclear transplantation for cloning
Donor cell Nucleus from the donor cell Reproductive cloning Blastocyst The blastocyst is implanted in a surrogate mother. A clone of the donor is born. The nucleus is removed from an egg cell. A somatic cell from an adult donor is added. The cell grows in culture to produce an early embryo (blastocyst). Therapeutic cloning Embryonic stem cells are removed from the blastocyst and grown in culture. The stem cells are induced to form specialized cells. Figure Nuclear transplantation for cloning 60

(embryonic stem cell)

11.15 CONNECTION: Therapeutic cloning can produce stem cells with great medical potential
When grown in laboratory culture, stem cells can divide indefinitely and give rise to many types of differentiated cells. Adult stem cells can give rise to many, but not all, types of cells. Student Misconceptions and Concerns 1. Students often fail to see the similarities between identical twins and cloning. Each process produces multiple individuals with identical nuclear genetic material. 2. Students often assume that clones will appear and act identically. This misunderstanding provides an opportunity to discuss the important influence of the environment in shaping the final phenotype. Teaching Tips 1. The political restrictions on the use of federal funds to study stem cells illustrate the influence of society on the directions of science. As time permits, consider opportunities to discuss or investigate this and other ways that science and society interact. 2. Preimplantation genetic diagnosis (PGD) is a genetic screening technique that removes one or two cells from an embryo at about the 6 to 10 cell stage. The cells that are removed are genetically analyzed while the remaining embryonic cell mass retains the potential to develop. This technique permits embryos to be genetically screened before implanting them into a woman. However, PGD has another potential use. Researchers can use PGD to obtain embryonic stem cells without destroying a human embryo. This procedure might be more acceptable than methods that destroy the embryo to obtain embryonic stem cells. © 2012 Pearson Education, Inc. 62

11.15 CONNECTION: Therapeutic cloning can produce stem cells with great medical potential
Embryonic stem cells are considered more promising than adult stem cells for medical applications. The ultimate aim of therapeutic cloning is to supply cells for the repair of damaged or diseased organs. Student Misconceptions and Concerns 1. Students often fail to see the similarities between identical twins and cloning. Each process produces multiple individuals with identical nuclear genetic material. 2. Students often assume that clones will appear and act identically. This misunderstanding provides an opportunity to discuss the important influence of the environment in shaping the final phenotype. Teaching Tips 1. The political restrictions on the use of federal funds to study stem cells illustrate the influence of society on the directions of science. As time permits, consider opportunities to discuss or investigate this and other ways that science and society interact. 2. Preimplantation genetic diagnosis (PGD) is a genetic screening technique that removes one or two cells from an embryo at about the 6 to 10 cell stage. The cells that are removed are genetically analyzed while the remaining embryonic cell mass retains the potential to develop. This technique permits embryos to be genetically screened before implanting them into a woman. However, PGD has another potential use. Researchers can use PGD to obtain embryonic stem cells without destroying a human embryo. This procedure might be more acceptable than methods that destroy the embryo to obtain embryonic stem cells. © 2012 Pearson Education, Inc. 63

Adult stem cells in bone marrow Cultured embryonic stem cells
Figure 11.15 Blood cells Adult stem cells in bone marrow Nerve cells Cultured embryonic stem cells Figure Differentiation of stem cells in culture Heart muscle cells Different culture conditions Different types of differentiated cells 64

THE GENETIC BASIS OF CANCER

11.16 Cancer results from mutations in genes that control cell division
Mutations in two types of genes can cause cancer. Oncogenes Proto-oncogenes are normal genes that promote cell division. Mutations to proto-oncogenes create cancer-causing oncogenes that often stimulate cell division. Tumor-suppressor genes Tumor-suppressor genes normally inhibit cell division or function in the repair of DNA damage. Mutations inactivate the genes and allow uncontrolled division to occur. Student Misconceptions and Concerns 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. (Answer: yes, as noted in Module 11.16). 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 website of the National Cancer Institute describes the risks of HPV infection at © 2012 Pearson Education, Inc. 66

Infection of a normal cell with oncogene-carrying viruses
Mechanisms by which a normal cell is converted to a cancer cell Infection of a normal cell with oncogene-carrying viruses Activation of oncogenes (proto-oncogene  oncogene) Inactivation of tumor-suppressor genes Cancer Proto-oncogene Cancer Tumor-suppressor gene Mutated allele

Proto-oncogene (for a protein that stimulates cell division)
Figure 11.16A Proto-oncogene (for a protein that stimulates cell division) DNA A mutation within the gene Multiple copies of the gene The gene is moved to a new DNA locus, under new controls Oncogene New promoter Figure 11.16A Alternative ways to make oncogenes from a proto-oncogene (all leading to excessive cell growth) Hyperactive growth- stimulating protein in a normal amount Normal growth- stimulating protein in excess Normal growth- stimulating protein in excess 68

Tumor-suppressor gene Mutated tumor-suppressor gene
Figure 11.16B Tumor-suppressor gene Mutated tumor-suppressor gene Normal growth- inhibiting protein Defective, nonfunctioning protein Cell division not under control Cell division under control Figure 11.16B The effect of a mutation in a tumor-suppressor gene 69

11.17 Multiple genetic changes underlie the development of cancer
Usually four or more somatic mutations are required to produce a full-fledged cancer cell. One possible scenario is the stepwise development of colorectal cancer. An oncogene arises or is activated, resulting in increased cell division in apparently normal cells in the colon lining. Additional DNA mutations cause the growth of a small benign tumor (polyp) in the colon wall. Additional mutations lead to a malignant tumor with the potential to metastasize. Teaching Tips Exposure to carcinogens early in life carries greater risks than the same exposure later in life. This is because damage in early life has more time to accumulate additional changes, potentially leading to disease. © 2012 Pearson Education, Inc. 70

An oncogene is activated A tumor-suppressor gene is inactivated
Figure 11.17A DNA changes: An oncogene is activated A tumor-suppressor gene is inactivated A second tumor- suppressor gene is inactivated Cellular changes: Increased cell division Growth of a polyp Growth of a malignant tumor 1 2 3 Figure 11.17A Stepwise development of a typical colon cancer Colon wall 71

1 mutation 2 mutations 3 mutations 4 mutations Chromosomes Normal cell
Figure 11.17B 1 mutation 2 mutations 3 mutations 4 mutations Chromosomes Normal cell Malignant cell Figure 11.17B Accumulation of mutations in the development of a cancer cell 72

11.18 Faulty proteins can interfere with normal signal transduction pathways
Proto-oncogenes and tumor-suppressor genes often code for proteins involved in signal transduction pathways leading to gene expression. Two main types of signal transduction pathways lead to the synthesis of proteins that influence cell division. Teaching Tips Mutations in the ras or p53 genes are like having car problems in which the gas pedal overaccelerates or the brakes on the car fail to function. In either situation, an accident is more likely to occur. © 2012 Pearson Education, Inc. 73

One pathway produces a product that stimulates cell division. In a healthy cell, the product of the ras proto-oncogene relays a signal when growth factor binds to a receptor. But in a cancerous condition, the product of the ras proto-oncogene relays the signal in the absence of a growth factor, leading to uncontrolled growth. Mutations in ras occur in more than 30% of human cancers. Teaching Tips Mutations in the ras or p53 genes are like having car problems in which the gas pedal overaccelerates or the brakes on the car fail to function. In either situation, an accident is more likely to occur. © 2012 Pearson Education, Inc. 74

Normal product of ras gene
Figure 11.18A Growth factor Receptor Target cell Hyperactive relay protein (product of ras oncogene) issues signals on its own Normal product of ras gene Relay proteins Transcription factor (activated) CYTOPLASM Figure 11.18A A stimulatory signal transduction pathway and the effect of an oncogene protein DNA NUCLEUS Transcription Translation Protein that stimulates cell division 75

A second pathway produces a product that inhibits cell division. The normal product of the p53 gene is a transcription factor that normally activates genes for factors that inhibit cell division. In the absence of functional p53, cell division continues because the inhibitory protein is not produced. Mutations in p53 occur in more than 50% of human cancers. Teaching Tips Mutations in the ras or p53 genes are like having car problems in which the gas pedal overaccelerates or the brakes on the car fail to function. In either situation, an accident is more likely to occur. © 2012 Pearson Education, Inc. 76

Growth-inhibiting factor
Figure 11.18B Growth-inhibiting factor Receptor Relay proteins Nonfunctional transcription factor (product of faulty p53 tumor-suppressor gene) cannot trigger transcription Transcription factor (activated) Normal product of p53 gene Figure 11.18B An inhibitory signal transduction pathway and the effect of a faulty tumor-suppressor protein Transcription Translation Protein that inhibits cell division Protein absent (cell division not inhibited) 77

11.19 CONNECTION: Lifestyle choices can reduce the risk of cancer
Carcinogens are cancer-causing agents that alter DNA. Most mutagens (substances that promote mutations) are carcinogens. Two of the most potent carcinogens (mutagens) are X-rays and ultraviolet radiation in sunlight. Student Misconceptions and Concerns Many students do not appreciate the increased risk of skin cancer associated with the use of tanning beds, which is still popular with many college-age populations. Teaching Tips 1. 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. Furthermore, people may feel obliged or be obligated to share this information with a potential mate or employer. 2. 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 website for the American Cancer Society at © 2012 Pearson Education, Inc. 78

11.19 CONNECTION: Lifestyle choices can reduce the risk of cancer
Healthy lifestyles that reduce the risks of cancer include avoiding carcinogens, including the sun and tobacco products, exercising adequately, regular medical checks for common types of cancer, and a healthy high-fiber, low-fat diet including plenty of fruits and vegetables. Student Misconceptions and Concerns Many students do not appreciate the increased risk of skin cancer associated with the use of tanning beds, which is still popular with many college-age populations. Teaching Tips 1. 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. Furthermore, people may feel obliged or be obligated to share this information with a potential mate or employer. 2. 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 website for the American Cancer Society at © 2012 Pearson Education, Inc. 79

Table 11.19 Table Cancer in the United States 80

DNA Technology and Genomics
Chapter 12 DNA Technology and Genomics

12.1 Genes can be cloned in recombinant plasmids
Bacterial plasmid Chromosome과 독립적으로 replication되는 small, circular DNA molecule Replication origin을 가진다 Host bacterium의 생존에 필수적이지 않다 Student Misconceptions and Concerns 1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant. Teaching Tips 1. Figure 12.1B is a synthesis of the techniques discussed in further detail in Modules 12.2–12.5. Figure 12.1B is therefore an important integrative piece that lays the foundation of most of the biotechnology discussion. Repeatedly referring to this figure in class helps students relate the text to your lecture. 2. The general genetic engineering challenge discussed in Module 12.1 begins with the need to insert a gene of choice into a plasmid. This process is very similar to film or video editing. What do we need to do to insert a minute of one film into another? We will need techniques to (a) cut and remove the minute of film to be inserted, (b) a way to cut the new film apart, and (c) a way to insert the new minute. In general, this is also like removing one boxcar from one train, and transferring the boxcar to another train. Students can become confused by the details of gene cloning through misunderstanding this basic editing relationship. Relaxed plasmid : high-copy number Stringent plasmid : low-copy number © 2012 Pearson Education, Inc. 83

12.1 Genes can be cloned in recombinant plasmids
Gene cloning The production of multiple copies of the gene Introduction of a recombinant plasmid into E. coli Transformation Electroporation Student Misconceptions and Concerns 1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant. Teaching Tips 1. Figure 12.1B is a synthesis of the techniques discussed in further detail in Modules 12.2–12.5. Figure 12.1B is therefore an important integrative piece that lays the foundation of most of the biotechnology discussion. Repeatedly referring to this figure in class helps students relate the text to your lecture. 2. The general genetic engineering challenge discussed in Module 12.1 begins with the need to insert a gene of choice into a plasmid. This process is very similar to film or video editing. What do we need to do to insert a minute of one film into another? We will need techniques to (a) cut and remove the minute of film to be inserted, (b) a way to cut the new film apart, and (c) a way to insert the new minute. In general, this is also like removing one boxcar from one train, and transferring the boxcar to another train. Students can become confused by the details of gene cloning through misunderstanding this basic editing relationship. © 2012 Pearson Education, Inc. 84

Figure 12.1B An overview of gene cloning
E. coli bacterium Plasmid A cell with DNA containing the gene of interest Bacterial chromosome 1 A plasmid is isolated. 2 The cell’s DNA is isolated. Gene of interest DNA 3 The plasmid is cut with an enzyme. Examples of gene use 4 The cell’s DNA is cut with the same enzyme. Gene of interest 5 The targeted fragment and plasmid DNA are combined. 6 DNA ligase is added, which joins the two DNA molecules. Genes may be inserted into other organisms. Recombinant DNA plasmid Examples of protein use Gene of interest Figure 12.1B An overview of gene cloning 7 The recombinant plasmid is taken up by a bacterium through transformation. 9 Recombinant bacterium Harvested proteins may be used directly. 8 The bacterium reproduces. Clone of cells 85

12.2 Enzymes are used to “cut and paste” DNA
Restriction endonuclease (enzyme) Most restriction enzymes recognize short nucleotide sequences in DNA molecules and cut at specific points within these recognition sequences Protection of bacteria against foreign DNA  methylase modifies the host DNA Sticky-end generating RE Blunt-end generating RE Restriction enzyme recognition sequence 1 DNA Restriction enzyme cuts the DNA into fragments Restriction enzyme cuts the DNA into fragments 2 Sticky end Addition of a DNA fragment from another source 3 Two (or more) fragments stick together by base-pairing Student Misconceptions and Concerns 1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant. Teaching Tips 1. The authors note the origin of the name restriction enzymes. In nature, these enzymes protect bacterial cells against foreign DNA. Thus, these enzymes “restrict” the invasion of foreign genetic material. 2. A genomic library of the sentence you are now reading would be all of the sentence fragments that made up the sentence. One could string together all of the words of this first sentence, without spaces between letters, and then conduct a word processing edit, placing a space between any place where the letter “e” is followed by the letter “n.” The resulting fragments of this original sentence would look like this and would be similar to a genomic library. Age nomiclibraryofthese nte nceyouare nowreadingwouldbeallofthese nte ncefragme ntsthatmadeupthese nte nce. 4 DNA ligase pastes the strand 5 Recombinant DNA molecule 86

3’-OH P-5’ 5’-P OH-3’ DNA ligase

12.4 Reverse transcriptase can help make genes for cloning
Reverse transcriptase: RNA  double-stranded DNA RNA-dependent DNA polymerase RNase DNA-dependent DNA polymerase Complementary DNA (cDNA) Student Misconceptions and Concerns 1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant. Teaching Tips 1. A cDNA library is a way to learn what portion of the genome is active at any given time in a cell’s life. In a very general way, it is like looking at the list of books checked out at a school library (assuming that the checked-out books are being used). 2. Reverse transcriptase is introduced in Module 10.20, where HIV is discussed. Even if students were not assigned this chapter, Module provides a meaningful background for the natural and significant roles of this enzyme. Eukaryotic gene을 prokaryote에서 expression시킬때, cDNA를 이용 © 2012 Pearson Education, Inc. 88

introns and joins exons)
Figure 12.4 CELL NUCLEUS Exon Intron Exon Intron Exon DNA of a eukaryotic gene 1 Transcription RNA transcript 2 RNA splicing (removes introns and joins exons) mRNA 3 Isolation of mRNA from the cell and the addition of reverse transcriptase; synthesis of a DNA strand TEST TUBE Reverse transcriptase Figure 12.4 Making an intron-lacking gene from eukaryotic mRNA cDNA strand being synthesized 4 Breakdown of RNA Direction of synthesis 5 Synthesis of second DNA strand cDNA of gene (no introns) 89

Gel electrophoresis https://www.youtube.com/watch?v=vq759wKCCUQ
Gel: agarose gel, polyacrylamide gel DNA, RNA have a negative charge The longer the DNA (RNA) molecule, the slower their migration rate Agarose polyacrylamide Mixture of DNA molecules of different sizes well anode Longer molecules Power source Gel Shorter molecules Glass plates Completed gel cathode

GENETICALLY MODIFIED ORGANISMS

12.6 Recombinant cells and organisms can mass-produce gene products
Recombinant cells and organisms constructed by DNA technologies are used to manufacture many useful products, chiefly proteins. Bacteria are often the best organisms for manufacturing a protein product because bacteria have plasmids and phages available for use as gene- cloning vectors, can be grown rapidly and cheaply, can be engineered to produce large amounts of a particular protein, and often secrete the proteins directly into their growth medium. Student Misconceptions and Concerns 1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms. 2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students. Teaching Tips As noted in Module 12.6, DNA technology is primarily used to produce proteins. Challenge your students to explain why lipids and carbohydrates are not typically produced by these processes. © 2012 Pearson Education, Inc. 92

Yeast cells are eukaryotes, have long been used to make bread and beer, can take up foreign DNA and integrate it into their genomes, have plasmids that can be used as gene vectors, and are often better than bacteria at synthesizing and secreting eukaryotic proteins. Student Misconceptions and Concerns 1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms. 2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students. Teaching Tips As noted in Module 12.6, DNA technology is primarily used to produce proteins. Challenge your students to explain why lipids and carbohydrates are not typically produced by these processes. © 2012 Pearson Education, Inc. 93

Mammalian cells must be used to produce proteins with chains of sugars. Examples include human erythropoietin (EPO), which stimulates the production of red blood cells, factor VIII to treat hemophilia, and tissue plasminogen activator (TPA) used to treat heart attacks and strokes. Student Misconceptions and Concerns 1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms. 2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students. Teaching Tips As noted in Module 12.6, DNA technology is primarily used to produce proteins. Challenge your students to explain why lipids and carbohydrates are not typically produced by these processes. © 2012 Pearson Education, Inc. 94

Table 12.6 Table 12.6 Some Protein Products of Recombinant DNA Technology 95

12.8 CONNECTION: Genetically modified organisms are transforming agriculture
Genetically modified (GM) organisms: any organism whose genetic material has been altered using genetic engineering techniques. GMO. =Transgenic organisms Student Misconceptions and Concerns 1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms. 2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students. Teaching Tips Roundup Ready Corn, a product of the agricultural biotechnology corporation Monsanto, is resistant to the herbicide Roundup. The general strategy for farmers is to spray fields of Roundup Ready corn with the herbicide Roundup, killing weeds but not the corn. A search of the Internet will quickly reveal the controversy associated with this and other genetically modified organisms (GMO), which can encourage interesting discussions and promote critical thinking skills. Module 12.9 discusses some of the issues related to the concerns over the use of GM organisms. © 2012 Pearson Education, Inc. 96

Figure 12.8B Figure 12.8B A mix of conventional rice (white), the original Golden Rice (light gold), and Golden Rice 2 (dark gold) 97

12.10 CONNECTION: Gene therapy may someday help treat a variety of diseases
Gene therapy is an alteration of an afflicted individual’s genes and attempt to treat disease. Gene therapy may be best used to treat disorders traceable to a single defective gene. Student Misconceptions and Concerns 1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms. 2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students. Teaching Tips 1. In 2008, the Genetic Information Nondiscrimination Act (GINA) was signed into law. The following link to a related US government web site characterizes the effect of the act as follows. GINA “… prohibits U.S. insurance companies and employers from discriminating on the basis of information derived from genetic tests.” The web site can be found at 2. As gene therapy technology expands, our ability to modify the genome in human embryos through in vitro fertilization permits genetic modification at the earliest stages of life. Future generations of humans, like our crops today, may include those with and without a genetically modified ancestry. The benefits and challenges of these technologies raise issues many students have never considered. Our students, and the generations soon to follow, will face the potential of directed human evolution. © 2012 Pearson Education, Inc. 98

human gene inserts into the cell’s chromosome.
Figure 12.10 Cloned gene (normal allele) 1 An RNA version of a normal human gene is inserted into a retrovirus. RNA genome of virus Retrovirus 2 Bone marrow cells are infected with the virus. 3 Viral DNA carrying the human gene inserts into the cell’s chromosome. Figure One type of gene therapy procedure Bone marrow cell from the patient 4 The engineered cells are injected into the patient. Bone marrow 99

12.11 The analysis of genetic markers can produce a DNA profile
Student Misconceptions and Concerns Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete. Teaching Tips Figure describes the general steps of DNA profiling. This overview is a useful reference to employ while the details of each step are discussed. 12.11 The analysis of genetic markers can produce a DNA profile DNA profiling is the analysis of DNA fragments to determine whether they come from the same individual. DNA profiling compares genetic markers from noncoding regions that show variation between individuals and involves amplifying (copying) of markers for analysis. © 2012 Pearson Education, Inc. 101

Crime scene Suspect 1 Suspect 2 DNA is isolated. The DNA of selected
Figure 12.11 Crime scene Suspect 1 Suspect 2 1 DNA is isolated. 2 The DNA of selected markers is amplified. Figure An overview of DNA profiling 3 The amplified DNA is compared. 102

12.12 The PCR method is used to amplify DNA sequences
Polymerase chain reaction (PCR) is a method of amplifying a specific segment of a DNA molecule. PCR relies upon a pair of primers that are short, chemically synthesized, single-stranded DNA molecules, and complementary to sequences at each end of the target sequence. PCR is a three-step cycle that doubles the amount of DNA in each turn of the cycle. Student Misconceptions and Concerns 1. Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete. 2. Students might expect DNA profiling for criminal investigations to involve an analysis of the entire human genome. Consider explaining why such an analysis is unrealistic and unnecessary. Modules 12.12–12.16 describe methods used to describe specific portions of the genome of particular interest. Teaching Tips In PCR, the product becomes another master copy. Imagine that while you are photocopying, every copy is used as a master at another copy machine. This would require many copy machines. However, it would be very productive! © 2012 Pearson Education, Inc. 103

PCR cycle (~30 cycles) Denaturation step (strand separation): 95C Annealing step (primer binding): 50-65C DNA synthesis step: 72C Limitation: Error-prone DNA synthesis due to weak proof-reading function of thermostable polymerases 장점: 매우 적은 양의 DNA 로부터 gene cloning 가능

yields eight molecules
Figure 12.12 Cycle 1 yields two molecules Cycle 2 yields four molecules Cycle 3 yields eight molecules Genomic DNA 3 5 3 5 3 5 5 5 3 1 Heat separates DNA strands. 2 Primers bond with ends of target sequences. 3 DNA polymerase adds nucleotides. 3 5 5 3 Target sequence 5 3 5 5 3 5 3 5 3 Figure DNA amplification by PCR Primer New DNA 105

Cycle 1 yields two molecules Genomic DNA 3 5 3 5 3 5 5 5 3
Figure 12.12_1 Cycle 1 yields two molecules Genomic DNA 3 5 3 5 3 5 5 5 3 1 Heat separates DNA strands. 2 Primers bond with ends of target sequences. 3 DNA polymerase adds nucleotides. 3 5 5 3 Target sequence Figure 12.12_1 DNA amplification by PCR (part 1) 5 3 5 5 3 5 3 5 3 Primer New DNA 106

yields eight molecules
Figure 12.12_2 Cycle 2 yields four molecules Cycle 3 yields eight molecules Figure 12.12_2 DNA amplification by PCR (part 2) 107

12.12 The PCR method is used to amplify DNA sequences
The advantages of PCR include the ability to amplify DNA from a small sample, obtaining results rapidly, and a reaction that is highly sensitive, copying only the target sequence. Student Misconceptions and Concerns 1. Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete. 2. Students might expect DNA profiling for criminal investigations to involve an analysis of the entire human genome. Consider explaining why such an analysis is unrealistic and unnecessary. Modules 12.12–12.16 describe methods used to describe specific portions of the genome of particular interest. Teaching Tips In PCR, the product becomes another master copy. Imagine that while you are photocopying, every copy is used as a master at another copy machine. This would require many copy machines. However, it would be very productive! © 2012 Pearson Education, Inc. 108

12.14 STR analysis is commonly used for DNA profiling
Repetitive DNA consists of nucleotide sequences that are present in multiple copies in the genome. Short tandem repeats (STRs) are short nucleotide sequences that are repeated in tandem, composed of different numbers of repeating units in individuals and used in DNA profiling. STR analysis compares the lengths of STR sequences at specific sites in the genome and typically analyzes 13 different STR sites. Student Misconceptions and Concerns 1. Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete. 2. Students might expect DNA profiling for criminal investigations to involve an analysis of the entire human genome. Consider explaining why such an analysis is unrealistic and unnecessary. Modules 12.12–12.16 describe methods used to describe specific portions of the genome of particular interest. Teaching Tips In most legal cases, the probability of two people having identical DNA profiles can be one in 10 billion or more. However, eyewitness testimony has been a standard part of the justice system. If you want to make the point about the unreliability of eyewitnesses in a trial, compared to techniques such as genetic profiling, consider this exercise. Arrange for a person who is not well known to the class to run into your classroom, take something you have placed near you (perhaps a bag, stack of papers, or box), and leave quickly. You need to take care that no one in the class is so alarmed as to do something dangerous. Once the “thief” is gone, tell the class that this was planned and do not speak. Have them each write a description of the person, including height, hair color, clothing, facial hair, behavior, etc. Many students will be accurate, but some will likely get details wrong. This is also an effective exercise to demonstrate the need for large sample sizes and accurate recording devices for good scientific technique. © 2012 Pearson Education, Inc. 109

The number of short tandem repeats do not match
Figure 12.14A STR site 1 STR site 2 Crime scene DNA The number of short tandem repeats match The number of short tandem repeats do not match Figure 12.14A Two representative STR sites from crime scene DNA samples Suspect’s DNA 110

Crime Suspect’s scene DNA DNA Longer STR fragments
Figure 12.14B Crime scene DNA Suspect’s DNA Longer STR fragments Figure 12.14B DNA profiles generated from the STRs in Figure 12.14A Shorter STR fragments 111

12.17 Genomics is the scientific study of whole genomes
Genomics is the study of an organism’s complete set of genes Student Misconceptions and Concerns The similarities in genotypes and phenotypes among members of a human family are expected and understood by most students. Yet many students have a difficult time extrapolating this knowledge and applying it to the phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool for modern systematics and genomics provides significant support for the other types of evidence for evolution. Teaching Tips The first targets of genomics were prokaryotic pathogenic organisms. Consider asking your students in class to suggest why this was a good choice. Students may note that the genomes of these organisms are smaller than eukaryotes and that many of these organisms are of great medical significance. © 2012 Pearson Education, Inc. 113

Exons (regions of genes coding for protein
Figure 12.18 Exons (regions of genes coding for protein or giving rise to rRNA or tRNA) (1.5%) Introns and regulatory sequences (24%) Repetitive DNA that includes transposable elements and related sequences (44%) Unique noncoding DNA (15%) Figure Composition of the human genome Repetitive DNA unrelated to transposable elements (15%) 114

Transposon (jumping gene)
DNA segment that can move from one location to another Discovered by Barbara McClintock in 1940s Transposons are present in both eukaryotic and prokaryotic genomes Transposition can lead to inactivation of a gene Transposase gene Repeated sequence

Transposon Cut-and-paste transposon Copy-and-paste transposon transposon transition

12.20 Proteomics is the scientific study of the full set of proteins encoded by a genome
Proteomics is the study of the full protein sets encoded by genomes and investigates protein functions and interactions. Student Misconceptions and Concerns The similarities in genotypes and phenotypes among members of a human family are expected and understood by most students. Yet many students have a difficult time extrapolating this knowledge and applying it to the phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool for modern systematics and genomics provides significant support of the other types of evidence for evolution. Teaching Tips 1. Challenge students to explain why a complete understanding of an organism’s genome and proteomes is still not enough to understand the full biology of an organism. Ask them to consider the role of the environment in development and physiology. (One striking example of the influence of the environment is that the sex of some reptiles is determined not by the inheritance of certain chromosomes, but by incubation temperature.) 2. Students may enter your course with little appreciation of the scientific questions that remain unanswered. Struggling with the details of what we now know can overwhelm our students, leaving little room to wonder about what is not yet understood. The surprises and questions noted in Modules 12.18–12.21 reveal broad challenges that await the work of our next generation of scientists. Emphasize the many opportunities that exist to resolve unanswered questions, here and throughout your course, as an invitation to future adventures for students. © 2012 Pearson Education, Inc. 117

How Genes Are Controlled

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