1. Chapter 11 How Genes Are Controlled
PowerPoint Lectures for
Campbell Biology: Concepts & Connections, Seventh Edition
Reece, Taylor, Simon, and Dickey
Lecture by Edward J. Zalisko
© 2012 Pearson Education, Inc.

2. CONTROL OF GENE EXPRESSION
© 2012 Pearson Education, Inc.

3. 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.

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

5. With few exceptions, operons only exist in prokaryotes.
A cluster of genes with related functions, along with the control sequences, is called an operon.
With few exceptions, operons only exist in prokaryotes.
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. The lactose (lac) operon includes
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.

7. 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. Operon turned off (lactose is absent): OPERON Regulatory gene
Figure 11.1B_1
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
Figure 11.1B_1 The lac operon (part 1)

9. Operon turned on (lactose inactivates the repressor):
Figure 11.1B_2
Operon turned on (lactose inactivates the repressor):
DNA
RNA polymerase is bound to the promoter
mRNA
Translation
Protein
Figure 11.1B_2 The lac operon (part 2)
Inactive repressor
Lactose
Enzymes for lactose utilization

10. 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. 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

12. Activators help control a wide variety of operons.
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.

13. 11.2 Chromosome structure and chemical modifications can affect gene expression
Differentiation
involves cell specialization, in structure and function, and
is controlled by turning specific sets of genes on or off.
Almost all of the cells in an organism contain an identical genome.
The differences between cell types are
not due to the presence of different genes but instead
due to selective 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.

14. 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.

15. 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.

16. Chemical modification of DNA bases or histone proteins can result in epigenetic inheritance.
Certain enzymes can add a methyl group to DNA bases, without changing the sequence of the bases.
Individual genes are usually more methylated in cells in which the genes are not expressed. Once methylated, genes usually stay that way through successive cell divisions in an individual.
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.

17. Removal of the extra methyl groups can turn on some of these genes.
Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance. These modifications can be reversed by processes not yet fully understood.
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. 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.
Inactivation occurs early in embryonic development, and all cellular descendants have the same inactivated chromosome.
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.

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

20. 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.

21. 11.5 Small RNAs play multiple roles in controlling gene expression
Only about 1.5% of the human genome codes for proteins. (This is also true of many other multicellular eukaryotes.)
Another small fraction of DNA consists of genes for ribosomal RNA and transfer RNA.
A flood of recent data suggests that a significant amount of the remaining genome is transcribed into functioning but non-protein-coding RNAs, including a variety of small RNAs.
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.

22. 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.

23. 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.

24. 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.

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

26. 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.

27. Root cells cultured in growth medium Cell division in culture Plantlet
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

28. 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.

29. 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.

30. The nucleus is removed from an egg cell.
Figure 11.13_1
Donor cell
Nucleus from
the donor cell
Blastocyst
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).
Figure 11.13_1 Nuclear transplantation for cloning (part 1)

31. The blastocyst is implanted in a surrogate mother.
Figure 11.13_2
Reproductive cloning
Blastocyst
The blastocyst is implanted in a surrogate mother.
A clone of the donor is born.
Therapeutic cloning
Figure 11.13_2 Nuclear transplantation for cloning (part 2)
Embryonic stem cells are removed from the blastocyst and grown in culture.
The stem cells are induced to form specialized cells.

32. 11.14 CONNECTION: Reproductive cloning has valuable applications, but human reproductive cloning raises ethical issues
Since Dolly’s landmark birth in 1997, researchers have cloned many other mammals, including mice, cats, horses, cows, mules, pigs, rabbits, ferrets, and dogs.
Cloned animals can show differences in anatomy and behavior due to
environmental influences and
random phenomena.
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. Students might not immediately understand why reproductive cloning is necessary to transmit specific traits in farm animals. They may fail to realize that unlike cloning, sexual reproduction mixes the genetic material and may not produce offspring with the desired trait(s).
2. The transplantation of pig or other nonhuman tissues into humans (called xenotransplantation) risks the introduction of pig (or other animal) viruses into humans. This viral DNA might not otherwise have the capacity for transmission to humans.
3. 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.

33. 11.14 CONNECTION: Reproductive cloning has valuable applications, but human reproductive cloning raises ethical issues
Reproductive cloning is used to produce animals with desirable traits to
produce better agricultural products,
produce therapeutic agents, and
restock populations of endangered animals.
Human reproductive cloning raises many ethical concerns.
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. Students might not immediately understand why reproductive cloning is necessary to transmit specific traits in farm animals. They may fail to realize that unlike cloning, sexual reproduction mixes the genetic material and may not produce offspring with the desired trait(s).
2. The transplantation of pig or other nonhuman tissues into humans (called xenotransplantation) risks the introduction of pig (or other animal) viruses into humans. This viral DNA might not otherwise have the capacity for transmission to humans.
3. 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.

34. Figure 11.14
Figure CC, the world’s first cloned cat (right), and her lone parent (left)

35. 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.

36. 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.

37. Adult stem cells in bone marrow
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