Biology Today and Tomorrow without Physiology 5th

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7
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GENE EXPRESSION AND CONTROL

Chapter Outline
7.1 RICIN RIP 7.8 CONTROL OF GENE EXPRESSION
7.2 GENE EXPRESSION Master Genes
7.3 TRANSCRIPTION: DNA TO RNA Sex Chromosome Genes
RNA Modifications Lactose Tolerance
7.4 THE GENETIC CODE DNA Methylation
7.5 TRANSLATION: RNA TO PROTEIN SUMMARY
7.6 PRODUCTS OF MUTATED GENES SELF-QUIZ

Chapter Seven
CRITICAL THINKING VISUAL QUESTION

Learning Objectives
7.1 Describe ribosome inactivating proteins (RIPs) and explain their toxic effects.
7.2 Explain the multistep process of gene expression.
7.3 Using a flowchart, explain the process of transcription.
7.4 Describe the significance of the genetic code for protein synthesis.
7.5 Explain the process of translation of mRNA into protein.
7.6 Discuss the negative consequences of genetic mutations.
7.7 Discuss the factors that govern gene expression in eukaryotic cells.

Key Terms
anticodon gene expression ribosomal RNA (rRNA)
Barr body genetic code RNA polymerase
base-pair substitution insertion translation
codon introns transcription
deletion knockout transcription factor
epigenetics master gene transfer RNA (tRNA)
exons messenger RNA (mRNA)
gene promoter

Lecture Outline
7.1 Ricin, RIP
A. Ricin is a powerful natural toxin produced in castor-oil plants.
B. It has long been used as a poison because of how lethal it is in very small doses.
C. Ricin blocks the action of ribosomes, disrupting a cell’s ability to manufacture proteins.
D. People who inhale ricin typically die in three days from low blood pressure and respiratory
failure.

7.2 Gene Expression

A. The DNA sequence of a gene encodes (contains instructions for building) an RNA or protein
product.
B. A chromosome region that encodes an RNA or protein product is called a gene.
1. Genes are used to code for RNA sequences through a process called transcription.
2. During transcription, enzymes read DNA as a template to create new RNA.
a. Since RNA is based on only one gene, RNA is much smaller than DNA molecules.
C. DNA and RNA are different in several ways.
1. DNA is double stranded, RNA is single stranded.
2. DNA has a deoxyribose sugar base, while RNA has a ribose sugar base.
3. In RNA, the nucleotide U-uracil is substituted for T-thymine.
D. RNA is used to create new proteins.
1. Genes are converted into mRNA (messenger RNA), which is used to create proteins in a
process called translation.

Gene Expression and Control

 2. mRNA dictates a sequence of amino acids based on a genetic code that is processed during
translation.
E. The processes of transcription and translation are part of gene expression, the process of
creating new proteins from DNA.

7.3 Transcription: DNA to RNA

A. During transcription, DNA acts as a template for the production of RNA.
1. Conversion of DNA into RNA is similar to DNA replication.
2. The base pairing is similar with the exception that uracil replaces thymine.
3. C pairs with G; G pairs with C; T pairs with A; and A pairs with U.
4. New RNA strands are complementary to DNA strands.
5. Each nucleotide provides the energy for its own attachment.
6. Unlike DNA replication, transcription involves copying only certain genes.
7. RNA polymerase is the enzyme that catalyzes transcription.
8. The result is a single strand of RNA.
B. The process of transcription.
1. Transcription occurs in the nucleus of eukaryotic cells.
2. Transcription initiates when RNA polymerase binds to a gene’s promoter.
3. RNA polymerase reads the gene and adds nucleotides to the growing RNA transcript.
4. When the polymerase reaches the end of the gene, the RNA transcript is released.
5. Typically, many transcripts of the same gene are made at the same time.
6. RNA is modified by excising introns and splicing together exons (coding regions).

7.4 The Genetic Code

A. mRNA and the genetic code.
1. mRNA is a disposable copy of a gene.
2. mRNA carries the genetic code for a protein to a ribosome.
3. Each genetic “word” consists of three letters, one codon.
4. With 4 possible bases in each of the 3 positions of a codon, there are 64 possible codons.
5. Collectively, the 64 codons represent the genetic code; the codons determine the sequence
of amino acids in the growing protein.
6. There are 20 amino acids; 64 codons represent redundancy in the code.
7. AUG is a start codon, and there are 3 stop codons.
8. The genetic code is highly conserved; there is little variation between organisms, with a few
exceptions in bacteria and mitochondria/chloroplasts.
B. rRNA and tRNA—the translators.
1. Ribosomes and tRNA (transfer RNA) interact to translate mRNA.
a. Each ribosome has a large and small subunit.
2. rRNA (ribosomal RNA) is a main component of ribosomal subunits.
3. During translation:
a. A small and large ribosomal subunit surrounds an intact mRNA strand.
b. tRNAs deliver amino acids to the ribosome by binding to the mRNA codon with the
tRNA anticodon.
c. As this process continues, tRNAs continue bringing new amino acids to the mRNA in
sequence, and as the mRNA is read, the peptide grows.
d. The elongation continues until the ribosome matches up with a stop codon; at that
point, the ribosome falls off of the mRNA, and the process is terminated.
4. rRNA has enzymatic properties; the rRNA is responsible for forming the peptide bond.

Chapter Seven
7.5 Translating the Code: RNA to Protein
A. Translation occurs in the cytoplasm.
1. The small ribosomal subunit binds to mRNA.
2. The initiator tRNA binds to the first AUG codon on the mRNA.
3. This causes the large ribosomal subunit to bind to the mRNA.
4. The ribosome assembles the polypeptide as the mRNA moves through the ribosome.
5. The initiator tRNA carries the amino acid methionine; another tRNA matches with the
second codon.
6. The ribosome joins the two amino acids by forming a peptide bond between them.
7. The first tRNA is released, and the ribosome moves onto the next codon.
8. A new tRNA brings in new amino acids; the ribosome forms a peptide bond.
9. This process continues along the mRNA until termination.
10. Termination occurs when the ribosome reaches a stop codon: UAA, UAG, or UGA.
11. No tRNA matches up with the stop codons, so the ribosome falls off of the mRNA.

7.6 Products of Mutated Genes

A. Mutations are changes in the DNA sequence.
B. If a mutation occurs in a gene-encoding region of DNA, it could result in an altered gene
product.
1. More than one codon sometimes codes for the same amino acid; some changes are minor.
C. A mutation in hemoglobin provides a good example of how a mutation can alter the function
of a protein.
1. Hemoglobin binds to oxygen and releases it at tissues.
2. Hemoglobin consists of four protein chains (2 alpha and 2 beta) and a heme group
(containing iron). Oxygen binds around the heme.
3. Changes in the protein can cause anemia, a state of decreased oxygen-binding potential.
4. A deletion mutation occurs when one or more nucleotides are removed from a gene.
a. One type of deletion causes thalassemia, a type of anemia.
b. Deletions cause a shift in the reading frame of the codons, which can change the
message after the deletion.
5. Frameshifts can also occur because of insertions of one or more nucleotides.
6. Base-pair substitutions occur when one or a few bases get replaced incorrectly, but the
overall number of nucleotides in the gene remains intact.
a. Sickle-cell anemia is caused by single-point substitution; the sixth amino acid becomes
valine instead of glutamic acid.
b. The change causes the beta chains to become sticky and clump together, forming the
red blood cell into a sickle shape.
c. The sickling blocks small blood vessels, disrupting circulation.
D. Mutations can be caused by many factors.
1. Insertions can be caused by transposable elements, segments of DNA that can insert
themselves into a chromosome. About 45% of human DNA consists of transposable
elements.
2. Mutations occur during DNA replication; DNA polymerase works rapidly and corrects
many mistakes. Those mistakes that remain are mutations.
3. Harmful environmental agents called mutagens can cause mutations. Examples are
ionizing radiation, free radicals, UV light, and natural and non-natural chemicals.

Gene Expression and Control

7.7 Control of Gene Expression
A. All cells contain the same DNA, yet each cell can become different and produce different
proteins at different times.
B. Differentiation is the process by which all cells become specialized, and it is mainly caused by
the activation of certain genes within a line of cells.
1. Which gene becomes activated defines which protein a cell produces.
2. Cells rarely use less than 10% of their genes at a given time.
3. Which genes are turned on is controlled by conditions in the cell and cytoplasm and the
type of cell.
4. Factors exist that can control the entire process of protein formation that can start, enhance,
slow, or stop gene expression. These proteins are called transcription factors.
C. Master genes.
1. Master genes affect the expression of many other genes.
2. Master genes cause cells to differentiate and specialize.
3. Homeotic genes regulate the formation of certain body parts.
4. Homeotic genes are one type of master gene, in that their expression affects many other
genes.
a. Many homeotic genes are known because of gene knockout studies where the gene
function has been removed and the resultant effect studied.
5. Homeotic genes are expressed during embryonic development, and their expression drives
the fundamental layout of the human body plan.
a. Homeotic control is often exerted in a gradient, where the direction of the gradient
determines how development will occur.
b. Homeodomains are fairly conserved in many species, a result of common ancestry.
D. Sex chromosome genes.
1. In humans, females have two X chromosomes while males have an X and a Y.
2. In females, one of the X chromosomes is tightly wound (Barr Bodies) and cannot be
accessed by the RNA polymerase.
a. The theory of dosage compensation explains that this probably prevents over-
expression of X chromosome genes in females.
3. The X chromosome contains 1,336 genes, most of which are not related to sexual traits.
4. The Y chromosome carries 307 genes.
a. SRY is the master gene for male sex determination.
b. Expression of SRY in an XY embryo leads to development of testes.
E. Lactose tolerance.
1. Most humans stop digesting lactose at age five, when gene transcription for lactase slows.
2. A mutation allows for about 1/3 of the human population to still digest lactose into
adulthood.
F. DNA methylation
1. Methylation continues through cell duplication unless the methyl group is removed by an
enzyme.
2. Various environmental factors can cause methylation or demethylation, which has impacts
on a cell’s activity.

Suggestions for Presenting the Material

Chapter Seven
  The content in this chapter builds on itself, and on content from chapter 6. Include
learning checkpoints for this material to keep students from getting lost. This can be a
dense chapter, especially for a student that gets behind.
 Construct physical models of DNA and RNA. The importance of the model of DNA, for
example, is that its simplicity defines its function.
 This may sound silly, but it is very effective: Use role playing to demonstrate what
happens during transcription and translation. Have students be all the major players:
DNA nucleotides, RNA polymerase, mRNA, tRNA, rRNA, and ribosomes. Engage the
students in the process, but also stop along the way to define roles and explain exactly
what is happening.
 Give the students several examples of DNA genes that they can transcribe and translate.
Start with a worked example that shows them the right answer. Then complete an
example with them. Then give them more freedom to complete the process on their
own.
 There are several good videos and tutorials out there that demonstrate transcription and
translation. Be careful which ones you select, though. Some work through the process
too rapidly to be effective. Choose materials that are more flexible; that is, those offering
controls that allow you to stop the animation and go back over the same steps again.
 The simplest and classic example of gene expression is the lac operon in E. coli. There are
many great resources for this prokaryotic system. The system has simple yet elegant
control based on the amount of carbohydrate in the environment.
 The text offers several examples of homeotic regulators. Identify the work by which
these molecules were identified, and use the images from that work to demonstrate the
effect of control exerted by master genes.
 Use a metaphorical story to relate the concepts of transcription and translation to
students who may not be familiar with the subject. For example, have the students
imagine the DNA as a king or queen with a decree for their kingdom. The king or queen
would not deliver that message themselves, so they would summon their messengers
(RNA polymerase). The messengers, not wanting to get the message wrong, would write
(transcribe) the message into a portable format (mRNA). Then the message could be sent
to the rest of the kingdom. However, the king would probably give the message in Latin
while the villagers might only speak some vernacular. Someone would have to decode
the message (ribosome) so that the people could understand it.

Classroom and Laboratory Enrichment

 Have a microbiologist help you complete the lac operon conditions in your lab.
 Look at slides of homeotic gene studies.
 Have the students work with a simulation of transcription and translation. Again, make
sure the simulation is flexible enough so that the students can manipulate the process to
aid in their understanding.
 Complete many examples.

Gene Expression and Control

  Give students original genes and mutated forms of the genes; include as many types of
mutations as possible. Have the students work out how differently the mutated product
would be and the potential impacts.
 Have students prepare projects for presentation about different mutagens and their
effects on cells.

Impacts, Issues: Classroom Discussion Ideas

 Why is ricin so dangerous?
 How does ricin cause a problem for our cells?
 How should such a dangerous commodity like ricin (castor-oil plants) be controlled?
 What are the implications of epigenetics when it comes to developing gene therapies?

Additional Ideas for Classroom Discussion

 What are the similarities and differences between transcription and translation?
 Where are points where transcription and translation could be controlled?
 What would be the effect of a mutation in RNA? Why wouldn’t it be a lasting effect?
 Describe the steps of initiation, elongation, and termination.
 How does interaction with a ribosome promote translation?
 How do cells become different from one another through differentiation?
 How do homeotic genes control the development of an embryo?
 What would be the effect of mutations on homeotic genes?
 Why are homeotic genes so important?
 How can understanding mutations to homeotic genes help understanding both common
ancestry and morphological changes in evolution?
 What is the difference between genetic variation and mutation?
 Are all mutations essentially bad? What determines the effect of a mutation?
 The text talks about sickle-cell anemia as an example of a simple mutation that causes a
problem. Was there ever a time when that mutation was beneficial, and why might that
have been the case?
 Why is the Y chromosome so important for determining sex in an embryo?
 Why is it difficult to treat cancers by developing drugs that generically stop protein
synthesis?

Videos, Animations, and Websites

Videos
Molecular and Cell Biology Learning Center—Virtual Cell Animation Collection
An animated video of transcription.
http://vcell.ndsu.edu/animations/transcription/movie-flash.htm

Chapter Seven
An animated video of regulated transcription.
http://vcell.ndsu.edu/animations/regulatedtranscription/movie-flash.htm

An animated video of mRNA processing.

http://vcell.ndsu.edu/animations/mrnaprocessing/movie-flash.htm

An animated video of mRNA splicing.

http://vcell.ndsu.edu/animations/mrnasplicing/movie-flash.htm

An animated video of translation.

http://vcell.ndsu.edu/animations/translation/movie-flash.htm

Cold Spring Harbor Laboratory—DNA Learning Center

Video overview of master genes controlling basic body plans.
http://www.dnalc.org/view/16760-Animation-37-Master-genes-control-basic-body-plans-.html

The University of Utah—Genetic Science Learning Science

This animated videos details an example of protein synthesis in a firefly.
http://learn.genetics.utah.edu/content/begin/dna/firefly/

Animations
The University of Utah—Genetic Science Learning Science
This is an interactive animation on transcription and translation.
http://learn.genetics.utah.edu/content/begin/dna/transcribe/

Websites
Estrella Mountain Community College—Online Biology Book
An overview of protein synthesis.
http://www.emc.maricopa.edu/faculty/farabee/biobk/biobookprotsyn.html

How Would You Vote? Classroom Discussion Ideas

 Monitor the online vote.
 Ricin has the potential to be used as a widespread biological weapon. Would you be
willing to be vaccinated against Ricin?

Term Paper Topics, Library Activities, and Special Projects

 Describe the times in a transcription and translation process where outside molecules
could affect and control the process.
 Pick a dangerous molecule like ricin that affects transcription or translation, and
describe the process by which that molecule affects the process.

Gene Expression and Control

  Describe the benefits of redundancy in the genetic code.
 Describe the process by which steroid hormones control protein synthesis.
 Pick a homeotic gene: 1) describe its function, 2) describe how we know what its
function is, and 3) describe what may happen if it were to become mutated.
 Disorders like sickle-cell anemia involve mutations to a single gene. Genetic therapy has
been touted as having the power to help repair genes like this. Investigate gene therapy
or gene replacement. Describe what work has been done in that field and what the
potential of these therapies may be.
 Pick a mutagen and describe how it causes a mutation and what effect it has on cells.

Answers to Self-Quiz Questions

1. d. a and b 12. d. either a or b
2. c. transcription; translation 13. c. from a female mammal
3. a. single-stranded; double-stranded 14. true
4. b. carry a translatable message 15. c. transcription; a. mRNA processing;
5. a. nucleus d. RNA leaves nucleus; b. translation
6. a. 15
16. c. can be epigenetic; g. extra nucleotide;
7. c. amino acid
h. binding site for RNA polymerase; e.
8. d. b and c are correct
read in threes; a. cells become
9. d. a and b
specialized; f. makes a man out of you;
10. b. they use different genes
b. cascades of control; d. assembles
11. d. all of the above
amino acids

Possible Responses to Critical Thinking Questions

1. A tRNA with the anticodon GCG would carry the amino acid arginine. A substitution
mutation that changes the C to a G would cause that tRNA to carry proline.

Chapter Seven
2. The minimum number of nucleotides per codon needed to code for all 20 amino acids is
three. For example. If a codon only included one base, there would only be four variations
that could code for four amino acids. If there were two nucleotides per codon with four
options at each spot – four possibilities in the first spot, times four possibilities in the
second spot – it would equal only 16 possible variations, or 16 possible amino acids that
could be coded for. With three nucleotides per codon, there could be four possibilities in
the first spot, times four possibilities in the second spot, times four possibilities in the third
– equaling 64 possible variations. This provides redundancy in the code.
3. Gene expression is a complex issue. Genes can be expressed completely, not at all, or
partially in some tissues and not others. There are many reasons for this, including, but not
limited to: genetic factors such as transcription factors, RNA binding genes, and mRNAs,
plus epigenetic factors such as chromatin complexity and methylation pattern.
4. This hairpin loop causes the RNA polymerase to be unable to bind to the DNA effectively,
therefore terminating transcription.

Visual Question

1. GGU-GAA-AAU-GAG-ACC-AUU-UGU-AGU
G-E-N-E-T-I-C-S

2. G-GUG-AAA-AUG-AGA-CCA-UUU-GUA-GU
V-K-M-R-P-F-V

Gene Expression and Control