Name: _____________________________________________________________ Period: _____

6.B Gene Changes & Regulation:

slides / vocab
Created for Bloomington HS South by Kirstin Milks (kirstinmilks.com).
Teachers: see the documents for the whole year here.

Table of contents (click to go to the heading)

Table of contents (click to go to the heading) 1
Unit 6.B guiding questions 1
6.5: Regulation of Gene Expression 2
6.6: Gene expression and cell specialization 4
6.7: Mutations 6
6.8: Biotechnology 9
Preparing for the AP Exam for Unit 6.B 13

Unit 6.B guiding questions

1. How is a species’s genetic information diversified from

generation to generation?
2. What mechanisms allow cell specialization and/or response
to changing environments?
3. ACTION: How can we use our knowledge of biology to
build useful, equitable molecular technologies?
6.5: Regulation of Gene Expression

SCIENCE SKILLS: Argumentation 6.A Make a scientific claim

IST-2.A Describe the types of interactions that regulate gene expression.

● IST-2.A.1 Regulatory sequences are stretches of DNA that interact with regulatory proteins to
control transcription.
● IST-2.A.2 Epigenetic changes can affect gene expression through reversible modifications of
DNA or histones.
● IST-2.A.3 The phenotype of a cell or organism is determined by the combination of genes that are
expressed and the levels at which they are expressed—
○ a. Observable cell differentiation results from the expression of genes for tissue-specific
proteins.
○ b. Induction of transcription factors during development results in sequential gene
expression.

IST-2.B Explain how the location of regulatory sequences relates to their function.
● IST-2.B.1 Both prokaryotes and eukaryotes have groups of genes that are coordinately
regulated—
○ a. In prokaryotes, groups of genes called operons are transcribed in a single mRNA
molecule. The lac operon is an example of an inducible system.

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 ○ b. In eukaryotes, groups of genes may be influenced by the same transcription factors to
coordinately regulate expression.

In class: HW:
- Review the feedback POGIL from earlier (can’t - (6.many) Notes on Unit 6B: Gene Changes &
legally post) Regulation
- Control of gene expression in prokaryotes
POGIL (can’t legally post)
- Modeling the Regulatory Switches of the PITX1
Gene (I’M BRINGING STICKLE-BACK) (YEAH)

VOCAB TO USE: regulatory switches, regulatory proteins, epigenetic changes, histones, transcription
factors, differentiation, operon, inducible, lac

YOU NEED TO PRACTICE:

Lactose digestion in E. coli begins with its hydrolysis by the enzyme β-galactosidase. The gene encoding
β-galactosidase, lacZ, is part of a coordinately regulated operon containing other genes required for lactose
utilization.

Which of the figures correctly depicts the interactions at

the lac operon when lactose is NOT being utilized?
(The legend defines the shapes of the molecules
illustrated in the options.)

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 The Trp operon is a coordinately regulated
group of genes (trpA–trpE) that are required
for tryptophan biosynthesis in E. coli. Based
on the figure above, which of the following
correctly describes the regulation of the Trp
operon?

A. In the absence of tryptophan, the

repressor is active and binds to the Trp
operator, preventing RNA polymerase from
transcribing the operon.
B. In the presence of tryptophan, the
repressor is active and binds to the Trp
operator, preventing RNA polymerase from
transcribing the operon.
C. In the absence of tryptophan, the trpR
gene is inactive, preventing the production of
the repressor that blocks expression of the
operon.
D. In the presence of tryptophan, the
trpR gene is inactive, preventing the
production of
the repressor that blocks expression of the operon.

6.6: Gene expression and cell specialization

SCIENCE SKILLS: Argumentation 6.B Support a claim with evidence from biological principles,
concepts, processes, and/or data.

IST-2.C Explain how the binding of transcription factors to promoter regions affects gene
expression and/or the phenotype of the organism.
● IST-2.C.1 Promoters are DNA sequences upstream of the transcription start site where RNA
polymerase and transcription factors bind to initiate transcription.
● IST-2.C.2 Negative regulatory molecules inhibit gene expression by binding to DNA and blocking
transcription.

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IST-2.D Explain the connection between the regulation of gene expression and phenotypic
differences in cells and organisms.
● IST-2.D.1 Gene regulation results in differential gene expression and influences cell products and
function.
● IST-2.D.2 Certain small RNA molecules have roles in regulating gene expression.

In class: HW:
- Modeling the Regulatory Switches of the PITX1 - finish the stickleback assignment :)
Gene

VOCAB TO USE: transcription factors, promoters, RNA polymerase, differential gene expression,
switches

YOU NEED TO PRACTICE

The p53 protein regulates a cellular response to DNA
damage. Based on the diagram at left, which of the following
best describes the role of p53 in the response to DNA
damage?

A. Phosphorylated p53 binds to DNA and repairs the

damage.
B. Phosphorylated p53 stimulates transcription of p21,
and the resulting p21 protein suppresses cell division until the
DNA damage is repaired.
C. Phosphorylated p53 binds cyclin−Cdk complexes,
and the resulting protein complex repairs the DNA damage.
D. Phosphorylated p53 activates p21 proteins, and the
p21 proteins in turn repair the DNA damage.

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Gibberellic acid stimulates the cells of germinating grass seeds to produce mRNA molecules that code
for hydrolytic enzymes. In this case the role of gibberellic acid can best be described as that of

A. a regulator of gene activity

B. a stimulator of hydrolase secretion
C. a stimulator of DNA replication
D. an allosteric activator of hydrolase
E. an activator of translation

6.7: Mutations

SCIENCE SKILLS: Visual Representations 2.C Explain how biological concepts or processes
represented visually relate to larger biological principles, concepts, processes, or theories.
Questions and Methods 3.D Make observations or collect data from representations of
laboratory setups or results.

IST-2.E Describe the various types of mutation.

● IST-2.E.1 Changes in genotype can result in changes in phenotype—
○ a. The function and amount of gene products determine the phenotype of organisms.
■ i. The normal function of the genes and gene products collectively comprises the
normal function of organisms.
■ ii. Disruptions in genes and gene products cause new phenotypes.
● IST-2.E.2 Alterations in a DNA sequence can lead to changes in the type or amount of the protein
produced and the consequent phenotype. DNA mutations can be positive, negative, or neutral
based on the effect or the lack of effect they have on the resulting nucleic acid or protein and the
phenotypes that are conferred by the protein.

IST-4.A Explain how changes in genotype may result in changes in phenotype.

● IST-4.A.1 Errors in DNA replication or DNA repair mechanisms, and external factors, including
radiation and reactive chemicals, can cause random mutations in the DNA—
○ a. Whether a mutation is detrimental, beneficial, or neutral depends on the environmental
context.
○ b. Mutations are the primary source of genetic variation.
● IST-4.A.2 Errors in mitosis or meiosis can result in changes in phenotype—
○ a. Changes in chromosome number often result in new phenotypes, including sterility
caused by triploidy, and increased vigor of other polyploids.
○ b. Changes in chromosome number often result in human disorders with developmental
limitations, including Down syndrome/ Trisomy 21 and Turner syndrome.

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IST-4.B Explain how alterations in DNA sequences contribute to variation that can be subject to
natural selection.
● IST-4.B.1 Changes in genotype may affect phenotypes that are subject to natural selection.
Genetic changes that enhance survival and reproduction can be selected for by environmental
conditions—
○ a. The horizontal acquisitions of genetic information primarily in prokaryotes via
transformation (uptake of naked DNA), transduction (viral transmission of genetic
information), conjugation (cell-to-cell transfer of DNA), and transposition (movement of
DNA segments within and between DNA molecules) increase variation.
○ b. Related viruses can combine/recombine genetic information if they infect the same host
cell.
○ c. Reproduction processes that increase genetic variation are evolutionarily conserved
and are shared by various organisms.

In class: HW:
- The Impact of Mutations (a.k.a. THE BELGIAN - finish The Impact of Mutations (a.k.a. THE
BLUE MOUND OF BEEF) BELGIAN BLUE MOUND OF BEEF)
- Modeling the rise of antibiotic resistance - Molecular genetics of the color mutations in rock
(and, if time, Origins of antibiotic resistance) pocket mice
- (6.many) Notes on Unit 6B: Gene Changes &
Regulation

VOCAB TO USE: genotype, phenotype, mutation, mitosis, meiosis, polyploidy, natural selection,
transformation, transduction, conjugation, transposition

YOU NEED TO PRACTICE

Methicillin-resistant Staphylococcus aureus (MRSA) can be a serious threat to human health. There is
evidence that S. aureus infections are common in hospitals and that MRSA have become resistant to other
antibiotics besides methicillin. This suggests that the rapid evolution of resistance in the bacteria poses a
serious public-health challenge. Which of the following best explains the ability of MRSA to evade existing
drug therapies?

A. MRSA have very long generation times and very large population sizes.
B. MRSA develop new alleles by intentionally introducing specific mutations that will give them a
selective advantage over other bacteria.
C. MRSA metabolize many drugs in their lysosomes and therefore evolve resistance at a high rate.
D. MRSA exchange genetic material with other antibiotic-resistant bacteria, which can spread resistance
in the S. aureus population.

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Sickle-cell anemia results from a point mutation in the HBB gene. The mutation results in the replacement of
an amino acid that has a hydrophilic R-group with an amino acid that has a hydrophobic R-group on the
exterior of the hemoglobin protein. Such a mutation would most likely result in altered

A. properties of the molecule as a result of abnormal interactions between adjacent hemoglobin

molecules
B. DNA structure as a result of abnormal hydrogen bonding between nitrogenous bases
C. fatty acid structure as a result of changes in ionic interactions between adjacent fatty acid chains
D. protein secondary structure as a result of abnormal hydrophobic interactions between R-groups in the
backbone of the protein

Figure 1. Percent survival of five strains of bedbugs treated with beta-cyfluthrin. A (+) indicates the gene is
present; a (−) indicates the gene is deleted. Error bars represent the 95% confidence interval.

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The common bedbug (Cimex lectularius) is a species of insect that is becoming increasingly resistant to
insecticides. Bedbugs possess several genes suspected of contributing to the resistance, including P450,
Abc8, and Cps. To investigate the role of these genes in insecticide resistance, researchers deleted one or
more of these genes in different strains of bedbugs, as indicated in Figure 1, and treated the strains with the
insecticide beta-cyfluthrin. Each strain was genetically identical except for the deleted gene(s) and was
equally fit in the absence of beta-cyfluthrin. The percent survival of each strain following beta-cyfluthrin
treatment is shown in Figure 1.

P450 encodes an enzyme that detoxifies insecticides. Abc8 encodes a transporter protein that pumps
insecticides out of cells. Cps encodes an external structural protein located in the exoskeleton that greatly
reduces the absorption of insecticides. Based on this information and the data in Figure 1, explain how a
deletion of both P450 and Abc8 results in lower survival in bedbugs compared with a deletion of Cps only.

6.8: Biotechnology

SCIENCE SKILLS: Argumentation 6.D Explain the relationship between experimental results
and larger biological concepts, processes, or theories.

IST-1.P Explain the use of genetic engineering techniques in analyzing or manipulating DNA.
● IST-1.P.1 Genetic engineering techniques can be used to analyze and manipulate DNA and
RNA—
○ a. Electrophoresis separates molecules according to size and charge.
○ b. During polymerase chain reaction (PCR), DNA fragments are amplified.
○ c. Bacterial transformation introduces DNA into bacterial cells.
○ d. DNA sequencing determines the order of nucleotides in a DNA molecule.
🆇 EXCLUSION STATEMENT—The details of these processes are beyond the scope of
this course. The focus should be on the conceptual understanding of the application of
these techniques.

In class: HW:
- Winging It: Analyzing a Scientific Paper

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 - Using CRISPR to Identify the Functions of - (6.many) Notes on Unit 6B: Gene Changes &
Butterfly Genes Regulation
(... we plan to do a transformation lab in Tri 3!) - Biotech showcase

VOCAB TO USE: electrophoresis, bands, polymerase chain reaction (PCR), bacterial transformation,
plasmid, antibiotic, CRISPR-Cas9, gene drive, DNA sequencing

YOU NEED TO PRACTICE

In a transformation experiment, a sample of E. coli bacteria was
mixed with a plasmid containing the gene for resistance to the
antibiotic ampicillin (ampr). Plasmid was not added to a second
sample. Samples were plated on nutrient agar plates, some of
which were supplemented with the antibiotic ampicillin. The results
of E. coli growth are summarized below. The shaded area
represents extensive growth of bacteria; dots represent individual
colonies of bacteria.

Plates I and III were included in the experimental design in order to

A. demonstrate that the E. coli cultures were viable

B. demonstrate that the plasmid can lose its ampr gene
C. demonstrate that the plasmid is needed for E. coli growth
D. prepare the E. coli for transformation

Plates that have only ampicillin-resistant bacteria growing include which of the following?

A. I only
B. III only
C. IV only
D. I and II

In a second experiment, the plasmid contained the gene for human insulin as well as the ampr gene. Which of
the plates shown would have the highest percentage of bacteria that are expected to produce insulin?

A. I only
B. III only
C. IV only

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 D. I and III

Samples of DNA were isolated from four different individuals and each sample was digested by the same
restriction enzymes. Gel electrophoresis was used to separate the resulting DNA fragments and the
results are shown above. These data best support which of the following hypotheses?

A. Individual 1 is the offspring of 2 and 3.

B. Individual 1 is the offspring of 3 and 4.
C. Individual 2 is the offspring of 1 and 3.
D. Individual 2 is the offspring of 1 and 4.
E. Individual 3 is the offspring of 1 and 4.

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Living and dead organisms continuously shed DNA fragments, known as eDNA, into the environment.
To detect eDNA fragments in the environment, the polymerase chain reaction (PCR) can be used to
amplify specific eDNA fragments. eDNA fragments of different lengths persist in the environment for
varying amounts of time before becoming undetectable (Figure 1).

To investigate whether silver carp, an invasive fish, have moved from a nearby river system into Lake
Michigan, researchers tested water samples for the presence of eDNA specific to silver carp (Figure 2).

Justify the use of eDNA sampling as an appropriate technique for detecting the presence of silver carp
in an environment where many different species of fish are found. Propose ONE advantage of
identifying long eDNA fragments as opposed to short fragments for detecting silver carp.

The researchers tested a large number of water samples from Lake Michigan and found eDNA specific to
silver carp in a single sample in the lake, as indicated in Figure 2. The researchers concluded that the single
positive sample was a false positive and that no silver carp had entered Lake Michigan. Provide reasoning
other than human error to support the researchers’ claim.

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Preparing for the AP Exam for Unit 6.B
● You should understand from the beginning of the school year that the location of a mutation in
the codon can affect the structure and function of a protein.
○ Common errors include stating that mutations result in the denaturation of a protein or that
point mutations cause frameshift mutations.
○ Students also tend to describe all mutations as having negative effects; I’ll exposure you
to examples of mutations that have no impact on phenotype to help prevent this
misunderstanding.

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