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Unit 4
Genetics
Chapters 13-20
All questions within each section of the Unit Study Guide will be due on the day of the unit
exam. Each section should be clearly labeled by section number and number of question for
complete points.
 4-1: Read 238—249
Meiosis
This is very important material, it sets the basis for both the why and how of many questions in
biology. The important figures are listed below.
 Fig 13.4 summarizes the all-important terms describing chromosomes.
 Somatic cells are any cells in the body that are not gametes. Somatic cells are diploid (2n)
meaning they have 2 sets of chromosomes (46).
 Gametes (sperm and egg) are haploid (n); they contain half the number of chromosomes of
somatic cells (23).
 One homologous chromosome from each pair is inherited from each parent; in other words, half
of the set of 46 chromosomes in your somatic cells was inherited from your mother, and the
other half was inherited from your father.
 Fig 13.5 summarizes terms associated with sexual reproduction, shows their relationship to one
another and places meiosis within that framework.
 Fig 13.6 is basically the same as 13.5. All that is being shown is that different kingdoms of
organisms place different emphasis in which part of the life cycle is the dominant (multicellular)
part of their lives.
1. In humans (and most animals), meiosis occurs during gamete production, and the diploid
zygote divides by mitosis to produce a diploid multicellular organisms.
2. In plants, and some algae, alternation of generations occurs, including a haploid and a
diploid stage in the life cycle. The diploid phase created haploid spores, which divided
mitotically to produce a gametophyte. The gametophyte produces haploid gametes
through mitosis, and the fertilization occurs, producing a diploid zygote that divides by
mitosis to produce a sporophyte.
3. In fungi, some protists, and algae, after gametes fuse to form the diploid zygote,
meiosis occurs to produce haploid cells. These cells then divide by mitosis, forming a
haploid, multicellular organism.
 Figures 13.7, 13.8, and 13.9 are the featured presentation. You must understand and remember
this material.
 Focus your understanding of meiosis on metaphase I. With this picture in your mind, and
understanding what meiosis is supposed to do, you can piece together the events leading to and
from metaphase I.
 The idea of independent assortment is introduced in Fig 13.10. You need to understand why it
happens:
– as related to events during meiosis (proximate cause) and
– as related to evolutionary (ultimate cause
 Fig 13.10 (Independent Assortment) and 13.11 (Crossing Over) are two sources of variation in a
population from sexual reproduction. A third source is random fertilization. (Another source of
variation comes from mutations which we discuss later.)
- Independent Assortment = In Metaphase I, homologous chromosomes line up randomly in
pairs on the metaphase plate; any combination can take place. These means that there is a
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50/50 chance that a particular daughter cell will get a maternal chromosome or a paternal
chromosome from the homologues.
- Crossing Over = During Prophase I, homologous chromosome synapse (“homologous huddle”)
and they exchange homologous parts of two non-sister chromatids. Then during metaphase
II, chromosomes that now have recombinant chromatids can face either of two poles with
respect to each other.
- Random Fertilization = all fertilization events are random because each sperm and egg is
different as a result of independent assortment and crossing over; each combination of
sperm and egg is unique.
 After understanding Fig 13.11, go back and re-read/study Figures 13.8 and 13.9
Questions (4-1):
1. What is meant by homologous chromosomes? (Must know, must know. . .)
2. Use the terms diploid, haploid, syngamy and zygote to explain why mitosis isn’t satisfactory for
producing gametes.
3. Make diagrams showing metaphase I and metaphase II of meiosis for a critter with three pairs
of chromosomes. (Complete understanding of the chromosomes arrangement during these two
phases will help tremendously when we discuss Mendel’s Laws!!!)
4. Describe three events that occur during meiosis I but not during mitosis.
5. Distinguish among the three life cycle patterns characteristic of eukaryotes, and name one
organism that displays each pattern.
6. Explain three sources of variation and explain the contribution of each to variation in a
population.
 4-2: 251—256 (Stop before “The Law of Independent Assortment” section)
Mendelian Genetics [Law of Segregation & The Testcross]
 Fig 14.3 introduces the terms that describe generations in studies of inheritance.
 The term allele is most important for understanding the patterns of heredity; Fig 14.4 will help
distinguish the terms allele versus gene.
 The most important Fig 14.5 summarizes the central idea of Mendelian inheritance. It explains
the 3:1 ratio common in simple dominant-recessive inheritance patterns but it also sets the style
for investigating other, more complex genetic patterns.
o The following are 4 related concepts that make up Mendel’s model explaining the 3:1
inheritance pattern that he observed among the F2 offspring:
- Alternate versions of genes cause variation in inherited characteristics among
offspring.
- For each character, every organism inherits one allele from each parent.
- If the two alleles are different, then the dominant allele will be fully expressed
in the offspring, while the recessive allele will have no noticeable effect on the
offspring.
- The each of the two alleles for a character separate during gamete production.
If the parent has two different alleles for a gene, each offspring as a 50%
chance of getting one of the two alleles; two alleles segregate (separate) and end
up in different gametes during Meiosis. This is Mendel’s Law of Segregation.
(Think of Metaphase II to Anaphase II)
 Fig 14.7 illustrates that the recessive phenotype is always use to perform a testcross because
its genotype is known (to show the recessive white requires two recessive alleles).
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Testcross refers to the crossing of a recessive homozygote with an individual exhibiting the
dominant phenotype, in order to find out if the organism is homozygous dominant or
heterozygous.
Questions (4-2):
1. What is meant by allele? How are alleles and genes related?
2. Distinguish between a trait and an allele.
3. State Mendel’s Law of Segregation in your own words. What does it mean? List and explain
the four components of Mendel’s hypothesis that led him to deduce the Law of Segregation.
4. Explain how independent assortment, crossing over, and random fertilization contribute to
genetic variation in sexually reproducing organisms.
5. What is a testcross? What can doing a test cross explain?
6. Now that we’ve covered meiosis and Mendel’s 2nd law, make an educated deduction and
explain why heritable variation is crucial to Darwin’s theory of evolution by natural selection.
(You may need to read page 444 “Summary of Natural Selection through page 446 (up to
“Concept 22.3”)

 4-3: Read 256—259
Law of Independent Assortment [w/ Di-hybrid Crosses]
 Mendel’s Law on independent assortment state each pair of alleles will separate independently
during gamete formation. (Think Metaphase I to Anaphase I)
 Fig 14.8 helps illustrate the important concept of Mendel’s Law of Independent Assortment. You
should be able to recite this law, describe its consequences in forming gametes and explain why
it happens as a consequence of the events of meiosis. This figure also shows what is called a
dihybrid cross; you should be able to draw the Punnett square given the genotypes of both
parents for two different genes (which sort independently). No need to draw the peas. 
 Learn the two rules governing the probability of certain genetic outcomes. Be able to apply them
to simple genetics problems.
 Thoroughly understand Fig 14.10, it shows Mendel’s laws still apply even when the outcome is
more complex than the simple 3:1 situations.
Questions:
1. Distinguish between: dominance and recessiveness, phenotype and genotype
2. State Mendel’s law of independent assortment in your own words.
3. Explain what the ratio 9:3:3:1 means. When can this ratio only be applied?
4. Page 272, problems 2, 3, 4, 7 & 8 (Show work including finding of probabilities, and Punnett
squares where possible.) [For #2, review pages 258-259]
Connection between sections,… (Now, go back and review both of Mendel’s Laws pgs. 253 & 256)
5. How do events of meiosis account for segregation and independent assortment? (Old AP
Free Response (essay) question!)
 4-4 Linked Genes
Read 274-281
 We will be see this reading again in section 4-7 (with additional pages added), but
understanding linked genes is important for understanding exceptions to Mendel’s Law of
Segregation (2nd Law).
 We will be covering sex-linked genes and Morgan’s fruit fly experiment in section 4-7;
if the “blip” on page 277 & 278 regarding genotypic notation is a little confusing, don’t
fret!
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Segregation and independent assortment can be applied to genes that are on different
chromosomes.
 Genes that are adjacent and close to each other (50 map units or less) on the same
chromosome are said to be linked genes and tend to move as a unit. The probability that they
will segregate as a unit is a function of the distance between them.
 During meiosis, unlinked genes follow independent assortment because they are located on
different chromosomes. Linked genes are located on the same chromosome and would not seem
to follow independent assortment.
 However, recombinations of linked genes are explained by crossing over. The father apart
two genes are on a chromosome, the higher the probability that a crossing over event will occur
between them and, therefore, the higher the recombination frequency.
 Relate Fig 15.5 (the Mendelian observations) to Fig 15.6 (the chromosomal basis for those
observations).
 Skim the Linkage Mapping Using. . . section to see how the ideas in Fig’s 15.5 and 15.6 were used
to “map” the location of genes on chromosomes.
Questions (4-4):
1. What are linked genes?
2. Explain the process through which linked genes are independently assorted. What determines
the likelihood of this being assorted independently?
3. What is chromosome mapping and how is it accomplished?

 4-5 Chi-square Statistical Analysis (There are no pages in your text to reference; preread the section in your note packet and the bulleted information below before lecture.)
 Analysis of data following an experiment can sometimes show that your hypothesis is not 100%
true and we can mistakenly say the hypothesis is invalid. One question that can be ask is was
this deviation from the expected results by chance or was there some type of outside influence
that caused this deviation. Quantifying this deviation, if possible, can be useful in answering this
question.
 The Chi-square (χ2) test allows us to calculate the probability of such chance deviations from
expected results and allow us to determine if the hypothesis is true even when the data deviates
from those expected results.

It has become a general scientific convention that a probability value of less than 5 percent is
to be taken as the criterion for rejecting the hypothesis. The hypothesis might still be true, but
we have to make a decision somewhere, and the 5 percent level is the conventional decision line.
In other words, you can be 95% (or higher) sure that your hypothesis is true based on your Chisquare calculations. 95% (or higher) is the scientific standard of acceptance.
 The logic is that, although results this far from expectations are expected 5% of the time even
when the hypothesis is true, we will mistakenly reject the hypothesis in only 5% of cases and we
are willing to take this chance of error.
*See your note packet and supplemental materials given to you for a full explanation of how to apply
the Chi-square test.
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Questions: 4-5
1. A genetics engineer was attempting to cross a tiger and a cheetah. She predicted a phenotypic
outcome of the traits she was observing to be in the following ratio 4 stripes only: 3 spots only:
9 both stripes and spots. When the cross was performed and she counted the individuals she
found 50 with stripes only, 41 with spots only and 85 with both. According to the Chi-square
test, did she get the predicted outcome?
2. Genes assort independently (are NOT on the same chromosome and NOT linked) if they follow
the 9:3:3:1 rule (on the 16 square Punnett square) resulting from a dihybrid cross. In this
dihybrid cross for Cheesapeak Bay Retrievers, red hair is dominant over blonde hair; golden eyes
are dominant over brown eyes.
(Hair Color/Eye Color)
Red/Golden
Red/brown blonde/Golden blonde/brown
Observed
556
184
193
61
Expected
559
186
186
62
Determine if the genes for hair color and eye color for this breed of dogs are on the same
chromosome or not and if they assorted independently. State both conclusion following your
Chi-square test.
 4-6: Read 260—268
Other Patterns ~ Other Exceptions to Mendel’s Laws
 As you read through the various other patterns of inheritance, try to visualize how they are all a
consequence of the same underlying principles and the same unifying thread of: genes coding
for proteins resulting in traits. While reading this section, focus on:
- Incomplete and co-dominance
- multiple alleles
- polygenic traits and continuous variation
 In section 14.4 you should:
- be able to follow, analyze and predict from a pedigree chart (Fig 14.14).
- know what a carrier is
- describe the genetics of sickle-cell disease and Tay-Sachs disease
 You can skim the rest of this section; the rest of the chapter is optional.
Questions:
1. Explain how the phenotypic expression of the heterozygote differs with complete dominance,
incomplete dominance, and co-dominance.
2. Explain why Tay-Sachs disease is considered recessive at the organismal level but co-dominant
at the molecular level.
3. Explain why dominant alleles are not necessarily a common in a population. Use an example with
your explanation.
4. Describe the inheritance of the ABO and explain why the IA and IB alleles are said to be
codominant.
5. Describe how environmental conditions can influence the phenotypic expression of a character.
Explain what is meant by “a norm of reaction”.
6. Explain how a lethal recessive allele can be maintained in a population.
7. Explain the concept of Heterozygous Advantage using the inherited disorder sickle-cell disease
and the effects of having this disorder on people who contract Malaria.
8. Page 272, problems 5, 6 & 13-15 (As before, show work.)
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 4-7: Read (Review/re-read 274-281 especially Morgan’s fruit fly experiment) & read on
282-284
Sex-Linked Genes
 Fig. 15.2 connects the events of meiosis to Mendel’s laws. A complete understanding of this
figure means you get it: the relationship of cellular events to the patterns of inheritance.
 Notice that fruit flies are sexed like humans: Xy = males, XX = females. However, due to
multiple alleles and a great variety of phenotypes for studied traits, we use a different system
to symbolize their alleles.
 Fig 15.4 is your introduction to sex-linkage.
 Sex-linked genes carry genes for many characters that are not related to sex. This is especially
true of the X chromosome, so the term “sex-linked” is usually used for genes that are found on
the X chromosome, rather than the Y chromosome.
 Fathers pass sex-linked genes onto their daughters but not their sons; sex-linked traits are
passed to sons from their mothers.
 Fig 15.10 shows more examples of sex-linkage. Note again how we must use a bit different
symbol system to include the fact that the chromosome possessing the allele need to be
indicated (although there are also other choices used for symbols).
 Knowing about Barr bodies is important because it helps demonstrate the relationship between
how much of a protein is made and the consequent effects on phenotype.
Questions:
1. What are sex-linked genes? Are sex-linked genes recessive or dominant expression?
2. Provide three examples and explain three types of sex-linked disorders.
3. How does the inheritance of sex linked traits differ from traits located on autosomes (non-sex
chromosomes)?
4. What are Barr bodies and how do they effect phenotypic expression in females for certain
traits? Include the concept of inactivation of X-chromosomes in your answer.
 4-8: Read 285—290
Abnormal Chromosomal Numbers & Genetic Disorders
 When the members of a pair of homologous chromosomes do not separate properly during
meiosis I, or sister chromatids don’t separate properly during meiosis II, nondisjunction occurs.
 As a result of nondisjunction, one gamete receives two copies of the gene, while the other
gamete receives none. In the next step, if the faulty gametes engage in fertilization, the
offspring will have an incorrect chromosome number = aneuploidy.
 Fertilized eggs that have received three copies of the chromosome in question are said to be
trisomic; those that have received just one copy of a chromosome are said to be monosomic for
the chromosome.
 Fig 15.12 shows non-disjunction. This leads to trisomy of which the most common example is
Down’s syndrome (an aneuploid condition-chromosome 21). You should understand how this
happens.
 Fig 15.14 shows examples of chromosomal alterations. The letters represent regions on the
chromosome to show how they become rearranged. Each may include many genes (some possibly
fragmented from the switch). [These alterations were/are sometimes referred to as
“chromosomal mutations” but this is not good practice because it confuses the much more
important usage of mutation that we will discuss in chapter 17.
 Skim section 15.5 to get an idea that, as usual, things are not always so simple.
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Questions (4-8):
1. Distinguish between linked genes and sex-linked genes.
2. Explain why sex-linked diseases are more common in human males.
3. What is a Barr body? Why is it produced?
4. Explain how nondisjunction can lead to aneuploidy.
5. Which chromosomal alteration shown in Fig 15.14 do you think is most disadvantageous? Why?
6. Why, in terms of protein production, would Down's individuals resemble each other while
appearing and functioning differently than the general population?
7. Why can Down’s individuals survive when any zygote with trisomy in chromosome one would not
come close to birth?
8. Page 291, problems 1, 2, 3, 7;
Review and understand solutions to genetics problems, Chapters 14 & 15.
 4-9: Read 293—298
Discovery of the Role of DNA
 The proof that DNA is the carrier of genetic information involved a number of important
historical experiments that include:
- Frederick Griffith’s experiments with bacteria and mice. Know what is meant by
transformation? The contributions of Avery, McCarty, and MacLeod to this experiment.
- The significance of the experiments of Hershey and Chase.
- Understand “Chargaff’s rules. What else did he notice that was important to our
recognition of DNA as the molecule of heredity?
- The contribution of Rosalind Franklin and Maurice Wilkins to the “DNA story”.
- The findings and importance of the work of James Watson and Francis Crick.
Questions:
1. Describe the structure of DNA. What properties make it capable of functioning as an
“information molecule”?
2. Diagram a four base-pair sequence for DNA using symbols for the components. What are the
important features that a good diagram should show?
3. Explain the contributions of Rosalind Franklin, Maurice Wilkins, James Watson and Francis Crick
to the discovery of the structure of DNA.
4. Explain the contributions of Griffith, Avery, McCarty and MacLeod to understanding how DNA
can be transmitted? What was still the skepticism following their experiments?
5. What was the significance of the Hershey and Chase experiment? (This is a biggie!)
 4-10: Read 309—314
Transcription & Translation
 Fig 17.2 shows a fairly simple experiment with an
insightful conclusion. This experiment links the
mechanisms of heredity to chemical events: “one gene,
one polypeptide”. In order to understand, you must
recognize their assumption that each strain of mutant
they produced had only one mutation making them
different than the other mutant strains. So, the basis
of their conclusion was to recognize that the
differences between some of the strains were small
enough to be due to the actions of a single protein (or
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polypeptide). So the structural difference of one mutated gene between two strains was
reflected in the functional difference of one strain not being able to perform a particular
reaction in an important pathway.
 Figures 17.3 and 17.4 show the big picture. In a way, this is the core of biology; it is sometimes
referred to as the “Central Dogma of Molecular Biology”. You need to have a complete
understanding of this material.
 Fig 17.5 This is one of the milestones of human intellectual achievement. This is the bridge
between information storage (DNA) and the mechanism through which that information is
carried out to form proteins. YOU NEED TO MEMORIZE THIS FIGURE…. Just kidding! 
Questions (4-10):
1. Briefly give an overview of the flow of genetic information.
2. Describe Beadle and Tatum’s experiments with Neurospora and explain the contribution they
made to our understanding of how genes control metabolism.
3. What is a codon? Why are they important? Why are they the length they are?
4. What is the function of mRNA? Why is the transcription of mRNA necessary?
5. Compare where transcription and translation occur in prokaryotes and eukaryotes.
6. What does it mean to say that the genetic code is redundant but never ambiguous?
 4-11: Read 315—319
Focus on Transcription
 Figure 17.7 shows most of what you want to know about transcription.
 Note the direction of transcription is antiparallel; therefore, DNA is read from 3’ to 5’ while
the mRNA strand is synthesized from 5’ to 3’.
 Fig’s 17.8 is a detail. You can summarize it by saying “transcription is initiated by certain
transcription factors”.
- The DNA sequence at which RNA polymerase attaches is called the promoter.
- The DNA sequence that signals the end of transcription is called the terminator.
- The entire stretch of DNA that is transcribed into mRNA is called a transcription unit.
 There are three main stages to transcription: Initiation, Elongation, and Termination.
 Fig’s 17.9 is another detail. Summarize with “the transcript has a cap and poly-A tail added”. The
tail and cap will help the mRNA be recognized by ribosomes and help protect the mRNA
transcript from degradation (depending on the length of the tail).
 RNA splicing takes place in eukaryotic cells where large portions of the of the newly synthesized
RNA strand are removed. Introns = sections spliced out; Exons = sections remaining are spliced
together.
 Fig 17.10 shows the “processing” of mRNA in eukaryotes. The importance of this is shown in Fig
17.12 (Fig 17.11 is a detail.)
Questions:
1. Describe the process of transcription, including the three major steps of initiation, elongation,
and termination.
2. Why have transcription involved when we could have used the DNA sequence directly (with
appropriate changes to the genetic code).
3. Define and explain the role of ribozymes? What major group of macromolecules do they belong
to?
4. What is the difference between an intron and an exon? What is the functional and evolutionary
significance of an intron?
5. What is meant by a domain? What are possible evolutionary advantages?
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 4-12: Read 320—327
Focus on Translation
 This is it! Possibly no concept is more central to understanding biology. With a thorough
understanding of translation, you can piece together transcription (provides the mRNA) and
replication (insures that the cell had the necessary DNA).
 Fig 17.13 introduces translation; it shows all the players involves and an overall idea of the
process.
 An understanding what tRNA is and does, is central to understanding translation. Fig 17.14 shows
how it is the tRNA that is the actual translator between a sequence of bases in the mRNA and
the sequence of amino acids in the polypeptide. Fig 17.15 demonstrates why a tRNA with a
particular anticodon will always also have a particular amino acid attached (when it’s loaded),
thanks to the specificity of enzymes.
 The ribosome is an incredibly large association of several proteins and multiple strands of RNA
(rRNA) acting to perform several enzymatic functions as well as assisting in base pair matching.
Be sure you understand Fig 17.16 before moving forward.
- P site = holds the tRNA that carries the growing polypeptide chain
- A site = holds the tRNA that carries the amino acid that will be added to the chain
next.
- E site = exit site
 Figures 17.17, 17.18 and 17.19 lead you through the details of translation; here’s how much you
should know: (Translation can also be divided into three stages)
- Initiation (translation): A tRNA loaded with methionine attaches to a start codon on the
mRNA and the ribosome assembles about it.
o Initiation factors (proteins) are also required in order for translation to begin.
- Elongation: Know all in the diagram (except for exactly where the GTP is needed). This
involves the recognition of codons by anticodons, the formation of peptide bonds
between amino acids added to the chain, and translocation = in which the tRNA in the A
site is moved to the P site and the tRNA in the P site is moved to the E site.
- Termination: The process (elongation) repeats itself until a stop codon is reached. Then
the new polypeptide is released and dissociates.
 Fig 17.21 shows how the first few amino acids of a growing polypeptide can direct where it will
end up.
Questions:
1. What features of tRNA allow it to serve as the translator molecule? In other words,
describe the structure and functions of tRNA.
2. List the players responsible for translation and briefly state the role of each.
3. Write a practice essay describing the process of translation (protein synthesis). Include:
small and large subunits, mRNA, 5’ and 3’, codon, initiation and the start codon, P site, A site,
tRNA, amino acids, anticodon, peptide chain, termination, E site.
4. What does the start codon have to do with the “reading frame”?
 4-13: Read 327—331
Mutations
 Notice, in Fig 17.22, how translation begins before transcription is even done in prokaryotes.
 Figures 17.23, 17.24 and 17.25 highlight the concept of mutations. This is highly important to
understanding diversity, evolution, disease and many more biological concepts and processes.
 Point mutations are alterations of just one base of a gene. They come in two basic types:
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1.
Base-pair substitution refers to the replacement of one nucleotide and its
complementary base pair in DNA with another pair of nucleotides.
o Missense mutations are those substitutions that enable the codon to still code
for an amino acid, although it might not be the correct one.
o Nonsense mutations are those substitutions that change a regular amino acid
codon into a stop codon, ceasing translation.
2. Insertion and deletions refer to the additions and losses of nucleotide pairs in a gene.
If they interfere with the codon groupings, they can cause a frameshift mutation, which
causes mRNA to be read incorrectly.
 Mutagens are substances (ex. smoke or other chemicals) or forces (ex. X-Ray or UV Rays) that
cause mutations in DNA.
 Whether or not a mutation is detrimental, beneficial, or neutral depends on the environmental
context. Mutations are the primary source of genetic variation.
 Fig 17.26 recaps the chapter. If you can articulate everything within that diagram, and
supplement with some talk about mutations, you have about 80% of the chapter under control.
Questions (4-13):
1. How does the existence of polyribosomes in bacteria confirm that mRNA is read from the 5’
to the 3’ end?
2. Compare protein synthesis in prokaryotes and eukaryotes.
3. Describe how point mutations can interfere with the reading frame. What is generally the
consequence?
4. Describe the types of point mutations. How are the possible effects of insertions or
deletions different from a substitution? Which type do you think is most important from an
evolutionary point of view?
* Be sure you can easily discuss all the concepts in Fig 17.26
*Study for protein synthesis quiz!
 4-14: Read 334—337
Intro to Viruses
 Smaller than ribosomes, the tiniest viruses are about 20 nm across. The genetic material of
viruses can be double- or single-stranded DNA or double- or single-stranded RNA.
 The viral genome is enclosed by a protein shell called a capsid. Some viruses also have viral
envelopes that surround the capsid and aid the viruses in infecting their host.
 Bacteriophages, or phages, are viruses that infect bacterial cells.
 Fig 18.5 serves as an introduction to how viruses reproduce (which is basically their “life”). You
should be very comfortable with the terms and the process; we will look at variations on this
theme next.
Questions:
1. Explain how a virus identifies its host cell.
2. Describe the structural components of a virus, what their functions are and, in general, how
they reproduce.
 4-15: Read 337—344 (up to “Emerging Viruses) [Skim: pages 344 – 352]
Viral Reproduction
 You should be able to describe the lytic and lysogenic cycles of bacteriophages; they serve as a
basis of understanding the behavior of animal viruses. Fig 18.6 is a detailed version of the left
half of Fig 18.7
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Skim Table 18.1 just to get an idea of the variety of viruses and the diseases they cause.
Both Figures 18.8 and 18.10 show life cycles of RNA viruses. Be able to describe differences
between the two diagrams. Focus on understanding the second diagram (HIV) and view the first
as a variation.
 Skim: pages 344 – 352 Here’s what you need to know:
- viral mutations lead to new diseases
- how bacterial chromosomes replicate, Fig 18.14 (review)
- bacteria can exchange genes through (be able to describe each with a sentence):
o Transformation – the alteration of a bacterial cell’s genotype and phenotype by the
uptake of foreign DNA from the environment.
o Transduction – a phage carries bacterial genes from one host cell to another as a
result of aberrations in the phage’s reproductive cycle.
o conjugation & plasmids
- transposable elements & transposons
Questions (4-15):
1. Why are viruses so host specific?
2. Describe the lytic and lysogenic cycles of bacteriophages.
3. Describe, in some detail, the structure and life cycle of HIV.
4. What is the origin of a viral envelope and of what advantage is it to the virus?
5. Briefly, why are transformation, transduction and conjugation important to bacteria
6. Describe the potential evolutionary importance of transposable elements & transposons.
7. Describe the best current medical defense against viruses. Explain how AZT helps to fight
HIV infections.


 4-16: Read 352—356
Operons (Genetic Control in Bacteria)
 Fig 18.20 suggests an important point: it’s not enough to just inhibit already manufactured
enzymes (by feedback inhibition), we must also be able to stop their production (by preventing
transcription) when not needed. The reason is to maximize efficient use of energy, materials,
space and time in the cell.
 Figures 18.21 and 18.22 are the topic of the day. Learn who the players are and what they do;
the repressor protein and the operator are the keys to understanding. Then be able to describe
how the two types of operons interact with repressors or inducers to promote or inhibit
transcription. Be able to state how each of the two strategies leads to efficiency. (The key to
understanding the difference in function between the two operons is answering the question,
“What is the difference between inhibiting and not promoting?”).
 In bacteria, genes are often clustered into operons, with one promoter serving several adjacent
genes. An operator site on the DNA switches the operon on or off. An operon consists of an
operator, promoter, and the genes they control - the entire stretch of DNA required for
enzyme production in a pathway.
 It is not important to know the details of Fig 18.23 but you should check it out to see that more
than just one factor regulates transcription in most cases (especially in eukaryotes). The action
of the additional regulatory factor, CAP, makes the cell even more efficient at when to
transcribe and translate polypeptides.
A.P. Biology
Genetics Study Guide
Page 12
Questions (4-16):
1. Explain the adaptive advantage of genes grouped into an operon.
2. Distinguish between structural and regulatory genes.
3. Using the trp operon as an example, explain the concept of an operon and the function of the
operator, repressor, and co-repressor.
4. Describe how the lac operon functions and explain the role of the inducer, allolactose.
5. Distinguish between positive and negative control and give examples of each from the lac
operon.
 4-17: Read 359—370
Genetic Control in Eukaryotes
 Both DNA regulatory sequences, regulatory genes, and small regulatory RNAs are involved in
gene expression.
 Gene regulation accounts for some of the phenotypic differences between organisms with similar
genes.
 Skim: 359 – 361 Here’s what’s important:
– follow the pictures going down Fig 19.2 for a mental image of how DNA is “packed”.
– know what a nucleosome is and what histones and chromatin are.
 Fig 19.3 summarizes the places in the process of gene expression where the action can be
stopped. You should be able to cite additional mechanisms for halting gene expression besides
inhibiting transcription.
 Skim: 363 [Regulation of. . .] – 370 Do know a little bit about:
– histone acetylation
- transcription factors/enhancers
– DNA methylation
- alternative RNA splicing (do study Fig 19.8)
 Fig 19.5 serves as a review but also introduces the additional regions in eukaryotic DNA
responsible for even finer control of transcription than found in prokaryotes.
 Fig 19.6 is important in that is graphically illustrates how several factors are necessary of
initiation of transcription.
 Don’t forget that we’ve already discussed in Unit 3 how certain signals can cause a cellular
response that leads to the activation of deactivation of specific genes.
Questions:
1. Compare the structure and organization of prokaryotic and eukaryotic genomes.
2. Describe the progressive levels of DNA packing in eukaryotes.
3. Provide, in a sentence or two, a description of four or five ways gene expression is regulated
in eukaryotes.
4. How might the complexity of initiating transcription in eukaryotes make them more
successful than with simple operons?
 4-18: Read 384—388
Biotechnology
 Fig 20.2 is a great overview of the main application of biotechnology. Although called “gene
cloning” in the text, the process is also referred to as recombinant DNA technology and is
usually what is referred to when people use the term “biotechnology”.
 Know the "DNA Toolkit": gene of interest, restriction enzymes, vectors (especially plasmids),
ligase, target (host) organisms, markers
 Restriction enzymes have made this technology possible, Fig 20.3 shows why (“sticky ends”).
A.P. Biology
Genetics Study Guide
Page 13
Restriction enzymes are used to cut strands of DNA at specific locations (called restriction
sites). These enzymes are what make genetic engineering possible.
 When a DNA molecule is cut by restriction enzymes, the result will always be a set of
restriction fragments, which will have at least one single-stranded end called a sticky end.
 Sticky ends can form hydrogen bonds with complementary single-stranded pieces of DNA sealed
with DNA ligase.
 Although the most important diagram in the chapter, Fig 20.4 has been made a bit complicated
for an introduction. When you first study it, ignore the talk about the lacZ gene. The use of the
lacZ gene only further assists the use of the ampicillin resistance gene (ampR) in helping find
the recombinant bacteria. Both are markers, genes which help locate which target cells have
taken up our plasmid (and, hopefully, the gene of interest). The ampR helps because only bacteria
that have taken up our plasmid survive.
 You should know what a nucleic acid probe is and does but the details (Fig 20.5) are not
important to study.
Questions (4-18):
1. Explain how advances in recombinant DNA technology have helped scientists study the
eukaryotic genome.
2. What is DNA cloning? Why is it important?
3. Describe, using the terms introduced above (DNA toolkit) how a gene from one organism is
introduced into a bacterium to be cloned.

 4-19: Read 391—398
Techniques of Biotech
 Skim: 388 [Storing. . .] –390
 You should definitely know the what and why of PCR but details of the process itself are not
important.
 Gel electrophoresis is a very important tool of molecular biology (probably second only to the
use of restriction enzymes). Fig 20.8 outlines the process, Fig 20.9 shows how it is useful in
analysis. With the help of a probe, electrophoresis can also be used to isolate our gene of
interest.
 Skim the text on southern blotting.
 Skim section 20.3 except DNA Sequencing
 Fig 20.12 shows the process developed by Fredrick Sanger (the “Sanger method”), still in use
today. One difference is in the use of fluorescent tags so the fragments can be “read” as show
in step 3. In the old days (that is, until about five years ago!) the analysis was done by
electrophoresis.
Questions:
1. What is the process and purpose of PCR?
2. Describe the purpose and process of gel electrophoresis.
3. How is the sequence of bases in a DNA fragment determined?
4. How are RFLP's used in "fingerprinting"?
A.P. Biology
Genetics Study Guide
Page 14
 4-20: Read 389—408
Applications of Biotechnology
 Focus on what is discussed in lecture and the rest of the chapter can be read lightly. Come away
with the ability to discuss four or five examples of the uses of recombinant DNA technology.
Questions:
1. List the potential applications of recombinant DNA technology in the fields of agriculture,
medicine and research.
2. What are some of the societal concerns involving biotechnology?
Whew!!