Learning Objectives
Genetics, Chapter1
These learning objectives are given as a study aid. After
studying my notes and/or the text, you should be able to answer
these questions. I will be taking my exam questions from the
study guides. I will also recommend questions from the end of
the chapter to work. I will usually use some of these for the
lab quizzes, but I would recommend working as many of the
questions as possible.
In addition to these learning objectives, the “How do we know what we know” sections are fair game.
Chapter 1: Be able to define:
Transmission/Mendelian Genetics, Cytogenetics, Molecular Genetics
Population Genetics
Know the contributions of Mendel; Correns, DeVries, and Von Tschermak; T.H. Morgan; Oswald Avery; Hershey and Chase; James Watson, Francis Crick, Maurice Wilkins, and Rosalind Franklin; Herbert Boyer, Stanley Cohen; Frederick Sanger; and J. Craig Venter
Learning Objectives-Chapter 2
1. How are chromosomes and genes related? What are chromosomes composed of? Why aren't individual chromosomes visible in a cell, except during mitosis?
2. What is a karyotype? How are chromosomes numbered? On a chromosome, be able to identify the P and Q arms, the centromere, and the telomeres.
3. Be able to identify or define the following terms:
diploid
haploid
karyotype
telomere
centromere
meta-, submeta, acro-, and telocentric
hetero- and euchromatin
sister chromatids
4. Be able to discuss mitosis and meiosis at the level
presented. In particular, be able to define:
cell cycle: Go, G1, S, G2, M phases
prophase & prometaphase
metaphase
anaphase
telophase
prophase I
leptotene
zygotene
pachytene
diplotene
diakinesis
4. (contd.) Define:
prophase, metaphase, anaphase, and telophases I and II in
meiosis
5. Describe how gametogenesis differs in male and female
gametes. Be able to define: spermatogonium/oogonium, primary and secondary spermatocyte/oocyte, polar body, spermatid/ootid, spermatozoa/ovum.
6. What are the “purposes” of meiosis?
Biol 330-1, Genetics
Learning Objectives, Chapters 10 & 11, Klug and Cummings
1. What is the CENTRAL DOGMA of MOLECULAR BIOLOGY? Be able to define replication, transcription, and translation in the context of the central dogma.
2. What is the evidence provided by the work of Avery et al., and Hershey and Chase that show DNA to be the genetic material? What are four functions that the genetic material must perform?
3. What is the structure of DNA? Specifically:
Be able to recognize the bases found in DNA and RNA, and the partners to which they pair.
Distinguish between a nucleoside & nucleotide
Understand the polarity of DNA and its antiparallel nature:
given a sequence, be able to give its complementary sequence.
Be able to identify the major and minor grooves of DNA.
Know what is meant by DNA being a right-handed helix, and by
supercoiling.
Be able to identify the coding and anticoding strands of DNA
when it is used as a template for transcription.
3. What is the evidence that DNA is replicated Semiconservatively? Bidirectionally? Semidiscontinuously?
4. How can you determine the size of DNA? Be able to define: denaturation, renaturation, and hybridization as it relates to DNA and RNA.
DNA Replication
1. Be able to describe DNA replication:
a. Properties of DNA polymerases
b. Functions of:
Primase- why is replication primed by RNA synthesis?
Dna A protein
Dna B & C complex-priming and helicase functions
single stranded binding protein
gyrase: why is it needed, and how is it thought to act?
polymerase I
ligase
c. You should be able to put all of the information about
these proteins into a model of a replication fork for DNA.
2. What is meant by bi-and uni-directional replication, and how
is it shown? What is a replicon?
3. What is meant by semi-discontinuous replication, and how is
it shown?
4. What is meant by rolling circle replication? Why is
duplicating the ends of a linear molecule a problem, & what is
one solution (in particular, telomerase as a solution)
5. Why do genes recombine? What are some of the possible
mechanisms for recombination? How does recombination explain gene conversion?
Genetics 330-1
Learning Objectives, Chapter 13, Klug and Cummings: The genetic code and transcription.
This chapter combines two important topics, the code and the basics of transcription. It provides some historical information,that we won’t be covering, however.
A. The genetic code: What is meant by the genetic code? Be able to define: codon, triplet, unambiguous, degenerate, initiation and termination as they relate to the code.
B. Describe the process of transcription.
What does RNA polymerase do? In particular, be able to define:
promoter
initiation, elongation, termination, rho factor
(open and closed promoter complexes)
sigma factor, core and holoenzyme RNA polymerases
-10 and -35 regions
operon
monocistronic and polycistronic mRNA
What are cis and trans acting elements?
How does transcription in eukaryotes differ from that in prokaryotes? In particular be able to compare the process in pro- and eukaryotes in terms of :
Number of polymerases; use of transcription factors; presence of enhancers; requirement for transport; processing after transcription. What are hnRNA, hnRNP’s, caps, tails and splicing as they relate to transcription in eukaryotes? (fig. 13.9, 13)
How are SNRNP’s involved with splicing? What are the products of the splicing reaction?
Chapter 14-
We won’t be reviewing protein structure, except in passing. You should be familiar with the following terms:
Amino acid
amino and carboxylic acid ends of a protein
peptide bond
primary, secondary, tertiary, and quaternary structure of a
protein.
Which structure determines the ultimate properties of a
protein?
What parts of a tRNA molecule are essential to its function?
What is an amino-acyl tRNA synthetase and a charged tRNA?
What is meant by degeneracy of the genetic code
What are the components of the ribosome. Which rRNA’s are in the small and large subunits of the prokaryote and eukaryotic ribosome? How big, in S units are the small, large and whole ribosomes in us and in prokaryotes?
Describe the events that occur in initiation, elongation, and
termination of translation. Be able to put the events of initiation in order.
What goes in the A, P, & E sites? What stops translation?
How does the translation process explain missense, nonsense,
frameshift, reversion, (and suppressor mutations)?
Biol 330-1, Genetics: Learning Objectives for Exam II
Learning Objectives, Chapter 15, Klug and Cummings
Mutations
1. Be able to define the following:
spontaneous vs induced mutations
somatic mutation
germ-line (gametic) mutation
Dominant and recessive autosomal mutations
X-linked mutations
morphological mutations
nutritional mutation
prototroph
auxotroph
lethal mutation
conditional mutation (temperature sensitive)
2. How does the translation process explain missense, nonsense,
frameshift, reversion. What is a transition, and transversion?
3. Describe how the following four events can lead to
spontaneous mutations:
tautomerization of bases
deamination of bases
activity of an insertion sequence or transposon
4. Describe how the following mutagens work, and the type of
mutations that they are likely to cause:
base analogues
alkylating agents
intercalating agents
UV & X-ray radiation
6. How does the Ames test identify carcinogens?
7. Describe how photoreactivation and excision repair work to
correct damaged DNA, either by the generation of AP sites (base excision repair), or without the generation of AP sites nucleotide excision repair. Why is DNA polymerase I needed in all cases of excision repair?
8. In cases of mismatch repair, how can the repair system
identify the new from the old strand?
9. How do recombination and SOS repair systems work to overcome
DNA damage? Why are they not really "repair" systems?
Transposable elements
NOTE: I may reduce the material on transposable elements
What are insertion sequences and transposons?
How would you identify a transposition event?
Chapter 16, Klug and Cummings: Regulation of Gene expression
1. Be able to define: inducible and repressible expression, constitutive expression, allosteric interaction.
2. Using the lac (and trp) operons as models, describe negative
and positive control of transcription in response to the
environment.
3. What is the effect of a mutation in the repressor gene of an operon? Of a mutation in an operator gene? What is a constitutive mutation?
4. What is meant by a cis acting and trans acting element?
5. What are some of the parts of a eukaryotic promoter (TATA, CAAT, GC rich regions), and what is an enhancer? How do we think enhancers work?
What patterns are found in regulatory sequences of DNA, and
the proteins that bind to them? (e.g., helix-turn helix, zinc fingers, leucine zippers)
6. How do steroid hormones stimulate trancription in eukaryotes?
Biol 330-1, Genetics
Learning Objectives, Chapter 17, Recombinant DNA technology
Be able to describe the steps involved in cloning a gene, beginning with an assay for finding the gene. In particular, be able to tell how the following are used:
Restriction enzymes: how do they allow cloning to take
place?
cloning vectors: how are plasmids and phages used as
cloning vectors, and what are the advantages/disadvantages of
each? What are the characteristics of a good cloning vector? What is a YAC?
How are recombinant plasmids and phages brought into a cell?
DNA ligase
What is a genomic library? a cDNA library?
How can you detect the presence of a cloned gene?
How can cloned genes be used to produce useful proteins?
How is DNA amplified by PCR?
What is a restriction fragment map, and a restriction fragment length polymorphism?
Be able to describe how Southern, northern, and western blots provide us information about DNA and RNA.
How is DNA sequenced?
Chapter 19- Biotechnology and its implications
I won’t be covering much of this chapter- however, I’ll be covering some important diagnostic and therapeutic tools that have come out of recombinant DNA technology.
How can RFLP’s Detect diseases?
How can genes be introduced into somatic cells for gene therapy?
What is a DNA microarray, and how can it detect differences in gene expression between two types of cells?
How are DNA fingerprints made?
You should be able to describe one use of biotechnology, that produces a product of value.
Learning Objectives for Exam III
Chapter 12: Chromosome structure and DNA sequence organization
Be able to convert a length measurement of DNA to a size measurement in kilobase pairs. (i.e., 1 bp= 0.34 nanometers, etc.)
Why do organisms need to package their DNA? Be aware that packaging is not the same as storing a long string; the DNA needs to be, at the same time, accessible for transcription and replication.
What proteins are associated with packaging of DNA in Bacteria?
In what ways are mitochondria and chloroplasts like bacteria? What is meant by the endosymbiotic hypothesis?
Do mitochondria and chloroplasts make all of the gene products that they need? In the mitochondria, where do most of the proteins come from ?
What are polytene and lampbrush chromosomes and why are they useful in studying chromosomes?
How do Eukaryotic cells fold their DNA? Be able to describe how DNA is packaged to produce nucleosomes, 30 nm fibers, looped domains, and the chromatids of a mitotic chromosome.
What is heterochromatin and euchromatin, and how are they different?
Be able to give examples of highly repetitive and middle repetitive DNA, and recognize the following as either highly repetitive or middle repetitive:
Satellite DNA, rRNA genes, VNTR’s, SINEs and LINES. What is a retrotransposon, and which elements are thought to be retrotransposons? Which are thought to be spread by activity of reverse transcriptase?
What is satellite DNA? How was it first identified? Where are two places that it is found?
What are VNTR’s? What is one application of VNTR’s?
Learning Objectives, Chapter 20, Genes and Development
What is the evidence that genes are not solely responsible for development?
At a genetic level, what causes one cell to be different from another?
Define: determination, differentiation, morphogen
[Possible learning objective: How would you determine if a gene is being transcribed more actively in one type of tissue than in another? How would you determine if a gene is still present in a tissue in which the gene is not expressed? (i.e., know how Southern and northern blots are done, and how they can be used to obtain the above information)]
Be able to describe the development of Drosophila through the
stage at which segmentation occurs. Be able to define :
syncytia, syncytial blastoderm, cellular blastoderm, pole cells, segments A1-A8 and T1-T3, parasegments, compartments, and imaginal discs.
What are the three main types of genes that control Drosophila development?
What are the three types of segmentation genes?
Given the description of a mutant phenotype, be able to identify it as the result of a maternal effect gene, segmentation gene (gap, pair-rule, segment polarity), or selector gene.
How can a gradient of a one protein (or two proteins) result in a second protein being only expressed in a narrow band? (fig 20-9).
What do most of the developmental genes code for (i.e., what type of proteins are they?)
Chapter 21, Genes and Cancer
1. What are the characteristics of cancer cells? Are all immortal cells cancerous?
2. What is a cell cycle checkpoint, and what are the two main ones in growing cells?
3. What is a protein kinase, and why are kinases important? Be able to give an example of how a kinase changes the activity of a protein. How do cyclins and CDK’s work together to stimulate a cell to the next phase of the cell cycle? What are some of the things that need to be completed before a cell continues in the cell cycle?
4. Be able to describe how the retinoblastoma, p53, and BRCA1 genes work as tumor suppressor genes.
5. What is a proto-oncogene and oncogene? What types of events can lead to the improper activity of an oncogene? (Table 21.6) In particular, be able to describe how the life cycle of a retrovirus allows it to cause cancer.
6. What is the function of the K-ras oncogene? How does its alteration result in cancer?
7. How does chronic infection with HBV increase a person’s risk of cancer? What is an example of an environmental factor that contributes to cancer? What is one piece of epidemiological evidence that lifestyle factors contribute to cancer risks?
Chapter 9: Microbial Genetics (Mapping in Bacteria and Bacteriophages)
1. What are some of the advantages to using bacteria to study genes? What types of traits can be studied in bacteria? Which bacteria is most often used in genetics? What are prototrophs and auxotrophs?
2. What are F+, Hfr, and F' strains of E. coli? How can Hfr
strains be used to map the location of a gene? [Possible L.O.: How can
complementation tell how many genes are involved in a process?]
3. What are specialized and generalized transduction? How can
generalized transduction and transformation be used to determine the order of three genes, and their relative distance from one another?
4. What is transformation? A competent cell?
5. [Possible L.O.: How are transposons used in genetic analysis?]
Learning Objectives: Last Section and Final Exam
Chapter 3- Medelian Genetics
Define:
gene
allele
gamete
linkage
segregation
independent assortment
phenotype
genotype
reciprocal matings
F1, F2 generations
testcross
monohybrid cross
dihybrid cross
Given a particular cross using parents of known genotype, be able
to give the expected percentages for each possible phenotype and
genotype.
Be able to use Chi-square analysis to determine whether data is
consistent with a certain hypothesis.
Be able to use the forked-line approach to determine the results of a cross when three or more genes are involved.
Be able to examine a human pedigree to determine if a trait is
dominant or recessive, and the probabilities of affected future
offspring, using the binomial distribution if necessary.
Be able to recognize the following as autosomal dominant or
recessive genetic diseases (Table 3.2)
Huntington's disease
achondroplasia
phenylketonuria
cystic fibrosis
albinism
Learning Objectives, Chapter 4
For the following terms be able to define and describe how these
conditions affect inheritance patterns.
incomplete dominance
codominance/multiple alleles
lethal mutation
epistasis and gene interaction: Using the example of coat color in mice, or the interactions of the H substance gene with blood type, and the production of flower color in peas, be able to describe how the interaction of two genes can change a typical 9:3:3:1 ratio to produce other ratios. Recognize the gene interaction in pea flower color as complementary gene action.
penetrance
expressivity
sex-linked gene; be able to predict the inheritance of such a
gene. Be able to recognize color-blindness and hemophilia as
sex-linked traits in humans. Be able to analyze a pedigree and determine that a gene is sex-linked.
sex influenced gene
Chapter 6- Quantitative genetics
What is a quantitative trait? Why are they also called polygenic? How would you tell that a trait is quantitative, as opposed to one that is the result of simple Mendelian inheritance? How can you estimate the number of genes that affect a quantitative trait?
Be able to define mean, variance, and standard deviation; what does standard
deviation mean in terms of a normal distribution?
How would you experimentally determine the effect of environment upon a phenotype? Of genes upon a phenotype? What is a common garden experiment?
Broad and narrow-sense heritability, including ways of measuring narrow-sense.
What are some of the problems in estimating the heritability of
quantitative traits in humans?
Learning Objectives, Chapter 7: Chromosome mutations: Variation in Number and Arrangement.
I. Variations in chromosome number- aneuploidy
Be able to define:
aneuploidy, monosomy, trisomy, non-disjunction
What types of aneuploidy are Down syndrome,
Turner syndrome, Klinefelter syndrome?
What is the relationship between the age of the mother and Down Syndrome?
II. Variations in chromosome number- euploidy.
What is a triploid, tetraploid, and hexaploid condition, in terms of N number?
Define:
autopolyploidy
allopolyploidy
Describe how chromosomal changes such as polyploidy and
aneuploidy can occur, and some of their results in humans
(Down's, Klinefelter's, Turner's syndromes, etc.). How is
polyploidy of value in plant breeding, and how is cholchicine used to produce a polyploid?
Give an example of a plant that is polypoid.
III. Variations in chromosome arrangement
Define: duplications, deletions, inversions, and
translocations, and describe how they can occur.
Why do inversions and translocations result in reduced fertility?
What is familial Down syndrome? What type of segregation produces a Down syndrome individual?
What is fragile X syndrome, and what is the molecular basis for the fragile sites?
Learning Objectives, Chapter 8
1. Define linkage; given a cross of individuals of two
different genotypes, be able to determine whether the two of the
genes are linked, and, if so, to what extent (i.e., by rate of
recombination).
2. Be able to interpret the results of a three-point cross,
determining the order and distance of genes from each other.
3. Be able to define and quantify interference, and relate it to
the behavior of chromosomes.
4. At what stage of meiosis does recombination occur, and why do
we know that? Be able to explain a tetrad analysis, as it occurs
in Neurospora.
5. How are genes mapped in people (possible learning objective)
Learning Objectives, Chapter 22: Population Genetics
Define:
Population
Gene pool
Polymorphic gene
Monomorphic gene
Genetic drift
Be able to calculate the frequency of both genotypes (P,H, &Q)
and alleles (p,&h) in a population.
Given the frequency of alleles and genotypes in a population, be
able to calculate the frequency of genotypes after 1 generation
of random breeding.
Be able to tell if a population is in Hardy-Weinberg equilibrium?
What is the effect of inbreeding and selection on the frequency
of an allele in the population? Be able to calculate the inbreeding coefficient in a pedigree, using the chain-counting method.
Genetics, Ethics and Society
While the bulk of this is not testable (at least not in the genetics course), you should know the contribution of genetics to evolutionary theory that produced neo-Darwinism.
Biology 330, Genetics, Study guide for Final Exam- Fall 2007
The exam will be about 70-75 questions, some one point each, and three problems, & five short discussion questions.
The first five or six will deal with an example of a gene being studied. We’ll use this example to show you understand basic terms and concepts in genetics:
genotype/phenotype; dominant/recessive/codominant; heterozygous/homozygous, complementation, law of segregation /independent assortment.
The questions will range from very easy to hard. Don’t let the fact that there are hard questions cause you to miss the easy ones- if it looks easy, it may be easy.
For CH’s 3-8, and 22:
You should be prepared to do a mono and di-hybrid cross, along with a Chi-square analysis.
Nature-Nurture- common garden experiment, heritability, determining the # of genes involved in a quantitative trait.
You should be able to determine the location of genes that are linked, and determine which gene is in the middle.
For CH 22, you should be able to determine P,H,Q, p,q, from data; you should be able to predict P,H,Q, given p & q.
You should be able to analyze a population to determine if it is in H-W equilibrium, including chi 2
You should be able to relate some of the phenomena that we examined in Mendelian genetics to what happens in molecular genetics: e.g., dominant and recessive traits; incomplete and co-dominance;
Much (but not all!!) of the rest is material that was covered in the previous exams.
First 50 pt quiz- omit
Some things I didn’t think we learned all that well:
Postive and negative control- examples, and how they differ.
cis and trans acting elements.
Questions we can answer with the techniques of molecular biology- Southern blots, northern blots, DNA sequencing, PCR, etc.
Prokaryote/eukaryote differences
metric system!
Short discussion questions. Answer question 1, and three out of the next four,or all four for up to five points extra credit.
1. (10 points) In a population of 200 goats, two alleles affect hair color: Brown (B1) and Blond (B2). homozygous individuals have either brown (B1B1) or blond (B2B2) hair; heterozygous individuals have grey (B1B2) hair. The population has 130 brown goats, 20 grey goats, and 50 blond goats
a. What is the frequency of the B1 and B2 alleles? (2 pts)
b. What is the expected frequency of brown, blond, and grey‑haired goats, if the population were breeding randomly? (3 pts)
c. Is this population in Hardy-Weinberg equillibrium? Show your work, using your Chi 2 chart.(4 pts)
d. What would be the INBREEDING COEFFICIENT in this population ?NOTE: f= 1-H/2pq
2. You are again a famous mad scientist, seeking to produce LONG LIVING PEOPLE. You wish to clone the hsf gene from humans. You wish to examine the promoter sequence from people who have lived a long time, and compare it to that of people who only live a normal life span. You have liver samples from both centenarians and people who died in their 70’s. You have the hsf gene from worms, and it is 90% homologous to the same gene in humans. Beginning with a liver sample the liver of a centenarian, describe how you would produce a library containing a clone the gene. Indicate what type of library you are producing, and indicate how you would find the hsf gene from the thousands of other genes in the library. ALTERNATELY: You know the sequence of the hsf gene in both humans and worms, and the sequence of the surrounding DNA from both humans and worms, although you don’t know how the promoter sequence might differ in people with different life expectancies.
3. We have studied a number of traits by Mendelian genetics and by molecular genetics. In cystic fibrosis (CF), the normal gene is dominant to the recessive gene. The functional gene codes for a chloride transport protein in the cell membrane.
a. At the molecular level, give two mutational events that might occur, to turn the CF gene from a dominant gene to one that is recessive and produces cystic fibrosis. For instance, perhaps the normal gene is overexpressed, resulting in CF (this is not true, but it’s an example of a change that might occur).
b. For one of your ways, describe how you would determine if this is actually what happened. You have at your disposal any genetic tools you need, including cloned copies of the CF gene, and a readily available test for chloride transport into and out of a cell.
4. What is heritabilty? Suppose you had a population of wild pigs, with an average weight of 100 kg, with a standard deviation of 20 kg. You want to see how heritable weight is in this pig population. What would you do to find this out? What kind of result would you get if weight had a heritability of 0.2? (NOTE: this is narrow-sense heritability)
5. Describe why the way chromosomes behave in meiosis accounts for Mendel’s laws of segregation and independent assortment.
Genetics-THE LAST QUIZ!!! Practice Quiz on linkage and Population genetics
1. Three genes are on the chromosome as shown; the distances are the frequency of crossover between them:
0.2 0.2
Z x y
z X Y
Give the gametes that will result from a double crossover, and the expected frequency at which they should occur.
2. You have three genes. The distance between q and l is 15 map units, and the distance between l and k is 5 map units, and the distance between q and k is 20 map units. What is the order of these three genes?
3. If two genes are NOT linked:
a. they will sort independently b. They will behave as if they have a crossover frequency of 50%
c. they may be far apart on the same chromosome d. all of the above are true.
4. A female insect of genotype XYZ/xyz for three genes was backcrossed, and the following progeny resulted:
|
XYZ 4,500 XYz 448 Xyz 54 XyZ 2 xyz 4,495 xyZ 452 xYZ 46 xYz __ 3_
10,000 |
|
The gene in the middle is: |
5. You have genes A
& B. Allele a is recessive to A and b is recessive to B. An organism heterozygous for alleles at these
loci (AaBb) is crossed with an aabb individual.
The offspring are
AaBb 23
aabb 27
Aabb 80
aaBb 70
What is the arrangement of genes on the parental chromosomes?
What is the recombination frequency between the A and B loci?
6. A group of interbreeding individuals of the same species that exists together in time and space is a:
a. colony b. population c. gene pool d. race e. community
7. In a population, if the initial frequencies of two alleles at a locus are 0.9 and 0.1, respectively, after 10 generations of random breeding the frequency of heterozygotes will be
a. 0.20 b. 0.81 c. 1.8 d. 0.18
8. What are two things that can result in a population NOT being in Hardy-Weinberg equilibrium?
9. (2 pts) In a population of goats, two alleles determine eye color. A1 A1 goats have brown eyes, A1 A2 goats have grey eyes, and A2 A2 goats have blue eyes. In a population of 100 goats, you have:
|
Brown eyes- A1A1 |
Grey eyes- A1 A2 |
Blue eyes A2 A2 |
|
50 |
20 |
30 |
a. What are the values for P, H, and Q?
b. What are the values for p & q?
11. For 2 points extra credit, use Chi2 analysis to determine if the population is in Hardy-Weinberg equilibrium. Use two degrees of freedom.
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