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Genetics chapters 16-19, 21


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A mutation in gamete-forming tissue.
An individual with the “new” germinal mutation will not show the phenotype but the mutation can be
transmitted to progeny.
Germinal Mutation
A mutation in any non-gamete producing tissue.
The individual with the “new” somatic mutation may exhibit a mutant phenotype but the mutation can't be
transmitted to progeny.
Somatic Mutation
The allele only expresses the mutant phenotype under certain environmental conditions.
(e.g.temperature sensitive)
The protein product functions at the permissive temperature but is non-functional at the
restrictive (non-permissive) temper
Conditional Mutation
The individual must be supplied with certain nutrients (amino acids, nucleotides, vitamins).
Commonly used when studying microorganisms.
2. WT is___________ (nutritionally self-sufficient).
1.Auxotrophic Mutation
Confers the ability to grow in the presence of an inhibitor. (e.g., antibiotic or virus/phage)
Antibiotic resistance mutations can arise from a mutation in the gene encoding the target of the drug or a
mutation in the gene encoding a transporte
Resistance Mutation
Germinal mutations are detected by the sudden appearance of the abnormal phenotype in a pedigree with
no previous record of abnormality.
Dominant mutations are relatively easy to detect.
Recessive mutations can go unnoticed for several gen
Human Genetics
Experiments designed to isolate mutants that affect a specific biological function.
Mutant Hunts
Techniques designed to separate rare mutant individuals from WT.
Need a selectable phenotype.
Only the appropriate mutants survive.
Genetic Selections
Strategies designed to identify desired mutant individuals (mutant phenotype) from a large number of
Genetic Screens
(Figure 16-4)
Used to increase mutation rates.
(e.g., chemicals or UV radiation)
Analyzing heritable mutant phenotypes at the genetic level before performing molecular analyses of the
isolated mutants.
Requires methods to identify the mutant genes (e.g., gene mapping)
Forward Genetics
This approach starts with a WT molecule (typically a cloned gene or a purified protein).
The WT gene is then mutated to identify the mutant phenotype.
Reverse Genetics
1) Grow as single cells in liquid culture or as colonies.
2) Easy to examine millions of individuals.
3) Isolated single cells generate a clonal population (colony) of genetically identical cells.
4) Mutants are easily identified (dominant
Single Cell Haploid Organisms-Bacteria and Fungi (advantages)
1) Grow mutant culture in minimal medium + supplement.
2) Plate cells on minimal medium without supplement.
3) Survivors are prototrophs.
The use of a mutagen in step 1 above will increase the mutation rate.
Forward Genetic Selections

Detection of Reverse Mutations (auxotrophprototroph)
1. The survivors can be a true reversion (WT genotype).
2. The survivors may be second site suppressors that result in the complete or partial
phenotypic reversion to WT.
a. The second site suppressor can be in a new gene.
Often ident
second site suppreseors
Auxotrophic selection in bacteria.
Penicillin kills actively growing cells by interfering with cell wall synthesis.
1) Grow cells in rich medium (with or without a mutagen).
2) Transfer to minimal medium.
3) Add penicillin (prototroph
Penicillin Enrichment
Resistance Mutations
1) Grow cells in liquid culture (with or without a mutagen).
2) Plate cells on selective medium (antibiotic or phage).
Resistance Mutations
Filter enrichment.
Prototrophs grow as fuzzy balls, auxotrophs do not grow.
1) Grow cells in rich medium (with or without a mutagen).
2) Transfer to minimal medium.
3) Filter cells and save the filtrate containing the auxotrophs.
Selection of Fungal Auxotrophs
(Figure 16-6)
1) Grow cells in rich medium (with or without a mutagen).
2) Plate cells and visually screen for abnormal colonies.
Identifies mutants that have defects in hyphal tip growth and branching
Morphogenesis Mutants in Fungi
(Figure 16-8)
1.Mutant screens of yeast are responsible for much of our understanding about the cell cycle.
2. _____________ were first obtained in a screen looking for mutants that blocked
the mitotic cell cycle at specific points.

1.Yeast Cell Cycle
2.cdc mutants(cell-division cycle) (Figure 16-9)
3.Comparitive genomics
Nobel Prize for yeast cell cycle
Leland Hartwell and Paul Nurse
A. Random Mutagenesis
Combine new mutants with a known mutation of the gene of interest.
Reverse Genetics
Mutagenize the WT parent.
a+a+b+b+ X aabb

a+a b+b a+abb aab+b
mutant 1 mutant 2
Diploid organism (germinal)
Mutagenize the individual.
Look for sectoring in a heterozygote.
Diploid organism (somatic)
See notes for exam 3.
Replace the wild type gene with a gene that has been disrupted by a drug resistance gene.
Gene-specific Mutagenesis
Gene Replacement (Inactivation)
(Figure 16-15)
See notes from exam 3.
Introduce point mutations, deletions or insertions in a gene of interest using mutagenic
Gene-specific Mutagenesis
Site-directed Mutagenesis
(Figure 16-16)
Use conditions in which PCR exhibits reduced fidelity of a coding region.
Then use a genetic selection or screen to identify interesting mutants.
Gene-specific Mutagenesis

Error-prone PCR
Applying mutagenic and selective techniques to animal and plant cell cultures.
Often only identify dominant mutations because the organism is diploid.
Somatic Cell Genetics
Once several mutants are identified in a selection or screen, it is important to identify the mutant genes.
There could be one or several different genes giving rise to a particular phenotype.
(e.g., the inability to grow in the absence of an a
Analysis of Recovered Mutations
A. __________
1. Use conjugation and transduction mapping techniques to localize the mutant gene.
2. Clone by complementation.
Use the complementation test.
Analysis of Recovered Mutation
B. Eukaryotes
Mechanisms exist to ensure that cell numbers remain balanced.
Cancer is a genetic disease of somatic cells that is caused by mutations that result in the failure of cell
cycle control and/or the failure of apoptosis (programmed cell death).
Cell Cycle Control and Apoptosis
G1 (Gap 1)Time between mitosis and DNA replication.
SDNA synthesis.
G2 (Gap 2) Time between DNA replication and mitosis.
G0Optional "resting" phase.
Eacly embryonic cells (no G0)
The Cell Cycle (G1-S-G2-M)
Progression of one stage of the cell cycle to the next depends on protein complexes
consisting of a cyclin and a cyclin-dependent protein kinase (CDK).
Protein kinases phosphorylate specific proteins.
Cyclins only expressed at specific cel
How does the cell “know” when to divide?
(Figure 17-2)
(Figure 17-3)
inhibit the kinase activity of the CDK until the cell is ready to progress
into the next stage of the cell cycle.
CDK-cyclin-binding proteins
E2F is a transcription factor that turns on genes encoding enzymes for DNA synthesis (i.e., replication).
Rb (retinoblastoma) protein binds to and inhibits E2F function.
cyclin A-Cdk2 complex phosphorylates Rb (i.e., Rb is the target protein).<
G1 to S Transition Checkpoint
(Figures 17-4 and 17-5)
Elimination of damaged (potentially harmful) cells through a self-destruct and disposal mechanism.
Activation of the self-destruct mechanism leads to fragmentation of the chromosomes, disruption of
organelle structure, and loss of normal cell s
Apoptosis (Programmed Cell Death)
(Figure 17-6)
The engines of self-destruction.
A group of enzymes that cleave other proteins (proteases).
In normal cells, each executioner caspase is present in an inactive state called the zymogen form.
The zymogen is converted to an active caspase by
(Figure 17-7)
1. Other zymogens
2. A protein responsible for inactivating a DNA endonuclease.
Leads to activation of the endonuclease and chromosomal fragmentation.
3. Actin (a component of the cytoskeleton)-leads to abnormal cell shape.
4. others<
Target proteins may include:
Cells communicate with each other via signal transduction pathways.
Intercellular Communication
A small molecule (ligand) is released from one cell and interacts with a membrane bound receptor of
another cell.
Signal Transduction
(Figure 17-11)
Cancerous cells are uncoupled from the regulatory mechanisms that keep cell proliferation in check.
Caused by multiple mutations in a single cell that causes it to:
1) Proliferate out of control.
2) Decrease the susceptibility to apoptosis
Mutations resulting in proteins that are activated when they shouldn’t be.
Typically these proteins are components of intracellular communication pathways such that the cell
always behaves as if it is receiving a signal to proliferate. (e.g.,
Dominant Oncogene Mutations
Ligand bound receptors dimerize.
Dimerized receptors autophosphorylate the cytoplasmic domain.
The phosphate is then transferred to another protein in the signaling pathway.
Often the next step in propagating the signal is to activate a G-
Signal Transduction
(Figure 17-13)
Mutations in genes whose proteins normally contribute to the inhibition of cell proliferation.
A. Proteins involved in inhibiting progression of the cell cycle (i.e., inhibitor protein is inactive).
B. Proteins involved in the repair of DNA dam
Recessive Tumor Suppresser Genes (Figure 17-5)
Autosomal recessive predisposition to skin cancer caused by a mutation in a gene involved in repairing
UV damaged DNA.
Xeroderma Pigmentosum
A. Hereditary Predisposition (Family history)
1) Inherited as RB rb (recessive).
2) rb rb is generated by rare mitotic X-overs.
Two eyes are often affected because only one mitotic X-over is required in each retina.
B. Sporadic (No pr
Retinoblastoma (Retinal cancer)
(Figure 17-20)
The study of the events that occur during the transfiguration of a single cell (fertilized egg) to an adult
organism that is composed of thousands, millions or trillions of cells organized into tissues and organs.
Cells adopt specific fates or the capacity to differentiate into specific types of cells (gradual process).
Periodic decisions are made in each cell lineage to more exactly specify the fates of the daughter cells.
In general, the same basic set
Cell determination
Establishing the body plan.
In addition to their role in determining cell shape, Microtubules and Microfilaments serve as molecular
highways in the cell.
Proteins, and vesicles are transported throughout the cell by molecular motors.
(e.g., kinesin and microtubules)
Role of the Cytoskeleton in Pattern Formation
(Figure 18-5)
The adult nematode is composed of only a few thousand cells.
The cell lineage has been traced from fertilized egg to adult.
(Figure 18-6)
P granules become restricted to one side of the egg upon fertilization and give rise
C. elegans
Generation of the egg cell.
Stem cellprimary oocyte16 cells, one of which becomes the oocyte itself.
The other 15 cells are nurse cells that dump their cytoplasmic contents into the oocyte.
1._______________ (RNA & protein) form at the posterior pole of the oocyte (tethered by the cytoskeleton).

2. Nuclear division without complete cell division forms a________________

3.______________ form at the posterior end, w
1.Polar granules
(Figure 18-7)
3.Pole cells
The Drosophila larva is highly differentiated along ___________
Formation of the Body Plan
(Figure 18-8)

the A/P & D/V axes.
~10 hrs after fertilization 14 body segments are formed along the A/P axis.
(3 head, 3 thoracic, 8 abdominal)
Each segment gives rise to body parts of the adult.
Segmentation Pattern
The egg contributes localized gene products that establish polarity along the A/P & D/V axes, which
ultimately determines cell fates.
Cell fate is determined during development by the selective local activation of a set of master regulatory
How are segmentation patterns established?
Concentration gradients of the maternal-effect proteins are established while the soma nuclei are part of
the syncitium (one common cytoplasm).
A/P Concentration Gradients
(Figure 18-9)
(A maternal-effect gene)
________ mRNA is localized to the anterior pole of the embryo by association with microtubules.
Following translation, BCD protein diffuses forming a concentration gradient from anterior to posterior.
BCD is a tran
BCD (bicoid)
(A maternal-effect gene)
______ mRNA is localized to the posterior tip of the embryo by association with microtubules.
Following translation, NOS protein diffuses forming a concentration gradient from posterior to anterior.
NOS protein is
NOS (nanos)
(A maternal-effect gene)
________mRNA is uniformly distributed throughout the embryo.
NOS represses translation of hb-m mRNA.
Thus, HB-M is most highly expressed in the anterior pole.
HB-M protein is also a transcription factor and is
HB-M (hunchback)
(different geographic positions) along the A/P & D/V
axes of the Drosophila embryo. which determine cell fate
As development continues a hierarchy of gene expression establishes the number of body segments, then
subsegments, then segment identity, etc...
Hierarchy of Gene Expression
BCD and HB-M are transcriptional regulatory proteins that activate and/or repress a set of genes called
cardinal genes (also called gap genes)
Segmentation Pattern
1.___________Repressed by high [BCD] but activated by low [BCD] and low [HB-M].
Activated by low [HB-M] and repressed by BCD.
Thus, kni is expressed more posteriorly than kr.
This differential gene expression is caused by BCD and H
Gap Genes (Figure 18-23a) (kruppel)
2.kni (knirps)(Figure 18-20)
1__________regulate expression of the 2___________.
3____________ genes encode transcription factors that regulate expression of 4_________ genes.
Some of the 5.___________genes also encode regulatory proteins while others encode different cla
1.Gap genes
2.pair-rule genes(Figure 18-23b)
Parallel cascades establish ___________
Segement Identity
Mutations in homeotic genes change the segmental identity into that of another.
(i.e., same number of segments but a duplication of one segment with another segment missing).
All homeotic genes encode transcription factors.
Gap gene protei
Homeotic Genes
(Figure 18-26)
(Figure 18-25a-c)
Homeotic (segment identity) genes exist in humans and mice, etc... (i.e.) homologous genes
Developmental strategies in animals are ancient.
Animals as divergent as Drosophila and humans develop using the same regulatory switches.
Applications to Higher Animals
Organisms don't live as isolated individuals; they live in populations.
__________________tries to understand the genetic composition of a population and the forces that
determine and change that composition.
Genetic variation within and b
Population genetics
Frequency Distribution of a Genotype
(e.g., MN blood types) (Table 19-1)
More typically the allele frequencies are used.
Determine the allele frequency by counting the homozygotes and half the heterozygotes.
A/A = 0.36; A/a = 0.48, a/
Allele Frequency
The occurrence in a population of several phenotypic forms associated with alleles of a particular gene.
Can easily see with the naked eye.
Doesn't tell you anything about what is actually changed.
Morphologic Variation
ABO Blood groups

2. ___________
(e.g., change in number of charged amino acids)
Only detects a few of the total number of changes.
Only examines protein-coding sequences.
Protein Polymorphism
(Figures 19-2, 19-3)
1.Immunologic polymorphism
(Table 19-2)
2.Amino acid sequence polymorphism
1. ________________
Only detects some of the changes.
Don't know where they are located.
Green sea turtle RFLP study.
Detects all of the changes, including regulatory changes.
DNA Sequence Polymorphism

1. RFLP Mapping
2. Complete Sequence
A/A A/a a/a
p2 + 2 pq + q2 = 1
Random mating results in an equilibrium distribution of genotypes after only one generation.
Sexual reproduction does not cause a reduction in genetic variation.
Genetic variation is maintained.
Hardy-Weinberg Equilibrium
1 0.3 0.0 0.7
2 0.2 0.2 0.6
3 0.1 0.4 0.5
1 p = f (A/A) 1/2 f (A/a) = 0.3 + 1/2(0) = 0.3 + 0.0 = 0.3
2 p = 0.2 + 1/2 (0.2) = 0.2 + 0.1 = 0.3
3 p = 0.1 + 1/2 (0.4) = 0.1 + 0.2 = 0.3
In each case: q = 1 – p = 0.7
Hardy-Weinberg Equilibrium
A/A A/a a/a
p2 + 2 pq + q2 = 1
The total frequency of heterozygotes for a given gene.
Heterozygosity can be calculated using the Hardy-Weinberg equilibrium (2pq).
Heterozygosity is greatest when several alleles of a gene exist in equal frequency.
(Figure 19-6)
Evolution is dependent on renewed variation.
rates are very slow and they take an extremely long time to be fixed into the population.
B. _______________
The generation of recombinants via intrachromosomal recombina
Sources of Variation
A. Mutation
B. Recombination
C. Immigration
Hardy-Weinberg assumes random mating but this is not always the case.
A. ____________
When mating between relatives is more common than what would occur purely by chance.
B. _____________
When mating between relatives is less common t
Non-random Mating
A. Inbreeding
B. Outbreeding
C. Positive Assortative Mating
D. Negative assortative mating
Differential rates of survival and reproduction of particular genotypes .
(Natural Selection)
Relative probability of survival and rate of reproduction of a phenotype or genotype.
Fitness is a consequence of the interaction of the phenotype with its environment.
The fitness of a particular phenotype (genotype) will differ in different e
Darwinian Fitness
The fitness of the individual does not depend on the composition of the population.
No competition.
(e.g., plants in a desert depend on depth of roots to obtain water)
Frequency Independent Selection
The fitness of the individual depends on the composition of the population.
(e.g., carnivores)
The allele with the highest average fitness increases in the population.
Frequency Dependent Selection
All populations are finite in size.
If two parents only have a small number of offspring, even in the absence of selective forces, the
frequency of a gene will not be exactly reproduced in the next generation (sampling error).
New mutation
Random Genetic Drift
Occurs when a small group breaks off from a larger population to found a new colony.
Probably responsible for the virtual lack of blood type B in Native Americans.
Founder effect
1. Populations of a given species includes individuals with varying characteristics
(i.e., different phenotypes and genotypes)
2. The population of the next generation will contain a higher frequency of those types that are most
Darwin's Theory of Evolution
(Figure 21-2)
13 different finch species with variation in form and function.

Evolution occurs within populations and not between individuals.
(i.e., the gene pool)
Darwin's Finches in the Galapagos Islands
(Figure 21-4)
A group of organisms which are capable of exchanging genes within the group but are genetically unable
to exchange genes in nature with other groups.
New species form as a result of geographic isolation.
(e.g., continental drift, different
1.The failure to form zygotes.

2.The failure of fertilized zygotes contribute gametes to future generations.
(e.g., sterility of the hybrids)
horse + donkey = sterile mule (horses and donkeys are different species)
1.Prezygotic Isolation
2.Postzygotic Isolation
Evolution consists of more than substitution of one allele for another.
In some cases, continuous transformation leads to new form and function without totally new genes.
(e.g., development of the mammalian inner ear from reptilian jaw bones)
Origin of New Genes
A. ______________
Duplication of the entire genome.
The duplicated genes can diverge and take on altered or new function.
Common occurrence in plants.
When n (haploid number) > 12, most plants have an even number of chromosomes.
Where does the DNA for new genes come from?

A. Polyploidy (Figure 21-9)
B. Duplications
1) _______________
(α2β2) α and β are 50% identical.
α on chromosome 16, β on chromosome 11

2)______________(α2γ2) γ and β are 75% identical.
γ and β are adjacent to one another on chromosome 11.

Human Hemoglobin
(Figure 21-10)(Figure 21-11)

1) Adult hemoglobin
2) Fetal hemoglobin
1) Mitochondria and chloroplasts
Bacterial engulfmentsymbiosisorganelle
2) Horizontal transfer
Transposable elements and plasmids can transfer DNA from one species to another.
Imported DNA
Mutations can have three consequences.
1) Decrease fitness
2) Increase fitness
3) No effect on fitness (neutral)
Molecular Evolution
Evolution of a gene proceeds according to a molecular clock that is dictated by the mutation frequency.
Synonymous substitutions occur at a faster rate than non-synonymous substitutions.

Different proteins have different molecular clocks.
Molecular Clock
(Figure 21-13)
(Figure 21-14)
in Evolution
All organisms are descended from a single common ancestor.
(Figure 21-15)
Common Ancestry

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