BISC 325 Genetics:

08/25/10- Lecture # 2 Chapter 1 (1.3,1.4,1.6)

Slide 1-5: Mendels experimental garden before 1922
-Mendel was product of age of European exploration
-europeans were traveling and bringing home collections of plants and
animals
-these plants were crossed together in 1715 resulting in new and valuable
phenotypes
-Mendel, unlike most of his contemporaries wanted to identify the fundamental
laws behind the phenomenon of producing hybrids
Had two advantages over other scientists
1) took courses under Doppler and had exceptional creativity
2) quantitative
Slide 6: Mendel and the Garden Pea
1) had acceptable generation time
2) strains were available that differed in a single well defined strain
3) the traits bred true
4) he could control the fertilization process
-generally the pea flowers are self-fertilizing and the stamen produces pollen
which fertilizes the pistil of the plant
-however Mendel wanted to cross pollinate so he would cut off stamen of
plants and take pollen from other plants that were different by 1 single trait
and cross bred them.
Mendels experiment:
A) -he crossed yellow pollen to green pistils and also did green pollen to yellow
pistil
-the f1 progeny all came out as yellow seeds
B) -took these yellow f1 seeds and planted them to give f1 plants
-self fertilized f1 plants and looked at f2 seeds
-found that the f2 progeny came out as 3:1 yellow to green
-he believed that 2 of the yellow were Yy and 1 was YY. According to his model if he
took the yellow seeds of F1 progeny
8/27/10 Lecture #3 chapter 3 (3.1,3.2,3.3) Chapter 2 (2.5)
-Chi square: (Observed- expected)^2/E
-if chi square values are less than .05 than it shows that the values are not
consistent with the hypothesis
-df= # of categories -1
-p= probability of observing a deviation from the expected results at least
as large as observed due to chance if the hypothesis is correct. P>.05
suggests hypothesis is correct.
-if p<.05 it suggests that hypothesis is not true. Assumptions are

A) segregation laws are in effect

B) assume all genotypes of pollen have same efficiency of fertilization
C) all fertilizations give rise to peas with equal probability
Mendel published his papers on independent segregation but noone understood the
significance. However by 1900 mitosis, meiosis and chromatin had been discovered so
there was a basis for understanding Mendels laws now.
Theodor Boveri (1862-1915)
Fertilized sea urchin eggs with large concentrations of sperm and obtained many eggs
that had been fertilized by two sperm. At first cleavage these eggs formed four mitotic
spindle poles and four cells (blastomeres) not two.
-he found that with four poles the 108 chromosomes will be distributed into four cells
yielding on average 27 chromosomes per cell. The normal number is 36. he saw that the
embryos didnt develop properly.
-he made another type of dispermic zygotes with 3 spindle poles. With three poles comes
3 cells and each cell had an average of 36 chromosomes. He expected that the embryos
would develop normally but they didnt. He concluded that it wasnt the # of
chromosomes that was important but the specific quality of the chromosomes that
mattered.
-he saw that with three spindle poles, even though many didnt develop properly, the rate
of success was much greater than that of 4 spindle poles. To find the exact probability of
success rate for 3 spindle poles he developed a test.
Boveris test:
-Made three sets of wooden balls numbered 1-18
-he would throw them down onto a plate and then place down wooden blocks to separate
the regions and looked for any instance in which a section had 1-18. with 3 poles he
found that 11% of the time a blastomere had at least one ball with each number of 1-18.
with 4 spindle poles he never observed an instance in which one section had at least 18
balls with numbers 1-18.
8/30/10 Lecture 4: Emphasis on all sections except 4.4 and 4.6; Ch 2 pg 46, 50; Ch 3 pg
103-106
The Boveri work and that of others proved the importance of chromosomes in
development.
Thomas Morgan: worked with flies because there generation time was only a few weeks
compared to a year for peas. Flies have 4 pairs of chromosomes
Experiment:
1) -took female from pure breeding red-eye strain
-took male from pure breeding white eye strain
-result all f1 progeny had red-eye

2) now mated f1 to another f1

found 3:1 ratio of red-eyed in f2
red-eyed females= 50%
red-eyed males= 25%
white eyed males=25%
-because of these results he believed he found a gene that coded for eye color that was on
the sex chromosome X
3) did reciprocal cross of white eyed true breeding female with a red male and found f1
of ( look at slides) didnt copy down fast enough
THIS WAS FIRST EXAMPLE O MENDELIAN FACTOR BEING FOUND ON A
SPECIFIC CHROMOSOME
Thomas wife Lillian worked with flies also.
-she found a funny looking female homozygous for the x-lined recessive gene yellow (y)
and crossed it to a male of normal color (y+)
-she found a wild type normal colored body (heterozygous tho) male
-she also found a yellow bodied female
-this doesnt make sense tho because it should be opposite.
Lillians explanation: the females lower part of the body was yellow while the upper part
was normal. Theorized that this weird animal arose because during development the
gamete cells had a Y chromosome too. (look at slides of lillians explanation square)
-significance of this observation is that it confirmed the linkage of genes to
chromosomes. Because attached X-females carry a Y chromosome, this confirmed the Y
does not determine maleness per se.
-This discovery is an example of serendipity (discoveries made by accident and
sagacity(still has wisdom to recognize it))
-Morgans lab was continually finding mutations that far outnumbered the number of
chromosomes. This suggested that chromosomes had more than 1 gene.
-for example they found a second mutation on the x chromosme of rudimentary
wings.
-the crossed a white female with normal wings with white eyes and
crossed to a red eyed rudimentary winged male. Expect 50% to be red eyed normal
winged females and 50% to be short winged white eyed males (look at slides for f2
expectations)
9/1/10 Lecture 5:
-did the same experiment using other genes that are sex-linked
-look at slides for the cross1
-did the experiment again using another sex-linked gene (yellow)

-look at the slides for cross1

-morgan concluded that maybe there were exchanges between chromosomes
-maybe yellow, rudimentary, and miniature wing genes differed in how far away
they were from white
-the likelihood of an exchange between white and the particular gene would also
vary
-work with yeast demonstrated that cross-over occurs when there are 4 strands
-frequency of recombination is different that frequency of recombination event
9/4/10 : Lecture #6 Chapter 2.6, 3.4-3.5, 4.6, All of Chapter 6
Crossing 3 Genes at a time:
Cross triple homozygous recessive fly with triple homozygous wildtype fly to make triple
heterozygous fly
-cross triple heterozygous with triple recessive tester male
-how many possible three locus genotypes would be expected
-2^3 genotypes
9/8/10: Lecture #7: Sturtevant Breakthrough led to Revolution in Molecular Medicine
-mutated genes that cause genetic disease can be located on a chromosome
-How do you make a genetic map in humans
-you cant make crosses between humans
-Pedigree analysis first used by bell and Haldane to show linkage of hemophila and color
blindness; both are X-linked
-Needs for Human Genetic Map
1) you first need DNA polymorphisms (markers) that are found throughout the genome of
unaffected individuals
-two different kinds of DNA markers used
-single nucleotide polymorphisms (SNPS)
-base changes that cause no harm
-Sometimes a marker can be found if at a snp site a RFLP is formed
-another way of detecting an snp genotype is by using a DNA chip.
-DNA chips can simultaneously determine the genotype at 1,000,000 different snp
sites in the genome
2) to locate these DNA markers with respect to one another. Need to be mapped using
pedigrees from different individuals
-find normal families and type each family member for many different markers
-by doing this you can construct the linkage map
3) pick polymorphisms that span the genome
-pedigrees from families affected with same disease must be found
-the disease causing gene must be located relative to these common markers

9/10/10- Lecture 8
-A genetic map of markers alone would be little help in finding a disease gene.
What we really want to know is the exact location in the chromosomal DNA of the
mutation that causes the disease.
*we need to find the position in the whole genome DNA sequence of the two genetic
makers that pedigree analysis told us flanked the disease gene
How do you find the position of the markers?
-well wee used PCR to amplify microsatellites
-to amplify a specific marker locus you need to know the flanking DNA
sequences that are unique to that locus
1) find markers by random cloning of small DNA pieces and sequencing
2) select microsatellites
3) find those that show variation
4) make genetic map of variable markers
5) choose a marker set to cover genome
6) do pedigree studies on affected families
7) find markers that flank the disease gene using lod score
8) find marker sequence in genome
9) disease gene must be in between
-Still a problem since the resolution of genetic mapping is low
-this means the candidate region for a disease gene may actually contain tens to
hundreds of different genes so each one must be considered
-A good candidate gene may be found among many possible genes because, for example,
the gene is known to function in the nervous system in the case of a neurological disease
-have to sequence all of the candidate genes in both affected and normals
-difficult to find which exact nucleotide is mutated because of the presence
of normal snps
9/13/10-9/15/10 Bacterial Conjugation in chapter 5
-Autosomal Dominant Inheritance: Marfans System
-it is pleiotropic because it is a mutation that affects many of the Bodies systems
-caused by different mutations in the Fibrillin-1 Gene located on Chromosome 15
-This gene is an important component of extracellular matrix microfibrils found in
connective tissues
-the mutation makes the microfibrils very fragile leading to degeneration
-Mouse studies overturned the idea that mfs pathology was directly due to the fibrillin
mutations effect on microfibrills
-an unexpected affect on cell signaling was found
-tested a high blood pressure drug that reduces the level of the abnormal signaling
pathway in blood vessels. This medication worked in mice and human trials are now
underway. It not only stopped the affects of MFS it reversed the disease and the
microfibrils became elastic again.

Autosomal Recessive Inheritance: Cystic Fibrosis

-Assume a study was done with families with 2 children and at least 1 child has CF:
-in 7 families 8 of 14 children have CF. How is this possible?
-It was possible because of the way the study was designed
-A better way to design the study would be to test couples whose parents both carry but
do not exhibit the disease.
*all recessive disorders exhibit ascertainment bias
CF is a multi-system disorder caused by mutation in CF transmembrane conductance
regulator. Western European origins exhibit the higher frequency (1/2500)
-CFTR is a choloride channel in epithelial cells in lung, liver, pancreas, digestive
tract(pleotropic)
-Diagnostic Hallmark: salty sweat
-66% of Caucasian disease chromosomes carry the Delta f-508 mutation which deletes
the phenylalanine codon which causes the genes protein to fold improperly.
-*this mutation is so prevalent because in early European populations there was a
heterozygous advantage that displayed resistance to cholera and typhoid fever
-Sounds like heterozygosity of Sickle cell anemia and alpha thalassemia which
have greater resistance to malaria
X-linked Recessive: Hemophelia
-males more affected
X-linked dominant Inheritance:
-very rare
-all daughters but no sons of father are affected
-50% of sons and daughters of affected mother should get it
Genetic Screening:
1) newborn: Screen about 4 million infants a year for genetic and metabolic
disorders. The disease must have a serious effect on health and be treatable or
preventable
2) carrier: screen a mother and father before pregnancy is detected to see if both are
carriers. Have option of not having children or having pre-implantation diagnosis.
Pre-implantation- based on invitro fertilization.
a) Hyper ovulation
b) Egg retrieval
c) Artificial insemination: PCR genotype blastomere
d) Embryo transferred to women
3) presymptomatic: screening individuals for disease before symptoms occur
Advantage: breast cancer, HNPCC, and other cancer syndromes patients may be
saved
Disadvantage: inferred diagnosis via testing of other family members

Archibald Garrod- Discoverer of inborn error of metabolism

-Studied children with black feces and urine.
Found that they turned black because of oxidation of homogentisic acid.
-induced that tyrosine was involved in the formation of homogentisic acid in patients
with alkaptonuria.
-in 1902 he found 9 families with a total of 48 children that had 9 affected children.
-40% affection rate
-Also in 60% of the families parents were first cousins
-in England only 3% of all marriages were between first cousins
-He postulated that alkaptonuria was an inborn error of metabolism that would convert
tyrosine to homogentisic acid through fermentations.
-Like mendel no one gave any thought to Garrods studies for 39 years
Beadle and Tatums 1941 Paper experiment
-rediscovery of Garrods studies
-*asexual spores produce hyphae
1) mutagenized asexual spores of neurospora and crossed with wild type of opposite
mating type
2) grew haploid ascospores on complete media(glucose,malt, yeast extract, inorganic
salts) so they will grow no matter what
3) Took some of the ascospores and put them on minimal media
4) If it didnt grow on minimal media take the original ascospores and plate to the
following minimal medias
A) Minimal control
B) Minimal + amino acids
C) Minimal+ vitamins
D) Complete media
5) If it grew on amino acid media then that meant there is a mutation that doesnt
allow the fungi to produce amino acids
6) So they then plate the original ascospores into tubes that each have a different
single amino acid
Were able to conclude that biochemical reactions promoted by enzymes in metabolism
could be determined by a single gene
9/17/10
15 Mutants were obtained that could not grow without arginine
Possibilities:
1) All mutants represented the same DNA mutation
2) Each mutation occurred in a different gene
Used complementation test to determine what it was

Assume two different strains are each homozygous for a recessive trait that doesnt grow
argining
Cross the two strains together and see what happens
-if you cross them and the progeny still shows the same trait then there is no
complementation and the mutations must have occurred within the same gene
-if you cross them and the progeny shows wild type then it shows
complementation which means the mutations are on different genes
Method for Interpreting Results of Complimentation Test
-Put all the genes of interest around a circle and connect the genes that show no
complementation (this means that they are in the same complementation group)
-In the beadle and tatum group they found that there were 7 groups that behaved as a
single mendelian gene.
-members of three groups were analyzed
-each group had ornithine, citrrulline, and arginine separately to see if they would grow.
9/20/10- Epistasis- alleles of one gene mask the expression of phenotype of alleles of
another gene
-interaction of genes at two or more loci
-in crosses the phenotypes can differ from what would be expected if one locuss
contribution to the phenotype was independent of that at the other locus.
-look at slides
If a certain allele is epistatic to another allele of a different locus that means it is the
dominant one and it effects the phenotype.
-Incomplete Penetrance:
BRCA-1 and BRCA-2
Environmental factors
-Compared groups of women who both carried the BRCA-1 and BRCA-2
mutations. Data showed that those women who were physically active had a later onset
of breast cancer than those who were inactive
Genetic Background
-The BRCA-1,2 and the HNPCC genes are tumor suppressor genes and are
recessive mutations so heterozygosity shouldnt lead to tumors
-what happens is only one cell Loses heterozygosity and this can ultimately cause
tumors to form
Expressivity:
Patients suffer variable severities of phenotypic

Sex-Influenced traits
When a genetic trait is expressed more frequently or severly in one sex than the other
Ex) premature baldness
Sex-limited
When a genetic trait is expressed in only one sex
Ex) uterine, ovarian, and prostate cancer
9/22/10- Microorganisms
-transformation-When DNA from local environment is incorporated into the bacteria
-Conjugation- A)unidirectional movement of small plasmids (Circular DNA) which has
its own origin of replication, into other bacterial cells
-Transduction-viruses can take up some bacterial DNA into their own genome
-Auxotroph: can only grow on complete media
Can select for spontaneous or induced mutations on minimal media
Mixing of Bacteria with Different Genotypes:
Took two reciprocal strains and added them together. Plated three different plates, one
that had both and two that each only had one type of strain. He found that he got
bacterial colonies growing on minimal media on the plate with both strains present
Was this due to actual physical contact and some kind of sex?
He maid a u shaped apparatus that had a small filter in it. The pores were small enough
so bacteria couldnt pass through but chemicals made by the bacteria could. Found that
no colonies were forming.
Discovered that gene exchange was always in one direction. One was always a donor
(has F+ plasmid) and the other was always a recipient
-the F+ plasmid allows for the formation of a pilus which brings the two cells
together. Then a pore opens up and a copy of the F+ plasmid goes into the recipient
Prototroph: can grow on minimal media