01 BIS101 S2014 Lect 1

BIS101-001, Spring 2014Genes and Gene Expression, R.L.
Rodriguez 2014
BIS101-001: Genes and Gene Expression
Welcome to BIS101-001 Spring 2014
Genes and Gene Expression
R.L. Rodriguez Instructor,
Mon - Wed 10:00 a.m. - 11:50 a.m.
3 Kleiber Hall
Introductory Lecture #1
1
BIS101-001, Spring 2014Genes and Gene Expression, R.L. Rodriguez 2014
BIS101 is a survey of the fundamental concepts
of genetics and molecular biology including
vocabulary, technology, experiment design, with
particular emphasis on gene structure and
function. Prokaryotic and eukaryotic molecular
models will be used to demonstrate basic
principles of gene mapping, chromatin structure,
genomics, replication, transcription, translation,
mutations, repair, gene regulation and genetic
engineering.
BIS101: Genes and Gene Expression: Introduction
2
BIS101-001, Spring 2014Genes and Gene Expression, R.L. Rodriguez 2014 3
Textbook: Genetic Analysis: An Integrative Approach,
Sanders and Bowman, 1
st
Ed.
Grade based on 500 points distributed among two
midterms, each worth 100 points, 100 points in online
assignments and a final exam worth 200 points.
Final exam is cumulative: approx. 50% (100 points)
from the first two midterms and 50% (100 points)
based on new material.
Requests for regrades must be submitted to the
Teaching Assistants using a Petition for Regrade
Form obtained on SmartSite. No midterms regraded
after the final and no regrading of final exams
4
There are no early, late or makeup exams. A
valid medical excuse is the only basis for missing
an exam or for petitioning for an incomplete (I)
grade. In the case of missed midterm exams,
the final exam will be weighted an additional 100
points. Sixty (60) minutes are allotted to each
midterm exam.
Past grade distribution is approx. as follows:
18% As, 33% Bs, 29% Cs, 10% Ds and 8% Fs.
Zero tolerance for cheating

5
MasteringGenetics is an online, interactive, problem-
solving program designed expressly for use with the
textbook.
Four MasteringGenetics assignments are required during
the quarter. The required assignments you complete will
be graded and submitted through Mastering. The
program provides feedback and hints for wrong answers
and uses automated grading to record your assignment
scores.
You can register for MasteringGenetics by going to:
MasterGenetics.com. Using the course code:
\MGENRODRIGUEZ78592, you can access class
assignments.
BIS101: MasteringGenetics
Course objective: To understand the true
relationship between genotype and
phenotype.
Definition of Genotype: The actual alleles
(alternation forms of a gene, or sequence of
DNA) in an individual.
Definition of Phenotype: An observable
characteristic (produced by the genotype).
Challenge: The path from genotype to
phenotype is not linear!
Why Genes, Gene Expression and Genomes?
BIS101-01 Spring 2014Genes and Gene Expression, R.L. Rodriguez 2014 7
Filters of Genetic Potential
Life span
Because of these gene modifiers, we do not have to be slaves
to our genes nor do we have to be victims of genetic determinism.
BIS101-001 Genes and Gene Expression
Mendels Principles:
Meiosis, Chromosomes and Probabilities
(Review: Chapter 2)
Mendels
Laws
Chromosome,
DNA
Behavior
Prediction
(Pedigree
Analysis)
Probability &
Statistics
Mendels
Laws
You should be here.
Achieving Integrated Genetic Fluency (IGF)
The information fundamental of life is encoded in
DNA.
Biological function emerges primarily from the
expressed forms of DNA (e.g., RNA and protein).
All life forms are part of a vast network of related
individuals.
The modular nature of the genome facilitates
rapid evolution
Powerful analytical tools and method of scientific
inquiry (p. 27), permit the dissection of the
genetic complexity for the good of humankind
Chapter 1: The Study of Biological Information
Mendels 1st and 2nd Laws of Inheritance.
Definitions
Using crosses to infer the nature of inheritance.
Test Crosses and recessive traits
Mitosis and Meiosis.
Mendelian inheritance and Chromosome Theory
Cell cycle and chromosome replication
Product and Sum Rules
Application of Product and Sum Rules in genetic
crosses.
This Lecture: Mendel and Chromosomes
Chapter 2 Vocabulary
Allele: An alternate form of the same gene, (e.g., the seed color gene in peas can be yellow or green).
Character: Any specific, true-breeding property of an organism. Synonymous with "trait or "phenotype."
Dihybrid Cross: A cross between two individuals with different alleles at two gene loci. A dihybrid is a heterozygous
individual with different alleles at two gene loci.
Diploid: A eukaryote cell or organism having two sets of chromosomes (or a pair of genes at each locus).
Dominant: An allele or trait that expresses its phenotype when heterozygous with a recessive allele, (e.g., A is dominant to
a because the phenotypes AA and Aa are the same).
Eukaryote: An organism or cell containing two sets of genes (diploid) for each character, where the entire genetic
complement is contained within a well-defined nucleus. Prokaryotes are 1N and have no defined nucleus (e.g.,bacteria)
F1: First filial generation. The progeny of a cross between two parental types that differ in one or more genes.
Gene: The basic unit of heredity that occupies a fixed chromosomal location (locus). The gene contains the information for
tRNAs, rRNAs and mRNA (i.e., proteins).
Genotype: The specific allelic composition of a cell or set of genes.
Haploid: A cell or organism having only one set of chromosomes (i.e., one gene at each locus or haploid).
Gamete: A haploid reproductive cell such as a sperm (or pollen) and egg (or ova).
Heterozygous: A diploid with dissimilar alleles at one or more loci and therefore not true-breeding for the trait(s)at that
locus or loci.
Homozygous: A diploid having the same allele at a given locus, therefore, true-breeding for the trait at that locus.
Locus: The region along the length of a chromosome where the alleles (pair of genes) for a particular trait resides.
Monohybrid Cross: A cross between two individuals with different alleles at one gene locus. A monohybrid is a
heterozygous individual with different alleles at one gene locus.
N: The haploid chromosome number. Prokaryotes are 1N while most eukaryotes are 2N.
Phenotype: The detectable outward biochemical or morphological manifestation of a specific genotype. The form a
character or trait takes in a specific individual.
Punnett Square: A cross-multiplication table used for determining the expected genetic outcomes of a mating.
Recessive: An allele or trait that does not express its phenotype in the heterozygous condition (e.g., a is recessive to A
when the phenotype of Aa is the same as AA).
Testcross: A cross between an F1 individual (unknown genotype) and the homozygous recessive parent of the F1, the
"tester." Because the genotype of the tester is known, the test cross reveals the genotype of the F1.
Patterns of Inheritance: Main Concepts
The existence of genes can be inferred by observing standard
ratios in the progeny of mating between two different
phenotypes
Discrete phenotypic differences in a trait can sometimes be due
to differences in a single gene
Each type of gene is represented twice in each cell, one on
each member of a chromosome pair.
Inheritance patterns are based on chromosome behavior at
meiosis
During gamete formation, each member of a gene pair
segregate producing two types of gametes
In gamete formation, gene pairs on different chromosome pairs
behave independently of one another (unless theyre linked).
Inference: the act or process of reaching a
conclusion about something from known
facts or evidence.
Inference and Integrated Genetic Fluency (IGF)
Ancient inferences about genetics
The Talmud made an ahead-of-its-time observation that inferred the existence of X-linked genes.
The authors of the Talmud ruled that if a woman bears two sons who die of bleeding after
circumcision, any additional sons that she has, should not be circumcised. They further state that
the sons of her sister must not be circumcised, whereas her brothers sons should be circumcised,
reflecting a clear understanding that this is a disease..
(passed from the mother to her sons).
Milestones of Modern Genetics
1853 Mendel begins pea breeding
experiments (p. 26-27)
Mendel's First Law (p.30): The Principle of Equal Segregation.
During the formation of gametes, the paired characters (alleles)
segregate (or separate) equally so that half of the gametes receive one
allele and half of the gametes receive the other member of the pair.

Mendel's Five Assumptions (p.35): (1) Hereditary determinants
(genes) are particulate in nature (therefore there is no blending of
characters). (2) Each adult pea plant has a pair of genes (alleles) for
each character (as can be seen in the F
1
, one member can be
dominant and one recessive) (3) Members of each gene pair
segregate equally into the gametes (pollen/ovule, sperm/egg) (4)
Consequently, each gamete carries one member of each gene pair (5)
The union of gametes from each parent (to form the zygote) is random.

Mendels 1st Law: Segregation of yellow (Y), green (y)
Parents YY x yy Points 1&2
Gametes Y only y only Points 4
1st Filial Generation (F
1
) Yy zygote
Ovule produced
Points 3
Pollen produced
1/2Y 1/2y
1/2Y
1/2y
1/4YY 1/4Yy
1/4Yy 1/4yy
Overall F
2
Genotypic Ratio 1YY : 2Yy : 1yy, or 3:1 Phenotypic ratio
Points 5
Mendels Experimental System (Fig. 2.1)
Mendels Seven True Breeding Characters
Pea Hybridization Techniques: Monohybrid Cross
Monohybrid
Cross of peas
with purple and
white flowers
(p.28)
P
purple white
F
1
All purple
anthers
removed
pollen placed
on stigma
Dominance and Recessive Traits (p.33)
The dominance or recessive
nature of a character, trait or
gene can be revealed by a
test cross involving the
F
1
and the homozygous
recessive parent.
Test crosses typically give
1:1 ratios for a monohybrid
cross involving a recessive
trait.
Counting traits from his monohybrid crosses, Mendel inferred
his 3:1 ratio, predicted by his Law of Equal Segregation.
Mendels strong inference based on large numbers
During the formation of gametes, the paired characters (alleles) segregate
(or separate) equally so that half of the gametes receive one allele and
half of the gametes receive the other member of the pair (p.32).
Mendels Second Law (p.35)
Independent Assortment:
Gene pairs on separate
chromosomes pairs, assort
themselves independently at
meiosis.
This can be seen from a
dihybrid cross between two
different characters (seed
shape and seed color) on
different chromosomes.
9:3:3:1 ratios are always
characteristic of a dihybrid
cross.
Mendels Law of Independent Assortment (p.80)
In the case of the 9:3:3:1 ratio produced from a
dihybrid cross, Mendel discovered that what looked
like an exception to the 3:1 ratio was in fact, a
mixture of two 3:1 ratios.
In the case of two characters, the members of both
pairs of alleles assort themselves independently into
gametes. The 16 genotypes shown on the next slide
can be broken down into 12:4 round to wrinkled
phenotypes and 12:4 yellow to green phenotypes. In
both instance we can see a 3:1 ratio.
Dihybrid Cross (2 monohybrid crosses) (Fig. 2.11)
The result of a dihybrid
cross are simply the
combination of two,
monohybrid crosses

In this example, the
ratio of round to
wrinkled seeds is
12:4 or 3:1.
Dihybrid Cross (2 monohybrid crosses) (Fig. 2.11)
The result of a dihybrid
cross are simply the
combination of two,
monohybrid crosses

In this example, the
ratio of yellow to
green seeds is 12:4
or 3:1.
Law of Independent Assortment: Summary
Although undiscovered for nearly 40 years, Mendel's
experiments laid the foundation for all future genetic
analysis, molecular biology and the revolutions in
gene cloning and genomics. His work made it
possible to infer the existence and nature of
hereditary material without ever seeing it; and predict
how they will appear in the offspring.
Mendels Laws of Equal Segregation and
Independent Assortment anticipated what would later
be found by microscopic observation in the nuclei of
cells and summarized in the Chromosome Theory of
Inheritance.
Mendels Second Law
Mendels Law of Independent
Assortment is also known as
interchromosomal
recombination and is
observed when dominant and
recessive gene pairs are
located on separate
chromosomes pairs or
unlinked.
As with the monohybrid cross,
a test cross can be use to
demonstrate the presence of
recessive alleles in the F
1

progeny
Dihybrid Test Cross (p. 38-40)
Mendels crosses always produced an F1 that looked like only one of the
two parents. For example, in the monohybrid cross RR x rr, the F1
progeny Rr looks like the round parent. The test cross can be used to
reveal the presence of the recessive allele in the F
1
. The test cross always
involves crossing the F1 progeny with the homozygous recessive parent.
For a monohybrid cross, the test cross progeny exhibit a 1:1 ratio of Rr and
rr. In the dihybrid cross shown above, a 1:1:1:1 ratio of RrYy; Rryy; rrYy;
rryy

RrYy Rryy rrYy rryy
1 : 1 : 1 : 1
ry
ry rY Ry RY
(these ratios occur only with unlinked genes)
Mendels Laws and Chromosome Behavior
Mendels
Laws
Chromosome,
DNA
Behavior
Prediction
(Pedigree
Analysis)
Probability &
Statistics
Mendels
Laws
Chromosome Behavior (mitosis-meiosis) (Ch. 3)
The dihybrid cross reflects the
behavior of chromosomes during
meiosis. Chromosome mechanics
during mitosis and meiosis was
unknown to Mendel.
Interphase Prometaphase Metaphase Anaphase Prophase
Cytokinesis
Telophase
Summary of Chromosome Behavior (p. 74)
Mitosis Meiosis
Chromosomes Duplication
Chromosome duplication and S-phase = DNA replication

Review of Chromosomes During Mitosis (p.70)
Review of Chromosomes During Meiosis (p.74)
Comparison of Mitosis and Meiosis:10 Points (p.73-79)
1. The products of mitosis are two daughter cells, each 2N. The products
of meiosis are four ga metes, each 1N.
2. During mitosis N goes from 2N to 4N to 2N as a result of 1
replication or S phase and 1 cell division. In meiosis, N goes from
2N to 4N to 2N to 1N as a result of 1 replication or S phase but 2 cell
division cycles.
3. Unlike mitotic prophase, the separate chromosomes of meiosis
zygotene prophase I are not distributed throughout the nucleus but
paired into bivalents (paired homologs). The number of bivalents
seen in this stage equal the haploid number of the organism.
4. There is no pairing of homologous chromosomes in mitosis. In meiosis
pairing of homologous chromosomes starts in zygotene and becomes
visible in pachytene.
5. In meiosis, the homologous chromosome pairs align themselves at the
metaphase plate of metaphase I while in mitosis, chromosomes align
at the metaphase plate separately, not in pairs.
6. In mitosis, centromeres divide at anaphase, In meiosis,
centromeres divide during anaphase II, not anaphase I.
7. S phase in cells about to undergo meiosis is longer than for
mitosis. In the newt, Triturus, it takes 12 hours to go through S
prior to mitosis while it takes 10 days in pre-meiotic cells.
8. In meiosis, the fibers coming from the centrosomes attach to the
two sister chromatids of each chromosome are pulled toward
the same pole in meiosis. In mitosis, fibers attached to each
centromere for each chromatid are oriented to opposite poles.
9. Prophase I of meiosis is much longer than prophase of mitosis.
Depending on the organism, the pachytene and diplotene stages
of prophase I may last weeks or years depending on the
organism.
10. Crossing over during the pachytene stage of prophase I of
meiosis can result in some exchanges of genetic material
between homologs.
Comparison of Mitosis and Meiosis (p.73-79)
1902: Sutton and Boveri
propose the chromosome
theory of inheritance.
Chromosome Theory of Inheritance (p.81)
Chromosome continuity. The chromosomes
one observes during one metaphase are exactly
the same as those observed in the next
metaphase (in the nucleus of the daughter cell).

During mitosis and meiosis, chromosomes
divide along the length of the chromosomes.

The pairing between chromosomes during
prophase of meiosis is specific, not random.

Chromosome individuality. Different
chromosome pairs are qualitatively different (i.e.,
carry different genes).

During meiosis, different chromosome pairs
assort themselves independently (Mendel's
dihybrid cross).

A pair of characters (like those described in
Mendels dihybrid cross) can assort themselves
independently during anaphase I of meiosis.
Independent Assortment and Meiosis
R
r
r
R
R R
r r
Y
Y y
y
Independent Assortment (Interchromosomal Recombination)
(p.80; Fig. 3.14)
Mendels Laws and Probabilities/Statistics (p.35-38)
Mendels
Laws
Chromosome,
DNA
Behavior
Prediction
(Pedigree
Analysis)
Probability &
Statistics
Mendels
Laws
Mendels Cross Reveals a Probabilistic Reality
The Punnett square at the left
is just a graphical
representation of probabilistic
outcomes for different
genotypes and phenotypes.
The utility of Punnett squares
breaks down, however, with
the addition of each new trait
to the cross (e.g., monhydrid =
4 squares, dihybrids = 16
squares, trihybrids = 64
squares or (2
n
)
2
where n = the
number of traits in the cross).
Mendels Cross Reveals a Statistical Reality (p. 44-45)
According to Mendels
Laws, the segregation of
alleles into gametes are
independent events.
Therefore, since the
union of gametes is
random, predicting the
outcome for progeny can
be determined using the
product rule and the
sum rule.
Product and Sum Rule (p.44-45)
The product rule states that the probability of independent
events occurring together is the product of the probabilities of
the individual events themselves (also called the and rule).
The sum rule states that the probability of either of two
mutually exclusive events occurring is the sum of their
individual probabilities (also called the or rule).
The product rule is useful for calculating the expected
frequency of a particular genotype while the sum rule is useful
in calculating the expected frequency of a phenotype.
Product Rule (p.44)
The possible outcomes of rolling dice follow the product rule
because the outcome on each separate die is independent of
the others. For example, the probability of rolling a pair of 4s
is calculate based on the probability of rolling one 4 on one
die, which is 1/6 (because the die has six sides and only one
side carries the 4). This probability is written as follows:
p (of a 4) = 1/6
Therefore the probability of rolling a pair of 4s can be written:
p (of two 4s) = 1/6 x 1/6 = 1/36

The product rule deals with one independent event and
another independent event occurring together (4 and 4).
Sum Rule
The sum rule deals with the probability of one mutually
exclusive event or another occurring (A or B). In other words,
either of the two outcomes satisfies the condition of the
probability question. We have already determined that the
probability of two 4s is 1/36. By the same way we can use the
product rule to calculate that the probability of two 5s is also
1/36 (1/6 x 1/6).
Now we can calculate the probability of either two 4s or two 5s
occurring. Because these outcomes are mutually exclusive,
the sum rule tell us that the probability of two 4s or two 5s is
1/18 (1/36 + 1/36). This probability can be written as:
p (of two 4s or two 5s) = 1/36 + 1/36 = 1/18
As you can see, the sum rule states that the probability of
either of two mutually exclusive events occurring is the sum of
their individual probabilities.
Mendels Cross Reveals a Statistical Reality
F1 RrYy (round, yellow)
Gametes: RY; Ry; rY; ry
p of R = 1/2
p of r = 1/2
p of Y = 1/2
p of y = 1/2

p of RY = 1/2 x 1/2 = 1/4
p of Ry = 1/2 x 1/2 = 1/4
p of ry = 1/2 x 1/2 = 1/4
p of rY = 1/2 x 1/2 = 1/4

Predicting frequency if RYRY
genotype in F2:

RYRY = 1/4 x 1/4 = 1/16
(1/2 x 1/2 x 1/2 x 1/2 = 1/16)
Mendels Cross Reveals a Statistical Reality
F1 RrYy (round, yellow)
Gametes: RY; Ry; rY; ry
p of R = 1/2
p of r = 1/2
p of Y = 1/2
p of y = 1/2

p of RY = 1/2 x 1/2 = 1/4
p of Ry = 1/2 x 1/2 = 1/4
p of ry = 1/2 x 1/2 = 1/4
p of rY = 1/2 x 1/2 = 1/4

Predicting frequency wrinkled
phenotype (rr--) in F2:

1/16 + 1/16 + 1/16 + 1/16 = 1/4

Product Rule Example
To create at homozygous tester plant line for five traits, a researcher had to
make the following cross:
A /a ; b /b ; C /c ; D /d ; E /e X A /a ; B /b ; C /c ; d /d ; E /e
What is the probability of finding a plant with the following genotype:
a /a ; b /b ; c /c ; d /d ; e /e
A/a x A/a a/a = 1/4
b/b x B/b b/b = 1/2
C/c x C/c c/c = 1/4
D/d x d/d d/d = 1/2
E/e x E/e e/e = 1/4
Product Rule = 1/256
The researcher will need a minimum of 256
progeny to get 1 homozygous plant at all 5 loci.

Product/Sum Rules
Mendels 1st and 2nd Laws of Inheritance.
Definitions
Using crosses to infer the nature of inheritance.
Test Crosses and recessive traits
Mitosis and Meiosis.
Mendelian inheritance and Chromosome Theory
Cell cycle and chromosome replication
Product and Sum Rules
Application of Product and Sum Rules in genetic crosses.
This Lecture: Mendel and Chromosomes
Achieving Integrated Genetic Fluency (IGF)
Mendels
Laws
Chromosome,
DNA
Behavior
Prediction
(Pedigree
Analysis)
Probability &
Statistics
Mendels
Laws
You should be here.

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