PORTLAND STATE UNIVERSITY BI 341

CHAPTER 3: THE CHROMOSOMAL BASIS OF

HEREDITY
Kim H. Brown, PhD
 So far in this class
Genetic material is passed from one generation to the next
• Chapter 1: Genetic material is contained in DNA-genes-
chromosomes
• Chapter 2: Pattern of inheritance of genetic material
depends on
• segregation (only one of two alleles parental are
inherited)
• independent assortment (combination of inherited
alleles is random)
To understand how inherited traits are passed from one
generation to the next we must understand how DNA is
replicated and sorted into gametes in a manner consistent
with Mendel’s laws: Meiosis!
 Cells divide to accomplish growth and
development

Mitotic Cell division:

organisms grow or
increase in number
Differentiation: After cell
division, daughter cells
may become specialized
for specific functions
Cell cycle: repeating
pattern of division,
growth, and
differentiation
 Objectives
The mechanism of meiosis predicts both segregation and independent
assortment of homologous chromosomes. To understand meiosis, we must
also understand:
1. Genes exist on chromosomes
• Chromosome structure and function
• Thomas Hunt Morgan: Theory of Chromosomal Inheritance: X-linked
traits
2. Chromosomes exist in homologous pairs in diploid organisms
• The generation of haploid gametes underlies patterns of gene
inheritance
3. In one phase of the cell cycle, mitosis partitions chromosomes into
dividing cells
4. Meiosis reduces the chromosome number from diploid to haploid in germ
cells and spores
5. Revisiting probabilities
• Some helpful rules
• Chi squared test: Relate hypothetical probabilities of patterns of
inheritance to “real life” observations associated with
 Eukaryotic Cell Cycle
Interphase:
1. G1 (growth phase 1)
acquisition of nutrients,
growth
2. S (DNA synthesis):
chromosome replication
3. G2 (growth phase 2)
completion of cell growth,
preparation for cell division
Cell division:
1. Mitosis: division of the
nucleus
2. Cytokinesis: cytoplasmic
division
 Prior to cell division, the DNA is replicated
A duplicated chromosome consists of two identical DNA
double helices, called sister chromatids, which are attached
to each other at the centromere
 Chromatin Remodeling
• In eukaryotes, DNA is
wrapped around proteins to
create a protein–DNA
complex called chromatin
• RNA polymerase (required
for transcription) cannot
access the DNA when it is
supercoiled within the
nucleus
• Chromatin remodeling
• DNA near the promoter
is released from tight
interactions with proteins
to allow transcription
http://micro.magnet.fsu.edu/cells/nucleus/chromatin.html
 Chromatin Structure
• In the nucleus of a nondividing cell,
chromatin fibers form discrete
chromosome territories
• Chromosome territories are
correlated with gene densities
• Territories of chromosome
domains that are relatively gene
rich tend to be located toward the
interior of the nucleus

Figure 03.18: Chromosome territories

formed by 30-nm chromatin fibers within the
Bozeman Science What are nucleus of a nondividing cell. Figure
courtesy of Tobias A. Knoch, Erasmus MC,
Chromosomes? Rotterdam, and Kirchhoff-Institute for
Physics, Ruperto-Carola University,
http://www.bozemanscience.com/what- Heidelberg
are-chromosomes/
 What Is Chromatin’s Basic Structure?
• Chromatin has a regular structure with several layers of
organization
• Chromatin contains nucleosomes
• Repeating, beadlike structures
 What Is Chromatin’s Basic Structure?
Nucleosomes consist of
• Negatively charged DNA
• Wrapped twice around eight
positively charged histone
proteins
• A histone protein called H1
functions to maintain the
structure of each
nucleosome
 What Is Chromatin’s Basic Structure?
• Between each pair of
nucleosomes, there is a “linker”
stretch of DNA
• H1 histones also may interact
with each other and with histones
in other nucleosomes to form
• A tightly packed structure
called a 30-nanometer fiber

• Chromatin’s elaborate structure

• Allows the DNA to be
packaged in the nucleus
• Plays a key role in regulating
gene expression
 Chromatin Structure
• Each nucleosome is composed of a core particle, ~55 base
pairs of DNA called linker DNA that links adjacent core
particles, and one molecule of histone H1 that binds the core
particle to the linker DNA
• Each core particle consists of an octamer of pairs for each
histone
 Chromatin Structure
• The spaces between the
chromatin domains form a
network of channels large
enough to allow passage of the
molecular machinery for
replication, transcription, and
RNA processing
• Replication takes place in
small discrete regions that
exhibit a reproducible
temporal and spatial pattern
• Transcription takes place in a
few hundred discrete locations
 Chromatin Structure
• Compact and heavily stained
regions of chromatin are known as
heterochromatin, which mainly
consists of highly repeated
noncoding DNA sequences—
satellite DNA

• The rest of the chromatin, which

becomes visible only after
chromosome condensation in
mitosis or meiosis, is called
euchromatin
• The number of genes located in
heterochromatin is small relative
to the number in euchromatin
 Chromosome Structure
• The centromere is essential
for chromosome segregation

• It serves as a central
component of the
kinetochore the complex of
DNA and proteins to which
the spindle fibers attach and
move the chromosomes in
both mitosis and meiosis

Time lapse video:

https://www.cellimagelibrary.org/images/10723
 Objectives
The mechanism of meiosis predicts both segregation and independent
assortment of homologous chromosomes. To understand meiosis, we must
also understand:
1. Genes exist on chromosomes
• Chromosome structure and function
• Thomas Hunt Morgan: Theory of Chromosomal Inheritance: X-linked
traits
2. Chromosomes exist in homologous pairs in diploid organisms
• The generation of haploid gametes underlies patterns of gene
inheritance
3. In one phase of the cell cycle, mitosis partitions chromosomes into
dividing cells
4. Meiosis reduces the chromosome number from diploid to haploid in germ
cells and spores
5. Revisiting probabilities
• Some helpful rules
• Chi squared test: Relate hypothetical probabilities of patterns of
inheritance to “real life” observations associated with
 The Chromosomal Theory of Inheritance
• Chromosome Theory of
Heredity: Genes are located
in chromosomes

• Early evidence that genes

are located on chromosomes
was found by Thomas Hunt
Morgan in 1910

• Morgan’s studied inheritance

patterns in Drosophila
melanogaster and found that
in some cases reciprocal
crosses yield different results
 The Chromosomal Theory of Inheritance
Thomas Hunt Morgan used fruit
flies (Drosophila melanogaster)
as a model organism for genetic
research
• Morgan’s first goal was to
identify different phenotypes
• Wild type: The most
common phenotype for each
trait
• Mutation: Phenotypes that
differed from the wild type
• Resulted from a change
in a gene
• Mutants: Individuals with
traits attributable to mutation
 Thomas Hunt Morgan’s Experiments
• Morgan identified
• Red eyes as the wild type for eye color
• White eyes as a mutation
 Thomas Hunt Morgan’s Experiments
He mated a wild-type female fly
with a mutant male fly
• All of the F1 progeny had red
eyes
When Morgan did the reciprocal
cross
• The F1 females had red eyes
• But the F1 males had white
eyes
These experiments suggest a
relationship between
• The sex of the progeny
• The inheritance of eye color
in Drosophila
 The Discovery of Sex Chromosomes

Nettie Stevens analyzed

beetle karyotypes and found
• Females’ diploid cells
contain 20 large
chromosomes
• Males’ diploid cells have
19 large and 1 small (Y)
chromosomes
• Y chromosomes pair
with the large X
chromosome during
meiosis I
 The Discovery of Sex Chromosomes
• X and Y chromosomes are
now called sex
chromosomes
• They determine the
sex of the offspring
• In beetles (like
humans)
• Females have two
X chromosomes
• Males have an X
and Y
• Other species have TedEd Video: Sex determination, more
complicated than you thought
other systems http://ed.ted.com/lessons/sex-determination-
more-complicated-than-you-thought
 X-Linked Inheritance
• Morgan put together his
experimental results with Stevens’
observations
• The gene for white eye color in
fruit flies is located on the X
chromosome
• Y chromosome does not carry an
allele of this gene
• X-linked inheritance (or X-linkage)
• Females (XX) have two copies of
the gene
• Males (XY) have only one
 X-Linked Inheritance and the Chromosome
Theory
• The various inheritance
patterns that can occur when
genes are carried on the sex
chromosomes
• Is termed sex-linked
inheritance or sex-
linkage
• Females and males have
different numbers of
alleles of that gene
• Non-sex chromosomes are
called autosomes
• Genes on autosomes are
said to show autosomal
inheritance
 X-Linked Inheritance and the Chromosome
Theory
• The discovery of X-linked
inheritance convinced most
biologists
• The chromosome theory
of inheritance was correct
• Mendel’s work was
rediscovered
• Researchers began to
analyze traits and alleles
whose inheritance was
more complicated
 Chromosomes & karyotype
• Chromosome complement = the complete set of
chromosomes
• The nucleus of each somatic cell contains a fixed number
of chromosomes typical of the particular species, this
number is independent of complexity

Gene Number vs. Organism

Complexity
https://www.dnalc.org/view/15
322-Gene-number-and-
complexity-Eric-Lander.html
 Chromosomes Come in Distinct Types

• Every organism has a

characteristic number of
chromosomes
• A karyotype
• Is the number and types of
chromosomes present in
an organism
• Humans have 46
chromosomes in every cell
(except their gametes)
• 1 pair of sex chromosomes
• 22 pairs of autosomes
 Homologous Chromosomes Have the Same
Genes
• Chromosomes of the same type
are
• called homologous
chromosomes or homologs
• Homologous chromosomes are
similar
• Carry genes for the same
inherited characteristics
• They are not identical: May
carry different versions of the
same gene
 Objectives
The mechanism of meiosis predicts both segregation and independent
assortment of homologous chromosomes. To understand meiosis, we must
also understand:
1. Genes exist on chromosomes
• Chromosome structure and function
• Thomas Hunt Morgan: Theory of Chromosomal Inheritance: X-linked
traits
2. Chromosomes exist in homologous pairs in diploid organisms
• The generation of haploid gametes underlies patterns of gene
inheritance
3. In one phase of the cell cycle, mitosis partitions chromosomes into
dividing cells
4. Meiosis reduces the chromosome number from diploid to haploid in germ
cells and spores
5. Revisiting probabilities
• Some helpful rules
• Chi squared test: Relate hypothetical probabilities of patterns of
inheritance to “real life” observations associated with
 Humans are Diploid, our Gametes are Haploid
• Chromosomes exist in
homologous pairs in diploid
organisms

• Somatic cells (body cells) of a

given species have a specific
number of chromosomes
• Present as homologous pairs
• E.g.: Humans: 46 chromosomes
(23 homologous pairs)
• Gametes (egg and sperm)
• Are haploid (23 chromosomes
in humans)
 Passing DNA from one cell to another
• In eukaryotes, transmission of
genetic material from one
generation of cells to the next
involves the production of
gametes which contain the
inheritable genes
• During sexual reproduction
• A haploid sperm and an
haploid egg unite to form a
new diploid individual
• This process is called
fertilization
 Fertilization Results in a Diploid Zygote
Fertilization: haploid
gametes fuse, creating
diploid zygote
• Each diploid individual
receives a haploid
chromosome set from both
its mother and its father
• Homologs are either
• Maternal
chromosomes
Paternal
chromosomes
 There are two types of cell division

Meiosis: Production of gametes

(eggs and sperm)
• Daughter cells have half the
amount of genetic material
as the parent cell
• Mitosis: production of somatic
cells
• Genetic material is copied
and then divided equally
• Daughter cells are
genetically identical to the
parent cell
 The Cell Cycle
There are a total of four phases in the cell cycle:
• M phase
• An interphase consisting of the G1, S, and G2 phases
Gap phases allow the cell to
• Grow large enough
• Synthesize enough organelles to ensure the daughter cells
• Be normal in size and function
 Chromosome Replication
• Before mitosis, each chromosome is replicated
• Each of the DNA copies in a replicated chromosome is called a
chromatid
• Chromatids are joined together along their entire length
• As well as at a specialized region of the chromosome called
the centromere
 Chromosome Replication
• Chromatids from the same chromosome are referred to as sister
chromatids
• A replicated chromosome consists of two chromatids
• It is still considered a single chromosome
 M Phase and Interphase
Growing cells cycle between two phases:
1. A dividing phase called the mitotic (M) phase
2. A nondividing phase called interphase
Chromosome replication occurs only during interphase
• It does not occur during M phase
• The stage in which DNA replication occurs is called the
synthesis (S) phase
 Interphase: Gap Phases
Interphase also includes two gap phases during which
• no DNA synthesis occurs during the gap phases
• Organelles replicate
• Additional cytoplasm is made in preparation for cell division
G1 phase Is the first gap before the S phase
G2 phase Is the second gap between S phase and mitosis

Cancer and the cell cycle,

chemotherapy:
http://www.youtube.com/watch
?v=VRhz3DhjG5M
 Chromosomes Change during the Cell Cycle
After replication during S phase, each chromosome consists of
• Two genetically identical sister chromatids attached at the
centromere
At the start of mitosis, the replicated chromosomes condense
 Mitosis Overview
• Mitosis results in
• The division of replicated chromosomes
• Formation of two daughter nuclei with identical
chromosomes and genes
• Mitosis is usually accompanied by cytokinesis (splitting of the
cytoplasm)
 Events in Mitosis
• During mitosis the two sister chromatids separate to form
independent chromosomes
• One copy of each chromosome goes to each of the two
daughter cells
• Each daughter cell receives a copy of the genetic
information that is contained in each chromosome
 The stages of
Mitosis

1. Prophase
2. Metaphase
3. Anaphase
4. Telophase

Note: your text considers

prophase = early + late
prophase= prophase +
prometaphase
 Prophase
• Prophase is marked by the
condensation of chromosomes.
Each chromosome is already
longitudinally double, consisting
of two subunits called
chromatids
• The chromatids in a pair are
held together at a specific
region of the chromosome
called the centromere.
 Metaphase
Metaphase:mitotic spindle forms
• The spindle is a bipolar structure
arching between the
centrosomes that consists of
microtubules
• The spindle fibers attach to
each chromosome in the region
of the centromere called the
kinetochore
• The chromosomes move toward
the center of the cell until all the
kinetochores lie on an imaginary
plane equidistant from the
spindle poles = the metaphase
plate
 Anaphase

• In anaphase, the
centromeres divide
longitudinally, and the two
sister chromatids of each
chromosome move toward
opposite poles of the spindle
• Once the centromeres divide,
each sister chromatid is
regarded as a separate
chromosome in its own right.
 Telophase
Telophase: nuclear envelope
forms around each compact group
of chromosomes, nucleoli are
formed, and the spindle disappears
• The chromosomes undergo
decondensation until they are no
longer visible as discrete entities
• The two daughter nuclei assume
a typical interphase appearance
• The cytoplasm of the cell divides
in two
 Objectives
The mechanism of meiosis predicts both segregation and independent
assortment of homologous chromosomes. To understand meiosis, we must
also understand:
1. Genes exist on chromosomes
• Chromosome structure and function
• Thomas Hunt Morgan: Theory of Chromosomal Inheritance: X-linked
traits
2. Chromosomes exist in homologous pairs in diploid organisms
• The generation of haploid gametes underlies patterns of gene
inheritance
3. In one phase of the cell cycle, mitosis partitions chromosomes into
dividing cells
4. Meiosis reduces the chromosome number from diploid to haploid in germ
cells and spores
5. Revisiting probabilities
• Some helpful rules
• Chi squared test: Relate hypothetical probabilities of patterns of
inheritance to “real life” observations associated with
 Meiosis and Mendel’s laws
The mechanism of meiosis
predicts both segregation
and independent
assortment of homologous
chromosomes
• Meiosis converts the
diploid number (2n) of
chromosomes to the
haploid number (n)
• Each chromosome sorts
into a gamete
independently of the
other chromosomes
 Meiosis Is Two Cell Divisions

Meiosis consists of two cell

divisions
1. Meiosis I
2. Meiosis II
• The two divisions occur
consecutively but differ
sharply

Animation: Bozeman Science Video Cell Cycle, Mitosis, Meiosis

http://www.bozemanscience.com/028-cell-cycle-mitosis-and-meiosis/
Explaining Mendelian Genetics

Figure 3.10a
Explaining Mendelian Genetics

Figure 3.10b
Explaining Mendelian Genetics

Figure 3.10c
 Meiosis Is a Reduction Division

• The outcome of meiosis

• reduction division:
reduction in
chromosome number
• In most plants and animals
• The original cell is diploid
• The four daughter cells
are haploid
• In animals, these daughter
cells become gametes
• This process is called
gametogenesis
 Meiosis Is a Reduction Division
• Meiosis is a more complex and
considerably longer process
than mitosis and usually
requires days or even weeks
• In animals, meiosis takes
place in specific cells called
meiocytes: the oocytes form
egg cells and the
spermatocytes form sperm
cells
• In the females of animals and
plants, only one of the four
products develops into a
functional cell (the other three
disintegrate)
 An Overview of Meiosis
• Meiosis reduces chromosome
number by half
• In diploid organisms, the
products of meiosis are haploid
• Just before meiosis begins,
each chromosome in the diploid
(2n) parent cell is replicated
• When replication is complete,
each chromosome
• Has two identical sister
chromatids
• They are attached at the
centromere
Bozeman Science:
http://www.bozemanscience.com/meiosis
 Meiosis Is Two Cell Divisions
Meiosis consists of two cell
divisions
1. Meiosis I
2. Meiosis II

The two divisions occur

consecutively but differ
sharply
 An Overview of Meiosis I
During meiosis I, the diploid
(2n) parent cell produces two
haploid (n) daughter cells
• The homologs in each
chromosome pair:
• Separate
• Go to different daughter
cells
• The daughter cells are haploid
(n)
• Each chromosome
consists of two identical
sister chromatids
 An Overview of Meiosis II

During meiosis II, the sister

chromatids of each chromosome
• Separate
• Go to different daughter
cells
Four haploid daughter cells are
produced by meiosis II
• They also have one of
each type of chromosome
• But now the chromosomes
are unreplicated
 The Phases of Meiosis I
Meiosis I is a continuous
process with four distinct
phases:
1. Prophase I
2. Metaphase I
3. Anaphase I
4. Telophase I

Note: your text considers prophase = early + late prophase= prophase +

prometaphase
 The Phases of Meiosis I

Early Prophase I
• The homolog pairs come
together in a pairing process
called synapsis
• The structure that results
from synapsis is called a
tetrad, consisting of two
homolog
• The chromatids of the
homologs are called non-
sister chromatids
 The Phases of Meiosis I

Late Prophase I
• The non-sister chromatids
begin to separate
• Exchange or crossing over
between homologous non-
sister chromatids occurs:
• Where chiasmata are
formed during this stage
Metaphase I
• The tetrads line up at the
metaphase plate
Metaphase I: Independent assortment
nonhomologous chromosomes.
 The Phases of Meiosis I
Anaphase I
• The paired homologs
separate
• Begin to migrate to
opposite ends of the
cell
Telophase I
• The homologs finish
migrating to the poles
of the cell
• Then the cell divides in
the process of
cytokinesis
 Anaphase I: Segregation
The physical separation of
homologous chromosomes in
anaphase I is the physical basis
of Mendel’s principle of
segregation
 The Result of Meiosis I

• The end result of meiosis I

one chromosome of each
homologous pair is
distributed to a different
daughter cell
• A reduction division has
occurred
• The daughter cells of
meiosis I are haploid: Still
in the form of sister
chromatids
The Phases of Meiosis II
Like meiosis I, meiosis II is a continuous process, but with four
distinct phases:
1. Prophase II
2. Metaphase II
3. Anaphase II
4. Telophase II
 The Phases of Meiosis II
Prophase II
• The spindle apparatus
forms
• One spindle fiber
attaches to the
centromere of each
sister chromatid
Metaphase II
• Replicated
chromosomes line up at
the metaphase plate
 The Phases of Meiosis II
Anaphase II
• Sister chromatids
separate
• The resulting daughter
chromosomes begin
moving to opposite sides
of the cell
Telophase II
• Chromosomes arrive at
opposite sides of the cell
• A nuclear envelope forms
around each haploid set
of chromosomes
• Each cell undergoes
cytokinesis
 The Result of Meiosis II

Meiosis II Results in four

haploid cells
• Each has one of each
type of chromosome

One diploid cell with replicated

chromosomes Gives rise to
four haploid cells with
unreplicated chromosomes

Bozeman Science Video: Phases of mitosis

http://www.bozemanscience.com/phases-of-meiosis
 Comparison of Meiosis and Mitosis
• The key difference between the two processes:
• Homologs pair in meiosis
• Homologs do not pair in mitosis
• Because homologs pair in prophase of meiosis I
• They can migrate to the metaphase plate together
• Then separate during anaphase of meiosis I
• Resulting in a reduction division
 Comparison of Meiosis and Mitosis
• Meiosis thus produces four daughter cells:
• Each cell has half the genetic material of the parents
• Mitosis produces two daughter cells
• They are genetically identical to the parent cells

Bioflix Mitosis Video:

https://vimeo.com/859
39821
Bioflix Meiosis Video:
https://vimeo.com/860
13234
 REVISITING PROBABILITY:

The Trihybrid Cross

Demonstrates That
Mendel's Principles Apply
to Inheritance of Multiple
Traits
THE TRIHYBRID CROSS
 Chi-Square Analysis Evaluates the Influence of
Chance on Genetic Data
• Chance deviation from an expected outcome is
diminished by larger sample size
 Chi-Square Calculations and Null Hypothesis

• When we assume that data will fit a given ratio, we

establish what is called the null hypothesis—so named
because it assumes that there is no real difference
between the measured values (or ratio) and the predicted
values (or ratio)
• The apparent difference can be attributed purely to
chance
• Chi-square (2) analysis is used to test how well the data
fit the null hypothesis
 Chi-Square Analysis
• Chi-square analysis requires that the degree of freedom
(df) be taken into account, since more deviation is
expected with a higher degree of freedom
df = Number of Genotypes – Number of Alleles,
where n is the number of different categories into
which each datum point may fall
In our case, this is the number of phenotypes
• Once the number of degrees of freedom is determined,
the 2 value can be interpreted in terms of a
corresponding probability value (p)
 Chi-Square Analysis
• The test of goodness of fit = test analyzes whether
observed data agree with theoretical expectation

• A conventional measure of goodness of fit is a value

called chi-square, 2

• 2 = ∑(observed – expected)2 / expected

• A value of 2 = 0 means that the observed numbers fit the

expected numbers perfectly

Bozeman Science Chi-squared test video:

http://www.bozemanscience.com/chi-squared-
test/
Chi-square (2) analysis is used to test how well
the data fit the PREDICTION
http://www.wikihow.com/Calculate-P-Value
P value calculator:
http://graphpad.com/quickcalcs/PValue1.cfm
 The table from your text

http://www.wikihow.com/Calculate-P-Value
P value calculator:
http://graphpad.com/quickcalcs/PValue1.cfm