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Unit 5 Heredity Student Notes Page 1

AP Biology

Unit 5

Student Notes
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Unit 5 Heredity Student Notes Page 2

Unit 5 Student Notes

Table of Contents

A. Chromosomes, Meiosis, and Sexual Reproduction—Pages 3-7

B. Important Terms Related to Chromosomes and Meiosis—Pages 3-5
C. Types of Reproduction—Page 6
D. Types of Life Cycles—Pages 7-8
E. Meiosis—Pages 8-14
F. Gametogenesis—Pages 14--16
G. Nondisjunction—Pages 16-20
H. Chromosomal Rearrangements—Page 21
I. Crossover Frequency/Chromosome Mapping—Page 22
J. Mitosis and Meiosis Compared and Contrasted—Page 23
K. Mendelian Inheritance —Pages 23-27
L. Important Terms Related to Mendelian Inheritance—Pages 23-25
M. Monohybrid Cross—Pages 25-27
N. Dihybrid Cross—Pages 27-28
O. Trihybrid or Larger Cross—Pages 28-29
P. Linked Genes and Dihybrid Crosses—Pages 29-30
Q. Non-Mendelian Inheritance Patterns—Pages 30-32
R. Pedigree Charts/Modes of Inheritance—Pages 33-37
S. Modes of Inheritance--Autosomal Dominant—Page 34
T. Modes of Inheritance--Autosomal Recessive—Page 34
U. Modes of Inheritance--X-linked Dominant—Page 35
V. Modes of Inheritance--X-linked Recessive—Pages 35-36
W. Modes of Inheritance--Y-linked—Page 36
X. Modes of Inheritance--Mitochondrial--Page 37
Y. Environmental Effects on Phenotype—Page 38
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Important Ideas/Enduring Understandings for this unit.
• Heritable information provides for the continuity of life.
• Organisms are linked by line of descent from common ancestry.
• Naturally occurring diversity among and between components within biological systems affects interactions with the
environment.

Chromosomes, Meiosis, and Sexual Reproduction

Important Terms

Heredity
Heredity refers to the transmission of traits from one generation to the next by INHERITING DNA from a single
parent (asexual reproduction) or from two parents (sexual reproduction). The genetic information transmitted via
the DNA provides for the continuity of life across generations. Major features of the genetic code and many of
the core metabolic pathways regulated by genes are conserved across all living things. All life forms possess
DNA, RNA, and ribosomes and carry out the processes of DNA replication, transcription, and translation (protein
synthesis) in very similar ways. This high level of conservation supports the concept of common ancestry for all
organisms.

Chromosome

Chromosomes are the packaged and organized structures of DNA found in cells. Chromosomes consist of
chains of linked genes and associated proteins. The chromosomal basis of inheritance can be used to explain
the pattern of transmission of genes from parent(s) to offspring.
A eukaryotic chromosome consists of a single molecule of DNA wrapped around proteins called histones.
The histones function to package and organize the DNA. They also play an important role in gene
regulation.
Eukaryotic chromosomes are only visible (with a microscope) just before and during cell division. During
other parts of the cell cell cycle, the DNA is present in an a less condensed form known as chromatin. In
this form, the DNA can be transcribed and replicated.
Each chromosome contains several genes and the other DNA sequences involved in the regulation of the
genes. Genes that are located on the same chromosome are said to be linked.
Eukaryotic chromosomes are said to have a linear shape.
After replication, eukaryotic chromosomes often have an “X-shaped” appearance. These structures are
more correctly referred to as bivalent chromosomes. They consist of two copies of the original
chromosome attached at a central point known as the centromere. While connected the two copies are
referred to as chromatids.
Chromosomes that are not involved in gender determination are called autosomes. Human cells contain 44
autosomes.
Chromosomes that are involved in the process of gender determination are called sex chromosomes. Human
females have two X sex chromosomes, while human males have one X and one Y sex chromosome.
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BIVALENT
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A prokaryotic chromosome is circular and resides in a cell region called the nucleoid. Prokaryotes typically have
only one chromosome per cell. The types of proteins found in prokaryotic chromosomes, known as the nucleoid-
associated proteins, differ from the histone proteins that appear in eukaryotic chromosomes and cause the prokaryotic
chromosomes to form looped structures. In addition to the single, circular chromosome, many prokaryotes also
contain plasmids. A plasmid is a small, circular, double-stranded DNA molecule that is distinct from a cell's
chromosomal DNA. Plasmids naturally exist in bacterial cells, and they also occur in some eukaryotes. Often, the
genes carried in plasmids provide bacteria with genetic advantages, such as antibiotic resistance. Plasmids can be
exchanged between bacterial cells during the process of conjugation. During conjugation the bacterial cells attach to
each other and exchange plasmids. This is an important process for increasing genetic variation within the population.

Gene
A gene is a segment of DNA which codes for a single polypeptide or protein. Each chromosome consists of a
chain of several genes and the accompanying regulatory sequences and associated proteins.

Genome
A genome is an organism's complete set of DNA, including all of its genes. Each genome contains all of the
information needed to build and maintain that organism. In humans, a copy of the entire genome—more than 3 billion
DNA base pairs—is contained in all cells that have a nucleus.

Haploid
Haploid refers to cells that have only one copy of each type of chromosome. Haploid cells are sometimes referred to
as N or 1N cells. In human cells, the haploid number is 23. The only haploid cells found in the human body are the
gametes or sex cells.

Diploid
Diploid cells have two copies of each type of chromosome. Diploid cells are sometimes referred to as 2N cells. In
human cells, the diploid number is 46. All of the human body’s somatic cells are diploid.

Locus
The location of a gene on a chromosome.
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Types of Reproduction
Asexual Reproduction
Asexual reproduction involves only ONE parent. During the process, the parent produces clones which are
genetically identical to itself. The benefits of asexual reproduction are that the process can occur rapidly,
the process requires less energy than sexual reproduction, and that only one organism is required to carry
out the process. Examples of asexual reproduction include binary fission in bacteria, budding in yeasts and
hydras, and vegetative propagation in some plants.
The major disadvantage of asexual reproduction is that it produces identical organisms. Since there is no
variation, the ability of the population to adapt/evolve is severely limited. Asexual reproduction works
well in stable environments (to which the organism is well adapted), but does not work well in changing
environments to which populations need to be able to adapt.

Sexual Reproduction
Sexual reproduction involves the combining of DNA from two parents to create an offspring. During
fertilization, two haploid games fuse together to form a zygote. Fertilization restores the diploid
number of chromosomes and maintains in from generation to generation. The major benefit of the
sexual reproduction is that it creates genetic diversity/variation within the population by combining the
DNA from two different individuals to form a new organism with new allele combinations. This
variation allows the population to adapt/evolve with a changing environment. The major
disadvantages of sexual reproduction are that two parents of opposite sexes are required (this may be
nearly impossible for endangered species to be able to do), the process takes much longer than asexual
reproduction, and the process requires more energy than asexual reproduction. Most animals and
plants reproduce sexually. Some protists and fungi also utilize sexual reproduction.
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Types of Life Cycle

Most living things follow one of three possible types of life cycles, based on the amount of DNA within their
cells.

Haploid Majority
Organisms with a haploid life cycle spend the majority of their lives as haploid cells. When two of the
haploid cells fuse, they form a diploid zygote. The zygote quickly undergoes meiosis to produce
more haploid cells that repeat the life cycle.
This haploid majority life cycle occurs mostly in Fungi and Protists.
The fusion of the haploid cells and the accompanying meiosis event, functions to create genetic
diversity/variation within the population.

Diploid Majority
Organisms with a diploid life cycle spend the majority of their lives as multicellular organisms
composed of diploid cells. In these organisms, diploid germ cells undergo meiosis to create haploid
gametes/sex cells. During fertilization, a haploid egg fuses with a haploid sperm to create a diploid
zygote. The zygote undergoes repeated rounds of mitosis to create a multicellular organism composed
of diploid cells. Most animals exhibit a diploid majority life cycle.

Alternation of Generations

Organisms which exhibit an alternation of generations alternate between a haploid sexual phase (the
gametophyte) and a diploid asexual phase (the sporophyte) of the life cycle.

The gametophyte generation begins with a spore produced by meiosis. The spore is haploid, and
all of the cells derived from it (by mitosis) are also haploid. In due course, this multicellular
structure produces gametes — by mitosis — and the fusion of two of these gametes then produces
the diploid sporophyte generation.

The sporophyte generation starts as a diploid zygote. Eventually, certain cells within the organism
undergo meiosis, forming spores. Each spore is capable of developing into a new haploid
gametophyte. Most plants exhibit an alternation of generations.
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In bryophytes, such as mosses and liverworts, the gametophyte is the dominant life phase, whereas
in angiosperms and gymnosperms the sporophyte is dominant. The haploid phase is also dominant
among fungi.

Meiosis

Meiosis is a specialized type of nuclear division (in sexually reproducing diploid organisms) that reduces the
chromosome number by half, creating four haploid cells, each genetically distinct from the parent cell that gave rise to
them. The haploid cells, after undergoing a period of maturation, become gametes.
The two main roles of meiosis are to create haploid gametes and to increase genetic diversity/variation within the
gametes.

In multicellular animals, meiosis occurs only in the sex organs/gonads. The only cells capable of doing meiosis are
specialized, diploid germ cells found in the gonads.

Before meiosis begins, the DNA is replicated during the S phase of interphase.

Meiosis involves two rounds of a sequential series of steps. These rounds are referred to as Meiosis I and Meiosis II.

Stages of Meiosis
Meiosis I
Prophase I
Meiosis begins with Prophase I. During Prophase I, the cell’s chromatin coils and condenses to form bivalent
chromosomes. The nucleolus disappears. The centrosomes form the spindle fibers and the nuclear envelope disintegrates.
Chromosomes of the same type/number (homologous chromosomes) pair up and join together during the process of
synapsis to form tetrads (groups of 4 homologous chromatids). The members of each pair contain the same genes in the
same order on the chromosome, but may contain different alleles or versions of the genes. After synapsis, the homologous
chromosomes undergo the process of crossing over in which they physically exchange segments. This is an example of
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genetic recombination. The process is an important source of genetic variation/diversity in the gametes that result at the
end of meiosis.

Metaphase I
During Metaphase I, the two members of each homologous pair of bivalent chromosomes align on each side of
the metaphase plate (middle of the cell). Each chromosome also attaches to the spindle fibers at a point on the
centromere known as the kinetochore. During the process of lining up, the paternal and maternal members of each
homologous pair randomly line up across from each other on either side of the metaphase plate. The pattern in which each
pair arranges itself is completely independent of the other homologous pairs. This process of random alignment, known as
independent assortment, can create up to 223 (8,388,608) possible alignments in human germ cells. Since the two rows
of chromosomes will eventually end up in different gametes, the process of independent assortment gives each human the
ability to create over 8 million genetically distinct types of gametes. Independent assortment increases genetic variation
by allowing daughter cells to each randomly receive a different proportion of paternal and maternal chromosomes.
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In the diagram above, red chromosomes represent maternal chromosomes and blue ones represent paternal chromosomes.
During independent assortment, both red, maternal chromosomes could face the top pole and both blue chromosomes
could face the bottom pole or both blue chromosomes could face the top pole and both red could face the bottom or one
red on the left and one blue on the right could face the top or one blue on the left and one red on the right could face the
top. It turns out the total possible combinations of alignments due to independent assortment can be found by raising 2 to
the number of homologous pairs contained within the cell. Number of combinations=2 number of homologous pairs
For example, a cell with 6 homologous pairs of chromosomes could independently assort into 2 6 or 64 different
arrangements.

Anaphase I
During Anaphase I, one member of each homologous pair of chromosomes is pulled toward each pole of the cell by the
microtubules of the spindle apparatus. This process is called Segregation. The individual chromatids of each bivalent
chromosome are not separated as they are during the anaphase stage of mitosis. Anaphase I separates the members of the
homologous pairs from each other. This process of separation ensures that each gamete receives a haploid (1N) set of
chromosomes comprised of a mixture of chromosomes from both parents.

Telophase I
During Telophase I, the homologous chromosome pairs reach the poles of the cell, the spindle fibers disappear, nuclear
envelopes form around each set of chromosomes, and cytokinesis follows to produce two cells. The two new cells are
haploid and have half the number of chromosomes as the original germ cell. It is important to note that we count
chromosomes by counting the number of centromeres present. Even though the chromosomes at the end of telophase I are
bivalent, each bivalent chromosome has one centromere and only counts as a single chromosome.
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Meiosis I is often referred to as reductive division, because it halves the number of chromosomes found in the two cells
which result from the process.

To summarize, Meiosis I begins with 1 diploid germ cell and ends with 2 haploid cells which both possess bivalent
chromosomes.

Interkinesis
Interkinesis is a short interphase-like period that occurs between Meiosis 1 and Meiosis 2. No DNA replication occurs
during interkinesis, however it does occur during the interphase I stage that occurs before meiosis begins. During
interkinesis, the single spindle of the first meiotic division disassembles and the microtubules reassemble into two new
spindles for the second meiotic division.

Meiosis 2

Prophase II

The nuclear envelopes and the nucleoli of each of the cells produced during Meiosis 1 disintegrate during prophase II.
The chromosomes condense and the centrosomes replicate and move towards opposite poles. Spindle fibers grow outward
from the centrosomes. Prophase II is almost identical to the Prophase stage of mitosis. No synapsis or crossing over occur
during this stage.

Metaphase II
The chromosomes in both cells become arranged on the metaphase plate, much as the chromosomes do in mitosis, and
are attached to the now fully formed spindle.
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Anaphase II
During Anaphase II, the centromeres of each chromosome (in both cells) separate and the sister chromatids—now called
individual chromosomes—move toward the opposite poles of the cells. Anaphase II is the process in which sister
chromatids are separated from each other.

Telophase II
During Telophase II, a nuclear envelope forms around each set of chromosomes and cytokinesis occurs, producing four
genetically different daughter cells, each with a haploid set of chromosomes.
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Meiosis Summary
Meiosis is the first step in the process of gametogenesis or gamete creation. Meiosis happens only in the gonads and
creates four haploid gametes (with single chromatid chromosomes) from each diploid germ cell that enters the process.
Sexual reproduction in eukaryotes involving gamete formation/meiosis (including crossing over, the random/independent
assortment of chromosomes during meiosis, and the subsequent fertilization of gametes) serves to increase the genetic
variation within a population.
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Gametogenesis
Gametogenesis is the process which creates gametes or sex cells. The process starts with meiosis. Meiosis is then
followed by a period of maturation.
The process of sperm creation is known as spermatogenesis. Spermatogenesis begins when a diploid germ cell, known
as a primary spermatocyte, undergoes the process of meiosis to create 4 haploid spermatids. The spermatids mature in the
epididymis to become functional sperm. Men can continue to carry out the process of spermatogenesis from puberty until
death.
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The process of egg creation is known as oogenesis. The diploid germ cells that have the potential to develop into ova are
called oogonia. In humans, all of a female's oogonia that she will make in her lifetime are created when she's still a fetus and
hasn't even been born yet. In fact, about one or two months before a baby girl is born, most of her approximately seven million
oogonia die, and the remaining surviving oogonia enter meiosis I and become primary oocytes. These primary oocytes press
the pause button on their development in prophase I, after they've replicated their genomes, but before they've made the first
meiotic division. They stay arrested at this stage of development for over a decade until the girl begins her first menstrual
cycle. Then, for about the next 30 to 45 years, on a monthly basis, some of the primary oocytes resume meiosis where they left
off and complete the first meiotic division.
When the primary oocyte does finally complete its first meiotic division, it divides the chromosomes evenly, just as you would
expect. However, it does not divide its cytoplasm equally. Almost all of the cytoplasm remains in one of the two daughter
cells, which becomes a secondary oocyte. The other daughter cell, which gets half of the chromosomes but very little
cytoplasm, is called a polar body. The polar body is not a functional oocyte, instead it degenerates and dies. The formation of
a polar body allows the primary oocyte to reduce its genome by half and conserve most of its cytoplasm in the secondary
oocyte. This allows the egg cell to be large enough to store the nutrients and proteins needed for a developing offspring.
The secondary oocyte still has bivalent chromosomes, so if it's going to become a fully-functional ovum, it must undergo the
Meiosis II. Meiosis II occurs only if the secondary oocyte is penetrated by a sperm cell. This division is also uneven, like the
first one, with half of the chromosomes going to another very small degenerate polar body and half of the chromosomes being
retained by the ovum (functional egg) along with almost all of the cytoplasm. In this way, the ovum achieves its haploid state
while conserving as much cytoplasm as possible. This means that during oogenesis, only one functional haploid egg is
created from each diploid germ cell.
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Nondisjunction

Nondisjunction is the failure of homologous chromosomes or sister chromatids to separate properly during cell division. There
are three forms of nondisjunction: failure of a pair of homologous chromosomes to separate in meiosis I, failure of sister
chromatids to separate during meiosis II, and failure of sister chromatids to separate during mitosis. Nondisjunction results in
daughter cells with abnormal chromosome numbers, a condition called aneuploidy. When nondisjunction occurs during
meiosis, it can result in gametes with the wrong number of chromosomes. If fertilized, the most common result is miscarriage.
Most human embryos cannot survive with an abnormal chromosome number.
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The letter “n” in the diagram included above indicates the normal chromosome number.
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There are some conditions in which the aneuploid zygote survives. The table below describes some of the conditions which
result.

Many of these conditions can be diagnosed either before or right after birth by the analysis of a karyotype. A karyotype is
simply a picture of a person’s chromosomes. In order to get this picture, the chromosomes are isolated, stained, and examined
under the microscope. Most often, this is done using the chromosomes in the white blood cells. A picture of the chromosomes
is taken through the microscope. Then, the picture of the chromosomes is cut up and the chromosomes are arranged by size
into homologous pairs. The chromosomes are lined up from largest to smallest. The autosomes are displayed are displayed
as pairs 1-22 and the sex chromosomes are shown as pair 23.
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Karyotype of a Normal Female

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Karyotype of Male with Down Syndrome

Karyotype of a Female with Turner Syndrome

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Chromosomal Rearrangements
In some cases, large chunks of chromosomes (but not entire chromosomes) are affected. Such changes are
called chromosomal rearrangements or chromosomal mutations. The rearranged chromosomes are called aberrant
chromosomes. The rearrangements often happen when crossing over doesn’t work correctly. There are four main
types of chromosomal rearrangements.
Duplication—A chromosome ends up with two or more copies of a gene segment.
Deletion—A chromosome ends up with no copies of a particular gene segment.
Inversion—A chromosomal region is flipped around so that it points in the opposite, wrong direction.
Translocation-- A piece of one chromosome is attached to another non-homologous chromosome.

Chromosomal rearrangements are responsible for several human disorders. These include:
Deletions—Cri Du Chat—Part of chromosome 5 is deleted. This leads to symptoms which include a high-pitched
cat-like cry, mental retardation, delayed development, distinctive facial features, small head size (microcephaly),
widely-spaced eyes (hypertelorism), low birth weight and weak muscle tone (hypotonia) in infancy.
Duplications—Fragile X syndrome—part of the X chromosome is duplicated. This leads to mental retardation.
Inversions—may not cause any problems—can lead to infertility
Translocations—Philadelphia chromosome—A segment of chromosome 9 is translocated to chromosome 22. This
leads to a severe form of leukemia.
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Crossover frequency

Genes that are located on the same chromosome are said to be linked. If the genes are located far apart from each other, they
appear to independently assort due to crossing over. If the genes are located near each other, they don’t independently assort
and are usually inherited together.

Scientists often use the crossover frequency of linked genes to estimate the order of the genes on the chromosome and their
relative distances from each other. The crossover frequency is essentially a measure of how often two genes that start out on
the same chromosome end up on opposite chromosomes after crossing over.

For example, let's suppose we have three linked genes, A, B, and C, and we want to know their order on the chromosome
(ABC? ACB? CAB?) If we look at recombination frequencies among all three possible pairs of genes (AC, AB, BC), we can
figure out which genes lie furthest apart, and which other gene lies in the middle. Specifically, the pair of genes with the largest
recombination frequency must flank the third gene:

By doing this type of analysis with more and more genes (e.g., adding in genes D, E, and F and figuring out their relationships
to A, B, and C) we can build up linkage maps of entire chromosomes. In linkage maps, you may see distances expressed as
centimorgans or map units rather than recombination frequencies. Luckily, there's a direct relationship among these values: a 1
percent recombination frequency is equivalent to 1 centimorgan or 1 map unit.
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Mitosis and Meiosis Compared and Contrasted
Mitosis and meiosis are both forms of nuclear division. They are similar in the way the chromosomes segregate but differ in
the number of cells produced and the genetic contents of the resulting cells. The table below summarizes the key similarities
and differences of the two processes.

Mendelian Inheritance
Gregor Mendel—Mendel is considered to be the “Father of Genetics” because of his groundbreaking work with
inheritance in pea plants. Mendel conducted his experiments at an Austrian monastery in the late 1800s. He discovered
the basic laws of inheritance. He was able to do this before science had an understanding of DNA, chromosomes, or
meiosis. One of the characteristics of Mendel’s work that made it so successful was that he quantitatively analyzed the
results of his pea plant breeding experiments. Most biologists, before Mendel, didn’t think that biological processes could
be mathematically analyzed. Mendel’s main conclusions included:
1. Each trait is controlled by a single pair of alleles. Mendel called them factors.
2. Some alleles are dominant and can mask the appearance of recessive alleles (Law of Dominance)
3. The alleles from a pair separate (during meiosis) and only one member of each pair is transmitted to an offspring from
each parent (Law of Segregation). Realize that Mendel did not know about meiosis, but essentially predicted its
existence.
4. The maternal and paternal alleles/factors from each pair assort independently from the alleles in the other pairs. All
possible combinations of alleles/factors occur in the gametes. We know today that independent assortment occurs
during Metaphase I of Meiosis. (Law of Independent Assortment).

We know today that Mendel’s Laws of Segregation and Independent Assortment apply only to genes that are
located on different chromosomes. Mendel was unaware of the existence of chromosomes and linked genes.

Important Terms

Trait—a genetically determined characteristic. Mendel hypothesized that each trait is determined by two alleles (one
inherited from each parent). Although this is often true, there are many exceptions to this rule. We will explore some of
those exceptions in the Non-Mendelian Inheritance section of the notes (included below).

Alleles--This term refers to different versions of a gene. For example, a gene might control the color of one’s eyes.
Different versions (alleles) of that gene might cause the individual to have brown, blue, or green eyes. Dominant alleles
are represented with capital letters, while recessive alleles are represented with lower case letters.
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Homozygous—An organism is said to be homozygous or pure bred for a trait if the two alleles it possesses for the trait
are identical. (TT or tt for example).

Heterozygous-- An organism is said to be heterozygous or a hybrid for a trait if the two alleles it possesses for the trait
are different. (Tt for example).

Phenotype--This term refers to the physical traits or appearance of an organism. (Blue eyes or Type A blood, would be
examples.)

Genotype--This term refers to an organism’s genetic (DNA) make-up for a trait. (Such as TT, Tt or tt.) A genotype of TT
might cause a pea plant to have the “tall” phenotype.
If the genotype of an organism is unknown, we can perform a TESTCROSS to determine it. To perform this test,
you must cross the individual with the unknown genotype with a homozygous recessive individual. The
phenotypes of the resulting offspring can then be used to deduce the genotype of the parent.
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Punnett Square--This is a chart which shows the possible genotypic outcomes for a mating cross based on the parents’
genotypes.

Monohybrid Cross
Monohybrid Cross—This is a cross in which only one trait is analyzed. To complete the cross, you must first
determine the possible gamete combinations of the parents. Remember that gametes are haploid. They should
only contain one allele for each trait. For example: If we crossed two purple flowered plants, with the genotype
Bb, the possible gametes for each plant are “B” or “b”. The gametes for one parent are written along the top of
the Punnett square, one haploid gamete per column. The gametes of the other parent are written along the left
hand side of the Punnett square, one haploid gamete per row. The boxes inside the square are then filled in using
the column and row headers as shown below.
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The cross illustrated above predicts a phenotypic ratio of 3 purple: 1 white and a genotypic ratio of 1 BB: 2Bb:1
bb

The rules of probability can be applied to analyze the passage of single-gene traits from parent to offspring.
The two rules commonly used in an AP Biology class are listed below:

If A and B are mutually exclusive (separate, unconnected events) then:

P(A or B)=P(A) + P (B)

The rule listed above is used to calculate the probability (P) of either event A or event B happening. The
probability that either event will occur is simply the sum of each of the individual events.

Product Rule

P (A and B)=P(A) X P(B)

The product rule is used to calculate the probability (P) that multiple independent events will each occur. The
probability that both event A and event B will occur is the product of the individual probabilities.

If you were asked to determine the probability that the cross above would produce a plant with white flowers,
your answer would be ¼ or 25% (from the Punnett square). If you were asked to determine the probability that
the cross would produce a plant with purple flowers, your answer would be ¾ or 75%.

If you were asked to determine the probability that the above cross would produce either a homozygous purple
(PP) or a homozygous white (pp) plant, you would: First use the Punnett Square to determine that the probability
of getting a homozygous purple plant is ¼ and the probability of getting a homozygous white plant is also ¼.
Then use:
P(A or B)= ¼ + ¼= ½

Suppose you were asked to determine the probability that the cross produced two purple-flowered plants in a
row?
To calculate this probability, you would need to use the product rule. The product rule states that in order to
determine the probability of two independent events occurring together, you must multiply the individual
probabilities of each event. In this example, we should multiple ¾ X ¾ to get a probability of 9/16 or 56.25%.
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Dihybrid Cross
Dihybrid Cross–A dihybrid cross is a cross in which the inheritance of two traits is analyzed at the same
time. For example: Suppose that in pea plants “R” is the allele for round seeds, “r” is the allele for wrinkled
seeds, “Y” is the allele for yellow seeds, and “y” is the allele for green seeds. The Punnett Square below
illustrates the cross between two plants that are heterozygous (RrYy X RrYy) for both traits, a true dihybrid
cross. To construct the cross, you must first determine the possible gametes that each parent can create. Each
gamete should contain only one allele from each gene. In this case, each allele contains only one R (either
upper or lowercase) and one Y (either upper or lowercase). All possible combinations of the parental alleles are
possible. This means that each of the two parents can create the following gamete combinations: RY; Ry; rY;
and ry.
To determine the possible number of unique gamete combinations, analyze each gene pair. For the R pair, each
parent has a single R and a single r, 2 different alleles. For the Y pair, each parent also has a single Y and a
single y, 2 different alleles. To calculate the number of possible unique gametes, multiply the number of unique
alleles in each gene pair together. In this case that would mean 2 (from the R pair) X 2 (from the Y pair) =4
unique gametes per parent.

Let’s say that one of the original parents had the following genotype: rrYy To calculate the number of possible
alleles from this parent, multiple 1 (from the unique alleles in the r pair) X 2 (from the unique alleles in the Y
pair) to get 2 possible unique gamete combinations. In this case those would be rY and ry.

Once the possible gamete combinations are determined, the gametes for one parent are written along the top of
the Punnett square, one haploid gamete per column. The gametes of the other parent are written along the left-
hand side of the Punnett square, one haploid gamete per row. The boxes inside the square are then filled in using
the column and row headers as shown below.
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In a true dihybrid cross (one in which both parents are heterozygous for both traits), the phenotypic ratio
will always be 9:3:3:1 as shown in the Punnett square above.

Trihybrid or Larger Cross

It is possible to construct Punnett Squares for trihybrid crosses (crosses in which the inheritance of three traits are
analyzed at the same time). These squares can be really large (up to 64 squares). You will typically not be asked
to draw a trihybrid Punnett Square on the AP exam. You might, however, be asked to answer questions like the
following:

How many different possible gametes can an individual with the following genotype produce Aa Bb Dd Ee?

To answer this question, use the same approach as that described above. Multiple the number of unique alleles
from each pair together. In this case. 2 unique alleles from the A pair X 2 unique alleles from the B pair X 2
unique alleles from the D pair X 2 unique alleles from the E pair to yield 16 total unique allele
combinations/gamete types.

If the genotype of the parent had instead been AA Bb cc, the calculation would have been:
1 unique allele from the A pair X 2 unique alleles from the B pair X 1 unique allele from the c pair to yield only
two possible gamete combinations. In this case, those combinations would be ABc and Abc.

What is the probability that the cross between the following genotypes:
Aa BB Dd Ee X Aa Bb Dd ee will produce an offspring with the genotype Aa BB dd Ee?

To answer this question, you could draw a huge Punnett Square, but the easiest and fastest approach is to use
the product rule. First, analyze each gene pair separately. Think of doing four separate Punnett squares.
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What is the probability that AA (from parent 1) and Aa (from parent 2) will yield (Aa) in the offspring? The
answer is ½.

What is the probability that BB (from parent 1) and Bb (from parent 2) will yield BB in the offspring? Again,
the answer is ½.

What is the probability that Dd (from parent 1) and Dd (from parent 2) will yield dd in the offspring? This
time, the answer is ¼.

What is the probability that Ee (from parent 1) and ee (from parent 2) will yield Ee in the offspring? This
time the answer is ½.

To determine the overall probability that the cross between parents Aa BB Dd Ee X Aa Bb Dd ee will
produce an offspring with the genotype Aa BB dd Ee, multiply the probabilities from each gene pair (in bold
above). In this case, the calculation is ½ (from the A pair) X ½ (from the B pair) X ¼ (from the C pair) X ½
(from the D pair) to yield an overall probability of 1/32.

Linked Genes and Dihybrid Crosses

Linked genes occur on the same chromosome, and therefore, tend to be inherited together (i.e., do not segregate
independently). When two heterozygotes are mated in a normal dihybrid cross with independent assortment of alleles, the
expected ratio in the offspring is 9:3:3:1. However, as shown in the figure below, in cases of dihybrid crosses involving
linkage, the ratio of the offspring produced is 3:1 and only the parental types, with no recombinants, are expected.
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Unit 5 Heredity Student Notes Page 30
The table below includes the actual observed results of the dihybrid cross involving the two heterozygotes described above.
Even though offspring with long wings/white eyes and offspring with short wings/red eyes weren’t expected, some were
produced. This often occurs in crosses involving linked genes because of the genetic recombination that occurs during
crossing over.

Non-Mendelian Inheritance
Although Mendel discovered some of the most basic laws of inheritance, scientists have discovered many exceptions to
the so-called laws of Mendelian inheritance. The processes/conditions described below are all examples on non-
mendelian inheritance patterns. In these situations, the patterns of inheritance do not follow the ratios predicted by
Mendel’s laws. Quantitative analysis of the results of such crosses reveals that the observed phenotypic ratios
statistically differ from the ratios predicted by Mendel’s laws.

Incomplete Dominance is a form of intermediate inheritance in which one allele for a specific trait is not completely
expressed over its paired allele. This results in a third phenotype in which the expressed physical trait is a combination or
blending of the phenotypes of both alleles. In some plants, there are alleles for red flowers (R) and for white flowers (r).
Heterozygous plants (Rr) end up with pink flowers (a blend between red and white).

Codominance—This is a condition in which both alleles in a pair are expressed at the same time. They are both equally
present in the phenotype (not blended). An example of codominance is human blood type. There are alleles for Type A
blood (IA), Type B (IB), and type O (i) blood. The alleles for type A and B code for different cell surface proteins that
occur on the surface of the red blood cells (RBCs). Individuals with two O alleles (ii) lack these proteins. Individuals
with either IAIA or IAi possess the type A proteins on their RBCs. Individuals with either I BIB or IBi possess the type B
proteins on their RBCs. Individuals with the I AIB genotype possess both the A and B proteins on the surface of their
RBCs.
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Another commonly cited example of codominance is the inheritance pattern of coat coloration in some cows.

There are two unique alleles (R) for red coat color and (W) for white color. Cows that inherit one of each allele (RW)
have a blotchy phenotype which includes both red and white patches. This type of coloration is known as roan.

Multiple Alleles—This is when three or more alternative forms of a gene (alleles) can occupy the same locus (location).
However, only two of the alleles can be present in a single organism. For example, the ABO system of blood types is
controlled by three alleles (IA, IB, i), only two of which are present in an individual.

Pleiotropy is a condition in which one gene affects multiple (seemingly unrelated) characteristics.
Sickle Cell Disease is a great example. The gene AFFECTS the shape of one of the polypeptide chains that make
up hemoglobin (the molecule that allows red blood cells to transport oxygen). The change in the polypeptide’s
shape also causes the red blood cells to change shape (from round to sickle shaped). This impedes the flow of
blood and leads to multiple symptoms all over the body such as anemia, physical weakness, impaired mental
function, lowered disease resistance, and paralysis. Individuals who are heterozygous for the sickle cell
mutation also possess resistance to the protozoan that causes malaria. This heterozygote advantage
explains why the normally harmful mutation is so common in human populations where malaria has consistently
been a problem.

Epistasis is a condition in which a gene at one locus affects a gene at a second locus. Albinism in humans is a good
example of epistasis. Albinism arises when individuals inherit two defective copies of the allele that normally codes for
the enzyme necessary for melanin (pigment) synthesis. Even though alleles at other loci may code for brown eyes, skin, or
hair, these individuals are albinos because they lack the ability to produce the pigment (melanin).
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Polygenic Inheritance occurs when a trait is governed by two or more sets of alleles. Examples of human traits that are
polygenic include height, skin color, and the prevalence of diabetes. Each individual possesses a copy of all the allelic
pairs. These may be located on different chromosomes. Each dominant allele has a quantitative effect on the phenotype
and the effects are additive. The population typically exhibits continuous phenotypic variations. If the frequency of the
different phenotypes were graphed, the graph would look like a bell curve. Human skin color is thought to be controlled
by 3 pairs of alleles (A, B, C). A person with the alleles AABBCC is very dark skinned, a person with aabbcc alleles is
very light skinned, and a person with AaBbCc (or any combo) has an intermediate skin color.

Multifactorial traits are those controlled by multiple genes that are also affected by physiological and environmental
influences. Hypertension, diabetes, schizophrenia, and allergic conditions are probably all multifactorial traits. Such traits
do not segregate in the predicted Mendelian patterns.

Lethal alleles—There are certain allele combinations which are lethal and prevent the birth of individuals with certain
genotypes. For example, Achondroplasia is an autosomal dominant form of human dwarfism. Individuals with the
genotype Aa are dwarfs. Individuals with the genotype aa are normal. The genotype AA is lethal. Individuals with this
genotype die before birth. The Punnett square for the cross between two dwarfs (Aa) would lead one to believe that ¾ of
their children should be dwarfs.

Due to the lethality of the AA genotype. the actual probability that a living dwarf child will be born is 2/3.
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Pedigree Charts/Modes of Inheritance

Important Terms
Pedigree Chart--A diagram showing the lineage or genealogy of an individual and all the direct ancestors, usually to
analyze or follow the inheritance of trait. The pattern of the inheritance of monohybrid, dihybrid, sex-linked, and
genetically-linked genes traits can often be predicted from data, including pedigrees, which indicate the genotypes
and/or phenotypes of parent and offspring.
Mode of Inheritance--The manner in which a genetic trait or disorder is passed from one generation to the next.
Autosomal dominant, autosomal recessive, X-linked dominant, X-linked recessive, Y-linked, and
mitochondrial inheritance are examples.
Autosome—A non-sex chromosome. Humans have 44 autosomes per diploid, somatic cell.

X and Y chromosomes—The two types of sex chromosomes in mammals, flies, and most other animals. These
chromosomes determine the sex of an individual. Females usually have 2 X chromosomes per somatic cell, while
males usually have only 1 X chromosome per cell. In certain species, the chromosomal basis of sex determination is
not based on X and Y chromosomes. Birds, butterflies, and snakes take everything we know about sex at the
chromosomal level and stand it on its head. Instead of X and Y chromosomes, they have Z and W
chromosomes.What's the difference? Everything. The XY and ZW chromosomes share no genes at all. What's more,
the ZW chromosomes flip the sex determination system. A male chicken - or peacock, or giant river prawn, or
komodo dragon - has ZZ chromosomes. A female has ZW chromosomes. For both XY and ZW systems, there are all
kinds of variations on what happens if one gene is missing or doubled. In mammals, an XO (an X chromosome and a
missing sex chromosome) usually results in a female. When it comes to fruit flies or crickets, a single X chromosome
results in a male. So sometimes the presence of a Y is required to produce a male, and sometimes it isn't. There
haven't been any ZO birds found, indicating they need at least two chromosomes to develop, but ZO, ZZW and
ZZWW all produce female butterflies. Snakes added to the confusion recently, when a female python produced
offspring despite not having been near any males. This parthenogenesis produced all-female offspring with WW
chromosomes — a combination not previously thought possible.

Carrier—An Individual who possesses only one copy of a recessive allele. This individual doesn’t express the trait,
but can pass the allele on to his/her offspring.
Gene Linkage—Genes are linked if they are found together on the same chromosome.

The diagram included below illustrates the symbols commonly used in pedigree charts.
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Modes of Inheritance—Autosomal Dominant
The genes for autosomal dominant traits are located on one of the 44 autosomes in a human cell. The genes are
dominant, which indicates that individuals with only one copy of the gene are affected. Characteristics of autosomal
dominant traits include:
• Males and females are equally likely to have the trait.
• Traits do not skip generations because there are no carriers for the traits.
• The trait is present whenever a single copy of the corresponding allele is present.
• There is male-to-male transmission. This means that fathers can pass to trait to their sons.
Some examples of human genetic conditions that are transmitted via the autosomal dominant mode of inheritance
include: Huntington’s Disease, Achondroplasia, Polycystic Kidney Disease, and Familial Hypercholesterolemia.
The pedigree chart included below depicts the transmission of an autosomal dominant trait.

Modes of Inheritance—Autosomal Recessive

The genes for autosomal recessive traits are located on one of the 44 autosomes in a human cell. The genes are
recessive, which indicates that individuals must possess two copies of the recessive allele in order to exhibit the trait.
Characteristics of autosomal recessive traits include:
• Males and females are equally likely to have the trait.
• Traits often skip generations (due to the possibility of carriers).
• Only homozygous recessive individuals have the trait.
• Traits may appear in siblings without appearing in their parents.
• If a parent has the trait, those offspring who do not have it are heterozygous carriers of the trait.
• Some examples of human genetic conditions that are transmitted via the autosomal recessive mode of inheritance
include: Tay Sachs Disease, PKU, and Cystic Fibrosis.

The pedigree chart included below depicts the transmission of an autosomal recessive trait.
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Modes of Inheritance—X-linked Dominant
Some traits are determined by genes located on sex chromosomes (either X or Y). Such traits are known as sex-linked
traits. The genes for X-linked dominant traits(a type of sex-linked trait) are located on the X chromosome in a human
cell. The alleles are dominant, so individuals with only one copy of the allele exhibit the trait. X-linked traits
(whether dominant or recessive) are always expressed in males (if the male’s X carries the allele) because males
possess only one X chromosome.

Characteristics of X-linked dominant traits include:

• The trait is present whenever the corresponding gene is present.

• There is no male-to-male transmission. Fathers cannot pass the trait to their sons.
• A female who has the trait may or may not pass the allele for the trait to her son or daughter.
• All of the daughters of a male with the trait will inherit the trait.

Some examples of human genetic conditions that are transmitted via the X-linked dominant mode of inheritance
include: hypertrichosis, porphyria, and Rett syndrome.

The pedigree chart included below depicts the transmission of an X-linked dominant trait.

Modes of Inheritance—X-linked Recessive

The alleles for X-linked recessive traits are located on the X chromosome in a human cell. The alleles are recessive,
so for a female to exhibit the trait she must possess the allele on both of her X chromosomes. Since a male has only
one X chromosome, he is affected if his X chromosome carries the allele. Characteristics of X-linked recessive traits
include:
• These traits are far more common in males than in females.
• Traits may skip generations.
• All daughters of a male who has the trait are either affected or are heterozygous carriers.
• The son of a female carrier has a 50 percent chance of having the trait.
• Mothers of males who have the trait are either heterozygous carriers or homozygous and express the trait.
• There is no male-to-male transmission. Fathers cannot pass the trait to their children.
•
Some examples of human genetic conditions that are transmitted via the X-linked recessive mode of inheritance
include: hemophilia, red/green colorblindness, Duchenne Muscular Dystrophy, and Lesch-Nyhan syndrome.
The pedigree chart included below depicts the transmission of an X-linked recessive trait.
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Unit 5 Heredity Student Notes Page 36

Modes of Inheritance—Y-linked
The alleles for Y-linked traits are located on the Y chromosome in a human cell. Since males possess only one Y
chromosome, the traits aren’t usually referred to as dominant or recessive. A man who possesses a Y-linked allele
will exhibit the trait it controls. Since females don’t possess a Y chromosome, they are not affected by Y-linked traits.

Characteristics of Y-linked traits include:

• Only males are affected.
• All sons of an affected male will also be affected.
• Females can’t possess or pass on the trait.

Some forms of Retinitis pigmentosum (a form of progressive blindness) are transmitted via the Y-linked mode of
inheritance
The pedigree chart included below depicts the transmission of an Y-linked trait.
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Modes of Inheritance—Mitochondrial
Some traits result from non-nuclear inheritance. The alleles for mitochondrial traits are located on the small circular
chromosome found in the mitochondria. Since children (in animals) of both sexes inherit their organelles (including
the mitochondria) from the egg of the mother, mitochondrial traits are always transmitted from mother to child. Since
the mitochondria only have one chromosome each, there are no dominant or recessive mitochondrial traits.
Individuals who possess a single copy of a mitochondrial allele express the trait. Characteristics of mitochondrial
traits include:
• All of the children of an affected female will express the trait. These traits are always maternally inherited.
• Males can express the trait but are unable to pass it on to their offspring.

The human mitochondrial chromosome is a very small piece of DNA and codes for only 13 proteins which are part of
the electron transport chain. Disorders related to mutations in the mitochondrial chromosome usually affect one’s
ability to make ATP.

In plants, both mitochondria and chloroplasts are transmitted in the ovule and not in the pollen. Since both organelles
contain their own single, circular chromosome, traits determined by the genes on the mitochondrial and chloroplast
chromosomes are always maternally inherited. Because chloroplasts and mitochondria are randomly assorted to
gametes and daughter cells, traits determined by chloroplast and mitochondrial DNA do not follow simple Mendelian
rules.

The pedigree chart included below depicts the transmission of a mitochondrial trait.
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Unit 5 Heredity Student Notes Page 38

Environmental Effects on Phenotypes

Environmental factors influence gene expression and can lead to phenotypic plasticity. Phenotypic plasticity occurs when
individuals with the same genotype exhibit different phenotypes in different environments. Natural environmental influences
include the phenomenon of color change in the Arctic fox (and other arctic animals) from red-brown in the summer months to
pure white during the winter season for better camouflage. The genes that produce the red-brown summer pigment are blocked
by cold temperatures, causing the hair to grow with no color (therefore, white). Another colorful example is the interaction
between the color of the hydrangea flower, which is blue in acidic soils and pink in alkaline soils. A recent study also linked
improved diet in infants and adolescents to a taller average height in the United States and Europe with the opposite effect in
famine-stricken populations. Some reptiles such as crocodilians and some turtles are known to display temperature-dependent
sex determination (TSD), where the ambient temperature of the developing eggs determines the individual's sex. For example,
in the American alligator's eggs, incubation at 33 ºC produces mostly males, while incubation at 30 ºC produces mostly
females. The genetic complement of an individual is inherited; however, the environmental effect on these genes may alter
their application and expression.