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DNA structure
-DNA (deoxyribonucleic acid): Nucleic acid that transmits genetic
information from parent to offspring and codes for the production of proteins
-It was already known that DNA is a polymer of nucleotides, each
consisting of three components: a nitrogenous (nitrogen-containing) base,
a pentose sugar called deoxyribose, and a phosphate group.
➢ The five-carbon sugar in a DNA nucleotide is called deoxyribose.
➢ The phosphate group consists of a phosphorus (P) atom bonded to
four oxygen (O) atoms.
➢ The nitrogenous base contains nitrogen (N) atoms and carbon (C)
atoms and is a base, accepts hydrogen ions.

-The base can be adenine (A), thymine (T), guanine (G), or cytosine (C). In
1950, he reported that the base composition of DNA varies from one species
to another.
• For example, he found that 32.8% of sea urchin DNA nucleotides
have the base A, whereas only 30.4% of human DNA nucleotides
have the base A and only 24.7% of the DNA nucleotides from the
bacterium E. coli have the base A. Chargaff’s evidence of molecular
diversity among species, which most scientists had presumed to be
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absent from DNA, made DNA a more credible candidate for the
genetic material.
-In the DNA of each species he studied, the number of adenines
approximately equaled the number of thymines, and the number of
guanines approximately equaled the number of cytosines.
• In sea urchin DNA, for example, Chargaff’s analysis found the four
bases in these percentages: A = 32.8% and T = 32.1%; G = 17.7% and
C = 17.3%. (The percentages are not exactly the same because of
limitations in Chargaff’s techniques.)
- Chargaff’s rules:
(1) the base composition of DNA varies between species.
(2) for each species, the percentages of A and T bases are roughly equal
and the percentages of G and C bases are roughly equal.
-DNA helix makes one full turn every 3.4 nm along its length. With the
bases stacked just 0.34 nm apart, there are ten layers of base pairs in each
full turn of the helix.
-The nitrogenous bases of the double helix are paired in specific
combinations: adenine (A) with thymine (T), and guanine (G) with
cytosine (C).
-Adenine and guanine are purines, nitrogenous bases with two organic
rings, while cytosine and thymine are nitrogenous bases called pyrimidines,
which have a single ring. Thus, purines (A and G) are about twice as wide
as pyrimidines (C and T).

-Each base has chemical side groups that can form hydrogen bonds with its
appropriate partner: Adenine can form two hydrogen bonds with thymine
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and only thymine; guanine forms three hydrogen bonds with cytosine and
only cytosine.
-DNA molecules have an antiparallel structure - that is, the two strands of
the helix run in opposite directions of one another. Each strand has a 5' end
and a 3' end.

-The order of nitrogenous bases on a chain of DNA is called its base

sequence.

-Complementary base pairing is important in DNA structure and function

for two reasons.

➢ The hydrogen bonds between the base pairs help hold the two
strands of a DNA molecule together.
➢ The complementary nature of DNA helps explain how DNA
replicates before a cell divides; one strand of a DNA molecule can
serve as a template for making a new complementary strand.
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Orientation
o Another unique feature of the DNA molecule is the direction, or
orientation, of the two strands; carbon molecules can be numbered
in organic molecules.
➢ The following Figure shows the orientation of the numbered
carbons in the sugar molecules on each strand of DNA.

o On the top rail, the orientation of the sugar has the 5', five-prime,
carbon on the left, and on the end of that rail, the 3', three-prime
carbon is on the right of the sugar-phosphate chain.
➢ The strand is said to be oriented 5' to 3'.
o The strand on the bottom runs in the opposite direction and is
oriented 3' to 5'.
➢ This orientation of the two strands is called antiparallel.
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Replication
-Semiconservative replication:

• Semiconservative replication describes the mechanism by which DNA is

replicated in all known cells.
• It derives its name from the fact that this
mechanism of transcription was one of 3
models originally proposed for DNA
replication, which are shown in the following
Figure:
➢ Semiconservative replication would
produce two copies that each contained
one of the original strands and one new strand.
➢ Conservative replication would leave the two original template
DNA strands together in a double helix and would produce a copy
composed of two new strands containing all of the new DNA base
pairs.
➢ Dispersive replication would produce two copies of the DNA, both
containing distinct regions of DNA composed of either both original
strands or both new strands.
• An overview of semiconservative replication is shown in the Figure.
• The process of semiconservative replication occurs in 3 main stages:
unwinding, base pairing, and joining.
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• The replication of a chromosome begins at particular sites called origins

of replication, short stretches of DNA having a specific sequence of
nucleotides.
• Proteins that initiate DNA replication recognize this sequence and
attach to the DNA, separating the two strands and opening up a
replication “bubble.” Replication of DNA then proceeds in both
directions until the entire molecule is copied.

Unwinding
• At each end of a replication bubble is a replication fork, a Y-shaped
region where the parental strands of DNA are being unwound. Several
kinds of proteins participate in the unwinding.
• Helicases are enzymes that untwist the double helix at the replication
forks, separating the two parental strands and making them available as
template strands. After the parental strands separate, single-strand
binding proteins bind to the unpaired DNA strands, keeping them from
re-pairing. The untwisting of the double helix causes tighter twisting and
strain ahead of the replication fork. Topoisomerase helps relieve this
strain by breaking, swiveling, and rejoining DNA strands.
• However, the enzymes that synthesize DNA cannot initiate the synthesis
of a polynucleotide; they can only add DNA nucleotides to the end of an
already existing chain that is base-paired with the template strand.
• The initial nucleotide chain that is produced during DNA synthesis is
actually a short stretch of RNA, not DNA.
• This RNA chain is called a primer and is synthesized by the enzyme
primase. Primase starts a complementary RNA chain from a single RNA
nucleotide, adding more RNA nucleotides one at a time, using the
parental DNA strand as a template. The completed primer, generally 5–
10 nucleotides long, is thus base-paired to the template strand. The new
DNA strand will start from the 3′ end of the RNA primer.
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Base Pairing
• Enzymes called DNA polymerases catalyze the synthesis of new DNA by
adding nucleotides to a preexisting chain.
• Most DNA polymerases require a primer and a DNA template strand,
along which complementary DNA nucleotides are lined up.
• DNA polymerases can add nucleotides only to the free 3′ end of a primer
or growing DNA strand, never to the 5′ end. Thus, a new DNA strand
can elongate only in the 5′ to 3′ direction.
• Along one template strand, DNA polymerase III can synthesize a
complementary strand continuously by elongating the new DNA in the
mandatory 5′ to 3′ direction. DNA pol III remains in the replication fork
on that template strand and continuously adds nucleotides to the new
complementary strand as the fork progresses. The DNA strand made by
this mechanism is called the leading strand. Only one primer is required
for DNA pol III to synthesize the entire leading strand.
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-To elongate the other new strand of DNA in the mandatory 5′ to 3′

direction, DNA pol III must work along the other template strand in the
direction away from the replication fork. The DNA strand elongating in this
direction is called the lagging strand.
Leading strand: 3’ to 5’ direction
Lagging strand: 5’ to 3’ direction
-In contrast to the leading strand, which elongates continuously, the
lagging strand is synthesized discontinuously, as a series of segments.
These segments of the lagging strand are called Okazaki fragments.

Okazaki Fragments
 These fragments are later connected by the DNA ligase.
 Each Okazaki fragment is about 100–200 nucleotides long in eukaryotes.
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 Because one strand is synthesized continuously and the other is

synthesized discontinuously, DNA replication is said to be semi-
discontinuous as well as semiconservative.

Joining
o Even though the leading strand is synthesized continuously, in
eukaryotic DNA replication there often are many areas along the
chromosome where replication begins.
o When the DNA polymerase comes to an RNA primer on the DNA, it
removes the primer and fills in the place with DNA nucleotides.
• When the RNA primer has been replaced, DNA ligase links
the two sections.
-only one primer is required on the leading strand, each Okazaki fragment on
the lagging strand must be primed separately. After DNA pol III forms an
Okazaki fragment, another DNA polymerase, DNA polymerase I (DNA pol
I), replaces the RNA nucleotides of the adjacent primer with DNA
nucleotides.
-But DNA pol I cannot join the final nucleotide of this replacement DNA
segment to the first DNA nucleotide of the adjacent Okazaki fragment.
Another enzyme, DNA ligase, accomplishes this task, joining the sugar-
phosphate backbones of all the Okazaki fragments into a continuous DNA
strand.
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Protein synthesis
(transcription and translation)
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-In prokaryotes, transcription and translation occur within the cytoplasm.

- In eukaryotes, however, transcription occurs in the nucleus, and then
mRNA passes through the nuclear envelope and into the cytoplasm, where
translation occurs.
-Genes provide the instructions for making specific proteins. But a gene
does not build a protein directly. The bridge between DNA and protein
synthesis is the nucleic acid RNA.
-RNA is chemically similar to DNA except that it contains ribose instead of
deoxyribose as its sugar and has the nitrogenous base uracil rather than
thymine. Thus, each nucleotide along a DNA strand has A, G, C, or T as its
base, and each nucleotide along an RNA strand has A, G, C, or U as its base.
An RNA molecule usually consists of a single strand.
-In DNA or RNA, the monomers are the four types of nucleotides, which
differ in their nitrogenous bases. Genes are typically hundreds or thousands
of nucleotides long, each gene having a specific sequence of nucleotides.
- Each polypeptide of a protein also has monomers arranged in a particular
linear order (the protein’s primary structure), but its monomers are amino
acids. Thus, nucleic acids and proteins contain information written in two
different chemical languages.
-Getting from DNA to protein requires two major stages: transcription and
translation.
• Transcription is the synthesis of RNA using information in the
DNA. DNA serves as a template for assembling a complementary
sequence of RNA nucleotides. For a protein-coding gene, the
resulting RNA molecule is a faithful transcript of the gene’s
protein-building instructions. This type of RNA molecule is called
messenger RNA (mRNA) because it carries a genetic message
from the DNA to the protein-synthesizing machinery of the cell.
• Translation is the synthesis of a polypeptide using the information
in the mRNA. The cell must translate the nucleotide sequence of
an mRNA molecule into the amino acid sequence of a
polypeptide. The sites of translation are ribosomes, molecular
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complexes that facilitate the orderly linking of amino acids into

polypeptide chains.
-Transcription occurs in the nucleus, and mRNA is then transported to the
cytoplasm, where translation occurs. But before eukaryotic RNA transcripts
from protein-coding genes can leave the nucleus, they are modified in
various ways to produce the final, functional mRNA. The transcription of a
protein-coding eukaryotic gene results in pre-mRNA, and further processing
yields the finished mRNA. The initial
RNA transcript from any gene,
including those specifying RNA that
is not translated into protein, is more
generally called a primary transcript.
-During transcription, the gene
determines the sequence of nucleotide
bases along the length of the RNA
molecule that is being synthesized.
For each gene, only one of the two
DNA strands is transcribed. This
strand is called the template strand
because it provides the pattern, or
template, for the sequence of
nucleotides in an RNA transcript. For
any given gene, the same strand is
used as the template every time the
gene is transcribed.
-An mRNA molecule is complementary rather than identical to its DNA
template because RNA nucleotides are assembled on the template according
to base-pairing rules. The pairs are similar to those that form during DNA
replication, except that U (the RNA substitute for T) pairs with A and the
mRNA nucleotides contain ribose instead of deoxyribose. Like a new strand
of DNA, the RNA molecule is synthesized in an antiparallel direction to the
template strand of DNA.
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-The mRNA nucleotide triplets are called codons, and they are customarily
written from 5’ to 3’ direction.
-During translation, the sequence of codons along an mRNA molecule is
decoded, or translated, into a sequence of amino acids making up a
polypeptide chain. The codons are read by the translation machinery from
5’ to 3’ direction along the mRNA.
- Each codon specifies which one of the 20 amino acids will be incorporated
at the corresponding position along a polypeptide. Because codons are
nucleotide triplets, the number of nucleotides making up a genetic message
must be three times the number of amino acids in the protein product.
• For example, it takes 300 nucleotides along an mRNA strand to code
for the amino acids in a polypeptide that is 100 amino acids long.

Transcription:
• An enzyme called an RNA polymerase pries the two strands of DNA
apart and joins together RNA nucleotides complementary to the
DNA template strand, thus elongating the RNA polynucleotide.
RNA polymerases can assemble a polynucleotide only from 5’ to 3’
direction. Unlike DNA polymerases, however, RNA polymerases are
able to start a chain from scratch; they don’t need a primer.
• Specific sequences of nucleotides along the DNA mark where
transcription of a gene begins and ends. The DNA sequence where
RNA polymerase attaches and initiates transcription is known as
the promoter, the sequence that signals the end of transcription is
called the terminator.
• The three stages of transcription they are: initiation, elongation, and
termination of the RNA chain.

Initiation:
• The promoter of a gene includes within it the transcription start point
and typically extends several dozen or more nucleotide pairs
upstream from the start point. RNA polymerase binds in a precise
location and orientation on the promoter, therefore determining
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where transcription starts and which of the two strands of the DNA
helix is used as the template. Certain sections of a promoter are
especially important for binding RNA polymerase.
o In bacteria, part of the RNA polymerase itself specifically
recognizes and binds to the promoter.
o In eukaryotes, a collection of proteins called transcription
factors mediate the binding of RNA polymerase and the
initiation of transcription. Only after transcription factors are
attached to the promoter does RNA polymerase II bind to it.
The whole complex of transcription factors and RNA
polymerase II bound to the promoter is called a transcription
initiation complex.
• Once the appropriate transcription factors are firmly attached to the
promoter DNA and the polymerase is bound in the correct
orientation, the enzyme unwinds the two DNA strands and begins
transcribing the template strand at the start point.

Elongation:
-As RNA polymerase moves along the DNA, it untwists the double helix,
exposing about 10–20 DNA nucleotides at a time for pairing with RNA
nucleotides. The enzyme adds nucleotides to the 3’ end of the growing RNA
molecule as it continues along the double helix.
-In the wake of this advancing wave of RNA synthesis, the new RNA
molecule peels away from its DNA template, and the DNA double helix re-
forms.
-Transcription progresses at a rate of about 40 nucleotides per second in
eukaryotes.

Termination:
-The mechanism of termination differs between bacteria and eukaryotes.
• In bacteria, transcription proceeds through a terminator sequence in
the DNA. The transcribed terminator (an RNA sequence) functions as
the termination signal, causing the polymerase to detach from the
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DNA and release the transcript, which requires no further

modification before translation.
• In eukaryotes, RNA polymerase II transcribes a sequence on the
DNA called the polyadenylation signal sequence, which specifies a
polyadenylation signal (AAUAAA) in the pre-mRNA.
• This is called a “signal” because once this stretch of six RNA
nucleotides appears, it is immediately bound by certain proteins in
the nucleus. Then, at a point about 10–35 nucleotides downstream
from the AAUAAA, these proteins cut it free from the polymerase,
releasing the pre-mRNA.
• The pre-mRNA then undergoes processing. Although that cleavage
marks the end of the mRNA, the RNA polymerase II continues to
transcribe. Since the new 5’ end isn’t protected by a cap, however,
enzymes degrade the RNA from the 5’ end. The polymerase
continues transcribing, pursued by the enzymes, until they catch up to
the polymerase and it dissociates from the DNA.

Modifying the pre-mRNA:

-In the eukaryotic gene, there are two kinds of segments beyond the
promoter: introns and exons.
-Introns are sections of a structural gene that are transcribed but are not
translated (noncoding parts).
-Exons are the sections of a structural gene that, when expressed, are
transcribed and translated (coding parts).

-eukaryotes can control gene expression by modifying RNA after

transcription. When transcription occurs, both introns and exons are
transcribed. The result is a large molecule known as pre-mRNA.

-Pre-mRNA is a form of messenger RNA (mRNA) that contains both introns

and exons. A molecule of mRNA is formed when introns are removed from
pre-mRNA and the remaining exons are spliced (joined) to one another.
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- Complex assemblies of RNA and protein called spliceosomes split the

pre-mRNA at each end of an intron and join the exons. The end result is an
mRNA molecule containing only the exons. The mRNA strand leaves the
nucleus and enters the cytoplasm to begin the manufacture of a protein on
the ribosomes.

-The removal of introns and splicing of an mRNA molecule have also been
found to occur in another way. Scientists have discovered that RNA
molecules can act as biological catalysts. RNA itself can act as a catalyst to
remove introns from mRNA molecules as they form in the nucleus. Until
this discovery, it was thought that all enzymes were proteins. RNA
molecules that act as enzymes are called ribozymes.

-Regulatory proteins in eukaryotes are known as transcription factors.

• Transcription factors help in the placement of RNA polymerase at the

correct area on the promoter. Many different transcription factors
may influence one gene. Transcription factors may also bind
sequences of DNA called enhancers. In general, enhancers are
located at a position far— thousands of nucleotide bases away—
from the promoter.
• A loop in the DNA may bring the enhancer and its activator (the
attached transcription factor) into contact with the RNA polymerase
and transcription factors at the promoter. Transcription factors bound
to enhancers can activate transcription factors bound to promoter.
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Translation
-In an mRNA, the instructions for building a polypeptide come in groups of
three nucleotides called codons. Here are some key features of codons to
keep in mind as we move forward:

• There are 61 different codons for amino acids

• Three “stop” codons mark the polypeptide as finished
• One codon, AUG, is a “start” signal to kick off translation (it also
specifies the amino acid methionine)

-In the process of translation, a cell “reads” a genetic message and builds a
polypeptide accordingly.

- The message is a series of codons along an mRNA molecule, and the

translator is called transfer RNA (tRNA). The function of tRNA is to
transfer amino acids from the cytoplasmic pool of amino acids to a
growing polypeptide in a ribosome.

-The ribosome, a structure made of proteins and RNAs, adds each amino
acid brought to it by tRNA to the growing end of a polypeptide chain.

-In translation, the codons of an mRNA are read in order (from the 5' end
to the 3' end) by molecules called transfer RNAs, or tRNAs.-Each tRNA has
an anticodon, a set of three nucleotides that binds to a matching mRNA
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codon through base pairing. The other end of the tRNA carries the amino
acid that's specified by the codon.

-tRNAs bind to mRNAs inside of a protein-and-RNA structure called

the ribosome. As tRNAs enter slots in the ribosome and bind to codons,
their amino acids are linked to the growing polypeptide chain in a chemical
reaction.

-Translation has three parts:

• Initiation ("beginning"): in this stage, the ribosome gets together with

the mRNA and the first tRNA so translation can begin.
• Elongation ("middle"): in this stage, amino acids are brought to the
ribosome by tRNAs and linked together to form a chain.
• Termination ("end"): in the last stage, the finished polypeptide is
released to go and do its job in the cell.

Initiation:
in order for translation to start, we need a few key ingredients. These
include:

• A ribosome (which comes in two pieces, large and small)

• An mRNA with instructions for the protein we'll build
• An "initiator" tRNA carrying the first amino acid in the protein,
which is almost always methionine (Met)
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During initiation, these pieces

must come together in just the
right way. Together, they form
the initiation complex, the
molecular setup needed to start
making a new protein.

-first, the tRNA carrying

methionine attaches to the
small ribosomal subunit.
Together, they bind to the 5'
end of the mRNA by
recognizing the 5' GTP cap
(added during processing in
the nucleus). Then, they
"walk" along the mRNA in the
3' direction, stopping when
they reach the start codon
(often, but not always, the first
AUG)
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Elongation:
-methionine-carrying tRNA starts out in the middle slot
of the ribosome, called the P site. Next to it, a fresh
codon is exposed in another slot, called the A site.
The A site will be the "landing site" for the next
tRNA, one whose anticodon is a perfect
(complementary) match for the exposed codon.
-Once the matching tRNA has landed in the A site, the
formation of the peptide bond that connects one
amino acid to another. This step transfers the
methionine from the first tRNA onto the amino acid of
the second tRNA in the A site.
-The methionine forms the N-terminus of the
polypeptide, and the other amino acid is the C-
terminus.
-the mRNA is pulled onward through the ribosome by
exactly one codon. This shift allows the first,
empty tRNA to drift out via the E ("exit") site. It also
exposes a new codon in the A site, so the whole cycle
can repeat.
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Termination:
-Termination happens when a stop codon in the mRNA (UAA, UAG, or
UGA) enters the A site.
-Stop codons are recognized by proteins called release factors, which fit
neatly into the P site (though they aren't tRNAs). Release factors mess with
the enzyme that normally forms peptide bonds: they make it add a water
molecule to the last amino acid of the chain. This reaction separates the
chain from the tRNA, and the newly made protein is released.
-translation "equipment" is very reusable. After the small and large
ribosomal subunits separate from the mRNA and from each other, each
element can (and usually quickly does) take part in another round of
translation.

Completing and Targeting the Functional Protein

-Polypeptides often need some "edits." During and after translation, amino
acids may be chemically altered or removed. The new polypeptide will also
fold into a distinct 3D structure, and may join with other polypeptides to
make a multi-part protein.
-Many proteins are good at folding on their own, but some need helpers
("chaperones") to keep them from sticking together incorrectly during the
complex process of folding.
-Certain amino acids may be chemically modified by the attachment of
sugars, lipids, phosphate groups, or other additions. Enzymes
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Genetics
Genetics Vocabulary
 A character is a heritable feature that varies among
individuals, such as flower color.
 A trait is each variant for a character, such as purple or white
color for flowers.
 True breeding occurs when over many generations of self-
pollination, the plant produces only the same variety as the
parent plant.
 Hybridization is the mating, or crossing, of two true-
breeding varieties.
 P generation is the true-breeding parents.
 The F1 generation is their hybrid offspring.
 F2 generation is the result of self-pollination of F1 hybrids.
 Alleles are the alternative versions of a gene.
 A homozygous gene stands for a gene that has a pair of
identical alleles for a character.
➢ The purple pea plant is homozygous for the dominant
allele (PP), while the white plant is homozygous for the
recessive allele (pp).
➢ Homozygous plants breed true because all of their
gametes contain the same allele—either P or p in this
example.
 A heterozygous gene stands for a gene that has a pair of
different alleles for a character.
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 Phenotype is an organism’s appearance or observable traits.

 Genotype is its genetic makeup.

 Testcross is breeding an organism of unknown genotype

with a recessive homozygote to reveal the genotype of that
organism.
 Monohybrid cross is a cross between monohybrids,
heterozygotes resulted from the F1 progeny produced in his
crosses of true-breeding parents.
 Dihybrid cross is a cross between dihybrids, F1 plants which
are heterozygotes for the two characters being followed in the
cross (YyRr).
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 Pleiotropy is a property that is affected by multiple

phenotypic effects.
➢ In humans, pleiotropic alleles are responsible for the
multiple symptoms associated with certain hereditary
diseases: such as cystic fibrosis and sickle-cell disease.
 Multifactorial characters are many factors, both genetic and
environmental, collectively influence phenotype.

-This type of relationship between alleles, with a heterozygote

phenotype intermediate between the two homozygote phenotypes,
is called incomplete dominance.
- codominance, both alleles are simultaneously expressed in the
heterozygote.
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Mendelian Genetics

Peas
• Reasons why Mendel chose peas are
➢ They are easy to cultivate
➢ They are hermaphrodite, have both male
and female sexual organs.
➢ Their cross-fertilization (Cross-Pollination)
can be easily controlled, as shown in the
following Figure.
➢ Their generation time is short
➢ They have many distinct traits, he tested 7,
as shown in the following Figure.
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Mendel’s Model
• Mendel developed a model to explain the 3:1 inheritance pattern
that he consistently observed among the F2 offspring in his pea
experiments.
• He describe 4 related concepts making up this model.
1. Alternative versions of genes account for variations in
inherited characters, as shown in the following Figure.
➢ The DNA at that locus, however, can vary slightly in its
nucleotide sequence.
➢ This variation in information content can affect the function
of the encoded protein and thus the phenotype of the
organism.
➢ The purple-flower allele and the white-flower allele are two
DNA sequence variations possible at the flower-color locus
on one of a pea plant’s chromosomes, one that allows
synthesis of purple pigment and one that does not.

2. For each character, an organism inherits 2 copies (that is,

two alleles) of a gene, one from each parent.
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➢ A genetic locus is actually represented twice in a diploid

cell, once on each homolog of a specific pair of
chromosomes.
➢ The two alleles at a particular locus may be identical, as in
the true-breeding plants of Mendel’s P generation.
➢ Or the alleles may differ, as in the F1 hybrids.
3. If the two alleles at a locus differ, then one, the dominant
allele, determines the organism’s appearance; the other, the
recessive allele, has no noticeable effect on the organism’s
appearance.
➢ Accordingly, Mendel’s F1 plants had purple flowers
because the allele for that trait is dominant and the allele for
white flowers is recessive.
➢ Although you might assume that the dominant allele for a
particular character would be more common than the
recessive allele, this is not a given.
4. The law of segregation, states that the 2 alleles for a
heritable character segregate (separate from each other)
during gamete formation and end up in different gametes.
➢ Thus, an egg or a sperm gets only one of the two alleles that
are present in the somatic cells of the organism making the
gamete.
➢ In terms of chromosomes, this segregation corresponds to
the distribution of the two members of a pair of
homologous chromosomes to different gametes in meiosis.
➢ Note that if an organism has identical alleles for a particular
character—that is, the organism is true-breeding for that
character—then that allele is present in all gametes.
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➢ But if different alleles are present, as in the F1 hybrids, then

50% of the gametes receive the dominant allele and 50%
receive the recessive allele.
➢ Mendel derived the law of segregation from experiments in
which he followed only a single character, such as flower
color.
➢ Since an egg with a purple-flower allele has an equal
chance of being fertilized by a sperm with a purple-flower
allele or one with a white-flower allele and the same is true
for an egg with a white-flower allele, there are 4 equally
likely combinations of sperm and egg, so we’ve to diagram
it.

Punnett Square
o It’s a handy diagrammatic device for predicting the allele
composition of offspring from a cross between individuals
of known genetic makeup.
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o The following Figure is an example of it.

Law of Independent Assortment

• It states that two or more genes assort independently, each pair
of alleles segregates independently of each other pair of
alleles—during gamete formation.
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• This law applies only to genes (allele pairs) located on different

chromosomes, nonhomologous chromosomes, or, to genes that
are very far apart on the same chromosome.
The following Figure represents an example.
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Probability
• The multiplication rule states that to determine the probability
of 2 events, we multiply the probability of one event (one coin
coming up heads) by the probability of the other event.
• The addition rule states that the probability that any one of two
or more mutually exclusive events will occur is calculated by
adding their individual probabilities.
• The following
Figure represents
an example.

-When tossing a coin, the outcome of one toss has no impact on the
outcome of the next toss. Each toss is an independent event, just
like the distribution of alleles into gametes.
-The multiplication rule states that to determine this probability,
we multiply the probability of one event by the probability of the
other event.
The probability that two coins tossed at the same time will
The probability that two coins tossed at the same time will land
heads up is ½ * ½ = ¼
Similarly, the probability that a heterozygous pea plant (Pp) will
self-fertilize to produce a white-flowered offspring (PP) is the
chance that a sperm with a white allele will fertilize an ovum with
a white allele is ½ * ½ = ¼
-in general: if both event X and event Y must happen in order for a
certain outcome to occur, and if X and Y are independent of each
other (don’t affect each other’s likelihood), then you can use the
 42

product rule to calculate the probability of the outcome by

multiplying the probabilities of X and Y.
-According to the addition rule, the probability that any one of two
or more mutually exclusive events will occur is calculated by
adding their individual probabilities.
- In general: If an outcome requires that either event X or event Y
occur, and if X and Y are mutually exclusive (if only one or the
other can occur in a given case), then the probability of the
outcome can be calculated by adding the probabilities of X and Y.
-We can apply and combine the rules of probability to predict the
outcome of crosses involving multiple characters.
 43

Non-Mendelian Genetics
 Mendelian genetics is identified by complete dominance.
➢ In such situations, the phenotypes of the heterozygote
and the dominant homozygote are indistinguishable.
 For some genes, neither allele
is completely dominant, and
the F1 hybrids have a
phenotype somewhere
between those of the two
parental varieties, so
incomplete dominance occurs.
➢ It is seen when red
snapdragons are crossed
with white snapdragons:
All the F1 hybrids have
pink flowers, as shown in
the following Figure.
➢ This third, intermediate phenotype results from flowers
of the heterozygotes having less red pigment than the red
homozygotes.
 Codominance occurs when the two alleles each affect the
phenotype in separate, distinguishable ways.
 Only two alleles exist for the pea characters that Mendel
studied, but most genes exist in more than two allelic forms,
that’s when multiple alleles are used.
➢ The ABO blood groups in humans, are determined by
three alleles of a single gene: IA, IB, and i; a person’s
blood group may be one of four types: A, B, AB, or O.
 44

➢ These letters refer to two carbohydrates—A and B—that

may be found on the surface of red blood cells.
➢ A person’s
blood cells may
have
carbohydrate A
(type A blood),
carbohydrate B
(type B), both
(type AB), or
neither (type O),
as shown in the
following
Figure.
Epistasis
• It’s the phenotypic expression of
a gene at one locus alters that of
a gene at a second locus.
• The following Figure represents
an example.
➢ A second gene determines
whether or not pigment will
be deposited in the hair.
➢ The dominant allele (E)
results in the deposition of
either black or brown
pigment, depending on the
genotype at the first locus.
 45

➢ But if the Lab is homozygous recessive for the second locus

(ee), then the coat is yellow, regardless of the genotype at
the black/brown locus (so-called golden Labs).
➢ In this case, the gene for pigment deposition (E/e) is said to
be epistatic to the gene that codes for black or brown
pigment (B/b).
Polygenic Inheritance
• Quantitative characters are many characters, such as human
skin color and height, are not one of two discrete characters, but
instead vary in the population in gradations along a continuum.
• Quantitative variation usually indicates polygenic inheritance,
an additive effect of two or more genes on a single phenotypic
character.
Pleiotropy
Some genes affect many different characteristics, not just a single
characteristic.
An example of this is Marfan syndrome, which results in several
symptoms (unusually tall height, thin fingers and toes, lens
dislocation, and heart
problems). These symptoms
don’t seem directly related, but
as it turns out, they can all be
traced back to the mutation of a
single gene.
 46

Incomplete dominance.
Two alleles may produce an intermediate phenotype when both
are present, rather than one fully determining the phenotype. Both
are recessive.
-An example of this is the snapdragon
plant. A cross between a homozygous
white-flowered plant (CWCW) and a
homozygous red-flowered plant
(CRCR) will produce offspring with
pink flowers (CRCW)
 47

Codominance
-Two alleles may be simultaneously
expressed when both are present, rather
than one fully determining the phenotype.
- In some varieties of chickens, the allele
for black feathers is codominant with the
allele for white feathers. A cross between a
black chicken and a white chicken will
result in chicken with both black and white
feathers.
-The symbols or letters are subscript while
in incomplete dominance are superscript.

Misconceptions:
• Some people confuse pleiotropy and polygenic inheritance. The
major difference between the two is that pleiotropy is when one
gene affects multiple characteristics (e.g. Marfan syndrome) and
polygenic inheritance is when one trait is controlled by multiple
genes (e.g. skin pigmentation).
• Codominance and incomplete dominance are not the same. In
codominance, neither allele is dominant over the other, so both will
be expressed equally in the heterozygote. In incomplete
dominance, there is an intermediate heterozygote (such as a pink
flower when the parents' phenotypes are red and white).
 48

Pedigree:
To start reading a pedigree:

1. Determine whether the trait is dominant or recessive. If the

trait is dominant, one of the parents must have the trait. Dominant
traits will not skip a generation. If the trait is recessive, neither
parent is required to have the trait since they can be heterozygous.

2. Determine if the chart shows an autosomal or sex-linked

(usually X-linked) trait. For example, in X-linked recessive traits,
males are much more commonly affected than females. In
autosomal traits, both males and females are equally likely to be
affected (usually in equal proportions).
 49

The diagram shows the inheritance of freckles in a family. The

allele for freckles (F) is dominant to the allele for no freckles (f).

At the top of the pedigree is a grandmother (individual I-2) who

has freckles. Two of her three children have the trait (individuals
II-3 and II-5) and three of her grandchildren have the trait
(individuals III-3, III-4, and III-5).
 50

Sex chromosomes in humans

Human X and Y chromosomes determine the biological sex of a
person, with XX specifying female and XY specifying male. Although
the Y chromosome contains a small region of similarity to the X
chromosome so that they can pair during meiosis, the Y
chromosome is much shorter and contains many fewer genes.

X-linked genes
When a gene is present on the X
chromosome, but not on the Y
chromosome, it is said to be X-
linked. X-linked genes have
different inheritance patterns than
genes on non-sex chromosomes
(autosomes). That's because these
genes are present in different copy
numbers in males and females.

Why is this the case? Recessive X-

linked traits appear more often in
males than females because, if a male receives a "bad" allele from
his mother, he has no chance of getting a "good" allele from his
father (who provides a Y) to hide the bad one. Females, on the
other hand, will often receive a normal allele from their fathers,
preventing the disease allele from being expressed.
 51

In Drosophila, the gene for eye color is located on the X

chromosome. Red eye color is wild-type and is dominant to white
eye color
 52

Morgan’s Experiments
 The first solid evidence associating a specific gene with a
specific chromosome came early in the 20th century from the
work of Thomas Hunt Morgan, an experimental
embryologist at Columbia University.
 Although Morgan was initially skeptical about both
Mendelian genetics and the chromosome theory, his early
experiments provided convincing evidence that
chromosomes are indeed the location of Mendel’s heritable
factors.
 While Mendel could readily obtain different pea varieties
from seed suppliers, Morgan was probably the first person to
want different varieties of the fruit fly.
Fruit Fly
• For his work, Morgan selected a species of fruit fly, Drosophila
melanogaster, a common insect that feeds on the fungi growing
on fruit.
• Fruit flies are prolific breeders; a single mating will produce
hundreds of offspring, and a new generation can be bred every
2 weeks.
• Morgan’s laboratory began using this convenient organism for
genetic studies in 1907 and soon became known as “the fly
room.”
• Another advantage of the fruit fly is that it has only 4 pairs of
chromosomes, which are easily distinguishable with a light
microscope.
 53

➢ There are 3 pairs of autosomes and one pair of sex

chromosomes.
➢ Female fruit flies have a pair of homologous X
chromosomes, and males have one X chromosome and one
Y chromosome.
• The phenotype for a character most commonly observed in
natural populations, such as red eyes in Drosophila, is called the
wild type, as shown in the following Figure.
• Traits that are alternatives
to the wild type, such as
white eyes in Drosophila,
are called mutant
phenotypes because they are
due to alleles assumed to
have originated as changes,
or mutations, in the wild-
type allele.
• Morgan and his students invented a notation for symbolizing
alleles in Drosophila that is still widely used for fruit flies.
➢ For a given character in flies, the gene takes its symbol
from the first mutant (non–wild type) discovered. Thus, the
allele for white eyes in Drosophila is symbolized by w.
➢ A superscript + identifies the allele for the wild-type trait:
w+ for the allele for red eyes, for example.
• Over the years, a variety of gene notation systems have been
developed for different organisms.
➢ For example, human genes are usually written in all
capitals, such as HD for the allele for Huntington’s disease.
 54

Correlating Behavior

Sex Linked Genes

 A gene located on either sex chromosome is called a sex-
linked gene; those located on the Y chromosome are called
Y-linked genes.
 The Y chromosome is passed along virtually intact from a
father to all his sons.
 Because there are so few Y-linked genes, very few disorders
are transferred from father to son on the Y chromosome.
➢ A rare example is that in the absence of certain Y-linked
genes, an XY individual is male but does not produce
normal sperm.
 55

 The human X chromosome contains approximately 1,100

genes, which are called X-linked genes.
 The fact that males and females inherit a different number of
X chromosomes leads to a pattern of inheritance different
from that produced by genes located on autosomes.
Sex Chromosomes
• The following Figure shows a picture
of X and Y chromosomes.
• Short segments at either end of the Y
chromosome are the only regions that
are homologous with regions of the X.
➢ These homologous regions allow the X and Y chromosomes
in males to pair and behave like homologs during meiosis in
the testes.
• There are several systems for determining sex, as shown in the
following Figure.
 56

• In humans, the anatomical signs of sex begin to emerge when

the embryo is about 2 months old.
➢ Before then, the rudiments of the gonads are generic—they
can develop into either testes or ovaries, depending on
whether or not a Y chromosome is present.
• In 1990, a British research team identified a gene on the Y
chromosome required for the development of testes.
➢ They named the gene SRY, for sex determining region of Y.
➢ In the absence of SRY, the gonads develop into ovaries.
• The biochemical, physiological, and anatomical features that
distinguish males and females are complex, and many genes are
involved in their development.
• In fact, SRY codes for a protein that regulates other genes.
• Researchers have sequenced the human Y chromosome and
have identified 78 genes that code for about 25 proteins (some
genes are duplicates).
➢ About half of these genes are expressed only in the testis,
and some are required for normal testicular functioning and
the production of normal sperm.
X-Linked Genes
• Because males have only one locus, the terms homozygous and
heterozygous lack meaning for describing their X-linked genes;
the term hemizygous is used in such cases.
• Any male receiving the recessive allele from his mother will
express the trait.
 57

➢ For this reason, far more males than females have X-linked
recessive disorders.
• However, even though the chance of a female inheriting a
double dose of the mutant allele is much less than the
probability of a male inheriting a single dose, there are females
with X-linked disorders.
• For instance, color blindness is almost always inherited as an
X-linked trait.
➢ A color-blind daughter may be born to a color-blind father
whose mate is a carrier.
➢ Because the X-linked allele for color blindness is relatively
rare, though, the probability that such a man and woman
will mate is low.
• The following Figure summarizes what was previously
mentioned.
 58

Down Syndrome
- It occurs because of possessing an extra copy of all or part of the 21st
chromosome. People with this syndrome have three copies of this
genetic material, instead of two. In some cases, the extra copy, or
trisomy, does not occur in every cell, producing what’s known as
mosaicism.
- Chromosome 21 contains the gene that encodes amyloid precursor
protein (APP), an Alzheimer’s disease risk factor, and possessing an
extra copy of this gene might cause the early onset of this fatal
disease.

• One aneuploid condition, Down syndrome, affects

approximately one out of every 830 children born in the United
States.
• As shown in the following Figure, Down
syndrome is usually the result of an extra
chromosome 21, so that each body cell has a
total of 47 chromosomes.
➢ Because the cells are trisomic for
chromosome 21, Down syndrome is often called trisomy
21.

Specialties
o Down syndrome includes characteristic facial features, short
stature, correctable heart defects, and developmental delays.
o Individuals with Down syndrome have an increased chance
of developing leukemia and Alzheimer’s disease but have a
 59

lower rate of high blood pressure, atherosclerosis (hardening

of the arteries), stroke, and many types of solid tumors.
o Although people with Down syndrome, on average, have a
life span shorter than normal, most, with proper medical
treatment, live to middle age and beyond.
➢ Many live independently or at home with their families,
are employed, and are valuable contributors to their
communities.
o Almost all males and about half of females with Down
syndrome are sexually underdeveloped and sterile.
-
• Effects:
- Children born with Down syndrome have distinctive facial features,
including a flattened face and bridge of the nose, eyes that slant
upward, and small ears. They usually have small hands and feet,
short stature, and poor muscle tone as well. The intellectual abilities
of people with Down syndrome are typically low to moderate,
although some graduate from high school and college, and many
successfully hold jobs.
- Other symptoms of Down syndrome can include hearing loss and
heart defects, and virtually everyone born with Down will develop
early-onset Alzheimer’s disease, often in their 40s or 50s.
 60

Klinefelter syndrome

o Klinefelter syndrome is a chromosomal condition in boys and men

that can affect physical and intellectual development. Males have
extra X chromosome (XXY)
o Most commonly, affected individuals are taller than average are
unable to father biological children (infertile).
o It occurs when there’s an extra X chromosome in a male,
producing XXY.
➢ It occurs approximately once in every 500 to 1,000 live
male births.
o People with this disorder have male sex organs, but the testes
are abnormally small and the man is sterile.
➢ Even though the extra X is inactivated, some breast
enlargement and other female body characteristics are
common.
o Affected individuals may have subnormal intelligence.

• Effects:
o Klinefelter syndrome may adversely affect testicular growth,
resulting in smaller than normal testicles, which can lead to lower
production of testosterone. The syndrome may also cause reduced
muscle mass, reduced body and facial hair, and enlarged breast
tissue. The effects of Klinefelter syndrome vary, and not everyone
has the same signs and symptoms.
o Most men with Klinefelter syndrome produce little or no sperm,
but assisted reproductive procedures may make it possible for
some men with Klinefelter syndrome to father children.
o They have higher risk for some forms of cancer and heart disease
 61

Prader-Willi syndrome
- Missing part of chromosome 15. Prader-Willi syndrome is a complex
genetic condition that affects many parts of the body.
• Effects:
o this condition is characterized by weak muscle tone (hypotonia),
feeding difficulties, poor growth, and delayed development.
Beginning in childhood, affected individuals develop an insatiable
appetite, which leads to chronic overeating (hyperphagia) and
obesity. Some people with Prader-Willi syndrome, particularly those
with obesity, also develop type 2 diabetes (the most common form of
diabetes).
o Behavioral problems are common, including temper outbursts,
stubbornness, and compulsive behavior such as picking at the skin.
Sleep abnormalities can also occur. Additional features of this
condition include distinctive facial features such as
a narrow forehead, almond-shaped eyes, and a triangular mouth;
short stature; and small hands and feet.

Turner syndrome
- Females missing all or part of an X chromosome Turner syndrome is a
chromosomal condition that affects development in females
o Monosomy X occurs about once in every 2,500 female births
and is the only known viable monosomy in humans.
o Although these X0 individuals are phenotypically female,
they are sterile because their sex organs do not mature.
➢ When provided with estrogen replacement therapy, girls
with Turner syndrome do develop secondary sex
characteristics.
o Most have normal intelligence.
 62

• Effects:
o The most common feature of Turner syndrome is short
stature, which becomes evident by about age 5. An early loss
of ovarian function (ovarian hypofunction or premature
ovarian failure) is also very common. The ovaries develop
normally at first, but egg cells (oocytes) usually die
prematurely and most ovarian tissue degenerates before birth.
Many affected girls do not undergo puberty unless they
receive hormone therapy, and most are unable to conceive
(infertile). A small percentage of females with Turner
syndrome retain normal ovarian function through young
adulthood.
o About 30 percent of females with Turner syndrome have
extra folds of skin on the neck (webbed neck), a low hairline
at the back of the neck, puffiness or swelling (lymphedema)
of the hands and feet, skeletal abnormalities, or kidney
problems. One third to one half of individuals with Turner
syndrome are born with a heart defect, such as a narrowing of
the large artery leaving the heart (coarctation of the aorta) or
abnormalities of the valve that connects the aorta with the
heart (the aortic valve).

Triple X Syndrome
o Females with trisomy X (XXX), which occurs once in
approximately 1,000 live female births, are healthy and have
no unusual physical features other than being slightly taller
than average.
➢ Triple-X females are at risk for learning disabilities but
are fertile.