GENERAL BIOLOGY 2

STUDY GUIDE

Prepared by:
Richie May A. Ramos
Created by: Richie May A.Associate Professor III
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Ramos

UM Faculty
Associate Professor III
UNIT 1: LAWS OF INHERITANCE
Genetics is the subdiscipline of biology that
focuses on heredity and genetic variation. In
biology, heredity, which is also called inheritance
or biological inheritance, refers to the transmission
or passing down of traits from the generation of
parents to their offspring.
Genetic variation, on the other hand, refers to the
degree of difference in the deoxyribonucleic acid
or DNA among individuals of a population. As you
can observe, genetics is centralized on the study
of genes or segments of DNA, how they are
inherited, and how different they are among the
members of a species.
EXAMPLES OF FIELDS UNDER GENETICS
the path to the priesthood as he entered the
Augustinian monastery of Saint Thomas and became
a monk. He was finally ordained in 1847. Thereafter,
he decided to work as an educator. However, due to
the poor quality of his answers, he failed his exams in
physics and natural history. Thus, he enrolled at the
University of Vienna to expand his knowledge in these
areas. Finally, in 1856, he began his hybridization
studies involving pea plants. His eight-year work on
experimental crosses was later recognized as a path-
breaking achievement in the field of biology.
Fig. 1
Gregor Mendel
(1822–1884), the father of
genetics, made vital
contributions to the science
of heredity through his pea
plant experiments at the
Augustinian monastery

Field Description Pea Plant as Mendel’s Model Organism

Molecular Molecular genetics deals with the
Genetics study of DNA and gene Mendel’s experiments were actually borne out of
expression and regulation. his interest for ornamental flowers. He even
Cytogenetics Cytogenetics deals with the study
performed separate experiments involving
of chromosomes and their
behavior during meiosis. honeybees. His study on garden peas or Pisum
Population Population genetics focuses on sativum brought him the greatest success in the
Genetics how the forces of evolution field of genetics.
influence the frequencies of genes
at the population level.
Transmission Transmission genetics deals with
Genetics the different patterns of
inheritance.

Gregor Mendel and His Pea Plant Hybridization

Experiments
Gregor Johann Mendel as the father of modern
genetics born in 1822 in Moravia located in the Czech
Fig. 2 Garden pea or Pisum sativum is a type of
Republic today (but was part of Austria when Mendel
legume.
was born), he grew up on a farm. He worked with his
father to improve the plants in their orchard by grafting Its flowers may either be violet or white. Being a
trees, a technique wherein two vegetative structures legume, its fruits are elongated or pod-shaped, with
from two plants are joined together. Later on, he took seeds attached to only one side of the fruit or pod wall.
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Mendel chose Pisum sativum for various reasons,
which are the following:
▪ First, it exhibits more vigorous growth
(approximately 70 to 80 days harvest period)
compared to other plants.
▪ Second, these plants are easy to cross-
fertilize. The flowers of peas contain both
male and female organs, particularly, the
stamens and pistil. Obtaining pollen grains
from the anthers from one plant and delivering
them to the stigma of another plant will allow
fertilization. If this is done between plants with
different traits, then hybridization is
performed. The offspring of the mating,
consequently, are referred to as hybrids
▪ Lastly, pea plants are also capable of self-
fertilization through self-pollination. A
modified petal of the pea flower is capable of
covering the reproductive structures. This
allows peas to naturally self-pollinate.
Review of Genetic Terminologies
In the discussion of transmission genetics, several
terminologies will be repeatedly used. You should
also understand them well to improve your skills in
solving genetic problems. Genes refers to the
basic unit of heredity. Mendel termed these genes
as “unit factors” that control the expression of
biological characteristics. A characteristic is any
heritable feature of an organism, which is under
the control of a particular gene. Different genes
control flower color, hair color, and skin color,
which are examples of characteristics. The
definite position that a gene occupies in a
chromosome is called a locus (plural, loci). A
gene for a particular characteristic usually has
different alternative forms, which are called
alleles. In the figure given below, two gene loci are
given: one for the height of a pea plant and
another for the texture of its pods. If you look at
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the gene for pod texture, two versions exist—one
for wrinkled pods and another for smooth pods.
Two chromosomes are used to represent genes
and alleles above. This is to emphasize that our
chromosomes, similar to most organisms, occur in
pairs called homologous chromosomes. The
members of each pair originate from each of our
parents. Thus, for animals and most plants, two
genes control the expression of a particular
characteristic. For us, humans, we inherit each of
these genes from our mother and father. Also, in
the individual has identical alleles for height (both
alleles for tall). Thus, this individual is said to be
homozygous for height. If this individual happens
to have inherited an allele for “dwarf” trait from its
parent 2, then its alleles will become different from
each other, making it heterozygous (or hybrid) for
height. This is the case for pod texture because of
the non-identical alleles. These combinations of
alleles that an individual possesses at a certain
locus, which can be homozygous or
heterozygous, refer to its genotype. The actual
manifestation of a genotype into observable traits
is called the phenotype. You usually describe
your classmates by enumerating their
phenotypes. In the given figure above, if the actual
phenotype of the plant is a round seed, then the
allele for round seed is said to be the dominant
allele. The other allele in which the expression is
masked (i.e., wrinkled allele) is called the
recessive allele.
Mendelian Laws of Inheritance
1. The Law of Segregation-Each inherited trait
is defined by a gene pair. Parental genes are
randomly separated to the sex cells so that
sex cells contain only one gene of the pair.
Offspring therefore inherit one genetic allele
from each parent when sex cells unite in
fertilization.
a. Mendel’s Monohybrid Cross- the initial Using Punnett Squares:
individuals that are mated comprise the P
To apply your knowledge of the principle of
generation or the parental generation. Particularly,
dominance and law of segregation in analyzing
the P generation consists of tall and dwarf parents.
other crosses, we can use the Punnett Square.
Note that P generations in all of Mendel’s crosses
This method, which was devised by Reginald
consist of true-breeding or homozygous
Punnett, is a basic technique that can be used to
individuals. These parents, when cross-pollinated.
represent the segregation of gametes in the
In this cross, only one characteristic is involved.
parents and the fertilization to produce the
However, the parents should have different or
possible offspring. By using the example earlier,
contrasting phenotypes.
Table 2 shows separate Punnett squares for P (tall
Interpretations of the Monohybrid Cross: × dwarf) and F1 generations (tall × tall). Note that
the first rows and columns below the parent
Two major observations can be made from the
genotypes represent the segregated gametes
monohybrid cross of Mendel. First, the F1 consists
(sperm and eggs). Combining them will give rise
of only one phenotype, which is tall. Second, the
to the possible genotypes of the offspring. The
dwarf phenotype reappeared in the F2
steps are summarized as follows:
generation. This implies that the tall trait is
dominant over the recessive dwarf trait. This is 1. Write down the genotypes of both parents for
best explained by the Principle of Dominance. each cross.
This states that when an individual is
a. P generation: TT, tt
heterozygous, the dominant allele tends to mask
b. F1 generation: both Tt
the expression of the recessive allele. For you to
understand better, let us establish notations to our 2. Write down the possible gametes for each
monohybrid cross. Let gene T code for height in genotype. Then, draw an empty version of the
the pea plant. This gene exists in two forms: the boxes below where you can write the gametes and
dominant T allele for tall trait and recessive t allele offspring.
for the dwarf trait. In the P generation, a TT (tall)
parent is crossed with a tt (dwarf) parent. In Table
a. TT: only T
1 below, note that the recessive allele is masked
b. tt: only t
in the heterozygous individuals in both F1 and F2
c. Tt: T or t
generations. Also, this explains that the recessive
phenotype is always true-breeding, whereas an
individual with the dominant phenotype may either
be homozygous or heterozygous.

Table 1. The conceptual approach to Mendel’s Table 2. Punnett squares for P and F1
monohybrid cross generations in a monohybrid cross

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2. The Law of Independent Assortment-Genes
for different traits are sorted separately from one
another so that the inheritance of one trait is not
dependent on the inheritance of another.
b. Mendel’s Dihybrid Cross -In Mendel’s dihybrid
cross, the same pattern applies as in the
monohybrid cross. However, this time, two
characteristics or two pairs of contrasting traits are
involved.
Interpretations of the Dihybrid Cross:
The F2 generation of the dihybrid cross of Mendel
has a characteristic phenotypic ratio of 9:3:3:1.
This result is best explained by Mendel’s Law of
Independent Assortment. According to this law,
the alleles from different genes are sorted into the
gametes independently of each other. This also
implies that genes are inherited independently of
each other. For example, in the given cross above,
the result of the dihybrid cross means that seed
color and seed shape are inherited independently.
The inheritance of one gene does not influence
that of the other. To better understand this, see
Table 3.
Table 3. Application of Punnett square to P and F1
generations of a dihybrid cross
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3. The Law of Dominance-An organism with
alternate forms of a gene will express the form that
is dominant. The alleles that are suppressed are
called the recessive traits while the alleles that
determine the trait are known as the dominant
traits.
The genetic experiments Mendel did with pea
plants took him eight years (1856-1863) and he
published his results in 1865. During this time,
Mendel grew over 10,000 pea plants, keeping
track of progeny number and type. Mendel's work
and his Laws of Inheritance were not appreciated
in his time. It wasn't until 1900, after the
rediscovery of his Laws, that his experimental
results were understood.
Using Pedigrees
Why Do We Perform Pedigree Analysis?
-A useful approach to study the inheritance of
traits in humans is pedigree analysis. As shown
in Fig.3 a pedigree is a graphical representation of
how a trait is inherited among the members of a
family. This is the first effective method introduced
to determine the mode of inheritance of a trait.
Given the periodic occurrence of a genetic
characteristic in a family, we can also assess the
risk of recurrence, especially if it is a genetic
disorder.
Fig. 3 Pedigrees are used to determine the
chances of a trait recurring in a family
However, as mentioned earlier, challenges in
studying the inheritance of traits in humans involve
problems in the collection of information. Usually,
one can construct an accurate pedigree of a family
from a survey or interview if the interviewee is
knowledgeable about the number of children, sex,
and the occurrence of the trait among his or her
relatives. Otherwise, false data can lead to wrong
interpretation of a pedigree.
Pedigree Analysis in Genetic Counseling
Genetic counseling is a procedure performed in
health institutions wherein advice is given to a
family afflicted with or at risk of getting a genetic
condition. A genetic counselor usually elaborates
on the genetic, psychological, and other
implications of the condition so that the family may
adapt as needed. The process of genetic
counseling entails the analysis of pedigrees
constructed from a series of questions answered
by the family to generate any pertinent
information. However, it will always be critical to
accurate genetic counseling that the family being
interviewed has a correct recollection of the
inheritance of traits among their relatives.
Constructing Pedigrees
Symbols and notations are used to construct a
pedigree. These symbols set the standard in all
genetic tests or analyses, and they are as follows:
1. Sex. Use squares for male individuals and
circles for females.
2. Traits. A shaded square or circle denotes that
an individual is affected by the condition.
Otherwise, the individual does not possess the
condition and is represented by an unshaded
shape.
3. Status. A slash is used to denote that an
individual is deceased. Not all pedigrees specify
this status of the individuals, however.
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4. Proband. Sometimes, pedigrees specify the
individual being studied or observed. Usually, a
proband is a member of the family who first sought
the attention of a genetic counselor. A proband is
represented by an arrow.
5. Carrier. A half-shade is used to represent that
an individual is a carrier for a genetic condition.
Specifically, the carrier individual is said to be
heterozygous for the condition. Take note that the
status of being a carrier is not always shown in a
pedigree.
6. Unknown Sex. Sometimes, the family being
interviewed prior to genetic counseling may be
certain about the number of children of a relative,
but not sure about their sexes. In such cases, a
diamond symbol is used.
7. Mating. Mating between a couple is denoted by
a horizontal line connecting them.
8.Offspring. The children of matings are
represented by a vertical line that connects to the
parents.
9. Consanguinity. Mating between genetically
related individuals, or a consanguineous mating,
is represented by a double horizontal line. ○ An
example of this is when cousins marry each other
and have children.
10. Twinning. Twins can be denoted by branching
from a common point. Connecting the members of
a twin represents a monozygotic or identical
condition. Otherwise, they are considered
dizygotic or fraternal.
11. Labels. Roman numerals are used to denote
generations. In each generation, individuals are
numbered consecutively from left to right. ○ For
example, individual II-2 is an affected son of
individuals I-1 and II-2, both of whom are
unaffected.

Analyzing Pedigrees
Identifying whether a trait that runs in the family is
dominant or recessive is crucial to the
determination of the chances of recurrence of that
trait in the family. This can also contribute to
continuously becoming a more extensive
understanding of how human traits are inherited.
It may not be as convenient as generating
hundreds of seeds in plant hybridization.
However, it can at least narrow down options
regarding the possible mode of inheritance of a
trait in humans
Fig.4 Symbols and notations used in constructing
human pedigrees
Conclusions from Mendel’s Experiments
▪ The genetic makeup of the plant is known as
the genotype. On the contrary, the physical
appearance of the plant is known as
phenotype.
▪ The genes are transferred from parents to the
offspring in pairs known as alleles.
▪ During gametogenesis when the
chromosomes are halved, there is a 50%
chance of one of the two alleles to fuse with
the allele of the gamete of the other parent.
▪ When the alleles are the same, they are
known as homozygous alleles and when the
alleles are different they are known as
heterozygous alleles.
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UNIT 2: MOLECULAR BIOLOGY
AND GENETIC ENGINEERING
History
Many people believe that American biologist
James Watson and English physicist Francis
Crick discovered DNA in the 1950s. In reality, this
is not the case. Rather, DNA was first identified in
the late 1860s by Swiss chemist Friedrich
Miescher. Then, in the decades following
Miescher's discovery, other scientists--notably,
Phoebus Levene and Erwin Chargaff--carried
out a series of research efforts that revealed
additional details about the DNA molecule,
including its primary chemical components and
the ways in which they joined with one another.
Without the scientific foundation provided by these
pioneers, Watson and Crick may never have
reached their groundbreaking conclusion of 1953:
that the DNA molecule exists in the form of a
three-dimensional double helix.
The First Piece of the Puzzle: Miescher
Discovers DNA
Although few people realize it, 1869 was
a landmark year in genetic research, because it
was the year in which Swiss physiological chemist
Friedrich Miescher first identified what he called
"nuclein" inside the nuclei of human white blood
cells. (The term "nuclein" was later changed to
"nucleic acid" and eventually to
"deoxyribonucleic acid," or "DNA.") Miescher's
plan was to isolate and characterize not the
nuclein (which nobody at that time realized
existed) but instead the protein components of
leukocytes (white blood cells).
Miescher thus made arrangement for a
local surgical clinic to send him used, pus-coated
patient bandages; once he received the
bandages, he planned to wash them, filter out the
leukocytes, and extract and identify the various
proteins within the white blood cells. But when he
came across a substance from the cell nuclei that
had chemical properties unlike any protein,
including a much higher phosphorous content and functions: (1) it contains the blueprint for making
resistance to proteolysis (protein digestion), proteins and enzymes; (2) it plays a role in
Miescher realized that he had discovered a new regulating when the proteins and enzymes are
substance. In addition, Chargaff’s rules state that, made and when they are not made; (3) it carries
“in DNA of any species and any organism, the this information when cells divide; and (4) it
amount of guanine should be equal to the amount transmits this information from parental organisms
of cytosine; and the amount of adenine should be
to their offspring. In this chapter, we will explore
equal to the amount of thymine”. Further, a 1:1
the structure of DNA, its language, and how the
stoichiometric ratio of purines (adenine and
guanine) and pyrimidines (cytosine and thymine) DNA blueprint becomes translated into a physical
bases should exist. Those purine and pyrimidine protein.
nucleotides are major energy carriers, subunits of
nucleic acids, and precursors for the synthesis of
nucleotide cofactors of NAD and SAM.
More than 50 years passed before the
significance of Miescher's discovery of nucleic
acids was widely appreciated by the scientific
community. For instance, in a 1971 essay on the
history of nucleic acid research, Erwin Chargaff
noted that in a 1961 historical account of
nineteenth-century science, Charles Darwin was
mentioned 31 times, Thomas Huxley 14 times, but
Miescher not even once. This omission is all the
more remarkable given that, as Chargaff also
noted, Miescher's discovery of nucleic acids was
unique among the discoveries of the four major
cellular components (i.e., proteins, lipids,
Fig. 5 DNA Structure
polysaccharides, and nucleic acids) in that it could
be "dated precisely... [to] one man, one place, one
A.DNA- Deoxyribonucleic acid
date."

DNA and RNA Physical Structure of DNA

Except for some viruses, life’s genetic code is
written in the DNA molecule (aka
deoxyribonucleic acid). From the perspective of
design, there is no human language that can
match the simplicity and elegance of DNA. But
from the perspective of implementation—how it is
actually written and spoken in practice—DNA is a
linguist’s worst nightmare. Most of the DNA, is
found inside the nucleus of a cell, where it
forms the chromosomes. Chromosomes haver
proteins called histones that bind to DNA. It has
two strands that twist into the shape of a spiral
ladder called a helix. DNA has four major
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Few people in literate societies can avoid
seeing a picture of DNA. Physically, DNA
resembles a spiral staircase. For our purposes
here, imagine that we twist the staircase to remove
the spiral so we are left with the ladder-like
structure depicted in Fig. 6. The two backbones to
this ladder are composed of sugars (S in the
figure) and phosphates (P); they need not concern
us further. The whole action of DNA is in the rungs.
Each rung of the ladder is composed of
two chemicals, called nucleotides or base pairs,
that are chemically bonded to each other. DNA
has four and only four nucleotides: adenine,
thymine, guanine and cytosine, usually
abbreviated by the first letter of their names—A, T,
G, and C. These four nucleotides are very
important, so their names should be committed to
memory. Inspection of Figure 6 reveals that the
nucleotides do not pair randomly with one another.
Instead A always pairs with T and G always pairs
with C. This is the principle of complementary
base pairing that is critical for understanding
many aspects of DNA functioning.
Fig. 6 DNA base-pairing
Because of complementary base pairing, if we
know one strand (i.e., helix) of the DNA, we will
always know the other helix. Imagine that we
sawed apart the DNA ladder in Figure 5 through
the middle of each rung and threw away the entire
right-hand side of the ladder. We would still be
able to know the sequence of nucleotides on this
missing piece because of the complementary
base pairing. The sequence on the remaining left-
hand piece starts with ATGCTC, so the missing
right-hand side must begin with the sequence
TACGAG. DNA also has a particular orientation in
space so that the “top” of a DNA sequence differs
from its “bottom.” The reasons for this are too
complicated to consider here, but the lingo used
by geneticists to denote the orientation is
important. The “top” of a DNA sequence is called
the 5’ end (read “five prime”) and the bottom is the
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3’ (“three prime”) end.1 If DNA nucleotide
sequence number 1 lies between DNA sequence
number 2 and the “top,” then it is referred to as
being upstream from DNA sequence 2. If it lies
between sequence 2 and the 3’ end, then it is
downstream from sequence 2.
DNA Replication
Complementary base pairing also assists in the
faithful reproduction of the DNA sequence, a
process geneticists call DNA replication. When a
cell divides, both of the daughter cells must
contain the same genetic instructions.
Consequently, DNA must be duplicated so that
one copy ends up in one cell and the other in the
second cell. Not only does the replication process
have to be carried out, but it must be carried out
with a high degree of fidelity. Most cells in our
bodies—neurons being a notable exception—are
constantly dying and being replenished with new
cells. For example, the average life span of some
skin cells is on the order of one to two days, so the
skin that you and I had last month is not the same
skin that we have today. By living into our eighties,
we will have experienced well over 10,000
generations of skin cells! If this book were to be
copied sequentially by 10,000 secretaries, one
copying the output of another, the results would
contain quite a lot of gibberish by the time the task
was completed. DNA replication must be much
more accurate than that.
Replication involves a series of protein and
enzymes that we will call the replication stuff. The
first step in DNA replication occurs when an
enzyme (cannot get away from those enzymes,
can we?) separates the rungs much as our
mythical saw cut them right down the middle (the
left-hand picture in Figure 6). Enzymes then grab
on to nucleotides floating free in the cell, glue them
on to their appropriate partners on the separated
stands, and synthesize a new backbone (right side
of Figure 6. The situation is analogous to opening
the zipper of your coat, but as the teeth of the not have the ladder-like structure of the DNA in
zipper separate, new teeth appear. One set of new Instead, RNA would look like Figure 5 after the
teeth binds to the freed teeth on the left hand side ladder was sawed down the middle and one half
of the original zipper, while another set bind to the of it discarded (with, of course, the added
teeth on the original right hand side. When you get provision that U would substitute for T in the
to the bottom, you are left with two completely remaining half).
closed zippers, one on the left and the other on the
Fourth, while there is one type of DNA,
right of your jacket front.
there are several different types of RNA, each of
which perform different duties in the cell. The
different types of importance for this text are listed
in Table 4. Note the abbreviations. In terms of
function, think of DNA as the monarch of the cell,
giving all the orders. Some occupy buildings in
outlying districts (ribosomal RNA), others
transport material to strategic locations (transfer
RNA), while yet others act as messengers to give
instructions on what to build (messenger RNA). As
we will see, the common language of the realm is
Fig. 7 DNA replication the genetic code and it is communicated by the
way of complementary base pairing.
B. RNA-Ribonucleic acid
Name Abbreviation Function
Before discussing the major role of DNA, Messenger mRNA Carries the
it is important to discuss DNA’s first cousin, RNA message from
ribonucleic acid or RNA. Besides its chemical the DNA to the
composition, RNA has important similarities and protein factory.
differences with DNA. First, like DNA, RNA has Transfer tRNA Responsible for
four and only four nucleotides. But unlike DNA, RNA bringing amino
RNA uses the nucleotide uracil (abbreviated as acid to the
U) in place of thymine (T). Thus, the four RNA ribosome.
nucleotides are adenine (A), cytosine (C), guanine Ribosomal rRNA Comprises part
RNA of the protein
(G), and uracil (U).
factory.
Second, the nucleotides in RNA also Small snRNA Process the pre-
exhibit complementary base pairing. The RNA nuclear mRNA to mature
nucleotides may pair with either DNA or other RNA RNA RNA.
molecules. When RNA pairs with DNA, G and C Micro RNA miRNA A guide by base-
always pair together, T in DNA always pairs with pairing with
target mRNA to
A in RNA, but A in DNA pairs with U in RNA.
negatively
When RNA pairs with RNA, then G pairs with C
regulate its
and A pairs with U. experession.
Third, RNA is single-stranded (usually) Table 4. Some important types of RNA
while DNA is double-stranded. That is, RNA does
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The Genetic Code
DNA is a blueprint. It does not physically construct
anything. Before discussing how the information in
the DNA results in the manufacture of a concrete
molecule, it is it important to obtain an overall
perspective on the genetic code. It is convenient
to view the genome for any species as a book with
the genetic code as the language common to the
books of all life forms. The “alphabet” for this
language has four and only four letters given by
four nucleotides in DNA (A, T, C, and G) or RNA
(A, U, G and C).
In contrast to human language, where a
word is composed of any number of letters, a
genetic “word” consists of three and only three
nucleotide letters and is called a codon. Each
genetic word symbolizes an amino acid. (We will
define an amino acid later.) For example, the
nucleotide sequence AAG is “DNAese” for the
amino acid phenylalanine, the sequence GTC
denotes the amino acid glutamine, and the
sequence AGT stands for the amino acid serine.
Like natural language, DNA has
synonyms. That is, there is more than one triplet
nucleotide sequence symbolizing the same amino
acid. For example, ATA and ATG in the DNA both
denote the amino acid tyrosine. The sentence in
the DNA language is a series of words that gives
a sequence of amino acids. For example, the DNA
sentence AACGTATCGCAT would be read as a
polypeptide chain composed of the amino acids
leucine-histidine-serine-valine. Because of the
triplet nature of the DNA language, it is not
necessary to put spaces between the words.
Given the correct starting position, the language
will translate with 100% fidelity.
Like natural written language, part of the
DNA language consists of punctuation marks. For
example, the nucleotide DNA triplets ATT, ATC,
and ACT are analogous to a period (.) in ending a
sentence—all three signal the end of a polypeptide
chain. They are called stop codons. TAC is a
start codon. It acts as the capital signaling the first
word in a new sentence. Biologically, it instructs
the cell to “start the peptide chain here.”
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Finally, DNA, just like a book, is organized
into chapters. The chapters correspond to the
chromosomes, so their number will vary from one
species to the next. The book for humans consists
of 24 different chapters, one for each chromosome
(22 autosomes plus the X and the Y). The book for
other species may contain fewer or more chapters
with little correlation between the number of
chapters and the complexity of the life forms.
Protein synthesis
A. Definition
We now examine the specifics of how
blueprint in the DNA guides the manufacture of a
protein. Although we have already spoken of
proteins and enzymes, we must now take a closer
look at these molecules. The basic building block
for any protein or enzyme is the amino acid.
Protein synthesis is the process in which cells
make proteins. It occurs in two stages:
transcription and translation. Transcription is the
transfer of genetic instructions in DNA to mRNA in
the nucleus. It includes three steps: initiation,
elongation, and termination.
There are three major sources for the amino
acids in our bodies. First, the cells in our bodies
can manufacture amino acids from other, more
basic compounds (or, as the case may be, from
other amino acids). Second, proteins and
enzymes within a cell are constantly being broken
down into amino acids. Finally, we can obtain
amino acids from diet. When we eat a juicy steak,
the protein in the meat is broken down into its
amino acids by enzymes in our stomach and
intestine. These amino acids are then transported
by the blood to other cells in the body
A series of amino acids physically linked
together is called a polypeptide chain. For now,
think of a polypeptide chain as a linear series of
boxcars coupled together. The boxcars are the
amino acids and their couplings the chemical
bonds holding them together. The series is linear
in the sense that it does not branch into a Y-like
structure. The notion of a polypeptide chain is
absolutely crucial for proper understanding of
genes, so permit some latitude to digress into
terminology.
We are now ready to define our old friend the
protein. A protein is one or more polypeptide
chains physically joined together and taking on a
three dimensional configuration. The polypeptide
chain(s) comprising a protein will bend, fold back
upon themselves, and bond at various spots to
give a molecule that is no longer a simple linear
structure. An example is hemoglobin, a protein in
the red blood cells that carries oxygen. It is
composed of four polypeptide chains that bend
and bond and join together.
B. The Process of Protein Synthesis: The
Central Dogma
Your DNA, or deoxyribonucleic acid, contains
the genes that determine who you are. How can
this organic molecule control your characteristics?
DNA contains instructions for all the proteins your
body makes. Proteins, in turn, determine the
structure and function of all your cells. What
determines a protein’s structure? It begins with the
sequence of amino acids that make up the
protein. Instructions for making proteins with the
correct sequence of amino acids are encoded in
DNA.
DNA is found in chromosomes. In eukaryotic
cells, chromosomes always remain in the nucleus,
but proteins are made at ribosomes in
the cytoplasm. How do the instructions in DNA get
to the site of protein synthesis outside the
nucleus? Another type of nucleic acid is
responsible. This nucleic acid is RNA or
ribonucleic acid. RNA is a small molecule that can
squeeze through pores in the nuclear membrane.
It carries the information from DNA in the nucleus
to a ribosome in the cytoplasm and then helps
assemble the protein. In short:
DNA RNA proteins
Discovering this sequence of events was a
major milestone in molecular biology. It is called
the central dogma of molecular biology. The
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two processes involved in the central dogma
are transcription and translation. In eukaryotic
cells, transcription takes place in the nucleus. It
uses DNA as a template to make an RNA
molecule known as messenger RNA (mRNA).
The RNA molecule then leaves the nucleus and
goes to a ribosome in the cytoplasm, where
translation occurs. Translation reads the genetic
code in mRNA and makes a protein.
b. 1 Transcription
The enzyme RNA Polymerase transfers
information from one strand of DNA to another
strand of RNA during transcription. Three parts of
the DNA strand are involved in this process: the
promoter, the structural gene, and the terminator.
DNA strands that synthesize RNA are
called template strands, and DNA strands that
Code for RNA are called coding strands. RNA
polymerases that are DNA-dependent bind to the
promoter and catalyze the 3' to 5' directions of
polymerization.
The newly synthesized RNA strand is
released from the terminator sequence as it
approaches the terminator. RNA strands released
after transcription undergo further modifications
post-transcriptionally.
b.2 Translation
Proteins are encoded by RNA by a
process called translation. Translation involves
energy and is an active process. The energy
comes from the charged tRNA Molecules.
The translation process is initiated by
ribosomes. Ribosomes are made up of two
subunits, one larger and one smaller. As a result,
the larger subunit consists of two tRNA Molecules
positioned together so that enough energy can be
expended to form a peptide bond.
The mRNA enters the smaller subunit and
is then held by the tRNA Molecules present in the
larger subunit that are complementary to the
codon. In this way, two codons are held together
by two tRNA Molecules placed close together and
a peptide bond is formed between them. This
process results in long polypeptide chains of
amino acids
Genetic Code
Proteins are manufactured from RNA and
their Genetic Code contains information about
them. In general, three nucleotides and four
nitrogenous bases collectively Code for an amino
acid, forming a triplet codon. As a result, there are
64 amino acids possible, including 4 x 4 x 4 amino
acids. There are 20 amino acids found naturally.
As a result, the Genetic Code
deteriorates. Due to the characteristics of the
Genetic Code, some amino acids are enCoded by
more than one codon at a time, causing the amino
acid to degenerate.
In total, there are 64 codons, of which
three are stop codons that end transcription and
one is an initiator codon, i.e. AUG, which Codes
for methionine.
Summary:
The central dogma states that the pattern
of information that occurs most frequently in our
cells is:
• From existing DNA to make new DNA
(DNA replication)
• From DNA to make new RNA
(transcription)
• From RNA to make new proteins
(translation)
Fig.8 DNA Structure
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Genetic Engineering
Genetic engineering, also called genetic
modification or genetic manipulation, is the
modification and manipulation of an
organism's genes using technology. It is a set
of technologies used to change the genetic
makeup of cells, including the transfer of genes
within and across species boundaries to produce
improved or novel organisms.
Brief History
Humans have altered the genomes of
species for thousands of years through selective
breeding, or artificial selection as contrasted
with natural selection. More recently, mutation
breeding has used exposure to chemicals or
radiation to produce a high frequency of random
mutations, for selective breeding purposes.
Genetic engineering as the direct manipulation of
DNA by humans outside breeding and mutations
has only existed since the 1970s. The term
"genetic engineering" was first coined by Jack
Williamson in his science fiction novel Dragon's
Island, published in 1951 one year before DNA's
role in heredity was confirmed by Alfred
Hershey and Martha Chase and two years
before James Watson and Francis Crick showed
that the DNA molecule has a double-helix
structure – though the general concept of direct
genetic manipulation was explored in rudimentary
form in Stanley G. Weinbaum's 1936 science
fiction story Proteus Island.
The process…
1. A small piece of circular DNA called a plasmid
is extracted from the bacteria or yeast cell.
2. A small section is then cut-out of the circular
plasmid by restriction enzymes called molecular
scissors.
3. The gene from human insulin (for example) is
inserted into the gap in the plasmid. This plasmid
is now genetically modified.
4. The genetically modified plasmid is introduced
into a new bacteria or yeast cell.
5. This cell then divides rapidly and starts making
insulin.
6.To create a large amounts of the cells, the
genetically modified bacteria or yeast are grown in
large fermentation vessels that contain all the
nutrients they need. The more the cell divide, the
more insulin is produced.
7.When fermentation is complete, the mixture is
filtered to release the insulin.
8. The insulin is then purified and packaged into
bottles and insulin pen for distribution to patients
with diabetes.
Years of GMO successful records:
1972-Paul Berg created the first recombinant
DNA molecules by combining DNA from the
monkey virus SV40 with that of the lambda virus.
1973- Herbert Boyer and Stanley Cohen created
the first transgenic organism by inserting antibiotic
resistance genes into the plasmid of
an Escherichia coli bacterium.
1975- A year later Rudolf Jaenisch created
a transgenic mouse by introducing foreign DNA
into its embryo, making it the world's
first transgenic animal.
1976-Genentech, the first genetic engineering
company, was founded by Herbert Boyer
and Robert Swanson and a year later the
company produced a human protein
(somatostatin) in E. coli. Genentech announced
the production of genetically engineered
human insulin in 1978.
1980-the U.S. Supreme Court in the Diamond v.
Chakrabarty case ruled that genetically altered life
could be patented.
1982- The insulin produced by bacteria was
approved for release by the Food and Drug
Administration (FDA).
1983-a biotech company, Advanced Genetic
Sciences (AGS) applied for U.S. government
authorisation to perform field tests with the ice-
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minus strain of Pseudomonas syringae to protect
crops from frost, but environmental groups and
protestors delayed the field tests for four years
with legal challenges.
1987-the ice-minus strain of P. syringae became
the first genetically modified organism (GMO) to
be released into the environment[36] when a
strawberry field and a potato field in California
were sprayed with it.
1992- he People's Republic of China was the first
country to commercialise transgenic plants,
introducing a virus-resistant tobacco.
1994-Calgene attained approval to commercially
release the first genetically modified food,
the Flavr Savr, a tomato engineered to have a
longer shelf life.
1995- Bt potato was approved safe by
the Environmental Protection Agency, after having
been approved by the FDA, making it the first
pesticide producing crop to be approved in the US.
2009- transgenic crops were grown commercially
in 25 countries, the largest of which by area grown
were the US, Brazil, Argentina, India, Canada,
China, Paraguay and South Africa.
2010-scientists at the J. Craig Venter
Institute created the first synthetic genome and
inserted it into an empty bacterial cell. The
resulting bacterium, named Mycoplasma
laboratorium, could replicate and produce
proteins.
2012-JenniferDoudna and Emmanuelle
Charpentier collaborated to develop
the CRISPR/Cas9 system, [48][49] a technique
which can be used to easily and specifically alter
the genome of almost any organism.
Applications
1.Medicine- Genetic engineering has many
applications to medicine that include the

manufacturing of drugs, creation of model
animals that mimic human conditions and gene
therapy.
2.Research- Genetic engineering is an important
tool for natural scientists, with the creation of
transgenic organisms one of the most important
tools for analysis of gene function.
3.Industrial- Organisms can have their cells
transformed with a gene coding for a useful
protein, such as an enzyme, so that they
will overexpress the desired protein.
4.Agriculture- One of the best-known
and controversial applications of genetic
engineering is the creation and use of genetically
modified crops or genetically modified livestock to
produce genetically modified food.
Fig. 9 GMO procedure
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UNIT 3: EARTH’S TIMELINE
AND EMERGENCE OF LIFE
Introduction
For decades, humans have explored
possible explanations for the origin of life on Earth.
Scientists started to formulate a series of theories
regarding the emergence of life forms on the
planet and relate it to the physical changes on
Earth’s environment. In this lesson, students are
expected to explore the geological timeline of
Earth together with the story on the early
emergence of life on the planet. In the end,
students must be able to construct Earth’s timeline
and identify the prevailing hypothesis regarding
the emergence of primitive life forms.
Brief History
Earth’s Geologic Time Scale Earth has
been around for billions of years and the way that
scientists make an estimate is through the
geologic time scale. This refers to a system of
dating the history of Earth in a chronological
manner using geological data. The entire geologic
time scale of the Earth reflects the entire history of
the geological history of our planet. The geologic
time scale is divided into eons, eras, periods,
and epochs.
EONS refer to the greatest expanse of time that
can be divided into the Phanerozoic and
Precambrian eons.
I. Precambrian eon (4 billion years ago)
represents the period between the birth of the
planet and the appearance of life forms. This is the
eon where the earth’s formation started to form in
three stages: Hadean (Earth’s surface was
possibly in the form of liquid rock and boiling sulfur
that built an ocean of hot materials), Archean
(Earth mostly cooled down and the water vapor
from the air condensed and formed the global
ocean) and Proterozoic (multicellular organisms
in the form of algae in the ocean started to free
oxygen that bonded with chemical elements such
as iron to form great mineral deposits around the known as the first appearance of first mammals
world). and first dinosaurs.
b.2 Jurassic period- Dinosaurs continued as the
II. Phanerozoic eon (542 million years ago) dominant species and evolved to be gigantic.
means ‘visible life’ that was constructed through Known for first bird appearance and dinosaur
rock units that bear abundant fossils. diversity.
b.3Cretaceous period- Major extinction of
ERAS which are the second-longest units of dinosaurs, first appearance of primates. The
geological time. The Phanerozoic eon is divided environment evolved to the point that flowering
into three eras: the Paleozoic, Mesozoic, and plants (angiosperms) began to appear for the first
Cenozoic. These time, eras were constructed time.
based on the major changes in available fossil
records and the PERIODS this is the basic unit of C. Cenozoic era is also known as the ‘age of
geologic time. Which means shorter time than the mammals’. In this period, scientists observed a
era. A Period lasts tens of millions of years, which series of speciation of mammals. Most
is the time it takes to form one type of rock system. importantly, this is the time when the first humans
appeared. It is subdivided into two periods
A. Paleozoic era is also known as the ‘age of including the tertiary (also sometimes referred to
invertebrates’ due to the presence of the fossils in terms of Paleogene and Neogene period) and
of animals without backbones, including trilobites quaternary.
and corals. It is divided into six periods. This time c.1 Tertiary period- mammals diversity.
period is represented by Cambrian, Ordovician, c.2 Quaternary period-human evolution.
Silurian, Devonian, Carboniferous, and Permian
periods.
a.1 Cambrian period- The explosion of life
occurred; first fish, and first chordates (animal with
backbone).
a.2 Ordovician period- Dominant animals were
marine invertebrates such as trilobites and corals.
a.3 Silurian period- It is marked by the first
appearance of land plants.
a4. Devonian period- fish diversity and first
amphibians.
a5. Carboniferous period- First seed plants and
first reptiles appeared.
a6. Permian period- It is marked by the extinction
of 90% of Earth’s species and reptiles diversity.

B. Mesozoic era is also known as the ‘age of

reptiles’. Within this time frame, reptiles,
especially dinosaurs, were abundant. It is divided
into three periods – Triassic, Jurassic, and
Cretaceous.
b.1 Triassic period- Dinosaurs evolved in the
late-Triassic period along with crocodilians, flying
reptiles, sea-reptiles, and mammals. This is Fig.10 Summary of events in each period

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Early theories regarding the origin of life on Earth
started during the 16th century in Europe. These
theories include the spontaneous generation
theory, primordial soup theory, and theory of
panspermia.
1. Theory of Spontaneous Generation-states
the idea that life comes from lifeless or
nonliving material through a mysterious
process. Abiogenesis is the process by which
life emerges naturally from inanimate or nonliving
materials. This theory was introduced by
Anaximander, a Greek philosopher in the 6th
century BCE. Other philosophers including
Aristotle adapted and expanded Anaximander’s
idea, where he explained that some organisms
appeared from inanimate objects spontaneously.
Another supporter of abiogenesis is John
Needham (1748), an English priest and biologist.
Needham tested whether life can arise
spontaneously after boiling. He boiled mutton
broth and sealed its container with cork to prevent
the entry of microorganisms.
2. Theory of Panspermia- suggests that building
blocks of life came from another planet. These
include comets colliding with Earth and depositing
living cells or the precursors of life, and aliens
making life-essential materials in a laboratory.
Fred Hoyle introduced this idea in the 19th
century, where he mentioned that life on Earth was
seeded from a celestial source. According to the
idea of this theory, bacteria and other
microorganisms might have traveled in dormant
stages within comets and asteroids that heated
the Earth.
3. Theory of Primordial Soup- This theory
suggests that life started in a primordial soup of
organic molecules. It tries to explain how catalysts
for nonliving things became living cells from
chemical compounds abundant on early Earth.
This idea of the primordial soup was originally
proposed by Alexander Oparin and John
Haldane. The theory states that if energy is added
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to the gases that made up Earth’s early
atmosphere.
UNIT 5: THEORIES OF
EVOLUTIONS
Evolutionary Thoughts
Our modern ideas regarding evolution come from
many sources. Among the most notable of these
are from Charles Darwin, who is widely
recognized as the father of evolution. Many of his
ideas are known to be among the earliest accurate
explanations for the diversity of life on Earth.
However, there have also been many other
concepts put forth that predate Darwin’s theory.
This lesson will tackle some of these concepts and
beliefs.
Older Evolutionary Beliefs
I. Ancient Beliefs
A. Aristotle-a Greek philosopher who lived
sometime between 384 and 322 B.C. Aristotle is
well known even in modern times due to his
contributions to ethics, the study of logic, and his
other philosophical work. His other work also
extensively tackled scientific topics including the
following:
-Historia Animalium (The History of Animals),
another preserved work of Aristotle, classified
animals based on their structure and functions.
-Scala naturae or “Natural Ladder” where he
organized all natural objects, from nonliving matter
to living organisms in a continuum which implies
that species are rather immutable or unchanging
entities.
B. Theophrastus (371–287 B.C.)- who was one
of Aristotle’s successors and has done extensive
work on plants in his Historia Plantarum (a study
on plant anatomy, structures, reproduction,
growth, and more), which earned him the moniker
the “Father of Botany”.
C. Pliny the Elder- a Roman military man, was
also a prominent natural historian and
philosopher. He lived sometime between 23 and
79 A.D. and wrote the work Naturalis Historia,
which is Latin for Natural History. This vast
publication spanned ten volumes that tackled
several fields such as biology, astronomy,
mathematics and many other branches of science.
Pliny’s observations on animals and plants have
been widely read even centuries after his death. In
fact, many of these ideas influenced his
contemporaries many years afterward.
D. Roman Catholic-creation story which states
that the world and all its inhabitants were created
over the course of six days. Some Islamic creation
myths are also very similar to the Catholic creation
story, with the world being fashioned out of
nothing. Buddhist mythology, on the other hand,
states that the universe has no beginning and end.
E. Pope Francis- in 2014, saying that the Big
Bang and the occurrence of evolution are indeed
scientific facts.
II. Other Beliefs in the Middle Ages
F. Al-Jahiz (776–869 A.D.)- was an Islamic
scholar born in Basra, Iraq. He published the
Kitab al-Hayawan, also known as the Book of
the Animals. This was a vast work that spanned
seven volumes and contained ideas that had
some influences from Aristotle. Al-Jahiz’ Kitab al-
Hayawan had multiple ideas that predated but
supported the idea of natural selection.
G. St. Thomas Aquinas (1225–1274) -was an
Italian Catholic priest who has also made
significant contributions to scientific thought. He
notably stated that there is no disconnect between
the Catholic creation myth and the natural
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observations that have been made by the natural
philosophers that have come before him.
H. Ibn Khaldun (1332–1406)-was born in Tunisia
and published the Muqaddimah. In his work, he
described the origins of Earth as being from basic
nonliving components. Later on, he described the
formation of plants and animals from simple life
forms to more complex ones.
The Lead-Up to the Theory of Evolution
The modern theory of evolution did not develop
overnight, and the ideas did not all just come from
a single scholar. The contribution of multiple
naturalists and the revision of ideas from one
scholar to another led to the theory of evolution as
we know it today. Many of the concepts that build
the modern theory of evolution were formulated in
the 1700s.
A. Charles Bonnet and Evolution (1720–1793)-
was a naturalist who was born to French parents
in Geneva, Switzerland. In Charles Bonnet’s
publication, the Considérations sur les Corps
Organisées (Considerations on Organized
Bodies), he used the term evolution to describe
his own concept of preformation, which is an idea
that states that a miniature version of organisms is
carried by females to give rise to future organisms.
B. Comte de Buffon’s Natural History of
Animals-was a French naturalist who published
an important work that contributed to the modern
idea of evolution. His work, entitled Natural History
of Animals, put forth ideas in comparative anatomy
that are closely related to today’s idea of evolution.
Some of his observations included noting the
similarities in the limbs of several vertebrates and
the specific structures and functions involved in
these limbs.
C.Jean-Baptiste Lamarck’s Transmutation of
Species-was a French naturalist who counted
Comte de Buffon as one of his mentors. His
contribution, though since been discredited, was
also a major step toward the development of
evolutionary theory. His transmutation of species
is an idea that species change over time and may
also be seen as a derivative of his mentor’s ideas.
Take note that some of his concepts, like many
other naturalists before him, were built and
adapted from earlier ideas put forth by other
naturalists. Lamarck’s concept of evolution had
two major ideas, with some significant differences
from Comte de Buffon’s proposals:
• Changes: The first idea aimed to explain
how organisms change over time. Simpler
forms of life are continuously formed
through spontaneous generation. These
simple life forms become more complex
as time passes through various changes
that occur in these organisms. The
changes that occurred are explained by
Lamarck’s theory of use and disuse,
which will be discussed later.
• Inheritance: The second idea aimed to
explain how these changes persist over
generations. According to Lamarck, the
traits that the organisms have acquired
through change can be passed onto their
offspring.
D. Robert Chambers’ Vestiges of the Natural
History of Creation- Another work that put forth
ideas regarding evolution was Robert Chambers’
(1802–1871) Vestiges of the Natural History of
Creation, published in 1844. This work was
published in the wake of the discrediting of
Lamarck’s theories. Vestiges presented ideas
regarding the origins of life on Earth. Important to
the concept of evolution, however, were his claims
that fossils show the progressive changes that
happen to organisms.
E. Charles Robert Darwin- on February 12, 1809
in England, he already showed interest regarding
the natural world even as a young child. As he
aged, his interest in the natural world further
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developed, which led him to formally study the
field of evolutionary biology and became a
naturalist by profession.
Darwin’s Theory of Evolution
Charles Darwin is credited for his
significant contributions to the development of the
modern theory of evolution, and rightfully so. The
main ideas put forth by Darwin were that species
change over long periods of time and that these
developed from ancestors to descendants. His
ideas were published in the book. On the Origin
of Species, which remains famous and relevant
until today.
On the Origin of Species
On the Origin of Species (sometimes
shortened to Origin) is undoubtedly Charles
Darwin’s most famous work. This book, published
on November 24, 1859, is still widely-read even in
modern times. As was mentioned in the previous
lesson, many ideas and explanations regarding
the development of life on Earth and the
diversification of species have already been put
forth. Darwin, in fact, derived many of his ideas
from these previous works. Some of the most
notable parts of Origin are the following:
● the proposal of branching evolutionary patterns
that show common ancestries between
organisms;
● explanations on the process of natural selection
and how it leads to evolution, and
● various pieces of evidence from Darwin’s own
findings and observations.
The Components of Darwin’s Theory of
Evolution
A. Common Descent -refers to how organisms
have descended from other organisms and
how species share a common ancestry.
Because of common descent, multiple species
can arise from just a single ancestor. This provides
one of the explanations for how life on Earth ended
up being enormously diverse.
B. Speciation- refers to the process by which
organisms change and evolve to form a
distinct new species. This process occurs
through different mechanisms that will be
discussed in the next unit. However, an important
thing to note about speciation and its mechanisms
is that there is a shift in the characteristics that
occur within the population. For example, a shift
may occur from a previously-dominant white
coloration in a population of insects to a population
mostly made up of black coloration.
C. Gradualism-Many theories attempted to
explain and estimate the Earth’s age, even before
Darwin’s time. Many of these explanations are
vastly inaccurate, being much shorter than Earth’s
4.54 billion years of age. A theory that Earth is
indeed older than what most people think was put
forth by Charles Lyell (1797–1875). Lyell was a
geologist who extensively studied Earth’s history
and explained much about the changes that
happened to the planet over its long course of
existence. Furthermore, he stated that the age of
Earth is ancient, contrary to what many other
studies claimed. This view is also reflected in his
view of evolution, stating that the change that
happens to species occur over very long
periods of time. The slow process of evolution
has occurred over the long history of Earth,
taking place in a gradual manner with small
changes happening to species through time.
D. Natural Selection-According to Darwin, the
preservation of traits can stem from how
organisms that have favorable traits within their
current environments are more likely to survive to
reproductive age, mate, reproduce, and
consequently pass on these traits to their
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offspring. Through natural selection, organisms
with favorable traits are more likely to survive, and
those with unfavorable traits have lower chances
of survival.
Differences from Earlier Explanations
Darwin’s ideas were significantly different from
the ideas of those that came before him, most
especially in terms of the following four points:
1. Physical and scientific explanations-unlike
many of the other works published regarding the
rise of species, Darwin’s work provided physical
and scientific evidence on how diversification
came to be.
2. Evolution occurs in stages-Darwin also gives
a stepwise explanation of how evolution occurs in
different stages, which was something that many
other publications were not able to provide.
3.Evolution occurs in groups-Unlike the
Lamarckian concept that predated Origins, Darwin
was able to correctly conclude that evolution and
speciation occur in groups of organisms instead of
individuals. In other words, evolution takes place
at the population level.
4.Environmental influence- Darwin also
recognized the fact that evolution happens due to
the differences in the success of organisms
depending on the environment that they are
exposed to.
The Unified Theory of Evolution
As was mentioned in the previous lesson,
Charles Darwin’s contributions, even without the
ideas of Gregor Mendel’s experiments, were
significant enough to revolutionize the
understanding of evolution. This remains true until
today, although many other concepts that have
been discovered since the publication of On the
Origin of Species have been incorporated into the
modern evolutionary theory. The inclusion of
these concepts unites several fields of biology
together, and these provide a more
comprehensive understanding of the evolutionary
process. Thus, the modern evolutionary theory is
also known as the unified theory of evolution,
which is sometimes also referred to as the
modern synthesis or neo-Darwinism.
1. Adaptation- refers to both the mechanism of
adjusting to environmental changes and the
features that organisms have or use to survive in
their habitats.
2. Genetic drift- refers to the change in the allele
frequencies that occur in a population as a result
of chance.
3.Phylogeny and Systematics-these fields
primarily deal with deciphering how species are
related to each other and how lineages have
diverged in order to form new species.
4. Phylogenetic change- refers to the changes
that occur during a species’ evolutionary history.
This means that phylogenetic changes are those
that occur across generations, which is in contrast
with the ontogenetic change, which deals with
those that occur in the lifespan of one organism.
5.Comparative Anatomy- studies the
comparisons between the structures of organisms
to establish their evolutionary relationships.
6. Biogeography- is a branch of biology that deals
with the distribution of species across the world. A
branch of biogeography, the historical
biogeography, concerns itself with the past and
present distribution of organisms.
Misconceptions about Evolution
1. Evolution Is a Theory-The name “theory of
evolution” has then led many people to believe
that evolution is not yet considered a fact and is
merely a supposition for how life diversified.
However, in truth, there are already many pieces
of irrefutable evidence that evolution is indeed real
and continuously occurring.
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2. Evolution Has a Goal-Some people believe
that evolution produces organisms that are
better than their ancestors and that evolution
has a goal of making organisms better over
generations.
3. Survival of the Fittest-This is inaccurate as
the statement implies that only the fittest will
survive in their environments. The more
accurate statement would be that natural
selection is closer to “survival of the fit” (or
“survival of the fit enough”), wherein
organisms that meet the requirements of their
environment have higher chances of survival
and passing on their genes to their offspring.
4. Humans Evolved from Chimps-It is true that
humans are very closely related to the great
apes, like chimpanzees, orangutans, gorillas,
and bonobos. In fact, chimpanzees are the
closest living relatives of humans. Many
people incorrectly believe, however, that
humans have directly descended from
chimpanzees. While humans are closely
related to the apes, we are not direct
descendants of the great apes. What we do
know is that we share common ancestors, and
our lineages diverged and produced the
extant species that are present on Earth
today.
UNIT 6: EVIDENCES OF
EVOLUTIONS
Fossil Formation and Classification
Fossils are not just indicators of life on
Earth. Another important use that scientists
have gained out of them is that they provide
 very important pieces of evidence for 2. Cast fossils -are formed when sediments and
evolution. Fossils give a glimpse of how minerals fill up the body cavities of an organism.
organisms that have long since become
3. Trace fossils-These are traces left behind by
extinct have lived and changed over very long
organisms in the past. In most cases, these fossils
periods of time. Our knowledge of past life
are not part of the body of the organism that left
forms can be attributed to fossils or the
them behind.
preserved remains of organisms from earlier
periods of Earth’s history. 4. True form fossils- are among the most useful
fossils in studying organisms since these are
The Process of Fossil Formation
entire organisms whose bodies have been
There are many different types of remains that preserved.
organisms can leave behind as fossils and each of
Fossil Dating Methods
these types form a certain way. In general,
however, fossils may form through the enclosure Estimating the age of a fossil allows us to
of the organism in a preserving substance, determine when the organism lived in Earth’s
through carbonization, permineralization, or history. This allows scientists to reconstruct the
through replacement. history of places, ecosystems, or the evolutionary
history of organisms and how they changed over
1. Permineralization-involves groundwater filling
time. Among the most useful fossil dating methods
up these spaces. Groundwater leaves behind
are relative dating and absolute dating.
minerals in these spaces which results in the
formation of a fossil in the image of the organism. 1. Relative dating methods- involve estimating
the sequence of events that are involved in Earth’s
2.Carbonization-involves organisms leaving
history.
behind the residual carbon while many other
elements are shed off. This usually happens when 2. Absolute dating methods- give a numerical
the remains of the organism are subjected to heat estimate of the age of rock layers and fossils.
and pressure. Possibly the most common method used in the
study of fossils is radiometric dating which uses
3. Replacement- involves the minerals in these
the decay of radioactive isotopes in order to
organisms’ bodies being replaced by other
determine the age of a subject.
minerals. For example, when minerals replace the
organic parts of a tree trunk to leave behind a Structural Evidence in the Study of Evolution
fossil.
The physical characteristics of organisms
Types of Fossils allow them to survive, grow, and reproduce. Most
of the physical characteristics that organisms have
There are many different types of fossils
are heritable. This means that if the organism
that form through different means. Some of the
survives, it has a chance of passing on its physical
major types of fossils that are useful for scientific
characteristics. As such, because of heritability,
studies are cast fossils, mold fossils, trace
scientists are able to use these as structural
fossils, and true form fossils.
evidence in studying evolution.
1. Mold fossils- form when substances like
1. Homologous Structures-refer to structures in
minerals or sediments press over the body of a
different organisms that are similar in terms of
dead organism.
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structure but may have different functions due to
evolutionary differences between organisms.

Fig. 13 Whales and other cetaceans (like

dolphins) have a vestigial pelvis.
Fig. 11 A photo showing the limbs of several 4. Embryological Evidence-Embryos refer to the
vertebrates unborn and still-developing organism in the early
stages of life. The similarities between embryos of
different species can be used for tracking
2. Analogous Structures-structures that have evolutionary relationships between them.
similar functions even though they have evolved
independently between different organisms. In
many cases, these organisms are only very
distantly related and do not share any recent
common ancestors that could have given them the
shared trait.

Fig. 14 Embryonic features of chordates

Fig. 12 Bird and insect wings are examples of
analogous structures
5.Structural Evidence from Fossils-are also
useful evidence for evolution since scientists are
able to observe the similarities and differences
between extinct organisms and the organisms of
today.

3. Vestigial Structures -Not all structures in

organisms are functional. Some have lost their
function over the course of an organism’s Fig. 15 Evolution of tetrapods and its relation
evolutionary history. to ancient fishes

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Biogeographical Evidence of Evolution 1. Continental Drift- In 1912, a scientist named
Alfred Wegener proposed the theory of continental
The study of the distribution of species
drift. He stated that the locations of the continents
over space and time is crucial to the study of
in Earth’s distant past were not the same as the
evolution. Knowing when and where species
locations that they are found in today. He
existed is important in determining evolutionary
proposed that the landmasses on Earth are
and ecological relationships. This is the primary
continually moving although at a very slow pace.
concern of the field of biogeography.

Fig.16 Difference between vicariance and

dispersal
Dispersal -refers to when a population moves
across a geographical barrier in order to settle in
a new location. If this population has the Fig.17 Image of Pangea
necessary adaptations to survive in the new area,
2. Climate and Sea Level Change-changes in the
then this population will most likely thrive.
sea levels on Earth affected the amount of land
Vicariance -refers to when a barrier appears available for organisms to thrive in. The lowering
which isolates two populations of the same of sea levels led to more land being exposed from
species that were once connected. An example is under the sea and may have allowed species to
when an earthquake causes a river to overflow colonize these areas.
and widen which causes two animal populations
on each side of the river to become isolated from
each other.
Factors and Phenomena That Shape
Biogeographical Patterns
There are many phenomena that scientists
believe help shape biogeographical patterns.
Some of these include continental drift, migration, Fig. 18 An example is this area between
climate, sea levels, geographic barriers, and Jerusalem and the Dead sea
centers of origin.
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3. Migration- refers to the movement of 5. Center of Origin- refers to a geographic
populations from one geographic location to location where multiple species have been proven
another. Migration can either be emigration or to have acquired distinct characteristics which
immigration, depending on where the population may have led to speciation.
moves.

Fig. 21 The geographic location of the East

Fig.19 Emigration and immigration in the
population
4.Geographical barriers- may be selective in
how they isolate populations from each other.
Some types of barriers may allow some species to
disperse through, whereas the same barrier
completely bars other species from movement.
Fig.20 The geographic barrier between
populations of lobster in Panama
Indies
The Hierarchy of Organization
The process of organizing organisms based on
taxonomic hierarchy involves classifying them into
multiple levels of the organization. These levels of
organization indicate the classification of
organisms based on general characteristics and
how scientists believe they are related to other
similar organisms.
Description
Domain The highest level of classification
which separates eukaryotes and
prokaryotes (bacteria and
archaeans).
Kingdom The kingdoms were traditionally
the highest level before domains
were introduced. Examples of
kingdoms are Animalia and
Plantae.
Phylum This is the uppermost level of
organization within kingdoms.
Examples are Chordata,
Arthropoda, and more.
Class The class is a rank below phylum
and above order. An example
includes the class Mammalia.

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Order Orders are classifications under
each class and organisms within
them show many similar
characteristics. An example is
Primata, where humans are
classified under.
Family The family is one of the lowest
levels of classification denoting
close relationships between
organisms.
Genus Organisms of the same genus
are very closely related and
usually with small differences.
Species Those that share the species
level are known as conspecifics,
which have genetic similarities.
Table 5. All organisms have a corresponding
classification in the taxonomic hierarchy.
Taxonomy The field of taxonomy is an important
field in biology. This field involves naming and
classifying organisms based on characteristics
and relatedness. Carl Linnaeus, also known as
Carl von Linnė or Carolus Linnaeus, is often called
the “Father of Taxonomy”. His system for naming,
ranking, and classifying organism is still in wide
use today. Giving an organism an appropriate
scientific name, for example, is one of the things
that taxonomy is in charge of. Although it seems
like a very simple field, taxonomy is essential to all
biological branches that involve studying
organisms.
A scientific name, in most cases, is composed of
two components: the genus name and the specific
epithet. These two must be included in a complete
scientific name, with both names being italicized if
in a digital format or separately underlined if
handwritten. For example:
The scientific name of the Philippine eagle:
Pithecophaga jefferyi
Genus: Pithecophaga
Specific epithet: jefferyi
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UNIT 7: TAXONOMIC
CONCEPTS & PRINCIPLES
Taxonomy refers to the science that deals with the
description, identification, nomenclature, and
classification of organisms. Taxonomy takes into
account how organisms are related, but it does not
totally reflect evolutionary relationships.
Particularly, the taxonomic processes mentioned
above can be described as follows.
1. Description. This basic procedure in taxonomy
entails the assignment of characteristics to an
organism for use in the succeeding steps.
-For example, one can describe the venation of a
corn plant as parallel.
2. Identification. This step determines whether
an organism already falls under a previously
identified organism.
-For example, a flower-bearing plant with netted or
reticulate venation can be used as a feature to
identify the dicot group.
3.Classification. This step involves the
assignment of an organism to a particular level or
rank in the taxonomic hierarchy.
-For example, at the phylum level, a red fox can
be classified under Chordata, which is similar to
that of humans.
4. Nomenclature. This a procedure in taxonomy
in which organisms are named by using a
standardized system. Particularly, formal scientific
names should be in Latin.
-For example, the standard scientific name for
humans, which should be in Latin similar to all
other organisms, is Homo sapiens.
Taxonomic classification groups organisms
according to their relatedness. In the classification
of the red fox, organisms are more distantly
related at the domain level and tend to share more
similarities as we go down the taxonomic
hierarchy. For example, a comparison between a
human and an ostrich is shown in Figure 22.
These two organisms fall under the same
classification from the domain down to the phylum
level.
Fig. 22 Taxonomic classification of red fox
Taxonomic Traits
Taxonomic traits are the characters used
to classify organisms according to their taxonomic
groups. These characters are very important in
quantifying the degree of relatedness of species
with one another. Taxonomic characters can be
classified into two general categories—ancestral
traits and derived traits.
1.Ancestral traits- are evolutionary traits that are
homologous within groups of organisms. It is
expected that they all descended from a common
ancestor, in which the ancestral trait first evolved
shares this similarity. Most of the time, ancestral
traits are useful in classifying organisms in the
domain, kingdom, or even until the phylum level.
Fig. 23 Evolution of fish, birds, and mammals
involving the presence of jaws
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2. Derived traits- are characters that are
present in a species but absent in their
ancestor. This can also be in vice versa condition,
where the structures that are not present in an
organism, but were present in its ancestors.
Derived traits are very useful in studying the
evolution of organisms. Most of the time, derived
traits are products of evolutionary changes that
allow organisms to adapt to their environment. In
taxonomy, derived traits are useful in classifying
organisms into their specific taxonomic groups.
Fig. 24 Importance of derived traits in studying
the evolution of organisms and in identifying
more specific traits to groups of organisms.
Taxonomic Evidence for Classification
1. Morphological traits- refer to the set of
physical features of living organisms. These can
be external or internal morphological features that
are useful for the classification of organisms.
2.Developmental traits- refer to the set of
developmental features that can be used for the
classification of organisms.
3. Physiological traits -are mainly focused on the
functional features of the structures. Physiological
traits are usually compared among organisms. In
some cases, the morphological structure of the
body parts can be highly different, but their
functions are the same.
4. Genetic traits -refer to specific sequences of
the DNA molecule in organisms. The use of
genetic sequences in comparing the similarities
and differences of organisms is highly useful in
delineating organisms until the species or even
until the subspecies level.
Phylogenetic Tree of Life
Phylogenetic trees- are illustrated diagrams that
show evolutionary relationships between featured
organisms and are based on hypotheses of how
the organisms are related. Taxonomists and
evolutionary biologists construct phylogenetic
trees based on morphological, genetic, and
behavioral data.
1. Morphological Data - These are the physical
traits that can be observed in organisms.
Examples are bone structure, body shape, or
muscle patterns.
2.Genetic Data - This refers to the DNA
sequences collected from the organisms. The
sequences are analyzed based on the number of
similarities in the DNA base pairs.
3.Behavioral Data - Many evolutionary biologists
consider observable behavior in constructing a
phylogenetic tree, especially for some animal
groups.
The following are the parts of a usual phylogenetic
tree:
a. Root - This is the origin point that represents
the position of the common ancestor of all species
included in the tree.
b. Nodes - Nodes represent diverging points in the
evolutionary history of the organism due to the
development of derived traits along the organism’s
history.
c. Branch - It shows the positioning order of each
organism within the phylogenetic tree.
d. Branch Length - For scaled phylogenetic trees,
the branch length may signify the estimated time
period for the evolutionary changes to happen
within the group of organisms included in the tree.
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e. Clade - This refers to the cluster of organisms
that were grouped together due to their great
similarities.
Development of Taxonomy
Taxonomy is the science of classifying and
naming organisms. Taxonomy classifies
organisms based on their relatedness which is
why phylogenetic trees are relevant in this field. At
the same time, evolutionary relationships of
organisms are also being considered to provide a
more comprehensive understanding of the overall
connection of one organism to another. In general,
the field of taxonomy can be divided into three
major functions. These are identification,
naming, and classification.
A. Identification and Description Taxonomy-
deals with the identification of organisms. To do
this, modern-day taxonomists provide
comprehensive taxonomic descriptions of all
documented species on Earth. The taxonomic
descriptions can be based on morphology,
behavior, and genetic data.
B. Naming- Taxonomy also deals with the naming
of species. This is particularly important for newly
discovered species that require their own scientific
names. The subfield of Taxonomy that deals with
the proper naming of organisms refers to
nomenclature.
C. Classification-Taxonomy deals with the
proper groupings of organisms based on their
morphological, genetic, and evolutionary
relatedness. This is usually done by studying the
phylogeny of the organisms. The process of
classifying organisms in a highly organized
manner refers to Systematics.
Significant taxonomists who contributed major
works in the development of the field in taxonomy
are as follows:
• Aristotle -is considered as one of the earliest
formally trained taxonomists. For example, he
defined humans as "rational animals" due to
their ability to think and decide on things.
Aristotle summarized all of his works in early
taxonomy in the History of Animals (Latin:
Historia Animalium), where he classified
organisms based on their similarities.
• Theophrastus-wrote early works on the
classification of all known plants in his work,
“De Historia Plantarum.”
• Dioscorides- documented many Roman and
Greek medicinal plants. He summarized all of
his works in a book, “De Materia Medica”,
which describes around 600 species.
• Plinius wrote many books about giving Latin
names to plants. In his only surviving work,
“Naturalis Historia” that contains 160
volumes, he described plants and then
provided them with Latin names.
• Caesalpino is considered as the "the first
taxonomist". He wrote “De Plantis,” a book
containing 1 500 species of plants that were
classified based on the growth habit, fruit, and
seed form.
• The Bauhin Brothers- wrote “Pinax Theatri
Botanici” in 1623. Their work tried to fix this
issue by recognizing the concept of genera
and species as major taxonomic levels.
• John Ray -wrote several important books
about taxonomy. He published a book,
“Methodus Plantarum Nova”, where he
tried to identify a total of 18 000 plant species
based on a relatively narrow species concept.
• Joseph Pitton de Tournefort-constructed a
botanical classification that was dominantly
followed in plant taxonomy until the time of
Carl Linnaeus. He published “Institutiones
Rei Herbariae”, which contains around 9 000
species from a total of 698 genera. He tried to
emphasize the classification of plants based
on genera.
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• Carolus Linnaeus started the modern
botanical and zoological taxonomy and is
considered the “Father of Taxonomy”. Also,
Linnaeus published “Systema Naturae” in 1758
that contains information for zoological
nomenclature.
The Importance of the Linnaean System
Classifying organisms into hierarchical
ranks and giving them binomial names have
several benefits. Some of these include
uniqueness, uniformity, and organization.
A. Uniqueness of the Name- all binomial names
are unique. This means that a scientific name can
refer to one species of organisms and that species
only. This can prevent confusion when referring to
different species of organisms.
B. Uniformity-The use of a binomial name is
universal. This means that the binomial name is
used by the scientific community all around the
world. This can prevent confusion because
species names tend to have local variations
depending on the area.
C. Organization-The use of ranks also provides
organization regarding the relationship between
organisms. Looking at the respective hierarchical
ranks can provide an indication of how closely-
related or distantly-related organisms are from
each other.
Species diversity- refers to the degree of
variation among species in a given ecosystem. For
example, a drop of pond water can be considered
rich in species diversity because it tends to harbor
a high diversity of protozoans, bacteria,
phytoplankton, and zooplankton species.
Measurement of Species Diversity
A. Species Richness- refers to the number of
unique species present in a specific area. This
measurement answers the question of how many
distinct species are present within a specified
area.
B. Species abundance- refers to the total number
of individuals that belong to one distinct species.
C. Species evenness- measures the diversity of
species while considering the abundance of each
species within the ecosystem. This is a measure
of how close the abundances of species are in a
given environment.
D. Species dominance- refers to the relative
importance of a species related to the degree of
influence it has on ecosystem components.
Cladistics- is a branch of taxonomy that deals
with the categorization or classification of species
based on their shared traits.
Cladograms -are diagrams that propose a
hypothesis for the relatedness between species
based on their shared characteristics.
Cladogram Character States
To fully understand a cladogram, one must know
specific terminologies to describe characteristics
based on their states (“character states”). The
following are cladistic terms that are used to
describe different character states in the
cladogram:
● Plesiomorphy is an event where ancestral
traits were retained in one or more taxa throughout
evolution. In the cladogram, it is possible for two
or more taxa to share plesiomorphic characters
even if they cluster into different groups.
● Apomorphy is an event where derived
characters were used to define specific clades in
the cladogram. Most of the time, this allows the
separation of one group to another due to the
presence or absence of derived traits. Apomorphic
characters can be classified as autapomorphic or
synapomorphic:
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Autapomorphies -happen when the derived trait
is exhibited by a single species or group.
Synapomorphies- happen when all species in
the entire clade possess the derived trait.
● Homoplasy refers to an event where a
character is shared by at least two organisms but
tends to be absent in common ancestors.
Willi Hennig was a German entomologist who laid
the foundation for the development of
“phylogenetic systematics”. During his time,
Hennig’s work on analyzing relatedness of
organisms based on their shared similarities was
heavily criticized by other taxonomic schools. But
eventually, Henng’s cladistics approach was
accepted by the scientific community and served
as the foundation for the works of modern-day
systematists.
References:
Berg, Linda R. Introductory Botany: Plants,
People, and the Environment. Belmont, CA:
Thomson Brooks/Cole, 2008.
Hickman, Cleveland P. Animal Diversity. New
York, NY: McGraw-Hill Education, 2015.
Miller, Stephen A., and John P. Harley. Zoology.
New York, NY: McGraw-Hill, 2010.
Russell, Peter J. Biology: The Dynamic Science.
Student Ed. Belmont, CA: Thomson/Brooks/Cole,
2008.
Starr, Cecie, Ralph Taggart, Christine A. Evers,
and Lisa Starr. Biology: the Unity and Diversity of
Life. Boston, MA: Cengage, 2019.
Mader, S.S. 2014. Concepts of Biology. New York:
McGraw-Hill Education. Reece, J.B., and
Campbell, N.A. 2011.
Campbell Biology. Boston: Benjamin
Cummings/Pearson.2014