BIO 101

Learning Module
in
Fundamentals of
Biology

Prepared by:
Ms. Evangeline Joyce D. Jungay
Introduction
This module is intended for second year undergraduate psychology
students of Batangas State University enrolled in the first semester,
AY 2020-2021. It covers and presents the fundamental concepts,
principles, the systems and processes of biology, with a
comprehensive focus on human biology. The course identifies and
elaborates basic themes in the study of biology, reviews important
concepts including the biochemical and structural basis of cell
function with a focus on the relation between structure and function
of cells as well as higher order assembly. Students may own their
learning by studying this material in their own convenient time
outside of class schedule as long as they comply with the completion
of all the learning tasks to be completed during the term.

This module is composed of 6 topics, and each topic is divided into 4

sections:

● Objectives
● Lesson Proper
● Learning Tasks
● References
Intended Learning Outcomes
Upon completion of the course, students should be able to:

1. define and characterize biology as a “unified science of life”;

2. explain the fundamental concepts, principles and processes of
biology as they relate to the real world situation;
3. apply the principles of scientific method in solving real life
problems;
4. distinguish the complexity of living organisms through a
thorough understanding of systems and processes, specifically
on the workings of the human body;
5. discover, analyze, interpret and record important points in the
fundamentals of biology perspective.
 Topic 1- Introduction to Biology

Learning Objectives:
1. Define Biology.
2. Characterize biology as a “unified science of life”.
3. Identify and explain the characteristics of life.
4. Assess the importance of studying biology.

What is Biology?

Biology is the study of life and living organisms. The word biology is derived
from the Greek words “bios”, which means life, and “logos”, which means
study. It is a study of the organism’s physical components and structure,
and delves into their chemical processes and molecular interactions. It is a
natural science that studies the physiological mechanisms, development
and evolution of all life forms.

Biology: The study of life

An animal or plant, or any living thing is called an organism.

Biology as a “unified science of life”

Biology is a vast subject that takes up a wide array of disciplines and

specializations. However, despite its many branches and broad scope,
unifying concepts serve as strong guiding principles and influences over all
recent study and research:

● the basic unit of life is cell

-All organisms are made up of cells and came from pre-existing cells.
● the basic unit of heredity are genes, composed of DNA or RNA
-All living organisms have genetic information that codes for a specific
structure or function of cells.
● a stable internal environment is found in all organisms
- All organisms must maintain a state of balance or homeostasis
● evolution is responsible for the unity and diversity among living
organisms
-It is the change over time that helps organisms adapt to their
environment and the driving force for biological diversity.
● all organisms survive by energy absorption and conversion
-Energy is required for all living organisms to survive.

The Characteristics of Life

In studying biology, there is always a difference between living organisms

and non-living things. Defining life is not an easy matter, and scientists do
not always agree with each other. Below is the list of known and accepted
characteristics of life:

1. Organisms require energy and nutrients

All living things require energy and nutrients. Both are essential to
maintain life’s organization and functioning.
Energy is the capacity to do work. A nutrient is a substance that an
organism needs for growth and survival but cannot make for itself.
However, what type of energy and nutrients are acquired varies
considerably depending on the type of organism. The differences
 allow us to classify all living things into two categories: producers
and consumers.
● Producers make their own food using energy and simple raw
materials they get directly from their environment.
● Plants are producers that use the energy of sunlight to make sugars
from water and carbon dioxide in a process called photosynthesis.
● Consumers cannot make their own food. They get their energy and
nutrients by feeding on other organisms. Animals are consumers.
● Decomposers are consumers that feed on the wastes and or
remains of other organisms.
● The leftover of consumer’s meals ends up in the environment, where
they serve as nutrients for producers. Said another way, nutrients
cycle between producers and consumers.
● Unlike nutrients, energy is not cycled. It flows in one direction: from
the environment, through organisms, and back to the environment. It
is a one-way flow because with each transfer, some energy escapes
as heat. Cells do not use heat to do work. Thus, all the energy that
enters the world of life eventually leaves it, permanently.

2. Organisms Sense and Respond to Change

Every living thing has the ability to respond and sense to conditions
both inside and outside of itself.

For example, after you eat, the sugars from your meal enter your
bloodstream. The added sugars set in motion a series of events that
cause cells throughout the body to take up sugar faster, so the sugar
level in your body quickly falls. This response keeps your blood sugar
level within a certain range, which in turn helps keep your cells alive
and your body functioning. Unless that internal environment (fluid in
your blood) is kept within certain ranges of composition, temperature,
and other conditions, your body cells will die.
Homeostasis is the name for this process, which is a state of balance.

3. Organisms use DNA

• Information encoded in the organism’s DNA (deoxyribonucleic acid)

guides the ongoing metabolic activities that sustain the individual
through its lifetime. Such activities include:
⮚ Growth – increase in cell number, size, and volume
 ⮚ Development- the process by which the first cell of a new individual
becomes a multicelled adult
⮚ Reproduction- processes by which parents produce offspring.

DNA is the basis of similarities in form and function among

organisms.

The Scientific Method

Critical thinking is the deliberate process of judging the quality of
information before accepting it.
Scientific method is a systematic study used in the sciences to make
observations, hypotheses, predictions, testing, and draw results and
conclusions. From the results and conclusions, another hypothesis can be
made. Hypothesis is a tentative answer to a query which can lead to
predictions that can be tested by observation or experimentation.

Key Terms
hypothesis
inductive reasoning
deductive reasoning
variables
independent/dependent variable

Learning Tasks

1. What is Biology?
2. Discuss briefly the meaning of biology “as a unified science of life”
4. Explain the importance of studying biology.
 Topic II – The Cell
Chemistry of Life

Learning Objectives:
1. Define cell and its components
2. Describe the function of the components of the eukaryotic cells
3. Identify the organic molecules of life
4. Explain the energy flow, metabolism and the movement of fluids

The Cell

A cell is the smallest unit of life. All biological systems are based on the
same organic molecules. Simple organic building blocks bonded in different
numbers and arrangements form different versions of the molecules of life.

Cells maintain reserves of small organic molecules that they can

assemble into complex carbohydrates, lipids, proteins, and nucleic acids.
When used as subunits of larger molecules, the small organic molecules
(simple sugars, fatty acids, amino acids, and nucleotides) are called
monomers. Molecules that consist of multiple monomers are called
polymers.

Cells build polymers from monomers, and break down polymers to

release monomers. Metabolism refers to activities by which cells acquire
and use energy as they make and break apart organic compounds. These
activities help cells stay alive, grow, and reproduce.

All organisms consist of the same kinds of molecules, but small

differences in the way those molecules are put together can have big
effects in a living organism. With this concept, we introduce you to the
chemistry of life.
 The human cell

Cell Structure and Function

A cell is the smallest unit that shows the properties of life. Cells vary
dramatically in shape and in function. However, all cells share certain
organizational and functional features. Every cell has a plasma
membrane, an outer membrane that separates the cell’s contents from its
environment. A plasma membrane is selectively permeable, which means it
allows only certain materials to cross. Thus, it controls exchanges between
the cell and its environments. All cell membranes, including the plasma
membrane, consist mainly of lipids.

The plasma membrane encloses a fluid or jellylike mixture of waters,

sugars, ions, and proteins called cytoplasm. Some or all of a cell’s
metabolism occurs in the cytoplasm, and the cell’s internal components,
including organelles, are suspended in it. Organelles are structures that
carry out special metabolic functions inside a cell.
 All cells start out life with DNA. We categorize cells based on whether
their DNA is housed in a nucleus or not. Only eukaryotic cells have a
nucleus (plural, nuclei), an organelle with a double membrane that
contains the cell’s DNA. In most bacteria and archeans, the DNA is
suspended directly in the cytoplasm.

Eukaryotic Cells

All protists, fungi, plants, and animals are eukaryotes. By definition, a

eukaryotic cell starts out life with a nucleus (eu- means true; karyon means
nut, or kernel).

The main components of eukaryotic cells

All eukaryotic cells start life with a nucleus and other membrane-
enclosed organelles.

Eukaryotic Cells

• Domain Eukarya
• Protists
• Fungi
• Plants
• Animals
• Cells contain:
• Membrane-bound nucleus
• Specialized organelles
• Plasma membrane
The functions of plasma membrane include:
• selectively permeable and surrounds the cellular contents.
• regulates the passage of materials into and out of the cell.
• participates in intercellular communications.

The cytoplasm (cytosol) is the gelatinous material inside the cell

membrane but outside the nucleus.
• The cytoplasm contains organelles which are sub-cellular structures
that perform discrete functions. True organelles are bounded by a
phospholipid membrane.
Organelles of a Typical Cell

Ribosome - production of proteins – located attached to ER or free-floating

- responsible for protein synthesis
Endoplasmic
Reticulum (ER) - Passageway for materials

*Rough - produces proteins & processes molecules for secretion

*Smooth - produces lipids & detoxifies drugs & stores Ca++

Golgi Apparatus - packages material for export & processes

macromolecules

Lysosome - contains digestive enzymes. Each contains one specific

enzyme.

Mitochondria - Aerobic cellular respiration:

C6H12O6 + 6O2 6CO2 + 6H2O +ATP
• The mitochondrion (plural, mitochondria) is a type of organelle that
specializes in making ATP.
• Aerobic respiration, an oxygen-requiring series of reactions that
proceeds inside mitochondria, can extract more energy from organic
compounds than any othe metabolic pathway.
• With each breath, you are taking in oxygen mainly for mitochondria in
your trillions of aerobically respiring cells.

Cilia, flagella, microvilli - surface projections – increase surface area &

produce movement

Nucleus - is a double-membrane organelle containing the nucleic acids

(DNA) and at least one nucleolus (contains ribosomal RNA).
- This organelle stores the genetic information and contains the
blueprints for almost all protein syntheses.
DNA - RNA - protein..

Lysosomes, Peroxisomes, Vacuoles are Vesicles

Vesicles – small, membrane-enclosed, saclike organelle: store transport,
or degrade their contents.
Vacuole – a fluid-filled organelle that isolates or disposes of waste, or toxic
materials.
Lysosome – take part in intracellular digestion
- contain powerful enzymes that can break down
carbohydrates, lipids, proteins, and nucleic acids.
- Vesicles inside white blood cells deliver ingested
bacteria, cell parts, and other
debris to lysosomes for destruction.
Peroxisome- is an enzyme- filled vesicle that breaks down amino acids,
fatty acids, and toxic substances.

Organelles without membranes

• Ribosomes – assembling polypeptide chains; responsible for protein

synthesis
• Centriole – anchor for cytoskeleton

Other Component: The Cytoskeleton

-cytoskeleton contributes to cell shape, internal organization,
movement
-elements of the cytoskeleton reinforce, organize, and move cell
structures, and often the whole cell.

Organic molecules (Carbohydrates)

The molecules of life are organic, which means they consist mainly of
carbon and hydrogen atoms.
❑ Carbohydrates- consist of carbon, hydrogen, and oxygen.
Carbohydrates are the most plentiful biological molecules.
❑ Three main types are monosaccharides, oligosaccharides, and
polysaccharides.
- Cells use some carbohydrates as:
a. structural materials
b. for fuel
c. to store or transport energy
Lipids

❑ Lipids are hydrophobic organic compounds

❑ Common lipids include triglycerides, phospholipids, waxes, and
steroids.
❑ Lipids are fatty, oily, or waxy organic compounds.
❑ Fatty acids, the main component of soap, has a hydrophobic tail
and a hydrophilic head.
❑ Fatty acids can be saturated or unsaturated.
saturated- have only single bonds in their tails.
unsaturated – tails have one or more double bonds.

Proteins

❑ Proteins are the most diverse biological molecule. All cellular

processes involve them.
❑ Cells build thousands of different types of proteins by stringing
together amino acids in different orders.
❑ Proteins are chains of amino acids. The order of amino acids in a
polypeptide chain dictates the type of protein.
❑ Polypeptide chains twist and fold into coils, sheets, and loops,
which fold and pack further into functional domains.
❑ A protein’s shape is the source of its function, therefore, changes
in a protein’s structure may also alter its function.

Nucleic acids

❑ Nucleotides are subunits of DNA and RNA. Some have roles in

metabolism.
 ❑ Nucleotides are small organic molecules that function as energy
carriers, enzyme helpers, and chemical messengers.
❑ Nucleotides are monomers of DNA and RNA, which are nucleic
acids.
❑ DNA’s nucleotide sequence encodes heritable information.

The Working Cell and Transport Across Membranes

We define energy as the capacity to do work. Work occurs as a result

of an energy transfer. For example, making ATP is work, so it requires
energy. Most cellular work occur by the transfer of chemical energy from
one molecule to another. For example, cells make glucose by transferring
chemical energy from ATP to other molecules.

Every time energy is transferred, a bit of it disperses. The energy lost

from the transfer is usually in the form of heat.

An organized body is hardly dispersed. Energy becomes

concentrated in each new organism as the molecules of life organize into
cells. Even so, living things constantly use energy to grow, to move, to
acquire nutrients, to reproduce, and so on. Inevitable losses occur during
the energy transfers that maintain life. Unless those losses are replenished
with energy from another source, the complex organization of life will end.

Energy flows from the environment into living organisms, and then
back to the environment (from the sun, through producers- the plants, then
consumers). Energy’s spontaneous dispersal is resisted by chemical
bonds. The energy in chemical bonds is a type of potential energy,
because it can be stored. Think of all the bonds in the countless molecules
that make up your heart, skin, liver, fluids, and other body parts. Those
bonds hold the molecules together.

Reactants and Products

Cells store energy in chemical bonds, and access the energy stored
in chemical bonds by breaking them. Both processes change molecule.
Any process by which such chemical change occurs is called a reaction.
 During a reaction, one or more reactants (molecules that enter a
reaction) become one or more products (molecules that remain at the
reaction’s end).

In most reactions, the free energy of reactants differs from the free
energy of products. Reactions in which reactants have less free energy
than products will not proceed without a net energy input. Such reactions
are endergonic, which means “energy in”. In other reactions, reactants
have greater free energy than products. Such reactions are exergonic,
which means “energy out”, because they end with a net release of energy.

ATP – The Cell’s Energy Currency

Cells pair reactions that require energy with reactions that release
energy. ATP is often part of that process. ATP, or adenosine triphosphate,
functions as an energy carrier by accepting energy and delivering energy.
Energy from such transfers drives cellular work.

Cells constantly use up ATP to drive endergonic reactions, so they

constantly replenish it. When ATP loses a phosphate, ADP (adenosine
diphosphate) forms. ATP forms again when ADP binds phosphate in an
endergonic reaction. The cycle of using and replenishing ATP is called the
ATP/ADP cycle.

Enzymes

Centuries might pass before sugar would break down to carbon

dioxide and water on its own, yet the same conversion takes just seconds
inside your cells. Enzymes make specific reactions occur much faster than
they would on their own. Enzymes enhance the rate of metabolic reactions
without being changed by them, a process called catalysis. Each type of
enzyme works best within a characteristic range of temperature, salt
concentration, and pH.

Most enzymes are proteins, but some are RNAs. Each kind
recognizes specific reactants, or substrates, and alters them in a specific
way. For instance, the enzyme hexokinase adds a phosphate group to the
hydroxyl group on the sixth carbon of glucose. Such specificity occurs
because an enzyme’s polypeptide chains fold up into one or more active
sites, which are pockets where substrates bind and where reactions
proceed. An active site is complementary in size, shape, polarity, and
charge to the enzyme’s substrate. This fit is the reason why each enzyme
acts in a specific way on specific substrates.

When we talk about activation energy, we are really talking about the
energy required to break the bonds of the reactants. Depending on the
reaction, that energy may force substrates close together, redistribute their
charge, or cause some other change. The change brings on the transition
state, when substrate bonds reach their breaking point and the reaction will
run spontaneously to product. Enzymes can help bring on the transition
state by lowering activation energy. They do this by following four
mechanisms, which work alone or in combination:

1. Helping substrates get together

Binding at an active site brings two or more substrates close together.
The closer the substrates are to one another, the more like they are
to react.
2. Orienting substrates in positions that favor reaction
On their own, substrates collide from random directions. By contrast,
binding at an active site positions substrates so they align
appropriately for a reaction.
3. Inducing a fit between enzyme and substrate
By the induced-fit model, an enzyme’s active site is not quite
complementary to its substrate. Interacting with a substrate molecule
causes the enzyme to change shape so that the fit between them
improves. The improved fit may result in a stronger bond between
enzyme and substrate, or it may better bring on the substrate’s
transition state.
4. Shutting out water molecules
Metabolism occurs in water-based fluids, but water molecules can
interfere with certain reactions. The active sites of some enzymes
repel water, and keep it away from the reactions.

Help From Cofactors

Cofactors are atoms or molecules (other than proteins) that

associate with enzymes and are necessary for their function. Some are
metal ions. Organic molecules that are cofactors are called coenzymes.
Vitamin C is a coenzyme, and many B vitamins are remodeled into
coenzymes.
 Coenzymes in some reactions are tightly bound to an enzyme. In
others, they participate as separate molecules. Unlike enzymes, many
coenzymes are modified by taking part in a reaction. They typically become
regenerated in other reactions.

We can use an enzyme called catalase as an example of how

cofactors work. Like hemoglobin, catalase has four hemes. The iron atom
at the center of each heme is a cofactor. Iron is a metal, and metal atoms
affect nearby electrons. Catalase works by holding a substrate molecule
close to one of its iron atoms. The iron pulls on the substrate’s electrons,
which brings on the transition state.

Transport Across Membranes

Cells conserve energy and resources by making only what they need-
no more, no less – at any given moment. Several mechanisms help a cell
maintain, raise, or lower its production of thousands of different
substances.

Other mechanisms more actively regulate enzymes. Certain

molecules in a cell govern how fast enzyme molecules are made, or
influence the activity of enzymes that have already been built. For example,
the end product of a series of enzymatic reactions may inhibit the activity of
one or the enzymes in the series, an effect called feedback inhibition.

Some regulatory molecules or ions activate or inhibit an enzyme by

binding directly to its active site. Others bind to allosteric sites, which are
regions of an enzyme (other than the active site) where regulatory
molecules bind. Allo- means other, and steric means structure. Binding of
an allosteric regulator alters the shape of the enzyme in a way that
enhances or inhibits its function.

Most other molecules and ions in particular, cross only with the help
of membrane transport proteins. In passive transport, the solute simply
binds to the passive transport protein, and the protein releases it to the
other side of the membrane. In active transport, a transport protein uses
energy to pump a solute against it gradient across a cell membrane. After a
solute binds to an active transporter, an energy input (often in the form of a
phosphate-group transfer from ATP) changes the shape of the protein. The
change causes the transporter to release the solute to the other side of the
membrane.

A calcium pump is an example of an active transporter. This protein

moves calcium ions across cell membranes. Cotransporters are active
transport proteins that move two substances at the same time, in the same
or opposite directions across a membrane. Nearly all of the cells in your
body have cotransporters called sodium-potassium pumps. Sodium ions in
the cytoplasm diffuse into the pump’s open channel and bind to its interior.
A phosphate-group transfer from ATP causes the pump to change shape.
Its channel opens to extracellular fluid, where it releases the sodium. Then,
potassium ions from extracellular fluid diffuse into the channel and bind to
its interior. The transporter releases the phosphate group and reverts to its
original shape. The channel opens to the cytoplasm, where it releases the
sodium.

Bulk substances and large particles move across plasma membranes

by endocytosis and exocytosis. With exocytosis, a cytoplasmic vesicle
fuses with the plasma membrane, and its contents are released to the
outside of the cell. The vesicle’s membrane lipids and proteins become part
of the plasma membrane. Endocytosis takes up substances near the cell’s
surface. With phagocytosis and other processes of endocytosis, a patch
of plasma membrane balloons into the cell, and forms a vesicle that sinks
into the cytoplasm, which delivers its contents to an organelle or stores
them in cytoplasm.

Learning Task

1. Define cells and organic compounds such as carbohydrates

lipids, proteins and nucleic acids
2. Why is protein structure important?
3. Explain briefly the chemistry of life
4. Water molecules tend to diffuse in response to their own
concentration gradient. Explain how water can be more or less
concentrated.
 Topic III – Cellular Energy Transformations

Objectives:
1. Discuss the importance of photosynthesis in plants
2. Describe the processes important in living organisms.
3. Discuss the transformation and production of energy during
photosynthesis and respiration.

Green Energy

Plants have stored energy in chemical bonds. Autotrophs harvest

energy directly from the environment, and obtain carbon from inorganic
molecules (auto – means self; troph refers to nourishment). Plants and
most other autotrophs make their own food by photosynthesis, a process
in which they use the energy of sunlight to assemble carbohydrates from
carbon dioxide and water. Photosynthesis feeds most other life on Earth.
Animals and other heterotrophs get energy and carbon by breaking down
organic molecules assembled by other organism (hetero- means other).

A lot of energy is locked up in the chemical bonds of molecules made

by plants. That energy can fuel heterotrophs, as when animal cell powers
ATP synthesis by breaking the bonds of sugars. Oxygen is used to break
bonds and, in the process, produce carbon dioxide.

Plants convert light energy to chemical energy to use in driving

cellular work. The first step is capturing light. In order to understand how
that happens, you have to understand a little about the nature of light.

Visible light is the energy that drives photosynthesis. Light makes up

a small portion of the electromagnetic spectrum, which is a vast,
continuous range of electromagnetic radiations propagated through space
and matter. All radiations in the electromagnetic spectrum behave as
though they travel in waves. A wavelength is the distance from one wave
peak to the next. At one end of the spectrum are gamma rays with
extremely short wavelengths, measured in nanometers. At the other end of
the spectrum are radio waves with wavelengths so long that they are
measured in full meters.
 The portion of the electromagnetic spectrum from 380 and 760
nanometers is called the visible spectrum because humans can see it. The
visible spectrum includes all the colors of the rainbow. Ultraviolet radiation
(UV), which is invisible to the human eye, has a shorter range of
wavelengths than visible light, and infrared (IR) radiation, also invisible, has
a longer range.

Light is composed of small particles, or packets, of energy called

photons. The amount of energy in a photon depends on the wavelength of
light. The shorter the wavelength is, the more energy there is per photon;
the longer the wavelength, the less energy per photon. Thus, the energy of
a photon is inversely proportional to its wavelength.

Photosynthesis depends on visible light rather than some other

wavelength of radiation. The reason may be that most of the radiation
reaching our planet from the sun is within this portion of the
electromagnetic spectrum. Only radiation in the visible-light portion of the
spectrum excites certain types of biological molecules, causing their
reaction to jump into higher energy levels. Wavelengths of radiation that
are longer than visible light (microwaves, television waves, and radio
waves) do not possess enough energy to excite biological molecules.
Wavelengths shorter than visible light (ultraviolet radiation, X-rays, gamma
rays) possess so much energy that they disrupt biological molecules by
breaking chemical bonds.

In plants and algae, photosynthesis takes place in chloroplasts

If you examine a section of leaf tissue in a microscope, you see that

the green pigment, chlorophyll, is not uniformly distributed in the cell but is
confined to organelles called chloroplasts. In plants, chlorophyll lies
mainly inside the leaf in the cells of mesophyll, a layer with many air spaces
and a high concentration of water vapor. The interior of the leaf exchanges
gases with the outside through microscopic pores called stomata (sing.,
stoma). Each mesophyll cell has 20 to 100 chloroplasts.
The chloroplast is enclosed by outer and inner membranes. The inner
membrane encloses a fluid-filled region, the stroma, which contains most
of the enzymes required to produce carbohydrate molecules. Suspended in
the stroma is a third system of membranes that forms an interconnected
set of flat, disclike sacs called thylakoids. The thylakoid membrane
encloses a fluid-filled interior space, the thylakoid lumen. In some regions
of the chloroplast, thylakoid sacs are arranged in stacks called grana (sin.,
granum). Each granum looks something like a stack of coins, with each
“coin” being a thylakoid.
Thylakoid membranes contain several kinds of pigments, which are
substances that absorb visible light. Different pigments absorb different
wavelengths. Chlorophyll, the main pigment of photosynthesis, absorbs
light primarily in the blue and red regions of the visible spectrum. Green
light is not appreciably absorbed by chlorophyll. Plants usually appear
green because some of the green light that strikes them is scattered or
reflected to your eyes.

There are several kinds of chlorophyll. The most important is

chlorophyll a, the pigment that initiates photosynthesis. Chlorophyll b is an
accessory pigment that also participates in photosynthesis. It differs slightly
from the structure of the chlorophyll a molecule. This difference shifts the
wavelengths of light absorbed and reflected by chlorophyll b, making it
appear yellow-green, whereas chlorophyll a appears bright green.

Plants and algae also have accessory photosynthetic pigments, such

as carotenoids, which are yellow and orange. Carotenoids absorb
wavelengths of light different from those absorbed by chlorophyll, thereby
expanding the spectrum of light that provides energy for photosynthesis.
The large quantity of chlorophyll in most leaves usually masks the
presence of carotenoids in spring and summer; in autumn, when the
chlorophyll breaks down, other pigments, including carotenoids, become
visible.

Chlorophyll may be energized by light directly (by energy from the

light source) or indirectly (by energy passed by the accessory pigments that
have become energized by light). When a carotenoid molecule is
energized, its energy can be transferred to chlorophyll a. Carotenoids also
protect chlorophyll and other parts of the thylakoid membrane from excess
light energy that could easily damage the photosynthetic components.
 The principal raw materials for photosynthesis are water and carbon
dioxide. The reactions of photosynthesis occur in two stages: the light-
dependent reactions (the photo part of photosynthesis) and the carbon
fixation reactions (the synthesis part of photosynthesis). Each set of the
reactions occur in the different part of the chloroplast.

The light dependent reactions capture energy

Light energy is converted to chemical energy in the light-dependent

reactions, which are associated with the thylakoids. The light-dependent
reactions begin as chlorophyll absorbs light energy, which causes one of its
electrons to move to a higher energy state. The energized electron is
transferred to an acceptor molecule and is replaced by an electron from
water. During this process, water is split and molecular oxygen (O 2) is
released. Some of the energy of the energized electrons is used to make
adenosine triphosphate (ATP), a temporary energy storage molecule. In
addition, nicotinamide adenine dinucleotide phosphate (NADP +) becomes
reduced , forming NADPH. The products of the light-dependent reactions,
ATP and NADPH, are both needed in the energy-requiring carbon fixation
reactions.

The carbon fixation reactions produce carbohydrates

The ATP and NADPH molecules produced during the light-dependent

phase are suited for transferring chemical energy but not for long-term
energy storage. For this reason, some of their energy is transferred to
chemical bonds in carbohydrates, which can be produced in large
quantities and stored for future use. Carbon fixation is a cyclic series of
reactions that fixes carbon dioxide and produces carbohydrate. These
reactions “fix” carbon atoms from CO2 to existing skeletons of organic
molecules. Because the carbon fixation reactions have no direct
requirement for light, they were previously referred to as the “dark”
reactions. However, they do not require darkness; in fact, many of the
enzymes involved in carbon fixation are more active in the light than in the
dark. Furthermore, carbon fixation reactions depend on the products of the
light-dependent reactions. Carbon fixation reactions take place in the
stroma of the chloroplast.
Most plants use the Calvin cycle to fix carbon

The reactions of the Calvin cycle, which occur in the stroma, are
divided into three phases: CO2 uptake, carbon reduction, and RuBP
regeneration. Let us begin with ribulose biphosphate (RuBP), a five-carbon
sugar that was activated by the addition of a phosphate group.
1. CO2 uptake. First, a key enzyme, rubisco, combines a molecule of CO 2
with RuBP (Rubisco is an acronym for the enzyme ribulose biphosphate
carboxylate/oxygenase). Instantly, this six-carbon molecule splits into two
three-carbon molecule called phosphoglycerate (PGA). Because the first
detectable molecules to be formed contain three carbon atoms, the Calvin
cycle is also referred to as the C3 pathway.

2. Carbon reduction. The PGA molecules are then converted to

glyceraldehyde-3-phosphate (G3P) using NADPH and ATP. For every six
turns of the Calvin cycle, 2 of the 12 G3P molecules “leave” the cycle to be
used in carbohydrate synthesis. Each three-carbon molecule of G3P is
essentially half of a six-carbon sugar molecule; G3P molecules are joined
in pairs to produce glucose or fructose.
In some plants, glucose and fructose then combine to form the
disaccharide sucrose, or common table sugar. This we harvest from
sugarcane, sugar beets, or maple sap. Plants also use glucose to produce
the polysaccharides, cellulose (a constituent of plant cell walls), and starch
(the principal storage compound in plants).

3. RuBP regeneration. Note that although 2 of the 12 G3P molecules

formed during six turns of the cycle were removed from the cycle, 10 G3Ps
remain, containing 30 carbon atoms in all. Through a series of reactions,
these 30 carbons and their associated atoms are rearranged into six
molecules of the five-carbon compound ribulose phosphate (RP). ATP from
the light-dependent reactions is expended to add a second phosphate to
ribulose phosphate. This reaction converts ribulose phosphate to ribulose
biphosphate (RuBP), which is where the cycle began.
In summary, the inputs required for the carbon fixation reactions are CO2,
NADPH, and ATP. The light-dependent reactions of photosynthesis provide
the ATP and NADPH. In the end, carbohydrate molecules are
manufactured.
Aerobic and Anaerobic Pathways

Every organism must extract energy from the organic fuel molecules
that it either manufactures (for example, when plants photosynthesize).
These fuel molecules are transported to all the cells of a multicellular
organism, where they are broken down to provide the energy for cellular
work.

Within each plant cell, glucose and other fuel molecules are broken
down during cellular respiration, a series of chemical reactions that break
apart fuel molecules and transfer the energy stored in their bonds to
adenosine triphosphate (ATP) for use in cellular work.

Cells use three different catabolic pathways to extract energy from

fuel molecules: aerobic respiration, anaerobic respiration, and fermentation
(another type of anaerobic pathway). Cells that live in environments where
oxygen is plentiful use an aerobic pathway, one that requires O2. Cells that
inhabit waterlogged soil or polluted water where oxygen is absent must use
anaerobic pathways (either anaerobic respiration or fermentation) that do
not require O2.

Photosynthetic autotrophs capture energy from the sun and store it in

the form of carbohydrates. They and most organisms use energy stored in
carbohydrates to run the diverse reactions that sustain life. However,
carbohydrates rarely participate in such reactions, so how do cells harness
their energy? In order to use the energy stored in carbohydrates, cells must
first transfer it to energy carriers such as ATP, which does participate in
many of the energy-requiring actions that a cell runs. The transfer occurs
by breaking the bonds of the carbohydrates, which releases energy that
drives ATP synthesis.

There are a few different pathways that breakdown carbohydrates,

but aerobic respiration is the one that typical eukaryotic cells use at least
most of the time. Aerobic respiration is the process by which cells use
oxygen to break down organic molecules, with the release of energy that
can be used for biological work. The chemical reactions of aerobic
respiration are grouped into four stages: (1) glycolysis (2) Acetyl coenzyme
A formation (transition reaction) (3) the citric acid cycle (Krebs cycle) (4)
electron transport.
 Aerobic respiration begins with the same reactions in the cytoplasm.
Glycolysis is the first stage of cellular respiration, in which glucose is split
into two molecules of pyruvate for a net yield of two ATP. The term
glycolysis is derived from two Greek words that, taken together, mean
“splitting sugar.” The reactions of glycolysis occur in the cytoplasm. The
reactions of glycolysis can be divided into two phases. The first phase
requires the input of energy and phosphates from two molecules of ATP.

Glycolysis begins when a molecule of glucose enters a cell through a

glucose transporter. The cell invests two ATP that begin the pathway. In
the first reaction, a phosphate group is transferred from ATP to the glucose,
thus forming glucose-6-phosphate. Hexokinase is the enzyme that
catalyzes this reaction.

Glycolysis continues as glucose-6-phosphate accepts a phosphate

group accepts a phosphate group from another ATP, then splits in two,
forming two PGAL (phosphoglyceraldehyde). A second phosphate group is
attached to each PGAL, so two PGA (phosphoglycerate) form. During the
reaction, two electrons and a hydrogen ion are transferred from each PGAL
to NAD+ (oxidized state), thereby becoming reduced to NADH (reduced
state), so two NADH form.

Next, a phosphate group is transferred from each PGA to ADP, so

two ATP form. Two more ATP form when a phosphate group is transferred
from another pair of intermediates to two ADP. This and any other reaction
that transfers a phosphate group directly from a substrate to ADP is called
a substrate-level phosphorylation.

Glycolysis ends with the formation of two three-carbon pyruvate

molecules. These products may now enter the second stage reactions of
aerobic respiration. Remember, two ATP were invested to initiate the
reactions of glycolysis. A total of four ATP form, so the net yield is two ATP
per molecule of glucose that enters glycolysis.

Pyruvate is converted to acetyl CoA

Pyruvate, the end product of glycolysis, contains most of the energy
that was present in the original glucose molecule. Pyruvate molecules
move into the mitochondrion, where all subsequent reactions of aerobic
respiration take place.
 Pyruvate molecules move into the matrix of the mitochondrion, the
pyruvate is converted in a multistep, enzyme-controlled reaction to the two-
carbon compound acetyl CoA. In the first reaction, an enzyme splits each
molecule of pyruvate into one molecule of CO 2 and a two-carbon acetyl
group. CO2 diffuses out of the cell. Then, the two-carbon fragment
remaining is oxidized; the hydrogens removed during this oxidation are
accepted by NAD+, forming NADH. Finally, the oxidized fragment, an acetyl
group, is attached to coenzyme A. The product of this reaction is acetyl-
CoA.

The citric acid cycle oxidizes acetyl CoA

The citric acid cycle is also known as the Krebs cycle after sir Hans
Krebs, a British biochemist who worked out the details of the pathway in
the 1930’s.

The citric acid cycle is the common pathway for the final oxidation
reactions of the cell’s fuel molecules with the carbons being released as
CO2. The citric acid cycle also takes place in the mitochondrion.

The first reaction of the citric acid cycle occurs when acetyl CoA
transfers its two-carbon acetyl group to the four-carbon compound
oxaloacetate, forming citrate, a six-carbon compound. In later reactions,
two CO2 form and depart the cell. Two NAD+ are reduced when they accept
hydrogen ions and electrons, so two NADH form. ATP forms by substrate-
level phosphorylation, and FAD and another NAD + are reduced. The final
steps of the pathway regenerate oxaloacetate.

Remember, glycolysis converted one glucose molecule to two

pyruvate, and these were converted to two acetyl-CoA when they entered
the matrix of a mitochondrion. There, the second stage reactions convert
the two molecules of acetyl CoA to six CO2. At this point in aerobic
respiration, one glucose molecule has been broken down completely: Six
carbon atoms have left the cell, in six CO2. Two ATP formed, which adds to
the small net yield of glycolysis. However, six NAD + were reduced to six
NADH, and two FAD were reduced to two FADH2.

Most of the energy made available by the oxidation steps of the citric
acid cycle is transferred as energy-rich electrons to NAD +. For each acetyl
group that enters the citric acid cycle, three molecules of NAD + are reduced
to NADH. In addition, electrons are transferred to FAD, forming one
molecule of FADH2 for each acetyl group entering the cycle.

What is so important about reduced enzymes? A molecule becomes

reduced when it receives electrons and electrons carry energy that can be
used to drive endergonic reactions.

Because two acetyl CoA molecules are produced from each glucose
molecule, the citric acid cycle must turn twice to process each glucose. At
the end of each turn of the cycle, a four-carbon oxaloacetate is all that is
left, and the cycle is ready for another turn.

Only one molecule of ATP is produced directly with each turn of the
citric acid cycle. Thus at this point in aerobic respiration, the energy of one
glucose molecule has resulted in the formation of only four ATPs (two
ATP’s from glycolysis and two ATPs from two turns of the citric acid cycle).

Electron Transfer Phosphorylation

The third and last stage of aerobic respiration, electron transfer

phosphorylation, also occurs in the mitochondria. Remember that electron
transfer phosphorylation is a process in which the flow of electrons through
electron transfer chains ultimately results in the attachment of phosphate to
ADP (adenosine diphosphate).

The third stage reactions take place at the inner mitochondrial

membrane. They begin with the coenzymes NADH and FADH 2, which
became reduced in the in the first two stages of aerobic respiration. These
coenzymes donate their cargo of electrons and hydrogen ions to electron
transfer chains embedded in the inner mitochondrial membrane. As the
electrons pass through the chains, they give up energy little by little. Some
molecules of the transfer chains harness that energy to actively transport
hydrogen ions across the inner membrane, from the matrix to the
intermembrane space. The ions that accumulate in the intermembrane
space set up a hydrogen ion gradient across the inner mitochondrial
membrane.

This gradient attracts hydrogen ions back toward the matrix.

However, ions cannot diffuse through a lipid bilayer on their own. H + can
only cross the inner mitochondrial membrane by flowing through the interior
of ATP synthases. The flow causes these membrane transport proteins to
attach phosphate groups to ADP, so ATP forms. The coenzymes that were
reduced in the first two stages can drive the synthesis of about thirty-two
ATP in the third stage.

Oxygen accepts electrons at the end of the mitochondrial electron

transfer chains. Aerobic respiration, which literally means “taking a breath
of air,” refers to oxygen as the final electron acceptor in this pathway. When
oxygen accepts electrons, it combines with H+ to form water, which is one
product of the third stage. A typical net yield of aerobic respiration is 36
ATP per glucose.

Anaerobic Pathways

Prokaryotes and some other organisms that inhabit waterlogged soil

or stagnant ponds where oxygen is absent must engage in anaerobic
respiration. In anaerobic respiration, energy is released from glucose and
other fuel molecules without O2; that is, oxygen is not the final electron
acceptor in the electron transport chain. Instead, an inorganic compound,
such as nitrate, (NO3-) or sulfate ( SO4 2-), serves as the final acceptor of
electrons.

Fermentation, another anaerobic pathway, also degrades glucose

and other organic molecules without oxygen. Like aerobic respiration,
fermentation depends on the reactions of glycolysis. The final acceptor of
hydrogen in fermentation is an organic molecule. Two common types of
fermentation are alcohol fermentation and lactate fermentation.

Yeasts (unicellular fungi) and certain plant cells carry out a type of
fermentation known as alcohol fermentation. First, they degrade glucose to
pyruvate through the process of glycolysis. When deprived of O 2, these
cells split CO2 off from pyruvate, eventually forming ethyl alcohol. Alcohol
fermentation is the basis for the production of beer, wine, and other
alcoholic beverages using yeast, which is also used in baking to produce
CO2 that causes the dough to rise. The root cells of rice plants grown in
flooded conditions also carry out extensive alcohol fermentation.

Certain fungi and prokaryotes carry on lactate fermentation. In this

pathway, pyruvate produced during glycolysis is converted to lactate.
Lactate fermentation occurs when bacteria cause milk to sour or ferment
cabbage to form sauerkraut.

Alcohol, the end product of fermentation, contains a lot of energy and

can even be burned as automobile fuel. Lactate, a three-carbon compound,
contains even more energy than the two-carbon alcohol. Fermentation
produces a net profit of only 2 ATPs from one glucose molecule.

Learning Task:
1. What are the products of Glycolysis?
2. What are the products of Krebs cycle?
3. What is the end product of Electron Transport System (Chain)?
 Topic IV- Cell Reproduction and Genetics

Objectives:
1. Define the cell cycle and mitosis
2. Explain how cells divide
3. Describe the stages of mitosis and meiosis
4. Define homozygous and heterozygous
5. Describe dominant and recessive alleles

The Cell Cycle

The cell cycle is the period from the beginning of one division to the
beginning of the next division. It consists of two main phases, interphase
and M phase. Timing of the cell cycle varies widely from one cell type to
another and from one species to another, but in actively growing plant and
animal cells, it is usually about 8 to 20 hours.

M phase involves two main processes, mitosis and cytokinesis.

Mitosis is the division of the nucleus, and cytokinesis is the division of the
cytoplasm to form two cells. Mitosis is the division of the cell nucleus
resulting in two daughter nuclei, each with the same number of
chromosomes as the parent nucleus. Cytokinesis is the stage of cell
division in which the cytoplasm divides to form two daughter cells. Before a
eukaryotic cell divides by cytokinesis, its nucleus must undergo mitosis, a
process that precisely distributes complete sets of chromosomes to each
daughter nucleus. As a result of mitosis, each new cell contains the
identical number and types of chromosomes present in the original parent
cell.

Interphase is the stage of the cell cycle between successive cell

divisions. A meristematic cell spends most of its life in interphase, a period
of active growth and maintenance that precedes mitosis. Interphase
(“between phases”) is so named because it occurs between the phases of
successive cell divisions. During interphase, the cell synthesizes needed
materials and grows. Chromosomes undergo duplication during interphase,
although the process is not readily visible. Then, during mitosis, they
condense into visibly separate structures and are distributed to the two
daughter nuclei.
Interphase is subdivided into three periods; G 1, S, and G2. The first
period, G1, or the first gap phase, is the time between the end of the
previous cell division and the beginning of DNA replication. The cell grows
during the G1 phase, which is typically the longest phase. Cells that are not
actually dividing usually remain in this part of the cell cycle. Toward the end
of G1, the cell synthesizes certain enzymes used in DNA replication. These
activities make it possible for the cell to enter the S phase.

The second period of interphase, called the S phase or synthesis

phase, involves the replication of DNA. Other materials, such as proteins
that are components of chromosomes, are also synthesized at this time so
that the cell can make duplicate copies of its chromosomes.

Following the completion of the S phase, the cell enters a second

gap phase, or G2. At this time, increased protein synthesis occurs as the
cell prepares to divide. For many cells, the G 2 phase is short relative to the
G1 and s phases. The beginning of mitosis marks the completion of the G2
phase. To summarize, here is the sequence of interphase and M phase in
the eukaryotic cell cycle:

G1 phase – S phase – G2 phase (interphase) mitosis and

cytokinesis(M phase)

The completion of interphase is signaled by the beginning of mitosis,

in which visible changes associated with the division of the nucleus take
place. Most other cellular activities, such as protein synthesis, are
suspended during mitosis, which is a relatively brief period of the cell’s life.
Mitosis is a continuous process, but for descriptive purposes, it is divided
into four stages: Prophase, metaphase, anaphase, telophase.

● Duplicated chromosomes condense and become visible during

prophase
● During metaphase, duplicated chromosomes line up on the midplane
● Chromosomes move toward the poles during anaphase
● During telophase, two separate nuclei form
● Cytokinesis forms two daughter cells
Meiosis

Sexual reproduction mixes up the genes of two parents, so only

about half of each parent’s genetic information is passed to offspring. An
individual’s genes collectively contain the information necessary to make a
new individual.

The somatic (body) cells of multicelled organisms that reproduce

sexually contain pairs of chromosomes. Typically, one chromosome of
each pair is maternal and the other is paternal. The two chromosomes of
every pair carry the same set of genes. Different forms of the same gene
are called alleles.

What Meiosis Does

Sexual reproduction involves the fusion of reproductive cells from two

parents. It requires meiosis, a nuclear division mechanism that halves the
chromosome number. The process of sexual reproduction begins with
meiosis in germ cells, which are immature reproductive cells. Meiosis in
germ cells produces mature reproductive cells called gametes. A sperm is
an example of a male gamete. An egg is a female gamete.

Gametes have a single set of chromosomes, so they are haploid (n):

their chromosome number is half of the diploid (2n) number. Human body
cells are diploid, with 23 pairs of homologous chromosomes. Meiosis of a
human germ cell (2n) normally produces gametes with 23 chromosomes:
one of each pair (n). the diploid chromosome number is restored at
fertilization, when two haploid gametes (one egg and one sperm) fuse to
form a zygote, the first cell of a new individual.

The first part of meiosis is similar to mitosis. A cell duplicates its DNA
before either nuclear division process starts. As in mitosis, the microtubules
of a spindle move the duplicated chromosomes to opposite spindle poles.
However, meiosis sorts the chromosomes into new nuclei not once, but
twice, so it results in the formation of four haploid nuclei. The two
consecutive nuclear divisions are called meiosis I and meiosis II. In some
cells, no resting period occurs between these two stages. In others,
interphase with no DNA replication separates meiosis I and II.

DNA replications occurs prior to meiosis, so a cell’s chromosomes

are duplicated by the time meiosis I begins: Each chromosome consists of
two sister chromatids. The nucleus is diploid (2n): It contains two sets of
chromosomes, one from each parent.

Meiosis I

The first stage of meiosis I is prophase I. During this phase, the

chromosomes condense, and homologous chromosomes align tightly and
swap segments. The centrosome gets duplicated along with its two
centrioles. One centriole pair moves to the opposite side of the cell as the
nuclear envelope breaks up. Spindle microtubules begin to extend from the
centrosomes.

By the end of prophase I, microtubules of the spindle connect the

chromosomes to the spindle poles. Each chromosome is now attached to
one spindle pole, and its homologous partner is attached to the other. The
microtubules lengthen and shorten, pushing and pulling the chromosomes
as they do. At metaphase I, all of the microtubules are the same length,
and the chromosomes are aligned midway between the poles of the
spindle.

In anaphase I, the spindle microtubules separate the homologous

chromosomes and pull them toward opposite spindle poles. During
telophase I, the chromosomes reach the spindle poles. New nuclear
envelopes form around the two clusters of chromosomes as the DNA
loosens up. Each of the two haploid (n) nuclei that form contains one set of
(duplicated) chromosomes. The cytoplasm may divide at this point to form
two haploid cells. Interphase occurs in some cells at the end of meiosis I,
but the DNA is not replicated before meiosis II begins.

Meiosis II

During prophase II, the chromosomes condense as a new spindle

forms. One centriole moves to the opposite side of each nucleus, and the
nuclear envelopes break up. By the end of prophase II, microtubules
connect the chromosomes to the spindle poles. Each chromatid is now
attached to one spindle pole, and its sister is attached to the other. The
microtubules lengthen and shorten, pushing and pulling the chromosomes
as they do. At metaphase II, all of the microtubules are the same length,
and the chromosomes are aligned midway between the spindle poles.
In anaphase II, the spindle microtubules pull the sister chromatids
apart. Each chromosome now consists of one molecule of DNA. During
telophase II, the chromosomes, (now unduplicated) reach the spindle
poles. New nuclear envelopes form around the four clusters of
chromosomes as the DNA loosens up. Each of the four haploid (n) nuclei
that form contains one set of unduplicated chromosomes. The cytoplasm
may divide, so four haploid cells form.

How Meiosis Introduces Variations in Traits

The previous section mentioned briefly that duplicated chromosomes

swap segments with their homologous partners during prophase I. It also
showed how each chromosome aligns with and then separates from its
homologous partner during anaphase I. Both events introduce novel
combinations of alleles into gametes. Along with fertilization, these events
contribute to the variation in combinations of traits among the offspring of
sexually reproducing species.

Crossing over in Prophase I

Early in prophase I of meiosis, all chromosomes in a germ cell

condense. When they do, each is drawn close to its homologue. The
chromatids of one homologous chromosome become tightly aligned with
the chromatids of the other along their length. This tight, parallel orientation
favors crossing over, a process in which a chromosome and its
homologous partner exchange corresponding pieces of DNA. Homologous
chromosomes may swap any segment or segments of DNA along their
length, although crossovers tend to occur more frequently in certain
regions.

Swapping segments of DNA shuffles alleles between homologous

chromosomes. It breaks up the particular combinations of alleles that
occurred on the parental chromosomes, and makes new ones on the
chromosomes that end up in gametes. Thus, crossing over introduces
novel combinations of traits among offspring.
Segregation of Chromosomes Into Gametes

Normally, all of the new nuclei that form in meiosis I receive the same
number of chromosomes. However, whether a new nucleus ends up with
the maternal and paternal version of a chromosome is entirely random. The
chance that the maternal or the paternal version of any chromosome will
end up in a particular nucleus is 50%.

The process of chromosome segregation begins in prophase I.

imagine one of your own germ cells undergoing meiosis. Just call the
twenty-three chromosomes you inherited from your mother the maternal
ones, and the twenty-three from your father the paternal ones.

During prophase I, microtubules fasten your cell’s chromosomes to

the spindle poles. Chances are fairly slim that all of the maternal
chromosomes get attached to one pole and all of the paternal
chromosomes get attached to the other. Microtubules extending from a
spindle pole bind to the centromere of the first chromosome they contact,
regardless of whether it is maternal or paternal. Each homologous partner
gets attached to the opposite spindle pole. Thus, there is no pattern to the
attachment of the maternal or paternal chromosomes to a particular pole.

Inheritance in Modern Terms

DNA was not proven to be hereditary material until the 1950’s, but
Mendel discovered its units, which we now call genes, almost a century
before then. Today, we know that individuals of a species share certain
traits because their chromosomes carry the same genes. Offspring tend to
look like their parents because they inherited their parent’s genes.

The DNA sequence of each gene occurs at a specific location, or

locus (plural, loci), on a particular chromosome. The somatic cells of
humans and other animals are diploid, so they have pairs of genes, on
pairs of homologous chromosomes. In most cases, both genes of a pair are
expressed.

The two genes of a pair may be identical, or they may be slightly

different. Alternative forms of a gene are called alleles. An individual with
identical alleles of a gene is said to be homozygous for the allele. The
particular set of alleles that an individual carries is called genotype.

Alleles are the major source of variation in a trait. New alleles arise by
mutation. A mutation may cause a trait to change, as when a gene that
causes flowers to be purple mutates so the resulting flowers are white.
Flower color is an example of phenotype, which refers to an individual’s
observable traits. Any mutated gene is an allele, whether or not it affects
phenotype.

The offspring of a cross, or mating, between individuals that breed for

different forms of a trait are hybrids. Hybrids carry different alleles of a
gene, so they are said to be heterozygous for the alleles. An allele is
dominant when its effect masks that of a recessive allele paired with it.
Usually, italic capital letters signify dominant alleles, and lowercase italic
letters signify recessive ones. Thus, a homozygous dominant individual
carries a pair of dominant alleles. A homozygous recessive individual
carries a pair of recessive alleles. A heterozygous, or hybrid, individual
carries a pair of nonidentical alleles.

Learning Task:
1. What is the difference between mitosis and meiosis?
2. Distinguish homozygous and heterozygous.
3. Differentiate a dominant and recessive allele.
 Topic V – Animal Tissues

Learning Objectives:
1. Distinguish each type of animal tissue as to location, structure and
function
2. Identify the specialized connective tissues
3. Describe muscle contraction

In all animals, development produces a body with cells of several to

many types. Four types of tissue occur in all vertebrate bodies:

1. Epithelial tissue covers body surfaces and lines the internal cavities
such as the gut.
2. Connective tissue holds body parts together and provides structural
support.
3. Muscle tissue moves the body or its parts.
4. Nervous tissue detects stimuli and relays information.

Different types of cells characterize different tissues. For example,

contractile cells are found in muscle tissue, but not in nervous tissue or
epithelial tissue. A human heart includes all for tissue types. The wall of the
heart is made up mostly of cardiac muscle tissue. A sheath of connective
tissue encloses the heart. And the heart’s internal chambers are lined with
epithelial tissue. Nervous tissue delivers signals to and from the heart.

Epithelial Tissue

Epithelium (plural, epithelia), or epithelial tissues, is a sheetlike tissue

consisting of cells with extracellular material between them. It covers outer
body surfaces and lines internal tubes and cavities. Blood vessels do not
run through epithelium, so nutrients reach cells by diffusing from vessels in
an adjacent tissue.
 Tight junctions occur only in epithelial tissue. These junctions join the
plasma membranes of adjacent cells so securely that fluids cannot seep
between the cells. An epithelium with tight junctions can keep fluid
contained within a particular body compartment. For example, tight
junctions join the epithelial cells that line the gut. This epithelium serves as
a barrier that prevents acid secreted into the stomach from leaking out and
damaging the underlying tissue.

Epithelial tissues that are subject to mechanical stress such as those

of the skin have may adhering junctions. These junctions function a bit like
buttons that hold a shirt closed. They connect the plasma membrane of
cells at distinct points but do not for a tight seal.

Types of Epithelium

A simple epithelium is one cell thick. Cells in squamous epithelium

are flattened or scalelike. Cells of cuboidal epithelium are short cylinders
that look like cubes when viewed in cross-section. Cells in columnar
epithelium are taller than they are wide.

Three Types

Simple squamous epithelium

● Lines blood vessels, the heart, and air sacs of lungs.
● Allows substances to cross by diffusion

Simple cuboidal epithelium

● Lines kidney tubules, ducts of some glands, reproductive tract
● Functions in absorption and secretion, movement of materials

Simple columnar epithelium

● Lines some airways, parts of the gut
● Functions in absorption, secretion, and protection

Connective Tissues
 Connective tissues provides structural and functional support. There
are two kinds of soft tissues – loose and dense. Cartilage, bone tissue,
adipose tissue, and blood are specialized connective tissues.

Soft Connective Tissues

Loose and dense connective tissues have the same components but
in different proportions and arrangements. In both tissues, the most
abundant cells are fibroblasts, cells the secrete complex carbohydrates and
fibers of the structural proteins collagen and elastin.

The most common type of connective tissue in the vertebrate body is

https://meet.google.com/lookup/aairjmr44o?authuser=0&hs=179. It holds
organs and epithelia in place, and its fibroblasts and fibers are dispersed
widely through the matrix.

In dense, irregular connective tissue, the matrix is packed full of

fibroblasts and collagen fibers. It makes up the deep skin layers. It supports
intestinal muscles and also forms capsules around organs that do not
stretch, such as kidneys.

Dense, regular connective tissue has fibroblasts in orderly rows

between parallel, tightly packed bundles of fibers. This organization helps
keep the tissue from being torn apart when placed under mechanical
stress. Tendons and ligaments are mainly dense, regular connective tissue.
Tendons connect skeletal muscle to bones. Ligaments attach one bone to
another and are stretchier than tendons. Elastic fibers in the ligament
matrix facilitate movements around joints.

Specialized Connective Tissues

Cartilage has a matrix of collagen fibers and rubbery, compression-

resistant glycoproteins. Sharks have cartilage skeleton. In human embryos,
cartilage forms a model for the developing skeleton, then bone replaces
most of it. After birth, cartilage still supports the outer ears, nose, and
throat. It cushions joints and is a shock absorber between vertebrae. Blood
vessels do not extend through cartilage, as they do in other connective
tissues. As a result, nutrients and oxygen must diffuse from blood vessels
in nearby tissues. Cartilage tissues do not divide often in adults. Therefore,
injured cartilage does not repair itself. As other connective tissues do.
 Adipose tissue is the body’s main energy reservoir. Most cells can
convert excess sugars and lipids into droplets of fat. Small blood vessels
that run through the tissue carry fats to and from the cells. In addition to its
energy-storage role, adipose tissue cushions and protects body parts, and
a layer of adipose tissue under the skin functions as insulation that helps
keep the body’s internal temperature within an optimal range.

Bone tissue is a connective tissue with living cells imprisoned in their

own calcium-hardened secretions. This is the main tissue of bones, the
organs that interact with muscles to move a body. Bones also support and
protect soft internal organs. Blood cells form inside the spongy interior of
some bones.

Blood is considered a connective tissue because its cellular

components (red blood cells, white blood cells, platelets) are descended
from stem cells in bone. Red blood cells are filled with hemoglobin
transport oxygen. White blood cells defend the body against pathogens.
Platelets function in clot formation. The cellular components of blood drift
along in the plasma, a fluid consisting mostly of water, dissolved proteins,
nutrients, gases, and other substances.

Muscle Tissues

In muscle tissues, cells contract (shorten) in response to stimulation,

then they relax and passively lengthen. Coordinated contractions of layers
or rings of muscles move the body or move material through the body.
Muscle tissue occurs in most animals, but we focus here on the
arrangements of muscle found in vertebrates.

Skeletal Muscle

Skeletal muscle tissue, the functional partner of bone (or cartilage), helps
move and maintain the positions of the body and its parts. Skeletal muscle
tissue has parallel arrays of long, cylindrical muscle fibers. The fibers are
not single cells. They form during embryonic development when groups of
cells fuse together. Each fiber contains multiple nuclei between long
strands with row after row of contractile units. These rows give skeletal
muscle a striated, or striped appearance.
 Skeletal muscle tissue makes up 40 percent or so of the weight of an
average human. Reflexes activate it, but we can also make it contract when
we want to. Thus skeletal muscles are commonly called “voluntary”
muscles.

Cardiac Muscle

Cardiac muscle tissue is found only in the heart wall. Like skeletal
muscle, it appears striated. Unlike skeletal muscle tissue, it has branch-
shaped cells. Cardiac muscle cells abut at their ends, where adhering
junctions prevent them from being ripped apart during forceful contractions.
Signals to contract pass swiftly from cell to cell at gap junctions along their
length. The signals make all cells in cardiac muscle tissue contract as a
unit.

Cardiac muscle and smooth muscle are said to be “involuntary”

muscle because most people cannot make these types of muscle contract
at will.

Smooth Muscle

We find layers of smooth muscle tissue in the wall of some blood vessels
and soft internal organs, such as the stomach, uterus, and bladder. This
tissue’s unbranched cells contain a nucleus at their center and are tapered
at both ends. Contractile units are not arranged in an orderly repeating
fashion, so smooth muscle tissue does not appear striated. Smooth muscle
contracts more slowly than skeletal muscle, but its contractions can be
sustained longer. Smooth muscle contractions propel material through the
gut and adjust the diameter of some blood vessels.

Nervous Tissue

Nervous tissue consists of specialized signaling cells called neurons, and

the cells that support them. A neuron has a cell body with a nucleus and
other organelles. Projecting from the cell body are long cytoplasmic
extensions that allow the cell to receive and send electrochemical signals.

When a neuron receives sufficient stimulation, an electrical signal

travels along its plasma membrane to the ends of certain cytoplasmic
extensions. Here, the electrical signal causes release of chemical signaling
molecules. These molecules diffuse across a small gap to an adjacent
neuron, muscle fiber, or gland cell, and alter that cell’s behavior.

Your nervous system has more than 100 billion neurons. There are
three types. Sensory neurons are excited by specific stimuli, such as light
or pressure. Interneurons receive and integrate sensory information. They
store information and coordinate responses to stimuli. In vertebrates,
interneurons occur mainly in the brain and spinal cord. Motor neurons relay
commands from the brain and spinal cord to glands and muscle cells.

Neuroglial cells, also called neuroglia, keep neurons positioned

where they should be, and provide metabolic support. They constitute a
significant portion of nervous tissue. More than half of your brain volume is
neuroglia. Neuroglial cells also wrap around the signal-sending cytoplasmic
extensions of most motor neurons. They act as insulation and speed the
rate at which signals travel.

Learning Task:
1. What are the functions of epithelial tissue?
2. Differentiate connective, muscle, and nervous tissue.
3. Describe muscle contraction.
 Topic VI - Animal Biology
Protection, Support and Movement

Learning objectives:
1. Describe the human skin as an organ system
2. Describe the structure of the skin
3. Enumerate the functions of the skin
4. Identify the parts of a human skeleton
5. Explain how muscles contract
6. Describe the structure and function of the stomach

Of all vertebrate organs, the outer body covering called skin has the
largest surface area. Skin consists of two layers, a thin upper epidermis
and the dermis beneath it. The dermis connects to the hypodermis, a layer
of connective and adipose tissue.

Vertebrate skin has many functions. It contains sensory receptors

that keep the brain informed of external conditions. Skin serves as a barrier
to keep out pathogens and it helps control internal temperature. In land
vertebrates, skin also helps conserve water. In humans, reactions that take
place in the skin produce vitamin D.

Structure of the Skin

Epidermis is a stratified squamous epithelium with an abundance of

adhering junctions and no extracellular matrix. Human epidermis consists
mainly of keratinocytes, cells that make the waterproof protein keratin.

Mitotic cell divisions in deep epidermal layers continually produce

new keratinocytes that displace older cells upward toward the skin’s
surface. As cells move upward, they become flattened, lose their nucleus,
and die. Dead cells at the skin surface form an abrasion-resistant layer that
helps prevent water loss.
 Melanocytes, another type of epidermal cell, make pigments called
melanins and donate them to keratinocytes. Variations in skin color arise
from differences in the distribution and activity of melanocytes, and in the
type of melanin they produce. One melanin is brown to black. Another is
red to yellow. The effect of melanocytes can be seen with vitiligo, a skin
disorder in which destruction of these cells results in light patches of the
skin.

Dermis consists primarily of dense connective tissue with stretch-

resistant elastin fibers and supportive collagen fibers. Blood vessels, lymph
vessels, and sensory receptors weave through the dermis. Dermis is much
thicker than epidermis, and more resistant to tearing. Leather is animal
dermis that has been treated with chemicals to preserve it.

Sweat glands consist of epidermal cells that migrated into the dermis
during early development. The sweat they secrete is mostly water.
Evaporation of sweat can help cool the body surface when the temperature
is high.

Epithelial tissue embedded in the dermis also forms hair follicles. The
base of a hair follicle hold living hair cells. They divide every 24 to 72 hours,
making them among the fastest-dividing cells in the body. As the cells
divide, they push cells above them up, lengthening the hair. The part of a
hair that extends beyond the skin surface is keratin-rich remains of dead
cells. A smooth muscle attaches to each hair. Hair stands upright when this
muscle reflexively contracts in response to cold or fright.

Secretions from an oil gland next to each hair follicle keep the hair
and the skin surrounding hair soft and silky. Oil glands also consist of
epithelial tissue that migrated into the dermis during development.

Sun and the Skin

The melanin produced by the skin functions as a sunscreen, absorbing

ultraviolet UV radiation that could otherwise damage underlying skin layers.
When a patch of skin is exposed to sunlight, melanocytes in that region
make more of the brownish-black melanin, resulting in a “tan”.

A bit of UV exposure is a good thing; it stimulates production of a

molecule that the body later converts to vitamin D. We need vitamin D to
absorb calcium ions from food. However, UV exposure also causes the
breakdown of folate, one of the B vitamins. Among other problems, a
deficiency in folate during development damages the nervous system.

Variations in skin color among human populations probably evolved

as adaptations to differences in sunlight exposure. Humans arose in
equatorial Africa, where the sun’s rays are intense and daylength does not
decline dramatically in the winter. In this environment, melanin-rich skin
protected folate and still made enough vitamin D. Later, some humans
moved to more northerly regions, where sunlight is less intense, winter
days are short, and more time is spent indoors or bundled in clothing.
Under these circumstances, skin with fewer melanocytes is advantageous.
Such skin makes it easier to get enough sunlight to encourage adequate
vitamin D production even during cold, dark winters.

People with light skin often get a sunburn before they tan. Dark skin
protects people better than light skin. But in anyone, prolonged or repeated
UV exposure damages collagen and causes elastin fibers to clump. UV
harms DNA, and the damage increases the risk of skin cancer. Melanoma,
the most dangerous skin cancer, arises when melanocytes divide
uncontrollably.

Effects of Age

As people age, their epidermal cells divide less frequently. Glandular

secretions that kept the skin soft and supple dwindle. Thickness and
elasticity of the dermis decline as collage and elastin fibers become sparse.
Permanent wrinkles appear in places where facial expression once
produced temporary creases.

Excessive tanning accelerates skin aging. Smoking has a similar

effect. It lessens the flow of blood to the skin, depriving it of oxygen and
nutrients. Damaging effects of sun are localized to sun-exposed regions,
but smoking harms skin throughout the body.

Negative Feedback Control of Body Temperature

Think about when you exercise on a hot day. Muscle activity generates
heat, and the body’s internal temperature rises. Sensory receptors in the
skin detect the increase and signal the brain. The brain sends signals that
bring about the body’s response. Blood flow shifts, so more blood from the
body’s hot interior flows to the skin. The shift maximizes the amount of heat
given off to the surrounding air. At the same time, sweat glands in the skin
increase their output. Evaporation of sweat helps cool the body surface.
You breathe faster and deeper, speeding the transfer of heat from the
blood in your lungs to the air. As your activity level slows and your rate of
heat loss increases, your temperature falls.

Receptors in the skin also notify the brain when the external
environment becomes chilly. The brain then sends out signals that cause
diversion of blood flow away from the skin, lessening movement of heat to
the body surface, where it would be lost to the surrounding. With prolonged
cold, the brain commands skeletal muscles to contract ten to twenty times
a second. This shivering response dramatically increases heat production
by muscles.

SKELETON
Types of Skeleton

An animal skeleton can be internal or external. In either case, muscles

exert force against it to move body parts. Muscles bring about movement f
body parts by interacting with a skeleton. Many soft-bodied invertebrates
have a hydrostatic skeleton, an internal, fluid-filled chamber or chambers
that muscles exert force against. For example, earthworms have a coelom
divided into many fluid-filled chambers, one per segment.

An exoskeleton is a shell, cuticle, or other hard external body part

that receives the force of a muscle contraction. A clam’s muscles act on its
shell to pull the shell shut.

An endoskeleton is an internal framework of hard elements. Sea

stars have an endoskeleton made of hardened calcium-rich plates.
Vertebrates also have an endoskeleton.

Features of the Vertebrate Endoskeleton

The skeleton of sharks and other cartilaginous fishes consists of cartilage,

a rubbery connective tissue. Other vertebrate skeletons include some
cartilage but consist mainly of bone tissue.
 The term “vertebrate” refers to the vertebral column, or backbone, a
feature common to all members of this group. The backbone supports the
body, serves as an attachment point for muscles, and protects the spinal
cord that runs through a canal inside it. Bony segments called vertebrae
(singular, vertebra) make up the backbone. Intervertebral disks of cartilage
between vertebrae act as shock absorbers and flex points.

The vertebral column and bones of the head and rib cage constitute
the axial skeleton. The appendicular skeleton consists of the pectoral
(shoulder) girdle, the pelvic (hip) girdle, and limbs (or bony fins).

The Human Skeleton

The human skeleton has typical vertebrate features, as well as

modifications related to upright posture. The human skull’s flattened cranial
bones form a braincase that surrounds and protects the brain. The brain
and spinal cord connect through an opening at the base of the skull. Facial
bones include cheekbones and other bones around the eyes, the bone that
forms the bridge of the nose, and the jaw bones.

Both men and women have twelve pairs of ribs. Ribs and the
breastbone, or sternum, form a protective cage that encloses the heart and
lungs.

The vertebral column extends from the base of the skull to the pelvic
girdle. The shape of the human column the shape of the human vertebral
column is another adaptation to upright posture. Viewed from the side, our
backbone has an S shape, which keeps the head and torso centered over
the feet.

The lowest portions of the backbone are the sacrum and coccyx. The
sacrum consists of five vertebrae that have become fused as a large
triangular structure. The coccyx is four fused vertebrae derived from the
embryonic tail. At five weeks, the human embryo has a tail of 12 vertebrae.
As development proceeds, most of the tail is resorbed, leaving the shorter,
smaller coccyx.

The pectoral girdle consists of the scapula (shoulder blade) and

clavicle (collar bone). The thin clavicle transfers force from the arms to the
axial skeleton. When a person falls on an outstretched arms, excessive
force transferred to the clavicle frequently causes it to break.

The upper arm has one bone, the humerus. The forearm has two
bones, the radius and ulna. Carpals are bones of the wrist, metacarpals are
bones of the palm, and phalanges (singular, phalanx) are finger bones.

The pelvic girdle consists of two sets of fused bones, one set on each
side of the body. It protects organs inside the pelvic cavity and supports the
weight of the upper body when a person stands upright.

The largest bone of the body is the femur (thighbone). It attaches to

the bones of the lower leg (the tibia and fibula) at the knee, which is
protected by the patella (kneecap). Tarsals are ankle bones, and
metatarsals are bones of the sole of the foot. Like the bones of the fingers,
those of the toes are called phalanges.

SKELETAL-MUSCULAR SYSTEMS

Skeletal Muscle Function

Skeletal muscles allow us to dance, smile and to speak. They are

sometimes referred to as voluntary muscles because we control their action
at will. However, skeletal muscles also take part in reflex actions such as
the stretch reflex.

A sheath of dense connective tissue encloses each skeletal muscle

and extends beyond it to form a cordlike or straplike tendon. The tendon
connects a skeletal muscle to bone. Muscles and bones act like a lever
system, in which a rigid rod attaches to and moves about a fixed point.
Muscles connect to bones (rigid rods) near a joint (a fixed point). When a
muscle contracts, it transmits force to the bone it attaches and moves it.

The muscles of the upper arm: the biceps and the triceps. Two
tendons attach the upper part of the biceps to the scapula (shoulder blade).
At the opposite end of the muscle, a tendon attaches the biceps to the
radius in the forearm. When the biceps contracts (shortens), the forearm is
pulled toward the shoulder. You can feel the contraction happen if you
extend your arm outward, place your other hand over the biceps, then
slowly bend the elbow. Although the biceps shortens only a bit, it causes a
large motion of the bone to which it is connected.

Muscles can only pull; they cannot push. Often two muscles work in
opposition, with the action of one resisting or reversing action of another.
The human body has close to 700 skeletal muscles, some near the
surface, others deep inside the body wall. Collectively, skeletal muscles
account for about 40 percent of the body weight of a young man of average
fitness.
Most skeletal muscles move bones, but some have other functions.
Skeletal muscles that pull on facial skin cause changes in expression.
Others attach to and move the eyeball, or open and close eyelids. The
tongue is skeletal muscle, and sphincters of skeletal muscle provide
voluntary control of defecation and urination. Skeletal muscles function in
respiration and help keep blood circulating through the body.

Bear in mind, only skeletal muscle interacts with bone. Smooth

muscle is mainly a component of soft internal organs such as the stomach.
Cardiac muscle forms only in the heart wall.

STRUCTURE OF SKELETAL MUSCLE

A skeletal muscle’s function arises from its internal organization. Skeletal

muscle fibers run parallel with the muscle’s long axis. The multinucleated
fibers form during early development, when embryonic muscle cells fuse.
Many myofibrils – bundles of protein filaments- run the length of the fiber.
Each myofibril has light-to-dark crossbands that show up when a muscle is
stained for microscopy. The bands give the muscle fiber its striated, or
striped appearance. The bands give also define the units of muscle
contraction, or sarcomeres. The ends of a sarcomere are anchored to its
neighbors at a mesh of cytoskeletal elements called Z lines.

The sarcomere has parallel arrays of thin and thick filaments. Thin
filaments attached to Z lines extend inward, toward the sarcomere’s center.
Each thin filament consists of two chains of actin. Thicker filaments are
centered in the sarcomere. A thick filament consists of myosin, a protein
that has a clublike head. Each myosin head is positioned just a few
nanometers away from a thin filament.
 Muscle fibers, myofibrils, thin filaments, and thick filaments all have
the same orientation; they all run parallel with a muscle’s long axis. What
function does this repetitive orientation serve? It focuses the force of
contraction; all sarcomeres in all fibers of a muscle work together to pull a
bone in the same direction.

The Sliding-Filament Model

The sliding-filament model explains how interactions between thick and thin
filaments bring about muscle contraction. Neither actin nor myosin
filaments length and the myosin filaments do not change position. Instead,
myosin heads bind to actin filaments and slide them toward the center of a
sarcomere. As the actin filaments are pulled inward, the ends of the
sarcomere are drawn closer together, and the sarcomere shortens.

Part of the myosin head can bind ATP and break it into ADP and
phosphate. This reaction readies myosin for action. By analogy, binding of
ATP to a myosin head energizes the myosin like pulling back the rubber
band of a slingshot prepare it for action.

Muscle contraction occurs when nervous signals cause a rise in

calcium level. The rise in calcium allows the myosin heads to form cross-
bridges with actin filaments.

The ADP and phosphate bound to myosin earlier are released, and
each myosin head tilts like a slingshot snapping back to its unstretched
position. As a myosin head tilts, it pulls an actin filament and the attached Z
line toward the sarcomere center.

Binding of a new ATP and its breakdown to ADP and phosphate

detaches the myosin head from actin, and the head returns to its original
position. If calcium is still present, the head attaches to another binding site
on the actin, tilts in another stroke, and repeats the process. The
contraction of a sarcomere occurs when hundreds of myosin heads
perform a series of repeated strokes all along the length of the actin
filaments.
Digestion and Human Nutrition

Food supplies your body with raw materials and fuel. When the food you
eat contains more energy than you need at the time, you store the excess
as bond energy in organic compounds. The body’s largest energy store is
fat in adipose tissue. Putting on fat when food is abundant increases the
likelihood of survival if food later becomes scarce.

The Human Digestive System

Humans have a complete digestive system; a tubular gut with two

openings. If it were stretched out in a straight line, the gut would extend 6.5
to 9 meters. (21 to 30 ft). different regions specialize in digesting food,
absorbing nutrients, and concentrating and storing unabsorbed waste.
Salivary glands, the pancreas, and the liver are accessory organs that
secrete substances into the tube.

Food enters the body through the mouth, or oral cavity. The tongue,
an organ that consists of membrane-covered skeletal muscles, attaches to
the floor of the mouth. The tongue positions food for swallowing. It helps us
in speech, and many chemoreceptors at its surface contribute to our sense
of taste.

Swallowing forces food into the pharynx, or throat. The presence of

food at the back of the throat triggers a swallowing reflex. When you
swallow, the epiglottis flops down and the vocal cords constrict, so the
route between the pharynx and larynx is blocked. The reflex keeps food
from getting stuck in an airway and choking you.
 Swallowed food enters the esophagus, the muscular tube between
the pharynx and stomach. Wavelike smooth muscle contractions, called
peristalsis, move food through the esophagus to the stomach, and through
the rest of the digestive tract. The stomach is a stretchable sac that stores
food, secretes acid and digestive enzymes, and mixes them all together.

The stomach empties into the b the part of the gut where most
carbohydrates, lipids, and proteins are digested and where most of the
released nutrients and water are absorbed. Secretions from the liver and
pancreas assist the small intestine in these tasks.
The colon (large intestine) absorbs water and ions, thus compacting
the wastes. Wastes are briefly stored in a stretchable tube, the rectum,
before being expelled from the gut’s terminal opening, or anus.

Digestion in the mouth

Mechanical digestion begins when teeth rip and crush food. Human adults
have thirty-two teeth of four types. Each tooth consists mostly of bonelke
dentin. Dentin-secreting cells in a central pulp cavity are serviced by nerves
and blood vessels that extend through the tooth’s root. Enamel, the hardest
material in the body, covers the tooth’s exposed crown.

Chemical digestion begins when food mixes with saliva secreted by

salivary glands, exocrine glands that open into the mouth. Saliva contains
enzymes, bicarbonate, and mucins. One enzyme, (salivary amylase)
begins the breakdown of starch. Another enzyme, salivary lipase, starts the
chemical digestion of fats. Bicarbonate, a buffer, keeps the pH in the mouth
from becoming too acidic. Mucins are proteins that combine with water and
form mucus. Mucus makes the chewed-up bits of food stick together in
easy-to-swallow clumps.

Structure and Function of the Stomach

The stomach is a muscular, stretchable sac with a sphincter at either end.

A sphincter is a ring of muscle that controls the passage of material through
a tubular organ or a body opening.
 The stomach has three functions. First, it stores food and controls the
rate of passage to the small intestine. Second, it mechanically breaks down
food. Third, it secretes substances that aid in chemical digestion.

When the stomach is empty, its inner surface is highly folded. As it

fills with food, these folds smooth out, increasing the stomach’s capacity. In
an average adult, the stomach can expand enough to hold about 1 liter of
fluid.

A glandular epithelium, or mucosa, lines the stomach’s inner wall.

Cells of this lining secrete about 2 liters of gastric fluid each day. Gastric
fluid includes mucus, hydrochloric acid, and pepsinogen, an inactive form
of the protein-digesting enzyme pepsin.

The stomach has an internal pacemaker. Spontaneous action

potentials generated in the upper portion of the stomach cause the smooth
muscle in the stomach wall to contract rhythmically about three times a
minute. The contractions mix gastric fluid with food to form a semiliquid
mass called chyme. They also propel a bit of chyme out through the pyloric
sphincter and into the first segment of the small intestine.

Chemical digestion of proteins begins in the stomach. The acidity of

chyme denatures proteins and exposes their peptide bonds. High acidity
also converts pepsinogen into pepsin. Pepsin breaks peptide bonds,
snipping proteins up into smaller polypeptides.

The stomach steps up or slows down its acid secretion depending on

when and what you eat. Arrival of food in the stomach, especially protein,
triggers endocrine cells in the stomach lining to secrete the hormone
gastrin into the blood. Gastrin acts on acid-secreting cells of the stomach
lining, causing them to increase their output. When the stomach is empty,
gastrin secretion and acid secretion decline. This prevents excess acidity
from damaging the stomach wall.

Structure of the Small Intestine

Chyme forced out of the stomach through the pyloric sphincter enters the
duodenum, the initial portion of the small intestine. The small intestine is
“small” only in terms of its diameter- about 2.5 cm (1 inch). It is the longest
segment of the gut. Uncoiled, the small intestine would extend for about 5
to 7 meters (16 to 23 feet). In addition, the small intestine has an immense
surface area. Most digestion and absorption take place at the surface of the
small intestine.

The small intestine has a highly folded lining. Unlike the folds of the
empty stomach, those of the small intestine are permanent. The surface of
each fold has many villi (singular, villus). A villus is a hairlike multicelled
projection about 1 millimeter long. The millions of villi that project from the
intestinal lining give the lining a furry or velvety appearance. Blood vessels
and lymph vessels run through the interior of each villus.

Epithelial cells at the surface of a villus have even a tinier projections

called microvilli (singular, microvillus). The 1700 or so microvilli at the
surface of a cell make its outer edge look like a brush. Thus, these cells are
sometimes called brush border cells. Collectively, the many folds and
projections of the small intestinal lining increase its surface area by
hundreds of times.

Digestion and Absorption in the Small Intestine

The process of chemical digestion that began in the mouth and continued
in the stomach is completed in the small intestine. The small intestine
receives chyme from the stomach, enzymes and bicarbonate from the
pancreas, and bile from the gallbladder. Pancreatic enzymes work in
concert with enzymes at the surface of the brush border cells to complete
the breakdown of large organic compounds into absorbable subunits. The
bicarbonate provided by the pancreas buffers the chyme, raising the pH
enough for digestive enzymes to function.

Carbohydrate Digestion and Absorption

In the small intestine, carbohydrates are broken down into

monosaccharides, or simple sugars. This process began in the mouth,
where salivary amylase broke polysaccharides into disaccharides (two-unit
sugars). A pancreatic amylase carries out the same reaction in the small
intestine. Disaccharides are substrates for enzymes embedded in the
plasma membrane of the brush border cells. The enzymes split
disaccharides into monosaccharides. For example, sucrase breaks sucrose
into glucose and fructose subunits. Lactase splits lactose into glucose and
galactose. Monosaccharides are actively transported into a brush border
cell, then out into the interstitial fluid inside a villus. From here they enter
the blood.

Protein Digestion and Absorption

Protein digestion began n the stomach, where pepsin broke proteins into
polypeptides. It is completed in the small intestine. The pancreas secretes
proteases such as trypsin and chymotrypsin that break polypeptides into
peptide fragments. Enzymes at the surface of the brush border cell break
these fragments into amino acids.

Like monosaccharides, amino acids are actively transported into

brush border cells, then out into the interstitial fluid. From here they enter
the blood.

Fat digestion and absorption

Chemical digestion of fats begins with the action of salivary lipase, but most
fat digestion occurs in the small intestine. Here bile increases the
effectiveness of lipases secreted into the small intestine by the pancreas.
Bile contains salts, cholesterol, and lipids. It is made in the liver, then
stored and concentrated in the gallbladder. A fatty meal causes the
gallbladder to contract, forcing bile out through a short duct into the small
intestine.

Bile enhances fat digestion by aiding emulsification, the dispersion of

droplets of fat in a fluid. Water insoluble triglycerides from food tend to
clump together as fat globules. Oscillating movements of the small intestine
break big globs of fat into smaller droplets, the bile salts coat the droplets
so they remain separated. Compared to big globules, the many small
droplets present a much greater surface area to the lipases that break
triglycerides into fatty acids and monoglycerides.

Being lipid soluble, fatty acids and monoglycerides produced by fat

digestion can enter a villus by diffusing across the lipid bilayer of brush
border cells. Inside these cells, triglycerides form and become coated with
proteins. The resulting lipoproteins are moved by exocytosis into interstitial
fluid inside a villus. From the interstitial fluid, triglycerides enter lymph
vessels that eventually drain into the general circulation.
Fluid Absorption

Each day, eating and drinking puts 1 to 2 liters of fluid into the lumen of
your small intestine. Secretions from your stomach, accessory glands, and
the intestinal lining add another 6 to 7 liters. About 80 percent of the water
that enters the small intestine moves across the intestinal lining and into
the internal environment by osmosis. Transport of salts, sugars, and amino
acids across brush border cells create an osmotic gradient. Water flows
that gradient from chyme into the interstitial fluid.

The Large Intestine

Structure and Function

Not everything that enters the small intestine can be or should be

absorbed. Contractions propel indigestible material, dead bacteria and
mucosal cells, inorganic substances, and some water from the small
intestine into the colon, or large intestine. The large intestine is wider than
the small intestine, but much shorter – only about 1.5 meters (5 ft long).

As the wastes travel through the colon, they become compacted as

feces. The colon concentrates wastes by actively pumping sodium ions
across its wall, into the internal environment. Water flows by osmosis.

The first part of the colon is a cup-shaped pouch called the cecum.
The short, tubular appendix projects from the cecum. Beyond the cecum,
the colon ascends the wall of the abdominal cavity, extends across the
cavity, descends, and connects to the rectum..

Contraction of the smooth muscle in the colon wall mixes the colon’s
contents and propels this material along. Compared with other gut regions,
wastes move more slowly through the colon, which also has a moderate
pH. These conditions favor growth of bacteria such as Escherichia coli.
This species is part of our normal gut flora. It make vitamin B 12 that we
absorb across the colon lining.

After a meal, signals from autonomic nerves cause much of the colon
to contract forcefully and propel feces to the rectum. The rectum stretches,
which activates a defecation reflex to expel feces. The nervous system can
override the reflex by calling for contraction of a sphincter at the anus.
Respiratory System

Respiration is the physiological processes that collectively supply body

cells with oxygen from the environment and deliver waste carbon dioxide to
the environment.

Functions of Human Respiratory System

The respiratory system functions in gas exchange, but it has many
additional tasks. We can speak, sing, or shout as air moves past our vocal
cords. We have a sense of smell because airborne molecules stimulate
olfactory receptors in the nose. Cells lining the nasal passages and other
airways of the system help defend the body; they intercept and neutralize
airborne pathogens. The respiratory system contributes to the body’s acid-
base balance by exhaling waste carbon dioxide that can make blood acidic.
Controls over breathing also help maintain body temperature, because
water evaporating from airways has a cooling effect.

From Airways to Alveoli

If you are healthy and sitting quietly, air usually enters through your nose,
rather than your mouth. As air moves through your nostrils, tiny hairs filter
out any large particles. Mucus secreted by cells of the nasal lining captures
fine particles and airborne chemicals. Ciliated cells in the nasal lining also
help remove inhaled contaminants.

Air from the nostrils enters the nasal cavity, where it gets warmed and
moistened. It flows next to pharynx, or throat. It continues to the larynx, a
short airway commonly known as the voice box because of the pair of vocal
cords that span it. Each vocal cord is skeletal muscle with a cover of
mucus-secreting epithelium. Contraction of the vocal cords changes the
size of the glottis, the gap between them.

When the glottis is wide open, air flows through it silently. When
muscle contraction narrows the glottis, outgoing air flowing through the
tighter gap makes the vocal cords vibrate, giving rise to sounds. The
tension on the cords and changes in position of the larynx alter the sound’s
pitch.
 A flap of tissue called the epiglottis can fold over and cover the
larynx. When you are breathing, the epiglottis points up and air moves
through the larynx into the trachea, or windpipe. When you swallow, the
epiglottis points down and covers the larynx entrance, so food and fluids
enter the esophagus. The esophagus connects the pharynx to the
stomach.

The cartilage-reinforced trachea branches into two bronchi (singular,

bronchus). Each bronchus delivers air to a lung. Ciliated and mucus-
secreting cells in the epithelial lining of the bronchi help fend off respiratory
tract infections. Bacteria and airborne particles get caught in the secreted
mucus, then cilia sweep the mucus toward the throat for expulsion.

The Paired Lungs

Two cone-shaped lungs reside in the thoracic cavity, one on each side of
the heart. The rib cage encloses and protects the lungs. A two-layer thick
pleural membrane covers each lung’s outer surface and lines the inner
thoracic cavity wall.

Inside each lung, air flows through finer and finer branchings of a
“bronchial tree.” All of these branches are bronchioles. The finest
bronchioles lead to the respiratory alveoli., the little air sacs where gases
are exchanged. Collectively, alveoli provide an extensive surface for gas
exchange.

Air in alveoli exchanges gase with blood flowing through pulmonary

capillaries. At this point, a different organ system is involved. The
circulatory system transports oxygen to the body tissues and carries carbon
dioxide away from them.

Muscles and Respiration

A broad sheet of smooth muscle beneath the lungs, the diaphragm,

separates the thoracic cavity and the abdominal cavity. It is the only
smooth muscle that can be controlled voluntarily. The diaphragm and the
intercostal muscles- the skeletal muscles between the ribs- act together to
change the volume of the thoracic cavity during breathing. There are two
sets of intercostal muscles. One set is external to the rib cage and
functions in inhalation. The other set is inside the rib cage and acts during
forced exhalation.

Circulatory and Transport System

The Human Cardiovascular System

Like other mammals, humans have a four-chambered heart that pumps

blood through two circuits. Each circuit includes a network of blood vessels
that carry blood from the heart to a capillary bed and back to the heart. In
each circuit, the heart pumps blood out of a ventricle and into branching
arteries. Arteries are wide-diameter blood vessels that carry blood away
from the heart and to organs. Within an organ, arteries branch into smaller
vessels called arterioles. Arterioles in turn branch into capillaries, the
smallest vessels. Exchanges between the blood and interstitial fluid take
place as blood flows through the capillaries. Several capillaries join up to
form a venule, a vessel that carries blood to a vein. Veins are large-
diameter vessels that return blood to the heart. Blood from veins empties
into one of the two atria.

The shorter pulmonary circuit carries blood to and from the lungs.
Oxygen-poor blood is pumped out of the heart’s right ventricle into
pulmonary arteries. One pulmonary artery delivers blood to each lung. As
blood flows through pulmonary capillaries, it picks up oxygen and gives up
carbon dioxide. Oxygen-rich blood then returns to the heart by way of the
pulmonary veins, which empty into the left atrium.

Oxygenated blood pumped out of the heart travels through the longer
systemic circuit. The heart’s left ventricle pumps blood into the body’s
largest artery, the aorta. Arteries that branch from the aorta carry blood to
various body parts. For example, the renal artery delivers blood to the
kidneys, and the coronary arteries supply heart cells. Each artery branches
into arterioles and then capillaries. Blood gives up oxygen and picks up
carbon dioxide as it flows through the capillaries. The oxygen-poor blood.
The oxygen-poor blood that leaves the capillaries flows through venules
and veins to the heart’s right atrium.

Most blood moving through the systemic circuit flows through only
one capillary bed. However, after blood passes through the capillaries in
the small intestine, it flows through a vein (the hepatic portal vein) to a
capillary bed in the liver. This two-capillary journey allows the blood to pick
up glucose and other substances absorbed from the gut and deliver them
to the liver. The liver stores some of the absorbed glucose as glycogen. It
also breaks down some absorbed toxins, including alcohol.

The Human Heart

The heart lies in the thoracic cavity, beneath the breastbone and between
the lungs. It is protected and anchored by pericardium, a sac of connective
tissue. Fluid between the sac’s two layers provides lubrication for the
heart’s continual motions. The heart’s wall consists mostly of cardiac
muscle cells, and its chambers and blood vessels are lined with
endothelium, a type of epithelium.
Each side of the human heart has two chambers: An atrium receives
blood from veins, and a ventricle pumps blood into arteries. Pressure-
sensitive valves function like one-way doors to control the flow of blood
through the heart. High fluid pressure forces a valve open. When fluid
pressure declines, the valve shuts and prevents blood from moving
backward.

Flow To, Through. And From the Heart

Two big veins deliver oxygen-poor blood from the body to the right atrium.
The superior vena cava delivers blood from the upper regions of the body.
The inferior vena cava delivers blood from the lower regions. Blood from
the right atrium flows through the right atrioventricular (AV) valve into the
right ventricle. The right ventricle pumps it through the pulmonary valve and
into the pulmonary trunk, a vessel that branches into two pulmonary
arteries. Each pulmonary artery carries blood to a lung.

After passing through the lung, the now oxygenated blood returns to
the left atrium via pulmonary veins. The blood then flows through the left
atrioventricular (AV) valve into the left ventricle. The left ventricle pumps
the blood through the aortic valve into the aorta, and from there it flows to
tissues of the body.

The Cardiac Cycle

The events that occur from the onset of one heartbeat to another are
collectively called the cardiac cycle. During this cycle, the heart’s
chambers alternate through diastole (relaxation) and systole (contraction).
First, the relaxed atria expand with blood. Fluid pressure forces AV valves
to open and blood to flow into the relaxed ventricles, which expand as the
atria contract. Once filled, the ventricles contract. Contraction raises the
fluid pressure inside the ventricles and forces the aortic and pulmonary
valves to open. Blood flows through these valves and out of the ventricles.
Now emptied, the ventricles relax while the atria fill again.

Contraction of ventricles drive circulation; atrial contraction only helps

fill ventricles. The structure of the cardiac chambers reflects their different
functions. Atria need only generate enough force to squeeze blood into the
ventricles, so they have relatively thin walls. Ventricle walls are more thickly
muscled because their contraction has to generate enough pressure to
propel blood through an entire cardiovascular circuit. The left ventricle,
which pumps blood throughout the long system circuit, has thicker walls
than the right ventricle, which pumps blood only to the lungs and back.

During the cardiac cycle a “lub-dup” sound can be heard through the
chest wall. Each “lub” is the heart’s AV valves closing. Each “dup” is the
heart’s aortic and pulmonary valves closing. If a valve does not close
properly, blood is forced backward through the defective valve, making a
whooshing sound known as a heart murmur. Most valve defects that cause
heart murmurs do not threaten health. Those that do require a surgical
repair.

Characteristics and Functions of Blood

Functions of Blood

Vertebrate blood is a fluid connective tissue with many functions. It carries

essential oxygen and nutrients to cells, and carries their metabolic wastes
to the organs that dispose of them. It facilitates internal communications by
distributing hormones and serves as a highway for cells and proteins that
protect and repair tissues. In birds and mammals, blood helps maintain a
stable internal temperature by distributing heat generated by muscle
activity to the skin, where it can be lost to the surroundings.
Plasma
The fluid portion of the blood, known as the plasma, constitutes about 50
to 60 percent of the blood volume. Plasma is mostly water with hundreds of
different plasma proteins dissolved in it. Some plasma proteins transport
lipids and fat-soluble vitamins; others have a role in blood clotting or
immunity. Dissolved sugars, amino acids, vitamins, and some gases travel
through the bloodstream in plasma.

Red Blood Cells

The cellular portion of blood consists of blood cells and platelets. All arise
from stem cells in the red marrow of bones.

Erythrocytes, or red blood cells, transport oxygen from lungs to

aerobically respiring cells and facilitate movement of carbon dioxide to the
lungs. Mature red blood cells are flexible disks with a depression at their
center. Their flexibility allows them to slip easily through narrow blood
vessels, and their flattened shape facilitates gas exchange.

Hemoglobin fills the interior of the mature red blood cell. Most oxygen
that enters the blood travels to the tissues while bound to the heme group
of hemoglobin. In addition to hemoglobin, a mature red blood cell has
enough stored sugars. RNAs and other molecules to live about 120 days.

White Blood Cells

Leukocytes, or white blood cells, carry out ongoing housekeeping tasks

and function in defense. The cells differ in their size, nuclear shape, as well
as function.

Neutrophils, the most abundant white cells, are phagocytes that

engulf bacteria and debris. Eosinophils attack larger parasites, such as
worms. Basophils secrete chemicals that have a role in inflammation.
Monocytes are white cells that circulate in the blood for a few days, then
move into the tissues, where they develop into phagocytic cells known as
macrophages.
Macrophages interact with lymphocytes to bring about immune responses.
There are two types of lymphocytes, B cells and T cells. B cells mature in
bone, whereas T cells mature in the thymus. Both protect the body against
specific threats.
Platelets and Homeostasis

A platelet is a membrane-wrapped fragment of cytoplasm that arises when

a large cell ( a megakaryocyte) break up. Once formed, a platelet will
remain functional up to nine days. Hundreds of thousands of plates
circulate in the blood, ready to take part in homeostasis. This process stops
blood loss from an injured vessel and provides a framework to begin
repairs.

When a vessel is injured, it constricts (narrows), reducing blood loss.

Platelets adhere to the injured site and release substances that attract mor
platelets. Plasma proteins convert blood to a gel and form a clot. During
clot formation, fibrinogen, a soluble plasma protein, is converted to
insoluble threads of fibrins. Fibrin forms a mesh that traps cells and
platelets.

Excretory, Osmoregulation

The Urinary System

Kidneys filter water, mineral ions, organic wastes, and other substances
from the blood. They adjust the volume and composition of this filtrate and
return most of it to the blood. The fluid not returned becomes urine.

Components of the System

A human urinary system has two kidneys, two ureters, one urinary
bladder, and one urethra. The kidneys filter blood and form urine. The other
organs collect and store urine and convey it to the body surface.

Kidneys are bean-shaped organs about the size of an adult fist. They
lie just beneath the peritoneum that lines the abdominal cavity, to the left
and right of the backbone. The outermost kidney layer, the renal capsule,
consists of fibrous connective tissue. The Latin renal means “relating to the
kidneys”. The bulk of tissue inside the renal capsule is divided into two
zones: the outer renal cortex and the inner renal medulla. A renal artery
transports blood to each kidney and a renal vein carries blood away from it.
 Inside each kidney, urine collects in a central cavity called the renal
pelvis. A tubular ureter conveys the fluid from each kidney to the urinary
bladder, a hollow, muscular organ that stores urine. When the bladder is
full, a reflex action occurs. Stretch receptors signal motor neurons in the
spinal cord. These neurons cause smooth muscle in the bladder wall to
contract. At the same time, sphincters encircling the urethra, the tube that
delivers urine to the body surface, relax. As a result, urine flows out of the
body. After age two or three, , the brain can override the spinal reflex and
prevent urine from flowing through the urethra at inconvenient moments.

A male’s urethra runs the length of the penis and it conveys urine and
semen at different times. A sphincter cuts off urine flow during erections. In
females, the urethra opens onto the body surface near the vagina. The
female urethra is a short tube, so infectious organisms can easily reach the
urinary bladder. That is one reason why women get bladder infections more
often than men do.

Nephrons

A kidney has more than 1 million nephrons – microscopically small

tubes of cuboidal epithelium associated with capillaries. Kidney tubules are
just one cell thick, so substances diffuse easily across them. Each nephron
begins in the cortex, where its wall balloons out and folds back to form a
cup-shaped Bowman’s capsule. Beyond the capsule, the nephron twists a
bit and straighten out as a proximal tubule (the part nearest the beginning
of the nephron). After extending down into the renal medulla, the nephron
makes a hairpin turn called the loop of Henle. The tubule reenters the
cortex and twists again, as the distal tube (the farthest from the start of the
nephron). The distal tubules of up to eight nephrons drain into a collecting
tubule. Many collecting tubules extend through the kidney medulla and
open into the renal pelvis. Like the cells lining the small intestine, cells of
the kidney tubules have microvilli. These tiny extensions increase the
surface area for absorption of substances.

Blood Vessels Associated with Nephrons

Inside each kidney, a renal artery branches into smaller arterioles.

Each arteriole in turn branches into a glomerulus (plural, glomeruli), a
cluster of capillaries in Bowman’s capsule. Glomerular capillaries have
gaps between the cells in their walls. These gaps make these capillaries
about a hundred times more permeable than a typical capillary. As blood
flows through the glomerulus, blood pressure forces some fluid out through
the gaps in the capillary wall and into Bowman’s capsule. Glomerulus is the
Greek word for filter.

The unfiltered portion of the blood flows out of the glomerulus and
into an efferent arteriole. This arteriole quickly branches into the peritubular
capillaries, which thread lacily around the nephron. These capillaries are
the site for exchanges between the fluid flowing through the kidney tubules
and the blood. From the peritubular capillaries, blood continues into
venules that carry it to the renal vein.

Learning Task
1. What happens when one organ of the body fails to function? What could
be the effects to other parts of the body?

2. Explain how homeostasis is maintained by the different body systems.

Textbook References:

Starr, Cecie et al. 2012. Biology: Applications and Concepts

Mader, Sylvia, Biology-Inquiry to Life, McGrawHill 2nd Edition, New York,

2015

Berg, Linda L. 2012. Introductory to Botany Cengage Learning