General Biology (Biol.

1012)

DU (2013)
Chapter One
Introduction
 Objectives of the Chapter
 Define the term biology
 Explain scientific methods

 Know the origin and the nature of life

 The meaning and scope of biology
 The term Biology is derived from two Greek words ‘bio'life and
logos ‘study of’
Study of life and living organisms, sometimes called Life
Science.
 Cont….d
 Coined at the late 1700s by Pierre-Antoine de Monet and Jean-
Baptiste de Lamarck
 Updated from pure Science to Biological Sciences, which is an
extensive study covering the minute workings of chemical
substances inside living cells to the broad scale concepts of
ecosystems and global environmental changes.
 Cont.…D
 Biological Sciences study about:

 Physical characteristics and behaviors of organisms

 How they came into existence and what relation they
possess with each other and their environments
(ecology)?
 The origin and nature of life
 life's origin is still a big debating issue in science
 The evolution of life on earth has involved in the following
sequence of events.
1. The first living things to appear were the simplest creatures,
single-celled organisms, which are responsible for creation of more
complex, multi-cellular organisms (Endosymbiosis) through
billions of years of changes (Evolution)
 Theories on Origin of life
 Theories which offer their own explanation on the possible
mechanism of origin of life are
 Theory of Special Creation
 all the different forms of life on planet earth have been created by
God, the almighty.
 Theory of Spontaneous Generation

(e.g. Aristotle, the Greek philosopher (384-322 BC).

 living organisms could arise suddenly and spontaneously from any
kind of non-living matter.
 Cont.…D

 Theory of Catastrophism (Uniformitarianism)

 Modification of the theory of Special Creation
 several creations of life by God, each preceded by a
catastrophe resulting from some kind of geological
disturbance.
 since each catastrophe completely destroyed the existing
life, each new creation consisted of life form different
from that of previous ones.
 Cont.…D
 Cosmozoic Theory (Theory of Panspermia)
 life has reached this planet from other heavenly bodies such as
meteorites, in the form of highly resistance spores of some
organisms.
 Proposed by Richter in 1865 and supported by Arrhenius (1908)
and other contemporary scientists.
 Absence of evidence and lack of support lead the theory to be
discarded
 Cont.…D
 Theory of Chemical Evolution (Materialistic Theory or
Physico-chemical Theory).
 Origin of life on earth is the result of a slow and gradual process of
chemical evolution that probably occurred about 3.8 billion years
ago.
 Proposed by A.I.Oparin, a Russian scientist in 1923 and J.B.S
Haldane, an English scientist, in 1928.
 Nature and characteristics of life
 Life is defined as a "condition" that distinguishes animals and
plants from inorganic materials and dead organisms.
 The most sophisticated form of life is man as a result of this we
focuses upon the nature of the life and death of man.
 Cont….d
 Man demonstrates three lives or aspects of life:
Life of the body (physical),

life of the mind and

life of the spirit.
 Living tissues and organisms exhibit:

 Irritability: the ability to be excited or detect stimuli and to

respond thereto
 Growth and reproduction: power of multiplication and
duplication, regeneration and differentiation
 Cont….d
 Adaptability: permitting both change and maintenance of balances
(homeostasis)
 Metabolism: The transformation of energy and the use of nutrients.

 excretion and osmoregulation regulation are two important

homeostatic processes occurring in living cells, helping them to
maintain a constant internal environment.
 Excretion is the removal from the cell of waste products of
metabolism.
 In plant cells the major excretory products are oxygen and carbon
dioxide from cell respiration.
 Scientific methods
 Process for experimentation that is used to explore observations and
answer questions or
 Technique used in the construction and testing of a scientific hypothesis.

 Five basic steps of SM

 Make an observation.

 Ask a question.

 Form a hypothesis, or testable explanation.

 Make a prediction based on the hypothesis.

 Test the prediction.

 Iterate: use the results to make new hypotheses or predictions.

 Chapter Two: Biological Molecules
 Referred to as the molecules of life (bio-molecules) categorized as
organic and inorganic molecules.
 vital for every organism on Earth, these are:
 Organic;
 Proteins
 Carbohydrates
 lipids and
 nucleic acids.
 inorganic molecules
 water and minerals
 Carbohydrates

 is made of atoms; carbon, hydrogen and oxygen.

 source of energy and provide structural support for cells and

help in cell-cell recognition.
 They are found in the form of sugar or many sugars linked
together (saccharides).
 Divides into monosaccharides, disaccharides and
polysaccharides.
 bonded together through the glycosidic linkage
 Carbohydrates are polyhydroxy aldehydes or ketones or
substances that yield these compounds on hydrolysis.
 Carbohydrates

 Example: Glucose is aldehyde and fructose is Ketone.

 Based on number of carbons (3, 4, 5, 6), a monosaccharide is a
triose, tetrose, pentose or hexose.
 Disaccharides - 2 monosaccharides covalently linked
 Oligosaccharides - a few monosaccharides covalently linked.

 Polysaccharides - polymers consisting of chains of

monosaccharide or disaccharide
Cont.…D
 Cont.…D

•
 Monosaccharides

 Contains aldoses (reducing sugars) and ketoses group (non-

reducing sugars).
 GLUCOSE
 the most important carbohydrate fuel in human cells
 Two glucose molecules react to form the dissacharide maltose.

 Starch and cellulose are polysaccharides made up of glucose

units.
 Cont.….D

 GALACTOSE

 very similar to glucose molecules because it exists as α and β

forms.
 reacts with glucose to make the disaccharide lactose.
 It cannot play the same part in respiration as glucose because the
precise arrangement of atoms in a molecule, is so important.
 Fructose
 Fructose, glucose and galactose are all hexoses.
 It also has a five-atom ring rather than a six-atom ring.
 Fructose reacts with glucose to make the dissacharide sucrose.
 Cont.…D

Ribose and deoxyribose

 Ribose and deoxyribose are pentoses.
 The ribose unit forms part of a nucleotide of RNA.
 The deoxyribose unit forms part of the nucleotide of DNA.
 Disaccharides
 Most sugars found in nature are disaccharides.
 Disaccharides are soluble in water, but they are too big to pass through
the cell membrane by diffusion.
 They are broken down in the small intestine during digestion to give the
smaller monosaccharides that pass into the blood and through cell
membranes into cells.
 Cont.…D

 This is a hydrolysis reaction and is the reverse of a condensation

reaction and it releases energy.
 A condensation reaction takes place by releasing water.

 A glycosidic bond forms and holds the two monosaccharide units

together.
 The three most important disaccharides are sucrose, lactose and
maltose.
 Sucrose is a non-reducing sugar.

 Lactose and maltose are reducing sugars.

 Cont.…D

 Monosaccharides are used very quickly by cells.

 However, a cell may not need all the energy immediately and it
may need to store it.
 Monosaccharides are converted into disaccharides in the cell

 Further condensation reactions result in the formation of

polysaccharides.
 These are giant molecules which, importantly, are too big to escape
from the cell.
 These are broken down by hydrolysis into monosaccharides when
energy is needed by the cell.
 Polysaccharides

 Monosaccharides can undergo a series of condensation reactions, polysaccharides

are formed.

 This is called condensation polymerisation, and the building blocks are called

monomers.

STARCH

insoluble plant’s energy storage unit, exists as amylose (unbranched)

and amylopectin(branched polymer of α-glucose.

Glycogen

Animal energy storage unit made of amylopectin with very short

distances between the branching side-chains.

 Polysaccharides

Cellulose

 made from β-glucose molecules and the polymer molecules are 'straight'.

 It makes up the cell walls in plant cells.

 tougher than cell membranes due to the arrangement of glucose units in

the polymer chain and the hydrogen-bonding between neighboring chains.

 Cellulose is not hydrolysed easily and, therefore, cannot be digested so it

is not a source of energy for humans.

 The stomachs of Herbivores contain a specific enzyme called cellulase

which enables them to digest cellulose.

 Lipids

 variable forms, include fats, oils, waxes and some steroids.

 They are esters of fatty acids and alcohol (glycerol or chains of

alcohols).

 The primary function of lipids is to store energy.

 A lipid called a triglyceride is a fat if it is solid at room temperature

and an oil if it is liquid at room temperature.

 In addition, triglycerides are stored in the fat cells , also called

adipocytes or lipocytes, and are responsible in storing fats and

lipids which will facilitate energy store in animal‟s body.

 Cont…D

 White fat cells store one large lipid drop while brown fat cells

store smaller and multiple droplets of lipids spreading in the

whole body of the cell.

 Various types of lipids occur in the human body, namely 1)

triacylglycerol, 2) cholesterol, and 3) polar lipids, which include

phospholipids, glycolipids and sphingolipids.

 Plant leaves are coated with lipids called waxes to prevent water

loss, and the honeycomb in a beehive is made of beeswax.

 Cont.…D

Properties of lipids
 Hydrophobic, less soluble
 Double bonds increase solubility
 Melting points:
 Depend on chain length and saturation
 Double bonds lead acyl chain disorder and low melting temperatures
 Unsaturated fatty acids are solid at room temperature.
Importance of lipids
 As the main component of cell membranes (phospholipids)

 Insulation of heat and water,

 Storing energy, protection and cellular communication.

 Proteins

 made of amino acids, small compounds that are made of carbon,

nitrogen, oxygen, hydrogen, and sometimes sulfur.

 There are 20 different variable groups, and proteins are made of

different combinations of all 20 different amino acids.

 Several covalent bonds called peptide bonds join amino acids

together to form proteins,

 A peptide forms between the amino group of one amino acid and
the carboxyl group of another.
 Cont.…D

 Based on the variable groups contained in the different amino acids,

proteins can have up to four levels of structure.
 The number of amino acids in a chain and the order in which the amino
acids are joined define the protein‟s primary structure.
 After an amino acid chain is formed, it folds into a unique three-
dimensional shape, which is the protein‟s secondary structure.
 A protein might contain many helices, pleats, and folds.
 The tertiary structure of many proteins is globular, such as the
hemoglobin protein, but some proteins form long fibers.
 Some proteins form a fourth level of structure by combining with other
proteins.
 Cont.…D

 make up about 15% of your total body mass and are involved in
nearly every function of your body.
 your muscles, skin, and hair all are made of proteins.
 about 10,000 different proteins that provide structural support,
transport substances inside the cell and between cells,
communicate signals within the cell and between cells, speed up
chemical reactions, and control cell growth.
 NUCLEIC ACIDS

 Complex macromolecules that store and transmit genetic information.

 made of smaller repeating subunits called nucleotides, which are composed of
carbon, nitrogen, oxygen, phosphorus, and hydrogen

 There are six major nucleotides, all of which have three units a
phosphate, a nitrogenous base, and a ribose sugar.
 Cont.…D

The two forms are deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA).
The sugar of one nucleotide bonds to the phosphate of another nucleotide.

There are five different bases found in nucleotide subunits that make up
DNA and RNA, Adenine, Cytosine, Guanine, Thymine and Uracil.
 Cont.….d

 A nucleotide with three phosphate groups is adenosine

triphosphate (ATP).
 ATP is a storehouse of chemical energy that can be used by cells
in a variety of reactions.
 It releases energy when the bond between the second and third
phosphate group is broken.
 VITAMINS
 Needed in small amounts for metabolic activities.

 Many vitamins help enzymes function well.

 Vitamin D is made by cells in your skin.

 Some vitamins like B and vitamin K are produced by bacteria, living in

the large intestine.
 most vitamins cannot be made by the body,so a well-balanced diet can
provide the vitamins that are needed.
 fat-soluble vitamins can be stored in the liver and fatty tissues of body

 Other vitamins are water-soluble and cannot be stored in the body.

 Foods providing an adequate level of these vitamins should be included

in a person‟s diet on a regular basis.
 Water

 formed by covalent bonds that link two hydrogen (H) atoms to one
oxygen (O) atom,
 tasteless and odorless, plentiful and essential of compounds
existing in gaseous, liquid, and solid states.
 Water molecules have an unequal distribution of charges and are
called polar molecules, meaning that they have oppositely charged
regions.
 Minerals

 inorganic compounds used by the body as building material, and

they are involved with metabolic functions.
 the mineral iron is needed to make hemoglobin and it binds to
hemoglobin in red blood cells and is delivered to body cells as
blood circulates in the body.
 Calcium, and other minerals, is an important component of bones
and is involved with muscle and nerve functions and they serve as
cofactors for enzymes.
 Magnesium is an important component of the green pigment,
chlorophyll, involved in photosynthesis.
 Chapter Three
3. The Cellular Basis of Life
 English scientist named Robert Hook was the first to observe plant cells

with a crude microscope in 1600’s.

 German scientists Mathias Schleiden and Theodore Schwann

proposed that all living things are composed of cells , in1830.

 German pathologist, Rudolph Virchow extended this idea by

contending that cells arise only from other cells.

3.1. The Cell Theory

A cell is the basic structural and functional unit of living organisms.

All cells arise from pre-existing cells .

 Eukaryotic cell has 3 major parts:

 The plasma membrane: the outer boundary of the

cell.
 The cytoplasm: the intracellular fluid packed with
organelles
 The nucleus: an organelle that controls cellular
activities.
• An organelle is a specialized subunit within a cell
that has a specific function.
 Cont.…..d

 Eukaryotic organelles are double layer

 Prokaryotes are cells that do not have membrane
bound organelles.
• These organelles are found in the cytoplasm, a
viscous liquid found within the cell membrane that
houses the organelles and
• is the location of most of the action happening in
a cell.
Fig: 3.1. Animal cell
 There are two kinds of cell organelles on the basis
membrane covering, membranous and non
membranous organelles
Membranous organelles are:
 Endoplasmic reticulum (Rough and Smooth),
 Golgi bodies, mitochondria, chloroplasts and nucleus etc.
non-membrane bound cell organelles are;
• ribosomes (70S and 80S), centrosomes, cilia and flagella,
microtubules, basal bodies and microfilaments.
 3.3. Structure and function of organelles

A. The nucleus
 The nucleus spherically shaped double-layered
membrane.
 In it DNA directs protein synthesis and serves as a
genetic blueprint during cell replication.
 Nucleus governs most cellular activities and
serves as the cell's master.
 Cont.….d

 In the gametes, the DNA blueprint serves to pass

the genetic characteristics to future generation
The Nuclear envelope: surrounds nuclear
material and consists of outer and inner membrane
 perforated at intervals by nuclear pores through
this pores most ions and water soluble molecules
to transfer b/n nucleus and cytoplasm.
 Chromatin: The term chromatin means "colored material" and

refers to the fact that this material is easily stained for viewing with

microscope

 Nucleoli: The nuclei of most cells contain one or more lightly

stained structures called nucleoli that actively engage in

synthesizing of ribosomes.

 The nucleolus becomes enlarged when a cell is synthesizing proteins

 B. The Cytoplasm
 The Cytoplasm is highly organized membrane-enclosed
organelles- dispersed within a complex jelly – like marrow
called the „cytosol‟.
 These organelles occupy about half of the total cell
volume.

 The remaining part of the cytoplasm is cytosol.

 All cells
contain six Endoplasmic
Peroxisomes
main types of reticulum
organelles-

Mitochondria lysosomes

Golgi complex Vacuoles

 C. Endoplasmic reticulum (ER)
 ER is a fluid-filled present throughout the cytosol.
 The ER is one continuous organelle with many communicating
channels.
 ER is two types; smooth and rough ER.
 The smooth ER is a meshwork of interconnected tubules, whereas the
rough ER projects outwards from the reticulum as stacks of flattened
sacs.
 The outer surface of the rough ER contains dark particles called
ribosomes, that produce protein.
 Smooth ER does not have ribosomes, and does not produce proteins
• Fig:3.2. Endoplasmic reticulum
 All new proteins and fats pass from ER gathered in the
smooth ER.
 Transport vesicles move to the Golgi complex for further
processing of their cargo.
 In liver cells, it contains enzymes involved in detoxifying
harmful endogenous or exogenous substances
 The detoxifying enzymes alter toxic substances so that
they could be easily eliminated in the urine.
 It has a special role in skeletal muscle cells.
 It plays a crucial role in the process of muscle
contraction.
D. The Golgi Complex:
• The Golgi complex is elaborately associated with the ER and contains
sets of flattened, curved, membrane- enclosed sacs, or cisternae,
stacked in layers.
Functions of Golgi complex
• Processing the raw material into finished products.
• Sorting and directing finished product to their final destination.
• Enzymes within the smooth ER can inactivate or destroy a variety of
chemicals including alcohol, pesticides, and carcinogens.
• In skeletal muscle cells, a modified form of smooth ER stores Ca2+
to be released for muscle contraction.
Fig:3.3. Golgi apparatus
 E. Lysosomes
o Lysosomes are membrane-enclosed sacs containing
powerful hydrolytic enzymes capable of intracellular
digesting and removing unwanted cellular debris and
foreign materials
o Lysosomes can take up old organelles and break
down into their component molecules.
• Those molecules that can be released are reabsorbed
into the cytosol, and the rest are dumped out of the cell.
 Cont.….d
 The process by which worn-out organelles are digested is called
autophagy a human liver cell recycles about half its content every
week.
 In the inherited condition known as lysosomal storage disease (Tay-
Sachs disease)
 As a result, harmful waste products accumulate disrupting the
normal function of cells, often with fatal results
 F. Mitochondria

 Mitochondria are the “power houses” of a cell

 They extract energy from nutrients in food and
transform it into usable form to energize cell activity.
 Each is enclosed by a double membrane - a smooth outer
that surrounds the mitochondria, and an inner membrane
that forms a series of enfolding called cristae (jelly-like
matrix).
 Cont.….d

 These cristae contain proteins that convert much of the

energy in food into a usable form (the electron transport
protein).
 The enfolding increase the surface area available for
keeping these important proteins.
Fig. 3.4. Mitochondrial structure
 The matrix contains dissolved enzymes that preparing nutrient
molecules for the final extraction of usable energy by the cristae
proteins.
 In the matrix they have their own unique DNA called mitochondrial
DNA.
 Mitochondria have the ability to replicate themselves even when the
cell to which they belong is not undergoing cell division.
 ATP is the universal energy carrier the common energy “currency”
of the body.
 Cells can “cash in” ATP to pay the energy “price” for running the
cellular machine.
To get immediate usable energy cells can split

 terminal phosphate bond of ATP, which yields ADP with phosphate

group attached - plus inorganic phosphate (Pi) plus energy.

G. Chloroplasts

 Chloroplasts participate in the process of photosynthesis

 They are located in outer surface of the cell to receive enough

light.

 Chloroplasts are green colored due to the chlorophyll pigments

found in its internal parts.

Fig: 3.5. Structure of plant cell
 Vesicles are membrane bound sacs that are used to store or
transport substances around the cell.
 Vacuoles are essentially larger Vesicles, and they are
formed by the joining together of many Vesicles.
 Vacuole in plant cells maintaining Turgor Pressure.

Cytoskeleton
 The cytoskeleton is a complex protein network that act as the “bone
and muscle” of the cell.
 It has at least four distinct elements: Microtubules, Microfilaments,
Intermediate filaments and Microtubular lattice.
• The different parts of the cytoskeleton are
structures linked and functionally coordinated to
provide integration of the cell.
• The microtubule is the largest of the group;
slender, long, hollow tubes composed of a globular
protein molecule tubulin.
The microtubule
 coordinate numerous complex cell movements
in transport of secretory vesicles from region to
region of the cell,
 movements of cilia and flagella,
Generally, cytoskeletons
provide:
• The shape of a cell
• Structural support
• Organizing its contents
• Substances movement through
cell (cilia, flagella) and
• Contribute to the movements of
the cell as a whole.
 H. Plasma membrane /cell membrane

• PM is thin layer of lipids and proteins forming outermost

boundary of living cell and enclosing the intracellular fluid (ICF).

• It serves as a mechanical barrier that traps needed molecules

within the cell;

• PM plays an active role in determining the composition of cell by

selective permeability of substances to pass between the cell and

its ECF environment.

• The PM is a fluid lipid bilayer embedded with proteins.

 Cont.…d

• The PM is a fluid lipid bilayer embedded with proteins.

• It appears as trilaminar layer structure having two dark layers

separated by a light middle layer as a result of specific

arrangement of the constituent molecules.

Fig: 3.6. Structure of cell membrane
• All PM are made up of lipids and proteins plus small amount of
carbohydrates.
• Phospholipids are most abundant with a lesser amount of
cholesterol.
• Phospholipids have a polar charged head having a negatively
charged phosphate group and two non-polar (electrically
neutral) fatty acid tails.
• The polar end is hydrophilic (water loving) because it can interact
with water molecule, which is also polar; the non-polar end is
hydrophobic (water fearing) and will not mix with water.
• Such two-sided molecule self assemble into a lipid bilayer, a
double layer of lipid molecules when in contact with water.
• The hydrophobic tails bury themselves in the center away
from the water, while the hydrophilic heads line up on both
sides in contact with water.
• Cholesterol provides to the fluidity as well as the stability
• Cholesterol lies in between the phosphate molecules,
preventing the fatty acid chain from packing together and
crystallizing that could decrease fluidity of the membrane.
• The PM is asymmetrical; the two surfaces are not the
same; carbohydrate is only on the outer surface
• Different amount of different proteins are on the outer
and inner surfaces and even the lipid structures of the
outer and inner half is not the same.
• The PM is highly complex, dynamic, regional
differentiated structure.
• The lipid layer forms the primary barrier to diffusion

• whereas proteins perform most of the specific membrane

functions.
 • 1. Some form channels, allow ions to pass through
without coming in direct contact with lipid interior.
Channels open and close in response to a controlling
mechanism.
• 2. Other proteins serve as carrier molecule that
transport specific molecule that cannot cross on their
own.
Membra • 3. Many proteins serve as „receptor sites‟ that recognize
ne and bind with specific molecules in the cell environment.
proteins • 4. Another group of proteins act as membrane-bound
have the enzymes that control specific chemical reactions
followin • 5. Some proteins are arranged as filaments
g special network/meshwork on the inner side and are secured
functions to certain internal protein elements of the
in PM cytoskeleton. They maintain cell shape.
• 6. Other proteins function as cell adhesion molecules
(CAMs). These molecules protrude from the
membrane surface that grip each other and grip the
connective tissue fibers that interlace between cells.
• 7. Some proteins, especially in conjunction with
carbohydrate are important in the cell's ability to
recognize „self‟ and in cell-to-cell interactions.
 Fig: 3.7. Membrane protein
-
 3.4. Cellular diversity

 Cells are very diverse in their size, shape and their

internal structure

3.4.1. Cell Shape and size

 Cells have different shapes due to appropriate function.

-Skin cells have a shape which is flat

-Egg cells have shape which is like sphere

 3.4. Cellular diversity

-some bacteria are rod in shape

-Some plant cells are rectangular.

 Some cell can be seen without using magnification

instruments

 Example, egg of birds/reptiles and a neuron cell of

giraffe
 Fig: 3.8. Various types of animal cells (shape)

1
 3.5. Transport across the cell membranes

 Lipid-soluble substances and small ions can passively diffuse

through the plasma membrane down their electro-chemical
gradients.
 Highly lipid-soluble particles are able to dissolve in the lipid
bilayer and pass through the membrane.
 Uncharged/non-polar molecules such as oxygen, carbon dioxide
and fatty acids are highly lipid-soluble and readily permeate the
membrane.
 Charged particle sodium/potassium ions and polar molecules such as
glucose and proteins have low lipid solubility, but are very soluble in water.

 Particles with low lipid-permeability and too large for channels,

cannot permeate the membrane on their own.
There are 4 basic mechanisms:

1. Diffusion and facilitated diffusion

2. Osmosis
3. Active transport

4. Bulk transport
1. Diffusion is the net movement of molecules (or ions) from a region
of their high concentration to a region of their lower concentration.
Factors that influence the rate of net diffusion

Surface
Permeabili
area of the
ty of the
membrane
membrane

Distance
through Molecular
which weight of
diffusion the
must take substance
place
 N.B:- Increasing all the factors increases rate of net diffusion,
except distance - thickness, that if increased, decreases the rate
of diffusion; and molecular weight if increased, decreases rate
of diffusion.
• Diffusion molecules reach an equilibrium when there is no net
movement of molecules from either side.
• Movement of charged particles is also affected by their electrical
gradient.
• If a relative difference in charges exist between two adjacent
areas, the cations tend to move towards more negatively charged
area, whereas the anions tend to move toward the more positively
charged areas.
• The simultaneous existence of an electrical and concentration
(chemical) gradient for a particular ion is referred to as an electro-
chemical gradient.
 Fig: 3.10. Concentration difference (A) and diffusion (B)
• -
 Fig:3.11. Diffusion of lipid molecules
• -
 Carrier- Mediated Transport
 All carrier proteins span the thickness of the
plasma membrane and are able to undergo
reversible changes in shape so that specific binding
site can alternately be exposed at either side of the
membrane.
 This transport displays three characteristics:

1. Specificity: each cell possesses protein specified to transport a

specific substance amino acid cannot bind to glucose carrier, but
similar amino acids may use the same carrier.
2. Saturation: in a given time only a limited amount of a substance
can be transported via a carrier; limited number of carrier is known
as transport maximum (Tm). When the Tm is reached, the carrier is
saturated, and the rate of transport is maximum.
3. Competition: Several closely related compounds may compete for
ride across the plasma membrane on the same carrier.
 3. Facilitated Diffusion
• Facilitated diffusion uses a carrier protein to
facilitate the transfer of a particular substance
across the membrane ''downhill'' from higher to
lower concentration.
• Active transport requires protein carrier to transfer
a specific substance across the membrane,
transporting against concentration gradient.
 Osmosis

 Osmosis is the net diffusion of water down its own

concentration gradient.

• Water can readily permeate the plasma membrane.

• The driving force for diffusion of water is its concentration

gradient from area of higher water concentration (low

solute) to the area of lower water (high solute) concentration.

 Fig:3.12. diffusion of water molecules
• -
• Two forces are involved in facilitating movement across the
plasma membrane:

1. Passive force: not require the energy for movement

2. Active force: requiring energy for movement
Active transport
• Active transport is energy consuming transport of molecules or
ions across a membrane against its natural tendency to diffuse
in the opposite direction.
• The movement of molecules in active transport is in one
direction only.
 The transfer of sodium and potassium across the membrane is
brought about by the changes in the shape of the protein
 The pump is essential in controlling the osmotic balance in animal
cells (osmoregulation)
 If the pump is inhibited, the cell swells and bursts because of the
building up of Na+,
 which results in excess water entering in to the cell by osmosis .
 The pump is also important in maintaining electrical activity in
nerve and muscle cells and in driving active transport of some other
substances such as sugar and amino acids.
• High concentration of potassium are needed inside cells
for protein synthesis, glycolysis, photosynthesis and
other vital processes.

Na+-K+-pump plays three important roles

I. It establishes sodium and potassium concentration

gradients across the plasma membrane of all cells;
these gradients are important in the nerve and muscle to
generate electrical signals.
II. It helps regulate cell volume by controlling the
concentration of solutes inside the cell and thus
minimizing osmotic effects that would induce swelling or
shrinking of the cell.

III. serves as the energy source for the transport of glucose

and amino acids across the membrane (intestine and
kidney cell).
 Table 3.1 How molecules cross cell membrane
• -
 Exocytocis and Endocytisis
 Endocytosis and exocytosis are active processes involving the bulk
transport of materials through membranes, either in to cells
(endocytosis)or out of cells (exocytosis). Exocytosis is the reverse
process of endocytosis
 Endocytosis of fluid is called pinocytosis cell (drinking), whereas
endocytosis of large multimolecular particle is known as
phagocytosis (cell eating).
 Fig: 3.14. Exocytosis and Endocytosis
• 1
CHAPTER 4

Cellular Metabolism and Metabolic Disorders

95
 4.1 Cellular metabolism

• Metabolism is thus the sum of chemical reactions that takes

place within each cell of a living organism and that provides
energy for vital processes and synthesizing of new organic
materials.
• Broadly, these reactions can be divided into catabolic reactions
that convert nutrients to energy and anabolic reactions that
lead to the synthesis of larger biomolecules.

96
 4.2. Enzymes and their role in metabolism
What Are Enzymes?
 Most enzymes are
Proteins (tertiary and
quaternary structures)
 Act as Biological Catalyst to
accelerates a reaction
 Not permanently changed in
the process

97
 ENZYMES…
 Are specific for what they will catalyze
 Are Reusable
 End in –ase
-Sucrase
-Lactase
-Maltase
 Most enzymes are protein in nature.
 Depending on the presence and
absence of a non protein component
with the enzyme, enzymes can exist as,
simple enzyme or holoenzyme

98
 Cont’d…
1. Simple enzyme: It is made up of only protein molecules not
bound to any non proteins. Example: Pancreatic
Ribonuclease.
2. Holo enzyme is made up on protein groups and non-
protein component. „
 The protein component of this holo enzymes is called
apoenzyme and „the non-protein component of the holo
enzyme is called a cofactor.
 If this cofactor is an organic compound it is called a
coenzyme and if it is an inorganic groups it is called
activator. (Fe 2+, Mn 2+, or Zn 2+ ions). If the cofactor is
bound so tightly to the apoenzyme and is difficult to remove
without damaging the enzyme it is sometimes called a
prosthetic group.
99
 Cont’d…
COENZYMES-
 Coenzymes are derivatives of vitamins without which the
enzyme cannot exhibit any reaction.
 One molecule of coenzyme is able to convert a large number
of substrate molecules with the help of enzyme. „
 Coenzyme accepts a particular group removed from the
substrate or donates a particular group to the substrate „
 Coenzymes are called co substrate because the changes that
take place in substrates are complimentary to the changes in
coenzymes.
 „ The coenzyme may participate in forming an intermediate
enzyme-substrate complex
 Example: NAD, FAD, Coenzyme A
100
 Cont’d…
Metal ions in enzymes
 Many enzymes require metal ions like

for their activity.

 Metal-activated enzymes-form only loose and easily
dissociable complexes with the metal and can easily release
the metal without denaturation.
 Metalloenzymes hold the metal tightly on the molecule and
do not release it even during extensive purification.
Properties of Enzymes
Active site: the active site binds the substrate, forming an enzyme-
substrate (ES) complex. ES is converted to enzyme-product (EP); which
subsequently dissociates to enzyme and product.
Enzyme turnover number :refers to the amount of substrate converted per
unit time 101
 Cont’d…
Classification of Enzymes on the basis of the reactions they
catalyze

102
Cont’d…

103
 Cont’d…
How do enzymes
Work?
Enzymes work by weakening
bonds which lowers
activation energy

 Activation Energy is
needed to convert
potential energy into
kinetic energy.

104
Cont’d…

105
 Enzyme-Substrate Complex
 The substance (reactant) an enzyme acts on is the
substrate

Substrate

Active Site
 A restricted region of an enzyme molecule which
binds to the substrate.

106
 Cont’d…
Models of How Enzymes Work
1. Lock and Key model
 Substrate (key) fits to the active site (lock) which provides a
microenvironment for the specific reaction.
2. Induced Fit model
 A change in the shape of an enzyme’s active site
 Induced by the substrate

Substrate “almost” fits into the

active site, causing a strain on the
chemical bonds, allowing the
reaction.

107
 Cont’d…
Factors that Affect Enzymes
 Environment (Temperature & pH)
 Cofactors
 Coenzymes
 Inhibitors
 Allosteric Sites
Environment
 Factors that change protein structure will affect
an enzyme.
 Examples:
 pH shifts
 temperature
 salt concentrations 108
 Cont’d…
Temperature & pH
 High temperatures denature enzymes (Most enzymes like
normal body temperatures)
 Most enzymes function near neutral pH (6 to 8)
 Denatured (unfolded) by ionic salts

109
 Cont’d…
Cofactors
 Inorganic substances (zinc, iron, copper) are sometimes
need for proper enzymatic activity.
 Non-protein helpers can bond to the active site of enzymes
to help in reactions
 Example:
Iron must be present in the quaternary
structure of hemoglobin in order for it
to pick up oxygen.
Coenzymes
 Organic molecules that act as cofactors which help
enzymes.
 Examples:
 vitamins
110
 Cont’d…
Two examples of Enzyme Inhibitors
a. Competitive inhibitors: are chemicals that resemble an
enzyme’s normal substrate and compete with it for the
active site.
b. Noncompetitive inhibitors:
Inhibitors that do not enter the active site, but bind to
another part of the enzyme causing the enzyme to change
its shape, which in turn alters the active site.
Control of Metabolism
 Is necessary if life is to function.
 Controlled by switching enzyme activity "off" or "on” or
separating the enzymes in time or space

111
 Cont’d…
Types of Control
1. Switching on or off the genes that encode for specific
enzyme production
2. Allosteric sites
3. Feedback inhibition
4. cooperativity
Allosteric Regulation
 The control of an enzyme complex by the binding of a regulatory
molecule.
 Regulatory molecule may stimulate or inhibit the enzyme
complex.
 Allosteric site is a specific receptor site on some part of the
enzyme molecule away from the active site
 When activated, this site changes the shape of the enzyme to
inhibit it or to stimulate it

112
 Cont’d…

Feedback Inhibition
 When a metabolic pathway is switched off by its end-product.
 End-product usually inhibits an enzyme earlier in the pathway.
 Prevents the cell from wasting chemical resources

113
 4.3 Bioenergetics and biosynthesis
4.3.1. Cellular respiration
• Most living organisms obtain energy by breaking down organic
molecules (catabolism) during cellular respiration.
• This catabolic process can be divided into 3 phases.
• Phase I - Breakdown of large complex biomolecules like
polysaccharides, proteins and lipids into their respective building
blocks (hydrolysis). The chemical reactions occurring during this
stage do not release much energy.
• Phase II - These building blocks are usually oxidized to a common
intermediate, acetyl - CoA. Additionally, pyruvate or other citric acid
cycle intermediates may also be formed (in glycolysis and other
pathways).
• Phase III – This consists of the citric acid cycle (i.e. oxidation of
acetyl - CoA to CO2, formation of NADH and FADH2) followed by
electron transport and oxidative phosphorylation. Energy released
by electron transport to O2 is coupled to ATP synthesis. This cycle is
responsible for the release of much energy ( TCA cycle and ETC)
 Molecular structure of ATP

 Adenosine triphosphate (ATP) is a nucleoside triphosphate

used in cells as a coenzyme.
 It is often called the "molecular unit of currency" of
intracellular energy transfer.
 ATP transports chemical energy within cells for
metabolism.
 It is one of the end products of photophosphorylation,
cellular respiration, and fermentation and used by enzymes
and structural proteins in many cellular processes,
including biosynthetic reactions, motility, and cell division.
• Substrate level phosphorylation, oxidative
phosphorylation in cellular respiration, and
photophosphorylation in photosynthesis are three
major mechanisms of ATP biosynthesis.
• Metabolic processes that use ATP as an energy source
convert it back into its precursors.
• ATP is therefore continuously recycled in organisms.
• One molecule of ATP contains three phosphate
groups, and it is produced by a wide variety of
enzymes, including ATP synthase, from adenosine
diphosphate (ADP) or adenosine monophosphate
(AMP) and various phosphate group donors.

ATP consists of a base, in this case adenine (red), a ribose (magenta) and a phosphate chain
(blue).
 4.3.1.1 Anaerobic respiration

• Anaerobic respiration is a form of respiration using

electron acceptors other than oxygen.
• Anaerobic metabolic processes do not require oxygen.
Glycolysis
 Glycolysis (from glycose, an older term for glucose + -lysis
degradation) is the metabolic pathway that converts
glucose C6H12O6, into pyruvate, CH3COCOO− + H+.
 The free energy released in this process is used to form the
high-energy compounds ATP (adenosine triphosphate) and
NADH (reduced nicotinamide adenine dinucleotide).
• Glycolysis does not require or consume oxygen.
• The terms "aerobic glycolysis" and "anaerobic
glycolysis" refer to glycolysis in the presence or
absence of oxygen, respectively.
• Glycolysis occurs, with variations, in nearly all
organisms, both aerobic and anaerobic.
• The wide occurrence of glycolysis indicates that it is
one of the most ancient known metabolic pathways.
• It occurs in the cytosol of the cell.
The entire glycolysis pathway can be separated into two phases:
1. The Preparatory Phase – in which ATP is consumed and is hence also
known as the investment phase
 The first five steps are regarded as the preparatory (or investment)
phase, since they consume energy to convert the glucose into two
three-carbon sugar phosphates (G3P).
2. The Pay Off Phase – in which ATP is produced.
 Characterized by a net gain of the energy-rich molecules ATP and
NADH.
 This yields 2 NADH molecules and 4 ATP molecules, leading to a net
gain of 2 NADH molecules and 2 ATP molecules from the glycolytic
pathway per glucose.
 Substrate-level phosphorylation is the mechanism to produce ATP
during glycolysis.
Biochemical logic for the presence of regulatory steps
 The existence of more than one point of regulation indicates that
intermediates between those points enter and leave the glycolysis
pathway by other processes.
 For example, in the first regulated step, hexokinase converts
glucose into glucose-6-phosphate. Instead of continuing through
the glycolysis pathway, this intermediate can be converted into
glucose storage molecules, such as glycogen or starch.
Glycolysis involves ten enzymatic reactions as described below
 4.3.1.2 TCA(Tricarboxylic Acid) cycle and
ETC(Electron Transport Chain): Aerobic respiration
• One fate of pyruvate is that it enters to TCA cycle for complete oxidation.
But there are intermediate processes: The Oxidation of Pyruvate to form
Acetyl CoA for Entry Into the Krebs Cycle
• 2 NADH's are generated (1 per pyruvate)
• 2 CO2 are released (1 per pyruvate)
• The Krebs Cycle (citric acid cycle, TCA cycle)
 is considered as central pathway of aerobic metabolism, as
it serves two purposes-bioenergetics and biosynthesis
1. Bioenergetics:The cycle carries out complex degradation of
acetyl group in acetyl - CoA to CO2, resulting in release of energy
(ATP or GTP) and reducing power (NADH and FADH2).
2. Biosynthesis: It supplies precursors for several biosynthetic
pathways of amino acids, pyrimidines, purines etc
Example:- α-ketoglutarate and oxaloacetate are used for synthesis of a
number of amino acids like glutamic acid, asparatic acid etc
• Acetyl - CoA is the starting material for fatty acid biosynthesis.
• 6 NADH's are generated (3 per
Acetyl CoA that enters)
• 2 FADH2 is generated (1 per
Acetyl CoA that enters)
• 2 ATP are generated (1 per
Acetyl CoA that enters)
• 4 CO2's are released (2 per
Acetyl CoA that enters)

Therefore, the total numbers of

molecules generated in the
Oxidation of Pyruvate and the
Krebs Cycle is: 8 NADH, 2 FADH2,
2 ATP and 6 CO2
 4.3.1.3. Electron transport chain

• In aerobic respiration, electron transport is the final step in the

break-down of glucose.
• It also is the point at which most of the ATP is produced. High-
energy electrons and hydrogen ions from NADH and FADH2
produced in the Krebs cycle are used to convert ADP to ATP.

The maximum net Energy

Production from Aerobic
Respiration is 36-38.
 Biosynthesis
 Biosynthesis is a multi-step, enzyme-catalyzed process
where substrates are converted into more complex
products in living organisms.
 In biosynthesis, simple compounds are modified, converted
into other compounds, or joined together to form
macromolecules.
 This process often consists of metabolic pathways.
 Some of these biosynthetic pathways are located within a
single cellular organelle, while others involve enzymes that
are located within multiple cellular organelles.
 Examples of these biosynthetic pathways include the
production of lipid membrane components and
nucleotide.

127
 Cont’d…
 The prerequisite elements for biosynthesis include:
precursor compounds, chemical energy (e.g. ATP), and
catalytic enzymes which may require coenzymes
(e.g.NADH, NADPH).
 These elements create monomers, the building blocks for
macromolecules.
 Some important biological macromolecules include:
proteins, which are composed of amino acid monomers
joined via peptide bonds, and
 DNA molecules, which are composed of nucleotides joined
via phosphodiester bonds.

128
 Requirements of Biosynthesis
I. Photosynthesis
 Energy is transformed all around us every day.
 Batteries convert chemical energy into electric energy, and
radios convert electric energy into the energy carried by
sound waves.
 Similarly, some autotrophs convert light energy into
chemical energy through photosynthesis.
The importance of photosynthesis
 The processes of all organisms, from bacteria to humans
require energy and to get this energy, many organisms
access stored energy by eating food.
 Carnivores eat other animals and herbivores eat plants. But
where does the stored energy in food originate?
129
 Cont’d…
 All of this energy can be traced back to the process of
photosynthesis and light energy from the sun.
 Photosynthesis is essential to all life on earth.
 It is the only biological process that captures energy from
outer space (sunlight) and converts it into chemical energy in
the form of Glyceraldehyde3-phosphate (G3P), which in turn
can be made into sugars and other organic compounds such
as proteins, lipids, and nucleic acids.
 Plants use these compounds in all of their metabolic
processes.
 Unlike plants, animals need to consume other organisms to
consume the molecules they need for their metabolic
processes.

130
 The process of photosynthesis
 During photosynthesis, molecules in leaves capture sunlight
and energize electrons, which are then stored in the
covalent bonds of carbohydrate molecules.
 That energy within those covalent bonds will be released
when they are broken during cell respiration.
 How long lasting and stable are those covalent bonds?
 The energy extracted today by the burning of coal and
petroleum products represents sunlight energy captured
and stored by photosynthesis almost 200 million years ago.
 Photoautotrophs
 Are organisms(plants, algae, and some bacteria) which have
a capability of performing photosynthesis and they use light
to manufacture their own food.

131
 Cont’d…
 Heterotrophs: are organisms, such as animals, fungi, and
most other bacteria, they must rely on the sugars produced
by photosynthetic organisms for their energy needs.
 Chemoautotrophs: are very interesting group of bacteria
synthesize sugars, not by using sunlight's energy, but by
extracting energy from inorganic chemical compounds.
 The importance of photosynthesis is not just that it can
capture sunlight's energy.
 A lizard sunning itself on a cold day can use the sun's energy
to warm up.
 Photosynthesis is vital because it evolved as a way to store the
energy in solar radiation (the photo part) as high energy
electrons in the carbon-carbon bonds of carbohydrate
molecules (the ''synthesis'' part).
132
 Cont’d…
Other variant of photosynthesis
 Commonly known photosynthetic processes is the one
known as oxygenic photosynthesis.
 The other type is termed as anoxygenic photosynthesis.
 The general principles of anoxygenic and oxygenic
photosynthesis are very similar,
 But oxygenic photosynthesis is the most common and is seen
in plants, algae and cyanobacteria.
 During oxygenic photosynthesis, light energy transfers
electrons from water (H2O) to carbon dioxide (CO2), to
produce carbohydrates.
 In this transfer, the CO2 is "reduced," or receives electrons,
and the water becomes "oxidized," or loses electrons.
Ultimately, oxygen is produced along with carbohydrates.
133
 Cont’d…
 On the other hand, anoxygenic photosynthesis uses electron
donors other than water.
 The process typically occurs in bacteria such as purple
bacteria and green sulfur bacteria, which are primarily
found in various aquatic habitats.
The photosynthetic apparatus
 Plastids
 Photosynthetic eukaryotic organisms contain organelles
called plastids in their cytoplasm.
 Plastids generally contain pigments or can store nutrients.
 Colorless and nonpigmented leucoplasts store fats and
starch, while chromoplasts contain carotenoids and
chloroplasts contain chlorophyll.
134
 Cont’d…
 Photosynthesis occurs in the
chloroplasts; specifically, in the grana
and stroma regions.
 The grana is the innermost portion of
the organelle; a collection of disc-
shaped membranes, stacked into
columns like plates.
 The individual discs are called
thylakoids. It is here that the transfer
of electrons takes place.
 Chloroplasts are similar to
mitochondria, the energy centers of
cells, in that they have their own
genome, or collection of genes,
contained within circular DNA

135
 Cont’d…
Pigments
 Pigments are molecules that bestow color on plants, algae
and bacteria, but they are also responsible for effectively
trapping sunlight.
 Pigments of different colors absorb different wavelengths of
light. There are 3 main group of pigments.
1. Chlorophylls
 These green-colored pigments are capable of trapping blue
and red light.
 Chlorophylls have three subtypes, dubbed chlorophyll a,
chlorophyll b and chlorophyll c.
 There is also a bacterial variant aptly named
bacteriochlorophyll, which absorbs infrared light.
 This pigment is mainly seen in purple and green bacteria,
which perform anoxygenic photosynthesis. 136
 Cont’d…
2.Carotenoids: these red, orange or yellow-coloured pigments
absorb bluish-green light. Examples of carotenoids are
xanthophyll (yellow) and carotene (orange) from which
carrots get their color.
3.Phycobilins: these red or blue pigments absorb wavelengths
of light that are not as well absorbed by chlorophylls and
carotenoids. They are seen in cyanobacteria and red algae.
Antennae
 Pigment molecules are associated with proteins, which allow
them the flexibility to move toward light and toward one
another.
 A large collection of 100 to 5,000 pigment molecules
constitutes antennae. These structures effectively capture
light energy from the sun, in the form of photons.
137
 Cont’d…
Reaction centers: the pigments and proteins, which convert light energy
to chemical energy and begin the process of electron transfer, are known
as reaction centers.
The photosynthetic process
 The reactions of plant photosynthesis are divided into those that require
the presence of sunlight and those that do not.
 Both types of reactions take place in chloroplasts: light dependent
reactions in the thylakoid and light-independent reactions in the stroma.
 Light-dependent reactions :When a photon of light hits the reaction
center, a pigment molecule such as chlorophyll releases an electron.
 The released electron manages to escape by traveling through an
electron transport chain, which generates the energy needed to produce
ATP (adenosine triphosphate, a source of chemical energy for cells) and
NADPH.
 The "electron hole" in the original chlorophyll pigment is filled by taking
an electron from water. As a result, oxygen is released into the
atmosphere.
138
 Cont’d…
 light-independent reactions (also called dark reactions and
known as the Calvin cycle): Light reactions produce ATP and
NADPH, which are the rich energy sources that drive dark
reactions.
 Although NADPH and ATP provide cells with large amounts
of energy, these molecules are not stable enough to store
chemical energy for long periods of time.
 Thus, there is a second phase of photosynthesis called the
Calvin cycle in which energy is stored in organic molecules
such as glucose.
Three chemical reaction steps make up the Calvin cycle:
 Carbon fixation,
 Reduction and
 Regeneration.
139
 Cont’d…
 These reactions use water and
catalysts.
 The carbon atoms from carbon
dioxide are ''fixed,'' when they
are built into organic molecules
that ultimately form three-
carbon sugars. These sugars are
then used to make glucose or
are recycled to initiate the
Calvin cycle again.

140
 Cont’d…
Alternative Pathways
 The environment in which an organism lives can impact the
organism's ability to carry out photosynthesis.
 Environments in which the amount of water or carbon
dioxide available is insufficient can decrease the ability of a
photosynthetic organism to convert light energy into
chemical energy.
 For example, plants in hot, dry environments are subject to
excessive water loss that can lead to decreased
photosynthesis.
 Many plants in extreme climates have altered native
photosynthesis pathways to maximize energy conversion.

141
 Cont’d…
 C4 plants one adaptive pathway that helps plants maintain
photosynthesis While minimizing water loss is called the C4
pathway.
 The C4 pathway occurs in plants such as sugar cane and
corn and these plants are called C4 plants because they fix
carbon dioxide into four-carbon compounds instead of
three-carbon molecules during the Calvin cycle.
 C4 plants also have significant structural modifications in
the arrangement of cells in the leaves.
 In general, C4 plants keep their stomata closed during hot
days, while the four carbon compounds are transferred to
special cells where CO2 enters the Calvin cycle.
 This allows for sufficient carbon dioxide uptake, while
simultaneously minimizing water loss.
142
 Cont’d…
 CAM plants Another adaptive pathway used by some plants
to maximize photosynthetic activity is called crassulacean
acid metabolism (CAM photosynthesis).
 The CAM pathway occurs in water conserving plants that
live in deserts, salt marshes, and other environments where
access to water is limited.
 CAM plants, such as cacti, orchids, and the pineapple allow
carbon dioxide to enter The leaves only at night, when the
atmosphere is cooler and more humid.
 At night, these plants fix carbon dioxide into organic
compounds.
 During the day, carbon dioxide is released from these
compounds and enters the Calvin cycle.
 This pathway Also allows for sufficient carbon dioxide
uptake, while minimizing water loss. 143
CHAPTER 5

GENETICS AND EVOLUTION