BiologyUnit Review Note

Unit-1: The science of biology

The methods of science

      What is Science?

 Science is a system of acquiring knowledge based on the scientific method.

 Experimental science is the use of experiments to obtain information and build scientific knowledge. It
could generally include biology, chemistry and physics.

 Applied science is the use of the scientific method and knowledge to develop practical solutions for
real-world problems. It includes areas such as engineering, computer science, medicine, psychology,
agricultural science, statistics and mathematics.

What is the science of biology?

 Biology is a branch science that deals with living organisms and their vital processes. It encompasses
diverse fields, including botany, zoology, genetics, biomedicine, microbiology, physiology,
morphology, evolution, ecology, entomology, oncology, biochemistry, astrobiology and paleobiology.

What is the Scientific method?

 Scientific method is scientific method is the process by which scientists approach their work. It is a
systematic approach to interpreting observations that involve reasoning, predicting, experimenting
and drawing conclusions.

What are the main steps of the scientific method?

 Scientific method involves a series of steps. These include observation, asking a question,
conducting background research, constructing a hypothesis, designing and carrying out experiment,
analyzing results, drawing conclusion, reporting results and peer review.

⇒⇒  Observation: It is the act of noticing and describing events or processes in a careful, orderly way. It
is the first step in any scientific research.
⇒⇒  Asking a question: It involves identifying and defining a specific problem based on the observation.
⇒⇒  Conducting background research: It involves gathering information about the problem identified
using reliable resources. This could be done by reviewing previous scientific studies and experiments
through online searches or in a library.
⇒⇒  Constructing a hypothesis: Hypothesis is a statement or an educated guess that explains
observed facts and predicts new outcomes. It has to be stated in such a way that it can be tested by an
experiment
⇒⇒  Designing and conducting an experiment: A planned and controlled experiment is carried out to
test the hypothesis.
⇒⇒  Analyzing results and drawing conclusion: This step involves using the experimental data as an
evidence to draw a valid conclusion of the experiment. If the experiment does not support the hypothesis,
then a new hypothesis is made, and an experiment is designed to test the new hypothesis.
⇒⇒  Reporting the results and peer review: This involves sharing the findings of the research and
evaluation of a person’s work done by others in the same field.

Experimental variables

 Experimental variables are factors or conditions that can be manipulated (changed), controlled for, or
measured in an experiment. Examples may include temperature, amount of light, concentration of a
substance, the number of organisms, time and the availability of nutrients.

Types of experimental variables

 Independent variable (also called the manipulated variable): the factor that the scientist changes, or
manipulates, to see its effect on the dependent variable. There is only ever one independent variable
in an experiment.

 Dependent variable: the factor that the scientist observes or measures to see if it changes when the
independent variable is changed

 Controlled variable: the factor other than the independent variable that is kept constant in order to
avoid influencing results. There can be multiple control variables in an experiment.

 Confounding variable: a factor that cannot be controlled which may influence the result of the
experiment

Cause and effect relationships of experimental

variables
 Scientific experiments try to establish cause and effect relationships between variables. They try to
prove that a change in the independent variable (the cause) brings about a change in the dependent
variable (the effect).

Control and experimental groups of a controlled

experiment
 Control group: The standard group in an experiment in which the experimental groups are
compared with. It is exposed to the same conditions as the experimental group except for the
independent variable under investigation.

 Experimental group: The group which is being experimented on. This group is exposed to changes
in the independent variable being tested.
 Controlled experiment: an experiment in which all the variable factors in an experimental group and
a control group are kept the same except for the independent variable in the experimental group that
is changed or altered

How did the scientific method disprove the idea of

spontaneous generation?
 Spontaneous generation: a belief that living organisms could come from non-living matter

 Francesco Redi: He was the first person to challenge the theory of spontaneous generation
experimentally. He used jars covered with gauze to show that flies cannot be produced from rotting
meat. However, he was unable to disprove the belief that micro-organisms could arise by
spontaneous generation.

 Louis Pasteur: He disproved the theory of spontaneous generation once and for all using swan-
necked flasks filled with boiled broths.

Accuracy, reliability and validity in scientific

experiments
 Accuracy refers to how precisely you measure or count something in the experiment. It is
determined by the quality of the measuring devices used.

 Reliability refers to how consistently a method measures something. An experiment is reliable if it

gives the same or very close results when you repeat the entire experiment.

 Validity refers to how accurately a method measures what it is intended to measure.

How do we write reports on scientific experiments?

 A typical report format on a scientific experiment usually includes such sections as title, hypothesis,
materials required, experimental procedure, results obtained, conclusion and evaluation.

1.2 The tools of a biologist

What do biologists use in the laboratory?

 Some of the basic tools biologists use in the laboratory include:

⇒⇒ Measuring cylinders, pipettes and syringes are used to measure the volume of a liquid or a gas.
⇒⇒ Balances are used for measuring mass
⇒⇒ Dissecting kit is used to cut apart or separate tissue of an organism. It usually contains a
magnifying glass, scalpels, scissors, forceps (tweezers) and mounted needles.
⇒⇒ Petri dishes: These are round dishes made from glass or from plastic. They are usually used to
culture (grow) some microorganisms. Agar is a jelly-like substance obtained from seaweed, used for
culturing micro-organisms.
⇒⇒ Centrifuges are machines that spin to separate solids from liquids where simple filtration is not
adequate for the task. Ultracentrifuges are used to separate the various components of animal and plant
cells.
⇒⇒ Microscopes are devices that are used to see objects that are too small to be seen with unaided
(naked) eye. They magnify and resolve specimens.
⇒⇒  Magnification: the ability of a microscope to enlarge the image size of a specimen
⇒⇒ Resolution: the ability of a microscope to distinguish between two points that are close together. It is
the measure of how much detail a microscope is able to show.
⇒⇒ Microscopes can be optical microscopes or electron microscopes.
⇒⇒ Optical microscopes use a beam of light to form the image of a specimen. They are used to study
both living and non-living specimens. However, their magnification and resolution are limited by the wave
length of light.
⇒⇒ Electron microscopes use a beam of electrons to form the image of a specimen. They provide
better magnification and resolution. However, they are not used to study living specimens.
⇒⇒ There are two main types of electron microscopes. These are the transmission electron microscope
(TEM) and the scanning electron microscope (SEM).
⇒⇒ TEM uses a beam of electrons that passes through specimens to show the details of the internal
structures of cells or other specimens. It provides the greatest magnification and resolution. However, it
forms a two-dimensional image of a specimen.
⇒⇒ SEM uses a high-energy beam of electrons to produce three-dimensional, detailed images of the
surfaces of specimens. However, it provides less magnification and resolution than TEM.

What do biologists use in the field?

 Some of the equipment biologists use in the field are listed below:

⇒⇒ Quadrats like a metal square are used to estimate the abundance of organisms on land or under
water. Quadrats laid by the side of the transect line (a straight line on an area, such as a tape measure or
a long rope marked off every meter) are also used to show how the numbers of a particular species
changes across an area.
⇒⇒ Plastic jars or plastic bags are used to collect and keep small plant parts, such as leaves and
flowers.
⇒⇒ Plant press is used to preserve parts of plants.
⇒⇒ Pit fall trap is a container sunk into the ground to collect insects that crawl on the ground.
⇒⇒ Sweep nets are nets with canvas bags that are used to collect insects and other invertebrates from
long grasses.
⇒⇒ Funnel is for collecting insects from the soil.
⇒⇒ Potter (aspirator) is used to collect or suck small organisms on tree trunks or leaf.
⇒⇒ Data logger is used for recording information.
⇒⇒ Flow meter is used to measure the rate of flow of water.
⇒⇒ Field microscope is used to investigate the structures of specimens in the field while they are fresh.
⇒⇒ Theodolite is used to measure the height of trees or slopes in an area.
⇒⇒ Global positioning system (GPS) is used for recording positions (or area maps) quickly and
accurately.
⇒⇒ Balances are used for measuring mass.
1.3 The relevance and promise of biological science
 Biological science plays a major role in agriculture, medicine and environmental well-being.

Biology and agriculture

 Biologists are carrying out research into how to produce crop plants that are adaptive to new
conditions, high yielding, drought resistant and disease resistant.

Biology and medicine

 Biologists are involved in medical research to find out how pathogens function and spread and
develop new drugs to treat diseases. They are also able to give advice on ways of reducing the rate
of population growth by recommending effective methods of contraception.

Biology and the environment

 Biologists carry out research into how best to conserve the environment and reduce the impact of
global warming on the environment.

 Biotechnology is the use of microorganisms and enzymes that will benifit mankind. This technology
has huge applications that include:

⇒⇒ Cures for genetic diseases

⇒⇒ treatments for degenerative diseases
⇒⇒ establishing biologically controlled industrial processes
⇒⇒ genetically modifying plants to meet a specific need
⇒⇒ cloning of productive animals and plants
⇒⇒ production of monoclonal antibodies
⇒⇒ using stem cells to repair damaged organs

 Genetic engineering: is a process which involves altering an organism's genotype by inserting

another organism's gene into its DNA.

The relevance of Biology in Ethiopia

 Biology is very relevant in Ethiopia considering the issue of overpopulation, food security,
environmental well-being, health care and natural resource conservation.

1.4 Biology and HIV/AIDS

 Acquired immune deficiency syndrome (AIDS) is a sexually transmitted disease that reduces the
body's 

       immune functioning.
 It is caused by the human immuno deficiency virus (HIV), which attacks T-helper cells that help in
fighting diseases.
 The routes of HIV transmission includes

⇒⇒ unprotected sexual contact with an infected person

⇒⇒ during blood transfusion
⇒⇒ sharing infected sharp objects like needles
⇒⇒ from mother to child during pregnancy, birth or breast feeding

How can biology help in the fight against AIDS?

 There are several methods of combating the spread of AIDS.

       These include:

⇒⇒ breaking the transmission pathway of HIV

⇒⇒ producing drugs that kill the virus or at least stop it from reproducing
⇒⇒ producing a vaccine against the virus.

The life cycle of HIV and anti-retroviral drugs

 HIV is a retrovirus. Retroviruses are viruses that copy their RNA into DNA by an enzyme called
reverse transcriptase.

 HIV and other retro viruses have a life cycle with four main stages:

⇒⇒ Entry phase
⇒⇒ Viral genetic material is converted to DNA
⇒⇒ The new DNA enters the host cell DNA
⇒⇒ The new DNA ‘instructs’ the cell to make more HIV.

 Anti-retroviral drugs are drugs that target retroviruses and prevent them replicating. There are
different anti-retroviral drugs that target different stages in the life cycle of the virus.

 Highly active anti-retroviral therapy, or HAART is HIV treatment using a combination of different
anti-retroviral drugs.

Control and prevention of HIV/AIDS

 Methods of prevention of HIV/AIDS include:

⇒⇒ avoid having more than one sexual partner

⇒⇒ avoid sharing sharp objects like needles
⇒⇒ circumcision of males reduce HIV transmission
⇒⇒ creating awareness in the society about the issues related to responsible sexual behavior
⇒⇒ Creating consciousness about the ABC rules especially among the young.
A — abstain from sexual contact
B — be faithful to one sexual partner
C — use condoms

Unit-2: Biochemical molecules

2.1 Inorganic and organic molecules

Classification of biochemical molecules

 Biochemical molecules can be inorganic or organic.
 Inorganic molecules do not contain both hydrogen and carbon.
 Organic molecules always contain both carbon and hydrogen.

Which chemical elements are found most 

frequently in living organisms?
 An element is a substance that is made of only one kind of atom.
 Most biological molecules are built from carbon, hydrogen, oxygen, nitrogen, sulfur and phosphorus.

Atoms, molecules and compounds

 Atoms are the smallest particles of a chemical element.
 Molecules are groups of two or more atoms of the same element  (e.g. O2) or different elements
(e.g. H2O) held together by chemical bonds.

 A compound is a substance made from molecules containing more than one kind of atom in a fixed
ratio.

What is water?
 Water is the most abundant inorganic molecule in living things. It contains two hydrogen atoms
bonded to one oxygen atom.

 Water is a polar molecule. The oxygen and hydrogen atoms share electrons unevenly to form
opposite ends of the molecule, known as dipoles.
 A dipole refers to the separation of charges within a molecule between two covalently bonded atoms
or atoms that share an ionic bond. In a water molecule, the oxygen side of the molecule carries  a net
negative charge, while the side with the two hydrogen atoms  has a net positive electrical charge.

 Water molecules are interlinked by a hydrogen bond, which joins the oxygen in one water molecule
(the slightly negative part) to the hydrogen in another water molecule (the slightly positive part). 

Why is water so important to living things?

Water is important to living things in a number of ways, such as:

 It serves as a habitat for many organisms.

 It is a transport medium in living organisms.
 It is a reactant in many chemical reactions, such as photosynthesis and hydrolysis. Hydrolysis is a
reaction that uses water to split large molecules into smaller ones.

 It is a medium for chemical reactions due to its low viscosity (high flow) and its ability to dissolve
many solutes.

 It is involved in temperature regulation as you lose body heat through sweating.

Properties of water

 It is transparent. This allows light to reach aquatic plants and algae.

 It is a versatile solvent as it can dissolve different kinds of solutes because of its polarity and ability to
form hydrogen bonds easily with polar and charged solutes.

 It has low viscosity. Viscosity is the measure of a fluid's resistance to flow. The low viscosity of water
makes it an ideal medium for chemical reactions because the particles can move around and come
easily into contact with each other.

 It has a high surface tension; the surface of water acts as a thin elastic sheet. This property of water
is due to the strong hydrogen bonding between the water molecules at the surface and the molecules
from the sides of a mass of water. The high surface tension of water enables small animals like water
strides to walk on water easily.

 It has a high specific heat capacity as it takes a lot of energy to heat water up. Water also loses heat
quite slowly. As a result, water stays more or less the same temperature. This is very important to
aquatic organisms as the function of their enzymes is affected by changes in temperature.

 It has a high latent heat of vaporization; it takes a lot of heat to vaporize liquid water. As a result,
water bodies like ponds do not dry up too quickly in hot weather. This property also helps us lose a lot
of body heat while sweating during a hot day.
 Ice is less dense than liquid water. This is because water expands when it freezes.

Organic molecules
 Organic molecules are molecules of carbon and hydrogen. The carbon atoms are covalently bonded
to hydrogen atoms (C-H bonds).

 Many of the organic compounds in living cells are so large that they are known as macromolecules.

 Most macromolecules are formed by a process known as polymerization, a process by which smaller
units, or monomers, join together to form large compounds, or polymers.

 Biologically important groups of organic molecules include carbohydrates, lipids, proteins and nucleic
acids (RNA and DNA).

Carbohydrates
 They contain carbon, hydrogen and oxygen atoms, usually with a hydrogen-oxygen atom ratio of 2:1.
The general formula of carbohydrates is (CH2O)n, where n > 3.

Importance of carbohydrates

 They are the main source of energy for the body. Glucose is the main respiratory substrate of most
organisms.

 They are convenient for storing energy. Starch is the main carbohydrate energy store in plants.
Glycogen is the only carbohydrate energy store in animals.

 Some carbohydrates are used to build structures. Structural carbohydrates include:

⇒⇒ cellulose, which is the main constituent of plant cell wall

⇒⇒ chitin, which occurs in cell walls of fungi and in the exoskeleton of insects
⇒⇒ peptidoglycan, which occurs in bacterial cell wall
Classification of carbohydrates

 Carbohydrates are generally classified into three based on the number of sugar units they are made
from.  These are monosaccharides, disaccharides and polysaccharides.

Monosaccharides
 Monosaccharides are the simplest carbohydrates that contain only one sugar unit. Examples include
glyceraldehyde, dihydroxyacetone, ribose, deoxyribose, ribulose, glucose, galactose and fructose.
Classification of monosaccharides                 
 Monosaccharides are classified according to how many carbon atoms are present in the molecule.
These include triose, pentoses and hexoses.

Trioses
 Trioses contain 3 carbon atoms, with the chemical formula C3H6O3.
 The two naturally occurring trioses are glyceraldehyde and dihydroxyacetone. They are important in
cellular respiration.

 Each triose has the same number of each kind of atom, but the atoms are put together in a different
way. They are isomers of each other. Isomers are compounds that have the same chemical formula
but different arrangement of atoms.                  

Pentoses
 Pentoses have five carbon atoms - C5H10O5. Examples include ribose, deoxyribose and ribulose.
They are isomers of each other. Ribose occurs in RNA, coenzymes and ATP molecules, and
deoxyribose occurs in the DNA molecule.

Hexoses
 Hexoses have six carbon atoms - C6H12O6. Examples include glucose, galactose, mannose and
fructose. They are isomers of each other.

Functional groups of monosaccharides

 There are two functional groups in monosaccharides. These are the aldehyde group, with the formula
(-CHO) and the ketone group, with the formula (C=0). A functional group is a group of atoms
responsible for the reactions of a particular compound.

 Monosaccharides are also classified as aldoses or ketoses based on the functional group that they
possess.

Aldoses
 Aldoses contain an aldehyde functional group. Examples include glyceraldehyde, ribose, glucose and
galactose.

Ketones
 Ketones contain a ketone functional group. Examples include dihydroxyacetone, ribulose and
fructose.

Structures of monosaccharides
 The structures of monosaccharides appear in straight chain and ring forms. The straight chain
structures are often changed into ring forms when they are in solution.

 The straight form of glucose produces two ring forms, namely, a-glucose and b-glucose.

 The straight chain form of fructose produces only one ring form.

Disaccharides
 Disaccharides are carbohydrates which are formed from two monosaccharides joining together.
Examples include maltose, sucrose and lactose.

⇒⇒ Maltose (malt sugar) is formed from two α-glucose molecules.

⇒⇒ Sucrose (table sugar) is formed from an α-glucose molecule and a fructose molecule.
⇒⇒ Lactose (milk sugar) is formed from a β-glucose molecule and a β-galactose molecule.

 Disaccharides are formed from monosaccharides by a type of reaction called condensation.

Condensation is the process in which two small molecules combine to form a large molecule,
producing a smaller molecule (often water) as a by-product. The bond that holds the two
monosaccharide units together is called glycosidic bond.

C6H12O6+C6H12O6⟶C12H22O11+H2OC6H12O6+C6H12O6⟶C12H22O11+H2O

 A molecule of water is formed from a hydroxyl group from one monosaccharide and hydrogen atom
from the other.

Polysaccharides (Complex sugars)

 Polysaccharides are complex and stable carbohydrates whose molecules consist of many hundreds
of monosaccharide molecules bonded together in a condensation reaction. Examples include starch,
glycogen, cellulose and chitin.

Some importance of polysaccharides

 Some are storage molecules. Examples are starch in plants and glycogen in animals.

 Others are structural carbohydrates. These include cellulose, chitin and peptidoglycan.
Starch
 Starch is a plant storage polysaccharide containing two polymers of α-glucose called amylose and
amylopectin.

 Amylose is a straight chain polymer of α-glucose molecules joined by α-1,4-glycosidic bonds. It gives
a blue black color in iodine solution.

 Amylopectin is a branched polymer of α-glucose molecules joined by α-1,4-glycosidic bonds and α-

1,6-glycosidic bonds. The α-1,6-glycosidic linkages cause the branched structure of amylopectin. The
side branches of amylopectin allow it to be quickly hydrolyzed by enzymes.

Glycogen
 Glycogen is a branched, storage polysaccharide in animals having α-1, 4-glycosidic linkages and α-
1,6-glycosidic linkages.

How the structures of starch and glycogen are suited

to their functions
 Starch and glycogen are ideal for storing energy because they are very compact, insoluble and have
side chains that can be quickly hydrolyzed by enzymes.

Cellulose
 Cellulose is a straight chain polymer of β-glucose molecules joined by β-1,4-glycosidic bonds.

 Cellulose microfibrils are formed when many cellulose molecules are bind together by hydrogen
bonds. This fibrous nature of cellulose gives the plant cell walls their strength.

What are lipids?

 Lipids are organic molecules made from fatty acids and alcohols. They contain the elements carbon,
hydrogen and oxygen, with much less oxygen than carbohydrates. Examples of lipids include
triglycerides, phospholipids and waxes.

 Lipids are the most efficient energy store in body as they provide over twice as much energy as
carbohydrates.

mportance of lipids
 They store energy, provide insulation and buoyancy, make up cell membranes, provide building
blocks for hormones and form water-repellent layers on leaves and feathers (waxes).

Triglycerides
 A triglyceride molecule is an ester formed from one molecule of glycerol and three fatty acid
molecules. A fatty acid molecule consists of a hydrocarbon chain joined to a carboxyl functional
group.

 Fatty acid molecules can be either saturated (all carbon–carbon bonds are single), monounsaturated
(one carbon–carbon double bond) or polyunsaturated (more than one carbon–carbon double bond).

How are triglycerides formed?

 Triglycerides are formed when three fatty acids are joined to a glycerol molecule in a condensation
reaction. The bond formed between the carboxyl group of a fatty acid and the hydroxyl group of a
glycerol molecule is called ester bond.

Phospholipids
 A phospholipid molecule consists of two fatty acids and a phosphate group bonded to a molecule of
glycerol. The phosphate group gives the molecule a hydrophilic (water-loving) ‘head’ and the fatty
acids give the molecule hydrophobic (water-hating) ‘tails’. Phospholipid bilayers are the basis of
biological membranes.

Waxes
 Waxes are lipids formed from fatty acids and long-chain alcohols in a condensation reaction.

Proteins
 Proteins are polymers of amino acids. They contain carbon, hydrogen, oxygen and nitrogen. Amino
acids have two functional groups – the amino group (–NH 2) and the carboxyl group (–COOH), as well
as an '' R'' group, which can be an element or a hydrocarbon chain.

Importance of proteins
 They are structural components of the cell membrane as ion channels, transport proteins and
receptors.
 They are used in the immune system as antigens and antibodies.
 They control the rate of chemical reactions as enzymes.
 They are the structural components of chromosomes. The protein histone covers the DNA molecule.

How are proteins formed?

 Proteins are formed from amino acids when they join together in a condensation reaction. A peptide
bond is a covalent bond formed between two amino acids when the carboxyl group of one amino acid
reacts with the amino group of the other amino acid, releasing a molecule of water ( H2O).

 A polypeptide is a linear polymer consisting of many amino acids bonded together in a long chain.

Structures of proteins
 Proteins have several levels of structure:

⇒⇒ The primary structure is the linear sequence of amino acids in a polypeptide chain.
⇒⇒ The secondary structure is formed by the folding of the primary structure into either an α-helix or a β-
pleated sheet, which are held together by hydrogen bonds.
⇒⇒ The tertiary structure is the three-dimensional folding of the secondary structure into fibrous (string-
like) or globular (ball-like) shape due to further bonding of the side chains or R groups by hydrogen
bonds, disulphide bridges and ionic bonds.
⇒⇒ The quaternary structure is formed when two or more polypeptide chains, each with a tertiary
structure, are bonded together. Examples of proteins with quaternary structures include hemoglobin with
4 polypeptide chains and collagen with 3 polypeptide chains.

 Based on their molecular shapes, proteins can be fibrous or globular. Fibrous proteins like collagen
and keratin have string like shape. Globular proteins like enzymes and receptor proteins have ball like
shape.

Nucleic Acids

 Nucleic acids are biological molecules made from structures called nucleotides. Examples are RNA
and DNA.

 DNA is the genetic material found in the chromosomes. It is a huge molecule that contains the genes
that determine the features of organisms. A gene is a short section of DNA that codes for a specific
protein and, as a result, determines a particular feature.

 DNA has two strands which wound into a double helix.

 RNA is a single-stranded nucleic acid found both in the nucleus and the cytoplasm. It comes in
different types-messenger RNA, transfer RNA and ribosomal RNA.

 RNA carries the genetic code from the DNA in the nucleus to the ribosomes in the cytoplasm and
allows protein synthesis.

 DNA and RNA are polymers of nucleotides.

 A nucleotide contains a phosphate group, a pentose sugar and a nitrogenous base.

       Table: The differences between DNA and RNA

  

Food Test
Iodine test for starch: Starch reacts with a solution of iodine to give a blue-black color.
Test for reducing sugars: Reducing sugars like glucose, fructose, maltose and lactose react with
Benedict’s solution when heated to give a yellow/orange/red precipitate.
Biuret test for protein: Proteins react with Biuret reagent to give a mauve/purple color.
Emulsion test for lipids: It produces a milky-white color in water.

Unit-3: Enzymes
3.1 Nature of Enzymes

What are enzyme molecules like?

 An enzyme is a globular protein with a unique tertiary structure, which gives it a unique shape and a
uniquely shaped active site.

 Active site is the part of an enzyme that binds with its substrate.
 Substrate is a substance upon which an enzyme acts in a biochemical reaction. During a reaction, a
substrate binds with the active site of an enzyme to form an enzyme-substrate complex.

 Enzyme-substrate complex is the intermediate formed, temporarily, when an enzyme binds to its
substrate.
           E+S⟶ES⟶P+EE+S⟶ES⟶P+E    
 E = enzyme    S = substrate   ES = Enzyme-substrate complex     P = product

Properties of enzymes
 All enzymes are globular proteins.
 They are biological catalysts: they speed up a reaction.
 They catalyze chemical reactions without being charged or used up.
 They can be used over and over again.
 They lower the energy needed for reactions to take place.
 They are specific: they catalyze one reaction only.
 They are affected by pH, temperature, the concentration of their substrate and the presence of
inhibitors.

What are catalysts?

 A catalyst is a substance that speeds up a reaction; the reaction itself is unaltered. There is no
overall change to:

⇒⇒  the catalyst itself

⇒⇒  the nature of the products
⇒⇒  the energy change that takes place during the reaction

 Not all catalysts are proteins. Some RNA molecules can catalyze some biological reactions.

Why are enzymes specific?

 Enzymes are specific because they have a uniquely shaped active site. The conformation of the
active site (the way in which it is shaped) allows an enzyme to bind to only a certain substrate or
combination of substances. 

How do we name and classify enzymes?

 Different enzymes are named in different ways:

⇒⇒  by adding the suffix – ase to the name of the substrate; e.g. sucrase, lipase, urease, etc.
⇒⇒  by the type of reaction that they catalyze; e.g. polymerase, dehydrogenase, etc.
⇒⇒  by the source from which they were first identified; e.g. papayin, intestinal protease, etc.
⇒⇒  by ending the name of the enzyme with 'in', indicating that they are proteins; e.g. pepsin, trypsin,
erypsin, etc.

Some enzymes and the reactions that they catalyze

 Proteases: enzymes that act on proteins. Examples include Pepsin, trypsin and erypsin
 Carbohydrases: enzymes that act on carbohydrates. Examples include maltase, sucrase, lactase
and cellulase
 Lipase: an enzyme that hydrolyzes lipids
 ATPase: an enzyme that hydrolyzes ATP
 Dehydrogenase: an enzyme that removes hydrogen ions from a substance
 Polymerase: an enzyme that joins monomers to form a polymer

Enzyme classification and the systematic

nomenclature of enzymes
 Enzymes are grouped into six based on the type of reactions that they catalyze:

1. Oxidoreductases — transfer of hydrogen and oxygen atoms or electrons from one substrate to
another. E.g. Dehydrogenases and oxidases
2. Transferases — transfer of a specific group (a phosphate or methyl, etc.) from one substrate to
another E.g. Transaminases and Kinases
3. Hydrolases — hydrolysis of a substrate E.g. Esterases and digestive enzymes
4. Isomerases — change of the molecular form of a substrate E.g. Fumarases and
Phosphohexoisomerase and
5. Lyases — non -hydrolytic removal of a group or addition of a group to a substrate E.g. Decarboxylases
and aldolases
6. Ligases (Synthetase) — joining of two molecules by the formation of new bonds E.g. Citric acid
synthetase

 In a systematic naming of enzymes decided by the enzyme commission, each enzyme has a name
associated with numbers, such as EC 3.4.11.1. Each part tells us something about the enzyme.

What do Enzymes do for us?

 Some enzymes commonly used in industries include:

⇒⇒  Biochymosin: It is used to produce cheese.

⇒⇒  Lactase: It is used to produce lactose-free milk.
⇒⇒  Proteases, lipases and amylases: They are used in biological washing powders to remove
biological stains. Proteases and amylases are also used in dishwasher detergents. In textiles, proteases
are used to remove hair whereas lipases are used to degrease animal hides.
⇒⇒  Cellulase: It is used in textiles to ‘bio-polish’ cotton fabrics and ‘bio-stone’ denim.
⇒⇒  Pectinase: It is used in food processing to clarify fruit juice.
⇒⇒  Glucose oxidase: It allows easy diagnosis of diabetes by testing urine
⇒⇒  Streptokinase: It is used to dissolve clots of heart-attack patients

3.2 Functions of enzymes

How do enzymes act as catalysts?
 In order for a chemical reaction to take place the reacting molecules must first collide and then have
sufficient energy to trigger the formation of new bonds.

 Activation energy is the energy which is required to produce a collision that is powerful enough to
start off a chemical reaction.

 An enzyme is able to catalyze a reaction by lowering the activation energy required for the reaction.
More reactants molecules can meet this lower energy requirement and so the reaction proceeds
more quickly.

How do enzymes lower activation energy?

 There are two models of enzyme action; the Lock-and-key model and the induced-fit-model.

1. Lock-and-key model — this model proposes that the shapes of the substrate molecules are
complementary (completely fit) to that of the active site. The complementary substrate molecule binds
with the active site of the molecule to form the enzyme-substrate complex. The complex causes the
reactants to enter a transition (intermediate) state in which the activation energy is lowered. However, the
model does not explain how the intermediate reduces activation energy. This model was first proposed by
a German biochemist named Fischer.
2. Induced-fit-model — this model suggests that the active site and the substrate are not naturally
complementary in shape, but the binding of substrate molecules produces a conformational change
(change in shape) in the active site that allows the substrate and active site to bind fully. In the induced-fit-
mode, the conformational charge of the active site puts the substrate molecules under tension, so they
enter a transitional state and are able to react due to the lowed activation energy. This model was
proposed by Koshland.

Why do some enzymes need cofactos?

 Holoenzyme is an active enzyme which is made from two molecules called apoenzyme and cofactor.
 Apoenzyme is the protein part of a Holoenzyme.
 Cofactor is a small non-protein particle of the Holoenzyme.
 Cofactors include mineral ions or coenzymes (organic molecules, usually derived from vitamins
which act as cofactors). NAD and FAD are coenzymes derived from the vitamins niacin and riboflavin
respectively.

3.3 Factors affecting the functions of enzymes

 The turnover rate is the number of molecules of reactants that form enzyme-substrate complexes
with each molecule of an enzyme per second.
 The turnover rate and, therefore, the activity of the enzyme are influenced by a number of external
factors including temperature, pH, substrate concentration and inhibitors.
 Enzymes work best within specific ranges of temperature and pH.
 Optimum temperature is the temperature at which an enzyme works most efficiently.
 Effect of temperature: Increasing the temperature generally increases reaction rates because the
molecules are moving more quickly and are more likely to come into contact with each other.
 The Effect of pH: Enzymes function in a narrow pH value. Significant changes in temperature and
pH denature enzymes.
 Denaturation is the alternation of the tertiary structure of a protein.
 The Effect of substrate concentration: Increasing the concentration of the substrates usually
increases the rate of enzymatic activities by increasing collusions among substrate molecules.
However, increasing the concentration beyond Vmax (the maximum rate of enzyme action) will have no
effect on the activity of an enzyme.

 The effect of enzyme concentration: increasing the concentration of an enzyme will increase the
reaction time. However, this will not increase the activity of the enzyme.

How do other substances affect enzyme activity?

 Inhibitors are substances that bind to enzymes and prevent them from forming enzyme-substrate
complexes. There are two types of inhibitors:

1. Irreversible inhibitors bind strongly to enzymes, usually by covalent bond, permanently altering the
structure of the enzyme molecule and inactivating it. . 
2. Reversible inhibitors bind to enzymes only weakly and the bond that holds breaks easily releasing
the inhibitor. This allows the enzyme to become active again.
There are two main kinds of reversible inhibitors; competitive inhibitors and non-competitive inhibitors.
Competitive inhibitors are molecules that inhibit enzyme activity by competing with the substrate for the
active site. They have shapes that are complementary to all, or part, of the active site of an enzyme. In
competitive inhibition, increasing substrate concentration decreases the effect of the inhibitor.
Non-competitive inhibitors are molecules that alter the conformation of the active site by binding with
the allosteric sites of the enzymes; they prevent the substrates from binding and inhibit enzyme activities.
They do not compete with the substrates for the active site. In non-competitive inhibition, increasing
substrate concentration has no effect on the effectiveness of the inhibitor.
Allosteric site is a binding site on an enzyme other than the active site.

How do inhibitors control enzyme activity in living cells?

 Many substances are produced in cells as a result of a metabolic pathway (a series of reactions),
controlled by different enzymes.        

 Inhibition of any enzyme in a metabolic pathway will interrupt the whole process.

 In some metabolic pathways in living cells, the end product of a pathway acts as a non-competitive
inhibitor of the enzyme that catalyzes the first stage of the series.

 End-product inhibition is a type of enzyme inhibition that occurs when an end product inhibits the
enzyme controlling the first stage of a reaction sequence.
 When the end product is required by the cells, it will be removed by a chemical substance; so it stops
acting like an inhibitor.

 Activator is a substance that removes an inhibitor.

  

Unit-4: Cell biology

 Cells are the smallest building units of living organisms.

 Living organisms can be unicellular (one-celled) or multicellular (many celled).

4.1 The Cell Theory

 Cell theory is a collection of ideas which describes the cells.

A timeline for the development of the 

cell theory          
 1665 Robert Hooke: the first person to see and describe cells. He saw dead cells of the cork tissue
using one of the earliest compound microscope.

 1674 Anton Van Leeuwenhoek: the first person to see living cells. He saw moving unicellular
organisms (protoctistans), bacteria, blood cells and spermatozoa for the first time using a simple
microscope with only one lens.

 1824 Rene Dutrochet: the first man to state that all organisms are made up of cells.

 1839 Matthias Schleiden and Theodor Schwann: they put forward the first clearly stated cell
theory. It stated that:

1. The cell is the unit of structure, physiology and organization in living things.
2. The cell retains a dual existence as a distinct entity, and a ‘building block' of organisms.
3. Cells form by free-cell formation (spontaneous generation); this idea was later disproved.

 1858 Rudolf Virchow: the first person to state that a cell can only arise from another cell like it. 
 The first two accepted ideas of Schleiden and Schwann, and the idea forwarded by Virchow are the
fundamental tenets of modern cell theory.

 Modern cell theory includes the following main ideas:

1. All known living things are made up of cells.

2. The cell is a structural and functional unit of all living things.
3. All cells come from pre-existing cells by cell division.
4. Cells contain hereditary information which is passed from cell to cell during cell division.
5. All cells have basically the same chemical composition.
6. All energy flow (the metabolism and biochemistry of life) occurs within cells.  

4.2 Types of cells

 Cells can be grouped into two types based on their structure and complexity; prokaryotic cells and
eukaryotic cells.

Prokaryotic cells
 They are believed to be the first type of cells to be formed when life first evolved.
 They are small (1-10µm) and simple cells that lack distinct nucleus and membrane-bound organelles.
 They have cell wall, cell membrane, cytoplasm, ribosomes and genetic material (DNA). Their DNA is
arranged in a circular loop and their ribosomes are smaller than those present in eukaryotic cells
(70S).
 Archaebacteria and eubacteria are prokaryotic cells.

Eukaryotic cells
 They are cells that have distinct nucleus and membrane-bound organelles.
 They are much larger (10-100µm) and more complex cells than prokaryotic cells.
 They have linear DNA associated with histone proteins to form chromosomes.
 They have larger ribosomes than those present in prokaryotic cells (80S).
 They have sub-cellular structures called organelles. The nucleus, mitochondria, chloroplast, vacuole,
endoplasmic reticulum, Golgi apparatus and lysosomes are membrane-bound organelles. On the
other hand, ribosomes and centrosomes are membrane less organelles.
 Protozoa, fungal cells, algal cells, plant cells and animal cells are all eukaryotic cells.

How did eukaryotic cells originate?

 Endosymbiont theory is an evolutionary theory which states that the various organelles in eukaryotic
cells, such as mitochondria and chloroplast, were once free living prokaryotic cells that were ingested
by a large anaerobic prokaryote. This theory was first proposed by the biologist Lynn Margulis.
Steps of endosymbiont theory:
1. An ancestral prokaryotic cell developed foldings from its cell membrane.
2. The foldings eventually pinched off the cell membrane and formed the endoplasmic reticulum, Golgi
body and the nuclear membrane.
3.   The primitive cell with the nucleus engulfed smaller aerobic prokaryotic cells. The engulfed
prokaryotes developed into the mitochondria of the eukaryotic cells. These aerobic, heterotrophic cells
evolved through time into animal, fungal and protoctistan cells.
4.   Some of the cells with their ‘primitive mitochondria’ also engulfed other, smaller, photosynthetic
prokaryotes. In time, these engulfed cells developed into chloroplasts. Through time, these cells with
chloroplasts evolved into plant cells.

4.3 Parts of the cell and their functions

 Eukaryotic cells have three major parts. They are cell membrane, nucleus and
cytoplasm.                                                                       
 Cell membrane (plasma membrane) is the thin, flexible, semi-permeable membrane that separates
the interior of a cell from the outside environment (the extracellular space).

Importance of the cell membrane

⇒⇒  It functions as a selectively permeable membrane, controlling what enters and leaves the cell.
⇒⇒  It provides support and keeping the cell’s form.
⇒⇒  It allows cell signaling and communication.

Structure of the cell membrane

 There are several models which explain the structure of the cell membrane.

       The Davson–Danielli model and the fluid mosaic model are two such models.

The Davson–Danielli model

 This model was proposed in 1935 by Hugh Davson and James Danielli.  
 The Davson–Danielli mode suggested that the cell membrane consists of a phospholipid bi-layer
covered on both surfaces with thin sheets of proteins. They also suggested the presence of protein-
lined pores through the phospholipid bilayer. However, the model could not properly explain how
molecules move across the membrane.

The fluid mosaic model

 It is a widely accepted model introduced by S. Singer and G. Nicolson in 1972.
 The fluid mosaic model states that the cell membrane is a flexible membrane made up of a
phospholipid bilayer with cholesterol, protein and carbohydrate molecules embedded in it. It is a
mosaic of different components dispersed in a fluid bilayer of phospholipid.
 Components of the cell membrane in the fluid mosaic model include the following:

⇒⇒   Phospholipid bilayer, which is the basis for the membrane

⇒⇒   Membrane proteins: the cell membrane has two groups of membrane proteins; integral proteins
and peripheral proteins.
1. Integral (intrinsic) proteins: these are proteins firmly embedded within the phospholipid bilayer. The
majorities are trans-membrane proteins, which span the entire cell membrane. There are two main types
of integral transport proteins:

⇒⇒   Channel proteins: integral proteins with pores which allow ions to pass through the membrane
⇒⇒  Carrier proteins: integral proteins that bind to specific solutes and transfer them across the lipid
bilayer by undergoing conformational changes. They move medium-sized molecules through the
membrane by facilitated diffusion or active transport.
Pumps are carrier proteins that move ions across the cell membrane in active transport.
2. Peripheral proteins: proteins that span only one layer of the cell membrane. They are not embedded
in the lipid bilayer at all; they are loosely bound to the outer or inner surface of the membrane. Some are
enzymes, while others anchor integral proteins to the cytoskeleton.

 Glycoproteins and glycolipids: protein and lipid molecules that have carbohydrate chains attached
to them. They are always found on the outside surface of a cell and serve as signals to other cells,
allowing cell to cell communication or act as receptor sites for hormones and drugs.

 Cholesterol: A sterol lipid found between phospholipids. It reduces the fluidity of the phospholipids
and stabilizes the structural integrity of the cell membrane.

ow do substances cross the plasma membrane?   

 Substances cross the plasma membranes in two main ways; passive transport and active transport.

1. Passive transport: the movement of substances along or down the concentration gradient (from
an area of higher concentration to an area of lower concentration) using only the kinetic energy of
the particles of substances. They need no extra energy from the cell's metabolism.

Examples include simple diffusion, facilitated diffusion and osmosis.

2. Active processes: the movement of substances across the cell membrane up or against the
concentration gradient (from an area of lower concentration to an area of higher concentration)
using the energy from the cell's metabolism in the form of ATP. Examples include endocytosis
(phagocytosis, pinocytosis and receptor-mediated endocytosis) and exocytosis.

Simple diffusion
 Simple diffusion is the net or overall movement of particles down the concentration gradient until the
particles are distributed uniformly throughout the available space.
 For simple diffusion to take place there must be a concentration difference between the two regions.
It does not necessarily require membrane to move particles.

 Simple diffusion occurs until the two concentrations are the same. Once the two concentrations are in
equilibrium (have the same concentration), the particles will move equally in both directions, so there
will not be net movement of the particles.

 To pass through the plasma membrane by simple diffusion, particles must be small, lipid-soluble and
non-polar (non-charged).

Factors affecting the rate of simple diffusion

 Diffusion occurs faster at bigger concentration gradient, larger surface area and higher temperatures.
However, a longer diffusion distance results in slower diffusion.

Facilitated diffusion
 Facilitated diffusion is the passive movement of ions and medium-sized particles through channel
proteins with an ion pore, or a carrier protein.

 Like simple diffusion, facilitated diffusion depends on a concentration gradient to move particles and
always takes place down the concentration gradient. However, the particles must be helped to diffuse
across the cell membrane by a channel protein or a carrier protein.

 Increase of temperature, concentration gradient and the number of channel proteins or carrier
proteins on the cell membrane increases the rate of facilitated diffusion. However, facilitated diffusion
is not affected by the surface area of the membrane.

Osmosis 

 Osmosis is the movement of water from a system with a higher (less negative) water potential to a
system with a lower (more negative) water potential across a partially permeable membrane.

 Water potential refers to the concentration of water molecules. Pure, liquid water has a higher water
potential than any other system. The water potential of water is zero. All other systems have a water
potential that is lower than that of water; thus, their water potential values are negative.

 Osmosis is a special type of diffusion where only water moves across a partially permeable
membrane. For osmosis to take place, there must be a difference in water potential between two
systems, and the two systems must be separated by a partially-permeable membrane, which allows
the movement of water molecules, but not the solutes dissolved in it.
Factors affecting the rate of osmosis
 Osmosis occurs faster at bigger difference in water potential, larger surface area of the membrane
and higher temperatures. However, the longer the distance the water molecules must travel, the
slower the rate of osmosis.

What happens to cells placed in solutions of different

concentrations?
 When comparing the water potential of a solution to that of a cell, the solution surrounding the cell
could be:

* *   Isotonic — having the same water potential as the cell

* *   Hypertonic — having a lower (more negative) water potential than the cell
* *   Hypotonic — having a higher (less negative) water potential than the cell    

Animal cells
 In a hypertonic solution, animal cells lose water by osmosis and shrink.
 In a hypotonic solution, animal cells gain water by osmosis and swell up. If the cells continue to gain
water by osmosis, they eventually burst. The bursting of animal cells when they gain too much water
by osmosis is called cytolysis (Hemolysis refers to the bursting of red blood cells).

 In an isotonic solution, animal cells neither gain nor lose water by osmosis. Thus, they retain their
original shape and weight.

Plant cells
 In a hypertonic solution, the cytoplasm of plant cells loses water by osmosis and shrinks. The cells
become much less rigid and are said to be flaccid. If the cells continue to lose water by osmosis,
eventually the cytoplasm pulls away from the cell walls and the cells are said to be plasmolysed.

 In a hypotonic solution, plant cells gain water by osmosis, making the cytoplasm swell and press
against the plant cell walls. The cells become hard and rigid, and are said to be turgid. Turgidity
keeps the leaves and stems of plants rigid and firm so that they are able to stand upright. Unlike
animal cells, plant cells in hypotonic solution cannot become much larger and burst because of the
presence of the cell wall.

 In an isotonic solution, plant cells neither gain nor lose water by osmosis. Thus, they retain their
original shape and weight.

Active transport
 Active transport is the movement of ions, medium-sized and non-lipid soluble particles across the cell
membrane against a concentration gradient. This process involves using carrier proteins (pumps)
and  metabolic energy (ATP).

Endocytosis
 Endocytosis is the process by which large particles are engulfed by the plasma membrane that
invaginates and forms a vesicle. This process requires ATP to move the membrane around the
particles to form the vesicle.

 In endocytosis, particles can be ingested either from a higher concentration to a lower concentration
or from a lower concentration to a higher concentration.

Types of endocytosis
* *   Phagocytosis: the process of engulfing very large particles or even whole organisms by creating
pseudopodia (extensions of the plasma membrane)
* *   Pinocytosis: the process of engulfing small particles by using part of the cell membrane. Unlike
phagocytosis, pinocytosis does not require the formation of large pseudopodia to engulf the particles.
* *   Receptor-mediated endocytosis: the process of ingesting particles by using part of the cell
membrane that infolds only in regions where particles bound to specific receptors.

Exocytosis
 Exocytosis is the process of secreting large particles out of a cell by using ATP and a secretory
vesicle formed in the cell. The secretory vesicle merges with the cell membrane to release the
substance. It is the process by which enzymes and hormones are secreted. ATP is used to alter the
configuration of the membrane.

 In exocytosis, particles can be secreted either from a higher concentration to a lower concentration or
from a lower concentration to a higher concentration.

The other cell organelles—what are they like and what do they do?
Nucleus-The “brain” of a cell

 The nucleus is the part of a cell which controls all the activities of the cell. It typically occupies about
10% of the volume of a cell.

 The nucleus has three main components:

✓✓  The nuclear envelope: it is a semi-permeable, double membrane that surrounds the nucleus. It

has many nuclear pores, which allow the passage of molecules between the nucleus and the cytoplasm.
✓✓ The nucleolus: it is a membrane less organelle within the nucleus which synthesizes the
components of ribosomes.
✓✓  Chromatin: it consists of DNA molecules bound with proteins called histones. Just before a cell is
about to divide, the loosely dispersed chromatic fibers condense into distinct, recognizable structures
called chromosomes.                 
Mitochondria-The power houses of a cell

 Mitochondria are rod-shaped organelles that carry out most of the reactions of aerobic respiration.
They are surrounded by a semi-permeable double membrane.

 The inner membrane is folded into cristae to increase the available surface area for reactions. Some
of the reactions of aerobic respiration take place in the fluid matrix.

Ribosomes-The protein factories of a cell

 Ribosomes are tiny, membrane less structures in a cell which are essential for protein synthesis.
They can be found free in the cytoplasm, but are also bound to the membrane system of the rough
endoplasmic reticulum.

 Each ribosome comprises two subunits that are made from RNA and protein. The subunits are
manufactured in the nucleolus.

Endoplasmic reticulum (ER)-The transport system of a cell

 Endoplasmic reticulum is a three-dimensional system of tubules found throughout the cytoplasm of

eukaryotic cells.

 There are two types of endoplasmic reticulum:

* *  Rough ER: it has ribosomes on its surface and is responsible for the manufacture and transport of
proteins. Rough ER is extensive in cells that manufacture a lot of protein, such as cells that manufacture
enzymes to be secreted into the lumen of the intestine.
* *   Smooth ER: it has no ribosomes on its surface. It is concerned with the synthesis of lipids,
carbohydrate metabolism and detoxification.
Golgi apparatus (or Golgi body)

 The Golgi apparatus is a stack of membrane-bound sacs in a cell. It is involved in sorting, modifying,

tagging, packaging and distribution of cell products like proteins and lipids.

Lysosomes-The “suicidal bags” of a cell

 Lysosomes are small sacs containing powerful digestive enzymes that break down cellular wastes
and debris. They have no specialized internal structure and are surrounded by a single membrane.
Lysosomes are formed in the Golgi apparatus.

Cell wall
 The cell wall is a tough, non-living and freely permeable outer covering of plant cells, fungal cells and
bacteria. It provides strength and protection to the cells. The cell wall is also important in maintaining
the shapes of cells.

Vacuole

 The vacuole in a plant cell is a fluid-filled sac that stores a range of solutes. It is also important in
maintaining the turgidity of a cell.

Chloroplast

 The chloroplast is an oval-shaped organelle found in the cells of autotrophic eukaryotes, such as
plants and algae. Like the mitochondrion, the chloroplast is bounded by a double membrane;
however, the inner membrane is not folded.

 There are two main regions in chloroplasts that are linked to the stages of photosynthesis:

* *   Grana (singular: granum): they are stacks of thylakoids containing chlorophyll. This is where the
light-dependent reactions of photosynthesis occur.
* *   Stroma: it is a thick fluid in between grana, where the light-independent reactions of photosynthesis
occur.

How have biologists been able to study the different organelles?

 Cell fractionation is a technique for separating cellular components into layers by spinning them in a
centrifuge at different speeds for an extended period.

 Cell fractionation separates cellular organelles based on their densities. After being centrifuged, the
densest organelle settles first to the bottom of the test tube, whereas the least dense organelle settles
last at the top of the suspension.

 The order of settlement of the organelles in a centrifuged mixture, from the bottom (the densest
organelle that settles first) to the top (the least dense organelle that settles last), is as follows:
nucleus, chloroplast, mitochondrion, endoplasmic reticulum and ribosome.
Unit-5: Energy transformation
5.1 Cellular Respiration

 Cellular respiration is the metabolic pathway that converts the biochemical energy stored in nutrients,
such as glucose, into usable energy in the form of adenosine triphosphate (ATP). The reactions
involved in cellular respiration are catabolic reactions, which break large molecules into smaller ones,
releasing energy in the process. Cellular respiration is therefore an exergonic process that releases
energy from food molecules.

 Respiratory substrates are organic molecules that can be respired. Glucose is the most commonly
respired substrate in living organisms.

 Although cellular respiration technically includes both aerobic and anaerobic processes, the term is
commonly used to refer only to the aerobic process.

         What is ATP?

 ATP (Adenosine Tri-Phosphate) is the single energy providing and energy storing molecule for all the
processes in living cells. It is sometimes described as a phosphorylated nucleotide because ATP is
the adenine nucleotide with two extra phosphate groups added on.

 ATP is formed in both photosynthesis and cellular respiration.

ADP+Pi+ energy ⟶ATPADP+Pi+ energy ⟶ATP          

 When energy is required for cellular work, ATP is broken down in a hydrolysis reaction.

 ATP + water ⟶ ADP +P+ Energy  ATP + water ⟶ ADP +P+ Energy 

 Cellular processes that require energy from ATP include the synthesis of macromolecules – such as
proteins, active transport across a plasma membrane, muscle contraction, conduction of nerve
impulses and the initial reactions of respiration.

  How is ATP produced in respiration?

 In respiration, ATP can be produced either in the presence of oxygen (aerobic respiration) or in the
absence of oxygen (anaerobic respiration and fermentation).

How is ATP produced in aerobic respiration?

 In aerobic respiration, ATP is produced either by oxidative phosphorylation or by substrate level

phosphorylation.
 Oxidative phosphorylation is the oxygen-dependent production of ATP from ADP and inorganic
phosphate (Pi) using the enzyme ATP synthase. The hydrogen ions released from glucose are used
to spin the rotor of the ATP synthase in a way that catalyzes ATP production. Oxidative
phosphorylation produces about 90% of the ATP produced in aerobic respiration.

 Substrate level phosphorylation is the production of ATP by using a molecule (substrate), such as
phosphoenol pyruvate, which transfers a phosphate group directly to ADP. This process does not
involve ATP synthase. Substrate level phosphorylation produces about 10% of the total ATP
produced in aerobic respiration.

How are hydrogen ions transferred from 

glucose to ATP synthase?
 Hydrogen ions released from glucose are transferred to NAD and FAD to produce NADH (reduced
NAD) and FADH2 (reduced FAD) respectively. NADH and FADH2 later release hydrogen ions that are
used to spin the rotor of ATP synthase.

         Cellular respiration

 There are 4 stages of cellular respiration:

1.   glycolysis
2.   the link reaction
3.   Krebs cycle (Citric Acid cycle)
4.   electron transport chain and chemiosmosis

         Glycolysis
 Glycolysis is the first stage of cellular respiration that converts glucose into two molecules of
pyruvate, a smaller molecule containing only three carbon atoms. It takes place in the cytoplasm.

 Glycolysis does not require oxygen and can occur under aerobic and anaerobic conditions.

Why is it necessary to convert glucose into pyruvate?

 The glucose molecule cannot diffuse through the mitochondrial membranes (it is a medium-sized
molecule and is not lipid soluble), and there are no carrier proteins to transport the glucose molecule
across the mitochondrial membranes.

What happens in Glycolysis?

 2ATP molecules are used to phosphorylate a glucose molecule. This makes the glucose more
reactive.
 The phosphorylated glucose is converted to fructose 1, 6 biphosphate.
 The fructose 1, 6 biphosphate is split into two molecules of the 3 carbon sugar glycealdehyde 3
phosphate (GP).
 Each GP is then converted into pyruvate, with the production of 2 ATP by substrate level
phosphorylation and one molecule of NADH.
 Since there are two molecules of GP, 2 molecules of pyruvate, 4 ATP molecules and 2 molecules of
NADH are produced from one molecule of glucose. As 2ATP molecules are used to phosphorylate
glucose, glycolysis produces a net of 2 ATP molecules.

 The summary of the overall reaction of glycolysis:

C6H12O6+2ATP+4ADP+2Pi+2NAD⟶2C3H4O3+2ADP+4ATP+2NADH+2H+
+2H2OC6H12O6+2ATP+4ADP+2Pi+2NAD⟶2C3H4O3+2ADP+4ATP+2NADH+2H++2H2O

The Advantage of Glycolysis

 The process is so fast that cells can produce thousands of ATP molecules in just a few milliseconds.

 The process does not require oxygen. This means that glycolysis can quickly supply chemical energy
to cells when oxygen is not available.

 Pyruvate and other products of glycolysis follow either of the two pathways of respiration (aerobic
respiration or anaerobic respiration) depending on the presence or absence of oxygen in the cell.

 The aerobic pathway of respiration

 When oxygen is available, the pyruvate and NADH “outputs” generated during glycolysis become the
“inputs” for the next processes of cellular respiration.

The link (transition) reaction

 The link reaction connects glycolysis to the citric acid (Krebs) cycle. It takes place in the fluid matrix of
the mitochondrion.

 Through the processes of dehydrogenation and oxidative decarboxylation, the link reaction converts
the two molecules of the 3-carbon pyruvate from glycolysis into two molecules of the 2-carbon
molecule acetyl Coenzyme A (acetyl-CoA) and 2 molecules of carbon dioxide. As the two pyruvates
undergo dehydrogenation and oxidative decarboxylation, two molecules of NAD+ become reduced to
2NADH + 2H+.

 In the link reaction, the conversion of each pyruvate into acetyl-CoA takes place in two steps:
Step 1: First, a carboxyl group of each pyruvate is removed as carbon dioxide.
Step 2: Then, the remaining acetyl group combines with coenzyme
A (CoA) to form acetyl-CoA.

 The overall reaction for the link reaction:

2 pyruvate +2NAD++2CoA⟶2 acetyl-CoA +2NADH+2H++2CO22 pyruvate +2NAD+
+2CoA⟶2 acetyl-CoA +2NADH+2H++2CO2

 Since two molecules of acetyl-CoA are produced from a glucose molecule, two Krebs cycles take
place to completely break down the glucose molecule.

The Krebs cycle (Citric acid cycle)

 The Krebs cycle or Citric acid cycle is a series of enzyme-catalyzed reactions occurring in the fluid
matrix of the mitochondria, where the complete oxidation of glucose takes place. In this cycle, the
acetyl-CoA molecules formed in the link reaction are oxidized to form carbon dioxide, NADH,
FADH2 and ATP molecules.

 The Krebs cycle was named after Hans Krebs, who postulated the detailed cycle. Since the first
compound produced in this cycle is citrate (citric acid), the Krebs cycle is also known as the citric Acid
cycle.

 The Krebs cycle involves several steps, each catalyzed by a unique enzyme.

Step 1: The Krebs cycle begins when the two-carbon acetyl group of acetyl CoA combines with the four-
carbon compound, oxaloacetate, to form a six-carbon compound, called citrate. In this reaction, the
original CoA is regenerated for further reaction with pyruvate.
Step 2: Citrate loses a carbon atom (decarboxylation) and a hydrogen atom (dehydrogenation) to form a
five carbon compound and CO2 is produced. By losing a hydrogen atom with its electron, citric acid is
oxidized. The hydrogen atom is transferred to NAD +, reducing it to NADH.
Step 3: The five-carbon compound formed in step 2 is then further decarboxylated to form a four-carbon
compound and CO2 is again produced; a molecule of ATP is also synthesized from ADP by substrate
level phosphorylation. Once again, NAD is reduced to NADH.
Step 4: The four-carbon compound formed in step 3 undergoes several molecular transformations to
regenerate the original four-carbon compound (oxaloacetate) and the cycle is complete and can begin
again with oxaloacetate reacting with another molecule of acetyl CoA.
During these oxidation reactions, FAD is reduced to FADH2 and NAD+ is reduced to NADH.

 A summary of the overall reactions of one complete Krebs cycle:

1CH3CO⋅CoA(1 acetyl-CoA )+3NAD++1FAD+1C4H2O2−5(1 oxaloacetate )+1ADP+1Pi 
from a 1CH3CO⋅CoA(1 acetyl-CoA )+3NAD++1FAD+1C4H2O52−(1 oxaloacetate )+1ADP+1Pi from a 
 substrate ⟶2CO2+3NADH+1FADH2+1ATP+3H++1CoA+1C4H2O2−5 substrate 
⟶2CO2+3NADH+1FADH2+1ATP+3H++1CoA+1C4H2O52−
 Since two molecules of acetyl-CoA formed in the link reaction enter the Krebs cycle, all the gains of
ATP, NADH and FADH2 from the Krebs cycle must be doubled to get the total gain from each
molecule of glucose.

 A summary of the overall reactions of the Krebs cycle for a single molecule of glucose:

2CH3CO⋅CoA(2 acetyl-CoA )+6NAD++2FAD+2C4H2O2−5(2 oxaloacetate )+2ADP+2Pi 
from a 2CH3CO⋅CoA(2 acetyl-CoA )+6NAD++2FAD+2C4H2O52−(2 oxaloacetate )+2ADP+2Pi from a 
 substrate ⟶4CO2+6NADH+2FADH2+2ATP+6H++2CoA+2C4H2O2−5

Electron transport chain (ETC)

 Electron transport chain is a series of electron carriers that eventually transfers electrons from NADH
and FADH2 to oxygen. It is the last stage of aerobic respiration.

 The electron transport chain and chemiosmosis together make up the process of oxidative
phosphorylation.

 The reactions of the electron transport chain and chemiosmosis take place on the inner mitochondrial
membrane.  On the citrate, the following events take place:

 The hydrogen atoms carried by NADH and FADH2 are released and split into protons (hydrogen ions)
and electrons. NADH is oxidized into NAD+ and FADH2 is oxidized into FAD. NAD+ and FAD are
regenerated for reuse in the first three stages of cellular respiration.

 The electrons pass along a series of electron carriers that form the transport chain; they lose energy
as they pass from one carrier to the next.

 Three of the electron carriers (NADH dehydrogenase, ubiquinone and cytochrome complex) are also
proton pumps that move protons (hydrogen ions or H +) from the matrix of the mitochondrion to the
inter-membrane space located between the inner and outer mitochondrial membranes.

 As electrons are transferred through these three proton pumps, the energy they lose powers the
pumps which move the protons into the inter-membrane space. Electrons from NADH make this
happen at all three pumps because it is dehydrogenated (oxidized) by the NAD dehydrogenase
complex. FADH2 is dehydrogenated by ubiquinone. So, electrons from reduced FAD only operate
ubiquinone and cytochrome complex proton pumps.

 At the end of electron transport chain, the electrons combine with protons and with oxygen to form
molecules of water. Because of this, oxygen is known as the terminal (final) electron acceptor.

 Because of the action of the proton pumps, protons accumulate in the inter-membrane space creating
a higher concentration there than in the matrix. This proton gradient results in protons diffusing
through the ATP synthase molecule (down the concentration gradient) causing the rotor and rod of
 the ATP synthase to rotate or spin. The mechanical energy from this rotation is converted into
chemical energy as phosphate is added to ADP to form ATP. The production of ATP using the
enzyme ATP synthase is called oxidative phosphorylation.

 The diffusion of hydrogen ions through the ATP synthase is called chemiosmosis.

 The oxidation of one molecule of NADH results in six protons passing through ATP synthase, and so
leads to the synthesis of three molecules of ATP.

 The oxidation of one molecule of reduced FADH 2 results in four protons passing through ATP
synthase, and so leads to the synthesis of just two molecules of ATP.

 The summary of the overall reaction of the electron transport system:

6NADH (from Krebs' cycle) + 2NADH (from glycolysis) + 2NADH (from the link
reaction) + 2FADH26NADH (from Krebs' cycle) +2NADH (from glycolysis) + 2NADH (from the link
reaction) + 2FADH2
 (fom Krebs cycle) +34 ADP +34 Pi-2ATP (used in proton
pumps) →32ATP+10NAD+2FAD
Anaerobic pathway of respiration

 If oxygen is absent, the products of glycolysis may enter the alcoholic fermentation pathway or lactic
acid fermentation pathway that yields no additional ATP.

 Alcoholic fermentation: Yeasts and a few other microorganisms undergo alcoholic fermentation,
which produces ethanol (ethyl alcohol) and carbon dioxide.

 A summary of alcoholic fermentation after glycolysis:

2 pyruvate +2NADH⟶2 ethanol +2CO2+2NAD+2 pyruvate +2NADH⟶2 ethanol +2CO2+2NA
D+

 A summary of anaerobic respiration in yeast cells:

C6H12O6 (glucose) ⟶2C2H5OH(2 ethanol) +2CO2+2ATPC6H12O6 (glucose) ⟶2C2H5OH(2 e
thanol) +2CO2+2ATP

 Lactate fermentation: Animal cells like muscle cells produce lactate (lactic acid) when they ferment
glucose. Unlike alcoholic fermentation, lactic acid fermentation does not give off carbon dioxide.

 A summary of lactate fermentation after glycolysis:

2 pyruvate +2NADH⟶2 lactic acid +2NAD+2 pyruvate +2NADH⟶2 lactic acid +2NAD+

 A summary of anaerobic respiration in animal cells:

C6H12O6 (glucose) ⟶2C3H6O3 (2 lactic acid) +2ATPC6H12O6 (glucose) ⟶2C3H6O3 (2 lactic

acid) +2ATP

5.2 Photosynthesis

 Photosynthesis is the anabolic process by which plants and other organisms convert light energy into
chemical energy stored in organic compounds like glucose. This process involves endergonic
reactions, which take in energy to drive the reduction of carbon dioxide to glucose and the oxidation
of water to oxygen.

Chloroplast
 The chloroplast is an organelle with a double membrane where photosynthesis takes place. It has
thylakoids and stroma. Thylakoids are flattened sacs which contain photosynthetic pigments. The
stroma is the liquid inside the chloroplast.

 In the membranes of thylakoids, photosynthetic pigments are arranged inphotosystems that are
linked to electron transport chains. There are two types of photosystems, photosystem I and
photosystem II.

 In the membranes of the thylakoids, the first photosystem, photosystem II, is linked to the second
photosystem, photosystem I, by the first electron transport chain. Photosystem I is also linked to the
second electron transport chain.

 In a photosystem, various photosynthetic pigments are clustered around the reaction center
chlorophyll a molecule, which is positioned next to the electron transport chain.

 The overall process of photosynthesis is made up of two stages, the light-dependent reactions and
the light-independent reactions. 

Light-dependent reactions

 These reactions take place in the presence of light in the membranes of the thylakoids.

        Main events of the light-dependent reactions

1. Light energy is used to excite electrons from the chlorophyll molecules of photosystems I and II.
2. The energy lost by the electrons emitted from photosystem II causes the transfer of protons to the
inside of the thylakoid membrane as they pass along the first electron transport chain; this
eventually leads to the chemiosmotic formation of ATP.
 3. The electrons emitted from photosystem I pass along the second electron transport chain. The
electrons react with hydrogen ions and NADP at the end of the second electron transport chain to
form reduced NADP.
4. Light energy also causes photolysis of water into hydrogen ions, electrons and oxygen in
photosystem II. The electrons of water replace the electrons lost from the chlorophyll molecules in
photosystem II.

The electrons lost by the chlorophyll molecules in photosystem I are replaced by the electrons that have
passed down the first electron transport chain from photosystem II.

 The ATP and reduced NADP produced in the light-dependent reactions are used to drive the
synthesis of carbohydrates in the light-independent reactions of photosynthesis. 

         Photophosphorylation
 Photophosphorylation is the formation of ATP powered by the energy in the photons of light. It can be
cyclic or non-cyclic.

 Cyclic photophosphorylation involves only photosystem I. The electrons lost from the chlorophyll
molecule are returned to it. Oxygen and reduced NADP are not formed during cyclic
photophosphorylation.

 Non-cyclic photo phosphorylation involves both photosystems I and II. The electrons lost from the
chlorophyll molecule are not recycled.

The light-independent reactions 

     (The Calvin cycle)
 These reactions occur in the stroma of the chloroplasts.
 The light-independent reactions can take place in the presence or absence of light.
 In the light-independent reactions, the ATP and NADP formed in the light-dependent reactions are
used to reduce carbon dioxide and synthesize glucose in a complex cycle of reactions in the Calvin
cycle.

        The main stages of the light-independent reactions

1. Carbon dioxide reacts with ribulose bisphosphate (RuBP) – a five-carbon compound in the stroma;
the reaction is catalysed by the enzyme Rubisco.
2. The reaction forms two molecules of a three-carbon compound GP.
3. Each molecule of GP is converted to TP (triose phosphate – another three-carbon compound); this
is a reduction reaction using hydrogen ions from reduced NADP and energy from ATP.
 4. Some of the TP formed is used to regenerate the RuBP (ATP is again required) whilst some is
used to form glucose and other useful organic compounds. TP is the basis for the synthesis of all
organic molecules.
5. Six turns of the Calvin cycle would give an output of two molecules of TP – enough to make one
molecule of glucose.

Are there any other ways of photosynthesizing?

1. C3 photosynthesis and photorespiration

 C3 photosynthesis is a photosynthetic pathway in which the first compound formed in the light-
independent reactions of the Calvin cycle is glycerate 3-phosphate (GP), which contains three carbon
atoms.  Although this pathway occurs in all photosynthetic plants, C 3 photosynthesis is especially
adapted to plants living in temperate environments, where there is moderate sunlight and
temperature.

 C3 photosynthesis is less efficient in hot and dry conditions. In these conditions, the leaves of plants
close their stomata to reduce water loss. This reduces the amount of carbon dioxide in the leaves. In
the low concentrations of carbon dioxide, Rubisco binds with oxygen and catalyzes the reaction
between oxygen and RuBP, instead of carbon dioxide and RuBP. This process of oxidation of carbon
is called photorespiration. It reduces the photosynthetic efficiency of C 3 plants in tropics.

 Common examples of C3 plants are spinach, sunflower, rice, cotton and bean.

2. C4 photosynthesis
 C4 photosynthesis is a photosynthetic pathway in which the first compound formed in the light
independent reactions is a C4 compound called oxaloacetate. This pathway is common in tropical
plants, such as corn, millet, maize, crabgrass, sorghum and sugar cane.

 C4 photosynthesis reduces photorespiration by separating the initial carbon fixation and the Calvin
cycle in different types of cells.

1. The first carbon fixation takes place in mesophyll cells, which have chloroplasts with thylakoids. In
the mesophyll cells, carbon dioxide reacts with a C3 compound called PEP to form the C4
compound oxaloacetate. This reaction is catalyzed by the enzyme PEP carboxylase.
2. Oxaloacetate is converted into another C4 compound called malate.
3. Malate then passes from the mesophyll cell into a bundle sheath cell. In the bundle sheath cell,
malate is converted to pyruvate with the release of a molecule of carbon dioxide, which starts the
reactions of the Calvin cycle by binding with RuBP.
4. The pyruvate is converted back to PEP to be reused again; this reaction requires ATP.

 In C4 plants, the light-dependent reactions occur in mesophyll cells, which contain chloroplasts with
thylakoids. The bundle sheath cells of C4 plants contain chloroplasts without thylakoids. This means
 that the light-dependent reactions cannot occur here and so oxygen is not produced in these
chloroplasts. This helps to prevent photo respiration of RuBP and allows the Calvin cycle to take
place in these cells.

3. CAM photosynthesis

 CAM photosynthesis (Crassulacean acid metabolism) uses the same set of reactions as C4 plants,
but they separate the initial carbon fixation and the Calvin cycle not by carrying them out in different
types of cells, but by carrying them out at different times. This photosynthesis pathway is common in
plants, such as cacti and pineapple, which are well adapted to survive in the extreme heat of deserts.

 CAM plants must close their stomata during the day time to prevent water loss from their leaves. Due
to this, these plants open their stomata at night to allow in carbon dioxide.

 The CAM photosynthesis cycle is as follows:

1.  At night, the plants open their stomata to allow in CO2, which then reacts with PEP in mesophyll
cells to form oxaloacetate, and then malate just as in the C4 pathway.
2. The malate is then stored in the vacuoles of these cells overnight.
3. During the day, the light-dependent reactions generate ATP and reduced NADP so that the Calvin
cycle can continue.
4. Malate is released from the vacuoles and is broken down to glycerate, releasing carbon dioxide for
the reactions of the Calvin cycle.

Factors that affect the rate of photosynthesis

 Light intensity, carbon dioxide concentration and temperature are the major factors that affect the rate
of photosynthesis.

Light intensity
 The rate of photosynthesis usually increases with increasing light intensity.

Carbon dioxide concentration

 An increase in CO2 concentration increases the rate at which carbon is incorporated into
carbohydrate in the light-independent reaction. Thus, increasing the carbon dioxide concentration
increases the rate of photosynthesis until it is limited by the saturation of enzyme Rubisco.

Temperature
 An increase in temperature generally increases the rate of photosynthesis by increasing the rate of
collisions reacting molecules. However, at high temperatures, enzymes are denatured and this will
decrease the rate of photosynthesis.