Chapter 1-4

Biology and the Scientific Study of Life

 Biology is defined as the scientific study of life. This means it uses systematic and
evidence-based approaches to understand living organisms and their processes.
 Science itself is an approach to understand the natural world. This approach is based
on inquiry, which involves asking questions; analysis, which involves examining data;
and survey, which involves observation and gathering information. Science is essentially
a search for information, explanation and answers to specific questions.
 There are two main scientific approaches to studying life:
o Discovery science primarily focuses on searching for information, explanation
and answers to specific questions about the natural world. It is largely
observational and descriptive.
o Hypothesis-driven science is mostly about explaining nature. This is achieved
by conducting a search for explanations. This approach is done by formulating
a hypothesis to explain the natural world, that is tested.
 A hypothesis is defined as a tentative answer to a question, a proposed explanation
for a set of observations. It's also described as a tentative insight into the natural
world; a concept that is not yet verified but that if true would explain certain facts
or phenomena. For a statement to be considered a scientific hypothesis, it must be
testable and falsifiable. For example, the statement "Air pollution from automobile
exhaust can trigger symptoms in people with asthma" is considered a testable and
falsifiable hypothesis. Conversely, a statement like "Natural disasters, such as tornadoes,
are punishments for bad thoughts and behaviours" is not a scientific hypothesis because it
is not testable or falsifiable.
 Scientific investigations employ the scientific method, which is a series of steps, a
process used for investigations. It suggests a broad outline/steps for how discovery
might proceed. A crucial aspect of this method is that scientists test a hypothesis many
times and in different ways. Through this rigorous testing, a hypothesis may be
revised or even rejected.
 The concept of a scientific theory is distinct from a hypothesis. A theory is a
comprehensive explanation supported by abundant evidence. It is also described as a
well-tested explanation for a great variety of scientific observations. Compared to a
hypothesis, a theory is much broader in scope and can be enough to spin off many new
testable hypotheses. For instance, the hypothesis "Mimicking poisonous snakes is an
adaptation that protects nonpoisonous snakes from predators" is narrower than the
broader theory of "Adaptations such as mimicry evolve by natural selection". Theories
like the theory of evolution by natural selection become widely accepted when they are
validated by a large number of observation and experiments/evidences without any
contradiction.

Properties of Life

 Order: Life exhibits a high degree of order. Organisms are complex but organized,
with the cell being the basic unit of life. This order is evident in the hierarchical
organization of life, from atoms making up molecules, which form cell organelles and
 structures within a cell. In multicellular organisms, similar cells form tissues, tissues
collaborate to create organs (body structures with a distinct function), and organs work
together to form organ systems, ultimately making up an organism. This ordered
structure ensures that information flows in an ordered manner at all levels of
organization. Even unicellular organisms like bacteria display a complex internal
order.
 Energy processing: All living organisms require a source of energy to carry out their
metabolic activities. Some organisms capture energy from the sun and convert it
into chemical energy in food (photosynthesis). Others use chemical energy in
molecules they take in as food (cellular respiration). This involves the transformation
of energy from one form to another, as seen in a food chain. Metabolism is the vast
network of interconnected chemical reactions within living cells, where energy from
food is broken down and processed, and chemical bond energy is transformed into a
usable form like ATP. This energy and matter transformation is crucial, and if
disrupted, it can lead to problems as metabolic pathways are inhibited.
 Growth and development: Living organisms undergo regulated growth. At the cellular
level, individual cells become larger in size – GROWTH. In multicellular organisms,
growth occurs through the accumulation of many cells through cell division. Body
Growth depends on anabolic pathways that build large, complex molecules (proteins
and DNA, the genetic material). Organisms typically start out as a single cell and
have tens of trillions of cells as they develop. This pattern of growth and development is
controlled by information in the DNA.
 Reproduction: A fundamental characteristic of life is the ability to reproduce their own
kind, leading to population growth. In single-celled organisms, reproduction often
occurs by first duplicating their DNA, and then dividing it equally as the cell
prepares to divide to form two new cells, a process called binary fission.
 Regulation: Organisms exhibit regulation to maintain a stable internal environment. The
outside environment may change drastically, but the internal environment is always
adjusted and kept constant. Examples of internal functions regulated include nutrient
transport and blood flow. This maintenance of a stable internal environment is known
as homeostasis. Examples of regulatory mechanisms include osmoregulation, sweating
and dilation of blood vessels to loose heat in hot conditions, and vasoconstriction and
muscle movement to generate heat in cold conditions. Even the smallest organisms
require multiple regulatory mechanisms to coordinate internal functions.
 Response to the environment: Living organisms can respond/react to the given
stimulus in the environment. Examples of these responses include a plant's response to
infection, the carnivorous Venus fly trap's response to touch, and the Mimosa pudica's
response to touch. Phototropism (or light response) in plants and chemotaxis
(movement toward or away from chemicals) in bacteria are also examples of responses to
environmental stimuli.
 Evolution: Populations of living organisms can undergo evolution, meaning the
genetic makeup of a population may change over time. Evolution is a long-term
process wherein changes occur at the genetic level for a better functioning and
survival as a race. A clear example is the Giant leaf insect (Phyllium giganteum),
which has evolved to provide camouflage in its environment. Evolution is considered
a fundamental principle of life and a unifying phenomenon of all of biology. The
 evolution of the polar bear from the common brown bear through changes like its fur
colour to white for better camouflage in its arctic habitat is another example.

Major Themes in Biology

 Evolution by natural selection is highlighted as the core theme in biology, observable

at every level in the hierarchy of life. Natural selection does not promote changes
but edits the changes that have already occurred, and the product of natural
selection is adaptation. Examples include the different fur colours in bears (white in
polar bears and brown in grizzly bears) resulting from natural selection in their respective
environments, even though they are similar species sharing a common ancestor. Studies
on finches of the Galapagos Islands have shown how changes in beak size in response
to dry and wet years are measurable evidence of natural selection. Similarly, the
development of antibiotic-resistant bacteria is another example of natural selection. In
contrast to natural selection, artificial selection involves selecting breeding stocks with
certain traits, as seen in the customized crop breeding that has led to modern plants with
little resemblance to their wild relatives.
 The relationship between structure and function is a recurring theme, with a
correlation seen at every level of biological organization. The structure of lungs, for
example, is directly related to its function in gas exchange.
 Information flow is essential for life's functions, with every cell contain[ing]
information in the form of genes, hereditary units of information. This information
dictates growth, development, and other life processes.
 Energy transformations are crucial, as the conversion of energy from one form to
another makes life possible, as seen in photosynthesis and cellular respiration.
 Interconnections within systems are fundamental, with the study of life extend[ing]
from the microscopic level of molecules, all biological systems from molecules
–organelle –membrane bound cells-tissue-organ-organ system-organism-
population- community. Communities interact with their environment to form an
Ecosystem (all living organisms in a particular place and all non-living components of
the environment). The biosphere is the sum of all ecosystems and communities on
Earth, encompassing all places where life exists. Life's functions proceed in an ordered
manner due to these interconnections.

Diversity and Classification of Life

 There is a greatdiversity in the forms of life in nature, with millions of species on

earth. A species is defined as a taxonomic group whose members can interbreed and
share a genetic heritage, forming a population/group of organisms living in the same
place and time and are capable of interbreeding and producing healthy fertile
offspring. Examples of different species include humans (Homo sapiens), moose (Alces
laces), black bears (Ursus americans), and jack pines (Pinus banksiana). The
diversity of known life includes more than 290,000 plants, 52,000 animals with
backbones, and one million insects.
 To manage this diversity, scientists use taxonomy, which is the branch of biology that
names and classifies species by grouping them into logical categories. It involves a
 classification of organisms into groups based on similarities of structure or origin
etc.. Taxonomists use various observations, including morphological, behavioral,
genetic, and biochemical data. This results in an arrangement of species into a
hierarchy of broader and broader groups, often remembered by the mnemonic (D K P
C O F G S) for Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.
 At the broadest level, biologists divide the diversity of life into three
main domains:
Eubacteria, Archaea, and Eucarya. Every organism on earth belongs to one of these
three domains.
o Eubacteria (true bacteria) are small, prokaryotic, single-celled organisms
ranging in size from 1 to 10 um. They lack a nucleus and cell membrane-bound
organelles, and their cell wall contains a complex organic molecule called
Peptidoglycan.
o Archaea (ancient bacteria) also have a prokaryotic cell structure. However,
their DNA has large proportions of genes that are different from Eubacteria,
and their cell membranes have unique chemical structures, lacking fatty acids
and instead containing branched molecules called isoprenes. Archaea are also
known as extremophiles because they are often found in extreme environments.
o Eucarya includes organisms with eukaryotic cells and comprises three main
Kingdoms (Plantae, Fungi, Animalia) and the Protists. Most members of
Eucarya are multicellular. The Kingdoms are partly distinguished by how
organisms obtain food. Plantae are autotrophic, producing their own sugar and
food through photosynthesis. Fungi are heterotrophic decomposers, obtaining
food by digesting dead organisms and organic waste. Animalia are also
heterotrophic, obtaining food by ingesting and digesting other organisms.
Protists are a diverse catch-all group for eukaryotes that do not belong to the
other three kingdoms, and they are mostly single-celled microscopic organisms
such as amoeba or multicellular.

The Microscopic World of Cells

 The cell theory is a fundamental concept in biology, stating that all living things are
composed of cells and that all cells come from earlier cells. This implies that every
cell in our body (and in every other living organism on Earth) was formed by
division of a previously living cell.
 The countless cells on Earth fall into two basic categories: prokaryotic cells and
eukaryotic cells.
o Prokaryotic cells include Bacteria and Archaea. They are considered older
than eukaryotic cells, appearing about 3.5 billion years ago, while eukaryotes
appeared about 2.1 billion years ago. Prokaryotic cells are usually smaller than
eukaryotic cells and lack a nucleus. Their DNA is coiled into a nucleus-like
region called the nucleoid, which is without nuclear membranes. Prokaryotic
cells also lack other membrane-enclosed structures called organelles. However,
they do have several basic features: they are bounded by a thin plasma
membrane, have a thick, jelly-like fluid called the cytosol inside where cellular
components are suspended, have one or more chromosomes carrying genes
made of DNA, and have ribosomes for protein synthesis. Prokaryotes can also
 have pili (short projections for attachment), flagella (long projections for
wall, a
propulsion), and a capsule (a sticky outer coating). They also have a cell
rigid covering outside the plasma membrane that protects the cell and helps
maintain its shape. In Eubacteria, this cell wall contains peptidoglycan.
o Eukaryotic cells include protists, plants, fungi, and animals. They are
characterized by the presence of organelles, membrane-enclosed structures
that perform specific functions. The most important organelle is the nucleus,
which houses most of a eukaryotic cell’s DNA and is surrounded by a double
membrane. The region between the nucleus and the plasma membrane is the
cytoplasm, which consists of various organelles suspended in the liquid
cytosol. While eukaryotic cells are fundamentally similar, there are some
important differences between plant and animal cells. Only plant cells have
chloroplasts (where photosynthesis occurs), a cell wall (outside the plasma
membrane), and a large central vacuole. Only animal cells have lysosomes
(bubbles of digestive enzymes) and centrioles (most plant cells lack them). Both
plant and animal cells contain other organelles such as ribosomes, cytoskeleton,
plasma membrane, cytoplasm, mitochondrion, rough and smooth
endoplasmic reticulum (ER), and Golgi apparatus.

Executive Summary:

1. The Nature of Biology and Scientific Inquiry:

 Definition of Biology: Biology is defined as the "Scientific study of life".

 Science as an Approach: Science is presented as "an approach to understand the
natural world based on Inquiry, Analysis & Survey" and involves the "Search for
information, explanation and answers to specific questions".
 Two Main Scientific Approaches:Discovery Science: While mentioned, the excerpts
primarily focus on hypothesis-driven science.
 Hypothesis-Driven Science: This approach is described as "Mostly explaining nature -
search for explanations" and is "done by formulating a hypothesis to explain the
natural world, that is tested."
 Hypothesis: A hypothesis is defined as a "tentative answer to a question, proposed
explanation for a set of observations" and a "tentative insight into the natural world;
a concept that is not yet verified but that if true would explain certain facts or
phenomena."
 Scientific Method: This is presented as "A series of steps, process used for
investigations" that "Suggests a broad outline/steps for how discovery might
proceed." The process involves testing hypotheses repeatedly, with the understanding
that "A hypothesis may be revised or even rejected."
 Applying the Scientific Method: An example is provided regarding maple trees losing
leaves in the fall, illustrating observation, hypothesis formation ("cold weather causes
maple trees to lose their leaves in the fall"), testability (growing trees in a warm
environment), and falsifiability (if leaves still drop, temperature is not the main factor).
  Distinguishing Scientific Hypotheses: The example of air pollution and asthma is
presented as a testable and falsifiable scientific hypothesis, while the statement about
natural disasters being punishments is not.
 Hypothesis vs. Theory:Hypothesis: A tentative explanation.
 Scientific Theory: A "comprehensive explanation supported by abundant evidences"
and a "well-tested explanation for a great variety of scientific observations." Theories
are broader in scope than hypotheses and can "spin off many new testable hypotheses."
The example provided contrasts the hypothesis about mimicry in snakes with the broader
theory of adaptations evolving by natural selection.
 Theories gain wide acceptance when "Validatedby large number of observation and
experiments/evidences without any contradiction."

2. The Nature of Life - Seven Properties:

The document outlines seven fundamental properties that characterize life:

 Order: Life exhibits complex organisation, with the "cell basic unit". Organisms are
"highly organized into levels" from cells to organ systems. "Information flows in an
ordered manner at all levels of organization".
 Energy Processing: Organisms utilise energy for metabolic activities. Some capture
energy from the sun (photosynthesis), while others use chemical energy from food
(cellular respiration). "METABOLISM - Vast network of interconnected chemical
reactions –( within living cells)". Energy transformation and matter recycling are
crucial.
 Growth and Development: Growth and development are controlled by information in
DNA. "Living organisms undergo regulated growth." Growth involves individual cell
enlargement and, in multicellular organisms, cell division. Body growth depends on
anabolic pathways.
 Reproduction: Organisms reproduce "their own kind" leading to "Population growth".
This involves DNA duplication and cell division (e.g., binary fission in single-celled
organisms).
 Regulation: Organisms maintain a stable internal environment despite external changes,
a process called "Homeostasis". Examples include "Thermoregulations,
Osmoregulation".
 Response to the Environment: Organisms react to stimuli. Examples include plant
tropisms (phototropism), bacterial chemotaxis, and responses to infection or touch
(Venus fly trap, Mimosa pudica).
 Evolution: Populations can undergo evolution, with changes in their genetic makeup
over time for better survival. The giant leaf insect's camouflage is given as an example.
Evolution is described as a "Fundamental principle of life -Unifying phenomenon of
all of biology".

3. Major Themes in Biology:

Several overarching themes are highlighted:

  Evolution by Natural Selection: This is presented as the "core theme" in biology,
observable at all levels of life's hierarchy. Natural selection "edits the changes that have
already occurred" and the product is "ADAPTION". Examples include the fur colour of
polar bears and brown bears, and beak size changes in Galapagos finches in response to
environmental conditions. Artificial selection in crop breeding is also mentioned.
 Structure/Function Relationship: A "correlation seen at every level of biological
organization" (e.g., the structure of lungs is suited for gas exchange).
 Information Flow: "every cell contain information in the form of genes, hereditary
units of information". Life functions proceed in an ordered manner due to this
information flow at all levels.
 Energy Transformations: The conversion of energy from one form to another "makes
life possible".
 Interconnections within Systems: Life is studied from the microscopic level to the
biosphere, with all biological systems relying on interactions between components. This
hierarchy ranges from atoms to the biosphere, encompassing molecules, cells, tissues,
organs, organ systems, organisms, populations, communities, and ecosystems.

4. Diversity of Life and Taxonomy:

 Great Diversity: Nature exhibits a vast array of life forms, with millions of species.
 Species Definition: A "Taxonomic group whose members can interbreed -share a
genetic heritage" and capable of "producing healthy fertile offspring." Examples of
different species are provided (humans, moose, black bears, jack pines).
 Taxonomy: The "Branch of biology that names and classifies species by grouping
them into logical categories." Taxonomists use various observations (morphological,
behavioural, genetic, biochemical) to arrange species into a "hierarchy of broader and
broader groups" (Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species - D
K P C O F G S).
 Classification: Life is broadly divided into three domains: Eubacteria, Archaea, and
Eucarya.
 Eubacteria: Prokaryotic, single-celled, lack a nucleus and membrane-bound organelles,
cell wall contains peptidoglycan.
 Archaea: Prokaryotic, DNA has different genes than Eubacteria, unique cell membrane
structure (isoprenes instead of fatty acids), often found in extreme environments
(extremophiles).
 Eucarya: Includes three main Kingdoms (Plantae - autotrophic via photosynthesis, Fungi
- heterotrophic decomposers, Animalia - heterotrophic by ingestion) and the catch-all
group Protists (mostly single-celled).

5. The Microscopic World of Cells:

 Cell Theory: "all living things are composed of cells and that all cells come from
earlier cells."
 Two Major Cell Categories:Prokaryotic Cells: Include Bacteria and Archaea.
 Eukaryotic Cells: Include protists, plants, fungi, and animals.
 Basic Cell Features (Common to both):Bounded by a "thin plasma membrane".
  Contain "cytosol" (jelly-like fluid).
 Have "one or more chromosomes carrying genes made of DNA".
 Contain "ribosomes" for protein synthesis.
 Differences Between Prokaryotic and Eukaryotic Cells:Age: Prokaryotes (appeared
~3.5 billion years ago) are older than eukaryotes (~2.1 billion years ago).
 Size: Prokaryotic cells are generally smaller.
 Nucleus: Prokaryotic cells lack a nucleus; their DNA is located in a "nucleoid" region
without a nuclear membrane. Eukaryotic cells have a nucleus enclosed by a double
membrane, housing most of their DNA.
 Organelles: Eukaryotic cells possess "organelles, membrane-enclosed structures that
perform specific functions". Prokaryotic cells lack these.
 Prokaryotic Cell Structure (Details): Includes the plasma membrane, cell wall
(provides rigidity and shape), capsule (sticky coating for protection), flagella
(propulsion), pili (attachment), ribosomes, and nucleoid.
 Eukaryotic Cell Structure (Overview): The cytoplasm contains various organelles
suspended in the cytosol. Differences exist between animal and plant cells (e.g.,
chloroplasts and cell walls in plant cells; lysosomes and centrioles in animal cells).
Diagrams illustrate idealized animal and plant cells with key organelles labelled (nucleus,
mitochondria, endoplasmic reticulum, Golgi apparatus, ribosomes, cytoskeleton, etc.).

Molecules of Life

Introduction to Important Molecules of Life

 Key Elements: The 16 naturally occurring elements crucial for living systems are C, H,
O, N, P, S, K, Ca, Na, Cl, Mg, Fe, Cu, I, Mo, Zn.
 Organic Compounds: These are a vast group of carbon-containing chemical
compounds where at least one carbon atom is covalently linked to atoms of other
elements, most commonly H, N, or O.
 Carbon's Importance: Carbon is special because it forms the backbone of most
organic molecules. It can construct an endless diversity of carbon skeletons that vary
in size, can be straight, branched, or arranged in closed rings. Furthermore, atoms of
other elements can bond to these carbon skeletons.

Characteristics of Biological Molecules

 Monomers: These subunits serve as building blocks for larger molecules.

 Polymers: Polymers are formed when monomers are connected by covalent bonds.
 Dehydration Synthesis (Condensation): This is the process where two molecules are
joined covalently with the removal of a water molecule. Specifically, an -OH group is
removed from one monomer and an -H atom from the other. This is how monomers
like glucose and fructose join to form a disaccharide, releasing H₂O. If this process
continues with monosaccharides, a long, complex polysaccharide is formed.
 Hydrolysis: This is a chemical reaction in which water reacts with a compound to
produce other compounds, involving the splitting of a bond and the addition of the
hydrogen cation (H⁺) and the hydroxide anion (OH⁻) from the water. Hydrolysis
 breaks the bonds between monomers by adding a molecule of water, effectively
reversing the dehydration reaction. For example, a disaccharide plus water yields two
monosaccharides. This is how we break down food into smaller units.

Connectivity in Biomacromolecules

 Proteins: Amino acids are linked together by peptide bonds. These bonds form between
the carboxyl group of one amino acid and the amino group of another through
dehydration synthesis. The resulting bond is a peptide bond.
 Nucleic Acids: Nucleotides are joined by phosphodiester bonds.
 Lipids: Lipids are formed by ester bonds between glycerol and fatty acids. This is a
dehydration reaction where the hydroxyl group of glycerol reacts with the carboxyl group
of a fatty acid.
 Polysaccharides: Monosaccharides are linked by glycosidic bonds. For instance, two
glucose molecules join via a glycosidic bond to form maltose.

1) CARBOHYDRATES
 Principle Elements: Carbohydrates primarily consist of C, H, and O, often with a
characteristic formula Cn H2n On in a 1:2:1 ratio.
 Monomers: The monomers are monosaccharides, also known as simple sugars.
Examples include glucose, fructose, and galactose, all with the molecular formula
C6H12O6, as well as ribose (C5H10O5). The suffix -ose is typically used for sugars.
 Polymers: Long chains of monosaccharides linked by glycosidic bonds form
polysaccharides, also called complex carbohydrates.
 Solubility: Carbohydrates are generally water soluble (hydrophilic).
 Functions: Key functions include energy metabolism and serving as structural
components. They are also involved in cell-to-cell contacts and recognition, and fibre
of wastes.
(indigestible carbohydrates) aids in the elimination
 Disaccharides: These are formed when two monosaccharides join via dehydration
synthesis. Examples include:
o Maltose (malt sugar): glucose + glucose
o Sucrose (table sugar): glucose + fructose (not explicitly in the source, but a
common example)
o Lactose (milk sugar): glucose + galactose
 Polysaccharide Examples:
o Starch (amylose): A storage carbohydrate in plants, commonly found in rice,
potatoes, corn, wheat, and beans. It is composed of glucose monomers and is
digested into individual glucose molecules for absorption.
o Cellulose: A structural carbohydrate that makes up plant cell walls. Like
starch, it's made of glucose monomers, but humans cannot digest it, so it
functions as indigestible fibre or roughage, essential for a healthy digestive tract.
o Glycogen: The storage carbohydrate in animals, primarily stored in the liver
and muscles. It is a long chain of glucose molecules. Athletes may engage in
carb-loading to increase glycogen stores. Excess glycogen that isn't used for
energy can be turned into fat.
 o Chitin: Another structural polysaccharide, found in fungi cell walls and
arthropod exoskeletons. It is a polymer of beta-glucose molecules but also
contains a nitrogen-containing functional group and does not strictly follow the
Cn H2n On formula. It is indigestible like cellulose.
 High Fructose Corn Syrup (HFCS): This is made by processing glucose (often from
corn starch) using the enzyme glucose isomerase to convert it into fructose, which is
much sweeter. It is found in many sweeteners, often with negligible nutrients,
contributing to "empty calories". High consumption is linked to health issues like tooth
decay, weight gain, cancer, increased cholesterol, diabetes, high blood pressure, and
heart disease. The average 20 oz soda can contain 15 teaspoons of HFCS.
 Empty Calories: These are calories that provide energy but have no nutritional
balance, lacking significant amounts of nutrients other than carbohydrates. Most
sweeteners are considered empty calories.

2) LIPIDS
 Principle Elements: Lipids mainly contain C, H, and O, and some may also contain P
and N.
 Characteristics: Lipids are a diverse group including oils, fats, waxes, phospholipids,
and steroids. They are generally water insoluble (hydrophobic). Unlike other
macromolecules, they are not necessarily polymers and are typically smaller in size.
 Functions: Key functions include energy storage, protection and cushioning of body
organs, and serving as structural components of membranes.
 Major Types:
o Phospholipids: These are composed of fatty acids, phosphoric acid, and a
nitrogenous base. They are crucial components of cell membranes, forming a
phospholipid bilayer with a hydrophilic head (attracted to water) and
hydrophobic tails (repelled by water).
o Triglycerides (neutral fats): These are formed from one glycerol molecule and
three fatty acid molecules. They are the primary form of energy storage in the
body. Fatty acids can be saturated (containing no double bonds between
carbons, often solid at room temperature, and common in animal fats like
butter) or unsaturated (containing one or more double bonds between
carbons, often liquid at room temperature, and common in vegetable fats).
o Sterols (Steroids): These are organic compounds with a four-carbon ring
skeleton and various functional groups attached. Examples include:
 Cholesterol: A dietary lipid vital for cellular function and a precursor
to fat-soluble vitamins and steroid hormones.
 Sex hormones: Estradiol (oestrogen) and testosterone, which are
responsible for the anatomical and physiological differences between
the sexes.
 Corticosteroids: Found in vertebrates, involved in a wide range of
functions like immunity, inflammation, stress response, and
carbohydrate metabolism. Examples include cortisol, cortisone, and
aldosterone. Synthetic analogues are used to treat various conditions like
inflammation and pain. Oral corticosteroids can have side effects like
 fluid retention, high blood pressure, mood swings, upset stomach, and
weight gain. They can be detected in urine for up to 14 days.
 Anabolic steroids: Synthetic variants of testosterone that mimic its
effects, such as increasing muscle mass. They may be prescribed for
muscle wasting diseases but are also abused by athletes.
o Waxes: (Briefly mentioned as a diverse group of lipids, but not detailed further in
the source).
 Hydrogenation: This is a chemical process where hydrogen is added to liquid oils to
turn them into a solid form. Partially hydrogenated fats contain trans fats, which are
considered potentially harmful.
 Dehydrogenation: This is the reverse process of hydrogenation, involving the
removal of hydrogen from a molecule, converting saturated fats to unsaturated fats.

3) PROTEINS
 Principle Elements: Proteins contain C, H, O, and N.
 Monomers: The monomers are amino acids, of which there are 20 different kinds.
Each amino acid has a central carbon atom bonded to a carboxylic acid group (-
COOH), an amine group (-NH2), a hydrogen atom, and a variable R-group. The R-
group differs between the 20 amino acids and gives them their unique properties. Some
common functional groups found in R-groups include hydroxyl, carbonyl, amino,
sulfhydryl, phosphate, and methyl groups.
 Polymers: Polymers of amino acids are called polypeptides or proteins. Peptide bonds
link amino acids together. Functional proteins can vary in length from about 50 to
several thousand amino acids.
 Solubility: Proteins are generally water soluble.
 Bonds: The bond between two amino acids is a peptide bond, formed during
dehydration synthesis. The carboxyl group of one amino acid reacts with the amino
group of another, releasing water and forming the peptide bond.
 Structure: Protein structure has four levels:
o Primary structure: The linear sequence of amino acids in a polypeptide chain.
o Secondary structure: Localised, repeating folding patterns like the alpha helix
(e.g., in hair) and the beta-pleated sheet (e.g., in silk), stabilized by hydrogen
bonds between parts of the polypeptide backbone.
o Tertiary structure: The overall 3D configuration of a single polypeptide chain,
resulting from interactions between the R-groups of the amino acids (including
weak bonds). Examples include myoglobin and cytochrome.
o Quaternary structure: The association of two or more polypeptide chains
(subunits). Examples include haemoglobin (made of alpha and beta chains) and
antibodies (immunoglobulins).
 Functions: Proteins have diverse roles:
o Enzymes: Catalyse chemical reactions.
o Structural proteins: Provide support (e.g., collagen) (not explicitly named in the
source but implied).
o Chemical messengers: Involved in signalling between cells.
o Hormones: Some hormones are proteins.
 o Antibodies: Involved in the immune system, fighting infectious diseases.
o Transport proteins: Help transport substances (e.g., haemoglobin transports
oxygen).
o Contractile proteins: Aid in movement (e.g., actin and myosin) (not explicitly
named in the source but implied).
o Storage proteins: Provide amino acids for growth.
 Importance of Shape: Maintaining a specific shape, sequence, and 3D structure is
vital for a protein to function effectively. A single amino acid change in the primary
sequence can cause drastic changes in function, as seen in sickle cell anaemia, where the
6th amino acid in the beta chain of haemoglobin changes from glutamic acid to valine.
Misfolded proteins called prions are believed to cause diseases like BSE
(Mad Cow
Disease), Chronic Wasting Disease (CWD), and CJD (Creutzfeldt Jacob Disease).
These diseases are characterised by brain cell damage, progressive dementia, and loss of
muscle control. Denaturation of a protein refers to the loss of its specific shape, which
often leads to a loss of function.
 Bonds: The bond between fatty acids and glycerol is called an ester linkage. The bond
between two carbohydrates (monosaccharides) is a glycosidic bond.

4) NUCLEIC ACIDS
 Principle Elements: Nucleic acids contain C, H, O, N, and P.
 Monomers: The monomers are nucleotides, each consisting of a 5-carbon sugar (ribose
in RNA, deoxyribose in DNA), a phosphate group, and a nitrogenous base. The
nitrogenous bases are purines (adenine and guanine) and pyrimidines (cytosine, thymine
in DNA, and uracil in RNA).
 Polymers: Polymers of nucleotides are nucleic acids: DNA (deoxyribonucleic acid)
and RNA (ribonucleic acid). Nucleotides in a nucleic acid chain are linked by
phosphodiester bonds.
 Solubility: Nucleic acids are generally water soluble.
 DNA (Deoxyribonucleic Acid): DNA is typically double-stranded. Its sugar is
deoxyribose, and it contains the bases adenine (A), guanine (G), cytosine (C), and
thymine (T). DNA contains the information for almost all cell activities, serving as
the genetic instruction set.
 RNA (Ribonucleic Acid): RNA is usually single-stranded. Its sugar is ribose, and it
contains the bases adenine (A), guanine (G), cytosine (C), and uracil (U). RNA is
involved in protein synthesis. There are three main types:
o Messenger RNA (mRNA): Carries genetic instructions from the nucleus to the
cytoplasm.
o Ribosomal RNA (rRNA): A component of ribosomes, where protein synthesis
occurs.
o Transfer RNA (tRNA): Involved in ordering amino acids during protein
synthesis.
 ATP (Adenosine Triphosphate): ATP is a nucleotide composed of ribose (a 5-carbon
sugar), a phosphate group, and the nitrogenous base adenine (the source shows a
structure with a sugar, phosphate, and nitrogen base, and later mentions ATP has three
phosphate groups). It plays a crucial role in energy metabolism by undergoing
 hydrolysis to ADP (adenosine diphosphate) and inorganic phosphate (Pi), releasing
energy. ATP is also involved in protein synthesis (translation and transcription) and
cell division (DNA replication).

General Processes

 Dehydration Synthesis: This process forms bonds through the removal of water.
o Carbohydrates: Monosaccharide + Monosaccharide → Disaccharide + H₂O.
For example, glucose + fructose → sucrose + H₂O (not explicitly in the source for
sucrose formation, but the general principle is shown).
o Lipids: 1 Glycerol + 3 Fatty Acids → Lipid + 3 H₂O. Ester bonds are formed.
o Proteins: 2 Amino Acids → Dipeptide + H₂O. Peptide bonds are formed.
o Nucleic Acids: Nucleotides → Nucleic Acid + H₂O. Phosphodiester bonds are
formed.
 Hydrolysis: This process breaks bonds through the addition of water.
o Carbohydrates: Disaccharide + H₂O → Monosaccharide + Monosaccharide.
For example, lactose + H₂O → glucose + galactose.
o Lipids: Lipid + 3 H₂O → 1 Glycerol + 3 fatty Acids. Ester bonds are broken.
o Proteins: Dipeptide + H₂O → 2 Amino Acids. Peptide bonds are broken.

Executive Summary:

1. The Nature of Biology and Scientific Inquiry:

 Definition of Biology: Biology is defined as the "Scientific study of life".

 Science as an Approach: Science is presented as "an approach to understand the
natural world based on Inquiry, Analysis & Survey" and involves the "Search for
information, explanation and answers to specific questions".
 Two Main Scientific Approaches:Discovery Science: While mentioned, the excerpts
primarily focus on hypothesis-driven science.
 Hypothesis-Driven Science: This approach is described as "Mostly explaining nature -
search for explanations" and is "done by formulating a hypothesis to explain the
natural world, that is tested."
 Hypothesis: A hypothesis is defined as a "tentative answer to a question, proposed
explanation for a set of observations" and a "tentative insight into the natural world;
a concept that is not yet verified but that if true would explain certain facts or
phenomena."
 Scientific Method: This is presented as "A series of steps, process used for
investigations" that "Suggests a broad outline/steps for how discovery might
proceed." The process involves testing hypotheses repeatedly, with the understanding
that "A hypothesis may be revised or even rejected."
 Applying the Scientific Method: An example is provided regarding maple trees losing
leaves in the fall, illustrating observation, hypothesis formation ("cold weather causes
maple trees to lose their leaves in the fall"), testability (growing trees in a warm
environment), and falsifiability (if leaves still drop, temperature is not the main factor).
  Distinguishing Scientific Hypotheses: The example of air pollution and asthma is
presented as a testable and falsifiable scientific hypothesis, while the statement about
natural disasters being punishments is not.
 Hypothesis vs. Theory:Hypothesis: A tentative explanation.
 Scientific Theory: A "comprehensive explanation supported by abundant evidences"
and a "well-tested explanation for a great variety of scientific observations." Theories
are broader in scope than hypotheses and can "spin off many new testable hypotheses."
The example provided contrasts the hypothesis about mimicry in snakes with the broader
theory of adaptations evolving by natural selection.
 Theories gain wide acceptance when "Validatedby large number of observation and
experiments/evidences without any contradiction."

2. The Nature of Life - Seven Properties:

The document outlines seven fundamental properties that characterize life:

 Order: Life exhibits complex organisation, with the "cell basic unit". Organisms are
"highly organized into levels" from cells to organ systems. "Information flows in an
ordered manner at all levels of organization".
 Energy Processing: Organisms utilise energy for metabolic activities. Some capture
energy from the sun (photosynthesis), while others use chemical energy from food
(cellular respiration). "METABOLISM - Vast network of interconnected chemical
reactions –( within living cells)". Energy transformation and matter recycling are
crucial.
 Growth and Development: Growth and development are controlled by information in
DNA. "Living organisms undergo regulated growth." Growth involves individual cell
enlargement and, in multicellular organisms, cell division. Body growth depends on
anabolic pathways.
 Reproduction: Organisms reproduce "their own kind" leading to "Population growth".
This involves DNA duplication and cell division (e.g., binary fission in single-celled
organisms).
 Regulation: Organisms maintain a stable internal environment despite external changes,
a process called "Homeostasis". Examples include "Thermoregulations,
Osmoregulation".
 Response to the Environment: Organisms react to stimuli. Examples include plant
tropisms (phototropism), bacterial chemotaxis, and responses to infection or touch
(Venus fly trap, Mimosa pudica).
 Evolution: Populations can undergo evolution, with changes in their genetic makeup
over time for better survival. The giant leaf insect's camouflage is given as an example.
Evolution is described as a "Fundamental principle of life -Unifying phenomenon of
all of biology".

3. Major Themes in Biology:

Several overarching themes are highlighted:

  Evolution by Natural Selection: This is presented as the "core theme" in biology,
observable at all levels of life's hierarchy. Natural selection "edits the changes that have
already occurred" and the product is "ADAPTION". Examples include the fur colour of
polar bears and brown bears, and beak size changes in Galapagos finches in response to
environmental conditions. Artificial selection in crop breeding is also mentioned.
 Structure/Function Relationship: A "correlation seen at every level of biological
organization" (e.g., the structure of lungs is suited for gas exchange).
 Information Flow: "every cell contain information in the form of genes, hereditary
units of information". Life functions proceed in an ordered manner due to this
information flow at all levels.
 Energy Transformations: The conversion of energy from one form to another "makes
life possible".
 Interconnections within Systems: Life is studied from the microscopic level to the
biosphere, with all biological systems relying on interactions between components. This
hierarchy ranges from atoms to the biosphere, encompassing molecules, cells, tissues,
organs, organ systems, organisms, populations, communities, and ecosystems.

4. Diversity of Life and Taxonomy:

 Great Diversity: Nature exhibits a vast array of life forms, with millions of species.
 Species Definition: A "Taxonomic group whose members can interbreed -share a
genetic heritage" and capable of "producing healthy fertile offspring." Examples of
different species are provided (humans, moose, black bears, jack pines).
 Taxonomy: The "Branch of biology that names and classifies species by grouping
them into logical categories." Taxonomists use various observations (morphological,
behavioural, genetic, biochemical) to arrange species into a "hierarchy of broader and
broader groups" (Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species - D
K P C O F G S).
 Classification: Life is broadly divided into three domains: Eubacteria, Archaea, and
Eucarya.
 Eubacteria: Prokaryotic, single-celled, lack a nucleus and membrane-bound organelles,
cell wall contains peptidoglycan.
 Archaea: Prokaryotic, DNA has different genes than Eubacteria, unique cell membrane
structure (isoprenes instead of fatty acids), often found in extreme environments
(extremophiles).
 Eucarya: Includes three main Kingdoms (Plantae - autotrophic via photosynthesis, Fungi
- heterotrophic decomposers, Animalia - heterotrophic by ingestion) and the catch-all
group Protists (mostly single-celled).

5. The Microscopic World of Cells:

 Cell Theory: "all living things are composed of cells and that all cells come from
earlier cells."
 Two Major Cell Categories:Prokaryotic Cells: Include Bacteria and Archaea.
 Eukaryotic Cells: Include protists, plants, fungi, and animals.
 Basic Cell Features (Common to both):Bounded by a "thin plasma membrane".
 Contain "cytosol" (jelly-like fluid).
 Have "one or more chromosomes carrying genes made of DNA".
 Contain "ribosomes" for protein synthesis.
 Differences Between Prokaryotic and Eukaryotic Cells:Age: Prokaryotes (appeared
~3.5 billion years ago) are older than eukaryotes (~2.1 billion years ago).
 Size: Prokaryotic cells are generally smaller.
 Nucleus: Prokaryotic cells lack a nucleus; their DNA is located in a "nucleoid" region
without a nuclear membrane. Eukaryotic cells have a nucleus enclosed by a double
membrane, housing most of their DNA.
 Organelles: Eukaryotic cells possess "organelles, membrane-enclosed structures that
perform specific functions". Prokaryotic cells lack these.
 Prokaryotic Cell Structure (Details): Includes the plasma membrane, cell wall
(provides rigidity and shape), capsule (sticky coating for protection), flagella
(propulsion), pili (attachment), ribosomes, and nucleoid.
 Eukaryotic Cell Structure (Overview): The cytoplasm contains various organelles
suspended in the cytosol. Differences exist between animal and plant cells (e.g.,
chloroplasts and cell walls in plant cells; lysosomes and centrioles in animal cells).
Diagrams illustrate idealized animal and plant cells with key organelles labelled (nucleus,
mitochondria, endoplasmic reticulum, Golgi apparatus, ribosomes, cytoskeleton, etc.).

Tour of a Cell

 Basic Cell Features:

o All cells are enclosed by a thin plasma membrane.
o The interior of all cells contains a thick, jelly-like fluid called the cytosol. This
cytosol, along with the cellular components suspended within it (the organelles),
makes up the cytoplasm.
o Every cell possesses one or more chromosomes. These chromosomes carry genes
made of DNA , which hold the instructions for the cell.
o All cells also have ribosomes, which are tiny structures responsible for building
proteins based on the genetic instructions carried by DNA.
 Two Major Categories of Cells: The slides primarily focus on eukaryotic cells, which
are generally larger (ranging from 10 to 100 μm in diameter) compared to prokaryotic
cells (ranging from 0.1 to 5 μm in diameter).
 Animal vs. Plant Cells - Key Differences:
o Plant cells exclusively possess:
 Chloroplasts: These are the sites where photosynthesis occurs,
converting light energy into chemical energy.
 A cell wall: This is an outer layer providing structural support (while
mentioned in the diagram, its detailed composition isn't in these excerpts).
 A large central vacuole: This versatile compartment can store organic
nutrients, absorb water, and contain pigments or poisons.
o Animal cells exclusively possess:
 Lysosomes: These are membrane-enclosed sacs of digestive enzymes
that break down large molecules and recycle cellular components.
  Centrioles: These are involved in cell division but are noted as not being
present in most plant cells.
o Both animal and plant cells share:
 Plasma membrane: The outer boundary of the cell.
 Cytoplasm: The entire contents of the cell within the plasma membrane.
 Nucleus: The control centre containing DNA.
 Ribosomes: For protein synthesis.
 Mitochondria: Where cellular respiration and ATP production take place.
 Rough and smooth endoplasmic reticulum (ER): Involved in
manufacturing and transport.
 Golgi apparatus: For processing and packaging cellular products.
 Cytoskeleton: A network of fibres for support and movement.
 The Nucleus - Genetic Control:
o The nucleus is the control centre of the cell.
o It contains DNA , which carries the genes that store the necessary information to
produce specific proteins.
o The nucleus is separated from the surrounding cytoplasm by a double
membrane called the nuclear envelope.
o The nuclear envelope is punctuated by pores that allow certain materials to pass
between the nucleus and the cytoplasm.
o Within the nucleus, long DNA molecules and associated proteins form fibres
called chromatin.
o Each long chromatin fibre constitutes one chromosome.
o The nucleolus is a prominent structure within the nucleus and is the site where
the components of ribosomes are made.
o DNA transfers its coded information to a molecule called messenger RNA
(mRNA).
o mRNA then exits the nucleus through the pores in the nuclear envelope and
travels to the cytoplasm.
 Ribosomes - Protein Synthesis:
o Ribosomes are responsible for protein synthesis.
o In eukaryotic cells, the components of ribosomes are made in the nucleus and
then transported through the pores of the nuclear envelope into the cytoplasm.
o Some ribosomes are suspended in the cytosol and make proteins that remain
within the fluid of the cell.
o Others are attached to the outside of the nucleus or the endoplasmic
reticulum; these ribosomes make proteins that are incorporated into membranes
or secreted by the cell.
 Protein Sorting & The Endomembrane System - Manufacturing and Distribution:
o The endomembrane system is an internal network of membranes within a cell.
o It consists of the nuclear envelope, the endoplasmic reticulum (ER), the Golgi
apparatus, lysosomes, and vacuoles.
o These membranous organelles are either physically connected or linked by
vesicles, which are sacs made of membrane.
 The Endoplasmic Reticulum (ER):
o The endoplasmic reticulum (ER) is a major manufacturing facility in the cell.
 o It is connected to the nuclear envelope.
o The ER is composed of interconnected rough and smooth ER, which have
different structures and functions.
o Rough ER has ribosomes attached to its surface, giving it a "rough" appearance.
Cells that specialise in the production of proteins have a larger amount of rough
ER, such as cells of the pancreas and digestive tract. Some products
manufactured by rough ER are chemically modified and then packaged into
transport vesicles, which are sacs made of membrane that bud off from the rough
ER and can be dispatched to other locations in the cell.
o Smooth ER lacks surface ribosomes and is involved in several metabolic
processes. It produces lipids, including steroids such as hormones in the adrenal
cortex and endocrine glands, as well as steroid sex hormones in cells of the
ovaries and testes. The smooth ER also plays a crucial role in detoxifying a
number of organic chemicals, converting them to safer water-soluble products.
Liver cells, rich in smooth ER enzymes, detoxify products of natural metabolism,
drugs, and antibiotics. To assist with this, the smooth ER can double its surface
area within a few days when needed and return to its normal size later. The
smooth ER contains enzymes that catalyse reactions that make lipid-soluble
drugs and metabolic wastes water-soluble so they can be easily expelled from
the body.
 The Golgi Apparatus - Processing and Packaging:
o The Golgi apparatus consists of a stack of membrane plates.
o Products made in the ER reach the Golgi apparatus in transport vesicles.
o Proteins within a vesicle are usually modified by enzymes during their transit
from the "receiving" side to the "shipping" side of the Golgi apparatus.
o The "shipping" side of a Golgi stack acts as a depot where finished products
can be carried in transport vesicles to other organelles or to the plasma
membrane for secretion. The Golgi apparatus works in partnership with the ER.
 Lysosomes - Digestion and Recycling (Animal Cells):
o A lysosome is a membrane-enclosed sac of digestive enzymes found in animal
cells.
o The enzymes in a lysosome can break down large molecules such as proteins,
polysaccharides, fats, and nucleic acids.
o Lysosomes have several digestive functions. They fuse with food vacuoles
(formed when single-celled protists engulf nutrients) and expose the food to
digestive enzymes, resulting in small molecules that nourish the cell.
o Lysosomes can also destroy harmful bacteria, engulf and digest damaged
organelles (recycling their components), and play a role in sculpting tissues
during embryonic development, such as in the formation of fingers.
o Lysosomes are important for cell function and human health; hereditary
disorders called lysosomal storage diseases occur when one or more digestive
enzymes are missing, causing lysosomes to become engorged with indigestible
substances, eventually interfering with cellular functions and often being fatal in
early childhood.
o Most plant cells do not contain lysosomes but have lytic vacuoles that perform
similar functions.
 Vacuoles - Storage and More:
o Vacuoles are large sacs made of membrane that bud off from the ER or
Golgi apparatus.
o Certain freshwater protists have contractile vacuoles that pump out excess
water that flows into the cell from the hypotonic external environment, preventing
the cell from lysing (rupturing). This acts as a protective mechanism and helps
regulate the quantity of water inside the cell.
o A central vacuole can account for more than half the volume of a mature plant
cell and is a versatile compartment that can store organic nutrients, absorb
water, and contain pigments that attract pollinators or poisons that protect
against herbivores.
 Energy Transformations - Chloroplasts and Mitochondria:
o A cell converts energy obtained from the environment into usable forms.
Chloroplasts and mitochondria act as cellular power stations.
o Mitochondria are found in almost all eukaryotic cells and are the organelles
where cellular respiration takes place, producing ATP (adenosine triphosphate)
from the energy of food molecules. Cells use ATP as the direct energy source for
most of their work. A mitochondrion is enclosed by an envelope of two
membranes, and the inner membrane has numerous infoldings called cristae,
which increase the surface area for the chemical reactions of cellular respiration.
The inner membrane encloses a thick fluid called the mitochondrial matrix.
Mitochondria contain their own circular DNA (mtDNA) and ribosomes and can
grow and pinch in two, reproducing themselves. It is believed that mitochondria
evolved from ancient free-living prokaryotes that established residence within
other, larger host cells – a process called endosymbiosis. Different cells have
different amounts of mitochondria depending on their energy needs; for example,
muscle, liver, kidney, and brain cells have many mitochondria.
o Chloroplasts are unique to the photosynthetic cells of plants and algae and are
the organelles that perform photosynthesis, the conversion of light energy from
the sun to the chemical energy of sugar and other organic molecules. Chloroplasts
are also divided into compartments by two membranes. The stroma is a thick
fluid found inside the innermost membrane. Suspended in the stroma is a network
of membrane-enclosed disks and tubes that form another compartment. The disks
occur in interconnected stacks called grana, which are the structures that trap
light energy and convert it to chemical energy. Like mitochondria, chloroplasts
also contain their own circular DNA and ribosomes and can reproduce
themselves, also believed to have evolved through endosymbiosis.
 The Plasma Membrane - Barrier and Transport:
o The plasma membrane is a thin boundary that encloses the cell. It is selectively
permeable, controlling what enters and leaves the cell.
o Transport across the plasma membrane can be passive transport, which requires
no energy, or active transport, which requires energy.
o There are also mechanisms for the transport of large molecules and particles,
including endocytosis (movement into the cell) and exocytosis (movement out of
the cell).
 Passive Transport Details:
 o Passive transport requires no energy and occurs because of gradients in
concentration, pressure, or charge, moving substances from an area of high
concentration to an area of low concentration to equalize the gradient.
o Diffusion is a passive process where molecules move down their concentration
gradient. Gases and liquids have random molecular movement, causing them to
mix. For example, oxygen enters cells and carbon dioxide exits by diffusion.
Dialysis, used to remove wastes from blood in kidney failure, is an application of
passive diffusion across a semipermeable membrane.
o Facilitated diffusion is also a passive process but involves the passage of
substances down their concentration gradient through transport proteins in the
membrane. These proteins can be carrier proteins (or transporters) that bind to
a molecule and change shape to move it across the membrane (e.g., glucose
transporter), or channel proteins that provide a channel for small molecules or
ions to pass through (e.g., aquaporins for water transport, ion channels in nerves
and muscles). Facilitated diffusion allows polar and charged molecules that
cannot easily pass through the lipid bilayer to cross the plasma membrane without
the cell spending energy.
o Osmosis is the net movement of solvent (usually water) across a selectively
permeable membrane towards a higher solute concentration. It can also be
defined as the movement of water molecules from a higher to a lower
concentration of water or from a lower to a higher concentration of solute.
Osmosis can cause water to move into or out of a cell. The direction of water
movement is affected by the tonicity of the surrounding solution relative to the
inside of the cell: in a hypotonic solution, the outside solvent will flow into the
cell; in an isotonic solution, solutes are equal inside and out; and in a hypertonic
solution, solutes are greater outside the cell, causing fluid to flow out. Examples
of osmosis include the swelling of brain cells in response to excess water and the
turgidity of plant cells. Osmoregulation is the maintenance of water balance.
 Active Transport Details:
o Active transport is the movement of molecules against their concentration or
electrochemical gradient, requiring energy (usually provided by the hydrolysis
of ATP).
o An example is the sodium-potassium pump, which pumps 3 sodium ions (Na+)
out of the cell and 2 potassium ions (K+) into the cell, both against their
concentration gradients. This pump is crucial for maintaining osmotic balance and
cell volume.
 Endocytosis Details:
o Endocytosis is the process by which cells move large materials, particles,
organisms, or large molecules into the cell. The plasma membrane surrounds the
material, the edges of the membrane meet, and the membranes fuse to form a
vesicle containing the engulfed material.
o There are different types of endocytosis:
 Phagocytosis ("cell eating") is the process of engulfing large particles,
such as cells. Examples include how protozoa engulf food and how white
blood cells (phagocytes) engulf bacteria by wrapping them with their
 membrane and taking them into the cell. The engulfed material is
contained in a vacuole that then fuses with lysosomes for digestion.
 Pinocytosis ("cell drinking") is the process of engulfing liquids and the
materials dissolved in them, including waste and useful hormones. The
sacs formed are very small (vesicles) compared to phagocytosis, and
energy is used in this active process.
 Receptor-mediated endocytosis is a more specific process where
molecules from the cell's surroundings bind to receptor molecules on the
plasma membrane. The membrane then folds in and engulfs these
molecules. Examples include the transport of insulin into animal cells and
the uptake of iron carried by the transferrin protein.
 Exocytosis Details:
o Exocytosis is essentially the reverse of endocytosis, where membranous sacs
(vesicles) containing materials from the cell migrate to the plasma membrane and
fuse with it, releasing their contents outside the cell.
o Many materials are exported from the cell via exocytosis, such as mucus,
digestive enzymes, and molecules produced by nerve cells (neurotransmitters).
Examples include the release of salty tears by tear gland cells and the exocytosis
of neurotransmitters in the brain.
 The Cytoskeleton - Shape and Movement:
o The cytoskeleton is a network of fibres extending throughout the cytoplasm,
serving as both a skeleton and "muscles" for the cell, providing support and
enabling movement. It provides anchorage and reinforcement to many organelles,
such as holding the nucleus in place.
o Lysosomes can reach food vacuoles by gliding along microtubule tracks, and
microtubules guide chromosome movement during cell division.
o The cytoskeleton provides mechanical support to the cell and helps it maintain
its shape.
o It is made of three main types of fibres: microfilaments, microtubules (hollow
tubes of protein), and intermediate filaments (thinner and solid).
o A cell's cytoskeleton is dynamic; it can be quickly dismantled in one area and
reformed in another by adding or removing protein subunits. This rearrangement
can provide rigidity in a new location, change the shape of the cell, or even cause
the whole cell or parts of it to move, such as in amoeboid crawling and white
blood cell movement.
 Cilia and Flagella - Movement:
o In some eukaryotic cells, microtubules are arranged into structures called
flagella and cilia, which are extensions from the cell that aid in movement.
o Eukaryotic flagella are longer and usually occur singly, propelling cells through
an undulating, whiplike motion, as seen in human sperm cells. Problems with
flagella can lead to male infertility.
o Cilia (singular, cilium) are generally shorter and more numerous than flagella and
move in a coordinated back-and-forth motion, like oars. Both cilia and flagella
propel various protists through water. In humans, cilia on cells lining the trachea
help sweep mucus with trapped debris out of the lungs. Tobacco smoking can
 inhibit or destroy these cilia. Some men with hereditary sterility also suffer from
respiratory problems due to defects in the structure of their flagella and cilia.

Executive Summary

1. Fundamental Characteristics of All Cells:

The lecture begins by outlining the basic features shared by all cells, regardless of their
classification as prokaryotic or eukaryotic (though the focus of the provided material is clearly
on eukaryotic cells). These fundamental features include:

 Plasma Membrane: A thin outer boundary enclosing the cell.

 Cytosol: A jelly-like fluid within the cell, also referred to as the matrix of the cytoplasm,
where cellular components (organelles) are suspended.
 Chromosomes: One or more structures carrying genes made of DNA.
 Ribosomes: Tiny structures responsible for protein synthesis based on genetic
instructions.

2. Major Categories of Cells and Key Differences:

The document highlights the two major categories of cells, although the specifics of prokaryotic
cells are not detailed. Regarding eukaryotic cells, it notes important differences between plant
and animal cells:

 Plant Cells: Possess chloroplasts (for photosynthesis), a cell wall (providing structural
support), and typically a large central vacuole (for storage, water absorption, etc.). They
generally lack centrioles and lysosomes (though they have lytic vacuoles with similar
functions).
 Animal Cells: Possess lysosomes (containing digestive enzymes) and centrioles
(involved in cell division, though this is only implied by the diagram). They lack
chloroplasts and a cell wall.

The document includes idealized diagrams of both animal and plant cells, visually representing
these common and differing organelles.

3. The Nucleus: Genetic Control Centre:

The nucleus is presented as the cell's control centre, housing the genetic material (DNA). Key
features include:

 DNA and Genes: The nucleus contains DNA, which holds the genes necessary for
producing specific proteins.
 Nuclear Envelope: A double membrane separating the nucleus from the cytoplasm,
containing pores that allow regulated passage of materials.
 Chromatin and Chromosomes: Long DNA molecules and associated proteins form
chromatin fibres. Each long chromatin fibre constitutes one chromosome.
  Nucleolus: A prominent structure within the nucleus where components of ribosomes are
made.

The process of how DNA directs protein production is described:

 DNA's coded information is transcribed into messenger RNA (mRNA).

 mRNA exits the nucleus through nuclear pores and travels to the cytoplasm.
 In the cytoplasm, mRNA binds to ribosomes, which translate the genetic message into a
protein with a specific amino acid sequence.

4. Ribosomes: Protein Synthesis Machinery:

Ribosomes are explicitly identified as the sites of protein synthesis. Key points include:

 Origin: Components of ribosomes are made in the nucleolus and then exported to the
cytoplasm.
 Location and Function: Ribosomes can be suspended in the cytosol (producing proteins
that remain within the cell fluid) or attached to the outside of the nucleus and the
endoplasmic reticulum (producing proteins destined for membranes or secretion).

5. The Endomembrane System: Manufacturing and Distribution:

This section introduces the endomembrane system, an interconnected network of membranes

involved in manufacturing and distributing cellular products. It comprises:

 Nuclear envelope
 Endoplasmic reticulum (ER)
 Golgi apparatus
 Lysosomes
 Vacuoles

These organelles are either physically connected or linked by transport vesicles (membrane-
bound sacs).

6. The Endoplasmic Reticulum (ER): Two Forms, Diverse Functions:

The ER is described as a major manufacturing facility connected to the nuclear envelope,

existing in two forms:

 Rough ER: Studded with ribosomes, primarily involved in the synthesis and
modification of proteins (especially those destined for secretion or insertion into
membranes). The document notes that cells specialising in protein production have a
larger amount of rough ER. "Some products manufactured by rough ER are chemically
modified and then packaged into transport vesicles- Vesicles - sacs made of membrane
that bud off from the rough ER."
  Smooth ER: Lacks ribosomes, involved in lipid synthesis (including steroids and
hormones), detoxification of drugs and metabolic wastes, and contains enzymes that
catalyse various reactions. Liver cells, ovaries, and testes are highlighted as having
abundant smooth ER depending on their function. "It contains enzymes that catalyze a
number of reactions ; that can make lipid-soluble drugs and metabolic wastes into water-
soluble, so that these (drugs and waste) can easily be expelled out of the body ." The
ability of smooth ER to increase its surface area for detoxification is also mentioned.

7. The Golgi Apparatus: Processing and Packaging:

The Golgi apparatus is depicted as a stack of membrane plates involved in further processing and
packaging of molecules originating from the ER. Key aspects include:

 Receiving and Shipping Sides: Products arrive from the ER in transport vesicles at the
"receiving" side and are further modified by enzymes as they move through the Golgi.
 Dispatch: The "shipping" side acts as a depot from which finished products are carried in
transport vesicles to other organelles or the plasma membrane for secretion. "The
shipping side of a Golgi stack is a depot - finished products can be carried in transport
vesicles to other organelles or to the plasma membrane."

8. Lysosomes: Digestive Compartments:

Lysosomes are described as membrane-enclosed sacs of digestive enzymes found primarily in

animal cells (plant cells have functionally similar lytic vacuoles). Their functions include:

 Intracellular Digestion: Breaking down large molecules (proteins, polysaccharides, fats,

nucleic acids) from food vacuoles and damaged organelles. "Enzymes in a lysosome can
break down large molecules such as proteins, polysaccharides, fats, and nucleic acids."
 Autophagy: Engulfing and digesting parts of the cell's own organelles.
 Developmental Roles: Sculpting tissues during embryonic development (e.g., forming
fingers).
 Health Implications: Deficiencies in lysosomal enzymes lead to lysosomal storage
diseases, where indigestible substances accumulate, often with fatal consequences in
early childhood.

9. Vacuoles: Diverse Storage and Maintenance Compartments:

Vacuoles are large, membrane-bound sacs derived from the ER and Golgi. Their functions vary
depending on the cell type:

 Contractile Vacuoles (Freshwater Protists): Pump out excess water to maintain

osmotic balance and prevent lysis in hypotonic environments.
 Central Vacuole (Plant Cells): Can occupy a large portion of the cell volume and is
involved in storing organic nutrients, absorbing water, and containing pigments or
poisons. "A central vacuole can account for more than half the volume of a mature plant
 cell... store organic nutrients, absorb water, and contain pigments that attract pollinating
insects or poisons that protect against plant-eating animals."

10. Energy Transformations: Mitochondria and Chloroplasts:

These organelles are presented as the cell's power stations:

 Mitochondria: Found in almost all eukaryotic cells, the site of cellular respiration,
producing ATP (the cell's direct energy currency) from the energy of food molecules.
Key features include a double membrane, an inner membrane with folds called cristae
(increasing surface area for reactions), and the mitochondrial matrix (the inner fluid-filled
space). The document also notes that different cells have varying numbers of
mitochondria depending on their energy needs. "Mitochondria ... are the organelles in
which cellular respiration takes place, and produce ATP from the energy of food
molecules."
 Chloroplasts: Unique to photosynthetic cells of plants and algae, the site of
photosynthesis, converting light energy into the chemical energy of sugars and other
organic molecules. They also have a double membrane, an inner fluid called the stroma,
and interconnected stacks of membrane-enclosed disks called grana (where light energy
is trapped).

Both mitochondria and chloroplasts are highlighted as containing their own DNA and ribosomes,
enabling them to produce some of their own proteins and replicate independently. The
endosymbiotic theory, suggesting their evolution from ancient free-living prokaryotes that
established symbiotic relationships with host cells, is also mentioned.

11. The Plasma Membrane and Transport:

The plasma membrane is revisited as a selectively permeable barrier controlling the movement of
substances into and out of the cell. Different transport mechanisms are described:

 Passive Transport: Requires no energy, driven by gradients (concentration, pressure,

charge). Includes:
 Diffusion: Movement of molecules down a concentration gradient. Examples of gases
(oxygen, carbon dioxide) and the application in dialysis are given.
 Facilitated Diffusion: Movement of polar and charged molecules down a concentration
gradient with the help of membrane proteins (carrier proteins and channel proteins).
Examples of glucose transporters and aquaporins are provided.
 Osmosis: Net movement of solvent (usually water) across a selectively permeable
membrane towards a higher solute concentration. The concepts of hypotonic, isotonic,
and hypertonic solutions are explained, along with examples like turgor in plant cells and
osmoregulation in animals.
 Active Transport: Requires energy (usually ATP) to move molecules against their
concentration gradient. The sodium-potassium pump is given as an example, highlighting
its role in maintaining osmotic balance and cell volume.
 Bulk Transport: Movement of large materials across the plasma membrane:
  Endocytosis: Importing substances into the cell by forming vesicles from the plasma
membrane. Includes phagocytosis ("cell eating" of large particles), pinocytosis ("cell
drinking" of fluids), and receptor-mediated endocytosis (specific uptake of molecules
bound to receptors).
 Exocytosis: Exporting substances from the cell by the fusion of vesicles with the plasma
membrane. Examples include the secretion of mucus, digestive enzymes, and
neurotransmitters. "Reverse of endocytosis – when you cry, cells of tear glands use
exocytosis to export salty tears."

12. The Cytoskeleton: Cell Shape and Movement:

The cytoskeleton is introduced as a network of fibres throughout the cytoplasm, providing

structural support, anchorage for organelles, and enabling cell movement. Key components
include:

 Microfilaments: Thinner, solid fibres.

 Microtubules: Hollow tubes of protein.
 Intermediate Filaments: Thinner and solid, providing reinforcement.

The dynamic nature of the cytoskeleton, allowing for rapid rearrangement to change cell shape
or facilitate movement (like amoeboid crawling and white blood cell movement), is highlighted.

13. Cilia and Flagella: Motile Appendages:

These microtubule-based extensions from the cell are described as aids in movement:

 Flagella: Longer, usually fewer in number, propel cells with an undulating, whiplike
motion (e.g., sperm cells).
 Cilia: Shorter, more numerous, move in a coordinated back-and-forth motion (e.g., lining
of the trachea to sweep mucus).

The importance of proper flagellar function for sperm motility and the link between defects in
cilia and flagella structure to both sterility and respiratory problems are mentioned.

In conclusion, the provided lecture notes offer a comprehensive overview of eukaryotic cell
structure, detailing the functions of various organelles and the mechanisms of transport across
the plasma membrane. The interconnectedness of cellular components and processes is a
recurring theme, emphasizing the complexity and efficiency of cellular life.

Photosynthesis

What is Photosynthesis?

Photosynthesis is fundamentally a process where light energy is converted into chemical energy.
Green plants, algae, and certain bacteria achieve this by using sunlight to synthesise nutrients
from carbon dioxide and water. This process transforms light energy initially into chemical bond
energy in the form of ATP (adenosine triphosphate) and then uses this ATP to produce complex
organic molecules, most notably glucose. Essentially, photoautotrophs, which include plants,
algae, and certain bacteria, use sunlight to create their own food through photosynthesis. This is
in contrast to chemotrophs that obtain energy by oxidising organic or inorganic electron donors,
such as those found in hydrothermal vents.

The Overall Equation:

The process of photosynthesis can be summarised by the equation: Light

energy + 6 CO2 + 6
H2O → C6H12O6 + 6O2. This shows that carbon dioxide from the atmosphere and water are
the primary inorganic reactants, and in the presence of light energy, they are converted into
glucose, a sugar (C6H12O6), and oxygen (O2). The chemical energy captured during this
process is stored within the bonds of the resulting sugar molecules.

Where Does Photosynthesis Happen?

Photosynthesis occurs within chloroplasts, which are light-absorbing organelles present in all
the green parts of a plant. These organelles are often highly concentrated in the interior cells of
leaves. The green colour of chloroplasts comes from chlorophyll, a pigment molecule that plays
a central role in absorbing solar energy and converting it into chemical energy. Within the
chloroplast, there are membranes called thylakoids, which form a framework where many of the
light-dependent reactions take place. The fluid-filled space within the chloroplast surrounding
the thylakoids is called the stroma, which is the site of the light-independent reactions (Calvin
cycle). Carbon dioxide enters the leaves through tiny pores called stomata, while oxygen exits
through these same pores.

Reactants and Products:

 Reactants:
o Light energy: Sunlight is a form of electromagnetic energy or radiation,
characterised by different wavelengths. Chlorophyll molecules absorb about 80%
of the visible light spectrum.
o Carbon dioxide (CO2): Enters the leaf through stomata.
o Water (H2O): Absorbed by the plant's roots and transported to the leaves.
 Products:
o Glucose (C6H12O6): A sugar molecule that serves as a primary source of energy
and a building block for other organic molecules. The chemical energy is stored in
its bonds.
o Oxygen (O2): Released as a byproduct and exits the leaf through stomata.

Two Main Stages of Photosynthesis:

1. Light-Dependent Reactions (Photo Reactions):

o These reactions occur in the thylakoid membranes.
o They are initiated by the absorption of sunlight by pigment molecules like
chlorophyll a, chlorophyll b, and carotenoids, which are organised into
 photosystems (Photosystem II and Photosystem I). These pigments are built
into the thylakoid membranes and organised into light-harvesting complexes.
o Sunlight behaves as both waves and discrete packets of energy called
photons. The shorter the wavelength of light, the greater the energy of its
photons.
o When a pigment molecule absorbs a photon, one of its electrons becomes excited
to a higher energy level. This excited state is unstable, and the electron usually
falls back to its ground state, releasing energy as heat or sometimes as fluorescent
light.
o In photosystems, the energy is passed from one pigment molecule in the antenna
complex to another until it reaches the reaction center, which contains a specific
chlorophyll a molecule.
o At the reaction center, an excited electron is transferred to a primary electron
acceptor molecule, effectively converting light energy into chemical energy.
o Photosystem II (PSII) occurs first. Its reaction center chlorophyll a absorbs light
optimally at 680 nm (P680). The excited electrons from PSII are passed through
an electron transport chain (ETC). As electrons move down the ETC, energy is
released and used to pump protons (H+) from the stroma into the thylakoid space,
creating a proton gradient.
o Water is split by an enzyme associated with PSII, releasing electrons to replace
those lost by chlorophyll, protons (H+) into the thylakoid space, and oxygen (O2)
as a byproduct.
o The proton gradient across the thylakoid membrane drives the synthesis of ATP
through a process called chemiosmosis, where protons flow back down their
concentration gradient through an enzyme complex called ATP synthase. This
process is similar to ATP production in cellular respiration.
o Electrons from the ETC eventually reach Photosystem I (PSI). Its reaction center
chlorophyll a absorbs light optimally at 700 nm (P700). Light energy re-excites
these electrons in PSI.
o These high-energy electrons from PSI are then transferred through another series
of electron carriers and ultimately used to reduce NADP+ to NADPH. NADPH is
another energy-carrying molecule used in the Calvin cycle.
o In summary, the light-dependent reactions convert light energy into chemical
energy in the form of ATP and NADPH, produce oxygen from water, and
occur in the thylakoid membranes.
2. Light-Independent Reactions (Calvin Cycle or Dark Reactions):
o These reactions take place in the stroma of the chloroplast.
o They do not directly require light but rely on the ATP and NADPH produced
during the light-dependent reactions to synthesise sugar from carbon dioxide.
o The process begins with carbon fixation, where carbon dioxide from the
atmosphere is incorporated into an existing organic molecule in the stroma.
Specifically, CO2 combines with a 5-carbon sugar called ribulose-1,5-
bisphosphate (RuBP). This reaction is catalysed by the enzyme ribulose
bisphosphate carboxylase (RuBisCo).
o The resulting unstable 6-carbon molecule immediately breaks down into two
molecules of 3-phosphoglycerate (3-PGA).
 o Using the energy from ATP and the reducing power of NADPH, 3-PGA is
converted through a series of steps into glyceraldehyde-3-phosphate (G-3-P).
o Glyceraldehyde-3-phosphate (G-3-P) is considered the initial three-carbon
sugar product of photosynthesis. For every six molecules of CO2 fixed, 12
molecules of G-3-P are produced.
o Some of the G-3-P molecules are used to regenerate RuBP, allowing the Calvin
cycle to continue. This regeneration requires ATP.
o The remaining G-3-P molecules are considered the net gain of the Calvin cycle
and can be used to synthesise glucose and other organic compounds, including
other simple sugars that can be used as building blocks for ATP, RNA, DNA, and
other carbohydrates like starch and cellulose. G-3-P can also be converted into
lipids for storage or phospholipids for cell membranes, and it can serve as a
carbon skeleton for the construction of amino acids needed to form proteins. G-3-
P can also be broken down during cellular respiration to produce ATP.
o In summary, the Calvin cycle uses ATP and NADPH from the light-
dependent reactions to fix carbon dioxide and produce G-3-P, which can then
be used to create various organic molecules.

Photosystems:

 Photosystems I (PSI) and II (PSII) are complexes of proteins and pigment molecules
embedded in the thylakoid membranes.
 Each photosystem has an antenna complex consisting of hundreds of chlorophyll and
accessory pigment molecules that capture light energy. Accessory pigments like
chlorophyll b and carotenoids absorb light at different wavelengths than chlorophyll a
and transfer this energy to chlorophyll a in the reaction center.
 The reaction center contains a special chlorophyll a molecule and a primary electron
acceptor. When the energy from the antenna complex reaches the reaction center, an
electron in the chlorophyll a molecule is excited and transferred to the primary electron
acceptor, initiating the light-dependent reactions.
 PSII (P680) absorbs light optimally at a shorter wavelength (680 nm) than PSI (P700).
 Although named in the order of their discovery, PSII functions before PSI in the linear
electron flow of the light-dependent reactions. PSII provides electrons to the electron
transport chain that ultimately leads to PSI.

Importance of Photosynthesis:

 Photosynthesis is the fundamental process that sustains most life on Earth by producing
organic molecules (food) for autotrophs.
 It is also responsible for the release of oxygen (O2) into the atmosphere, which is
essential for the respiration of many organisms.
 The fixation of atmospheric carbon dioxide during the Calvin cycle plays a crucial role
in the global carbon cycle. This process helps to reduce the concentration of carbon
dioxide in the atmosphere.
  Deforestation, the removal of photosynthetic plant life, reduces the biosphere's ability to
absorb carbon dioxide. Conversely, planting new forests can increase carbon fixation,
potentially mitigating the effects of greenhouse gases and global climate change.

Executive Summary:

Main Themes and Important Ideas:

1. The Fundamental Process of Photosynthesis:

 Photosynthesis is defined as "the process by which green plants and some other
organisms use sunlight to synthesize nutrients from carbon dioxide and water."
 It transforms light energy into chemical bond energy, initially stored in ATP and then
used to create complex organic molecules like glucose.
 The overall reaction is summarised as: "Light energy + 6 CO2 + 6 H2O → C6H12O6 +
6O2," or in simpler terms, "carbon dioxide + water → Glucose + Oxygen."
 This process is carried out by autotrophs, which can produce their own food using either
sunlight (photoautotrophs) or chemical energy (chemotrophs). Plants, algae, and certain
bacteria are photoautotrophs.

2. Chloroplasts: The Sites of Photosynthesis:

 Chloroplasts are "light-absorbing organelles present in all green parts of a plant" and are
the primary sites where photosynthesis occurs.
 They are often concentrated in the interior cells of leaves.
 The green pigment chlorophyll within chloroplasts "plays a central role in converting
solar energy to chemical energy."

3. The Nature of Sunlight and Chloroplast Pigments:

 Sunlight is a form of "radiation, or electromagnetic energy," characterised by

wavelengths.
 Chlorophyll absorbs approximately 80% of the visible light spectrum.
 Leaves appear green because green light is "poorly absorbed by chloroplasts and is thus
reflected or transmitted toward the observer."
 Other pigments, such as chlorophyll b and carotenoids, absorb different wavelengths of
light, broadening the spectrum of light that can be used for photosynthesis.
 Carotenoids (yellow-orange pigments like beta-carotene and lycopene) also have a
"protective function" by dissipating excessive light energy that could damage chlorophyll
and some are important human nutrients.
 The vibrant colours of autumn foliage are due to the presence of carotenoids becoming
visible as chlorophyll levels decrease.

4. Harvesting Light Energy in Photosystems:

  Chloroplast pigments are organised into "light harvesting complexes called
Photosystems" within the thylakoid membranes.
 Light behaves as both waves and particles called photons. Shorter wavelengths have
photons with greater energy.
 When a pigment molecule absorbs a photon, an electron becomes "excited," entering an
unstable high-energy state.
 This excited electron typically releases energy as heat and sometimes as fluorescent light
when it returns to its "ground state."
 Photosystems contain an "antenna complex" of numerous chlorophyll and accessory
pigment molecules that capture light energy and transfer it to a central "reaction center"
(a chlorophyll a/protein complex).
 At the reaction center, an excited electron is passed to a "primary electron acceptor
molecule," initiating the light-dependent reactions.

5. The Light-Dependent Reactions:

 These reactions are "initiated by the excited electrons which result by capturing sun
light."
 They occur in the thylakoids and involve two photosystems: Photosystem II (PS II) and
Photosystem I (PS I).
 "PS II occurs first and feeds its excited electrons to PS I."
 Light energy captured by PS II is used to split water molecules, releasing oxygen ("The
oxygen is released into the environment as O2"), electrons (which replace those lost by
chlorophyll in PS II), and protons.
 Excited electrons from PS II are passed through an "electron-transport chain (ETC),"
similar to that in cellular respiration. This process establishes a "proton gradient" across
the thylakoid membrane.
 The flow of protons back across the membrane through "ATP synthase" drives the
synthesis of ATP from ADP and inorganic phosphate (phosphorylation).
 Light energy is also captured by PS I, and its excited electrons are ultimately transferred
to NADP+, reducing it to NADPH.
 In summary, the light-dependent reactions produce ATP and NADPH, energy-rich
molecules that will fuel the Calvin cycle.

6. The Light-Independent Reactions (Calvin Cycle):

 These reactions "use the products of the light reactions to make sugar from carbon
dioxide" and occur in the stroma of the chloroplast.
 They are indirectly dependent on light because they require the ATP and NADPH
produced during the light-dependent reactions.
 The Calvin cycle involves "carbon fixation," where carbon dioxide from the atmosphere
is incorporated into an existing organic molecule.
 This process begins with CO2 combining with a 5-carbon molecule called ribulose
bisphosphate (RuBP), a reaction catalysed by the enzyme RuBisCo (ribulose
bisphosphate carboxylase).
  The resulting unstable 6-carbon molecule quickly breaks down into two 3-carbon
molecules.
 Using ATP and NADPH, these 3-carbon molecules undergo a series of reactions,
ultimately leading to the formation of glyceraldehyde-3-phosphate (G-3-P). This pathway
is referred to as the "C3 photosynthetic pathway."
 "G-3-P and not sugar is the initial product of photosynthesis."
 Some G-3-P molecules are used to regenerate RuBP, ensuring the continuation of the
Calvin cycle, while others are used to synthesise glucose and other organic compounds,
including complex carbohydrates like starch and cellulose, lipids, and amino acids.

7. Energy Transformations and the Interplay with Cellular Respiration:

 Photosynthesis is a chemical transformation that requires a significant input of energy,

which is provided by sunlight absorbed by chlorophyll.
 It is presented as the "opposite" of cellular respiration in terms of electron transfer:
"Electrons are boosted 'uphill' and added to carbon dioxide to produce sugar," whereas
cellular respiration involves the "fall' of electrons from food molecules to oxygen."
 The energy stored in the glucose produced during photosynthesis can later be released
through cellular respiration to generate ATP for the plant's metabolic activities.

8. Photosynthesis and the Environment:

 "The initial incorporation of carbon from the atmosphere into organic compounds is
called carbon fixation." This process helps to reduce the concentration of carbon dioxide
in the atmosphere.
 Deforestation "reduces the ability of the biosphere to absorb carbon," while planting new
forests can have the opposite effect, potentially mitigating the effects of greenhouse gases
and climate change.

How do Cells aquire Energy

ATP and Cellular Work

 ATP (adenosine triphosphate) is indeed the primary nucleotide that manages the
transfer of chemical energy within living cells. Its structure comprises adenosine and a
tail of three phosphate groups.
 The crucial aspect for energy storage and release lies in the bonds
holding the last two
phosphate groups, which are high-energy phosphate bonds that are easily broken. This
chemical energy is stored when ATP is synthesised and released when it is broken down.
 The tail of three negatively charged phosphate groups is key to providing energy for
cellular work, as these negative charges repel each other.
 ATP powers cellular processes by transferring a phosphate group to another
molecule, a process known as phosphorylation. This transfer is facilitated by enzymes
that couple the release of energy from ATP to cellular activities that require energy.
A good example is the movement of a muscle fibre when a cyclist pedals uphill, which
involves the transfer of a phosphate group from ATP to motor proteins.
  Cells continuously use and reform ATP; it's akin to a chargeable
battery. In fact, up to
10 million ATP molecules can be used and re-formed every second in a single cell.

Enzymes – Biological Catalysts

 Enzymes are proteins that act as biological catalysts, meaning they speed up
metabolic reactions without being consumed in the process. These metabolic reactions,
also known as biochemical reactions, involve the formation, breakdown, and
rearrangement of molecules to provide organisms with essential energy and building
blocks.
 Living organisms require energy to perform work, which they obtain either from visible
light or from the energy stored in covalent bonds through biochemical reactions. To
sustain life, these reactions need to occur at an extremely rapid rate.
 While raising the temperature can supply the necessary activation energy to start these
reactions (as done in a lab), this approach is not feasible in living organisms as it would
lead to the denaturation of proteins.
 Enzymes solve this problem by increasing the rate of reaction by lowering the
activation energy. They are globular proteins produced in small amounts within cells.
Each enzyme has a complex, specific structure and geometry determined by its unique
primary sequence of amino acids and resulting 3D shape.
 Enzymes exhibit specificity, acting on a specific substrate. The 3-dimensional shape,
size, and charge of the enzyme are responsible for allowing it to combine with a
reactant (the substrate) and lower the activation energy.
 The molecule to which the enzyme binds is called the substrate, and the temporary
molecule formed is the enzyme-substrate complex. The specific site where the substrate
binds is known as the active site or catalysis site.
 There are two main theories explaining enzyme specificity:
o The Lock and Key Model proposes that the enzyme's active site has a fixed
shape that is complementary to the shape of a specific substrate, like a lock fits a
specific key. This model primarily explains specificity.
o The Induced Fit Theory, proposed by Daniel Koshland, suggests that enzymes
are partially flexible, and the active site can be reshaped by interaction with the
substrate as it binds. The presence of the substrate causes the enzyme to mould
or adjust itself to the substrate, and the substrate plays a significant role in
determining the final shape of the active site.
 Enzymes can be used over and over again until they are worn out or damaged. Their
production is directly under the control of an organism's genetic material (DNA); the
instructions for their manufacture are found on the genes of the cell, and organisms make
their own enzymes. Enzymes are crucial for supporting almost all the chemical reactions
that maintain animal homeostasis.
 Enzyme activity is carefully regulated to ensure that metabolic activities occur in the
correct sequence and at the proper rate. This co-ordination prevents the formation of
essential products at the wrong times or in the wrong amounts, which could lead to cell
death.
  Enzyme inhibitors are molecules that attach themselves to an enzyme and interfere with
its ability to form an enzyme-substrate complex. There are two main types of inhibition
discussed:
o Competitive inhibition occurs when an inhibitor has a shape similar to the
normal substrate ("substrate imposter") and competes with the substrate for the
active site. While the inhibitor is bound, the active site is unavailable, and no
product is formed.
o Non-competitive inhibition involves an inhibitor binding to the enzyme at a site
remote from the active site. This binding changes the enzyme's shape, thus
preventing the substrate from binding at the active site.
o Negative feedback inhibition is another vital control mechanism where the
product of a reaction sequence acts as an inhibitor of one of the earlier enzymes
in the pathway. As the concentration of the end product increases, it binds to the
enzyme, reducing its activity. When the product level drops, the inhibition is
relieved, and the pathway resumes its activity.

Cellular Respiration

 Cellular respiration is defined as a process of aerobic harvesting of chemical energy

from organic fuel molecules. The overall net reaction is: C6H12O6 + 6O2 → 6CO2 +
6H2O + energy (~32 ATP + heat). Oxygen is involved in the breakdown of glucose to
carbon dioxide and water. The chemical-bond energy from glucose is released and stored
in the form of ATP .
 Cellular respiration is a multi-step process involving over two dozen steps. In eukaryotic
cells, it begins in the cytoplasm and is completed in the mitochondria. There are three
main enzymatic pathways or stages involved: Glycolysis, the Krebs cycle, and the
Electron transport chain.
o Glycolysis (glycos = sugar; lysis = split) takes place in the cytosol. It involves 10
steps catalysed by 10 enzymes. Glucose (a 6-carbon molecule) has energy added
to it from 2 ATP molecules, making it unstable and easier to break down. After
several enzymatic reactions, glucose is cleaved into 2 molecules of pyruvic acid
(3-carbon molecules). During this process, electrons released from the bond
splitting are picked up by NAD+ to form NADH. Glycolysis also produces 4
ATP molecules directly through substrate-level phosphorylation (transferring
phosphate groups from fuel molecules to ADP). Since 2 ATP molecules were
initially used, the net gain of ATP in glycolysis is 2 ATP per molecule of
glucose. Additionally, 2 NADH and 2 H+ are produced. The overall reaction for
glycolysis can be summarised as: Glucose + 2 ATP + 2 NAD+ → 4 ATP + 2
NADH + 2 Pyruvic acid.
o Between Glycolysis and the Krebs Cycle (Grooming of Pyruvate): The 2
molecules of pyruvic acid produced in the cytoplasm are transported into the
mitochondria. Here, they undergo a "grooming" process before entering the
Krebs cycle. Each pyruvate molecule loses a carbon atom, which is released as
CO2 . Electrons are stripped from the remaining 2-carbon fragment (acetate) and
transferred to NAD+, forming NADH. Finally, each acetate molecule is attached
to Coenzyme A (CoA), forming acetyl-CoA. For the two pyruvate molecules
 from one glucose, this stage yields 2 NADH and releases 2 CO2 molecules. No
ATP is directly produced here.
o Krebs Cycle (Citric Acid Cycle): This cycle takes place in the matrix region of
the mitochondrion. The acetyl portion of acetyl-CoA (a 2-carbon molecule) is
transferred to a 4-carbon compound called oxaloacetate, forming a 6-carbon
molecule, citrate. The CoA is released to participate in another reaction with
pyruvate. For every acetyl-CoA molecule that enters the cycle, two CO2
molecules are released as waste. Some energy released during the cycle is used
to produce ATP directly (via substrate-level phosphorylation). However, most of
the energy is captured in the form of high-energy electrons carried by NADH and
FADH2. For each acetic acid molecule (acetyl group) entering the cycle, 3
NADH, 1 FADH2, and 1 ATP are produced, and 2 CO2 molecules are
released. Since two acetyl-CoA molecules are formed from one glucose
molecule, the Krebs cycle yields a total of 2 ATP, 6 NADH, 2 FADH2, and 4
CO2 . Oxaloacetate is regenerated at the end of each cycle, allowing the cycle to
continue. All carbon atoms that enter the cell as fuel are eventually accounted for
as CO2.
o Electron Transport Chain (ETC) and Chemiosmosis: The NADH and FADH2
produced during glycolysis, pyruvate grooming, and the Krebs cycle now move to
the innermitochondrial membrane (cristae) to undergo the final stage of
aerobic respiration. The ETC is a series of redox reactions where electrons
carried by NADH and FADH2 are passed along a sequence of protein
complexes. As these electrons move through the complexes, they lose energy,
which is used to pump hydrogen ions (protons) from the mitochondrial
matrix into the intermembrane space, creating an electrochemical gradient.
Oxygen serves as the final electron acceptor in the chain. When the electrons
are added to oxygen, it becomes negatively charged (O--) and combines with
hydrogen ions to form water. This is why the process is aerobic. The
accumulation of H+ ions in the intermembrane space creates a concentration
gradient and a charge difference (more positive in the intermembrane space).
This potential energy is harnessed by an enzyme complex called ATP synthase,
which is embedded in the inner mitochondrial membrane. As the H+ ions flow
back down their concentration gradient through special channels in ATP
synthase, the enzyme uses the energy from this flow to phosphorylate ADP,
forming ATP. This process of ATP synthesis driven by the proton gradient is
called chemiosmosis. For each glucose molecule, the ETC and chemiosmosis are
estimated to produce about 26-28 ATP, depending on various factors. A total of
10 NADH and 2 FADH2 are produced from one glucose molecule during the
earlier stages, which feed electrons into the ETC.
 In summary, the approximate ATP yield from one molecule of glucose through aerobic
cellular respiration is around 2 ATP (net) from glycolysis + 2 ATP from the Krebs
cycle + 26-28 ATP from the ETC and chemiosmosis, totalling about 30-32 ATP.

Fermentation
  Fermentation is an anaerobic (without O2) harvest of food energy. It involves the
incomplete oxidation of glucose. Typically, glucose undergoes glycolysis, producing 2
ATP and pyruvic acid. The crucial role of fermentation is to regenerate NAD+ from
NADH so that glycolysis can continue in the absence of oxygen, as NAD+ is required for
one of the steps in glycolysis.
o Lactic Acid Fermentation: In this type, pyruvic acid is reduced to lactic acid.
This process regenerates NAD+ from NADH. The net profit of ATP is 2 ATP
per glucose molecule, which is solely from glycolysis. Lactic acid fermentation
is seen in muscle cells when oxygen supply is insufficient (leading to muscle
fatigue or oxygen debt) and in some bacteria used in the production of curd, sour
cream, cheeses, and other fermented dairy products. Lactic acid causes milk
protein to coagulate and solidify. Red blood cells in the human body also rely on
lactic acid fermentation for energy as they lack mitochondria.
o Alcoholic Fermentation: In other organisms, such as yeast cells, pyruvic acid is
reduced to ethanol (alcohol) and carbon dioxide. This process also regenerates
NAD+. The net ATP gain is again 2 ATP per glucose, from glycolysis. Alcoholic
fermentation is used in making bread (the trapped CO2 makes it leavened, and the
alcohol evaporates during baking) and in winemaking (where ethanol is the
desired product). Champagne and other sparkling wines are products of
fermentation that retain both carbon dioxide and alcohol.
 Organisms that can perform anaerobic respiration can be classified as:
o Facultative Anaerobes (switch hitters): These organisms, like yeast, can perform
aerobic respiration if oxygen is present but will switch to anaerobic
respiration (fermentation) if oxygen is absent.
o Obligate or Strict Anaerobes: These organisms can only perform anaerobic
respiration and can actually be killed by the presence of oxygen (e.g., some
types of bacteria).
 It's important to note that some prokaryotes can also perform anaerobic cellular
respiration, where they use substances other than oxygen as the final electron acceptor in
an electron transport chain. These acceptors can include sulfur, nitrogen, or other
inorganic or organic molecules like pyruvic acid. These organisms often lack the
necessary enzymes for the Krebs cycle or ETC that uses oxygen. Fermentation is
specifically defined as anaerobic pathways that oxidize glucose using an organic
molecule as the ultimate hydrogen (electron) acceptor.

Metabolic Processing of Molecules Other than Carbohydrates

 Fat Respiration: Before fats can be used for energy, they must be broken down into
smaller compounds by digestion. Most fatty acids have a glycerol backbone, which is
converted to glyceraldehyde-3-phosphate, an intermediate that directly enters
glycolysis. The remaining fatty acids, often long chains of carbons, must first enter the
mitochondria, where each long chain is hydrolysed into 2-carbon fragments. These 2-
carbon fragments are then converted to acetyl-CoA, which enters the Krebs cycle. Due
to the high number of carbons in fatty acids, each fat molecule can release up to 10
times more ATP than a molecule of glucose.
  Protein Respiration: Proteins are first digested into individual amino acids. Each amino
acid then needs to have its amino group removed by a process called deamination,
which primarily takes place in the liver. The non-nitrogenous part of the amino acid is
converted to keto-acids, which can then enter the Krebs cycle at various points. In the
Krebs cycle, electrons are removed from these keto-acids and sent to the ETC, where
their energy is used to generate ATP. The amino group that was removed is converted
into ammonia, a toxic product. In mammals, the liver converts ammonia to urea or uric
acid, which are then released from the cell through the blood and kidneys. Excess fluid
intake can help the kidneys efficiently remove these waste products, especially with a
high-protein diet. Unlike fats and carbohydrates, proteins cannot be stored in the body.

Extensive Notes:

1. ATP and Cellular Work

Main Theme: ATP (adenosine triphosphate) is the primary energy currency of the cell,
powering cellular work by storing chemical energy released from the breakdown of fuel
molecules.

Key Ideas/Facts:

 Fuel molecules like carbohydrates and fats cannot be directly used by cells. Their
breakdown releases chemical energy that is stored in ATP. "Chemical energy released by
the breakdown of these fuel molecules are stored in the form of ATP."
 ATP is a nucleotide with three phosphate groups. The bonds between the last two
phosphates are high-energy bonds that are easily broken. "The bonds holding the last 2
phosphates are the high-energy phosphate bonds, which are easily broken."
 The hydrolysis of ATP releases energy that can be used to power cellular processes. "The
chemical energy is stored when ATP is made and is released when it is broken."
 The tail of three negatively charged phosphate groups is crucial for ATP's energy-
providing function due to electrostatic repulsion. "The tail of 3 phosphate groups in the
ATP is the key part that provides energy for cellular work... Each phosphate is negatively
charged and these negative charges repel each other."
 ATP powers cellular work through phosphorylation, the transfer of a phosphate group to
another molecule, making it more reactive. "Able to power cellular processes by
transferring a phosphate group to another molecule (a process called phosphorylation)."
 Enzymes facilitate this energy transfer by coupling ATP hydrolysis to energy-requiring
cellular activities. "This transfer is carried out by enzymes that couple the release of
energy from ATP to cellular activities that require energy."
 The ATP cycle involves continuous spending and reformation of ATP, similar to a
rechargeable battery. "Cells spend ATP continuously ATP is like a chargeable battery...
Upto 10million ATPs are used and re-formed every second in a cell."

2. Enzymes – Biological Catalysts

Main Theme: Enzymes are protein catalysts that speed up metabolic reactions by lowering the
activation energy required for the reactions to occur, without being consumed in the process.

Key Ideas/Facts:

 Enzymes are essential for life as they accelerate biochemical reactions necessary for
energy provision and building blocks. "Proteins that speed up metabolic reactions without
being consumed by them... The formation, breakdown and rearrangement of molecules to
provide organisms with essential energy and building blocks are known as Biochemical
reactions."
 Biochemical reactions require an initial energy input called activation energy. "The input
of energy required to get these reactions started is called Activation energy."
 Raising the temperature can provide activation energy (in the lab), but this denatures
proteins in living organisms. "Raising the Temperature routinely helps in supplying the
activation energy, (in Lab) however, this rise in temperature results in denaturation of the
proteins."
 Enzymes act as catalysts to increase reaction rates without harming cells. "The use of
catalyst helps in increasing the rate of the reaction, without affecting the cells proteins."
 Enzymes lower the activation energy, allowing reactions to proceed rapidly at normal
cellular temperatures. "Enzymes work by lowering the activation energy."
 Enzymes are proteins whose production is controlled by an organism's genes (DNA).
"The production of these proteins is directly under the control of an organism’s genetic
material (DNA)."
 Enzymes are highly specific to their substrates due to their unique 3D shape and active
site. "Enzymes Bind selectively to Substrates... The 3-Dimentional shape, size and charge
are responsible for allowing the enzyme to combine with a reactant and lower the
activation energy... Site where substrate binds is known as Active site i.e. catalysis site."
 The "lock and key" model and the "induced fit" theory explain enzyme specificity. The
induced fit model suggests the enzyme's active site can change shape to better fit the
substrate. "INDUCED FIT THEORY : DANIEL KOSHLAND Since enzymes are
partially flexible in structure ,the active site can be reshaped by interaction with substrate
as it interacts with enzyme... The fit is induced because the presence of the substrate
causes the enzyme to mold or adjust itself to the substrate as the two come together."
 Some enzymes are regulated by the binding of small molecules, which can either increase
or decrease their activity, providing feedback regulation.
 Enzymes play a crucial role in maintaining animal homeostasis by supporting almost all
chemical reactions. "ENZYMES are BIOCATALYSTS or biological catalysts
responsible for supporting almost all of the chemical reactions that maintain ANIMAL
HOMEOSTASIS."
 Cellular control processes rely on the coordinated action and regulation of enzymes to
ensure metabolic pathways occur in the correct sequence and at the proper rate.
 Enzyme inhibitors can interfere with enzyme function. Competitive inhibitors bind to the
active site, while non-competitive inhibitors bind elsewhere, changing the enzyme's
shape.
  Negative feedback inhibition is a regulatory mechanism where the end product of a
metabolic pathway inhibits an earlier enzyme in the pathway, controlling the amount of
product formed.

3. Cellular Respiration

Main Theme: Cellular respiration is a process that harvests chemical energy from organic fuel
molecules, primarily glucose, in the presence of oxygen (aerobic) to produce ATP.

Key Ideas/Facts:

 Cellular respiration is an aerobic process that completely oxidises organic fuel molecules.
"Cellular respiration is defined as a process of aerobic harvesting of chemical energy
from organic fuel molecules."
 The net reaction for aerobic cellular respiration is: C6H12O6 + 6O2 → 6CO2 + 6H2O +
energy (~32 ATP + heat).
 Cellular respiration involves a series of enzyme-controlled redox reactions where glucose
loses electrons (oxidation) and oxygen gains electrons (reduction). "The chemical
activities that remove electrons from glucose result in the glucose being oxidized... In
aerobic cellular respiration oxygen serves as the terminal electron acceptor... LEO says
GER."
 High-energy electrons released from glucose are captured by electron carriers like NADH
and FADH2. "Electron transfer molecules like NADH and FADH2 temporarily hold the
electrons and transfer them to other electron carriers."
 ATP is formed when these electrons are passed down an electron transport chain.
 In eukaryotes, cellular respiration begins in the cytoplasm (glycolysis) and is completed
in the mitochondria (Krebs cycle and electron transport chain).
 Glycolysis: Occurs in the cytosol, breaks down glucose (a 6-carbon molecule) into two
molecules of pyruvic acid (a 3-carbon molecule), produces a net gain of 2 ATP molecules
and 2 NADH molecules. "Glycolysis (glycos = sugar; lysis = split) takes place in the
cytoplasm of the cells and results in the breakdown of glucose with the release of
electrons and the formation of ATP... Net gain of ATP is 2 ATP per molecule of glucose
in glycolytic pathway."
 Grooming of Pyruvate: Before entering the Krebs cycle, pyruvate is converted to
acetyl-CoA in the mitochondrial matrix, producing CO2 and NADH.
 Krebs Cycle (Citric Acid Cycle): Occurs in the mitochondrial matrix, completes the
oxidation of glucose by further breaking down acetyl-CoA, releasing CO2, ATP (via
substrate-level phosphorylation), and generating large amounts of NADH and FADH2.
"The acetyl-coenzyme A proceeds through the Krebs cycle and is completely oxidized...
For every acetic acid molecule that enters the cycle, two CO2 molecules are released as
waste... most energy is captured in the form of NADH and FADH2."
 Electron Transport Chain (ETC) and Chemiosmosis: Occurs on the inner
mitochondrial membrane (cristae). NADH and FADH2 donate electrons to the ETC, a
series of protein complexes. As electrons are passed down the chain, energy is released
and used to pump protons (H+) across the inner membrane, creating a proton gradient.
 "Electron transport system... These are a series of redox reactions with oxygen as the
final electron acceptor."
 Chemiosmosis: The potential energy stored in the proton gradient is used by ATP
synthase, an enzyme complex in the membrane, to phosphorylate ADP to ATP as protons
flow back down their concentration gradient. "The H+s then diffuse down their
concentration gradient through an ATP Synthase enzyme that produces ATP... Process
produces about 32 ATP."
 Oxygen acts as the final electron acceptor in the ETC, combining with electrons and
hydrogen ions to form water.

4. Fermentation (Anaerobic Respiration)

Main Theme: Fermentation is an anaerobic process that allows cells to produce a small amount
of ATP from glucose in the absence of oxygen.

Key Ideas/Facts:

 Fermentation is the incomplete oxidation of glucose without the use of oxygen.

"Anaerobic (without O2) harvest of food energy... Anaerobic respiration is the
incomplete oxidation of glucose."
 It typically starts with glycolysis, producing pyruvic acid and a small amount of ATP.
 Pyruvic acid is then further reduced to other organic molecules, regenerating NAD+
needed for glycolysis to continue.
 Alcoholic Fermentation: Pyruvic acid is converted to ethanol and carbon dioxide.
Carried out by yeast. "In some organisms pyruvic acid is reduced to alcohol and carbon
di oxide... Alcoholic fermentation is the anaerobic respiration that the yeast cells follow
when oxygen is lacking………………….the cell profits 2 ATPs in this fermentation."
 Lactic Acid Fermentation: Pyruvic acid is converted to lactic acid. Occurs in some
bacteria and animal muscle cells during strenuous activity when oxygen supply is limited.
"In some organisms pyruvic acid is reduced to lactic acid... Here also net profit is 2ATPs
per glucose... Seen in curd, sour cream, cheeses, and other fermented dairy products... In
human body... Muscle cells can do both aerobic and anaerobic respiration."
 Anaerobic organisms may lack the enzymes for the Krebs cycle or ETC and use
alternative electron acceptors. "Some organisms do not have the necessary enzymes
required for Krebs cycle or ETC. Most of these are prokaryotes... These organisms do not
require oxygen as the final electron acceptor and hence are called anaerobic and they
perform anaerobic cellular respiration... These organisms utilize certain inorganic and
organic molecules as their final electron acceptors."
 Facultative Anaerobes: Can switch between aerobic respiration (if oxygen is present)
and anaerobic respiration/fermentation (if oxygen is absent), e.g., yeast. "Facultative
Anaerobes= (Switch hitters) – If O2 is present, it will do aerobic respiration – If no O2
then it will do anaerobic respiration – Ex. Yeast."
 Obligate Anaerobes: Can only survive in the absence of oxygen and are poisoned by its
presence, e.g., some bacteria. "Obligate or Strict Anaerobes= only do anaerobic
respiration – They can die in the presence of O2 – Ex. Some types of bacteria."
5. Metabolic Processing of Other Fuel Molecules

Main Theme: Cells can also obtain energy from fats and proteins, which are converted into
intermediates that enter the cellular respiration pathways.

Key Ideas/Facts:

 Fat Respiration: Fats are first broken down into glycerol and fatty acids. Glycerol enters
glycolysis, while fatty acids are broken down into 2-carbon fragments that are converted
to acetyl-CoA and enter the Krebs cycle. Fats can yield significantly more ATP per
molecule than glucose. "Glycerol forms the backbone of most fatty acids. It is converted
to glyceraldehyde-3-phosphate, which directly enters glycolysis... each long chain of
carbons is hydrolyzed into 2-carbon fragments... Next, each 2-carbon fragment is
converted to acetyl which enters krebs cycle... Thus each fat molecule can release upto 10
times more ATP than glucose."
 Protein Respiration: Proteins are digested into amino acids. Amino groups are removed
(deamination), and the remaining carbon skeletons (keto-acids) can enter different stages
of cellular respiration, often the Krebs cycle. Ammonia, a toxic byproduct of
deamination, is converted to urea or uric acid and excreted. Proteins are not typically
stored as an energy reserve. "Proteins……..digested to individual amino acids... Each
amino acid then needs to have the amino group removed by deamination that take place
in liver... The non-nitrogenous part of the protein is converted to keto-acids... Acids enter
Krebs cycle……..keto acids."

Reproduction Of cells

Cellular Reproduction

 Cell division is fundamentally the process by which a single cell gives rise to two new
cells. Your sources highlight three main types of cell division:
o Binary Fission: This type of division is observed in prokaryotic cells. A key
feature is that the single loop of DNA replicates, and these two DNA loops then
separate. Following this separation, a new cell membrane forms between the
two DNA molecules, resulting in two daughter cells. This process ensures that
the genetic information in the parent and daughter cells remains the same.
o Mitosis: This occurs in eukaryotic cells. The outcome of mitosis is the
production of daughter cells that are genetically identical to the parent cells.
Mitosis plays crucial roles in asexual reproduction, growth, and the
maintenance of multicellular organisms. Source further elaborates on its
importance in multicellular organisms, noting its role in growth, replacement of
lost cells, healing of injuries, and even the formation of reproductive cells
which eventually lead to new organisms that themselves grow by cell division.
o Meiosis: This is also a process that occurs in eukaryotic cells. Its primary
function is the production of gametes – specifically, egg and sperm cells, and
this process takes place only in reproductive organs. Unlike mitosis, the
 daughter cells produced through meiosis possess only half the genetic
information of the parent cells.
 Parthenogenesis is a distinct process described in source as the production of
organisms by a female without the involvement of a male. In this fascinating
phenomenon, an unfertilized egg develops into a new individual. This is noted as being
common among insects and some other arthropods, and interestingly, it has even been
noticed in the Komodo Dragon at the Chester Zoo, referred to as the "World’s Largest
Lizard".

Importance of Cell Division by Mitosis

 Source emphasises that the ability to divide through mitosis is one of the fundamental
characteristics of life, outlining three main roles:
o Ability to Grow
o Ability to Reproduce (specifically asexual reproduction)
 The importance of mitosis differs slightly between single-celled and multicellular
organisms:
o In single-celled organisms, mitosis serves as the primary method of increasing
their numbers.
o In multicellular organisms, as mentioned earlier, mitosis is essential for growth,
the replacement of lost cells, the healing of injuries, and the formation of
reproductive cells. Source highlights that this formation of reproductive cells in
turn leads to new organisms that subsequently grow by cell division.
 A crucial point from source is that when a cell undergoes reproduction or cell division via
mitosis, the two "daughter" cells produced are genetically identical not only to each
other but also to the "parent" cell. This genetic consistency is a defining characteristic
of mitosis. This is made possible because before a parent cell splits into two, it
meticulously duplicates its chromosomes.

Eukaryotic Chromosomes

 Source informs us that in eukaryotic cells, most genes are located on chromosomes,
although a few genes can also be found in the DNA of mitochondria and chloroplasts.
Each eukaryotic chromosome contains one very long DNA molecule, which typically
carries thousands of genes.
 Chromosomes are not just naked DNA; they are made of chromatin, which is a complex
of roughly equal amounts of DNA and protein molecules. These protein molecules,
particularly histones, play a vital role in organising the chromatin and also help to
control the activity of its genes.
 Source notes that often, chromosomes exist as thin chromatin fibers that are much
longer than the nucleus they are stored in. Source provides a remarkable example,
stating that if fully extended, the DNA in just one of your cells would be more than two
meters long!
 To manage this immense length, the DNA in a cell is packed into an elaborate,
multilevel system of coiling and folding. Source specifically mentions that histones are
 proteins used to package DNA in eukaryotes, and a nucleosome is formed when
DNA is wound around histone molecules.
 As a cell prepares to divide, these thin chromatin fibers coil up, forming compact
chromosomes that become visible under a light microscope. Conversely, when a cell is
not actively dividing, the chromosomes are typically too thin to be seen under a light
microscope.
 Before cell division begins, source explains that the DNA molecule of each
chromosome is copied through the process of DNA replication, and new histone
protein molecules attach as needed. This replication results in each chromosome
producing two identical copies called sister chromatids, which contain identical genes.
These two sister chromatids are joined together tightly at a narrow "waist" called
the centromere.
 During cell division, specifically in mitosis, the sister chromatids of a duplicated
chromosome separate from each other. Once separated, as described in source, each
chromatid is then considered a full-fledged chromosome and is identical to the
original chromosome. This process ensures that each daughter cell receives a complete
and identical set of chromosomes.

Cell Cycle and Mitosis

 Source defines the cell cycle as an ordered sequence of events that extends from the
time a cell is first formed from a dividing parent cell until its own division into two.
It is described as a continuous process encompassing all stages of growth and division
for a eukaryotic cell. Importantly, source notes that different cells vary in the time
spent in various stages of the cell cycle.
 The cell cycle is broadly divided into two major phases:
o Interphase: This is the longest stage of the cell cycle, typically occupying about
90% of the time. During interphase, the cell engages in metabolic activities and
prepares for cell division. It is further subdivided into three distinct phases:
 G1 phase: In this phase, the cell gathers nutrients and other resources,
grows in volume, and carries out its metabolic roles such as producing
transfer RNA (tRNA), messenger RNA (mRNA), ribosomes, enzymes,
and other cellular components. Source adds that in multicellular
organisms, metabolic functions in G1 can include specialised activities
like protein production for muscle contraction, photosynthesis, or
glandular-cell secretion. Cells can also enter the G0 phase during G1.
 G0 phase: Source explains that cells may become differentiated or
specialised in their function in G0, citing examples like muscle, heart,
and nerve cells. Cells in G0 do not move forward in the cell cycle, and
this phase is also referred to as the quiescent
phase
(dormant/motionless). Source notes that some cells, like nerve cells, may
stay in G0 permanently, while others can re-enter the S phase and continue
the cycle.
 S phase: This is the stage where DNA synthesis occurs, leading to
chromosome duplication. Source clarifies that during this phase, the cell
distributes the copies of genetic information as chromosomes to the
 daughter cells. The DNA in chromosomes is wrapped around histone
proteins to form nucleosomes, which then coil into chromatin, and these
chromatin strands further coil to form chromosomes. As chromosomes
become visible during mitosis, source mentions the formation of two
thread-like structures called chromatids. Source defines a chromatid
as one of the two parallel parts of chromosomes, with each
chromosome containing one DNA molecule. Sister chromatids,
therefore, are the two chromatids of a chromosome produced after
replication, possessing the sameDNA.
G2 phase: This is the final stage of interphase, where the cell prepares
the necessary components for division, such as proteins required for
chromosome movement. At this stage, the nuclear membrane is still
intact, and while the chromatin has replicated, individual
chromosomes are not yet visible. Importantly, source notes that the
nucleolus, the site of ribosome manufacture, is still visible during G2.
o Mitotic (M) phase: This is the stage of the cell cycle where the cell divides its
genetic material and typically lasts for about 10% of the time. Source highlights
that two main events occur during eukaryotic cell division:
 Karyokinesis: The distribution of genetic material equally, essentially
the division of the nucleus.
 Cytokinesis: The division of the cytoplasm, resulting in two separate
daughter cells. The mitotic phase itself is further divided into four phases:
Prophase, Metaphase, Anaphase, and Telophase. Finally, source
provides an interesting exception, noting that red blood cells (RBCs) lack
nuclei and therefore cannot undergo mitosis.

Executive Summary:

Main Themes and Important Ideas/Facts:

1. Cell Division: The Generation of New Cells

 Definition: Cell division is the "process in which one cell generates two new cells."
 Types of Cell Division: The document identifies three main types:
 Binary Fission: Occurs in prokaryotes. A single loop of DNA replicates, the two loops
separate, and a new cell membrane forms, resulting in two genetically identical daughter
cells. This "ensures that the genetic information in parent and daughter cells are the
same."
 Mitosis: Occurs in eukaryotic cells. It results in daughter cells that are "identical to
parent cells" and is responsible for "asexual reproduction, growth and maintenance of
multicellular organisms."
 Meiosis: Occurs in eukaryotic cells, specifically in reproductive organs, for the
"production of gametes – egg and sperm." Daughter cells produced through meiosis
"possess half the genetic information of parent cells."
  Parthenogenesis: Briefly mentioned as a process where an unfertilized egg develops into
a new individual, common in some insects and arthropods, and observed in the Komodo
Dragon.

2. Importance of Cell Division by Mitosis

 Cell division by mitosis is fundamental to life, fulfilling three main roles:

 Ability to Grow: In multicellular organisms, cell division is crucial for increasing size.
 Ability to Reproduce: In single-celled organisms, it is the primary method of increasing
numbers. In multicellular organisms, it contributes to the formation of reproductive cells,
which "in turn leads to new organisms which in turn grow by cell division."
 Replacement and Repair: Mitosis "replaces damaged or lost cells" and facilitates the
"healing of injuries."
 Genetic Identity: A key outcome of mitotic cell division is that the "two 'daughter' cells
are produced that are genetically identical to each other AND the 'parent' cell." This is
ensured by the duplication of chromosomes before cell division.

3. Eukaryotic Chromosomes: Packaging Genetic Information

 Location of Genes: In eukaryotic cells, "most Genes are located on Chromosomes and a
few genes are found in DNA of Mitochondria and Chloroplasts."
 Structure: Each eukaryotic chromosome contains "one very long DNA molecule,
typically bearing thousands of genes." Chromosomes are composed of chromatin, which
consists of "roughly equal amounts of DNA and protein molecules, which help organise
the chromatin and control the activity of its genes."
 Chromatin Organisation: During most of the cell cycle, chromosomes exist as "thin
chromatin fibers that are much longer than the nucleus they are stored in." These fibres
condense into "compact chromosomes that can be viewed under a light microscope" as
the cell prepares to divide.
 DNA Packaging: The DNA is packed into a "multilevel system of coiling and folding."
Histones are the "proteins used to package DNA in eukaryotes," and nucleosomes are
formed by "DNA wound around histone molecules."
 Chromosome Duplication: "Before a cell begins the process, the DNA molecule of each
chromosome is copied through the process of DNA replication & new histone protein
molecules attach as needed." This results in sister chromatids, which are "two copies" of
a chromosome containing "identical genes."
 Centromere: Sister chromatids are joined tightly at a narrow region called the
centromere.
 Separation of Sister Chromatids: During cell division, the sister chromatids separate,
and "once separated from its sister, each chromatid is considered a full-fledged
chromosome and is identical to the original chromosome."

4. Cell Cycle and Mitosis: The Ordered Events of Cell Division

 Cell Cycle Definition: The cell cycle is the "ordered sequence of events that extend from
the time a cell is first formed from a dividing parent cell until its own division into two."
  Features of the Cell Cycle: It is a "continuous process" consisting of "all stages of
growth and division for a eukaryotic cell." The duration of the different stages varies
between cell types.
 Interphase: This is the "longest stage of cell cycle" (accounting for "90% of time"),
during which the "cell engages in metabolic activities and prepares for cell division." It is
divided into three phases:
 G1 Phase: The cell "gathers nutrients and other resources," grows in volume, and carries
out metabolic roles like producing essential molecules. Cells may also enter a resting
phase called G0 where they become differentiated (e.g., nerve cells) and do not move
forward in the cell cycle. Some cells remain permanently in G0.
 S Phase: This is the stage where "DNA synthesis occurs" and "chromosome duplication"
takes place. The replicated DNA is associated with histone proteins to form nucleosomes,
which are coiled into chromatin. Chromatin further coils to form visible chromosomes.
Each chromosome at this stage consists of two "thread like structures" called
chromatids, specifically sister chromatids containing identical DNA.
 G2 Phase: The final stage of interphase where the "cell prepares the components needed
to divide like proteins to move the chromosomes." The nuclear membrane is intact, the
chromatin has replicated but individual chromosomes are not yet clearly visible, and the
nucleolus is still present.
 Mitotic (M) Phase: This phase ("10% of time") is where "cell division" occurs,
involving the division of the genetic material and the cytoplasm. It consists of:
 Karyokinesis: "Distribution of genetic material equally," which involves the four stages
of mitosis:
 Prophase
 Metaphase
 Anaphase
 Telophase
 Cytokinesis: "Division of cytoplasm."
 Note on Red Blood Cells (RBCs): The document mentions that "RBCs lack nuclei and
cannot undergo mitosis."

Imp points:

 "Cell division - Process in which one cell generates two new cells"
 "ensures that the genetic information in parent and daughter cells are the same"
(regarding binary fission)
 "Results in daughter cells that are identical to parent cells" (regarding mitosis)
 "Responsible for asexual reproduction, growth and maintenance of multicellular
organisms" (regarding mitosis)
 "Production of gametes – egg and sperm .occur only in reproductive organs" (regarding
meiosis)
 "Daughter cells possess half the genetic information of parent cells" (regarding meiosis)
 "When a cell undergoes reproduction / cell division, TWO “daughter” cells are produced
that are genetically identical to each other AND the “parent” cell."
 "Each eukaryotic chromosome contains one very long DNA molecule, typically bearing
thousands of genes."
  "Chromosomes are made of chromatin, fibers composed of roughly equal amounts of
DNA and protein molecules, which help organise the chromatin and control the activity
of its genes."
 "Histones are proteins used to package DNA in eukaryotes."
 "Nucleosomes consist of DNA wound around histone molecules."
 "As a cell prepares to divide, its chromatin fibers coil up, forming compact chromosomes
that can be viewed under a light microscope."
 "the DNA molecule of each chromosome is copied through the process of DNA
replication"
 "Two sister chromatids are joined together tightly at a narrow “waist” called the
centromere."
 "Once separated from its sister, each chromatid ⮚ is considered a full-fledged
chromosome and ⮚ is identical to the original chromosome."
 "Ordered sequence of events that extend from the time a cell is first formed from a
dividing parent cell until its own division into two" (definition of cell cycle)
 "Longest stage of cell cycle" (regarding interphase)
 "Stage of cell cycle where the cell divides its genetic material" (regarding mitosis)
 "Cell gathers nutrients and other resources...Cell grows in volume and carries out its
metabolic roles..." (regarding G1 phase)
 "Cells may become differentiated or specialized in their function...Cells do not move
forward in the cell cycle. This is also referred as quiescent phase (dormant / motionless)"
(regarding G0 phase)
 "Stage where DNA synthesis occurs" (regarding S phase)
 "Cell prepares the components needed to divide like proteins to move the chromosomes"
(regarding G2 phase)
 "Distribution of genetic material equally :- karyokinesis"
 "Division of cytoplasm :- Cytokinesis"
 "RBCs lack nuclei and cannot undergo mitosis"

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