Introduction to Biochemistry

Biochemistry is the scientific study of the chemical and physical processes that occur within
living organisms. Emerging around the beginning of the 20th century, it combines principles
from chemistry, physiology, and biology to explore the structure, behavior, and interactions
of complex biological molecules that form cells, tissues, and entire organisms.

-​ Biochemistry is the branch of science that explores the chemical processes,

substances, and molecular interactions occurring within living organisms,
bridging biology and chemistry. It focuses on the structure and function of
cellular components like proteins, carbohydrates, lipids, and nucleic acids
to explain how life functions.

Principles of Biochemistry
●​ Cells are the basic structural units of life, highly organized and requiring continuous
energy to maintain their ordered state.
●​ Living systems involve thousands of chemical reactions that must be precisely
regulated and integrated to sustain life.
●​ Essential biochemical reactions such as glycolysis are conserved across almost all
organisms.
●​ All living organisms use similar biomolecules: carbohydrates (CHO), proteins, lipids,
and nucleic acids.
●​ Instructions for growth, reproduction, and development are encoded in DNA.

●​ Cellular Organization and Energy: Cells, the basic structural units of living organisms, are
highly organized. Maintaining this ordered state requires a constant supply of energy.
●​ Regulation of Chemical Reactions: Living processes involve thousands of chemical reactions.
Life depends on the precise regulation and integration of these reactions.
●​ Universality of Reactions: Certain key reactions, such as glycolysis, are found in almost all
organisms, highlighting fundamental biochemical pathways.
●​ Common Molecular Building Blocks: All organisms utilize the same types of molecules:
carbohydrates (CHO), proteins, lipids, and nucleic acids.
●​ Genetic Information: The instructions for growth, reproduction, and development in each
organism are encoded in their DNA.

Cell Structure
Basics of Cells
●​ Cells are the smallest living units of an organism capable of growth, reproduction,
energy use, adaptation, and response to the environment.
●​ Cells vary greatly in size and shape, depending mainly on function.
●​ Types of cells include unicellular and multicellular organisms.
 -​ Cells are the structural, functional, and biological units of all living beings. A cell can replicate
itself independently. Hence, they are known as the building blocks of life. Each cell contains a fluid
called the cytoplasm, which is enclosed by a membrane. Also present in the cytoplasm are several
biomolecules like proteins, nucleic acids and lipids.

Cell Size and Shape

●​ The cell size is generally measured in micrometers (µm), where 1 µm = 1/1000
millimeter.
●​ Examples:
○​ Smallest cell: Mycoplasma (~0.1 µm)
○​ Largest cell: Ostrich egg (~18 cm)
○​ Human examples: Sperm (~5 µm), Ovum (~120 µm), nerve cells can be as
long as 1 meter.
●​ Shape varies by function:
●​ Cell shape varies greatly and is typically related to the cell's function. Some cells, like
Euglena and Amoeba, can change their shape, while most have a fixed form.
○​ Red blood cells (RBCs): circular biconcave for efficient capillary passage.
○​ Nerve cells: branched to conduct impulses.
○​ White blood cells (WBCs): can change shape to engulf pathogens.

Shape Example Why this shape?

Biconcave Disc Red Blood Cells Increases surface area for oxygen
exchange and allows them to "fold"
through narrow capillaries.

Long & Branching Nerve Cells (Neurons) Long extensions (axons) allow
them to transmit signals over long
distances (like from your spine to
your toe).

Spindle-Shaped Muscle Cells These long, tapered cells are

designed to contract and pull,
generating movement.
 Columnar/Cuboidal Skin or Gut Cells These "brick-like" shapes allow
cells to pack tightly together to
form protective barriers.

Irregular/Amoeboid White Blood Cells Being "shapeless" allows them to

squeeze through vessel walls to
reach sites of infection.

As a cell grows larger, its volume increases much faster than its surface area. If a cell gets too big:

1.​ Nutrients can’t get in fast enough.

2.​ Waste can’t get out fast enough.
3.​ DNA becomes "overloaded" trying to manage too much cytoplasm.

Key Cell Components

●​ Plasma membrane: Thin, elastic, semi-permeable membrane composed of lipid
bilayer with embedded proteins; regulates cell shape, protects cell contents, and
controls substance passage.
-​ The main role of the cell membrane is to provide protection to the cell from its
surroundings. The cell membrane or plasma membrane controls the passage of some
solutes and water into and out of the cell.
●​ Cell wall: Found in plants and bacteria, rigid non-living outer layer made of
cellulose, hemicellulose, and pectin; provides shape, rigidity, and protection.
-​ The cell wall is the protective, semi-permeable outer layer of a plant cell. A major
function of the cell wall is to give the cell strength and structure, and to filter
molecules that pass in and out of the cell.
●​ Nucleus: Spherical organelle containing DNA and surrounded by a double
membrane (nuclear envelope with pores); controls cell activities, stores hereditary
information, nucleolus inside synthesizes RNA.
-​ The nucleus contains the hereditary material of the cell, the DNA.
-​ It sends signals to the cells to grow, mature, divide and die.
-​ The nucleus is surrounded by the nuclear envelope that separates the DNA from the rest of the
cell.
-​ The nucleus protects the DNA and is an integral component of a plant’s cell structure.
●​ Cytoplasm: Jelly-like aqueous portion (cytosol) containing biomolecules and
organelles.
-​ Cytoplasm is the gel-like substance, primarily composed of water, salts, and proteins,
that fills the interior of a cell, surrounding the nucleus in eukaryotes. It acts as the
site for most cellular metabolic reactions, supports organelles, maintains cell shape,
and facilitates the transport of molecules.

Organelles within Cytoplasm

 ●​ Endoplasmic Reticulum (ER): Network of membranes; Rough ER (RER) is studded
with ribosomes and synthesizes proteins; Smooth ER (SER) synthesizes lipids,
detoxifies substances, and stores calcium ions.
-​ The Endoplasmic Reticulum (ER) is a continuous membrane-bound network of
tubules and sacs (cisternae) in eukaryotic cells that acts as a manufacturing,
packaging, and transport system for proteins and lipids.
●​ Golgi body: Stacked membranous sacs that modify, sort, package proteins and lipids;
produces vesicles, lysosomes, and plasma membrane components.
-​ The Golgi apparatus (or Golgi complex/body) is a membrane-bound organelle in
eukaryotic cells, composed of stacked, flattened pouches called cisternae, it receives
proteins and lipids from the endoplasmic reticulum, then sorts, modifies, and packages
them into vesicles for secretion or delivery to other organelles.
●​ Lysosomes: Membrane-bound sacs containing hydrolytic enzymes; digest large
molecules, foreign invaders, and worn-out organelles.
●​ Vacuoles: Membrane sacs for storage of liquids, food, and waste; large in plants
providing turgor pressure, smaller and temporary in animals.
●​ Mitochondria: Double membrane organelles with inner folded membrane (cristae);
produce ATP through cellular respiration and contain their own DNA.
-​ Mitochondria are double-membrane-bound organelles found in most eukaryotic cells,
commonly known as the "powerhouse of the cell". They generate most of the cell's
supply of adenosine triphosphate (ATP), used as a source of chemical energy, through
a process called aerobic respiration. They also manage calcium storage, heat
production, and cell death.
●​ Plastids: Double membrane organelles in plants and algae involved in food synthesis
and storage; chloroplasts contain chlorophyll for photosynthesis.
●​ Centrosomes: Contain centrioles; involved in chromosome movement during cell
division and formation of cilia and flagella.
●​ Cytoskeleton: Composed of microtubules (tubulin) and microfilaments (actin);
maintains cell shape, structural strength, and enables movement.

Cell Types

Feature Prokaryotic Cells Eukaryotic Cells

Nucleus Undeveloped Well-developed with

nuclear membrane

Chromosomes Single chromosome Multiple chromosomes

Membrane-bound Absent Present

organelles
 Size range 0.5-5 µm 5-100 µm

Examples Bacteria, Cyanobacteria Plants, Animals, Fungi,

(blue-green algae) Protists

Prokaryotic cells, found in bacteria and archaea, are small, simple, and lack a
membrane-bound nucleus or organelles, with DNA stored in a nucleoid. In contrast,
eukaryotic cells, found in plants, animals, fungi, and protists, are larger, more complex,
possess a nucleus, and contain membrane-bound organelles like mitochondria.

Types of ER:

1. Rough Endoplasmic Reticulum (RER) Studded with ribosomes on its surface.

Function: Synthesizes proteins destined for secretion, plasma membrane, or lysosomes. Found
abundantly in cells that secrete large amounts of protein (e.g., pancreas, plasma cells).

2. Smooth Endoplasmic Reticulum (SER) Lacks ribosomes and appears smooth.

Functions: Lipid and steroid hormone synthesis Detoxification of drugs and poisons (especially in
liver cells) Carbohydrate metabolism Calcium ion storage (especially in muscle cells as sarcoplasmic
reticulum

Biomolecules
Biomolecules are the chemical building blocks of cells. Animal and plant cells contain
thousands of kinds of biomolecules. Water constitutes 50-95% of cell weight, while ions like ,
, and contribute about 1%. Most biomolecules are organic (based primarily on carbon,
hydrogen, oxygen, nitrogen, sulfur, phosphorus).

-​ A biomolecule is a chemical compound found in living organisms. These include

chemicals that are composed of mainly carbon, hydrogen, oxygen, nitrogen, sulfur and
phosphorus. Biomolecules are the building blocks of life and perform important
functions in living organisms.

Major Classes of Biomolecules

●​ Carbohydrates
●​ Proteins
●​ Lipids
●​ Nucleic Acids

1. The Main Element in an "Organic" Molecule

The main element in an organic molecule is carbon. Organic molecules are defined as carbon-based
compounds, typically containing carbon atoms covalently bonded to hydrogen, oxygen, and other
elements. Carbon is essential because its ability to form four stable covalent bonds allows it to build
complex, long-chain structures necessary for life.

2. How Monomers are Related to Polymers

Monomers are the smaller, individual building block molecules that link together to form larger,
complex molecules called polymers.

●​ Relationship: Monomers are the subunits; polymers are the chains made of these repeating
units.
●​ Process: The process of connecting monomers to form polymers is called polymerization
(often via dehydration synthesis).
●​ Analogy: If a polymer is a necklace (the chain), the monomer is a single bead.

3. The Four Main "Organic" Molecules Needed by Living Organisms

The four major classes of biological macromolecules (organic molecules) necessary for life are:

1.​ Carbohydrates: Composed of monosaccharides (sugars), they serve as primary energy

sources and structural components.
2.​ Lipids: Composed of fatty acids and glycerol, they are used for long-term energy storage,
insulation, and cell membrane structure.
3.​ Proteins: Composed of amino acids, they function as enzymes, structural building blocks,
and transporters.
4.​ Nucleic Acids: Composed of nucleotides, they store and transmit genetic information
(DNA/RNA).

Carbohydrates
●​ Known as sugars and starches; also include cellulose, chitin, and glycogen.
●​ Most abundant biomolecules in nature.
●​ Composed of monosaccharides (monomers) forming disaccharides and
polysaccharides.
●​ Examples:
○​ Disaccharides: Sucrose (table sugar)
○​ Polysaccharides: Starch (plant energy storage), Glycogen (animal energy
storage), Cellulose (plant structural fibrous material)
○​ Chitin: forms exoskeleton in arthropods and used in surgical threads.

Monosaccharides (Simple Sugars)

●​ Definition: The simplest form of carbohydrates, consisting of a single sugar molecule (3–7
carbon atoms).
●​ Examples: Glucose (energy source), Fructose (fruit sugar), Galactose (found in milk).
●​ Characteristics: White, sweet, crystalline solids soluble in water.

Disaccharides (Double Sugars)

 ●​ Definition: Formed when two monosaccharides are linked by a dehydration (condensation)
reaction, forming a glycosidic bond.
●​ Examples:
○​ Sucrose: Glucose + Fructose (table sugar).
○​ Lactose: Glucose + Galactose (milk sugar).
○​ Maltose: Glucose + Glucose (malt sugar).
●​ Characteristics: Soluble in water.

Polysaccharides (Complex Carbohydrates)

●​ Definition: Long chains of 10 or more monosaccharide units (polymers) linked together by

glycosidic bonds.
●​ Examples:
○​ Starch: Energy storage in plants.
○​ Glycogen: Energy storage in animals (stored in liver/muscles).
○​ Cellulose: Structural component in plant cell walls.
○​ Chitin: Structural component in fungal cell walls and arthropod exoskeletons.
●​ Characteristics: Not sweet, generally insoluble in water,, and high molecular weight.
●​ Carbohydrates are important for short-term energy storage, structural components of plant
cell walls, and parts of cell membranes.

Sugar Structures

Carbohydrates include various sugar types—trioses (C3H6O3), pentoses (C5H10O5), and

hexoses (C6H12O6, e.g., glucose). Glucose exists in linear and ring forms, with two ring
conformations α-glucose and β-glucose differing at the position of the OH group on carbon
1.

1.​ Carbohydrates are essential biomolecules composed of carbon, hydrogen, and oxygen, that
serve as the primary energy source and structural components for living organisms. They are
classified as monosaccharides (simple sugars), disaccharides, and polysaccharides (complex
carbs), with glucose being a key metabolic fuel.

Key facts about carbohydrates as biomolecules include:

●​ Structure: They are polyhydroxy aldehydes or ketones, often existing in ring structures.
●​ Energy and Storage: Glucose is used immediately for energy, while excess is stored as
glycogen in animals and starch in plants.
●​ Structural Role: They provide structural integrity, such as cellulose in plant cell walls and
chitin in fungal cell walls and insect exoskeletons.
●​ Functions: Beyond energy, they are crucial for cell recognition, immune system function,
and are part of nucleic acids (ribose/deoxyribose).
●​ Classification:
○​ Monosaccharides: Simple sugars like glucose, fructose, and galactose.
○​ Disaccharides: Two sugars linked, such as sucrose (table sugar) and lactose (milk
sugar).
○​ Polysaccharides: Long chains like starch, glycogen, and fiber.

Proteins
●​ Polymers of amino acids (typically 50-300 amino acids long).
●​ 20 different amino acids commonly found in human proteins.
 ●​ Amino acids have an amino group, a carboxyl group, a hydrogen atom, and a
variable R group.
●​ Amino acids are classified based on the polarity and charge of their R groups into
non-polar, polar, positively charged (+), and negatively charged (-) categories.
●​ Divided into essential amino acids (must be consumed) and non-essential amino
acids (can be synthesized in the body).
●​ Proteins have multiple levels of structure: primary (amino acid sequence), secondary
(α-helices and β-sheets), tertiary (3D folding), and quaternary (multiple subunits).
●​ Protein functions include enzymatic catalysis, defense (antibodies), support (keratin),
motion (actin/myosin), transport (hemoglobin), and regulation (hormones like
insulin).
1.​ Proteins are essential macromolecules (biopolymers) composed of amino acid chains folded
into complex 3D shapes, determined by genetic code. They are built from 20 amino acids,
forming structures that facilitate crucial biological roles including enzymatic catalysis,
structural support, transport, and immune defense.

Key Facts About Protein Structure and Composition:

●​ Amino Acid Chains: Proteins consist of one or more polypeptide chains, which are long,
linear chains of amino acids linked by peptide bonds.
●​ 20 Amino Acids: Only 20 different amino acids are commonly found in proteins, yet they
combine in vast, unique, and complex sequences.
●​ Shape Determines Function: The specific 3D shape is crucial for function, and it is
determined by the sequence of amino acids.
●​ Chemical Stability: Hydrophilic (water-loving) groups are typically on the surface, while
hydrophobic (water-averse) elements are tucked inside for stability in aqueous environments.

Primary Functions and Roles:

●​ Catalysis: Enzymes act as biological catalysts, accelerating chemical reactions by a factor of

a million or more.
●​ Structure: Proteins provide structural support for cells and tissues (e.g., collagen, keratin).
●​ Signaling/Regulation: Hormones, such as insulin and growth hormone, regulate body
processes.
●​ Defense: Antibodies are specialized proteins that protect the body from pathogens.
●​ Transport & Movement: Proteins move molecules (e.g., hemoglobin) and enable muscle
contraction (e.g., actin and myosin).

Protein Abnormalities

●​ Sickle-cell anemia arises from a mutation in hemoglobin structure, substituting

glutamic acid with valine, causing abnormal cell shape and reduced oxygen-carrying
capacity.
●​ Denaturation refers to loss of a protein's native structure, impairing function.
●​ Protein misfolding can cause disease due to aggregation, toxic gain of function, or
loss of function.
●​ Chaperonins assist in proper protein folding using ATP-driven conformational
changes.

Lipids
●​ Include fats, oils, and waxes; composed of glycerol and fatty acids.
 ●​ Classified by saturation: saturated fatty acids have single bonds, unsaturated have
one or more double bonds.
●​ Triglycerides formed from glycerol plus three fatty acids.
●​ Provide long-term energy storage, form structural components of cell membranes
(phospholipid bilayer), and act as hormones and waterproof coverings.
●​ Lipids are organic compounds that are fatty acids or derivatives of fatty
acids, which are insoluble in water but soluble in organic solvents. For eg.,
natural oil, steroid, waxes.
-​ Lipids are oily or greasy nonpolar molecules, stored in the adipose tissue of the body.
-​ Lipids are a heterogeneous group of compounds, mainly composed of hydrocarbon chains.
-​ Lipids are energy-rich organic molecules, which provide energy for different life processes.
-​ Lipids are a class of compounds characterised by their solubility in nonpolar solvents and
insolubility in water.
-​ Lipids are significant in biological systems as they form a mechanical barrier dividing a
cell from the external environment known as the cell membrane.

Nucleic Acids
●​ Composed of nucleotides containing carbon, hydrogen, oxygen, nitrogen, and
phosphorus.
●​ DNA and RNA store and transmit hereditary information.
●​ Nucleotides have three components: a nitrogenous base, a sugar (ribose or
deoxyribose), and phosphate groups.
●​ Nitrogenous bases are purines (adenine, guanine) with double-ring structures and
pyrimidines (cytosine, thymine in DNA, uracil in RNA) with single-ring structures.
●​ DNA provides the blueprint for life through gene sequences; RNA translates genetic
information into proteins.
●​ The main function of nucleic acid is the transfer of genetic information and synthesis of
proteins by processes known as translation and transcription. The monomeric unit of nucleic
acids is known as nucleotide and is composed of a nitrogenous base, pentose sugar, and
phosphate.
●​ There are 4 major nitrogenous bases found in DNA: adenine, guanine, cytosine, and thymine.
In RNA, thymine is replaced by uracil. The DNA structure is described as a double-helix or
double-helical structure which is formed by hydrogen bonding between the bases of two
antiparallel polynucleotide chains.

Enzyme Action
●​ Enzymes are biological catalysts, mostly proteins, that increase reaction rates by
decreasing activation energy.
●​ Enzymatic activity depends on precise 3D structure and is sensitive to temperature
and pH.
●​ Specificity means enzymes bind only particular substrates—like a lock and key.
●​ Mechanism:
1.​ Substrate binds enzyme's active site.
2.​ Enzyme stabilizes the substrate complex, weakening internal bonds.
3.​ Catalysis lowers activation energy, product forms and is released.
4.​ Enzyme is free to bind more substrate molecules.

Biochemical Reactions
 ●​ Metabolism: Sum of all chemical reactions in a living organism, divided into:
○​ Anabolism: Energy-requiring biosynthesis of molecules.
○​ Catabolism: Breakdown of molecules to produce energy.
●​ Reactions require activation energy; enzymes as catalysts decrease this energy barrier
and speed reactions.
●​ Common reaction types:
○​ Nucleophilic substitution: One atom/group replaces another.
○​ Elimination reaction: Formation of double bond by removal of atoms.
○​ Addition reaction: Two molecules combine into one product (e.g., hydration).
○​ Isomerization: Intramolecular rearrangement of atoms or groups.
○​ Oxidation-reduction (redox): Electron transfer between molecules.
○​ Hydrolysis: Breaking bonds by water addition.

Maintenance of Cellular Internal Order

●​ Synthesis of biomolecules for structure and function.
●​ Selective transport across membranes regulates ion and molecule passage.
●​ Cell movement and intracellular transport maintain life-sustaining processes.
●​ Removal of metabolic wastes to prevent toxicity