Basic Biology and Chemistry

1. Structure of Atoms

 Atom: Fundamental unit of matter, retaining the properties of an element.

o Components:

 Protons: Positively charged, located in the nucleus.

 Neutrons: Neutral charge, also in the nucleus.

 Electrons: Negatively charged, orbiting the nucleus in energy levels or shells.

2. Molecules and Compounds

 Molecule: Two or more atoms bonded together, can be the same or different elements.

o Types:

 Elemental Molecules: Consist of one type of atom (e.g., O₂).

 Compound Molecules: Consist of different atoms (e.g., CO₂).

 Compound: A substance with atoms of two or more different elements bonded chemically.

o Characteristics:

 Fixed ratio of elements.

 Chemical bonds that are either ionic (atoms exchange electrons) or covalent
(atoms share electrons).

3. Basic Chemistry Relevant to Biological Processes

 Chemical Reactions: Processes where reactants convert into products, essential in all biological
systems.

o Examples:

 Photosynthesis.

 Cellular respiration.

 Water’s Role:

o Universal solvent in biological systems, facilitating reactions.

o Transports substances, regulates temperature, and maintains homeostasis.

 pH Importance:

o Critical for enzyme function and metabolic activities.

o The body meticulously maintains pH within a narrow range.

4. Table of Comparison: Atom, Molecule, Compound

Category Atom Molecule Compound

Definition Smallest unit of an Group of two or more Chemical substance of two or more
element. bonded atoms. different elements bonded.

Example Helium (He) Oxygen gas (O₂) Water (H₂O)

Bond N/A Mostly covalent; Ionic or covalent, depending on

Type sometimes ionic elements involved
Cell Biology

1. Structure and Function of Cell Organelles

 Cell Organelles: Specialized structures within cells that perform specific functions.

o Nucleus: Contains the cell’s DNA and controls its activities.

o Mitochondria: Known as the powerhouses of the cell; they generate ATP through
respiration.

o Ribosomes: Sites of protein synthesis; found floating within the cytoplasm or attached
to the endoplasmic reticulum.

o Endoplasmic Reticulum (ER):

 Rough ER: Studded with ribosomes; involved in protein synthesis.

 Smooth ER: Lacks ribosomes; synthesizes lipids and detoxifies toxins.

o Golgi Apparatus: Modifies, sorts, and packages proteins and lipids for storage or
transport out of the cell.

o Lysosomes: Contain enzymes for breaking down waste materials and cellular debris.

2. Differences Between Prokaryotic and Eukaryotic Cells

 Prokaryotic Cells:

o Do not have a nucleus or membrane-bound organelles.

o DNA is circular and floats freely within the cell.

o Example: Bacteria.

 Eukaryotic Cells:

o Contain a nucleus and membrane-bound organelles.

o DNA is linear and housed within the nucleus.

o Example: Plant and animal cells.

3. Cellular Processes

 Metabolism: The set of life-sustaining chemical reactions in organisms.

o Catabolism: Breakdown of molecules to obtain energy.

o Anabolism: Synthesis of all compounds needed by the cells.

 Protein Synthesis: Process by which cells build proteins; involves transcription (in the nucleus)
and translation (at ribosomes).

 Cell Division (Mitosis):

 o Mitosis: Process by which a eukaryotic cell separates its duplicated chromosomes into
two nuclei.

o Stages: Prophase, Metaphase, Anaphase, Telophase, followed by Cytokinesis.

4. Table of Comparison: Prokaryotic vs. Eukaryotic Cells

Feature Prokaryotic Cells Eukaryotic Cells

Nucleus Absent Present

Organelle No membrane-bound organelles Membrane-bound organelles present

s

DNA Circular, not enclosed Linear, enclosed within the nucleus

Size Generally smaller Generally larger

Examples Bacteria, Archaea Plants, Animals, Fungi

Genetics

1. DNA Structure and Function

 DNA (Deoxyribonucleic Acid): Carries the genetic instructions for the development, functioning,
growth, and reproduction of all known organisms.

o Structure: Double helix made up of nucleotides; each nucleotide consists of a phosphate

group, a sugar group (deoxyribose), and a nitrogenous base.

o Nitrogenous Bases: Adenine (A), Thymine (T), Cytosine (C), and Guanine (G).

o Base Pairing: A pairs with T, and C pairs with G.

2. Genetic Code and Protein Synthesis

 Genetic Code: The set of rules by which information encoded in genetic material (DNA or RNA
sequences) is translated into proteins by living cells.

o Transcription: Process of copying a segment of DNA into RNA.

o Translation: Process where the sequence of the RNA is used to produce proteins; occurs
at the ribosome.

o Codons: Triplet bases in mRNA that determine which amino acid is added during protein
synthesis.

3. Inheritance Patterns and Genetic Diseases

 Mendelian Genetics: Patterns of inheritance that are characteristic of organisms that reproduce
sexually.

o Dominant and Recessive Traits: Dominant alleles mask the presence of recessive alleles
in heterozygous pairings.

o Punnett Square: A diagram used to predict the genotype and phenotype combinations
in a genetic cross.

 Non-Mendelian Genetics: Include incomplete dominance, codominance, and multiple alleles.

 Genetic Diseases: Disorders caused by abnormalities in an individual's DNA.

o Examples: Cystic fibrosis, sickle cell disease, Huntington's disease.

o Hereditary: Transmitted from parent to offspring through genes.

4. Table of Comparison: DNA vs. RNA

Characteristi DNA RNA

c

Sugar Type Deoxyribose Ribose

Strand Type Double-stranded Usually single-stranded

Base Pairs Adenine with Thymine, Cytosine with Adenine with Uracil, Cytosine with
Guanine Guanine

Function Stores genetic information Translates genetic information into

protein
Ecology and Environmental Science

1. Symbiotic Relationships

 Symbiosis: A close and long-term biological interaction between two different biological
organisms.

o Mutualism: Both species benefit from the interaction.

 Example: Bees and flowers; bees get nectar for food, flowers get pollinated.

o Parasitism: One organism (the parasite) benefits at the expense of the other (the host).

 Example: Tapeworms in humans; tapeworms absorb nutrients, harming human

health.

o Commensalism: One organism benefits, and the other is neither helped nor harmed.

 Example: Barnacles on whales; barnacles get transportation, whales are

unaffected.

2. Biodiversity and Conservation

 Biodiversity: The variety of life in the world or in a particular habitat or ecosystem.

o Levels of Biodiversity: Genetic diversity, species diversity, ecosystem diversity.

 Conservation: Efforts to preserve the natural world and prevent biodiversity loss.

o Strategies: Protected areas, wildlife management, restoration ecology, legislation.

3. Ecological Impacts of Human Activities

 Pollution: Release of harmful materials into the environment.

o Types: Air, water, soil, and noise pollution.

o Effects: Health issues, loss of biodiversity, ecosystem degradation.

 Climate Change: Changes in global or regional climate patterns, largely due to increased levels of
atmospheric carbon dioxide produced by fossil fuels.

o Effects: Rising sea levels, altered weather patterns, impacts on all life forms.

o Response: Mitigation (reducing emissions) and adaptation (adjusting to changes).

4. Table of Symbiotic Relationships

Relationship Type Benefit Harm Example

Mutualism Both None Bees and flowers

Parasitism Parasite Host Tapeworms in humans

Commensalism One None Barnacles on whales

Evolution and Taxonomy

1. Evolutionary Theories and Natural Selection

 Evolution: The process by which different kinds of living organisms are thought to have
developed and diversified from earlier forms during the history of the earth.

o Natural Selection: Mechanism of evolution where individuals with beneficial traits are
more likely to survive and reproduce, passing those traits to the next generation.

o Key Concepts:

 Variation: Organisms within a population exhibit variations in traits.

 Inheritance: Traits must be heritable to be passed on to the next generation.

 Differential Survival: Not all offspring survive to reproduce due to limited

resources and competition.

2. Species Concepts and Classification Systems

 Species Concepts:

o Biological Species Concept: Species are groups of actually or potentially interbreeding

natural populations which are reproductively isolated from other such groups.

o Morphological Species Concept: Species are classified based on shared physical

characteristics.

o Phylogenetic Species Concept: Species are the smallest detectable group of organisms
sharing a common ancestor.

 Classification Systems:

o Developed to organize and categorize the diversity of life.

o Binomial Nomenclature: Two-part scientific naming of species (Genus species, e.g.,

Homo sapiens).

o Taxonomic Hierarchy: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.

3. Phylogenetic Trees and Cladistics

 Phylogenetic Trees: Diagrams that show the inferred evolutionary relationships among various
biological species or entities based upon similarities and differences in their physical and/or
genetic characteristics.

o Cladistics: Method of classification based on common ancestry. A clade is a group of

species that includes an ancestral species and all its descendants.

o Branches: Represent lineages evolving through time that branch off due to speciation
events.

4. Table of Species Concepts

Species Concept Definition Focus

Biological Species Groups that breed naturally and are Reproductive isolation
Concept reproductively isolated.

Morphological Species Classification based on physical form and Physical characteristics

Concept structure.

Phylogenetic Species Smallest groups sharing a common Common ancestry and

Concept ancestor. genetic lineage
Physiology and Organ Systems

1. Human Body Systems

Circulatory System:

 Function: Transports blood, nutrients, gases, and wastes throughout the body.

 Components:

o Heart: A muscular organ that pumps blood through the blood vessels of the circulatory
system. It has four chambers: two atria and two ventricles.

o Arteries: Blood vessels that carry oxygen-rich blood away from the heart to the tissues
of the body.

o Veins: Blood vessels that carry oxygen-poor blood back to the heart from the tissues.

o Capillaries: Small blood vessels where the exchange of water, oxygen, carbon dioxide,
and many other nutrient and waste chemical substances between blood and the tissues
occurs.

Respiratory System:

 Function: Facilitates the exchange of oxygen and carbon dioxide between the external
environment and the body’s cells.

 Components:

o Lungs: Main organs of the respiratory system, responsible for gas exchange. They fill
with air, oxygenate depleted blood, and remove carbon dioxide.

o Trachea: Also known as the windpipe, it connects the pharynx and larynx to the lungs,
allowing the passage of air.

o Bronchi: The two main branches from the trachea that lead into the lungs and further
branch into smaller bronchioles.

o Alveoli: Tiny sac-like structures at the end of bronchioles where gas exchange occurs
with the blood through the capillaries that line their walls.

Nervous System:

 Function: Controls and coordinates body activities by transmitting electrical signals to and from
different parts of the body.

 Components:

o Brain: The control center of the nervous system, located in the skull and responsible for
processing sensory information, regulating blood pressure, breathing, and more.
 o Spinal Cord: A long, thin, tubular structure made up of nervous tissue, which extends
from the brainstem to the lower back, conducting signals to and from the brain through
nerve fibers.

o Nerves: Bundled axons that form neural "cables" connecting the central nervous system
to the body, muscles, and glands.

Digestive System

Function: Processes food for energy and nutrient absorption while expelling waste.

Components and Functions:

Mouth:

 Function: Begins the digestion process by mechanically breaking down food through chewing
and mixing it with saliva, which contains enzymes that begin the breakdown of carbohydrates.

 Salivary Glands: Produce saliva, which moistens food for easier swallowing and contains
enzymes such as amylase that start the digestion of starches.

Esophagus:

 Function: A muscular tube that transports food from the mouth to the stomach using rhythmic
muscle contractions known as peristalsis.

 Structure: Lined with mucus to facilitate the smooth passage of food and protect the lining from
abrasion and acid reflux.

Stomach:

 Function: Further breaks down food using stomach acid (hydrochloric acid) and enzymes (such
as pepsin) that digest proteins, turning the food into a semi-liquid substance called chyme.

 Components:

o Gastric Glands: Produce gastric juice which contains acid and enzymes.

o Sphincters: Muscular rings (like the pyloric sphincter at the exit of the stomach) control
food entry and exit, preventing backflow.

Small Intestine:

 Function: Main site for digestion of nutrients and absorption. Enzymes from the pancreas and
bile from the liver aid in digesting fats, proteins, and carbohydrates.

 Components:

o Duodenum: Receives chyme from the stomach along with bile and pancreatic juice.

o Jejunum: Primarily involved in nutrient absorption.

o Ileum: Absorbs remaining nutrients not absorbed by the jejunum and transfers
remaining waste to the large intestine.
 o Villi and Microvilli: Increase the surface area for absorption dramatically.

Large Intestine (Colon):

 Function: Absorbs water and salts from the material that has not been digested as food, and is
thus involved in the formation of solid waste (feces).

 Components:

o Cecum: Connects the ileum to the colon.

o Colon: Composed of the ascending, transverse, descending, and sigmoid sections, it

further absorbs water and mineral nutrients from food residue.

o Rectum and Anus: Store and regulate the expulsion of feces.

Liver:

 Function: Produces bile, which helps digest fats. It also processes nutrients absorbed from the
small intestine.

 Bile: Stored in the gallbladder between meals and released into the small intestine when
needed.

Gallbladder:

 Function: Stores and concentrates bile from the liver, releasing it into the small intestine to aid in
the digestion of fats.

Pancreas:

 Function: Produces digestive enzymes and bicarbonate, which are released into the small
intestine to aid in digestion and neutralize stomach acid.

 Enzymes Include:

o Amylase: Breaks down starches.

o Lipase: Breaks down fats.

o Proteases: Break down proteins into amino acids.

Digestive Processes:

1. Ingestion: Intake of food.

2. Digestion: Mechanical and chemical breakdown of food into absorbable units.

3. Absorption: Uptake of nutrients by the cells of the small intestine for transport into either the
blood or lymph system.

4. Egestion: Removal of unabsorbed waste as feces.

Endocrine System

 Function: Produces and secretes hormones that regulate the activity of cells or organs, crucial
for maintaining homeostasis.

 Components:

o Glands: Specialized organs that produce, store, and release hormones into the
bloodstream.

 Pituitary Gland: The "master gland" that controls other glands and influences
growth, metabolism, and regeneration.

 Thyroid Gland: Regulates metabolism, energy generation, and nervous system

activity.

 Adrenal Glands: Produce hormones that help control heart rate, blood pressure,
and other critical functions.

 Pancreas: Besides its digestive role, it secretes insulin and glucagon to regulate
blood sugar levels.

o Hormones: Chemical messengers that transmit information from the endocrine system
to target organs for regulation of various physiological processes.

2. Plant Physiology

Photosynthesis:

 Process: Plants convert light energy into chemical energy stored in glucose.

 Equation: 6CO2+6H2O+light→C6H12O6+6O26CO_2 + 6H_2O + \text{light} \rightarrow

C_6H_{12}O_6 + 6O_26CO2+6H2O+light→C6H12O6+6O2.

 Components:

o Chloroplasts: Organelles in plant cells where photosynthesis occurs. They contain

chlorophyll, which absorbs light energy for photosynthesis.

o Chlorophyll: A green pigment located within the chloroplasts, crucial for the absorption
of light that drives the initial reaction of photosynthesis.

Plant Structures:

 Roots: Structures that absorb water and minerals from the soil, anchor the plant, and store food.

 Stems: Support structures for plants, transporting fluids between roots and leaves, and storing
nutrients.

 Leaves: The main site of photosynthesis and transpiration in plants. They contain chloroplasts
and facilitate gas exchange through stomata.
4. Summary of Photosynthesis in Plants

Photosynthesis:

 Light-dependent Reactions: Convert solar energy into chemical energy in the form of ATP and
NADPH.

 Calvin Cycle: Uses ATP and NADPH from the light-dependent reactions to convert CO2CO_2CO2
into glucose, which is used as a form of chemical energy for growth and development.
Microbiology

1. Structure, Function, and Classification of Bacteria

 Bacteria:

o Structure: Typically single-celled organisms with a cell wall, cell membrane, cytoplasm,
and genetic material (DNA).

 Cell Wall: Provides structure and protection; made of peptidoglycan in most

bacteria.

 Flagella: Some bacteria have flagella for movement.

o Function: Can be either beneficial (e.g., gut flora aiding digestion) or pathogenic (causing
disease).

o Classification: Based on shape, Gram staining properties, and metabolic activity.

 Shapes: Cocci (spherical), Bacilli (rod-shaped), Spirilla (spiral-shaped).

 Gram Staining:

 Gram-positive: Thick cell wall that retains purple dye.

 Gram-negative: Thin cell wall with an additional outer membrane; does

not retain purple dye.

2. Structure, Function, and Classification of Viruses

 Viruses:

o Structure: Consist of genetic material (DNA or RNA) encased in a protein coat,

sometimes with a lipid envelope.

o Function: Cannot replicate on their own; must infect a host cell to reproduce.

o Classification: Based on type of genetic material, replication method, and morphology.

 Examples: HIV (retrovirus with RNA), Influenza virus.

3. Mechanisms of Microbial Infection and Immunity

 Infection:

o Pathogen Entry: Through physical contact, contaminated food/water, or airborne

droplets.

o Invasion and Multiplication: Microbes invade host tissues, evade the immune response,
and multiply.

 Immunity:

o Innate Immunity: Non-specific first line of defense (e.g., skin, mucous membranes).
 o Adaptive Immunity: Specific immune response involving recognition of antigens,
activation of lymphocytes, and production of antibodies.

 Cell-mediated Immunity: Involves T cells that destroy infected host cells.

 Humoral Immunity: Involves B cells that produce antibodies to neutralize

pathogens.

4. Table of Microbial Classification

Type Characteristics Examples

Bacteri Single-celled, peptidoglycan cell walls, various E. coli (rod-shaped), Staphylococcus

a shapes. (spherical)

Viruses Genetic material in protein coat, require host HIV, Influenza virus
cells.
 Chemistry
Atomic Structure

Basic Concepts of Atomic Structure

 Atom: The smallest unit of an element that retains the properties of that element. Consists of a
nucleus surrounded by electrons.

 Nucleus: The central part of an atom, containing protons and neutrons.

 Protons: Positively charged particles in the nucleus of an atom.

 Neutrons: Neutral particles in the nucleus that add mass but no charge.

 Electrons: Negatively charged particles that orbit the nucleus in electron shells.

Subatomic Particles

 Proton (p+): Determines the atomic number and identity of an element. Located in the nucleus.

 Neutron (n0): Contributes to the atomic mass but not to the atomic number. Helps stabilize the
nucleus.

 Electron (e-): Very light compared to protons or neutrons. Determines the atom’s charge and
chemical properties by its arrangement around the nucleus.

Atomic Number and Mass Number

 Atomic Number (Z): Number of protons in the nucleus of an atom, defining the element.

 Mass Number (A): Total number of protons and neutrons in an atom’s nucleus.

 Isotopes: Atoms of the same element that have the same number of protons but different
numbers of neutrons. They have different mass numbers but the same chemical properties.

Electronic Configuration

 Electron Shells: Layers around the nucleus where electrons are likely found. Each shell can hold a
certain maximum number of electrons.

 Electron Configuration: Distribution of electrons in an atom’s shells, usually noted in terms of

energy levels (e.g., 1s² 2s² 2p⁶).

Periodic Table and Electron Configuration

 Periodic Table: A chart where elements are organized in order of increasing atomic number.
Element properties are periodic functions of their atomic numbers.

 Groups: Vertical columns in the periodic table. Elements in the same group have similar chemical
properties because they have the same number of valence electrons.
  Periods: Horizontal rows in the periodic table. Atomic size and reactivity show trends across a
period.

Sample Electron Configurations

 Hydrogen (H): 1s¹

 Carbon (C): 1s² 2s² 2p²

 Oxygen (O): 1s² 2s² 2p⁴

 Iron (Fe): 1s² 2s² 2p⁶ 3s² 3p⁶ 3d⁶ 4s²

Periodic Table and Element Properties

Introduction to the Periodic Table

 Definition: The periodic table organizes all known chemical elements in an informative array.
Elements are arranged from left to right and top to bottom in order of increasing atomic number.

 Purpose: To display the periodic trends in the properties of elements, which help predict the
characteristics and chemical behaviors of these elements.

Layout of the Periodic Table

 Groups (Columns): Also known as families, these vertical columns contain elements with similar
chemical and physical properties due to their having the same number of electrons in their
outermost shell.

 Periods (Rows): Horizontal rows where elements are organized by increasing atomic number.
Properties change predictably across a period.

Major Groups in the Periodic Table

 Alkali Metals (Group 1): Highly reactive, especially with water, soft, silver-colored, low density;
example: Sodium (Na).

 Alkaline Earth Metals (Group 2): Slightly less reactive than alkali metals, higher densities, higher
melting points; example: Calcium (Ca).

 Transition Metals (Groups 3-12): Moderate to high reactivity, good conductors of electricity and
heat, high luster, high melting points; example: Iron (Fe).

 Halogens (Group 17): Very reactive nonmetals, poor conductors of heat and electricity, react
with metals to form salts; example: Chlorine (Cl).

 Noble Gases (Group 18): Colorless, odorless, extremely unreactive, monatomic gases at room
temperature; example: Helium (He).

Special Categories of Elements

 Lanthanides and Actinides: Often shown separately at the bottom of the periodic table, these
elements fill the f-orbitals and include many radioactive elements.

 Metals, Nonmetals, and Metalloids: Metals are good conductors of heat and electricity,
nonmetals are not, and metalloids have properties intermediate between metals and nonmetals.

Periodic Trends

 Atomic Radius: Generally decreases across a period and increases down a group.

 Ionization Energy: The energy required to remove an electron. Increases across a period and
decreases down a group.

 Electronegativity: A measure of the tendency of an atom to attract a bonding pair of electrons.

Increases across a period and decreases down a group.
  Electron Affinity: The amount of energy released when an electron is added to a neutral atom to
form a negative ion. Increases across a period and can vary down a group.

Element Classification Based on Electron Configuration

 Elements in the same group have similar valence electron configurations, which explains their
similarities in chemical properties.

Significance of the Periodic Table in Chemistry

 Provides a useful framework for analyzing chemical behavior, and aids in predicting the
properties of new elements or those not yet thoroughly studied.
Chemical Bonds and Interactions

Overview of Chemical Bonds

 Definition: Chemical bonds are the attractive forces that hold atoms together in compounds.
They are formed due to interactions between electrons from different atoms.

Types of Chemical Bonds

 Ionic Bonds:

o Formed when one atom donates an electron to another atom, creating ions. This usually
occurs between metals and nonmetals.

o Characterized by the electrostatic attraction between positively charged cations and

negatively charged anions.

o Example: Sodium chloride (NaCl).

 Covalent Bonds:

o Occur when two atoms share one or more pairs of electrons. Generally involves
nonmetals.

o Can be single, double, or triple bonds, depending on how many electron pairs are
shared.

o Example: Water (H₂O), where each hydrogen shares an electron with oxygen.

 Metallic Bonds:

o Found in metals, where electrons are not bound to any particular atom and can move
freely about the metal’s lattice.

o Contributes to properties such as conductivity, malleability, and ductility.

o Example: Iron (Fe) in its metallic state.

Molecular Geometry

 VSEPR Theory (Valence Shell Electron Pair Repulsion): A model used to predict the geometry of
individual molecules from the number of electron pairs surrounding their central atoms.

 Shapes: Linear, trigonal planar, tetrahedral, bent, trigonal pyramidal, etc., each shape dependent
on the number and arrangement of electron pairs.

Intermolecular Forces

 Types and Importance:

o Van der Waals Forces: Weak attractions between molecules, including dipole-dipole
interactions and London dispersion forces.
 o Hydrogen Bonds: Strong type of dipole-dipole interaction involving a hydrogen atom and
a more electronegative atom (N, O, or F), leading to higher boiling points and unique
properties in substances like water.

Bond Strength and Chemical Reactions

 Bond Energy: The energy required to break a bond. Higher bond energy means a stronger bond.

 Influence on Reactions: The type and strength of bonds affect the rate and outcome of chemical
reactions. For example, stronger bonds generally lead to slower reactions under the same
conditions.

Electronegativity and Polarity

 Electronegativity: The ability of an atom to attract shared electrons in a chemical bond.

Differences in electronegativity between bonded atoms create polar bonds.

 Polar vs. Nonpolar Molecules: Polar molecules have uneven distribution of charges (partial
positive and negative ends), while nonpolar molecules have an even distribution of electrons.

Chemical Bonding in Everyday Life

 Applications: From the water we drink (polar covalent bonds) to the salt in our food (ionic
bonds), and the metals used in technology and construction (metallic bonds), chemical bonding
is essential to both natural processes and human-made technologies.
States of Matter and Intermolecular Forces

Introduction to States of Matter

 Definition: The physical forms in which all matter naturally exists on Earth—primarily as solids,
liquids, and gases.

 Determined by: Temperature and pressure conditions, which influence the energy and
movement of particles in a substance.

States of Matter

 Solids:

o Properties: Definite shape and volume, particles closely packed in a fixed position, only
vibrate in place.

o Examples: Ice, diamond, iron.

 Liquids:

o Properties: Definite volume but no definite shape, particles are close but can move
around each other.

o Examples: Water, mercury, oil.

 Gases:

o Properties: No definite shape or volume, particles move freely at high speeds.

o Examples: Oxygen, carbon dioxide, nitrogen.

 Plasma:

o Properties: Ionized gas with some electrons removed from atoms, conducts electricity,
affected by magnetic fields.

o Examples: Stars, neon signs, plasma displays.

Intermolecular Forces (IMFs)

 Overview: Forces of attraction or repulsion which act between neighboring particles (atoms,
molecules, or ions).

 Types of IMFs:

o Van der Waals Forces: Weakest intermolecular forces including:

 London Dispersion Forces: Temporary polarizations of electron clouds in

nonpolar molecules.

 Dipole-Dipole Forces: Attractions between oppositely charged ends of polar

molecules.
 o Hydrogen Bonds: Strong type of dipole-dipole force occurring between hydrogen and F,
O, or N, notable for their role in water's unique properties.

Impact of Intermolecular Forces

 Boiling and Melting Points: Stronger intermolecular forces result in higher boiling and melting
points because more energy is required to overcome these forces.

 Solubility: Like dissolves like; substances with similar intermolecular forces are more likely to be
soluble in each other.

 Viscosity and Surface Tension: Higher intermolecular forces increase viscosity (resistance to
flow) and surface tension (the elastic tendency of liquids).

Phase Changes

 Melting: Solid to liquid.

 Freezing: Liquid to solid.

 Vaporization: Liquid to gas.

 Condensation: Gas to liquid.

 Sublimation: Solid to gas (bypassing the liquid state).

 Deposition: Gas to solid (bypassing the liquid state).

State Diagrams and Phase Changes

 Phase Diagram: A graphical way to depict the effects of pressure and temperature on the state
of a substance.

 Critical Point and Triple Point: Specific points on a phase diagram that describe the unique
states where substances can coexist in different phases.
Chemical Reactions

Introduction to Chemical Reactions

 Definition: A process in which one or more substances, the reactants, are converted to one or
more different substances, the products.

 Indicators of a Chemical Reaction: Production of gas, change in color, energy change, formation
of a precipitate.

Types of Chemical Reactions

 Synthesis (Combination) Reactions:

o Definition: Two or more simple substances combine to form a more complex substance.

o Example: A+B→ABA + B \rightarrow ABA+B→AB

o Specific Example: 2Na+Cl2→2NaCl2Na + Cl_2 \rightarrow 2NaCl2Na+Cl2→2NaCl

 Decomposition Reactions:

o Definition: A compound breaks down into two or more simpler substances.

o Example: AB→A+BAB \rightarrow A + BAB→A+B

o Specific Example: 2H2O→2H2+O22H_2O \rightarrow 2H_2 + O_22H2O→2H2+O2

 Single Replacement (Displacement) Reactions:

o Definition: An element reacts with a compound and takes the place of another element
in that compound.

o Example: A+BC→AC+BA + BC \rightarrow AC + BA+BC→AC+B

o Specific Example: Zn+2HCl→ZnCl2+H2Zn + 2HCl \rightarrow ZnCl_2 +

H_2Zn+2HCl→ZnCl2+H2

 Double Replacement Reactions:

o Definition: The ions of two compounds exchange places in an aqueous solution to form
two new compounds.

o Example: AB+CD→AD+CBAB + CD \rightarrow AD + CBAB+CD→AD+CB

o Specific Example: AgNO3+NaCl→AgCl+NaNO3AgNO_3 + NaCl \rightarrow AgCl +

NaNO_3AgNO3+NaCl→AgCl+NaNO3

 Combustion Reactions:

o Definition: A substance combines with oxygen, releasing a large amount of energy in the
form of light and heat.
 o Example: CxHy+O2→CO2+H2OC_xH_y + O_2 \rightarrow CO_2 + H_2OCxHy+O2→CO2
+H2O

o Specific Example: CH4+2O2→CO2+2H2OCH_4 + 2O_2 \rightarrow CO_2 + 2H_2OCH4

+2O2→CO2+2H2O

Balancing Chemical Equations

 Purpose: To satisfy the Law of Conservation of Mass, which states that mass is neither created
nor destroyed in a chemical reaction.

 Method: Adjust the coefficients of the reactants and products to make the number of atoms of
each element equal on both sides of the equation.

Stoichiometry

 Definition: The calculation of reactants and products in chemical reactions.

 Stoichiometric Calculations: Used to determine the amount of products/reactants that are

produced/consumed in a given reaction.

Energy in Reactions

 Exothermic Reactions: Release heat energy; ΔH<0\Delta H < 0ΔH<0.

 Endothermic Reactions: Absorb heat energy; ΔH>0\Delta H > 0ΔH>0.

 Activation Energy: The minimum energy required to initiate a chemical reaction.

Reaction Rates

 Factors Influencing Rate: Concentration, surface area, temperature, and the presence of
catalysts.

 Catalysts: Substances that speed up chemical reactions without being consumed.

Chemical Equilibrium

 Dynamic Equilibrium: The rate of the forward reaction equals the rate of the reverse reaction.

 Le Chatelier's Principle: If a dynamic equilibrium is disturbed by changing the conditions, the

position of equilibrium moves to counteract the change.
Acids, Bases, and pH

Introduction to Acids and Bases

 Definition of Acids: Substances that donate protons (H⁺ ions) or accept electrons during
chemical reactions.

 Definition of Bases: Substances that accept protons or donate electrons.

 Properties of Acids: Sour taste, corrosive, can conduct electricity, turn blue litmus paper red.

 Properties of Bases: Bitter taste, slippery feel, can conduct electricity, turn red litmus paper
blue.

The pH Scale

 Definition: A scale from 0 to 14 that measures the acidity or alkalinity of a solution; pH stands
for 'potential of Hydrogen'.

 Neutral pH: A pH of 7 is considered neutral, indicative of pure water.

 Acidic Solutions: Have a pH less than 7. The lower the pH, the more acidic the solution.

 Basic Solutions: Have a pH greater than 7. The higher the pH, the more basic the solution.

Ionization of Water

 Autoionization: Water naturally ionizes into H⁺ and OH⁻ ions in a reversible reaction where
H2O↔H++OH−H_2O \leftrightarrow H^+ + OH^-H2O↔H++OH−.

 Ion Product of Water (Kw): At 25°C, Kw=[H+][OH−]=1.0×10−14Kw = [H^+][OH^-] = 1.0 \times

10^{-14}Kw=[H+][OH−]=1.0×10−14.

Acid and Base Strength

 Strong Acids and Bases: Dissociate completely in solution, providing high concentrations of ions
(e.g., HCl for acids, NaOH for bases).

 Weak Acids and Bases: Only partially dissociate in solution, resulting in lower concentrations of
ions (e.g., acetic acid for acids, ammonia for bases).

Conjugate Acids and Bases

 Definition: When an acid donates a proton, it forms a conjugate base; when a base accepts a
proton, it forms a conjugate acid.

 Example: NH3+H2O↔NH4++OH−NH_3 + H_2O \leftrightarrow NH_4^+ + OH^-NH3+H2

O↔NH4++OH− (Ammonia is the base, and ammonium NH4+NH_4^+NH4+ is its conjugate acid).

Buffer Systems

 Definition: Solutions that resist changes in pH upon the addition of small amounts of acids or
bases.
  Components: Typically composed of a weak acid and its conjugate base, buffering the pH by
neutralizing added acids or bases.

 Biological Importance: Buffers are crucial in maintaining the pH of blood and cellular fluids.

Applications of Acids and Bases

 Industrial: Used in manufacturing, treatment processes, and synthesis of various products.

 Household: Found in cleaning products, baking ingredients, and personal care products.

 Environmental: Monitoring of acid rain and the health of aquatic environments.

Titration

 Purpose: A laboratory method of quantitative chemical analysis used to determine the

concentration of an identified analyte.

 Process: Involves the gradual addition of a titrant solution to a known volume of a sample (or
vice versa) until the reaction reaches the desired chemical equivalence point indicated by a color
change (endpoint).
Organic Chemistry Basics

Introduction to Organic Chemistry

 Definition: Organic chemistry is the study of carbon compounds, which includes a vast number
of substances that form the basis of life (biomolecules) and many synthetic materials.

 Importance: Essential for understanding biological processes, the development of

pharmaceuticals, and the creation of synthetic materials.

Carbon: The Basis of Organic Chemistry

 Unique Properties: Carbon's ability to form four covalent bonds and its capacity to catenate
(form chains with other carbon atoms) make it uniquely suited to form complex and diverse
molecules.

 Hybridization: sp³ (tetrahedral), sp² (trigonal planar), and sp (linear) hybridizations dictate the
geometry of carbon compounds.

Types of Hydrocarbons

 Alkanes: Saturated hydrocarbons with single bonds only. Example: Methane (CH₄).

 Alkenes: Unsaturated hydrocarbons with one or more double bonds. Example: Ethene (C₂H₄).

 Alkynes: Unsaturated hydrocarbons with one or more triple bonds. Example: Ethyne (C₂H₂).

 Aromatic Hydrocarbons: Compounds that contain benzene rings, which are stable due to
resonance. Example: Benzene (C₆H₆).

Functional Groups in Organic Chemistry

 Alcohols: Contain an -OH group. Example: Ethanol (CH₃CH₂OH).

 Carboxylic Acids: Contain a -COOH group. Example: Acetic acid (CH₃COOH).

 Amines: Contain an -NH₂ group. Example: Aniline (C₆H₅NH₂).

 Ethers: Contain an -O- between two alkyl groups. Example: Diethyl ether (CH₃CH₂OCH₂CH₃).

 Aldehydes and Ketones: Contain a carbonyl group (C=O). Aldehydes have it at the end of the
carbon chain, while ketones have it within the chain.

Common Organic Reactions

 Addition Reactions: Typical in alkenes and alkynes where π bonds are broken and new atoms are
added.

 Substitution Reactions: Common in saturated hydrocarbons like alkanes and aromatic

hydrocarbons where one atom is replaced by another.

 Elimination Reactions: Opposite of addition, where elements of the starting material are
removed resulting in a double or triple bond.
  Polymerization: Molecules combine to form a polymer. Example: Polymerization of ethene to
form polyethylene.

Isomerism

 Structural Isomers: Molecules with the same molecular formula but different structural
formulas.

 Stereoisomers: Same molecular and structural formulas but different spatial orientations.
Includes geometric (cis/trans) and optical isomers.

Applications of Organic Chemistry

 Pharmaceuticals: Design and synthesis of drugs.

 Agriculture: Pesticides and herbicides.

 Material Science: Plastics, fibers, and other synthetic materials.

 Environmental Science: Understanding pollutants and their breakdown.

Solutions and Solubility

Introduction to Solutions

 Definition: A solution is a homogeneous mixture of two or more substances. The substance in

the greatest amount is known as the solvent, and the substance(s) in lesser amounts are called
solutes.

 Characteristics: Solutions are uniform in composition and phase; particles of solute are not
visible by the naked eye and do not settle out on standing.

Types of Solutions

 Gaseous Solutions: Homogeneous mixtures of gases, such as air (a solution of oxygen, nitrogen,
and other gases).

 Liquid Solutions: The most common type, where a solid, liquid, or gas is dissolved in a liquid
solvent. Example: Salt water.

 Solid Solutions: Alloys like bronze and steel where the solutes are metals mixed at the molecular
level with metallic solvents.

Solubility

 Definition: The ability of a substance to dissolve in a solvent. It is often expressed as the

maximum amount of solute that can dissolve in a specific amount of solvent at a specified
temperature.

 Factors Affecting Solubility:

o Temperature: Generally, solubility of solids in liquids increases with an increase in

temperature.

o Pressure: For gases in liquids, solubility increases as the pressure of the gas above the
solution increases (Henry's Law).

o Nature of Solute and Solvent: Dictated by the principle "like dissolves like" (polar
solvents dissolve polar solutes, and nonpolar solvents dissolve nonpolar solutes).

Solution Concentration

 Units of Concentration:

o Molarity (M): Moles of solute per liter of solution.

o Molality (m): Moles of solute per kilogram of solvent.

o Percentage (%): Weight or volume of solute in a given volume of solution.

o Parts per million (ppm) and parts per billion (ppb): Used for very dilute solutions.

Dissolution Process
  Dissolving Mechanism: Involves solute-solvent interactions that overcome the internal energy of
solute particles and spread them throughout the solvent.

 Entropy and Spontaneity: Increased disorder (entropy) often drives the dissolution process,
making it energetically favorable.

Saturation

 Unsaturated: A solution that can dissolve more solute at a given temperature.

 Saturated: A solution that contains the maximum amount of solute that can dissolve.

 Supersaturated: A solution that contains more solute than it can theoretically hold at a given
temperature; unstable and can precipitate.

Colligative Properties

 Definition: Properties that depend on the number of solute particles in a solution, not on the
type of particles.

o Boiling Point Elevation: Boiling point increases when a nonvolatile solute is added.

o Freezing Point Depression: Freezing point decreases with the addition of a solute.

o Osmotic Pressure: Pressure required to stop osmosis; depends on the concentration of

solute particles.

Applications of Solutions

 Medical: Delivery of drugs in solution form for faster absorption.

 Industrial: Use in chemical synthesis, cleaning processes, and materials production.

 Environmental: Monitoring of pollutant levels in water and air.

Biochemistry Essentials

Introduction to Biochemistry

 Definition: Biochemistry is the branch of science that explores the chemical processes and
substances that occur within living organisms.

 Relevance: Biochemistry bridges biology and chemistry, providing insights into the molecular
mechanisms that drive biological processes, including metabolism, enzyme action, and genetic
expression.

Core Biomolecules in Biochemistry

 Proteins:

o Function: Catalyze biochemical reactions (enzymes), structural components (collagen),

signal and regulatory molecules (hormones), transport and storage.

o Structure: Made up of amino acids linked by peptide bonds forming complex structures
essential for their function.

 Carbohydrates:

o Function: Main source of energy (glucose), structural components (cellulose in plants,

chitin in arthropods), and involved in cell recognition processes (glycoproteins).

o Types: Simple sugars (monosaccharides), disaccharides (sucrose), polysaccharides

(starch, glycogen).

 Lipids:

o Function: Structural components of cell membranes (phospholipids), energy reserves

(fats), signaling molecules (steroids).

o Categories: Fats and oils, phospholipids, steroids, waxes.

 Nucleic Acids:

o Function: Storage, transmission, and use of genetic information.

o Types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

Metabolism

 Overview: Metabolism involves all chemical reactions that occur within an organism to maintain
life.

 Pathways:

o Catabolism: Breakdown of molecules to obtain energy.

o Anabolism: Synthesis of all compounds needed by the cells.

 Enzyme Action:
 o Role: Enzymes are proteins that catalyze biochemical reactions without being consumed
in the process.

o Mechanisms: Lower the activation energy required for reactions, increasing the rate of
reactions.

Genetics and Biochemistry

 Gene Expression: The process by which information from a gene is used to synthesize a
functional gene product (often a protein).

 Central Dogma of Molecular Biology: DNA → RNA → Protein. This flow of information highlights
the role of nucleic acids in protein synthesis.

Cellular Signaling and Regulation

 Signal Transduction: The transmission of molecular signals from a cell's exterior to its interior,
leading to functional changes.

 Hormones and Receptors: Chemical signals that travel through the body to initiate responses at
specific target cells.

Techniques in Biochemistry

 Chromatography, Electrophoresis, and Spectroscopy: Used for analyzing and separating

biomolecules.

 PCR and Gel Electrophoresis: Techniques for studying genetic material.

Applications of Biochemistry

 Medical: Development of pharmaceuticals and diagnostics.

 Agricultural: Enhancements in crop and livestock production.

 Environmental: Bioremediation and pollution control.