Basics of Chemistry

Matter, Atoms, and Elements

• Everything is made of matter, which is composed of atoms.

• Atoms consist of protons and neutrons in the nucleus, with electrons orbiting around.

• Different kinds of atoms make up elements, each with a unique number of protons (atomic number).

• Life requires approximately 25 chemical elements, with carbon, hydrogen, oxygen, and nitrogen making up 96% of living matter.

• Isotopes are atoms of the same element with different numbers of neutrons, some of which are unstable and undergo nuclear reactions.

Atomic Structure and Behavior

• The number of protons in an atom determines its element and atomic number, which also equals the number of electrons.

• All atoms of the same element exhibit identical chemical properties.

• Elements in the same row of the periodic table have the same number of electron shells.

• Moving from left to right in the periodic table, elements have a sequential addition of protons and electrons.

• Atoms tend to complete or empty their outer (valence) electron shell, following the Octet rule, which drives chemical reactions.

Chemical Bonds

• Ionic bonds involve the transfer of electrons, forming positive and negative ions.

• Covalent bonds entail the sharing of electron pairs between atoms, forming molecules.

• Double and triple covalent bonds involve sharing multiple pairs of electrons and are very strong.

• Polar covalent bonds result from unequal sharing of electrons, creating a polar molecule.

• Hydrogen bonds occur between a hydrogen atom and an electronegative atom like oxygen, contributing to unique properties of water.

Importance of Chemistry in Biology

Foundation of Biology

• Chemistry forms the foundation of biology, as biological processes rely on chemical interactions.

• Approximately 25 chemical elements are essential for life, with carbon, hydrogen, oxygen, and nitrogen being predominant.

• Understanding chemistry is crucial for comprehending biological functions and processes.

Role of Chemical Bonds

• Chemical reactions in biological systems involve the making and breaking of chemical bonds.

• Strong and weak chemical bonds play vital roles in the chemistry of life.

• The biological function of a molecule is closely related to its shape and the bonds it forms.

Importance of Water

Water's Unique Properties

• Water's unique properties enable life on Earth.

• Key concepts include polarity, hydrogen bonding, high specific heat, 'stickiness', ability to dissolve, ice's lower density, and pH.

• Life depends on hydrogen bonds in water, which is a polar molecule with slightly charged regions.

• Hydrogen bonds form between slightly positive hydrogen atoms and slightly negative atoms.

• Polarity involves unequal sharing of electrons, with oxygen being negative and hydrogen being positive.

Hydrogen Bonding

• Hydrogen bonds are crucial for proteins folding, DNA structure, and water's unique properties.

• Proteins fold into specific shapes due to hydrogen bonds.

• DNA forms a double helix structure because of hydrogen bonding.

High Specific Heat

• Water's high specific heat allows it to absorb and retain energy.

• Coastal regions have stable temperatures due to water's specific heat.

• Earth's position in the 'Goldilocks zone' is maintained by water's specific heat.

• Water's specific heat prevents rapid temperature changes, supporting diverse life forms.

Adhesion and Cohesion

• Water exhibits adhesion (sticks to other substances) and cohesion (sticks to itself).

• Adhesion allows water to climb up plants' vascular system through capillary action.

• Cohesion is essential for water's surface tension and the ability to form droplets.

• Adhesion and cohesion are vital for life, enabling swimming and water transport in plants.

Ability to Dissolve

• Water is known as the universal solvent due to its ability to dissolve many substances.

• Solutions are formed when one substance dissolves in another, creating a homogeneous mixture.

• Polar solvents dissolve polar solutes, while nonpolar solvents dissolve nonpolar solutes.

• Water's ability to dissolve various compounds supports life processes.

Chemistry of Water

Ice's Density and pH

• Ice floats on water due to its lower density.

• Fish live underneath ice, and its floating property prevents the world from getting colder.

• A neutral solution has a pH of 7, with acids releasing hydrogen ions and bases removing them.

Universal Solvent and pH in Biology

• Water's ability to dissolve substances makes it the universal solvent.

• Blood, cytoplasm, and oceans are examples of solutions vital for life.

• pH levels in the human body affect acidity, with most areas maintaining a pH of 7.

Water in Biology

• Water's properties enable it to move from roots to leaves in plants.

• Water's cohesive and adhesive behavior supports life processes.

• Water's surface tension allows insects to stand on water surfaces.

• Ice floats due to water molecules' cohesive behavior and hydrogen bonding.

• Water's high specific heat means it can absorb and retain energy.

• H2O's atoms are held together by covalent bonds.

• Water's universal solvent property is enabled by its hydrogen bonds.

Introduction to Macromolecules

Macromolecules Overview

• Macromolecules are large organic molecules found in living organisms.

• They are essential for various biological functions.

• Monomers are the building blocks of macromolecules.

• Polymers are formed by joining monomers through covalent bonds.

Dehydration Synthesis and Hydrolysis

• Dehydration Synthesis: Monomers join to form polymers with the release of water.

• Hydrolysis: Polymers are broken down into monomers with the addition of water.

• Enzymes are required to catalyze both processes.

Carbohydrates

Structure and Function of Carbohydrates

• Carbohydrates serve as a source of energy and for structural purposes.

• Monosaccharides are the monomers of carbohydrates.

• Disaccharides and polysaccharides are formed by the bonding of multiple monosaccharides.

• The ratio of elements in carbohydrates is 1:2:1 (C:H:O).

Types of Carbohydrates

• Monosaccharides: Simple sugars like glucose, fructose, and galactose.

• Disaccharides: Examples include maltose, lactose, and sucrose.

• Polysaccharides: Complex carbohydrates like glycogen, starch, cellulose, and chitin.

Functions of Carbohydrates

• Short-term energy storage in animals and energy storage in plants.

• Provide support in organisms, such as cell walls in plants.

• Act as transferable energy when consumed by animals.

Lipids

Lipids Overview

• Lipids are a diverse group of macromolecules insoluble in water.

• They play crucial roles in energy storage, insulation, and cell structure.

Types and Functions of Lipids

• Triglycerides: Formed by glycerol and three fatty acids, categorized as saturated or unsaturated.

• Phospholipids: Compose cell membranes with hydrophilic heads and hydrophobic tails.

• Wax: Hydrophobic lipid that resists water, used for waterproofing.

Additional Lipid Functions

• Long-term energy storage compared to carbohydrates.

• Insulation in cold climate animals.

• Building blocks of cell membranes and waterproofing.

Proteins in Biology

• Proteins are essential macromolecules with diverse functions in living organisms.

• Functions of proteins include structural support (e.g., hair, nails), movement (muscles), enzymatic activity, transportation of molecules, hormonal signaling, defense mechanisms (antibodies), and storage of amino acids.

• Example: Hemoglobin, a protein, transports oxygen in the blood.

Protein Structure Levels

• Proteins have four structural levels: primary, secondary, tertiary, and quaternary.

• Primary structure: Linear sequence of amino acids determined by DNA.

• Secondary structure: Local folding patterns like alpha-helix and beta-sheet.

• Tertiary structure: Overall 3D shape influenced by R-group interactions.

• Quaternary structure: Formed by the association of multiple polypeptide chains.

• Example: Sickle cell anemia results from a single amino acid change in the primary structure.

Factors Holding Proteins Together

• Proteins are held together by hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.

• Denaturation disrupts protein structure through factors like pH, temperature, and salt concentration.

• Some proteins can refold into their functional shape after denaturation.

Amino Acids and Protein Building

• Proteins are composed of amino acid monomers linked by peptide bonds.

• There are 20 different amino acids with unique properties determined by their R-groups.

• Amino acids can be nonpolar, polar, charged, large, or small.

• Example: Cysteine forms disulfide bridges in proteins.

Nucleic Acids

Nucleic Acid Structure

• Nucleic acids are polymers made of nucleotide monomers.

• Nucleotides consist of a nitrogenous base, a phosphate group, and a 5-carbon sugar.

• DNA and RNA are examples of nucleic acids with distinct functions.

Nucleotide Composition

• Nucleotides are composed of a nitrogenous base (purines or pyrimidines), a phosphate group, and a 5-carbon sugar.

• Purines (adenine, guanine) have a double-ring structure, while pyrimidines (cytosine, thymine, uracil) have a single-ring structure.

• In DNA, adenine pairs with thymine, and guanine pairs with cytosine via hydrogen bonds.

DNA Structure and Function

• DNA forms a double helix structure with hydrogen bonds between complementary base pairs.

• The sequence of bases encodes genetic information passed from parent to offspring.

• Adenosine Triphosphate (ATP) is a modified nucleotide crucial for energy transfer in cells.