Atoms, Chemical Bonds, Water, and Introduction to Macromolecules

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Atoms and Atomic Structure

Definition and Properties of Atoms

Atoms are the smallest units of matter that retain the properties of an element. They are composed of subatomic particles and are the building blocks of all matter.

Subatomic particles include protons, neutrons, and electrons.
Protons have a mass of 1 and a positive charge.
Neutrons have a mass of 1 and no charge.
Electrons have negligible mass and a negative charge.

Elements and the Periodic Table

92 elements occur naturally.
Elements are composed of atoms with unique properties.
Atoms are organized in the periodic table by their properties.
Six elements (C, H, N, O, P, S) are fundamental to living organisms.

Atomic Neutrality

Atoms are electrically neutral because the number of protons equals the number of electrons.

Isotopes

Isotopes are atoms of the same element with the same number of protons but different numbers of neutrons.

Most elements have several isotopes; most are stable.
Some isotopes have special names (e.g., hydrogen isotopes: 1H, 2H, 3H).
Example: Carbon has isotopes 12C (6 neutrons), 13C (7 neutrons), 14C (8 neutrons).

Electrons and Chemical Behavior

Electrons are located in orbitals arranged in shells around the nucleus.
The outermost shell (valence shell) determines how atoms interact and bond.
Atoms are most stable when their outermost shell is full (octet rule: 8 electrons).
Reactive atoms have unpaired electrons in their valence shell.
The energy level of each shell increases with distance from the nucleus.

Elements, Molecules, and Compounds

Definitions

Element: A pure substance containing only one kind of atom.
Molecule: An electrically neutral group of two or more atoms held together by chemical bonds (e.g., O2).
Compound: A molecule made up of two or more different elements in a fixed ratio (e.g., H2O, NaCl).
Molecular weight: The sum of atomic weights of all atoms in a molecule.

Chemical Bonds

Types of Chemical Bonds

Covalent Bonds: Attractive forces that link two atoms together by sharing electrons.
Polar covalent bonds: Unequal sharing of electrons (e.g., H2O).
Nonpolar covalent bonds: Equal sharing of electrons (e.g., C-H bond).
Electronegativity: The ability of an atom to attract electrons in a bond. The more electronegative an atom, the more strongly it pulls shared electrons.

Ions and Ionic Bonds

Ions: Electrically charged particles formed when atoms lose or gain electrons.
Cations: Positive ions.
Anions: Negative ions.
Ionic bonds: Formed by the electrical attraction of positive and negative ions (e.g., NaCl).
Salts are ionically bonded compounds and can interact with polar molecules (salts dissolve in water).

Hydrogen Bonds

Form between polar molecules (e.g., between water molecules).
Weaker than covalent or ionic bonds but important in biological molecules (e.g., DNA, proteins).

Chemical Reactions

Nature of Chemical Reactions

Chemical reactions involve the making and breaking of chemical bonds.
Reactants: Starting molecules of a reaction.
Products: Final molecules of a reaction.
Law of Conservation of Matter: Chemical reactions cannot create or destroy matter (1st law of thermodynamics).

Water: Properties and Importance

Special Properties of Water

Water is a polar molecule, making it a good solvent for many substances.
Water is essential for life and many biochemical reactions.
Water forms hydrogen bonds, leading to unique properties.
Water's covalent bonds are polar.

Hydrophilic and Hydrophobic Molecules

Hydrophilic: Water-loving molecules that form hydrogen bonds with water.
Hydrophobic: Water-fearing molecules (e.g., hydrocarbons) that do not interact with water.

Hydrogen Bonding in Water

Hydrogen bonds form between water molecules, contributing to water's high specific heat, cohesion, and surface tension.

Specific Heat and Heat of Vaporization

Specific heat: The amount of heat required to raise the temperature of 1 gram of water by 1 degree Celsius = 1 calorie.
Water's high specific heat helps buffer temperature changes in organisms and environments.
Heat is absorbed when hydrogen bonds break; heat is released when they form.
Heat of vaporization: The amount of energy required to change water from liquid to gas.
Ice floats because it is less dense than liquid water.

Cohesion and Surface Tension

Cohesion: Water molecules stick together due to hydrogen bonding.
Surface tension: Water molecules at the surface are more strongly attracted to each other than to the air above.

Water as an Acid and Base

Water can act as both a weak acid and a weak base:

Ionization of water is important for biological reactions.

Acids, Bases, and pH

Definitions

Acids: Release hydrogen ions (H+) in solution.
Strong acids ionize fully; weak acids do not.
Bases: Accept hydrogen ions (H+) in solution.
Strong bases ionize fully; weak bases do not.

pH Scale

Water is neutral (pH 7).
Acidic solutions: pH less than 7.
Basic solutions: pH greater than 7.
Most biological fluids have pH values in the range of 6 to 8.

Biological Importance of pH

pH influences the rates of biological reactions.
pH can change the 3-D structure of biological molecules.

Homeostasis: Maintaining pH

Living organisms maintain constant internal conditions (homeostasis).
Organisms use various mechanisms to minimize pH changes in cells and tissues.
Buffers are weak acids and their corresponding bases that help maintain constant pH by absorbing or releasing H+ or OH-.

Introduction to Macromolecules

Carbon: The Backbone of Life

Carbon has four valence electrons and can form four covalent bonds with a variety of atoms (especially H, O).
This allows carbon to form large, complex molecules and chains.
Carbon chains form the skeletons of most organic molecules and can vary in length and shape.

Isomers

Isomers are molecules with the same chemical formula but different arrangements of atoms.
Structural isomers: Atoms are bonded differently.
Optical isomers: Molecules are mirror images of each other.

Functional Groups and Macromolecule Function

Macromolecules may contain many different functional groups.
Each functional group participates in chemical reactions in a characteristic way.
Functional groups determine the shape and function of molecules and their interactions with other macromolecules.