chapter 2 Comprehensive Guide to Chemistry of Life: Atoms, Bonds, Water, Organic Molecules, and Energy

Matter

Anything that takes up space and has mass

Mass

Amount of matter contained in a substance; Determines weight

Atom

Building block of all matter; Smallest stable unit

Proton

Found in nucleus; Mass: one amu; Charge: +1

Neutron

Found in nucleus; Mass: one amu; Charge: 0

Electron

Orbits nucleus; Mass: ~1/1800th amu; Charge: -1; Arranged into electron shells (energy levels)

Element

Simplest matter with unique chemical properties; Possess only one kind of atom; Identified by unique symbols

Minerals

Inorganic elements extracted from soil by plants; Significant to body structure and physiology

Atomic Number

# of protons

Atomic Mass

# protons + neutrons

Atomic Weight

Average mass of all elemental isotopes

Isotopes

Same # of protons, but different # of neutrons

Chemical Stability

Full valance shell = chemical stability; Atom is inert

Chemical Bonds

Ionic, Covalent, Hydrogen

Molecule

Two or more atoms held together by a bond; May be identical or different elements

Compound

Atoms of two or more elements held together by a bond; Held together by chemical bonds

Ions

Charged particles; # protons ≠ # electrons; Formed when atoms gain or lose electrons

Cations

Lost one or more electrons; Positive charge; Atoms with 1 - 3 valence electrons

Anions

Gained one or more electrons; Negative charge; Atoms with 4 - 7 valance electrons

Electrolytes

Salts that ionize in water; Form solutions capable of conducting electricity

Free Radicals

A particle with an unpaired electron; Harmful and highly reactive

Ionic Bonds

Formed between two or more atoms; Results in ionic compound; Weaker than covalent bonds

Covalent Bonds

Atoms share electrons; Common and strong; Atoms can share multiple e- pairs

Polar Covalent

Electrons shared unequally

Nonpolar covalent

Electrons shared equally

Electronegativity

"Pull" an atom has on electrons

Hydrogen Bonds

Attraction between a δ+ H and a δ- N or O

Basic Water Facts

Around 50 - 75% of body weight

Water Formula

H2O

Polar molecule

A molecule with a V-shaped structure that contributes to polarity.

Chemical reactivity

Participates in chemical reactions and disassociates into H+ and OH-.

Thermal stability

Stabilizes body temperature due to high heat capacity from hydrogen bonds.

Cohesion

Water molecules cling to each other, contributing to surface film and surface tension.

Adhesion

Water molecules cling to other substances, reducing friction.

Solvency

Ability to dissolve other chemicals.

Hydrophilic

Substances that will dissolve in water.

Hydrophobic

Substances that won't dissolve in water.

Amphipathic molecules

Molecules that have both hydrophilic and hydrophobic regions.

Suspension

Particles settle when mixture stands, scatters light, and is cloudy/opaque.

Colloid

Remains mixed when mixture stands, scatters light, and is cloudy/opaque.

Solution

Remains mixed when mixture stands, is a homogenous mixture of solute and solvent.

Emulsion

Suspension of one liquid in another.

Neutralization

Mixing acids and bases can form water and salts, bringing pH to 7.

Buffer

Solutions which resist changes in pH and assist with maintenance of body fluid pH.

Acidosis

Abnormally low blood pH.

Alkalosis

Abnormally high blood pH.

Denaturation of enzymes

H+ ions disrupt bonds and chemical structure

Energy

Capacity to do work (move something)

Potential energy

Energy of position (stored energy)

Kinetic energy

Energy of motion

Chemical Reactions

Forming new bonds or breaking old bonds

Reactants

Substances present at start of reaction

Products

Substances present at end of reaction

Metabolism

Sum of all chemical reactions in a cell or organism

Activation energy

Energy required for a chemical reaction to begin

Enzymes

Lower the energy cost for starting a reaction and act as catalysts: increase reaction rate

Specificity

Matched to specific substrate; active site only fits substrate

Saturation Limits

All enzymes busy = saturation; need to add more enzyme to increase rate

Regulation

Functional if active site is open; can be 'turned off' by adding inhibitors

Cofactors

Many enzymes require a non-protein 'partner' to function

Organic compounds

Contain carbon and hydrogen; primarily covalent bonds; often large, complex

Inorganic molecules

Typically do not contain carbon; includes water, oxygen, and carbon dioxide

Polymers

Molecules made of repeating subunits called monomers

Carbohydrates

Source of chemical energy; short-term, easy access; converted into glycogen or fat for storage

Monosaccharides

Simple sugars; primary cellular energy source

Disaccharides

Composed of two joined monosaccharides

Polysaccharides

Long chains of monosaccharides

Glycogen

Animal storage form of glucose; produced by liver, muscles, etc.

Cellulose

Structural polysaccharides for plants; indigestible by humans (lack enzyme)

Lipids: Fatty Acids

Hydrocarbon chains with a 'Head' end possessing a carboxyl group (-COOH) that is hydrophilic and a 'Tail' that is a chain of 4 -24 carbons, where saturated means no double bonds and unsaturated means one or more double bonds.

Lipids: Triglycerides

Combination of glycerol, a three-carbon alcohol, and three fatty acid chains, serving functions such as energy storage, insulation (adipose tissue), and protection (adipose tissue).

Lipids: Phospholipids

Combination of glycerol, two fatty acid chains, and a phosphate group, making them amphipathic with hydrophilic heads and hydrophobic tails, serving as structural components of the plasma membrane.

Lipids: Eicosanoids

Derived from arachidonic acid and act as local signaling molecules.

Prostaglandins

Coordinate/direct local cell activities, produced in most tissues, with roles in pain sensation, labor, inflammation, clotting, etc.

Lipids: Steroids

Contain four hydrocarbon rings, derived from cholesterol, serving as chemical messengers between cells, and can be ingested from animal products or synthesized.

Bile acids

Aid in digestion and absorption of lipids.

Proteins

Monomers made of amino acids, composed of carbon, hydrogen, oxygen, nitrogen, and often sulfur, with numerous functions.

Conformation

The 3D shape of proteins that varies with function and can denature when exposed to extreme pH or heat.

Peptide

Two or more amino acids joined by peptide bonds, with the name depending on the number of amino acids present.

Amino Acids

20 found in humans, each with a distinctive structure including an amine group (-NH2), a carboxyl group (-COOH), and a variable group (R group) that determines unique properties.

Protein Structure: Primary

Sequence of amino acids joined by peptide bonds.

Protein Structure: Secondary

Coiled or folded 3D shape held together by hydrogen bonds, with the most common forms being alpha helix or beta sheet.

Protein Structure: Tertiary

Result of hydrophobic/hydrophilic side chain interactions, typically resulting in globular or fibrous shapes.

Protein Structure: Quaternary

Association of two or more polypeptides with each other due to ionic bonds and R group interactions; not all proteins have this structure.

Protein Function: Structure

Proteins serve as structural components of cells and tissues, providing strength, durability, and flexibility.

Protein Function: Communication

Proteins serve as hormones and local signaling molecules and act as receptors for chemical messengers.

Protein Function: Membrane transport

Proteins form channels in cell membranes and act as carriers for other substances.

Protein Function: Catalysis

Enzymes participate in metabolic reactions.

Protein Function: Recognition and protection

Glycoproteins serve as cell identification molecules and participate in immunity, especially antibodies.

Protein Function: Movement

Proteins provide the basis for movement through contractile and motor proteins.

Nucleic Acids

Composed of nucleotide monomers including a pentose sugar (ribose or deoxyribose), a phosphate functional group, and a nitrogenous base.

Nucleic Acids: DNA

Deoxyribonucleic acid, stores genetic information directing protein synthesis, double stranded, uses AGCT only, found in the nucleus.

Nucleic Acids: RNA

Ribonucleic acid, participates in protein synthesis, single stranded, uses AGCU only, found in nucleus and cytoplasm.

Nucleotide: Adenosine Triphosphate

Primary energy-transfer molecule required to perform most of the body's work, with the reaction ATP + H2O → ADP + Pi + energy.

Producing ATP

Requires glucose or other fuel and involves a multi-stage process including anaerobic fermentation and aerobic respiration.

Anaerobic fermentation

Does not require oxygen, produces fewer ATP, occurs in cytoplasm, and produces lactate.

Aerobic respiration

Requires oxygen, produces more ATP, and is more efficient, occurring in mitochondria.