Chapter 2 | Chemistry Principle

Chemistry (definition)

The study of interactions between atoms and molecules.

Atom (definition)

The smallest unit of matter; cannot be subdivided into smaller substances.

What are atoms composed of?

Electrons (negatively charged), protons (positively charged), and neutrons (uncharged).

Nucleus (atomic) composition

Protons and neutrons; electrons move around the nucleus.

Chemical element (definition)

Atoms with the same number of protons; each element has a different number of protons.

Atomic number (slide definition)

The number of protons in the nucleus.

Atomic mass (slide definition)

The total number of protons and neutrons in an atom.

Isotopes (slide definition)

Atoms of an element with different numbers of neutrons.

Electron shells

Regions where electrons are arranged, corresponding to different energy levels.

Valence (slide definition)

The number of missing or extra electrons in an atom's outermost shell.

Chemical bond (slide definition)

An attractive force between atomic nuclei formed by valence electrons of combining atoms.

Compound (slide definition)

A molecule that contains two or more kinds of atoms (e.g., water: 2 hydrogen + 1 oxygen).

What determines the number of protons and electrons in a neutral atom?

They are equal.

Ion (slide definition)

A charged atom that has gained or lost electrons.

Cation

An atom that loses electrons and becomes a positively charged ion.

Anion

An atom that gains electrons and becomes a negatively charged ion.

Ionic bond (slide definition)

An attraction between ions of opposite charge; one atom loses electrons while another gains them.

Covalent bond (slide definition)

Forms when two atoms share one or more pairs of electrons; stronger and more common in organisms than ionic bonds.

Hydrogen bond (slide definition)

Forms when a hydrogen atom covalently bonded to O or N is attracted to another O or N atom in another molecule.

Molecular mass (slide definition)

The sum of the atomic masses in a molecule.

Mole (slide definition)

The molecular mass of a substance expressed in grams.

Dalton

The unit used to express molecular mass.

Chemical reaction (slide definition)

Involves the making or breaking of bonds between atoms, with a change in chemical energy.

Endergonic reaction (slide definition)

A reaction that absorbs energy.

Exergonic reaction (slide definition)

A reaction that releases energy.

Synthesis reaction / Anabolism

Atoms, ions, or molecules combine to form new, larger molecules; called anabolism in a cell.

Decomposition reaction / Catabolism

A molecule is split into smaller molecules, ions, or atoms; called catabolism in a cell.

Exchange reaction (slide definition)

A reaction that is part synthesis and part decomposition.

Reversibility of chemical reactions

Reactions can go in either direction; each direction may require special conditions.

Organic vs. inorganic compounds

Organic compounds always contain carbon and hydrogen and are typically structurally complex; inorganic compounds typically lack carbon and are usually small and simple.

Water's key properties (slide)

Inorganic, polar molecule with unequal charge distribution; acts as a solvent; hydrogen bonds allow it to absorb heat, making it a temperature buffer.

Acid (slide definition)

A substance that dissociates into one or more hydrogen ions (H+) and one or more negative ions.

Base (slide definition)

A substance that dissociates into one or more hydroxide ions (OH-) and one or more positive ions.

Salt (slide definition)

A substance that dissociates into cations and anions, neither of which is H+ or OH-.

pH and organism growth

Most organisms grow best between pH 6.5 and 8.5.

Effect of increasing H+ or OH- concentration

Increasing H+ increases acidity; increasing OH- increases alkalinity.

Organic compound composition (slide)

Commonly contain hydrogen, oxygen, and/or nitrogen in addition to carbon.

Carbon skeleton (slide definition)

The chain of carbon atoms in an organic molecule.

Functional groups (slide definition)

Groups that bond to carbon skeletons and are responsible for most of an organic compound's chemical properties.

Macromolecule / monomer / polymer

Macromolecules are polymers made of many small repeating molecules called monomers, joined by dehydration synthesis or condensation reactions.

Carbohydrates (slide role)

Serve as cell structures and cellular energy sources; include sugars and starches; consist of C, H, and O.

Carbohydrate isomers

Molecules with the same chemical formula but different structures.

Monosaccharide examples

Glucose and deoxyribose.

Disaccharide

Formed when two monosaccharides join via dehydration synthesis; can be broken down by hydrolysis.

Polysaccharide

Consists of tens or hundreds of monosaccharides joined by dehydration synthesis (e.g., starch, glycogen, dextran, cellulose).

Lipids (slide role)

Primary components of cell membranes; consist of C, H, and O; nonpolar and insoluble in water.

Simple lipids (fats/triglycerides)

Contain glycerol and fatty acids, formed by dehydration synthesis.

Saturated vs. unsaturated fat

Saturated fat has no double bonds in the fatty acids; unsaturated fat has one or more double bonds.

Cis vs. trans fatty acid

Cis: hydrogen atoms on the same side of the double bond. Trans: hydrogen atoms on opposite sides of the double bond.

Complex lipids

Contain C, H, O plus P, N, and/or S; includes phospholipids (glycerol, two fatty acids, and a phosphate group) which have polar and nonpolar regions.

Steroids (slide description)

Four carbon rings with a functional group attached to one ring; part of membranes, helping keep them fluid.

Proteins (slide functions)

Made of C, H, O, N, and sometimes S; function as enzymes, transporter proteins, flagella, and some bacterial toxins/cell structures.

Amino acid structure

Contains an alpha-carbon attached to a carboxyl group, an amino group, and a side group.

Peptide bond (slide definition)

A bond between amino acids formed by dehydration synthesis.

Primary protein structure (slide)

A polypeptide chain.

Secondary protein structure (slide)

Occurs when the amino acid chain folds and coils into a helix or pleated sheet.

Tertiary protein structure (slide)

Occurs when the helix or sheet folds irregularly, forming disulfide bridges, hydrogen bonds, and ionic bonds.

Quaternary protein structure (slide)

Consists of two or more polypeptides.

Denaturation

Occurs when proteins encounter hostile environments (e.g., temperature, pH) and lose their shape and function.

Conjugated protein types (slide examples)

Glycoproteins, nucleoproteins, and lipoproteins.

Nucleotide components (slide)

A five-carbon (pentose) sugar, a phosphate group, and a nitrogen-containing (purine or pyrimidine) base.

Nucleoside components (slide)

A pentose sugar and a nitrogen-containing base.

DNA (slide description)

Deoxyribonucleic acid; contains deoxyribose; exists as a double helix; adenine pairs with thymine, cytosine pairs with guanine.

RNA (slide description)

Ribonucleic acid; contains ribose; single-stranded; adenine pairs with uracil, cytosine pairs with guanine; plays roles in protein synthesis.

ATP composition (slide)

Ribose, adenine, and three phosphate groups.

ATP function (slide)

Stores chemical energy released by chemical reactions; releases phosphate groups by hydrolysis to liberate usable energy for the cell.