Mastering Microbiology Chapter 2: Chemical Principles: Atomic Structure and Organic Compounds

Chemistry

the study of interactions between atoms and molecules

Atom

smallest unit of matter and cannot be subdivided into smaller substances

Molecule

forms when atoms interact

Electrons

negatively charged particles

Protons

positively charged particles

Neutrons

uncharged particles

Nucleus

composed of protons and neutrons

Chemical Element

Atoms with the same number of protons are classified as the same chemical element

Atomic Number

number of protons in the nucleus

Atomic Weight

total number of protons and neutrons in an atom

Isotopes

atoms with different number of neutrons

Valence

The number of missing or extra electrons in the outermost shell

Chemical Bonds

molecules hold together because of the valence electrons combining atoms to form an attractive force between the atomic nuclei

Compound

a molecule that contains two or more kinds of atoms

Water (H2O)

two atoms of hydrogen, one atom of oxygen

Ions

charged atoms that have gained or lost electrons

Cations

atoms that lose electrons and become positively charged ions

Anions

atoms that gain electrons and become negatively charged ions

Ionic Bonds

attractions between ions of opposite charge

Covalent Bonds

form when two atoms share one or more pairs of electrons

Hydrogen Bonds

form when hydrogen atom that is covalently bonded to an O or N atom is attracted to another N or O atom in another molecule

Molecular Weight

The sum of the atomic weights in a molecule

Mole

is its molecular weight in grams of substance

Chemical Reactions

Involve the making or breaking of bonds between atoms.

Endergonic

Reactions that absorb energy.

Exergonic

Reactions that release energy.

Synthesis Reactions

Occur when atoms, ions, or molecules combine to form a new, larger molecule.

Anabolism

The synthesis of molecules in a cell (ex: making proteins from amino acids or making starch from sugar molecules).

Decomposition Reactions

Occur when a molecule is split into smaller molecules, ions, or atoms.

Catabolism

Decomposition reactions in a cell (ex: digesting proteins or starch).

Exchange Reactions

Are part synthesis and part decomposition.

Reversibility of Chemical Reactions

Can readily go in either direction; each direction may need special conditions.

Organic Compounds

Always contain carbon and hydrogen; typically structurally complex.

Inorganic Compounds

Typically lack carbon; usually small and structurally simple.

Polar Molecule

Unequal distribution of charges.

Solvent

Polar substances undergo dissociation in water, forming solutes.

Acid

Substances that dissociate into one or more H+ (protons) and one or more negative ions (ex: HCl→H+ + Cl-).

Base

Substances that dissociate into one or more OH- (hydroxide) ions (ex: NaOH→Na+ + OH-).

Salts

Substances that dissociate into cations and anions neither of which is H+ or OH- (ex: NaCl).

Acid Base Balance

The Concept of pH.

pH

The concentration of H+ in a solution is expressed as pH; pH=-log10 [H+].

Macromolecules

Polymers consisting of many small repeating molecules called monomers.

Monomers

Join by dehydration synthesis or condensation reactions.

Function Groups

Bond to carbon skeletons and are responsible for most of the chemical properties of a particular organic compound.

Carbohydrates

Serve as cell structures and cellular energy sources.

Carbohydrates

Include sugars and starches.

Carbohydrates

Consist of C, H, and O with the formula (CH2O)n.

Isomers

Molecules with the same chemical formula, but different structures.

Monosaccharides

Simple sugars with three to seven carbon atoms.

Examples of Monosaccharides

Glucose and deoxyribose.

Disaccharides

Formed when two monosaccharides are joined in dehydration synthesis.

Hydrolysis

Process by which disaccharides can be broken down.

Polysaccharides

Consist of ten or hundreds of monosaccharides joined through dehydration synthesis.

Examples of Polysaccharides

Starch, glycogen, dextran, and cellulose.

Lipids

Very important organic compounds that make up most of cell membranes.

Composition of Lipids

Composed of C, H, O (no 2:1 ratio for H/O).

Simple Lipids

Fats = triglycerides, formed by glycerol + fatty acids.

Saturated Fat

No double bonds in the fatty acids.

Unsaturated Fat

One or more double bonds in the fatty acids.

Cis Configuration

H atoms on the same side of the double bond.

Trans Configuration

H atoms on opposite sides of the double bond.

Complex Lipids

Phospholipids that contain P, N, S, in addition to C, H, O.

Steroids

Structurally different from lipids, have 4 interconnected carbon rings.

Proteins

Made of C, N, O, N and sometimes S, essential in cell structure and function.

Amino Acids

Organic molecules with C, H, O, N and (S), make up to 50% of cell's dry weight.

Peptide Bonds

Formed between amino acids by dehydration synthesis.

Levels of Protein Structure

Primary, secondary, tertiary, and quaternary structures.

Denaturation

Occurs when proteins encounter hostile environments and lose their shapes and functions.

Nucleic Acids

Consist of subunits called nucleotides (A, T, C, G).

DNA

Deoxyribonucleic Acid, contains deoxyribose and exists as a double helix.

RNA

Ribonucleic Acid, contains ribose and is single stranded.

Adenosine Triphosphate (ATP)

The principal energy carrying molecule in cells.

ATP Hydrolysis

Liberates useful energy for the cell.