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Mastering Microbiology Chapter 2: Chemical Principles: Atomic Structure and Organic Compounds
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1
Chemistry
the study of interactions between atoms and molecules
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2
Atom
smallest unit of matter and cannot be subdivided into smaller substances
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3
Molecule
forms when atoms interact
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Electrons
negatively charged particles
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Protons
positively charged particles
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Neutrons
uncharged particles
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Nucleus
composed of protons and neutrons
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Chemical Element
Atoms with the same number of protons are classified as the same chemical element
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Atomic Number
number of protons in the nucleus
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10
Atomic Weight
total number of protons and neutrons in an atom
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11
Isotopes
atoms with different number of neutrons
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12
Valence
The number of missing or extra electrons in the outermost shell
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13
Chemical Bonds
molecules hold together because of the valence electrons combining atoms to form an attractive force between the atomic nuclei
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14
Compound
a molecule that contains two or more kinds of atoms
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15
Water (H2O)
two atoms of hydrogen, one atom of oxygen
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Ions
charged atoms that have gained or lost electrons
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17
Cations
atoms that lose electrons and become positively charged ions
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18
Anions
atoms that gain electrons and become negatively charged ions
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19
Ionic Bonds
attractions between ions of opposite charge
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20
Covalent Bonds
form when two atoms share one or more pairs of electrons
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21
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
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22
Molecular Weight
The sum of the atomic weights in a molecule
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23
Mole
is its molecular weight in grams of substance
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24
Chemical Reactions
Involve the making or breaking of bonds between atoms.
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Endergonic
Reactions that absorb energy.
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Exergonic
Reactions that release energy.
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Synthesis Reactions
Occur when atoms, ions, or molecules combine to form a new, larger molecule.
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Anabolism
The synthesis of molecules in a cell (ex: making proteins from amino acids or making starch from sugar molecules).
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Decomposition Reactions
Occur when a molecule is split into smaller molecules, ions, or atoms.
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Catabolism
Decomposition reactions in a cell (ex: digesting proteins or starch).
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Exchange Reactions
Are part synthesis and part decomposition.
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Reversibility of Chemical Reactions
Can readily go in either direction; each direction may need special conditions.
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Organic Compounds
Always contain carbon and hydrogen; typically structurally complex.
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Inorganic Compounds
Typically lack carbon; usually small and structurally simple.
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Polar Molecule
Unequal distribution of charges.
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Solvent
Polar substances undergo dissociation in water, forming solutes.
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Acid
Substances that dissociate into one or more H+ (protons) and one or more negative ions (ex: HCl→H+ + Cl-).
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Base
Substances that dissociate into one or more OH- (hydroxide) ions (ex: NaOH→Na+ + OH-).
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Salts
Substances that dissociate into cations and anions neither of which is H+ or OH- (ex: NaCl).
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Acid Base Balance
The Concept of pH.
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pH
The concentration of H+ in a solution is expressed as pH; pH=-log10 [H+].
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Macromolecules
Polymers consisting of many small repeating molecules called monomers.
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Monomers
Join by dehydration synthesis or condensation reactions.
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Function Groups
Bond to carbon skeletons and are responsible for most of the chemical properties of a particular organic compound.
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Carbohydrates
Serve as cell structures and cellular energy sources.
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Carbohydrates
Include sugars and starches.
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Carbohydrates
Consist of C, H, and O with the formula (CH2O)n.
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Isomers
Molecules with the same chemical formula, but different structures.
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Monosaccharides
Simple sugars with three to seven carbon atoms.
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Examples of Monosaccharides
Glucose and deoxyribose.
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Disaccharides
Formed when two monosaccharides are joined in dehydration synthesis.
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Hydrolysis
Process by which disaccharides can be broken down.
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Polysaccharides
Consist of ten or hundreds of monosaccharides joined through dehydration synthesis.
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Examples of Polysaccharides
Starch, glycogen, dextran, and cellulose.
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Lipids
Very important organic compounds that make up most of cell membranes.
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Composition of Lipids
Composed of C, H, O (no 2:1 ratio for H/O).
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Simple Lipids
Fats = triglycerides, formed by glycerol + fatty acids.
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Saturated Fat
No double bonds in the fatty acids.
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Unsaturated Fat
One or more double bonds in the fatty acids.
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Cis Configuration
H atoms on the same side of the double bond.
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Trans Configuration
H atoms on opposite sides of the double bond.
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Complex Lipids
Phospholipids that contain P, N, S, in addition to C, H, O.
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Steroids
Structurally different from lipids, have 4 interconnected carbon rings.
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Proteins
Made of C, N, O, N and sometimes S, essential in cell structure and function.
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Amino Acids
Organic molecules with C, H, O, N and (S), make up to 50% of cell's dry weight.
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Peptide Bonds
Formed between amino acids by dehydration synthesis.
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Levels of Protein Structure
Primary, secondary, tertiary, and quaternary structures.
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Denaturation
Occurs when proteins encounter hostile environments and lose their shapes and functions.
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Nucleic Acids
Consist of subunits called nucleotides (A, T, C, G).
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DNA
Deoxyribonucleic Acid, contains deoxyribose and exists as a double helix.
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RNA
Ribonucleic Acid, contains ribose and is single stranded.
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Adenosine Triphosphate (ATP)
The principal energy carrying molecule in cells.
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ATP Hydrolysis
Liberates useful energy for the cell.
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