Basic Chemistry - Atomic Structure

Basic Chemistry - Atomic Structure

• Atoms consist of protons, neutrons, and electrons.
• An atom in its elemental state has a neutral charge due to the number of protons equaling the number of electrons.
• Electron configuration determines how an atom will react with other elements.
• Electrons in the lowest available energy level are in the ground state.
• An atom that absorbs energy has electrons that move to a higher energy level and the atom is said to be excited.
• Isotopes are atoms of the same element with varying numbers of neutrons but the same number of electrons.
  • Carbon-12 has 6 neutrons, while carbon-14 has 8 neutrons.
• Radioisotopes are radioactive isotopes used to diagnose and treat diseases and to measure the age of fossils.

Bonding

• A bond forms when two atoms attract electrons, releasing energy and requiring energy to break.

Ionic Bond

• Electrons are transferred between atoms.
  • An atom that gains an electron becomes an anion (negative charge).
  • An atom that loses an electron becomes a cation (positive charge).

Covalent Bond

• Atoms share electrons.
  • The resulting structure is molecule.
  • A single covalent bond involves two atoms sharing one pair of electrons.
  • A double covalent bond involves two atoms sharing two pairs of electrons.
  • A triple covalent bond involves two atoms sharing three pairs of electrons.
• Two types include polar and nonpolar covalent bonds.

Nonpolar Covalent Bond

• Electrons are shared equally between identical atoms.
  • Examples: H₂(H-H) and O₂(O=O).

Polar Covalent Bond

• Electrons are shared unequally between unlike atoms.
  • Examples: CO (C=O) and H₂O (H-O-H).

Intermolecular Attraction

• Molecules attract each other in three types.

Polar-Polar Attraction

• Occurs when molecules are either polar (unbalanced) or non-polar (balanced).
• Strong attractions exist between polar molecules.

Hydrogen Bond

• Found between water molecules.
• It attaches DNA strands together.
• Involved in the secondary protein structure.

Non-polar Molecules

• The weakest attractions (van der Waals forces) exist between non-polar molecules.
• The phosphodiester bond is a covalent linkage between a phosphate group of one nucleotide and the 3' carbon of the deoxyribose sugar of an adjacent nucleotide, forming the sugar-phosphate backbone of DNA.

Hydrophilic and Hydrophobic

• Hydrophilic substances love water.
• Hydrophobic substances hate water.
• Polar substances dissolve in water.
• Non-polar substances do not dissolve in water.

Characteristics of Water

• Water is asymmetrical, very polar, and exhibits strong intermolecular attractions and hydrogen bonds.
• High specific heat means it takes a lot of heat to increase temperature of 1 gram of water by 1 degree Celsius.
  • Oceans absorb a lot of heat and resist changes in temperature.
• Evaporation of sweat cools the body.
• High adhesion properties help water flow up from plant roots to leaves, important for plant survival.
• Water is a universal solvent.
  • It dissolves all polar and ionic molecules.
• Water has strong cohesion tension, helping molecules stick together.
  • Facilitates water movement up tall trees without energy expenditure, referred to as transpiration-pull cohesion tension.
  • Results in surface tension, allowing insects to walk on water.
• Ice is less dense than water, so it floats.

pH

• Measurement of acidity and alkalinity of a solution.
• Negative logarithm of the hydrogen ion concentration.
• Internal pH of living cells is close to 7.
• Biological systems use buffers to regulate pH by absorbing or donating hydrogen ions.
  • Bicarbonate ion (HCO3) is the most important buffer in human blood.
• Acidity is inversely proportional to pH level.
• Acidity is directly proportional to hydrogen ion concentration.

Organic Compounds

• Contain carbon.
• Carbon is the most abundant element in the body.
• There are four classes: carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates

• Consist only of carbon, hydrogen, and oxygen.
• Provide quick energy.
• 1 gram releases 4 calories.
• Three classes: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides

• Chemical formula C₆H₁₂O₆.
  • Examples: glucose, galactose, and fructose.

Disaccharides

• Chemical formula C₁₂H₂₂O₁₁.
• Consist of two monosaccharides joined by dehydration synthesis.
  • Glucose + Glucose → Maltose + water.
  • Glucose + Galactose → Lactose + water.
  • Glucose + Fructose → Sucrose + water.
• Hydrolysis breaks down compounds.

Polysaccharides

• Many monosaccharides linked by dehydration synthesis.
• Four Important Polysaccharides:
  • Cellulose makes up plant cell walls.
  • Starch is the way plants store carbohydrates.
  • Chitin makes up the exoskeleton in arthropods and cell walls in mushrooms.
  • Glycogen is the way animals store starch.

Lipids

• Are classified according to the chemical structure.
• Simple lipids: oils, fats, and waxes.
• Complex lipids: phospholipids
• Lipid derivatives: cholesterol, and some hormones (steroids)

Simple Lipids

• Diverse class including fats, oils, and waxes.
• Made up of 1 glycerol and 3 fatty acids.
  • Glycerol is an alcohol, and fatty acids are hydrocarbon chains with a carboxyl group at one end.
• Fatty acids exist in two groups.
  • Saturated fats come from animals, and are solid at room temperature
    • Contain Single bonds between carbon atoms
  • Unsaturated fats extract from plants and are liquid a room themperature
    • Have double bonds between carbon atoms

Lipid Derivatives

• Derived from simple and complex lipids by hydrolysis.
• Examples: cholesterol and steroids.
• Steroids: lipids that don't have the same general structure as other lipids.
  • Consist of four fused rings.
  • Examples: testosterone and estradiol.

Complex Lipids

• Phospholipids present in the cell membrane of all cell types.
• Contain carbon, hydrogen, and oxygen.
• Consist of 1 glycerol, 2 fatty acids, 1 phosphate, and 1 choline group.

Lipid Function

• Energy storage: Each gram releases 9 kcal.
• Structural: Phospholipids bilayer make up the cell membrane.
• Endocrine: Steroid hormones.
• Cushioning of organs.
• Thermal insulation: Lipids form an insulating layer.
• Protective covering: Wax prevents evaporation of water.

Proteins

• Polymers of amino acids linked by peptide bonds.
• Amino acids consist of carboxyl, an amine, and an alkyl group.
• The R group differs for each amino acid.
• Enzymes are examples of proteins.
• 1 gram releases 4 calories.
• The amino acid contains an acidic and basic group
  • Carboxylic group is acidic.
  • Amino group is basic.
• Peptide bonds are between amino acids.
• 2nd and 3rd protein structures depend on 1st and 3D protein shape
• Protein depends on the tertiary structure.

Nucleic Acids

• Two types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
• They carry hereditary information.
• They are polymers of nucleotides.
• Contains a phosphate, sugar, and nitrogenous base.
• In DNA, the bases are adenine, cytosine, guanine, and thymine.
• In RNA, the bases are adenine, cytosine, guanine, and uracil.
• Adenine and guanine are purines.
• Cytosine, thymine, and uracil are pyrimidines.

Notes

• 1 gram of carbohydrates yields 4 calories.
• 1 gram of lipids yields 9 calories.
• 1 gram of proteins yields 4 calories.
• Transpiration pull cohesion tension is when a water molecule is lost through transpiration it draws in more water through the roots.
• Capillary action results from combined forces of cohesion and adhesion.
• Ethanol or C2H5OH is a light alcohol and is a volatile, colorless and flammable liquid and is produced by fermentation.
  • Also known as ethyl alcohol.