Untitled

• Chapter 2 focuses on the molecules of life.
• Elements and atoms, chemical bonds and reactions, water, pH and buffers, and organic molecules are studied.
• Beijerinck isolated nitrogen-fixing microorganisms called rhizobia from the root nodules of legumes.

Elements and Atoms

• Elements consist of only one type of atom and cannot be chemically separated into simpler parts.
• Living matter is primarily composed of six elements: carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P), and sulfur (S).
• An atom, the basic unit of matter, has three major components: neutrons (uncharged), protons (positively charged), and electrons (negatively charged).
• A neutral atom has an equal number of protons and electrons and therefore has no charge

Atomic Structure

• The atomic number equals the number of protons found in the nucleus.
• The mass number refers to the sum of protons and neutrons, excluding electrons due to their negligible mass.

The Role of Electrons

• Electrons move in a cloud around the nucleus; it is impossible to determine the precise location of said electrons.
• Electrons are most likely to be within specific regions called shells.
• The shells closest to the nucleus fill first, and the innermost shell can hold up to two electrons.
• Biological molecules are most stable with eight electrons in the outer shell (octet rule).
• Valence electrons exist in the outer shell.

Isotopes

• Isotopes of an element differ in the number of neutrons.
• Atomic mass refers to the average of mass numbers of atoms of an element.
• Energy emitted from radioactive isotopes may be useful in diagnosis.

Chemical Bonds and Reactions

• Chemical bonds and reactions involve atoms losing, gaining, or sharing valence electrons to reach a more stable state
• This forms the basis for chemical bond formation which includes ionic, covalent, and hydrogen bonds.

Ionic and Ionic Bonds

• An ion refers to an atom that has gained or lost electron(s).
• Anions gain electron(s) and are negatively charged, while cations lose electron(s) and are positively charged.
• lonic bonds are formed because of attraction between negative and positive charges.
• Ionic bonds produce salts also called electrolytes because they conduct electricity.

Covalent Bonds

• Covalent bonds form when atoms share electrons, where one pair of shared electrons equals a single covalent bond.
• A molecule includes two or more atoms joined together by covalent bonds.
• A compound defines a molecule containing atoms of different elements.
• Carbon forms four covalent bonds, forming the basis for many diverse structures.
• Carbon bonds, with hydrogen, form organic compounds.
• Other compounds are inorganic compounds.

Types of Covalent Bonds

• In a non-polar covalent bond, electrons are shared equally.
• With a polar covalent bond, electrons are shared unequally.
• It has one atom more electronegative than the other, results in slight separation of charge, and important in biological systems.

Molarity

• A mole refers to 6.02 X 1023 particles.
• A mole of one substance contains the same number of particles as a mole of any other substance.
• Molarity (M) of a solution equals number of moles dissolved in 1 liter of the solution.

Chemical Reactions

• Chemical reactions transfer electrons, often involving the making and breaking of bonds.
• Reactants are starting components of a reaction that are changed to products.
• Synthesis reaction - A + B --> AB.
• Decomposition reaction - AB --> A + B.

Hydrogen Bonds

• Hydrogen bonds refer to weak bonds formed when a hydrogen atom in a polar molecule attracts an electronegative atom in the same or another polar molecule.
• Hydrogen bonds may be short-lived, but numerous bonds add strength.

Oxidation-Reduction (Redox) Reactions

• Oxidation-reduction reactions include electrons transferred from one reactant to another.
• The reactant that loses electrons is oxidized, and the reactant that gains electrons is reduced.
• Reducing agents are reactants that typically lose electrons.
• Oxidizing agents are reactants that typically gain electrons.

Enzymes

• Most biologically important chemical reactions would occur too slowly to be useful to a cell; enzymes are biological catalysts that speed the rate of reactions.
• Enzymes bind to one or more reactant molecules, positioning them in such a way that certain bonds are more likely to be broken or to form.
• Reactants in enzyme-catalyzed reactions are referred to as substrates.

Water and its properties

• Water (H₂O), a polar molecule, exhibits properties explained by hydrogen bonding.
• Liquids exhibit hydrogen bonds that continually form and break, allowing molecules to slide over another.
• Solids have each water molecule form 4 hydrogen bonds with surrounding water molecules, producing a less dense structure called ice.
• Polar nature makes water an excellent solvent in which solutes are dissolved.
• Polar and charged substances are hydrophilic ("water loving”) and dissolve in water.
• Non-polar substances are hydrophobic ("water fearing”) and do not dissolve in water.

pH and buffers

• pH serves as measure of acidity (H+ concentration).
• Water (H₂O) tends to split into H+ and OH- ions.
• Pure water consists of equal concentrations of H+ and OH- ions at a pH of 7, and a molarity of 10^-7.
• Acids increase H+ concentration (pH < 7), whereas bases decrease it (pH > 7).
• Each pH unit (0 to 14) represents a ten-fold change in H+ concentration.
• A buffer is a chemical that helps maintain a constant pH of a solution.
• When base is added, a buffer releases H+.
• When acid is added, a buffer releases H+.
• Buffers are important to action of enzymes and may change shape when pH changes.
• The combination of acids and a base reacting to form water and a salt involves the combination of H+ and OH- ions to generate water, which describes a neutralization reaction.

Organic Molecules

• Organic molecules contain carbon and hydrogen.
• Each carbon atom forms four covalent bonds, thus the incredible assortment of organic molecules exists.
• Covalent bonds joining carbon atoms within an organic molecule can be single, double, or triple.

Macromolecules

• Organic molecules are often macromolecules, where different classes of macromolecules are made up of different monomers.
• The four major classes of organic molecules are carbohydrates, lipids, proteins, and nucleic acids.
• Polymers include macromolecules made by joining monomers (subunits).
• Dehydration synthesis removes water and joins monomers to build polymers
• Hydrolysis requires water and breaks a polymer into monomers.

Carbon Skeletons

• A carbon skeleton refers to arrangement of carbon atoms in organic molecule.
• Functional groups, when attached to the carbon skeleton, contribute to molecule's properties.
• Carbohydrates refers to a structural component of cell walls; they are also an energy source.
• Lipids are an important component of cell membranes.
• Proteins are enzyme catalysts that serve as a structural portion of many cell components.
• Nucleic acids are the carrier of genetic information

Carbohydrates

• Carbohydrates are a diverse group that includes sugars and starches, and serve as an an energy source, an energy storage, and a carbon source.
• They are also a component of structural components in cells and in DNA and RNA.
• They have carbon, hydrogen, and oxygen in a 1:2:1 ratio (CH₂O).
• Monosaccharides can be glucose, galactose, mannose, or fructose.
• Disaccharides are composed of two monosaccharides - sucrose (glucose + fructose), lactose (glucose + galactose), and maltose (glucose + glucose).
• Covalent bond are formed and creates groups of monosaccharides.
• Polysaccharides are chains of monosaccharides.

Lipids

• Lipids are non-polar, hydrophobic molecules.
• They are defined based on slight solubility in water and are important in the structure of membranes.
• Not all lipids are composed of similar subunits.
• Fatty acids are linear carbon skeletons with a carboxyl group (-COOH) at one end.
• Saturated fatty acids have no double bonds.
• Unsaturated fatty acids include double bonds between carbon atoms.
• Trans has hydrogens on opposite sides of double bond.

Proteins

• Proteins are composed of one or more chains subunits and are called amino acids.
• Chains vary in length between proteins.
• They are folded into a complex three-dimensional form, where proper folding is crucial to a protein's function.
• Proteins perform catalysis (enzymes), transport (hemoglobin), signal reception (receptors), regulation and communication (hormones), motility (actin, myosin), support (collagen), energy storage (albumen, casein), and buffering (albumin).
• Amino acids have a common structure, including a central carbon, carboxyl group, and an amino group.
• Amino acids have side chains where characteristics depend on the shape that is mainly influenced by the amino acid sequence.
• All amino acids except glycine are known to exist as optical isomers.
• Peptide bonds are located in amino groups.
• Protein secondary structure have localized coiling or folding (pleated sheet) largely due to hydrogen bonding.
• Tertiary structure defines the overall 3-dimesional shape of folded polypeptide due to largely the interaction between R groups.
• Protein domains refer to a stable substructure associated with a specific function.

Protein Denaturation

• When a protein loses its characteristic shape, it is denatured, and can be caused to high temperatures, extreme pH. or certain solvents.
• Certain proteins may become non-functual, however enzyme function best within a narrow range of conditions.

Nucleic Acids

• Nucleic acids carry genetic information in a sequence of nucleotides and are composed of a pentose sugar, a phosphate group, and a nucleobase.
• Nucleobases are linked to other sugar groups in a nucleotide by phosphate.

Deoxyribonucleic (DNA) Acid

• DNA is genetic information needed to build and maintain a cell.
• DNA is typically double-stranded (composed of two nucleotide chains).
• Nucleotide sequences encode the amino acid sequences of proteins.
• Alteration in DNA sequence results in changing even a single amino acid which affects protein function.

Ribonucleic Acid (RNA)

• RNA (ribonucleic acid) exists in several protein synthesis forms.
• The sugar is ribose instead of deoxyribose.
• Uracil is the nucleobase instead of thymine.

The Role of ATP

• Adenosine triphosphate (ATP) involves energy currency of the cell.
• Three negatively charged phosphate groups repel one another making bonds unstable.
• High-energy phosphate bonds can break and release energy to drive cellular processes