The Chemistry of Life
2.1 What is Matter?
1. Any substance that occupies space is called matter. Matter is often equated to chemicals, which form the basis of all life.
2. Matter can be broken down into pure substances called elements. Elements are organized in the periodic table according to their number of subatomic particles. Bulk elements, those essential to life in large quantities, include carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus.
3. An atom is the smallest unit of an element. Subatomic particles include the positively charged protons and neutral neutrons that form the nucleus and the negatively charged, much smaller electrons that circle the nucleus.
4. Atomic number is an element's characteristic number of protons, and the atomic mass is the mass of its protons and neutrons. Isotopes of an element differ by the number of neutrons.
5. Compounds are built of bonded atoms of different elements, in a consistent ratio. A molecule is the smallest unit of a compound that retains the characteristics of that compound. A compound's characteristics differ from those of its constituent elements.
6. Chemical shorthand indicates the numbers of atoms and molecules in a compound. In a chemical reaction, different compounds are broken down and form, but the total number of atoms of each element remains the same.
7. Electrons move constantly; they are most likely to be found in volumes of space called orbitals, which contain levels of energy called shells. Electrons can absorb energy and move to higher shells.
8. An atom's tendency to fill its outermost or valence shell with electrons drives atoms to bond and form molecules.
9. Covalent bonds form between atoms that can fill their valence shells by sharing one or more pairs of electrons. These are the strongest of chemical bonds. Carbon atoms form up to four covalent bonds. Atoms in a nonpolar covalent bond share all electrons equally. Electronegative atoms involved in covalent bonds tend to attract electrons, forming polar covalent bonds, resulting in opposite partial charges on different parts of the molecule.
10. Two atoms may donate or receive electrons from each other to fill their valence shell. The resulting atoms possess a charge and are called ions. An ionic bond forms as two ions are attracted to each other. These are moderately strong bonds.
11. Hydrogen bonds form when a hydrogen in one molecule is drawn to part of a neighboring molecule because of unequal electrical charge distribution.
12. van der Waals attractions occur between parts of molecules that are temporarily oppositely charged.
2.2 How is Water Important to Life?
13. Most biochemical reactions occur in an aqueous environment. Water is cohesive and adhesive, enabling many substances to dissolve in it.
14. pH is a measure of H+ concentration, or how acidic or basic a solution is. Pure water has a pH of 7, which means that the numbers of H+ and OH- in water are equal. An acid adds H+ to a solution, lowering the pH below 7. A base adds OH-, raising pH to between 7 and 14. Buffer systems consisting of weak acid-and-base pairs maintain the pH ranges of body fluids.
15. Water helps regulate temperature in organisms because of its high heat capacity and high heat of vaporization.
2.3 Which Organic Molecules Are Important to Life?
16. Most of the large biological molecules are
composed of small subunit molecules called monomers, which possess characteristics distinct from the resulting polymers.
17. Monomers form into polymers by dehydration synthesis or are released from polymers by hydrolysis.
18. Carbohydrates provide energy and support. They consist of carbon, hydrogen and oxygen in the proportions 1:2:1. Monosaccharides are single-molecule sugars such as glucose. Two bonded monosaccharides form a disaccharide. Oligosaccharides are composed of 2 to 100 monomers, whereas polysaccharides are enormous molecules of hundreds of monomers.
19. Lipids are diverse organic compounds that provide energy, slow digestion, waterproof the outsides of organisms, cushion organs, and preserve body heat. Lipids include fats and oils, do not dissolve in water, and contain carbon, hydrogen, and oxygen but have less oxygen than carbohydrates. Triglycerides consist of glycerol and three fatty acids, which may be saturated (no double bonds), unsaturated (at least one double bond), or polyunsaturated (more than one double bond). Double bonds make a lipid oily at room temperature, whereas saturated fats are more solid. Sterols are lipids containing four carbon rings.
20. Proteins have many functions and a great diversity of structures. They consist of 20 types of amino acids, each of which consists of a central carbon atom bonded to a hydrogen, an amino group, a carboxyl group, and an R group. Amino acids join by forming peptide bonds through dehydration synthesis. A protein's conformation, or three-dimensional shape, is vital to its function and is determined by the amino acid sequence (primary structure) and interactions between the non-R group atoms (secondary structure) and ionic, covalent, and hydrophobic interactions between R groups (tertiary structure) in the sequence. A protein with more than one polypeptide has a quaternary structure.
21. Enzymes are proteins that accelerate specific chemical reactions under specific conditions and are involved in every aspect of life.
22. Nucleic acid sequences determine amino acid sequences. DNA and RNA are polymers consisting of a sugar-phosphate backbone and sequences of nitrogenous bases. DNA includes deoxyribose and the bases adenine, cytosine, guanine, and thymine. RNA contains ribose and has uracil instead of thymine. A nucleotide, a nucleic acid monomer, consists of a phosphate, a base, and a sugar. DNA carries genetic information. RNA copies the information to enable the cell to synthesize proteins.