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BIOLOGY OF THE CELL

CHEMICAL BASIS OF LIFE


Biology 1 Lecture 2 EPHRIME B. METILLO, PhD

Multiverse = matter and energy. Energy is the capacity to do work. Matter has mass and occupies space and composed of basic elements. Elements are substances consisting of one type of atom (C for diamond, gold or Au for gold. Greek philosophers thought an Name Charge Location Mass could not be broken down, but Proton +1 atomic nucleus 1.6726 X 10-27 kg Enrico Fermi broke atoms into Neutron 0 atomic nucleus 1.6750 X 10-27 kg subatomic particles: Electron -1 electron orbital 9.1095 X 10-31 kg

Atomic number = number of protons. It is characteristic and unique for each element.

Atomic mass (or atomic weight) = number of protons and neutrons in. Atoms of an element that have differing numbers of neutrons (but a constant atomic number) = isotopes.
Use of Isotopes: determine diet of mummified or fossilized human as proportions of isotopes in tissues; biochemical pathways; age of fossils and artifacts using radioactive isotopes, either directly on the fossil (if it is young enough) or on the rocks that surround the fossil (for older fossils like dinosaurs); radiation used in medical diagnostic and treatment procedures.

Some are radioisotopes, which spontaneously decay, releasing radioactivity. Others are stable.
E.g. radioisotopes - Carbon-14 (symbol 14C), and deuterium (Hydrogen-2; 2H). Stable isotopes are 12C and 1H.

Albert Einstein: E=mc2, electrons as particles and energy quantum Orbital = area of space, an electron will be found 90% of the time. s orbital is spherical. Each orbital = maximum of 2 electrons, so atomic numbers above 2 must fill the other orbitals, like px, py, and pz orbitals (dumbbell shaped, along the x, y, and z axes respectively)

Ionic bonds = formed between ions (atoms that gain or lose electrons). Chlorine with only 7 seven electrons in their outer shells, gain acquiring a charge of -1. Sodium with one electron in outer shell, usually lose election = +1 charge.

Sharing of electrons form covalent bonds or electron-sharing bonds form. Very fast moving electrons effectively fill or empty outer shells of atoms. Analogy - child custody: children are like electrons, spend some time with either parent. In a covalent bond, the electron clouds surrounding the atomic nuclei overlap (see Figure).

The sharing of a single electron pair is termed a single bond. When two pairs of electrons are shared, a double bond results, as in carbon dioxide. Triple bonds are known, wherein three pairs (six electrons total) are shared as in acetylene gas or nitrogen gas.

Polar covalent bond form when electrons spend so much time with > electronegativity or electron affinity causing that end to have slightly negative charge. Conversely, the loss of the electrons from the other end leaves a slightly positive charge.

slightly -

slightly +

Hydrogen bonds is the weak electrical attraction between the positive end of one molecule and the negative end of another. In a large enough quantity, H bonds are strong enough to hold molecules together or in a 3D shape.

Molecules are compounds in which the elements are in definite, fixed ratios, where atoms are held together usually by one of the three types of chemical bonds. E.g., the sugar glucose has 6 Carbons, 12 hydrogens, and 6 oxygens per repeating structural unit. The formula is written C6H12O6.

chemical reaction:

Reactants Products A + B AB
WATER:
Water has been referred to as the universal solvent of solutes:

Water disassociates into H+ and OH- ions, where oxygen retains electrons and only one hydrogen = hydroxide. Pure water has the same number (or concentration) of H+ as OH- ions.
Acidic solutions have more H+ ions than OH- ions. Basic solutions have the opposite. An acid causes an increase in the numbers of H+ ions and a base causes an increase in the numbers of OH- ions.

Organic molecules are those that: 1) formed by the actions of living things; and/or 2) have a carbon backbone (E.g. Methane - CH4). If we remove the H from one of the methane units below, and begin linking them up, while removing other H units, we begin to form an organic molecule.

When two methanes are combined, the resultant molecule is Ethane, which has a chemical formula C2H6. Molecules made up of H and C are known as hydrocarbons.

Polar molecules are attracted to water molecules and are hydrophilic. Nonpolar molecules are repelled by water and do not dissolve in water; are hydrophobic.
Hydrocarbon is hydrophobic but if with ionized carboxyl (acid) (COOH), then molecule is hydrophilic. Since cells are 70-90% water, if organic molecules have -OH (hydroxyl) group which enable a molecule to be water soluble. Isomers are molecules with identical molecular formulas but differ in arrangement of their atoms (e.g., glyceraldehyde and dihydroxyacetone).

Classes of macromolecules (polysaccharides, triglycerides, polypeptides, nucleic acids)

1. Carbohydrates - formula [CH2O]n, n = 3-6. For short-term energy storage (such as sugar); as intermediate-term energy storage (starch for plants and glycogen for animals); and as structural components in cells (cellulose in the cell walls of plants and many protists), and chitin in the exoskeleton of insects and other arthropods. Sugars are simplest carbohydrates, structural unit. Monosaccharides are single (mono=one) sugars: ribose (C5H10O5), glucose (C6H12O6), and fructose (glucose isomer).

Disaccharides = two monosaccharides bond together (sucrose = glucose + fructose; lactose = glucose + galactose; maltose two glucose)

Polysaccharides are large molecules composed of individual monosaccharide units. A common plant polysaccharide is starch:

2. Lipids for long-term energy storage. Insoluble in polar water. Other functions structural components (glycolipid; phospholipids in cell membranes) and "messengers" (hormones) within and between cells. Lipids are composed of three fatty acids (usually) covalently bonded to a 3-carbon glycerol. Fats and oils more complex storage form.

Phospholipid Cholesterol

3. Proteins have control functions (enzymes and protein hormones). Enzymes are catalysts that promotes but is not changed by a chemical reaction). Structural proteins function in the cell membrane, muscle tissue, etc. Amino acids are building blocks of proteins (amino, carboxylic acid, R group), 20 kinds.

STRUCTURES: Primary (polypeptide) Secondary (coil or pleat due to H-bond R groups) Tertiary (bonding and R repulsion) Quaternary (hemoglobin, more polypeptides)

4. Nucleic acids are polymers composed of monomer units known as nucleotides. Nucleotides are information storage (DNA), protein synthesis (RNA), and energy transfers (ATP and NAD). Nucleotides = sugar, a nitrogenous base, and a phosphate. Pentose sugars (ribose or deoxyribose). Nitrogenous bases are purines (Adenine and Guanine, double-ringed), and pyrimidines (Cytosine, Thymine and Uracil, single-ringed)

A mutation is any change in the DNA base sequence. Most mutations are harmful, few are neutral, and a very few are beneficial and contribute the organism's reproductive success. Mutations are the wellspring of variation, variation is central to Darwin and Wallace's theory of evolution by natural selection. DNA only in nucleus (except chloroplasts and mitochondrion) RNA both nucleus and cytoplasm: Messenger RNA (mRNA) is the blueprint for construction of a protein. Ribosomal RNA (rRNA) is the construction site where the protein is made. Transfer RNA (tRNA) is the truck delivering the proper amino acid to the site at the right time.

Put animation of protein synthesis:

http://highered.mcgrawhill.com/sites/0072437316/student_view0/chapter15/animations.html#