Sunday, November 27, 2005

Highly recommended: Biology 1A Lecture Notes (by Frank Orme, Merritt College, Oakland).



These EXCELLENT Flash Animations are 3D 'movies' that visualize many of the key processes that occur within cells, including info on amino acids, assembly of amino acids into proteins, folding of protiens into spirals and sheets, creation of proteins by the ribosome, a 3D model of how DNA is structured, how transcription works and how DNA is wound up to form chromosomes, cell membrane structure and function, mitosis, photosynthesis, how the Golgi apparatus works, etc. etc. Check it out, it's accurately done and provides a great feel for what goes on inside of a cell. FANTASTIC site. (by John Kyrk).


Good overview of bio-chemistry basics and parts of the cell (with pictures!)


The following chemistry summary is adapted from here.:


Acids - substance that donates H+ (protons) in a solution.
Base - substance that donates OH- (hydroxide ions) in a solution.
Organic compounds - contain carbon and hydrogen, consist of mainly covalent bonds. Large organic compounds are called macromolecules. Major organic compounds contain Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorous, Sulphur. (periodic table)

(The chemical properties of an atom will depend on the number of electrons in the atom's outermost (or valence) electron shell. Thus lithium behaves more similarly to hydrogen than it does to helium because both lithium and hydrogen have 1 electron in their outermost shell. (ref.)

Carbohydrates - includes sugars and starches
- functions are to provide energy to cell, building block of nucleic acids (DNA and RNA), cell wall of bacteria (major component of peptidoglycan)
- monosaccharides - contains 3-7 carbons, glucose has 6 carbons, ribose and deoxyribose have 5 C's.
- disaccharides - two monosaccharides put together
Example - sucrose (table sugar) = glucose + fructose
- polysaccharides - consist of many monosaccharides put together, often polymers of glucose

  • glycogen - storage form of glucose in animals, some bacteria

  • starch - storage form of glucose in plants

  • cellulose - cell walls of plants, most algae

  • peptidoglycan – polysaccharide + amino acids in bacterial cell walls

  • dextran - slime layer produced by some bacteria

  • mannan - cell wall of many yeasts

  • Lipids - fats and oils
    - consist mainly of C and H, very little O
    - non-polar, so does not mix w/ polar substances like water
    - simple lipids - consist of a molecule called glycerol plus 1, 2, or 3 fatty acids.
    - Can be saturated (no double bonds) or non-saturated(one or more double bonds)
    - Complex lipids - have other elements such as phosphorus (P), N, and S added.

  • phospholipids - major component of cell membranes, have polar and non-polar ends

  • waxes, glycolipids

  • steroids - highly ringed structure, add stability to cell membranes

  • Proteins - contain C, H, O, N, some contain S
    - make up enzymes; integral parts of cell membranes, bacterial cell walls; hormones, antibodies, some bacterial toxins, contractile proteins in muscle cells, etc.
    - proteins made up of many amino acids put together
    - about 20 dif. amino acids occur naturally in proteins (more...)
    - amino acids held together by peptide bonds
    - there are 4 levels of protein structure:

  • primary - pep. bonds

  • secondary - H-bonds

  • tertiary - H-bonds, rxn=s between R groups

  • quaternary

  • - shapes of proteins can be denatured by high temps, high or low pH's, or high salt concentrations

    Nucleic acids - DNA and RNA
    - made up of polymers of nucleotides
    - composed of 3 parts: pentose sugar, phosphate group, and a nitrogen-containing
    base - adenine, guanine, thymine, (uracil in RNA) or cytosine.

    - DNA : makes up genes, double stranded, pentose sugar is deoxyribose (can be magnetically aligned)
    - RNA : involved in protein synthesis, usu. single stranded, sugar is ribose
    - ATP : a nucleotide that does not form polymers. It is the principle energy carrier for the cell and has 3 phosphate groups bound together by high energy bonds.

    The ribosome's able to implement enzymatic reactions to break off each amino acid, each bound to a specific transfer RNA, and to connect it to its adjoining amino acid using a peptide bond.