Basic Biochemistry short notes

Basic Chemical Concepts

1. Atoms
   1. Def.- the smallest unit of an element that can combine chemically with other elementsStructure                                      
      
      1. Proton (+) charged
      2. Neutron (not charged)
      3. Electron (-) charged
         1. Electrons exist in distinct orbital clouds
         2. s, p, and d orbitals
         3. Orbitals combine to form energy levels: K, L, M, N, etc
      4. Protons and neutrons are the same mass and make up the nucleus
   2. Identification
      1. Atomic number: number of protons
      2. Atomic mass number: number of protons + neutrons
      3. Atoms are organized into groups in the periodic table
   3. Isotopes
      1. Two atoms with the same atomic number but different atomic mass numbers
      2. Differ only in the number of neutrons
      3. Some are radioactive (radioisotopes)
   B. Compounds
   
   1. Def: a combination of two or more elements which are joined chemically
   2. Chemical bonding
      1. Ionic: when an atom will either give or take an electron from another atom
         1. Cation: positive ion
         2. Anion: negative ion
         3. Electrostatic forces hold the atoms together
      2. Covalent: when atoms share electrons
         1. Forms single or multiple bonds
         2. Sharing of electrons hold the atoms together
      3. Hydrogen bonds: weak links between the hydrogen (+) end of one polar molecule and the negative end of another polar molecule
   C. Acids and Bases
   
   1. Acid: a substance which releases a H+ ion
   2. Base: a substance which releases an OH- ion
   3. pH scale
      1. A method of determining how acidic or basic a solution is
      2. Negative logarithmic scale: 0 (acidic) to 14 (basic) (alkaline)
      3. pH 7.0 is neutral (water)
   4. Buffers: a substance which limits the change of pH
   D. Basic chemical reactions
   
   1. Synthesis: two or more atoms or molecules are combined
   2. Decomposition: molecules are broken down into simpler forms
   3. Reduction
      1. The addition of electrons to a molecule
      2. Often accompanied by a gain of a hydrogen nucleus (proton)
   4. Oxidation
      1. The removal of electrons from a molecule
      2. Often accompanied by a loss of a proton
      3. Oxidized atoms are more reactive than reduced atoms

II. Basic Biochemistry Concepts
A. Building Materials of Life

1. Inorganic compounds
2. Organic compounds
   1. All contain some form of carbon
   2. Biosynthesis: the manufacture of things by a living organism
3. Carbohydrates
   1. Structure
      1. Contain only C, H, and O
      2. Ratio of O:H is 1:2 (same as water H₂O)
   2. Reactions involving carbohydrates
      1. Dehydration synthesis: joining two molecules by removing water
      2. Hydrolysis: splitting two molecules by adding water
   3. Types
      1. Monosaccharides (simple sugars)
         1. 5-carbon: ribose
         2. 6-carbon: C₆H₁₂O₆ (Glucose, Galactose, Fructose)
      2. Disaccharides
         1. Two monosaccharides joined together (dehydration synthesis)
         2. Sucrose (table sugar): Glucose + Fructose
         3. Maltose (malt sugar): Glucose + Glucose
         4. Lactose (milk sugar): Glucose + Galactose
      3. Polysaccharides
         1. Starch: straight chain of glucose (food storage in plants)
         2. Glycogen: branched chain of glucose (food storage in animals)
         3. Cellulose: Zig-zag chain of glucose (non-digestible roughage)
4. Lipids
   1. Fats (triglycerides)
      1. 3 fatty acid molecules + 1 glycerol joined by dehydration synthesis
      2. Saturated: no double bonds between carbons
      3. Unsaturated: at least one double bond
   2. Phospholipids
      1. 2 fatty acids + 1 glycerol + 1 phosphate
      2. Hydrophobic end (fat): water fearing (non-polar)
      3. Hydrophilic end (phosphate): water loving (polar)
      4. Used extensively in cell membranes
   3. Sterols: multi-ringed compounds
      1. Cholesterol
         1. HDL: High density lipoprotein ("good" cholesterol)
         2. LDL: Low density lipoprotein ("bad" cholesterol)
      2. Hormones: i.e. prostaglandins, cortisone, etc
5. Proteins
   1. Structure: composed of 20 basic amino acids
   2. Protein synthesis
      1. Two amino acids are brought together and dehydration synthesis between the amino acids forms a peptide bond
      2. Protein = polypeptide chain
      3. The order of the amino acids is critical to the function of a protein
   3. Enzymes: large proteins which catalyze reactions
      1. Structure
         1. Active site: attachment site for substrates
         2. Substrate: molecule which reacts with the enzyme and is changed
         3. Coenzyme: non-protein which helps to complete the active site (vitamins)
      2. Enzyme action
         1. Enzyme & substrate bind at the active site
         2. Reaction proceeds (lytic- splitting apart, synthetic - putting together)
         3. Enzyme and product(s) separate
6. Nucleic acids
   1. Consist of long chains of repeating subunits (nucleotides)
   2. Nucleotide structure
      1. 5-carbon sugar (ribose)
      2. Phosphate group (PO₄)
      3. Organic nitrogen-containing base
   3. DNA: Deoxyribonucleic acid
      1. Used to store biological information
      2. DNA base pairs
         1. Guanine - Cytosine (G - C)
         2. Adenine - Thymine (A - T)
      3. Double-stranded helix shape formed by hydrogen bonds
   4. RNA: Ribonucleic acid
      1. Used as working blueprints for protein synthesis
      2. RNA base pairs
         1. Guanine - Cytosine (G - C)
         2. Adenine - Uracil (A - U)
      3. Single strand

III. Energy and its Changes
A. Kinetic energy: energy of motion
B. Potential energy: energy of position (stored energy)
C. Kinetic and potential energy are interconvertable
D. Energy in chemical reactions

1. Exothermic: reactions which release energy (heat)
2. Endothermic: reactions which require energy
3. Activation energy: energy needed to start a chemical reaction