1. Chapter 3 Notes
Biochemistry

2. Objective
SC-HS-3.4.2: Students will understand that most cell functions involve chemical reactions. Food molecules taken into cells react to provide the chemical constituents needed to synthesize other molecules. Both breakdown and synthesis are made possible by a large set of protein catalysts, called enzymes. The breakdown of some of the food molecules enables the cell to store energy in specific chemicals that are used to carry out the many functions of the cell.

3. Carbon Compounds
Organic: compounds that contain C atoms that are covalently bonded to other C atoms and to other elements (H, O, N)
Inorganic: compounds that do NOT contain C atoms

4. Carbon Bonding
Atoms want to become stable – 8 electrons in their outermost energy level
C has 4 electrons in outermost level
Forms 4 covalent bonds with other elements to become stable
Can also form bonds with other C atoms and form straight chains, branched chains, rings

5. Functional Groups
Clusters of atoms that are the structural building block that determines the characteristics of the compound
Ex. –OH (hydroxyl group)
Alcohol: organic compound with a hydroxyl group attached to one of its C atoms
Polar (positive and negative end)
Ex. Ethanol, methanol, glycerol

6. Large Carbon Molecules
Monomers: small molecules put together to form large, complex molecules (polymers) which can combine to form macromolecules (large polymers)
Monomers to polymers: process = condensation reaction
Result: water released
Breakdown of polymers to monomers: process = hydrolysis
Reversal of condensation reaction
Water added to break apart the polymer

7. Energy Currency Life processes always need energy
Energy comes from ATP (adenosine triphosphate)
3 phosphate groups are covalently linked
When bonds break, lots of energy is released
Energy can be used by the cell to drive chemical reactions in the body

8. 4 Classes of Organic Compounds
Carbohydrates – composed of C, H, and O in a ratio of about 2H:1O and a varying # of C atoms
Proteins – composed mainly of C, H, O, and N
Lipids – large, nonpolar molecules that don’t dissolve in water; higher H:O ratio than carbs.
Nucleic Acids – very large, complex molecules that store important info in the cell.

9. Carbs Monosaccharide: simple sugar 1C:2H:1O (CH2O)n , n=3-8
Ex. glucose (C6H12O6; main source of energy for the cell), fructose (sweetest   and found in fruit), galactose (found in milk, usually combined with glucose or fructose)
Isomers – compounds with a single chemical formula but different forms

10. Disaccharides Polysaccharides
A double sugar formed from 2 monosaccharides combining
Ex. Sucrose (table sugar) composed of fructose and glucose
Polysaccharides
A complex molecule composed of 3 or more monosaccharides
Ex. Glycogen (sugar stored by animals in liver and muscles); starch (sugar stored by plants); cellulose (large sugar stored by plants to give strength and rigidity to cells)

11. Proteins Skin and muscles are mostly proteins
Catalysts found in animals and plants are proteins
Amino acids (a.a.), p. 56
Several together make a protein
20 different a.a.s
Basic structure: C atom in middle bonded to 4 other atoms or functional groups (R group)
Different a.a.s have different R groups which give them different shapes and so have different functions.

12. Dipeptide Polypeptide Enzymes 2 bonded a.a.s Bond = peptide bond
    A very long chain of a.a.s
Enzymes
    Organic molecules that act as catalysts
    Essential for functioning of cells
Most are proteins

13. Enzyme Action
Depend of fit of enzyme with its substrate (the reactant being catalyzed)
Shape of enzyme and substrate are like a lock and key, only one certain enzyme for a particular substrate
When enzyme binds to substrate, bonds are weakened allowing chemical reactions to occur with smaller amount of energy needed
After reaction, enzyme releases the products, which used to be the substrate
Acts as a catalyst of the reaction: speeds up the reaction but isn’t used up, so it can be reused in another reaction

14. Enzyme failure to work due to :
Wrong substrate (doesn’t fit)
Change in temperature or pH which can cause a change in the shape of the substrate or the enzyme

15. Lipids Store energy very efficiently
Composed of unbranched C chains called fatty acids (p. 58)
Structure of fatty acid: long, straight C chain with a carboxyl (-COOH) group attached to one end
Carboxyl group is polar and is attracted to water molecules (hydrophilic: “water loving”)
Hydrocarbon end is nonpolar and does not interact with water molecules (hydrophobic: “water fearing”)

16. Complex lipids
Triglyceride: composed of 3 molecules of fatty acid joined to one molecule of the alcohol glycerol
Saturated: shortening and animal fats; solid at room temp
Unsaturated: found in plant seeds and fruits; liquid at room temp
Phospholipids: 2 fatty acids joined by a glycerol
Cell membrane composed of 2 layers of phospholipids, which forms barrier between inside and outside of cell

17. Wax: type of structural lipid that has a long fatty-acid chain joined to a long alcohol chain
Highly waterproof; form protective coating on plants and in animals (earwax to protect middle ear)
Steroids
Composed of 4 fused C rings with various functional groups attached to them
Ex. Male hormone testosterone, cholesterol

18. Nucleic Acids
Very large and complex organic molecules that store important info in the cell
2 types:
DNA (deoxyribonucleic acid): contains info that is essential for almost all cell activities
RNA (ribonucleic acid): stores and transfers info that’s essential for making proteins
Made up of thousands of nucleotides (p. 59)
Structure: phosphate group, 5-C sugar, and a ring-shaped N base