Chapter 3: Bio-Chemistry

3-1 Water

3-2 Carbon Compounds

3-3 Molecules of Life

I. Polarity (i.e., polar molecule)• TWO opposing regions of slight ELECTRICAL charge:

(1) A Positive end (+)

(2) A Negative end (-)

3-1 Water

(1) Polar (e.g., water molecule)• With (+) charge, O atom PULLS on shared e- with GREATER force than (+) of H atoms.

II. Hydrogen Bonding• Weak force between O atoms and H atoms of adjacent water molecules.

(A) Cohesion and Adhesion: Two Properties of Water• COHESIVE force are STRONG enough to cause water to have a thin “SKIN” on its surface.

NOTE: ADHESION is force between UNLIKE substances (Ex: Water holding TWO glass microscope slides together)

•

(1) The SURFACE TENSION of water at room temperature is so great that you can actually “float” a small needle on the surface of water. (The needle doesn’t truly float—it is denser than water. It is held in place by the force of hydrogen bonding between water molecules lying below and around the needle.) If the water were HEATED, WHAT would LIKELY happen to the needle and WHY?

Critical Thinking

(1) Capillarity (result of BOTH cohesion AND adhesion of water)• Property of water to be PULLED UP a straw OR a stem of a plant.

(2) Most automobiles have water-cooled engines. What must be true about a SOLUTION that can replace water in the cooling system, such as ANTIFREEZE?

Critical Thinking

(3) Cells contain mostly WATER. What might happen to the stability of an organism’s INTERNAL TEMPERATURE with respect to environmental temperature changes if cells contained mostly OIL, which does NOT have extensive hydrogen bonding?

Critical Thinking

(B) Temperature Modification (Crucial to LIFE)• Water MUST gain or lose a HUGE amount of THERMAL energy for its temperature to SLIGHTLY change.

Advantage?

• A body that does not overheat easily (70% water)• A stable environment for aquatic ecosystems, freshwater and marine.

3-2 Carbon Compounds

I. Organic (vs. Inorganic) Compounds

• Carbon (organic) COVALENTLY bonded to C, H, O, and N atoms.

II. Carbon Bonding (single, double, AND triple bonds are POSSIBLE!!)• 4 e- in OUTER energy level (valence), carbon would PREFER 4 BONDS.

• A GROUP off a CARBON ATOM that influences the molecule.

III. Functional Groups (e.g., hydroxyl group = polarity)

(1) Alcohol (C-0H)• -OH group brings POLARITY to alcohols (i.e., ethanol, glycerol).

• POLYMERS are built from MONOMERS during chemical reactions.

III. Large Carbon Molecules (Monomer + Monomer Polymer)

(1) Condensation Reaction (a.k.a “Dehydration Synthesis”)• LINKS monomers TOGETHER to form POLYMERS releasing a WATER.

(2) Hydrolysis (i.e., “to BREAK with WATER”)• BREAKS DOWN polymers to MONOMERS requiring a WATER molecule. (i.e., the REVERSAL of condensation reaction)

(A) Energy Currency• NRG in a compound known as ATP used to run reactions

(a HIGH energy-yielding compound).

(1) Adenosine triphosphate (ATP)• HYDROLYSIS of ATP (ADP) and (Pi) + 7kcal of NRG.

3-3 Molecules of Life

I. Carbohydrates (3 CLASSES)• NRG yielding and structural molecules (sugars, starch, cellulose)

(A) Monosaccharides (i.e., simple sugars)• MONOMER of starch OR glycogen (e.g., glucose, fructose, and galactose) NOTE: The RATIO of C to H to O is 1:2:1. Formula is written as (CH2O)n.

Isomers include…

• Each monosaccharide has SAME molecular FORMULA, C6H12O6, BUT they are STRUCTURED (appear) differently…

Glucose Galactose

(1) Isomers (of monosaccharides)

Fructose

(B) Disaccharides (2-sugar unit) and Polysaccharides (many sugar unit)• Glycogen (animal storage), Starch (plant storage), Cellulose (plant STRUCTURAL component)

• CELLULOSE provides strength to PLANT cells, BUT have their glucose monomers CROSS-LINKED with H-bonds, and are UNABLE to be broken (via HYDROLYSIS) in humans due to a LACK of an ENZYME.

II. Proteins (tissue development, enzymes, NOT NRG)• Built by AMINO ACIDS (monomer of protein), made of N, C, H, and O. •Examples include…

Collagen

HemoglobinLactaseFibrinogen

(A) Amino Acids (20 different types; building blocks of proteins)•All begin with a CENTRAL carbon covalently bonded to 4 other atoms.

(1) A H atom at 1st site.

(2) A carboxyl group (-COOH) at 2nd site

(3) An amino group (-NH2) at 3rd site

(4) A functional group (-”R”) at 4th site (** SHAPE and FUNCTION **)

(B) Dipeptides and Polypeptides• Adjacent amino acids form a COVALENT bond PEPTIDE bond.

(1) Peptide Bond• Strong bond between N-H of 2 AMINO ACIDS in a PEPTIDE chain.

NOTE: A protein’s STRUCTURE and SHAPE are linked to FUNCTION. This will be influenced by TWO PHYSICAL conditions:

(1) Temperature

(2) pH

(C) Enzyme (weakens BONDS, lowers ACTIVATION NRG)• A protein that acts as a CATALYST during chemical rxns.

• Bonds and is catalyzed by an enzyme (broken up OR pulled together).

(1) Substrate (i.e., reactant)

(4) HIGH temperatures can WEAKEN bonds between different parts of a protein molecule, thus changing its SHAPE. How might this SHAPE change alter the EFFECTIVENESS of an enzyme?

Critical Thinking

III. Lipids (3 CLASSES)• NON-polar (do NOT dissolve in water) AND stores MORE NRG than carbs due to NUMEROUS C-H bonds (carbs LESS NRG C-O bonds)

(A) Fatty Acids (BUILDING BLOCKS of most LIPIDS)• Unbranched C chain with TWO ends of DIFFERENT properties:

(1) Hydrophilic

(2) Hydrophobic

• CARBOXYL end of chain, polar, and “water-LOVING”

• HYDROCARBON end of chain, non-polar, and “water-FEARING”

(B) Complex Lipids• Include 3 classes:

(1) Triglycerides

(2) Phospholipids

(3) Waxes

(1) Triglyceride (e.g., saturated (animal) and unsaturated (plant) fats• 3 fatty acids joined to a GLYCEROL molecule.

(5) Triglycerides in ANIMALS’ bodies are usually SOLID FATS, and those in PLANTS are usually OILS. However, many animal species living in the Arctic and Antarctic have a GREATER number of triglycerides that are OILS than do other animals. What advantage might the storage of body fat as OIL INSTEAD of SOLID FAT be to animals that inhabit freezing climates?

Critical Thinking

(2) Phospholipids• TWO fatty acids joined by a glycerol

(in CELL MEMBRANE, we call this the “LIPID BILAYER.”

(3) Wax (i.e., ear wax, plant cuticle)• STRUCTURAL lipid; long fatty-acid joined to an ALCOHOL.

(WATERPROOF)

(C) Steroids• Made using 4 carbon RINGS with various groups attached.

• Ex: Sex HORMONES (testosterone and estrogen), CHOLESTEROL, a key for nerve transduction AND cell membrane stability.

IV. Nucleic Acids (2 CLASSES, DNA and RNA)• Encrypt HEREDITARY data for cells.

(e.g., Sequence of bases READ like a CODE and is UNIQUE).

• BLUEPRINT for cellular activity; NEVER leaves nucleus of cell.

(1) Deoxyribonucleic Acid (DNA)

• 3 types of RNA; work with DNA to allow a cell to make its PROTEINS.

(2) Ribonucleic Acid (RNA)

• Made of 3 PARTS:

(1) Sugar deoxyribose (DNA) OR ribose (RNA)

(2) Phosphate Group (PO4)

(3) Nitrogenous Base (A, T, C, G) (U in RNA)

(1) Nucleotide (monomer for DNA and RNA, 4 types of nucleotides)

Extra Slides AND Answers for Critical Thinking Questions

(1) Solutions that can replace water as a coolant in automobiles must have the ability to absorb large quantities of heat.

(2) An organism’s internal temperature would likely change more abruptly and drastically in response to environmental temperature changes.(3) Heating the water would cause the water molecules to move about and the hydrogen bonds to break, thus allowing the needle to eventually fall through the surface of the water.

(4) Changing the shape of an enzyme may affect its ability to function because the enzyme may no longer physically interact appropriately with its substrate.

(5) Oil solidifies at a lower temperature than fat does; storing body fat as oil is helpful in freezing climates because oil is less likely to solidify in these climates than is fat.