AP BIO UNIT 1: chemistry of life

topic 3.

WATER

topic 3.

WATER

OVERVIEW:

• water and the importance of hydrogen bonds.

• pH

hydrogen and covalent bonds

polar covalent bond

a partial negative charge around the oxygen atom and a partial positive charge around the hydrogen atom.

adhesion

different molecules attract each other.

cohesion

like molecules attract each other.

high specific heat:

as a result of water’s ability to form hydrogen bonds, more energy is required to separate water molecules during phase changes, giving water a high specific heat.

moderating climate:

since water has a high heat capacity, it can absorb and release large amounts of energy. this stabilizes climates in locations near large bodies of water.

expanding upon freezing:

since water has the ability to form hydrogen bonds, there is more space between water molecules in the solid state than in the liquid state. as a result, ice had a lower density than that of liquid water, and thus ice floats on liquid water.

acting as a great solvent for other polar molecules and for ions:

water has a partially positive end and a partially negative end. thus, water can readily dissolve ionic compounds and other polar molecules.

pH

measures the concentration H+ ions in a solution.

buffers

crucial in maintaining relatively constant pH levels in living cells. buffers can form acids or bases in response to changing pH levels in a cell.

topic 4.

MACROMOLECULES

OVERVIEW:

• biological macromolecules

• protein structure

• nucleic acids

macromolecules necessary for life are primarily made up of six elements…

nitrogen, carbon, hydrogen, oxygen, phosphorus, and sulfur.

dehydration synthesis

biological macromolecules are formed from building blocks (i.e., monomers) that are linked by dehydration synthesis.

hydrolysis

these biological macromolecules are broken down by hydrolysis reactions.

carbohydrates

• polymers of sugar monomers

• used to store energy (such as starch or glycogen)

• can also have structural functions (such as cellulose)

• linkage: glycosidic bond or glycosidic linkage

lipids

• building blocks: fatty acids

• nonpolar macromolecules that function in energy storage, cell membranes, and insulation.

• linkage: ester linkages

unsaturated

fatty acids with at least one C=C double bond are called unsaturated, are liquid at room temperature, and usually originate in plants.

phospholipids

they are built from a glycerol molecule, two fatty acids, and a phosphate group. because fatty acids are nonpolar and the phosphate is polar, phosphlipids are amphipathic, meaning that they have both hydrophobic and hydrophilic regions.

nucleic acids

• polymers of nucleotides

• carriers of genetic information

• linkage: phosphodiester linkage

proteins

• polymers of amino acids

• have an amino group, a carboxylic acid group, a hydrogen atom, and a side chain (r-group) attached to a central carbon.

• functions in enzyme catalysis, maintaining cell structures, cell signaling, cell recognition, and more.

• linkage: covalent peptide bond

r-group

unique for each amino acid; it determines the amino acid’s identity and whether the amino acid will be nonpolar, polar, acidic, or basic.

protein structure

there are four levels of protein structure: primary, secondary, tertiary, and quaternary.

primary structure

amino acids are joined by peptide bonds. The resulting polypeptide chains have directionality, with an amino (NH2) terminus and a carboxyl (COOH) terminus. the order of the amino acids in the polypeptide chain determines the primary structure of the protein.

secondary structure

one the primary structure is formed, hydrogen bonds may form between adjacent amino acids in the polypeptide chain. this drives the formation of the secondary structure of the protein. these secondary structures include alpha helixes and beta-pleated sheets.

tertiary structure

the three-dimensional folded shape of a protein, often determined by the hydrophobic/hydrophilic interactions between r-groups in the polypeptide.

chaperonins

special proteins called chaperonins often help fold a polypeptide into its three-dimensional structure.

quaternary structure

some proteins consist of multiple polypeptide chains (subunits), which are joined together to form the complete protein and function as a unit.

nucleic acids

(DNA and RNA) are polymers of nucleotides. the genetic information is stored and communicated through the order of these nucleotides. nucleotides consist of a five-carbon sugar (deoxyribose or ribose), a nitrogenous base (adenine, thymine, cytosine, guanine, or uracil), and a phosphate group. nucleotides have directionality in that the phosphate group is always attached to the 5’ carbon in the sugar, and the 3’ carbon always has a hydroxyl group to which new nucleotides may be added.