AP Biology Biochemistry Review

Carbon, Hydrogen, Oxygen, Phosphorus, Nitrogen (CHOPNS)

elements that make up macromolecules

organic chemistry

the study of carbon compounds

organic molecules

molecules that contain carbon

the reason carbon is important to life

1) carbon can form four covalent bonds with different elements; 2) carbon can form single, double, or triple bonds; 3) carbon is the main component of organic molecules; 4) all organic molecules contain carbon (carbohydrates, lipids, proteins, nucleic acids)

inorganic compound

compounds that do not contain carbon

FUNCTIONAL GROUPS

parts of organic molecules that are involved in chemical reactions

carboxyl group

A -COOH group, found in organic acids.

hydroxyl group

OH-

carbonyl group

C=O

amino group

NH2

phosphate group

PO4

methyl group

CH3

sulfhydryl group

-SH

nonpolar

not soluable in water

polar

soluable in water

ion

atom becomes charged when it gains or loses an electron

macromolecules

large organic biomolecules

monomer

molecules that consist of a single unit

polymer

molecules that consist of many repeated monomers

dehydration synthesis

A reaction in which monomers are bonded together to form polymers by removing a water molecule

condensation / polymerization reaction

dehydration synthesis reaction that joins monomers together to form a polymer

hydrolysis reaction

the process of adding a water molecule to break a polymer into monomers

CARBOHYDRATE

macromolecule group used for short-term energy, structure, and cell-signalling

Carbohydrate Examples

glucose, fructose, sucrose, starch, glycogen, cellulose, monosaccharides, disaccharides, polysaccharides

-ose

suffix carbohydrates usually end in (gluc-ose, fruct-ose, malt-ose, galact-ose)

Monosaccharide

A single sugar molecule such as glucose or fructose, the simplest type of sugar.

Disaccharide

A double sugar, consisting of two monosaccharides joined by dehydration synthesis.

Polysaccharide

Carbohydrates that are made up of more than two monosaccharides

Starch

storage form of glucose in plants

Cellulose

Carbohydrate component of plant cell walls.

LIPIDS

macromolecule group used for long-term energy storage, cell signalling, and cell membrane structure

Lipid Examples

fatty acids, fats, saturated fats, unsaturated fats, steroids, phospholipids, cholesterol, triglycerides

glycerol

a carbon alcohol that is hydrophilic; component of many lipids

hydrocarbons

carbon and hydrogen atoms that are covalently bonded that make them stable and nonpolar

fatty acid

monomer of a lipid made of a hydrocarbon chain and a carboxyl group

monounsaturated fatty acid

kind of unsaturated fat that consists only has one double bond (the rest are single) between each pair of carbon atoms

polyunsaturated fatty acid

kind of unsaturated fat that has two or more double bonds between each pair of carbon atoms

Unsaturated Fat

A lipid made from fatty acids that have at least one double bond between carbon atoms.

food made of unsaturated fatty acids

plant & fish fats, vegetable oils; good fats; liquid at room temp

food made of saturated fatty acid

animal fats and butter; bad fats, solid at room temp

Saturated Fat

fat in which all three fatty acid chains contain the maximum possible number of hydrogen atoms

Triglyceride

an energy storage lipid made of three fatty acid molecules and one glycerol molecule

phospholipid

amphipathic lipid made of two hydrocarbon chains, glycerol, and a phosphate group; makes up cell membrane

amphipathic

having both hydrophobic and hydrophilic parts

the reason a phospholipid is amphipathic

the hydrocarbon chains (tails) are nonpolar, while the glycerol and phosphate group (head) is polar

phospholipid bilayer

the main structure of the cell membrane, made of phospholipids that are arranged with the fatty acid tails packed together and the glycerol and phosphate heads facing water in an aqueous solution

hydrophilic head

another name for the polar phosphate group in a phospholipid

hydrophobic tail

another name for the nonpolar hydrocarbon chain in a phospholipid

cholesterol

the most common steroid; is a component of the cell membrane as well as the precursor to all other steroids

Steroid

lipid molecule with four fused carbon rings

examples of steroids

cholesterol, sex hormones

Nucleic Acid Examples

DNA, RNA, (ATP and ADP are modified nucleic acids)

amino acid

building block (monomer) of proteins, composed of an amino group and a carboxyl group, a hydrogen atom, and an R-group

R group (side chain)

stands for the rest of the compound, different for each kind of amino acid, giving the amino acid its properties

peptide bond

covalent bond formed between the amino group and carboxyl group of amino acids

polypeptide chain

a long line of amino acids bonded together by peptide bonds

Protein Examples

antibodies, hemoglobin, enzymes, cell membrane channels and pumps, peptide and protein hormones

denatured

a change in the shape of a protein due to chemical treatments, temperature, change of pH, or high concentrations of polar or nonpolar substances; may or may not be irreversible

enzymes

proteins that speed up chemical reactions (reduce the activation energy required)

PROTEINS

a macromolecule group made chains of amino acids used for gene expression, structure, transport, storage, enzymes, defense, etc.

four levels of a proteins structure

primary structure, secondary structure, tertiary structure, quaternary structure

Primary Structure of a Protein

the amino acid sequence of the polypeptide chain

Secondary Structure of a Protein

alpha helix and beta pleated sheet result from hydrogen bonds

alpha helix

the spiral shape resulting from the coiling of a polypeptide due to hydrogen bonds in a protein's secondary structure

beta-pleated sheet

sheet-like secondary structure of proteins due to hydrogen bonds

Tertiary Structure of a Protein

3D protein structure resulting from hydrophobic and hydrophilic interactions, disulfide bridges, ionic and hydrogen bonds

Quaternary Structure of a Protein

results when a protein consists of multiple polypeptide chains

Disulfide Bridge

The covalent bond between two sulfur atoms (-S—S-) that holds tertiary protein structure together.

Hydrogen Bonds

weak bonds; occurs when a hydrogen atom in one molecule is attracted to the electronegative atom in another molecule

Ionic Interaction

the attraction between oppositely charged ions

Hydrophobic Interaction

the tendency for hydrophobic molecules to cluster together when immersed in water (important in protein folding and fatty acid lipid properties)

NUCLEIC ACIDS

group of macromolecule that stores, transfers, and expresses genetic information

nucleotide

monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base

DNA

deoxyribonucleic acid; sugar-phosphate backbone with bases A-T, C-G arranged in 2 anit-parallel strands; nucleic acid polymer

double helix

term used to describe the arrangement of a DNA strand

RNA

ribonucleic acid; sugar-phosphate backbone with bases A, G, C, U arranged in single strand

*how DNA differs from RNA

*the sugar in DNA is deoxyribose; Thymine bonds with Adenine; DNA is double-stranded

charge of the oxygen atom in a water molecule

slightly negative

charge of the hydrogen atoms in a water molecule

slightly positive

hydrogen bond in water

weak bond formed between water molecules that leads to cohesion

universal solvent

Property of water in which substances that are ionic or substances that have polar covalent bonds all dissolve in water.

aqueous solution

A solution in which water is the solvent.

high specific heat

property of water in which water changes temperature very slowly with changes in heat due to hydrogen bonding

the reason ice floats in liquid water

less dense as a solid; hydrogen bonds form crystalline structure that keeps the water molecules separate

reasons why ice floating is important to life

floating ice keeps the water below it from freezing; if ice would sink, it would remain frozen eventually freezing the entire body of water

the reason insects can walk on the surface of water

surface tension caused by the cohesion of water molecules

cohesion

the attraction of like substances; water molecules are attracted to other water molecules; this is due to the hydrogen bonding between water molecules

adhesion

the attraction of unlike molecules; water molecules are attracted to other polar surfaces

the reason water moves from the roots to the leaves of a plant

adhesion of water to walls of xylem ("plant veins") and cohesion between water molecules results in capillary action due to evaporation in leaves

pH

hydrogen ion concentration, measure of how acidic or basic

logarithmic scale

A method of displaying data in multiples of 10.

The amount of hydrogen ions a solution with pH 5 compared with pH 7

100 times

cis-trans isomers

carbons have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds

glycogen

An extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch.

Difference between starch and glycogen

the amount of branching in the polymer chains

Ratio of carbohydrates

1 carbon: 2 hydrogen: 1 oxygen

Picture of Amino Acid

base pairing rules

the rules stating that cytosine pairs with guanine and adenine pairs with thymine in DNA, and that adenine pairs with uracil in RNA

Function of RNA

function in the synthesis of proteins

Buffer

A solution that minimizes changes in pH when extraneous acids or bases are added to the solution.