AP Biology - The Chemistry of Life

elements

substances that cannot be broken down into simpler substances by chemical means

CHNOPS

an acronym representing the 6 key elements of life

carbon

key element of life; major component of ALL organic compounds, including all 4 types of macromolecules (sugars, fats, proteins, and nucleic acids); rarely found unbound to other elements

hydrogen

key element of life, highly involved in the creation of protein gradients that enable photosynthesis and respiration

nitrogen

key element of life, especially prevalent in proteins and nucleic acids; wastes based on excesses of this element must be excreted by organisms to prevent the accumulation of toxic ammonia in cells

oxygen

key element of life, involved in processes like oxidative phosphorylation and a major component of many organic compounds; exists in the atmosphere in molecular form, small enough to permeate most membranes by simple diffusion

phosphorous

key element of life; especially important for its role in phosphate and thus in ATP molecules, which store energy to fuel the majority of cellular work

sulfur

key element of life; especially important in proteins, where disulfide bridges composed of this element help anchor peptide chains into functional shapes (tertiary structure)

trace elements

elements that are required by organisms in only very small quantities, such as Fe, Cu, I, etc

atom

the smallest unit of an element that retains its characteristic properties; composed of subatomic particles such as protons, neutrons, and electrons

nucleus

the center core of an atom where the protons and neutrons are concentrated

protons

positively charged subatomic particles located in the nucleus of an atom; constant for all atoms of the same element

neutrons

subatomic particles that carry no charge; located in the nucleus of an atom; number can vary among atoms of the same element, leading to various isotopes (some of which are unstable, or radioactive, and spontaneously split due to instability)

isotopes

atoms of the same element that have different numbers of neutrons and thus different atomic masses; some are unstable, or radioactive

electrons

negatively charged subatomic particles that orbit the nucleus of an atom in a region of space called the "electron cloud"

valence electrons

the electrons of the outermost energy level of an atom that determine bonding characteristics

valence

the maximum number of bonds that an atom of a particular element can form; based on the number of valence electrons (8 - ve)

atomic number

the number of protons in all atoms of a specific element

mass number

the weighted average of the masses of the different isotopes of an element

atomic mass

the mass of an atom of a particular isotope of a particular element; equal to the number of protons plus the number of neutrons

compound

a combination of two or more different types of atoms in a fixed ratio

chemical reaction

the formation or destruction of chemical bonds between two or more atoms or compounds

chemical bond

forces that hold the atoms of a compound together, including ionic bonds, covalent bonds, hydrogen bonds, etc

ionic bond

chemical bond formed when an electron is transferred from one atom to another, creating a positive ion and a negative ion, which are then attracted to one another by electromagnetic forces

formula unit

two or more ions (monoatomic or polyatomic) held together by ionic bonds

covalent bond

chemical bond formed when an electron pair is shared between two atoms, contributing to the outer shell of electrons of both

molecule

two or more atoms held together by chemical bonds

nonpolar covalent bond

covalent bond where the electron pair is shared equally between both atoms with the same or similar electronegativities

polar covalent bond

covalent bond where the electron pair is pulled more towards one atom than the other, because one has a stronger electronegativity; creates slightly polar regions across molecules

single covalent bond

two atoms that share one electron pair

double covalent bond

two atoms that share two electron pairs

triple covalent bond

two atoms that share three electron pairs

coordinating covalent bond

two atoms that share an electron pair where one of the atoms donates both electrons

polar molecules

molecules that have partial positively charged and partial negatively charged regions (ie water); cannot permeate the nonpolar membranes of cells, but can dissolve better in water and other polar solvents than nonpolar molecules

hydrogen bonds

weak chemical bonds formed when a slightly positively charged hydrogen atom attached to a significantly more electronegative atom (such as O or N) by a polar covalent bond is also attracted to the negative region of another electronegative atom involved in another polar covalent bond

emergent properties of water

properties of water that arise from the ability of H20 molecules to form hydrogen bonds with one another; critical to many life functions; include cohesion, moderation of temperature, formation of a less dense solid form (ice), and ability to act as a nearly universal solvent

cohesion

the tendency of water molecules to stick together; enables transportation of H2O against gravity in vascular plants, because as water molecules evaporate through transpiration, they pull up their replacements

adhesion

the tendency of water molecules to stick to other substances; enables transportation of H2O against gravity in vascular plants, because molecules stick to sides of xylem

capillary action

the ability of water to flow against gravity up the xylem of plant vascular systems based on its cohesive and adhesive properties

surface tension

the resistance of water to being stretched or broken at the surface of a liquid due to cohesion

heat capacity

the ability of a substance to store heat, or to absorb thermal energy without changes in temperature (average thermal energy/atom); the quantity of heat required to raise the temperature of 1 g of a substance by 1 degree Celsius; water has a high specific heat b/c hydrogen bonds absorb energy before breaking and allowing atoms to move more quickly

heat of vaporization

the amount of heat that must be absorbed for 1 g of a substance to be converted from a liquid to a gas; high in water because a significant amount of heat must be absorbed to break hydrogen bonds

evaporative cooling

the decrease in temperature of an entire body of water as the molecules with the most thermal energy are lost through evaporation; helps moderate temperature

solution

a liquid that is a homogenous mixture between two substances

solvent

the dissolving agent of a solution

solute

the substance that is dissolved in a solution

hydration shell

sphere of water molecules surrounding a dissolved ion, attracted by the polar regions of the molecule

hydrophilic substances

substances that dissolve easily in water; the smaller and more charged the better

hydrophobic substances

substances that do not dissolve in water; usually larger and nonpolar/nonionic

amphipathic substances

substances with both hydrophobic and hydrophilic regions

molarity

the number of moles of a particular solute per liter of solvent

acid

substance that increases the molarity of hydrogen ions in a solution, decreasing pH (simultaneously diminishes the molarity of hydroxide ions, because product of the molarities of both is always 10^-14)

base/alkaline

substance that decreases the molarity of hydrogen ions in a solution, increasing pH (simultaneously increases the molarity of hydroxide, because the product of the molarities of both is always 10^-14)

neutral

solution with an equal concentration of hydroxide and hydrogen ions (10^-7 M); pH of 7

pH scale

measurement of the acidity/alkalinity of a solution; assigns a numerical value (opposite logarithm of the molarity of H+) to the concentration of hydrogen ions, thus implying the concentration of hydroxide ions; ranges from 1 - 14, and an increase of 1 equates to a tenfold decrease in the concentration of H+

organic compounds

chemical compounds found in living organisms that contain a carbon backbone

inorganic compounds

chemical compounds that do not contain carbon

functional groups

distinctive groups of atoms that play a key role in determining the chemical behavior and properties of the organic compounds of which they are a part; 7 main functional groups: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl

hydroxyl group

(-OH) hydrogen atom binded to an oxygen atom and then combined onto a carbon skeleton; called "alcohols;" polar, allowing them to give rise to hydrogen bonds

carbonyl

(-C=O) carbon atom double bonded to an oxygen atom; called "ketones" if located inside carbon skeleton and "aldehydes" if located at the end; create structural isomers, esp. in sugars

carboxyl

(-COOH) carbon atom double bonded to an oxygen atom and single bonded to a hydroxyl group; called "carboxylic acids;" acidic properties; important in amino ACIDS

amino

(-NH2) nitrogen atom attached to two separate hydrogens; called "amines;" alkaline properties; important in AMINO acids

sulfhydryl

(-SH) sulfur atom attached to a hydrogen atom; called "thiols;" can create disulfide bridges in protein 3D structures

phosphate

(-OPO3) phosphorous atom bonded to four oxygen atoms, two of which carry a negative charge; called "organic phosphates;" contribute negative charge; have potential to release energy

methyl

(-CH3) carbon atom attached to three hydrogen atoms; called "methylated compounds;" nonpolar; can effect expression of genes through "methlylation"

4 classes of organic molecules

1. carbohydrates 2. proteins 3. lipids 4. nucleic acids

polymer

molecule with repeating pattern of subunits of the same general type

dehydration reaction

joining of two molecules through the loss of a hydrogen molecule (one contributes the hydroxyl group, the other contributes a hydrogen)

carbohydrates

organic macromolecules that include carbon hydrogen and oxygen in a 1:2:1 ratio; aka sugars

monosaccharides

a single unit of sugar (1 ring); classified by number of carbons: trioses (3-C backbone), pentoses (5-C backbone), or hexoses (6-C backbone); classified by location of carbonyl group (C=O): aldoses (carbonyl group on the end) and ketoses (carbonyl group in the middle)

ring structure

in aqueous environments, most sugars form rings; most common example is glucose: C1 and C5 become linked by an O atom, and C6 attaches to C5

glucose

common monosaccharide; C6H12O6 aldose; hexagonal ring structure; two structural isomers: alpha glucose and beta glucose, which differ based on the position of the OH and H groups attached to C1 in the ring structure

fructose

common monosaccharide; C6H12O6 ketose; forms a pentagonal ring structure

disaccharides

two units of sugar joined in such a way that no more can attach to either end (2 rings)

glycosidic bond

the joining of 2 monosaccharides by a dehydration reaction in which a H2O molecule is lost (inverse = hydrolysis)

maltose

common disaccharide composed of two glucoses linked by a 1-4 glycosidic bond

sucrose

common disaccharide composed of glucose + fructose in a 1-2 glycosidic linkage

polysaccharides

macromolecules composed of repeating units of glucose joined by 1-4 glycosidic linkages; often used as storage of excess sugars for fast energy

starch

polysaccharide composed of repeating alpha glucose molecules that form a helical, easily compacted storage molecule typically used to store energy for respiration; 3 types: amylose, amylopectin, and glycogen

amylose

unbranched starch molecule found in plants

amylopectin

moderately branched starch (1-6 linkages) found in plants

glycogen

highly branched starch (1-6 linkages) found in animals

cellulose

polysaccharide composed of repeating beta glucose molecules that alternate orientation to form a perfectly straight molecule often used in protection or reinforcement of structures (esp. cell wall); cannot be digested by humans

chitin

variation of cellulose including a nitrogen-containing appendage on each repeating subunit

proteins

macromolecules formed from amino acid sequences, called polypeptide chains, that are folded into 3D shapes after many levels of organization

amino acids

organic molecules that serve as the building blocks of proteins; 20 common ones, each composed of an amino group (NH2) attached to a middle carbon attached to a carboxyl group (COOH) and an R group (variable)

R group

side chain of the amino acid, which determines properties; may be polar, nonpolar, or charged (each one effects protein folding in a different way)

peptide bond

dehydration reaction that links two amino acids together by joining an amino end to a carboxyl end

dipeptide

two amino acids joined by a peptide bond

polypeptide

chain of amino acids joined by hundreds or thousands of peptide bonds

primary structure of protein

sequence of amino acids in a polypeptide chain

secondary structure of protein

beta pleated sheets and alpha helices that form as a result of hydrogen bonds interacting between similar portions of a polypeptide chain

alpha helix

delicate coil in polypeptide chain held in place by hydrogen bonds between every fourth amino acid

beta pleated sheet

accordion fold in parallel stretches of a polypeptide chain laying side by side; locked into place by hydrogen bonds

tertiary structure of protein

development of a 3D shape due to hydrophobic interactions (folding in of hydrophobic regions in an aqueous environment) and interactions among R groups, including hydrogen and ionic bonds and disulfide bridges

quaternary structure of a protein

in some proteins, the aligning of several polypeptide chains to form a single macromolecule

lipids

organic molecules consisting of carbon, hydrogen, and oxygen, but not in a set a ratio; include fats, oils, phospholipids, and steroids

fats/triglycerides

hydrophobic molecule consisting of three fatty acid chains and a glycerol

fatty acid chains

hydrocarbon chains (usually 16 or 18 Cs long) with a carboxyl group at one end that forms an ester linkage with glycerol

glycerol

hydrophobic molecule with a three carbon backbone and three attached hydroxyl groups, each of which can attach to a fatty acid change by a dehydration reaction called an ester linkage