chemistry review ap biology. chapter 2: the chemical context of life

Chemistry Review

AP Biology

Chapter 2: The Chemical Context of Life

Matter, Elements, and Compounds• Matter

• Anything that takes up space or has mass

• Element• “Pure” substance that cannot be broken

down• 92 naturally occurring in nature

• Compound• Two or more elements combined in a fixed

ratio

Life’s chemical requirements

• 25 of 92 elements are required• Carbon, nitrogen, hydrogen and oxygen

make up 96% of living matter

• Trace elements• Required in minute quantities• Some needed by all life forms• Others only by certain species

Atomic StructureWhat are these called?

These have what charge?

These have what charge?

Reading the periodic table

Isotopes and Radioisotopes• Isotopes

• Different forms of element due to # of neutrons

• Radioisotopes• Nucleus decays

spontaneously• Date fossils• Used to trace atoms

through metabolisms• Can damage cellular

molecules

Electron configuration• Energy levels

• Closest shell = least energy

• Farthest shell = most energy

• Energy is gained/lost by moving shells

• Orbital• 3-D place where e- are

usually found• 2 e- per orbital

• Valence electrons and shell• Outermost e-• Complete outer shell =

non-reactive

Chemical Bonding

• Interactions between atoms• Covalent – shared e-

• Non-polar covalent• Polar covalent

• Ion – charged atom• Anion (-)• Cation (+)

• Ionic bond – “steals” e-

Weak chemical bonds• Hydrogen bonds

• Hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

• Hydrogen bonds, ionic bonds and other weak bonds help form proteins

Reactants and Products

• Chemical reactions• Make and break chemical bonds, change composition of

matter• Reactants and products

• Starting and ending materials of chem rxns• Matter cannot be destroyed, but rearranged

• Most chemical rxns are reversible• Chemical equilibrium

• When reactions offset one another• Rxns still happening, but no effect on reactant/product

concentrations• Reactants and products are NOT equal in concentration

Chapter 3: Water and the Fitness of the Environment

Polarity and Hydrogen Bonding

• Polar molecule• Has opposite charges

at different ends

• Each water molecule can bond to a max of 4 others

Water Properties and Organisms• Water molecules stick together

due to hydrogen bonds• In liquid form, bonds are fragile• Each bond lasts one trillionth a

second

• Cohesion – bonds collectively hold substance together• How plants transport water• Hydrogen molecules tug on

molecules further down the vessel• http://faculty.pingry.org/thata/

pingry_upload/movies/water_macromolecules/cohesion_transport.mov

• Adhesion• Clinging of one

substance to another

• Surface tension• Measure of how

difficult it is to break the surface of a liquid

Water & Earth

• Moderates temperatures, contributing to habitability

• Kinetic energy• Energy of motion

• Heat• Measure of total kinetic energy due to

molecular motion

• Temperature• Intensity of heat due to avg. kinetic

energy

• Celsius scale

Water and Earth, cont.• Calorie

• Amount of heat energy needed to raise 1g of water by 1°C

• Kilocalorie• Amount of heat energy

needed to raise 1kg of water by 1°C

• Joule• = 0.239 calories (one

calorie = 4.184 J)

Water and Earth, cont.• Specific heat

• Amount of heat absorbed or lost for 1g of substance to change 1°C

• Specific heat of water is 10x that of iron

• Water resists change in temp

• High specific heat of water makes ocean temp stable for life

• Organisms made mostly of water resist temp changes

Water and Earth, cont.• Liquid molecules moving

fast to overcome bonds enter air as gas• Vaporization or

evaporation• Takes 580 calories of heat

to evaporate 1g of room temp water

• Evaporative cooling• As substance evaporates,

surface of remaining substance cools down

Ice Floats

• Why oceans and lakes don’t freeze

• Water is less dense as a solid than as a liquid• Expands when frozen• Reaches its greatest density at 4°C

• If ice sank, all ponds, lakes, and oceans would freeze solid

• How would this affect life?

Water is the solvent of life• Solution

• Solvent + solute

• Solvent• Does dissolving

• Solute• What dissolves

• Aqueous solution• Solution with water as solvent

• Water works well, but not for everything, otherwise could not be stored

Water is the solvent of life, cont.• Hydrophilic

• Has affinity for water• Hydrophobic

• Repels water• Mole

• Equal in # to molecular weight of substance in grams

• Molecular weight• Sum of all weights of all atoms in

a molecules• Avagadro’s number = 6.02 x 1023

(# molecules/mole)• Molarity

• Moles of solute per liter of solution

Organisms and pH• Organisms are sensitive to

pH

• Hydrogen ion• (H+) single proton with charge

of +1

• Hydroxide ion• (OH-) charge of -1

• Dissociation • Transfer of hydrogen atoms

pH• Acid

• Substance that increases H+ concentration of a solution

• Donate H+ to a solution• When hydrochloric acid is added to water HCl H+ +

Cl-

• Base• Substance that increases OH- of a solution

• Concentrations of H and OH• Products of OH- and H+ concentrations are always

10-14

pH, cont.• pH scale

• Range from 0-14, expresses OH- and H+ concentrations

• Defined as –log[H+]• pH declines as H+ concentration increases• Each pH unit represents 10-fold difference in

OH- and H+ concentrations

pH, cont.• Buffers

• Substances that minimize changes in pH• Accepts and donates ions in solution when

needed• Ex: carbonic acid

Acid Precipitation & Environment

• Threatens the fitness of environment

• Acid precipitation• Rain, snow, or fog more acidic than pH 5.6

• Harms environment by killing plants and animals

Chapter 4: Carbon and the Molecular Diversity of Life

Carbon• Prominent role in evolution of life

• Can form molecules that are large, complex, and diverse

• Complexity is demonstrated in hemoglobin

Organic Chemistry• Study of carbon compounds

• 30% of a cell is carbon based compounds

• Common ingredients in carbon compounds: H, O, N, S, P

Carbon atoms are a versatile building block

• Carbon has 6 electrons• Little tendency to gain or lose

e- and form ionic bonds• Completes valence shell by

making 4 covalent bonds• Makes large, complex

molecules possible• Carbon is compatible with

many different elements• CO2 is the source of carbon for

all the organic molecules found in organisms

Variation = Diversity• Variation in carbon

skeletons contributes to the diversity of organic molecules

• Carbon chains form the skeletons of organic molecules

• Hydrocarbons• Organic molecules

consisting only of carbon and hydrogen

Variation = Diversity, cont.

• Isomers• Compounds with same

molecular formula, but different structures, hence different properties

• Structural isomers• Differ in the covalent

arrangements of their atoms

Variation = Diversity, cont.

• Geometric isomers• All have same

covalent partnerships, differ in their spatial arrangements

• Stereoisomers• Molecules are mirror

images of each other

Functional Groups• Contribute to the molecular diversity of

life• Hydroxyl group

• H atom bonded to a O atom, in turn bonded to the C skeleton

• Alcohol: organic compounds containing hydroxyl groups

• Polar because of electronegative oxygen

• Carboxyl• O double bonded to a C, bonded to

hydroxyl

Functional Groups, cont.

• Amino• N bonded to 2 H atoms

• Sulfhydral• S bonded to H

• Phosphate• P ion convalently attached by O atom to C

skeleton

Chemical Elements of Life: Review

• Living matter consists of mainly C, H, O

• Chemical behavior of carbon makes it a versatile building block