AP BiologyAP Biology

Chemistry

Biology Is MultidisciplinaryBiology Is Multidisciplinary

• Emergent Properties = new properties that result from the interaction of components at a lower level of organization

– Properties NOTNOT derived by adding original properties together

• Life is emergent properties• Hierarchy of life

Elements and CompoundsElements and Compounds• Chemistry = study of matter and interactions

• All living thing are made of matter• Matter = has space and mass

• Mass = amount of matter

• Weight = measure of force of gravity on matter

Elements and CompoundsElements and Compounds

• Elements = matter that cannot be broken down into simple substances by ordinary means

– 92 natural; ? Artificial

• 96% of all life = CHON

• Other 4% = Ca, K, S, Na, Cl, Mg.

• Trace elements = minute quantities, essential to life (B, Cr, Cu, I, Fe, Mn, Sn, Zn)

Elements and CompoundsElements and Compounds• Compounds = molecules composed of 2 or more

elements chemically combined in a fixed ratio (NaCl)

• Compounds have different properties from their original elements

Atomic Structure/behaviorAtomic Structure/behavior• 2 basic parts: nucleus and electron ‘cloud’

• Nucleus = ‘center’; Protons (+1) and neutrons (0) All mass

• Electron ‘cloud’- electron(s) (-), negligible mass

Structure/behaviorStructure/behavior• Atomic mass and number are written to the left of

the symbol; mass on top

• Atomic number = number of protons (+)

• Atomic mass = no. protons (at. no.) + no. neutrons; mass number = average of all isotopes found in nature

• Isotope = same atom with different atomic mass due to differing numbers of neutrons

– May be unstable - radioactive

• Atomic mass and number are written to the left of the symbol; mass on top

• Atomic number = number of protons (+)

• Atomic mass = no. protons (at. no.) + no. neutrons; mass number = average of all isotopes found in nature

• Isotope = same atom with different atomic mass due to differing numbers of neutrons

– May be unstable - radioactive

Unstable IsotopesUnstable Isotopes

• Radiation - spontaneous decay of subatomic particles or energy

– Alpha (α), Beta (β), Gamma(γ)

– Transformation into a stable element

• Radiation may be detected

• Radiation - spontaneous decay of subatomic particles or energy

– Alpha (α), Beta (β), Gamma(γ)

– Transformation into a stable element

• Radiation may be detected

Structure/behaviorStructure/behavior

• 3 uses for radiation;

– Dating

– Tracers

– Cancer treatment

• 3 uses for radiation;

– Dating

– Tracers

– Cancer treatment

Radioactive Dating Radioactive Dating • N2 absorbs energy from cosmic radiation

– Converted into C14

– C14 spontaneously decays into C12

• Living organisms absorb N2 and stop when they die; C14 begins decaying

• Half-life = length of time it takes for half the substance to decay. Half-life is known; age can be calculated by knowing ratio of stable/radioactive isotope in fossils vs living organisms

Radiation DatingRadiation Dating

• C14’s half life = 5,700 Yr.

• Beta radiation rate = 15 rad/minute

• If the sample = 7.5 rads/min. = ½ gone or 5700 y.o.

• If the sample is ¼ gone, then the sample = 11,400 y.o.

• If 1/8 = ?

Radioactive TracersRadioactive Tracers

• Radioactive isotopes behave the same chemically

– P, N2, used to determine structure of DNA

– I2 in thyroid

• Radioactive isotopes behave the same chemically

– P, N2, used to determine structure of DNA

– I2 in thyroid

PET scan

Radiation: Cancer Radiation: Cancer

• Treatment of cancer: Co

• Cause cancer; Chernobyl, Tokaimura; 3-Mile Island?

Structure/behaviorStructure/behavior

• Energy Levels: Electrons and orbitals

• Arrangement of outer electrons (valence) determines how atoms interact with other atoms (Chemistry)

• Electrons have potential energy because of their position (potential) relative to the nucleus

• Energy Levels: Electrons and orbitals

• Arrangement of outer electrons (valence) determines how atoms interact with other atoms (Chemistry)

• Electrons have potential energy because of their position (potential) relative to the nucleus

• Energy = the ability to do work; move

• Potential = stored energy; due to position

• Energy = the ability to do work; move

• Potential = stored energy; due to position

• Kinetic = energy of motion• Kinetic = energy of motion

Energy

• Water on top of the hill = potential energy

• Energy flowing down the hill (gravity) has kinetic energy

• Water at the bottom of the hill has less potential energy

Structure/behaviorStructure/behavior

• Electron ‘shells’, ‘orbitals’ = distances that electrons are from the nucleus

• Electrons in the outer shells are more reactive and cause ‘chemical changes’

• Outer shell = ‘valence shell’

• Valence electrons = more reactive

• Electron ‘shells’, ‘orbitals’ = distances that electrons are from the nucleus

• Electrons in the outer shells are more reactive and cause ‘chemical changes’

• Outer shell = ‘valence shell’

• Valence electrons = more reactive

Energy Energy • Electrons in the atom have

potential energypotential energy– Position relative to the nucleus– Electrons farther away from the nucleus have

greater potential energy• Electrons can absorb or lose energy

BondsBonds

• Attractions of atoms or molecules to form new compounds

• Three types:

– Covalent

– Ionic

– Hydrogen

Structure/behaviorStructure/behavior

• Bonding = attractions formed between atoms caused by the interactions of valence electrons

• Number of bonds = no. of electrons gained/lost, shared to fulfill octet rule

• Bonding = attractions formed between atoms caused by the interactions of valence electrons

• Number of bonds = no. of electrons gained/lost, shared to fulfill octet rule

Structure/behaviorStructure/behavior

• Octet Rule = atoms are most stable when outer ‘shell’ has 8 electrons

• Four = do not gain or lose electrons (ions) but ‘share’

– Carbon, silicon

• Octet Rule = atoms are most stable when outer ‘shell’ has 8 electrons

• Four = do not gain or lose electrons (ions) but ‘share’

– Carbon, silicon

How Many Bonds Will Atoms How Many Bonds Will Atoms Form?Form?

•Carbon -Carbon - 4 •NitrogenNitrogen - 3•OxygenOxygen - 2 •Hydrogen - 1

What Are The Types of Bonds?What Are The Types of Bonds?

• Covalent• Ionic • Hydrogen

Covalent BondCovalent Bond

• Strongest type

• Electrons shared

• Diatomic molecules

• Carbon;

– 4 valence electrons

– May be single, double, or triple

– Si (?)

• Strongest type

• Electrons shared

• Diatomic molecules

• Carbon;

– 4 valence electrons

– May be single, double, or triple

– Si (?)

Covalent Bond

• Electrons may not be shared equally

• Polar - one atom may ‘share’ the electron(s) more; imbalanced bond

– Polar Covalent Bond

• Nonpolar Covalent Bond = (?)

Covalent bonds

Covalent BondCovalent Bond

• Polarity or non-polarity causes reactions between MOLECULES

Ionic BondsIonic Bonds

• Ionic Bond = formed between atoms that gain/lose valence electrons

• Not as strong as Covalent

• Usually only a few atoms or groups (polyatomic ions, CO3, PO4)

• Electrical charge; easily dissociated

– One cause of pH

• Ionic Bond = formed between atoms that gain/lose valence electrons

• Not as strong as Covalent

• Usually only a few atoms or groups (polyatomic ions, CO3, PO4)

• Electrical charge; easily dissociated

– One cause of pH

Ionic bonds

Ionic BondsIonic Bonds• Ions may dissociate easily (freely) in water • Causes the water to become an electrolyte• In living systems, the amount of (+) or (–)

is measured as pH• Nervous, muscular system

Hydrogen BondsHydrogen Bonds

• Attraction between (+) and (-) of adjacent molecule

• “Most” important in biology • Weakest of the three• Molecules have polar sites in

their structure

Bonds and Function and Function• Shape of the molecule created

by bonding forces determines function

• Ex. Proteins have specific shapes that allow only another molecule with the right shape to fit; – Makes life chemistry

possible

• Shape of the molecule created by bonding forces determines function

• Ex. Proteins have specific shapes that allow only another molecule with the right shape to fit; – Makes life chemistry

possible

Structure/behaviorStructure/behavior• Chemical equations are shorthand for reactions• Reactants and Products• Chemical formula vs. structural formula• Equilibrium

WaterWater

Water• Life evolved in water (oceans)• ¾ of earth covered with water• 70-90% of organisms are water• Properties of water make life possible• Philic = loving• Phobic = fearing• Hydro = water

Exists in all 3 states on the planet

Properties of WaterProperties of Water

• Adhesive

• Cohesive

• Surface tension

• High specific heat

• Expands as is freezes

• Universal solvent

Water: Hydrogen bonding

Water PropertiesWater PropertiesWater PropertiesWater Properties

• Adhesive = adheres to other substances hydrophilic substances (glass, metals)

• Cohesive = adheres to itself

• Adhesion and cohesion create Capillarity in trees (transpiration)

• Adhesive = adheres to other substances hydrophilic substances (glass, metals)

• Cohesive = adheres to itself

• Adhesion and cohesion create Capillarity in trees (transpiration)

Water- PropertiesWater- Properties

• Surface tension - beading,

• ex. waterstriders

High Specific Heat

• Heat = total kinetic energy (motion) created by moving molecules.

• calorie = amount of heat needed to raise the T of 1 g of water 1o C.

• Kilocalorie = 1000 cal.; Kcal or C• Specific heat of water is very high

– H bond absorb heat when broken and release heat when formed.

• Slow to change Temperature

• Heat = total kinetic energy (motion) created by moving molecules.

• calorie = amount of heat needed to raise the T of 1 g of water 1o C.

• Kilocalorie = 1000 cal.; Kcal or C• Specific heat of water is very high

– H bond absorb heat when broken and release heat when formed.

• Slow to change Temperature

Water: Specific Heat

• Water will act as a heat ‘sink’, traps heat during summer…

• Slowly releases heat during winter

• Moderates earth’s climate; coastal areas milder

High Heat of Vaporization

• Heat of vaporization = amount of heat energy needed to cause a liquid to evaporate; (water = 540 cal/g)

– H bonds must be broken before water molecules can absorb heat energy

• Heat of vaporization = amount of heat energy needed to cause a liquid to evaporate; (water = 540 cal/g)

– H bonds must be broken before water molecules can absorb heat energy

High Heat of Vaporization• Evaporative cooling = cooling of a surface

as a liquid evaporates• Molecules with the highest energy

evaporate fastest, – Molecules with less heat energy are left

behind (less heat = cooler) Radiators, dogs pant, Homeostasis

• Evaporative cooling = cooling of a surface as a liquid evaporates

• Molecules with the highest energy evaporate fastest, – Molecules with less heat energy are left

behind (less heat = cooler) Radiators, dogs pant, Homeostasis

Expands as it FreezesExpands as it Freezes• Water contracts as it

cools until 4oC then it expands (9%); becomes less dense (floats). Bodies of water freeze at the top; insulation for life below

• Colder water from bottom re-circulates nutrients to the surface (life)

• Water contracts as it cools until 4oC then it expands (9%); becomes less dense (floats). Bodies of water freeze at the top; insulation for life below

• Colder water from bottom re-circulates nutrients to the surface (life)

‘Universal’ Solvent

• Non-polar substances

• Due to Polarity; (+) end pulls (-) end

• Solution = mixture of two or more substances

– Air

– Solvent = dissolving agent (water); aqueous solution, alcohol – tincture

– Solute = substance being dissolved

• Non-polar substances

• Due to Polarity; (+) end pulls (-) end

• Solution = mixture of two or more substances

– Air

– Solvent = dissolving agent (water); aqueous solution, alcohol – tincture

– Solute = substance being dissolved

Measurement of SolutionsMeasurement of Solutions

• Percentage

• Molarity – measure of the amount of solute dissolved in the solvent

• pH – measure of H ions in the solution

Molarity

• Mole = 1 molecular weight dissolved in 1 liter of solvent (water)

– Ex. 1 mole of glucose = 180g dissolved in 1 liter of water. 1M glucose

• Molarity is convenient for combining substances and for describing concentration (1.0M, 0.5M, 0.1M)

• Mole = 1 molecular weight dissolved in 1 liter of solvent (water)

– Ex. 1 mole of glucose = 180g dissolved in 1 liter of water. 1M glucose

• Molarity is convenient for combining substances and for describing concentration (1.0M, 0.5M, 0.1M)

pH

• Measure of amount of H+ in solution

• Range of measure from 1-14

• 1-7 = ‘acid’

• 7-14 = ‘base’, ‘alkaline’ (alkalinity)

• Measure of amount of H+ in solution

• Range of measure from 1-14

• 1-7 = ‘acid’

• 7-14 = ‘base’, ‘alkaline’ (alkalinity)

pH

• In water, (H20) a hydrogen atom may dissociate from the oxygen to form:

H2O + H2O H30+ + OH-

H30+ = (hydronium)

OH- = hydroxide

pHpHpHpH

• In ‘pure’ water, the amount of H3O+ = OH- :

H2O + H2O H3O+ + OH-

• Equilibrium (not ionized)

• In ‘pure’ water, the amount of H3O+ = OH- :

H2O + H2O H3O+ + OH-

• Equilibrium (not ionized)

pH

In equilibrium, number of H+ in solution = 1/10,000,000

• 10-7

• 7

• Equilibrium = pH 7 = ‘neutral’

• ‘p’ = concentration

• pH = concentration of H+

pH

• In equilibrium: • H+ = 10-7 (1/10,000,000)• OH- = 10-7 (1/10,000,000)• Total of H+ + OH- = 10-14 (14)• If H+ = 1/1,000,000 = 10-6 (6)• OH- = 10-8

pH

• A change in pH number (7 to 6) is exponential (tenfold)

• 1/10,000,000 (1 in 10 million) to: 1/1,000,000 (1 in 1 million)

• 7 to 5 = 100 fold increase in H+• 5.5 to 8.5 = 1000x increase (major change)

– Pollution

pH

• Acids (‘acidic’) are substances that cause water to release H+ in solution (lower pH)

• Bases (alkaline) release OH- in solution• pH always totals 14; if pH = 5 then

concentration of OH = (?)• If pH = 9, then concentration of OH (?)

pH• Most biotic solutions = 6-8;

– Stomach = 1.5-2• Acid rain

• SO2, NO2 mix w/ water in atmosphere– Lowers pH of lakes, soil

pHpH

• Buffers = substance that prevents sudden, large changes in pH, weak acids or bases (bicarbonate)

Properties of WaterProperties of WaterProperties of WaterProperties of Water

• Cohesive; H bond• Adhesive; H bond• High specific heat; H bond• High heat of vaporization; H bond• Expands as it freezes• ‘Universal’ solvent; polarity