AP Biology Prep Course Unit 1Fundamental Biology Skills and Knowledge

This unit connects basic chemistry knowledge to molecular biology by exploring water’s properties, carbon as the basic element of life, and the functional groups of vital biological molecules. In addition, there is a brief review of Latin roots and how to use them to decipher complex biological terminology.

OverviewChemistry, biology and other sciences often overlap information in one form or another. A strong foundation of chemistry knowledge is essential to understanding biology at the molecular level.

MatterAll organisms on Earth are made of matter. Matter is defined as any substance that takes up space and has mass. Matter is made up of atoms of elements. An element is a pure substance that cannot be broken down to a simpler substance by chemical means. Examples of elements include hydrogen (H), copper (Cu) and oxygen (O). A compound contains two or more different elements in a fixed ratio. Examples include potassium chloride (KCl) and carbon dioxide (CO2).

In Figure 1 you can see how the human body and the Earth’s crust contain many of the same elements but in different proportions.

Water Is EssentialWater covers about 71% of the Earth and is essential for life. A water molecule consists of two hydrogen atoms and one oxygen atom connected by covalent bonds. See Figure 2.

A covalent bond occurs when one atom shares electrons with another atom. Molecules held together by covalent bonds can be polar or nonpolar depending on the nature of the atoms in the bonds and the symmetry of the molecule.

For example, water is a polar molecule. This means that one end of a water molecule has a partial negative charge and the other end has a partial positive charge. The partial charges are a result of each atom’s individual electronegativity value, which is simply a number that reflects the ability of an atom to attract electrons in a covalent bond. A more electronegative element will be more likely to attract the shared electrons. In the case of water, oxygen is more electronegative than hydrogen, so the electrons are not equally distributed between the atoms in the bonds. This creates a difference of charge across the molecule. See Figure 3.

Polar molecules attract or interact more strongly with other polar molecules due to the attraction of unlike charges. The positive end of a water molecule is attracted to the negative end of a different water molecule. When water molecules interact with each other, they form hydrogen bonds. See Figure 4. Hydrogen bonds contribute to the essential properties of water and its important role in the biochemistry of living organisms.

Cohesion and AdhesionHydrogen bonding allows water to have unique properties, such as cohesion and adhesion. Cohesion refers to water’s ability to form hydrogen bonds with other water molecules, while adhesion refers to water’s ability to form hydrogen bonds with other substances.

Both of these properties contribute to the high surface tension of water. Water molecules on the surface of water experience a pull from all the water molecules below the surface due to cohesion. For example, the water molecules at the top of the water in a beverage glass do not have water molecules surrounding them from every angle, so they cling more closely to the water molecules they are touching. Surface tension is what allows bugs to walk on water.

Cohesion, adhesion and surface tension are responsible for capillary action in plants, which is the process by which a plant takes up water against gravity without using energy. Cohesion holds water molecules together as they are pulled up through the plant to replace water that has been lost through the leaves. Adhesive forces between the water molecules and the hydrophilic walls of the xylem allow the water to move against gravity. See Figure 6.

Density of WaterWhen water is in a solid state, water molecules are arranged in a crystal formation. The hydrogen bonds in the crystal formation of ice are locked, whereas the hydrogen bonds in liquid water are continuously breaking and reforming, which allows the liquid water molecules to be closer together. Because of the rigid crystal formation, ice has fewer water molecules per a given volume of water, resulting in a lower density than liquid water. When ice and water are together, the ice will float because it is less dense. For example, in the winter, a lake or pond may have a frozen layer of ice on top, which allows life below the ice to survive beneath the frozen surface. This is a unique property of water since, in general, solids are usually denser than liquids. However, liquid water is denser than ice.

The Universal SolventWater is often referred to as the universal solvent because many substances are able to dissolve in water due to the polar nature of water molecules. Substances that are hydrophilic have an affinity or are attracted to water. Ionic solids are hydrophilic and readily break apart when mixed with water. For example, NaCl, sodium chloride, breaks apart into Na+ and Cl– ions when added to water. The positive ends of the water molecules, the hydrogens, surround the negative chlorine ion, while the negative ends of the water molecules, the oxygen, surround the positive sodium ion. See Figure 7.

Although it is called the “universal solvent,” water does not actually dissolve every substance. Hydrophobic substances are not attracted to water because they are nonpolar. A hydrophobic layer or membrane to protect tissues from dissolving in water surrounds most living tissue!

pH and Living OrganismsAs mentioned previously, water is composed of two hydrogen atoms and one oxygen atom. Sometimes a hydrogen atom that is part of a water molecule will leave its original molecule and join a different water molecule. When that happens, a hydrogen ion (H+) is transferred from one molecule to another. The hydrogen ion is a single proton with a 1+ charge. The water molecule that lost a proton is now a hydroxide ion (OH–) and the water molecule that gained a proton is now a hydronium ion (H3O+). A hydronium ion is also referred to as an H+ ion.

This property of water is important in biology as H+ and OH– are very reactive ions. Changes in their concentration can drastically alter cellular proteins and other molecules. Furthermore, changes in concentration of these ions are measured by the pH scale. See Figure 8.

The concentration of H+ ions is inversely related to the pH value. pH is the negative log of the hydrogen ion concentration:

pH = –log[H+]

A neutral aqueous solution has an H+ concentration of 10–7 and an equal concentration of OH– ions. To determine the pH value:

pH = –log10–7 = – (–7) = 7

Notice that as the pH value declines, the hydrogen ion concentration increases. By knowing the hydrogen ion concentration, the hydroxide ion concentration can also be determined. The pH scale goes from 0 to 14. If the solution has a pH of 4, the hydrogen ion concentration, [H+], is 10–4, which implies the hydroxide ion concentration [OH–] is 10–10 according to the equation:

[H+][OH–] = 10–14

A buffer is a solution containing a weak acid and its corresponding base. Buffers are essential in biological fluids because their role is to resist changes in pH when acids or bases are added.

CarbonLiving matter on Earth primarily consists of carbon, oxygen, hydrogen and nitrogen. There are also small amounts of sulfur and phosphorus in biological molecules. Lipids, proteins, DNA and carbohydrates are present in living matter. These large molecules are comprised primarily of carbon. Biological diversity at the molecular level results from carbon’s ability to form numerous molecules with different shapes and chemical properties.

Carbon is capable of bonding to many other atoms such as oxygen, hydrogen and nitrogen. Carbon can also bond to other carbon atoms to form long organic carbon chains. Chains consisting of only carbon and hydrogen are known as hydrocarbons. Hydrocarbon chains in lipids (fats) store energy for later use.

Important Biological Functional GroupsFunctional groups can replace one or more of the hydrogens bonded to the carbon skeleton of a hydrocarbon to create different types of organic molecules. These functional groups participate in chemical reactions and sometimes contribute to function by affecting the shape of a molecule. See Figure 9 for a table describing common functional groups.

All functional groups, with the exception of the methyl group, increase the solubility of a molecule. The phosphate functional group deserves special mention as it is extremely important in many cellular processes. This ionized group contains a phosphorus atom bonded to four oxygen atoms. See Figure 10. The phosphate group is important because molecules with phosphate groups are able to react with water to release energy.

Adenosine triphosphate, ATP, is a type of organic phosphate and the primary energy-transferring molecule in cells. It consists of three phosphate groups with adenosine attached to one end. When ATP reacts with water, it forms an inorganic phosphate and ADP, adenosine diphosphate. This chemical reaction releases energy that is used by the cell. See Figure 11.

Root Words, Prefixes, and SuffixesBiology is full of specific terminology, but there are many common root words, prefixes and suffixes. Many words in the English language are formed by taking basic words and adding different prefixes and suffixes to them. The basic words are known as root words. By learning common prefixes and suffixes it becomes easier to decipher meanings of new, unfamiliar words. Figure 12 is a chart of the most common root words, prefixes and suffixes used in biological sciences.

Scientific Root Words, Prefixes, And Suffixes

a-, an- ab-

not, without, lacking, deficient away from, out from

centi- centr-

hudredth center

-escent eso-

becoming inward, within, inner

-able capable of cephal- head eu- well, good, true, normalac- to, toward cerat- horn eury- widen-aceous of or pertaining to cerebr- brain ex- out of, away fromacou-, acous- hear cervic- neck extra- beyond, outsidead- to, toward chel- claw -fer- bear, carry, produceaden- gland chem- dealing with chemicals ferro- ironadip- fat chir- hand fibr- fiber, threadaero- air chlor- green -fid, fiss- split, divided intoagri- field, soil chondr- cartilage -flect, -flex bend-al having the character of chrom-, -chrome color flor- floweralb- white chron- time flu-,fluct-,flux flowalg-, -algia pain -chym- juice foli- leafalto- high -cid-, -cis- cut, kill, fall fract- breakambi- both circa-, circum- around, about -gam- marriageameb- change, alternation cirru- hairlike curls gastr- stomachamni- fetal membrane co- with, together geo- land, earthamphi-, ampho- both cocc- seed, berry -gen, -gine producer, formeramyl- starch coel- hollow -gene- origin, birthana- up, back, again coll- glue -gest- carry, produce, bearandro- man, masculine coni- cone -glen- eyeballanemo- wind contra- against -glob- ball, roundang- choke, feel pain corp- body gloss- tongueangi- blood, vessel, duct cort-, cortic- outer layer gluc-, glyc- sweet, sugarante- before, ahead of time cosmo- world, order, form glut- buttockanter- front cotyl- cup gnath- jawantho- flower counter- against -gon angle, corneranti- against, opposite crani- skull -grad- stepantrhopo- man, human cresc-, cret- begin to grow -gram, graph record, writing-ap-, -aph- touch crypt- hidden, covered grav- heavyapo-, ap- away from -cul-, -cule small, diminutive -gross- thickaqu- water cumul- heaped gymno- naked, barearchaeo- primitive, ancient cuti- skin gyn- female-ary, -arium denotes a place for something cyan- blue gyr- ring, circle, spiralarteri- artery -cycle, cycl- ring, circle -hal-, -hale breathe, breatharthr- joint, articulation -cyst- sac, pouch, bladder halo- salt-ase forms names of enzymes cyt-, -cyte cell, hollow container hapl- simpleaster-, astr- star dactyl- finger hector- hundred-ate verb form – the act of de- away from, down -helminth- wormanther- fatty deposit deca- ten hem- blood-ation noun form – the act of deci- tenth hemi- halfatmo- vapor deliquesc- become fluid hepar-, hepat- liveraudi- hear demi- half herb- grass, plantsaur- ear dendr- tree hetero- different, otherauto- self dent- tooth hex- sixbacter-, bactr- bacterium, stick, club derm- skin hibern- winterbarb- beard di-, dipl- (Latin) two, double hidr- sweatbaro- weight di-, dia- (Greek) through, across, apart hipp- horsebath- depth, height dia- (Latin) day hist- tissuebene- well, good digit- finger, toe holo- entire, wholebi- (Latin) two twice din- terrible homo- (Latin) man, human

bi-, bio- (Greek) life, living dis- apart, out homo- (Greek) same, alike-blast- sprout, germ, bud dorm- sleep hort- gardenbrachi- arm dors- back hydr- waterbrachy- short du-, duo- two hygr- moist, wetbrady- slow -duct lead hyper- above, beyond overbranchi- fin dynam- power hyph- weaving, webbrev- short dys- bad, abnormal, difficult hyphno- sleepbronch- windpipe ec- out of, away from hypo- below, under, lesscac-. bad echin- spiny, prickly hyster- womb, uteruscalor- heat eco- house -iae person afflicted with diseasecapill- hair ecto- outside of -iasis disease, abnormal conditioncapit- head -elle small -ic (adjective former)carcin- cancer -emia blood -chthy- fishcardi- heart en-, endo-, ent- in, into, within ign- firecarn- meat, flesh -en made of in-, il-, im-, ir- notcarp- fruit encephal- brain in-, il-, im-, ir- to, toward, intocarpal- wrist enter- intestine, gut in- very, thoroughlycata- breakdown, downward entom- insects -ine of or pertaining tocaud- tail -eous nature of, like infra- below, beneath-cell- chamber, small room epi- upon, above, over inter- within, insidecen-, cene- now, recent -err- wander, go astray intra- betweencente- pierce erythro- red -ism a state or condition

iso--ist

equal, same person who deals with

oo- opthalm-

egg eye

saur- schis-, schiz-

lizard split, divide

-it is inflammation, disease opt- eye sci- know-ium refers to a part of the body orb- circle, round, ring scler- hard-kary- cell nucleus -orium, -ory place for something -scop- look, device for seeingkel- tumor, swelling ornith- bird -scribe, -script writekerat- horn orth- straight, correct, right semi- half, partlykilo- thousand oscu- mouth sept- partition, sevenkine- move -osis abnormal condition -septic infection, putrefactionlachry- tear oste- bone sess- sitlact- milk oto- ear sex- sixlat- side -ous full of -sis condition, stateleio- smooth ov- egg sol- sun-less without oxy- sharp, acid, oxygen solv- loosen, freeleuc-, leuk- white, bright, light pachy- thick som-, somat-, -some bodylign- wood paleo- old, ancient somn- sleeplin- line palm- broad, flat son- soundlingu- tongue pan- all spec-, spic- look atlip- fat par-, para- beside, near, equal -sperm- seedlith-, -lite stone, petrifying path-, -pathy disease, suffering -spher- ball, roundloc- place -ped- foot spir-, -spire breathe-log- word, speech -ped- child -spor- seed-logist one who studies pent- five stat-, -stasis standing, placed, staying-logy study of per- through stell- starslumin- light peri- around sten- narrow-lys, -lyt, -lyst decompose, split, dissolve permea- pas, go stern- chest, breastmacr- large phag- eat stom-, -stome mouthmalac- soft pheno- show strat- stratmalle- hammer -phil- loving, fond of stereo- solid, 3-dimensionalmamm- breast phon-, -phone sound strict- drawn tightmarg- border, edge -phore,, pher- bear, carry styl- pillarmast- breast photo- light sub- under, belowmed- middle phren- mind, diaphragm super-, sur- over, above, on topmeg- million, great phyc- seaweed, algae sym-, syn- togethermela-, melan- black, dark phyl- related group tachy- quick, swift-mer part -phyll leaf tarso- anklemes- middle, half, intermediate physic- nature, natural qualities tax- arrange, put in ordermet-, meta- between, along, after phyt-, phyte platn tele- far off, distant-meter, -metry measurement pino- drink telo- endmicro- small, millionth pinni- feather terr- earth, landmilli- thousandth plan- roaming, wandering tetr- fourmis- wrong, incorrect plasm-, -plast- form, formed into thall- young shootmito- thread platy- flat -the-, -thes- putmole- mass pleur- lung, rib, side -thel- cover a surfacemono- one, single pneumo- lungs, air therm- heatmort- death -pod foot -tom- cut, slicemot- move ply- many, several toxico- poisonmorph- shape, form por- opening top- placemulti- many port- carry trache- windpipemut- change post- after, behind trans- acrossmy- muscle pom fruit tri- threemyc- fungus pre- before, ahead of time trich- hairmycel- threadlike prim- first -trop- turn, changemyriad- many pro- forward, favoring, before -troph- nourishment, one who feelsmoll- soft p[roto- first, primary turb- whirlnas- nose pseudo- false, deceptive -ul-, -ule diminutive, smallnecr- corpse, dead psych mind ultra- beyondnemat- thread pter- having wings or fins uni- oneneo- new, recent pulmo- lung ur- urineneprho- kidney puls- drive, push -ura tail-ner- moist, liquid pyr- heat, fire vas- vesselneur- nerve quadr- four vect- carrynoct-, nov- night quin- five ven-, vent- come-node knot radi- ray ventr- belly, underside-nom-, -nomy ordered knowledge, law re- again, back -verge turn, slantnon- not rect- right, correct vig- strongnot- back ren- kidney vit-, viv- lifenuc- center ret- net, made like a net volv- roll, wander

ob- against rhag-, -rrhage burst forth -vor- devour, eatocul- eye rhe-, rrhea flow xanth- yellowoct- eight rhin- nose xero- dryodont- tooth rhiz- root xyl- wood-ond form, appearance rhodo- rose zo-, -zoa animalolf- smell roto- wheel zyg- joined togetheroligo--oma omni-

few, little abnormal condition, tumor all

rubr- sacchar- sapr-

red sugar rotten

zym- yeast

onc- mass, tumor sarc- flesh

Summary An element is a pure substance that cannot be broken down to other substances. A

compound contains two or more different elements in a fixed ratio.

The hydrogen and oxygen atoms of an individual water molecule are connected via covalent bonds. Water molecules bond with each other via hydrogen bonds.

Water is polar. The oxygen carries a partially negative charge and the hydrogen carries a partially positive charge.

Water’s cohesive and adhesive properties, density, and ability to act as a universal solvent all contribute to life on Earth.

pH is an expression of [H+]. Hydrogen ion concentration varies because of water’s ability to form hydronium and hydroxide ions, which interact with other ions dissolved in water.

Functional groups can replace a bonded hydrogen in a hydrocarbon to create different types of organic molecules.

Molecules with phosphate groups are able to react with water to release energy.

Biological diversity at the molecular level results from carbon’s ability to form numerous molecules with different shapes and chemical properties.

Root words, suffixes and prefixes are helpful in determining meanings of unknown words.

AP Biology Prep Course Unit 2Cells: Structure and Function

This unit introduces cell structure and function and explains how cells carry out essential life functions such as energy transfer and transformation, gas exchange, waste disposal, growth, and how cells interact with their environment.

OverviewThe goal of this unit is to understand that cells are responsible for essential life functions such as energy transfer and transformation, gas exchange, waste disposal, growth, reproduction and environmental interaction. Cells contain internal structures that carry out specialized life functions.

Prokaryotic and Eukaryotic Cells — Similarities and DifferencesCells are classified as either prokaryotic or eukaryotic. Both prokaryotic and eukaryotic cells share the following characteristics: both are enclosed by a plasma (cellular) membrane and contain DNA and ribosomes. The plasma membrane serves as a selective barrier between the components of the cell and its surrounding environment. The DNA, while different in structure between the two cell types, carries the cell’s genetic information on chromosomes. The ribosomes are essential for protein synthesis.

Prokaryotic cells are microorganisms such as bacteria and archaea. They are smaller than eukaryotic cells with a diameter of 0.1 to 5 µm. Prokaryotes also lack a membrane-bound nucleus. Instead, the chromosome is concentrated in a region known as the nucleoid. Many bacteria also have circular DNA molecules called plasmids, which replicate separately from the other chromosome. Prokaryotes may have a flagellum, which is a long appendage used for locomotion. Cilia may also be present and is used to control a cell’s movement.

Eukaryotic cells include plant and animal cells. The DNA of a eukaryotic cell is found in the nucleus. It is surrounded by a double membrane called the nuclear envelope. The DNA is in linear form and condenses into tightly-packed chromosomes prior to replication.

Eukaryotic cells are also filled with cytoplasm; a thick solution consisting of water, salts and proteins. Cytoplasm is located between the nuclear membrane and the plasma membrane. Eukaryotes contain a variety of organelles throughout the cytoplasm. (Organelles are not present in prokaryotic cells.) Eukaryotes are much larger than prokaryotes with an average diameter of 10-100 µm.

Plant cells and animal cells are types of eukaryotic cells.

Eukaryotic Organelles — A Detailed LookEukaryotes have a variety of different organelles, each with a specialized structure and function.

The endomembrane system consists of the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, vacuoles and the plasma membrane. The purpose of this system is to allow cells to exchange, process and transport materials throughout the cell.

The endoplasmic reticulum (ER) consists of folded, connected, membrane-enclosed sacs called cisternae. There are two types of endoplasmic reticulum—rough and smooth. The functions of the smooth ER are different depending on the cell’s type. The smooth ER can synthesize lipids, store calcium ions, process carbohydrates and also remove toxins. The rough ER has attached ribosomes while the smooth ER does not. The function of the ER is to fold/synthesize proteins (that are produced by the ribosomes) into sacs called transport vesicles, which end up at the Golgi apparatus.

After being processed or “finished” in the Golgi apparatus, proteins and other products of the ER are again packaged into transport vesicles. These vesicles then travel to their final destination. For example, a secretory protein will be transported to the plasma membrane. The Golgi apparatus can also manufacture macromolecules, such as polysaccharides.

The endomembrane system in animal cells also includes lysosomes. Lysosomes are sacs of hydrolytic enzymes that digest macromolecules. Macromolecules consist of food, cellular macromolecules and damaged organelles.

Cells use specialized organelles, called mitochondria and chloroplasts, to convert energy into a usable form. Mitochondria perform cellular respiration, which is the metabolic process that uses oxygen to produce ATP. In plant and algae cells, chloroplasts are the site of photosynthesis. Photosynthesis is the process by which light energy is converted to chemical energy.

The genetic instructions for a eukaryotic cell are found in the nucleus. The nucleus is surrounded by the nuclear envelope, which is connected to the rough ER and perforated by nuclear pores, which regulate the movement of molecules into and out of the nucleus. The

nucleus stores chromosomes, which are structures made of chromatin (DNA and proteins). A nucleus can contain one or more nuclei, regions within the nucleus that are responsible for the production of ribosomes.

Ribosomes consist of two subunits: a small ribosomal subunit and a large ribosomal subunit. Each subunit is comprised of ribosomal RNA and proteins. Ribosomes can be free in the cytoplasm or bound to the endoplasmic reticulum or nuclear envelope.

CytoskeletonCells have a cytoskeleton, which is a network of fibers extending throughout the cytoplasm that consists of microtubules, microfilaments and intermediate filaments. Microtubules shape the cell, guide organelle movement and separate the chromosomes of dividing cells. They are the largest component of the cytoskeleton at 25 nm in diameter. In animal cells, microtubules provide strength to the cytoskeleton.

Microfilaments are 7 nm in diameter and consist of two intertwined strands. The primary role of microfilaments is to bear tension. They also aid in maintaining cell shape, muscle contraction, cytoplasmic streaming, cell motility and cell division. Cytoplasmic streaming is the flow of cytoplasm throughout the cell in order to distribute materials evenly.

Intermediate filaments are fibrous proteins supercoiled into thicker cables. They are typically 8–12 nm in diameter and function to maintain cell shape, anchor the nucleus and other organelles, and help form the nuclear lamina, which provides structure to the nuclear envelope. See Figure 4.

Cellular Membranes — Phospholipid BilayerThe plasma membrane functions as a selective barrier that allows oxygen, nutrients and wastes to pass into and out of the cell. The plasma membrane is a phospholipid bilayer, meaning it has two layers of phospholipids. Phospholipids are amphipathic in that they have a hydrophobic (water-fearing) region and a hydrophilic (water-loving) region. The head of a phospholipid, the hydrophilic region, contains a phosphate group, which makes it polar. The hydrophobic tail contains fatty acid hydrocarbon chains, which are nonpolar. See Figure 5.

When phospholipids are placed into a solution, the hydrophobic tails will orient themselves facing inwards and toward each other, while the hydrophilic heads will be exposed to the “water” area. Hence, a lipid bilayer is formed. See Figure 6.

Cells are constantly exchanging molecules and ions across their membranes. This process is regulated by the selective permeability of the plasma membrane. Nonpolar substances are soluble in the lipid bilayer and easily pass through. Conversely, polar molecules and ions generally cannot pass through the lipid bilayer without the aid of transport proteins.

Cellular Membranes — Membrane Proteins

Phospholipids and proteins are arranged in cell membranes according to the fluid mosaic model. The membrane itself is a fluid structure containing various proteins embedded in or attached to the phospholipid bilayer. The unsaturated hydrocarbon tails of the phospholipid bilayer are kinked, which prevents them from packing tightly together and therefore ensuring membrane fluidity. It is important to note that plant cell walls have a different structure composed of cellulose fibers embedded in other polysaccharides and proteins.

There are two main types of membrane proteins: integral proteins and peripheral proteins. Integral proteins are embedded in the lipid bilayer. Peripheral proteins are attached to the membrane surface and not embedded in the lipid bilayer at all. The purpose of membrane proteins is to aid in transport, enzymatic activity, signal transduction, cell–cell recognition, intercellular joining, and attachment to the cytoskeleton and ECM. Animal cells secrete glycoproteins and glycolipids, which are short chains of sugars on the exterior side of the plasma membrane that are linked to proteins or lipids and interact with the surface molecules of other cells to form the extracellular matrix (ECM). See Figure 7.

Passive TransportThe primary rule of diffusion is that in the absence of other forces, molecules or particles will move from a region of higher concentration to a region of lower concentration. This is known as moving down its concentration gradient. When diffusion occurs across a biological membrane, such as a cell membrane, this is called passive transport. Passive transport is the diffusion of a substance through a biological membrane with no expenditure of energy.

Osmosis is an example of passive transport. Osmosis is the diffusion of water across a selectively permeable membrane. Water will flow from an area of lower solute concentration (called a hypotonic solution) to an area of higher solute concentration (hypertonic solution). If two solutions have an equal solute concentration, they are considered isotonic. Water molecules move through specialized channels called aquaporins.

Facilitated diffusion is a type of passive transport that occurs when a transport protein increases the speed at which a solute moves across a membrane down its concentration gradient. An ion channel assists in the diffusion of ions across a membrane using a channel protein. See Figure 8.

Gated ion channels use carrier proteins that open and close in response to a stimuli. See Figure 9. Even though facilitated diffusion uses transport proteins, it is still considered to be passive transport because the solutes are moving down a concentration gradient.

Active TransportWhen a solute moves across a biological membrane against a concentration gradient (from an area of low concentration to high concentration), it requires energy. This is called active transport. Active transport uses carrier proteins and energy from ATP to move a solute against the concentration gradient. One common process in a cell that uses active transport is the sodium/potassium pump.

Exocytosis & EndocytosisLarge molecules require packaging in vesicles to cross the plasma membrane. This type of bulk transport requires energy. Exocytosis is the transport of large substances produced inside the cell to the outside of the cell. The cell encloses a substance in a vesicle that fuses with the plasma membrane. The plasma membrane evacuates the contents of the vesicle to the interior of the cell. See Figure 10.

Endocytosis is basically the reverse of exocytosis. The cell takes in substances by forming new vesicles in the plasma membrane. A region of the plasma membrane will cave inwards toward the center of the cell. As the pocket forms, it pinches off the plasma membrane releasing the vesicle into the cell.

Cellular CommunicationCommunication among cells is continuous. Cell junctions connect adjacent plant and animal cells. Plant cells have plasmodesmata, channels that pass through adjoining cell walls connecting chemical environments to allow water and small solutes to move freely between the cells. Animal cells have tight junctions, desmosomes and gap junctions:

• Tight junctions prevent leakage of material through the space between cells by using proteins to bind the membranes tightly to each other.• Desmosomes function as rivets, fastening cells together.• Gap junctions consist of proteins that surround a pore and allow the passage of materials between cells.

Neurons and Cell SignalingWhen a person touches something very hot, they remove their hand as quickly as possible. This is possible because the body uses the nervous system to send and receive messages from one area to another. The nervous system processes information in three stages: sensory input, integration and motor output. In this example, the sensory input would be the sense of touch that is feeling the hot item, integration is how the central nervous system processes that message, and motor output signals the body to immediately remove the hand from the hot surface.

The central nervous system (CNS) consists of the brain and spinal cord. The peripheral nervous system (PNS) is made of neurons that deliver messages to and from the central nervous system to the rest of the body. Neurons have three general regions that perform

specific functions: dendrites, axons, and the cell body, which contains the nucleus and organelles. The majority of neurons have dendrites that receive information from neighboring neurons. The axon is an extension of the neuron that transmits electrical signals along its length to the synapse, which is the space between the axon of one neuron and the dendrite of the next neuron. The electrical signal triggers chemicals called neurotransmitters to move across the synapse and communicate the message to the next neuron, which in turn activates another electrical signal.

Neurons also communicate via electrical signals. At rest, cells have a particular voltage. When a message is sent via electrical signal, gated ion channels open and close to allow ions to enter and exit the cell. This increases the voltage and transmits the message.

Relationship of Surface Area to VolumeWhy are cells so small? Each region of a cells’ surface can only pass a limited amount of substances through it per second. Therefore, the ratio of surface area to volume is extremely important. Smaller cells have a greater ratio of surface area to volume than larger cells. This is because as an object increases in size, its volume increases at a greater rate than its surface area. Cells need a surface area that is large enough to accommodate

their volume. This is why living organisms have many small cells as opposed to fewer large cells.

Summary Prokaryotic and eukaryotic cells are different. Prokaryotic cells lack nuclei and

membrane-bound organelles. Eukaryotic cells have organelles that perform specific functions.

Some organelles are found in both plant and animal cells while others are exclusive to one or the other.

In eukaryotes, genetic instructions are found in the nucleus.

The endomembrane system consists of the nucleus, endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, vacuoles and plasma membrane. Its function is to process proteins, perform metabolic functions, and provide transportation of materials.

Mitochondria (animal and plant cells) and chloroplasts (plant cells) convert energy from one form to another.

The purpose of a cytoskeleton is to provide structural support and assist in motility.

Cellular membranes are considered fluid mosaics. Amphipathic proteins, consisting of integral proteins, peripheral proteins and glycoproteins, are embedded within the phospholipid bilayer of the membrane.

Cellular membranes are selectively permeable.

Passive transport is the diffusion of molecules from high to low concentrations across a membrane and does not require energy.

Active transport requires energy to move solutes against a concentration gradient across a membrane.

Larger volumes or molecules are transported across the plasma membrane by exocytosis and endocytosis.

Cells are small because objects with a high surface area to volume ratio are more efficient at moving molecules (or solutes).

Neurons transmit sensory messages to the central nervous system where they are integrated and motor responses are transmitted back to the peripheral nervous system.

Neurons transmit signals both chemically and electrically.

AP Biology Prep Course Unit 3

The Cell CycleThis unit illustrates how cells control their growth, and how they divide through the process of mitosis. It also explores the development and differentiation of the single-celled zygote into specialized cells that form different tissues and organs. Finally, it discusses what happens when cell cycle controls fail.

OverviewThe goal of this unit is to understand that cells of multicellular organisms continuously divide to make more cells for growth and repair. Furthermore, in multicellular organisms, the single celled zygote will continue to divide and differentiate into specialized cells that form different tissues and organs.

Cell Cycle Phases

Dividing cells are always in one of two phases: the mitotic phase or interphase. The mitotic phase (M phase) consists of mitosis and cytokinesis. Interphase consists of G1, S and G2 phases. In Figure 1 below, you can see that the mitotic phase (mitosis and cytokinesis) is relatively short compared to interphase. Cells spend approximately 90% of their time in interphase.

The process of mitosis copies and distributes DNA of a cell into two identical daughter cells. Cytokinesis is the division of the cytoplasm amongst the two daughter cells.

The G1 phase of interphase stands for “gap 1.” During the G1 phase, the cell grows and makes proteins that are necessary for DNA replication. During the S phase, also known as the synthesis phase, the chromosomes duplicate. Therefore, the quantity of DNA in the cell at that time has doubled. During the G2 phase of interphase, the cell continues to grow and proteins are synthesized that are necessary for mitosis.

During mitosis, the nucleus divides and DNA is distributed into two identical daughter cells. The cytoplasm is divided between the daughter cells through a

process called cytokinesis. Each daughter cell continues through the cell cycle starting back at the G1 phase.

The timing and frequency of cell division varies between different cells, tissue, organs and even species. Humans, for example, have regions where cells divide frequently such as the skin and esophagus. Conversely, in other areas of the body, such as the liver, cells can divide but only do so to repair damaged tissue. Furthermore, other cell types, such as nerve cells, never divide in a mature human. Cells that do not divide enter a phase called G0.

ChromosomesCell division is part of the cell cycle. The result of a cell going through the cell cycle is the production of two genetically identical daughter cells.

A cell’s DNA or genetic information is called its genome. In order for mitosis to occur successfully, the genetic material (DNA) must condense into structures called chromosomes. Genes are found within DNA and carry information that specify an organism’s inherited traits. The DNA and proteins that make up chromosomes are called chromatin. Each chromosome contains two identical sister chromatids. Sister chromatids are held together at the centromere. See Figure 2.

Human somatic cells (all cells except reproductive cells) contain 46 chromosomes, two sets of 23, one inherited from each parent. Reproductive cells, known as gametes, have half as

many chromosomes at 23. Different eukaryotic species have a different characteristic number of chromosomes. For example, chimpanzees have 48 chromosomes per somatic cell.

Mitotic Phase

The mitotic phase includes mitosis and cytokinesis. Mitosis is the cell cycle process during which duplicated chromosomes separate into two identical daughter cells. It is characterized by five stages: prophase, prometaphase, metaphase, anaphase and telophase. Cytokinesis is a division of the cytoplasm and follows mitosis. Animal cells perform cytokinesis by cleavage and plant cells form a cell plate.

The Five Stages of Mitosis Prophase is the first stage of mitosis. The chromatin condenses into discrete

chromosomes and the nucleolus disappears. The mitotic spindle begins to form as microtubules extend from a region called the centrosome. The centrosome contains centrioles, but these are not necessary for the spindle to form. In fact, plant cells do not have centrioles, but still form a mitotic spindle. The short microtubules on the non-spindle side of the centrosome are called asters.

Prometaphase is the second stage of mitosis. The nuclear envelope breaks apart and the spindle microtubules attach to a group of proteins associated with the centromere of each chromosome called a kinetochore. Each chromosome has two kinetochores. When a microtubule attaches to a kinetochore, it pulls the chromosome towards that microtubule’s pole. At the same time, a microtubule from the opposite pole attaches to the other kinetochore of the same chromosome, causing a pull in the opposite direction.

Metaphase is the third stage of mitosis. The spindle is complete and the chromosomes that are attached to the microtubules by their kinetochores align at the metaphase plate due to the “tug-of-war” described above. At this time, the asters extend to the plasma membrane.

Anaphase is the fourth stage of mitosis. The proteins holding the sister chromatids together deactivate allowing each chromosome to separate. The resulting daughter chromosomes begin "walking" towards opposite poles of the cell and the

kinetochore microtubules shorten. At the same time, the non-kinetochore microtubules reduce the overlap between them to elongate the entire cell.

Telophase is the final (fifth) stage of mitosis. The daughter nuclei form, the daughter chromosomes uncoil, and cytokinesis begins. Animal cells pinch at the cleavage furrow to separate into daughter cells. Plant cells develop a cell plate that fuses with the cell membrane to become a new cell wall between the daughter cells.

Prokaryotes and Cell Division EvolutionEukaryotes divide by mitosis, but prokaryotes, such as bacteria, divide using a process called binary fission. In binary fission, chromosomes replicate and move to opposite sides of the cell. Then the cell separates into two identical daughter cells. Binary fission also occurs in single-celled eukaryotes, such as Amoeba.

There is evidence that prokaryotes existed on Earth over a billion years before eukaryotes. It is plausible that mitosis evolved from the mechanisms of prokaryotic cell division.

Cell Cycle Control SystemsIt is necessary for cells to have checkpoints throughout the cell cycle to ensure that cells are replicating and dividing properly. If cells do not replicate and divide properly, then the growth and function of a cell may be adversely affected. For example, if the proteins that regulate cell division are not functioning properly, the result could be the replication and division of cancer cells.

The cell cycle is controlled by specific signaling molecules found in the cytoplasm. These molecules verify that necessary steps in the cell cycle have been accurately completed before the cell continues to the next step of the cycle.

There are three checkpoints of the cell cycle control system: G1, G2 and M. In mammals, the first and most important checkpoint is the G1 checkpoint. If a cell makes it through the G1 checkpoint, it will likely complete the subsequent stages and divide. If it does not, it will exit the cycle and remain in the G0 phase.

If the conditions are right, cyclin-dependent protein kinases (Cdks) allow a cell to proceed through the G1 and G2checkpoints. Cdks are present at constant concentrations and spend a majority of the time in an inactive form. To be active, Cdks must be attached to a cyclin. A cyclin is a protein that is present in fluctuating concentrations depending on the time of the cell cycle. Cyclin-dependent kinases require cyclin to function. Their activity level fluctuates based on the cyclin concentration in the cell. Several types of Cdk-cyclin complexes form during the cell cycle. One example is the complex called the maturation-promoting factor (MPF). MPF is formed when the cyclin level rises during the S and G2phase, and then abruptly decreases during the M phase. MPF triggers the cell to proceed past the G2 checkpoint initiating and regulating mitosis. See Figure 8.

The M checkpoint is the final checkpoint in the cell cycle. In order to pass the M checkpoint, all chromosome kinetochores must be attached to the spindle at the metaphase plate. Once attached, enzymes cause the sister chromatids to separate. This results in daughter cells with the appropriate number of chromosomes.

The Loss of Cell Cycle ControlEach checkpoint determines whether or not all of the components and conditions have been met for cell division to proceed. If the cell is halted at the G1 checkpoint, the cell never progresses to the synthesis phase during which the DNA is replicated. At the G2 checkpoint, any problems in the replicated DNA trigger the cell to halt in G2 until either repairs are made or apoptosis, cell death, is prompted. If an error is detected at the M checkpoint, mitosis is halted until repairs are made. If repairs are not possible or take too long at any of the checkpoints, apoptosis is triggered and the cell dies.

When these checkpoints fail and there is a rapid, uncontrolled growth of cells, cancer is a common result. Cancer cells exhibit abnormal traits and behaviors such as excessive division, unusual numbers of chromosomes, abnormal cell surfaces, detachment from neighboring cells and the extracellular matrix, and the ability to secrete molecular signals that attract a blood supply to provide a steady stream of nutrients. Detachment and a readily available supply of nutrients allow cancer cells to grow and spread to other areas, making the cancer malignant (harmful).

Normal cells require growth factors, proteins that stimulate cell division. However, cancer cells grow and divide even when growth factors are depleted or absent. Normal cells stop dividing when the cells become crowded; this is called density-dependent

inhibition. Cancer cells do not exhibit density-dependent inhibition and will grow in clumping, overlapping layers of cells.

Cancer treatments are used to attack weaknesses in cancer cells. For example, radiation damages the DNA in cancer cells, which lack the ability to repair such damage. Chemotherapy treatments interfere with the cell cycle and are toxic to actively dividing cells. For example, a chemotherapy drug may freeze mitotic spindles and thus prevent mitosis from proceeding beyond metaphase.

Gene Expression and Cell TypesAs a multicellular organism develops from a zygote, it grows more cells through mitosis. Those cells become specialized through cell division, cell differentiation and morphogenesis. First, the zygote goes through a series of cell divisions that result in a copious volume of cells. Next, during embryonic development, cells undergo cell differentiation where they become specialized in structure and function and are organized into tissues and organs. The process that gives an organism its shape is called morphogenesis. It is important to note that cells differ in structure and function because they express different portions of a common genome and not because they contain different genes.

Two processes direct cells to express particular genes during early development. In the first process, maternal substances within the egg’s cytoplasm (mRNA, proteins, organelles, etc.) called cytoplasmic determinates influence early development directly. Once fertilized, early mitotic divisions distribute the zygote’s cytoplasm into daughter cells. The cytoplasmic determinants are different from cell to cell because the cytoplasm divides without making additional cytoplasm. The different cytoplasmic determinants in each cell help to regulate development by regulating gene expression during cell differentiation.

The second process is called induction. During induction, gene expression is controlled through environmental signals sent from one cell to another. Signals from surrounding embryonic cells, such as contact between cell surfaces and binding of growth factors secreted by other cells, cause changes in target cells. This creates regions of differentiated cells.

Summary There are two main phases in the cell cycle—interphase and the mitotic phase: 

– Interphase consists of G1, S and G2 stages. – The mitotic phase consists of mitosis and is followed by cytokinesis.

DNA is packaged in chromosomes. Human somatic cells have 46 chromosomes and reproductive cells (gametes) have 23.

Mitosis consists of five stages: prophase, prometaphase, metaphase, anaphase and telophase.

Cells must have control mechanisms to control division so damaged cells do not continue to divide. There are three main checkpoints in the cell cycle control system: G1, G2 and M.

When cells no longer respond or follow cellular control mechanisms or checkpoints, cancer cells may develop.

Cells differ in structure and function because they express different portions of a common genome. They do not contain different genes. When different genes are expressed, different proteins are produced.

Cells are signaled to express genes by cytoplasmic determinates and induction.

AP Biology Prep Course Unit 4

Meiosis: Heredity and VariationThis unit introduces heredity and genetic variation. The stages of meiosis are illustrated and explained. The content explores how meiosis results in offspring with unique combinations of genes from their parents. In other words, offspring inherit traits from each parent but do not become an exact replica of either parent.

OverviewThe goal of this unit is to understand heredity and variation. We will explore how meiosis results in offspring with unique combinations of genes from their parents. In other words, offspring inherit traits from each parent but do not become an exact replica of either parent.

HeredityHeredity is the transfer of traits from one generation to the next. Inherited traits are transmitted on genes. Each gene in an organism’s DNA is found at a specific location on a chromosome called a locus. Humans inherit one set of chromosomes from their mother and the other set from their father, which leads to offspring that differ in appearance from each other and the parents.

Sexual reproduction combines a set of genes from each parent resulting in genetically diverse offspring. Conversely, asexual reproduction results in offspring that are genetically identical to the parent by mitosis. It simply copies all of its genes to its offspring without fusion of gametes.

Haploid and Diploid CellsA human somatic cell contains 46 chromosomes—2 sets of 23. Two chromosomes that compose a pair have the same length, centromere position, staining pattern and genes and are called homologous chromosomes. We inherit one chromosome of each pair from each parent. Therefore, of the 46 chromosomes in our somatic cells, there are two sets of 23 chromosomes. There is a maternal set of 23 chromosomes and a paternal set of 23 chromosomes, resulting in 46 total.

The number of chromosomes present in a single set is represented by n. A cell that has two chromosome sets is called a diploid cell, represented by the number 2n. Humans have a diploid number of 46 (2n = 46), which is the number of chromosomes present in our somatic cells. Conversely, gametes (reproductive cells) contain a single set of chromosomes and are known as haploid cells represented by n. In humans, the haploid number is 23 (2n = 46 so n = 23). Different species have different diploid numbers.

Human Life CycleThe human life cycle begins with fertilization. When a haploid sperm from the father fuses with a haploid egg from the mother, the fusion of their nuclei is called fertilization. The fertilized egg is called a zygote.The zygote is diploid because it contains two sets of chromosomes. The zygote develops by mitosis to create all the somatic cells of the human body. See Figure 1 for an overview of the human life cycle process.

The only cells that are not a result of mitosis in the human body are the gametes that develop from germ cells in the gonads. Gametes are haploid and not diploid because their offspring’s zygote must contain cells with the correct number of chromosomes. If two somatic diploid cells fused to make a zygote, those cells would each contain 92 chromosomes. This result would double the number of chromosomes present in each cell in the next generation. Meiosis reduces the number of sets of chromosomes by half in the gametes to counterbalance the doubling that occurs during fertilization. This process is essential for gamete formation. Gametes are the only haploid cells in the human body and thus contain 23 chromosomes.

The human zygote has 22 pairs of autosomes and two sex chromosomes, which determine the biological sex of the offspring. A zygote with a pair of X chromosomes will be female, while a zygote with one X and one Y chromosome will be male. The Y chromosome contains the SRY gene, which controls the release of hormones. These hormones signal the development of the male during prenatal development.

MeiosisBefore getting into the details of meiosis, it is important to understand some terminology. Sister chromatids are two copies of the same chromosome, which was replicated during interphase. The sister chromatids are attached by a centromere to make one duplicated chromosome. Furthermore, a homologous pair is two chromosomes—one from each parent. See Figure 2.

Unlike mitosis, meiosis has two cell divisions known as meiosis I and meiosis II that produce four haploid daughter cells. During meiosis I, the number of chromosomes is reduced from diploid to haploid.

Phases of Meiosis Prophase I: Homologous chromosomes pair and exchange segments of DNA. Paired

homologs become physically attached to each other by a protein structure called the synaptonemal complex. This state is known as synapsis. Crossing over is the exchange of corresponding segments of DNA between nonsister chromatids. The site of the crossover is known as the chiasma. See Figure 3.

Metaphase I: Chromosomes line up by homologous pairs on the metaphase plate. See Figure 4.

Anaphase I: Each pair of homologous chromosomes separates towards its respective pole. Sister chromatids remain connected. See Figure 5.

Telophase I and Cytokinesis: During cytokinesis, the cytoplasm separates. Two haploid cells form and each chromosome contains two sister chromatids. See Figure 6.

Meiosis II: Prophase II through Cytokinesis II: Similar events occur during meiosis II. However, there is no crossing over. The main activity of meiosis II is when the sister chromatids finally separate. This produces four haploid daughter cells containing unduplicated chromosomes. See Figure 7.

Mitosis vs. Meiosis—Similarities and DifferencesBoth types of cell division begin with a diploid parent cell that contains a duplicated set of chromosomes. The main difference between mitosis and meiosis is that mitosis preserves the number of chromosome sets producing cells that are genetically identical to the parent. If a cell that has 46 chromosomes undergoes mitosis, the resulting cells will also have 46 chromosomes. Meiosis reduces the number of chromosomes from diploid cells to haploid cells that are genetically different from the parent. If a cell that has 46 chromosomes undergoes meiosis, the resulting cells will have 23 chromosomes. Two daughter cells are produced in mitosis while four are produced in meiosis.

Three unique events occur in meiosis I that do not occur in mitosis:

Synapsis and crossing over occur during prophase I.

Homologous pairs gather at the metaphase plate. In mitosis, individual chromosomes gather at the metaphase plate.

Separation of homologs in anaphase I. Sister chromatids remain together at the centromere until they separate during meiosis II.

Genetic Variation and Contribution to EvolutionChromosomal behavior during meiosis and fertilization is responsible for the majority of genetic variation. There are three main factors that contribute to genetic variation among sexually reproductive species—independent assortment, crossing over and random fertilization.

During metaphase of meiosis I, homologous chromosomes orient randomly on the metaphase plate. Each homologous pair consists of one maternal and one paternal chromosome. It is completely random whether or not a particular maternal or paternal chromosome is nearest a given pole. Therefore, there is a 50% chance a particular daughter cell will inherit the maternal chromosome and a 50% chance it will inherit a paternal chromosome. In Figure 8, you can see that the paternal chromosome of homologous pair “A” will move towards pole 1 and the maternal chromosome will move towards pole 2.

Furthermore, each pair of homologous chromosomes align on the metaphase plate independently of the other chromosomes. In Figure 8, homologous pairs A, B and C are not influenced by each other. Whether or not the paternal or maternal chromosome moves towards pole 1 in homologous set “A” will not affect the orientation of the chromosomes of homologous pairs B and C and so on. This is called the law of independent assortment.

The number of possible different daughter cells is the number of chromosomes in a homologous pair (in most cases 2) raised to the number of haploid chromosomes (n):

2n = number of combinations possible for daughter cells

In Figure 8, the haploid number of chromosomes per cell is three. Since 23 = 8, there would be eight possible daughter cells.

Crossing over occurs in prophase I of meiosis I. This results in recombinant chromosomes, one chromosome carrying genes from each parent. Therefore, each chromosome in a gamete cannot be exclusively maternal or paternal. Crossing over is important because combining DNA from two parents in a single chromosome results in genetic variation in sexual life cycles.

Humans have a haploid number of 23. Therefore, the possible combinations of maternal and paternal chromosomes is 8.4 million. When taking fertilization into account, there are approximately 70 trillion diploid combinations (223 × 223). This does not account for the variations resulting from crossing over, which increases the number of possibilities exponentially. Therefore, each zygote is genetically unique.

Summary Heredity is the transmission of traits from one generation to the next.

Sexual reproduction combines a set of genes from two parents resulting in genetically diverse offspring.

Two chromosomes that have the same length, centromere position, genes and staining pattern are called homologous chromosomes.

When a haploid sperm from the father fuses with a haploid egg from the mother, the fusion of their nuclei is known as fertilization. The fertilized egg is called a zygote.

Gametes are the only haploid cells in the human body and contain 23 chromosomes.

Three unique events occur in meiosis I that do not occur in mitosis: – Synapsis and crossing over during prophase I. – Homologous pairs gather at the metaphase plate. In mitosis, individual chromosomes gather at the metaphase plate. – Separation of homologs in anaphase I. Sister chromatids remain attached at the centromere.

Meiosis creates the genetic variation that is responsible for the development of many different traits and phenotypes that may be better suited to improve evolutionary fitness.

AP Biology Prep Course Unit 5

Mendelian Genetics and Molecular Genetics

OverviewThe purpose of this unit is to describe the importance of genetics and inheritance. Genetic information is transferred in the form of DNA. The information from DNA determines the structure of various molecules that are responsible for heritable physical characteristics of organisms.

InheritanceGenetics is the study of genes. Genetics explains how genes are inherited resulting in the expression of different traits. Genes are a region of nucleotides that code for a protein. They are passed to the next generation by meiosis and sexual reproduction.

Mendelian GeneticsGregor Mendel is considered the father of modern genetics. Mendel studied the inheritance of traits using pea plants. To begin, we must first understand some terminology. A character is a heritable feature that is different among individuals. A trait is each variant of that character. For example, flower color is the character and the colors white and purple are the traits.

Through Mendel’s work, two laws of inheritance were developed. The Law of Segregation says genes have alternate forms called alleles. For example, the gene for flower color has various alleles that combine to determine whether the flower is purple or white. The combination of alleles is the genotype, while the color of the flower (the expressed trait) is the phenotype. Remember, diploid organisms have two copies of each chromosome and therefore two alleles for each gene. In diploid organisms such as humans, the two alleles separate during meiosis resulting in each sperm or egg carrying one allele from each pair. The offspring then inherits one allele from each parent.

Homozygotes have identical alleles of a given gene, such as AA (homozygous dominant) or aa (homozygous recessive). Heterozygotes have two different alleles, such as Aa. In the

case of heterozygotes, the phenotype of the dominant allele will always be expressed over the recessive allele. It is important to note that the law of segregation only follows one characteristic. Figure 1 displays a Punnett square of possible outcomes of a cross between two heterozygotes. During this process, the alleles separate so the offspring inherits only one from each parent. Therefore, the offspring will be either AA, Aa or aa.

The Law of Independent Assortment states that each pair of chromosomes segregates independently of all other chromosome pairs during gamete formation. Therefore, multiple characters could be studied at the same time. The Law of Independent Assortment explains that when two characters are analyzed together, each pair of alleles assort independently without influencing each other. This was supported by the dihybrid cross experiments Mendel performed using peas.

A dihybrid cross studies two traits—in this case seed shape and color. One parent expressed round yellow peas (RRYY) and the other parent expressed wrinkled green peas (rryy); this is the P generation. When Mendel crossed the P generation, an F1 generation was produced with a 100% round and yellow phenotype with a RrYy genotype. Since Mendel realized the entire F1 generation was the RrYy genotype, he crossed two F1 plants to produce an F2generation. This cross produced an F2 generation with four phenotypes in a 9:3:3:1 ratio confirming that alleles for seed shape are expressed independently of alleles for seed color. See Figure 2.

DNA StructureIn the 1950s, James Watson and Francis Crick began building the model of the double helix structure of DNA based on Chargaff’s base pairing rules and Rosalind Franklin’s work with X-ray diffraction photographs of DNA.

Watson and Crick’s research resulted in the discovery that DNA is made of two nucleotide chains forming a double helix. A nucleotide consists of a nitrogenous base, deoxyribose sugar and a phosphate group. In Figure 3, 1'–4' are used to designate carbon (C) atoms at the corners of the ring structure.

As mentioned previously, DNA forms a double helix. That double helix makes one complete turn every 3.4 nm in length and each base is 0.34 nm apart. DNA is also considered to be antiparallel, which means that the subunits run in opposite directions. To elaborate, one strand runs in the 5' to 3' direction while its complementary strand runs in the 3' to 5' direction. See Figure 4.

There are four different nucleotides: adenine (A), guanine (G), cytosine (C) and thymine (T). Adenine and guanine are considered purines, which have two organic rings, while cytosine and thymine are considered pyrimidines with a single organic ring. See Figure 5.

Fellow scientist Edwin Chargaff discovered that the composition of bases varies between species. However, he noticed that the number of adenine bases always equaled the number of thymine bases and the number of cytosine bases always equaled the number of guanine bases. Therefore, he was able to infer that adenine bonds to thymine and cytosine bonds to guanine. The bases form hydrogen bonds to make complementary base pairs.

DNA ReplicationDNA replication occurs via the semiconservative model. This means that the replicated double helix consists of one strand from the parents and one newly synthesized DNA strand. In order for DNA replication to occur the double helix has to uncoil. The first step of the replication process is the separation of the two DNA strands by the enzyme helicase. Once separated, each parental strand serves as a template strand to determine the order of the nucleotides along a new complementary strand. The complementary nucleotides align

and are connected at the sugar phosphate backbone to form new daughter DNA strands. See Figure 6.

Replication forks are found at the edges of the replication bubble and appear in a Y-shape. This is where the parental strands are separating. See Figure 7.

Helicases are enzymes that untwist and separate the two strands at the replication fork. Once the parental strands are separated, single strand binding proteins bind to the unpaired DNA strands, keeping them from re-pairing. To initiate DNA synthesis, a short RNA chain called primer is synthesized by the enzyme primase. Enzymes known as DNA

polymerases catalyze the synthesis of new DNA by adding nucleotides to the template strand.

DNA polymerases can add nucleotides only to the free 3' end of a primer or growing DNA strand. This is called the leading strand and DNA polymerase III synthesizes continuously on the leading strand. The lagging strand requires a few extra steps and is synthesized in short Okazaki fragments that are later joined together by DNA ligase. 

MutationsA genome contains all of the coding regions (genes) and noncoding regions of genetic material. Any time there is a change in the nucleotide sequence of a genome a mutation has occurred. A silent mutation causes very few or no changes in the resulting protein. Silent mutations can occur in a coding or noncoding region. When a silent mutation takes place in a coding region, it will code for the same amino acid as the original nucleotide sequence. In the example below, a mutation has occurred in the third position. However, it still codes for the same amino acid, so it is a silent mutation. See Figure 8.

An insertion mutation adds a piece of DNA that was not previously in the sequence. Conversely, a deletion removes a piece of DNA from the original sequence. Both types of mutations may result in a functional or nonfunctional protein. Missense mutations are mutations of one nucleotide that results in a different amino acid being produced. Missense mutations often have little effect on the protein produced because the new amino acid usually has similar properties to the amino acid that was replaced. Nonsense mutations replaces a nucleotide that results in a stop codon and translation is terminated prematurely resulting in a nonfunctional protein.

Insertions and deletions are frameshift mutations that occur in any quantity of bases that is not a multiple of three. If one base is inserted, it will shift the reading frame to result in a protein that is different from the original. See Figures 9a and 9b.

DNA Repair MechanismsDNA polymerase not only moves along a single strand of DNA forming the complementary strand, but it also proofreads for errors. DNA polymerase verifies that the newly formed double stranded DNA molecule contains all the proper bases. If any are missing or incorrect, they are corrected before DNA polymerase moves on.

DNA mismatch repair (MMR) is an evolutionarily conserved process that corrects mismatches generated during DNA replication that have escaped proofreading. When a mismatch repair occurs, enzymes remove and replace incorrectly paired nucleotides that were missed by DNA polymerase proofreading. Sometimes errors occur that involve more than one nucleotide. In these cases, a DNA fragment containing damage is cut out by a nuclease enzyme. This is known as a nucleotide excision repair.

Gene to ProteinGene expression is the process by which DNA directs the synthesis of proteins. The expression of genes that code for proteins occurs in two stages—transcription and translation. Transcription is the synthesis of RNA using the information in the DNA. This RNA is processed into mRNA or messenger RNA because it carries a genetic message from the DNA to a ribosome for protein synthesis. Transcription and RNA processing take place in the nucleus of the cell. Translation is the synthesis of a polypeptide using the information in the mRNA. Translation occurs in the ribosomes. See Figure 10 for an overview.

TranscriptionRemember that one strand of DNA runs in the 5' to 3' direction, while the complementary strand runs in the 3' to 5' direction. During transcription, an enzyme called RNA polymerase separates the two strands and joins the complementary RNA nucleotides to the DNA template strand to form pre-mRNA.

Transcription exists in three stages:

• Initiation. The transcription initiation complex consists of the promoter, transcription factors and RNA polymerase. Its main function is to separate DNA strands and begin RNA synthesis.• Elongation. The polymerase elongates the RNA transcript in the 5' to 3' direction. As polymerase travels down the strand the preceding region of the strand reconnects to reform the double helix.• Termination. The RNA transcript is released and the polymerase detaches from the DNA.

After transcription and before leaving the nucleus, mRNA molecules undergo RNA

processing. This process includes RNA splicing and the addition of a 5' cap to the 5' end and a poly-A tail to the 3' end.

The majority of eukaryotic genes are split into segments called exons (primary transcript remaining after processing) and introns (a noncoding sequence that is removed during RNA processing). The introns are removed and exons are joined during RNA splicing. RNA splicing is typically done by spliceosomes.

TranslationTranslation occurs when the mRNA code is read to produce a corresponding protein. This is also referred to as the synthesis of a polypeptide chain. Cells are able to translate a message from mRNA into a protein through the use of transfer RNA (tRNA).The function of tRNA is to transfer individual amino acids found in the cytoplasm into a properly organized polypeptide chain in a ribosome based on the sequence found in mRNA. A codon is a sequence of three nucleotides in DNA or RNA that corresponds to a specific amino acid. An amino acid is attached to one end of the tRNA while a specific anti-codon is located at the other end. The anti-codon is a triplet nucleotide code that is complementary to the codon of mRNA.

Ribosomes coordinate the three stages of translation—initiation, elongation and termination. A ribosome contains an mRNA binding site and three tRNA binding sites: A, P and E. The A site holds the tRNA carrying the next amino acid, the P site holds the tRNA attached to the growing polypeptide, and the E site contains the tRNA with the amino acid removed where it exits the ribosome. See Figure 11.

Summary A character is a heritable feature that varies amongst individuals. A trait is a variant

of that character.

According to the law of segregation, an individual has two alleles that segregate during gamete formation. 

– Homozygotes have two identical alleles. – Heterozygotes have two different alleles.

The law of independent assortment states that each pair of chromosomes segregates independently of all other chromosome pairs during gamete formation.

A single nucleotide of DNA consists of a nitrogenous base, deoxyribose sugar and a phosphate group.

There are four nitrogenous bases in DNA: adenine, guanine, thymine and cytosine. Recall: purines pair with pyrimidines and vice versa.

The structure of DNA is a double helix. It is also antiparallel, which means the subunits run in opposite directions.

DNA replication is semiconservative meaning that the replicated double helix consists of one old strand from the parent DNA molecule and one new strand.

There are several mutations that occur in DNA. Mutations can result in the production of the same protein, a different functional protein or a different nonfunctional protein.

Gene expression is the process by which DNA directs the synthesis of proteins. This consists of the transcription and translation processes. – Transcription is the synthesis of mRNA from DNA. – Translation is the formation of a polypeptide using the information in mRNA. This process requires the use of transfer RNA (tRNA).

Biology Prep Course Unit 6Evidence of EvolutionThis unit explores how Darwin came to describe evolution as "descent with modification." Five main lines of evidence are including changes in species composition over time, anatomical similarities between living species and fossils, patterns in DNA and amino acid sequences, and direct observation and experimentation. Relevant case studies illustrate how scientists use this unifying theory to explain how life interacts with the environment.

OverviewDarwin described evolution as "descent with modification" in the book On the Origin of Species. Descent meaning all life comes from a common ancestor, and modification meaning changes. Darwin’s unifying theory informs biologists’ understanding of how life interacts with its immediate environment. There are five main lines of evidence that support evolution as descent with modification:

• fossil evidence showing changes in species composition over geologic time;• similarities in anatomical structures of living species and fossils;• direct observation and experimentation;• patterns of similarities and differences in DNA sequences; and• patterns of similarities and differences in amino acid sequences.

To gain a comprehensive understanding of evolution, this evidence is studied collectively.

The Geologic TimelineThe Earth is 4.6 billion years old. Scientists developed the geologic timeline to categorize the Earth’s long history based on geology, climate and the evolution of life. Figure 1 shows the geologic history of Earth as a clock, with the formation of the earth at 12:00 and major milestones in the evolution of life as bands around the timeline.

Multicellular life evolved between 1.5 and 1.2 billion years ago. Models comparing DNA sequences estimate that the common ancestor of multicellular life evolved 1.5 billion years ago. The oldest fossil evidence comes from a multicellular algae that dates back 1.2 billion

years. These two lines of evidence are in basic agreement with each other. Evolutionary biologists and geologists use multiple lines of evidence to confirm the generally-accepted times in which major milestones in evolution occurred.

Evolutionary biologists group the Hadean, Achean and Proterozoic into the Precambrian because there is little fossil or DNA evidence. The Precambrian ended with a mass extinction and was followed by the Cambrian "explosion" 540 million years ago. Animal diversity “exploded” during the Cambrian period. Figure 2 outlines the geologic time periods and corresponding evolutionary milestones that make up the Paleozoic, Mesozoic and Cenozoic eras.

Absolute Radiometric DatingGeochemists reconstruct the geologic, climatic and evolutionary events of the past. Radiometric dating methods determine the absolute age of rocks based on the constant decay rate of radioactive isotopes. Isotopes are elements with different atomic masses due to variations in the numbers of neutrons. For example, carbon has three isotopes: carbon-12, carbon-13 and carbon-14. Carbon-12 is the most common isotope and is stable, meaning it does not decay. Carbon-14 is a radioisotope that decays to nitrogen. One neutron changes to a proton causing the release of one electron and the spontaneous creation of an antineutrino. Carbon-14 is the parent isotope and nitrogen-14 is the daughter isotope. The amount of time it takes for half of the carbon-14 isotopes to decay is called the half-life. In one gram of carbon, 15 carbon-14 atoms decay every minute. Carbon-14 has a half-life of 5,730 years and is useful in dating organic material up to 75,000 years old. Older samples have too little carbon-14 for accurate dating. See Figure 3.

Volcanic and metamorphic rocks are candidates for radiometric dating because, upon cooling, a rock will have a known ratio of parent isotopes and daughter isotopes. As time passes, the ratio changes as the parent isotopes decay into daughter isotopes. By comparing the ratios, geologists can determine the age of the rock. Fossils found in sedimentary rock are given a range of possible ages based on layers of metamorphic or volcanic rock that surround the geologic formation in which they are found. Isotopes with half-lives of more than 1 billion years are used to determine the age of rocks.

Relative DatingIn combination with absolute dating, relative dating is used to determine the sequence of events in the ancient past. Relative dating is the ordering of events in a sequence, but without attaching dates. The law of superposition states that strata (rock layers) are deposited in chronological order, with the oldest rocks on the bottom and the youngest rocks on the top. This is complicated by two main factors: the movement of plates and the erosion and weathering of rocks.

The theory of plate tectonics explains that the Earth’s crust is broken into about a dozen plates that interact with each other. The movement of these plates causes rocks to bend, break and move after they have been deposited. Older layers can be exposed by erosion, turned over or thrust above other rocks. This means that the youngest rocks are not necessarily still on top.

Figure 4 shows how older layers of rock can be pushed up and then exposed as the younger layers are eroded. Surface erosion and weathering occur at different rates depending on the topography, climate, composition of the rocks and influences from living things. Paleontologists must be knowledgeable of the geologic history of the area in order to determine the relative ages of the fossils they find.

Fossil RecordThe fossil record supports the claim that species composition changes over time; organisms in the past differed from those in the present. Fossils take many forms including bones, shells, footprints, microorganisms, plants and evidence of prokaryotes called stromatolites. Fossilized specimens from different time periods show incremental changes in the structures of species that are otherwise similar. Figure 5 displays how different species of extinct horses show a trend from a small to large body size as well as a reduction in the number of toes from a five-toed ancestor to the modern horse hoof.

Fossils also reveal the geographic distribution of organisms over time and important information about major extinction events. While fossils are an important form of evidence of evolution, most organic material decomposes instead of fossilizing. Organisms that died in mud, on sea floors, or due to catastrophic events where the bodies were buried suddenly fossilize more easily as do organisms with shells or bones. Some species are well represented while others, such as birds, are rarely fossilized. This bias is taken into account by scientists as they piece together Earth’s evolutionary history.

Fossils contribute to the understanding of the next line of evidence—anatomical structures.

Anatomical Structures and Molecular EvidenceThe two main lines of evidence used to determine how species are related to one another are morphological and molecular data. Molecular biologists compare DNA and amino acid sequences in living species and fossils. Paleontologists compare anatomical differences and similarities in fossils and living species. Each wants to confirm the other’s data by using their own methods. Morphological and molecular data provide the most accurate models of how species are related and when their most recent common ancestor lived.

Case Study—Deciphering Whale EvolutionThe recent discovery of key fossils has helped to confirm hypotheses regarding the lineage of mammals by comparing similar anatomical structures. Porpoises, whales and dolphins—marine mammals collectively known as Cetacea—were believed to have recently evolved from land mammals due to their bone structure and distinguishing mammalian traits. Without additional evidence, the hypothesis that mammals returned to the ocean after evolving on land was weak. It seemed unlikely that an aquatic mammal would arise separately from land mammals, but the data was not there to prove one theory over another.

Cetaceans have several derived anatomical structures, which are structures that evolved after the most recent common ancestor of land and marine mammals. Cetaceans have a unique ear for hearing underwater, no hind limbs, a tail fluke and flippers. Since the early 20th century, scientists have known that the bones in the flippers of Cetacea have the same pattern as the forelegs of mammals, an ancestral trait shared by all mammals. The unique shape of the flippers and the lengths of bones are derived traits.

In the late 1970s, scientists in Pakistan discovered the skull of a new species they named Pakicetus. Pakicetushad ear features similar to modern whales. This ear would have been an advantage if Pakicetus hunted underwater. Pakicetus also had four legs meant for walking.

The discovery of the Basilosaurus in 1989, a more recent whale with hind legs, a tail fluke, elongated body and the ear of modern whales helped add to the evolutionary history of whales. Basilosaurus’ hind legs were greatly reduced in size and it was fully aquatic. However, the common ancestor of whales and its closest land relative remained a mystery.

DNA evidence pointed to the hippopotamus as the closest living land relative to modern whales. However, without fossils to determine how they were related, the puzzle was incomplete. The discovery of a specialized anklebone, or astragalus, on an aquatic whale ancestor dubbed Artiocetus supported the DNA evidence. The astragalus of Artiocetus has two humps on each end, which aid in jumping; it is found only in artiodacyla such as goats, deer and the hippopotamus. Another whale ancestor, Rodhocetus, from the same time period also had this specialized anklebone. The fossils of Pakicetus, Basilosaurus, and Rodhocetus were transitional forms, each showing the emergence of derived, whale-like traits while retaining some ancestral traits of land mammals. See Figure 6.

Life HistoryThe morphologic and genetic similarities between Cetacea and other mammals are called homologies. Homologies are similarities resulting from a common ancestry. As species evolve, there are slight modifications to similar structures, but the overall structure remains the same. These structures are called homologous structures. An example of a homologous structure is the common bone structure seen in the forelimbs of mammals.

In the case of animals, a set of genes active early in development, called HOX genes, is nearly identical in many animal phyla. These genes dictate body plan including: bilateral symmetry, limbs and a head, to name a few. The similarity in the DNA leads to the similarity in the anatomical structure. The regulation of these genes and some very small

mutations account for large differences in phenotype such as the lengths of limbs and shapes of bones. Many homologies are even more universal:

• All life uses DNA with four identical nucleotide bases.• All life is composed of cells, which are made of the same basic chemical building blocks. Carbon is the central element for all of life.• All life uses a handful of similar mechanisms to gain energy and nutrients from the environment. Photosynthesis and chemosynthesis both turn inorganic molecules into organic molecules. Respiration, either anaerobic or aerobic, liberates energy from organic molecules.

This repetition of the same set of processes and types of molecules supports Darwin’s theory of one common ancestor.

Comparing Classical and Modern ClassificationClassifying organisms based on their most recent common ancestor using DNA has led to the rearrangement of the Linnaean classification system. When Carolus Linnaeus developed the classical classification system, he did not consider evolutionary theory because Linnaeus predates Darwin.

Linnaeus’ goal was to group organisms that had similar features and functions. Modern classification focuses on grouping organisms by how recently they shared a common ancestor. Many of Linnaeus’ groupings hold true because usually organisms with similar features are genetically similar.

However, some traits that are beneficial in a particular environment can evolve independently. For instance, wings are an advantageous trait for being able to use more of the ecosystem because movement in three directions is possible. Competition on the ground would favor selection for traits that evolve toward flight.

Animals with more ancient common ancestors evolved wings from separate genes. This process is called convergent evolution and the resulting structures are called analogous structures. The wings of birds and bats are analogous because their common ancestor had four legs, not wings. See Figures 7 and 8.

DNA mutation rates are used to predict the absolute length of time since two species diverged from a common ancestor. For example, a species undergoes an average of 1

mutation every 200 years. By counting the number of mutations, scientists can determine the amount of time since two species diverged. This helps researchers know where—in time and space—to look for fossils of common ancestors. Once the rate of mutation is determined, it is used as a molecular clock to determine the time of divergence. The molecular clock approach relies on the observation that mutation rates stay relatively constant for some genes and noncoding regions of the genome. This is calibrated using fossils of a known age. The molecular clock approach is a useful tool for decaying material up to 75,000 years old and can be used with DNA or amino acids sequences. All of this data is compiled to create “family trees” called phylogenetic trees.

Direct Observations of EvolutionScientists use mutation rates, decay of radioactive isotopes, geographic distribution of fossils, theory of plate tectonics and morphology of living species to develop a clear explanation of Earth’s history. What about direct experimentation? Biologists have induced and documented evolutionary change in thousands of instances, including peer-reviewed controlled trials and comparison studies.

One of the best documented instances is the evolution of antibiotic resistance in bacteria. Methicillin-resistant Staphylococcus aureus, MRSA, is a pathogenic form of S. aureus that lives on the skin and can cause infection if it enters through a wound. S. aureus evolves quickly, with documentation of penicillin being ineffective on the bacteria after only two years. In 1959, doctors started using methicillin, a powerful antibiotic, to treat S. aureus infections. Within two years, cases of drug resistance were emerging. The number of hospitalizations due to MRSA increased quickly, with less than 10,000 reported hospitalizations in 1993 to more than 350,000 reported hospitalizations in 2005. This indicates that the bacteria has evolved to increase the severity of infection and resistance to antibiotics. Bacteria reproduce by effectively cloning themselves, and mutations can occur during this process. Mutations can accumulate quickly since bacteria reproduce very quickly. Figure 9 shows the genome of MRSA.

In addition, bacteria have the unique ability to transfer bits of DNA from one organism to another in a process called conjugation. Conjugation most often occurs between members of the same species, but can also happen between species. Therefore, a nonpathogenic strain of bacteria could pass genes containing an advantageous trait to a pathogenic strain, rendering the pathogenic strain immune to the antibiotic. The conditions are ripe for evolution when antibiotics are administered.

Another documented case of evolutionary change is the peppered moth in London. Peppered moths varied in color from light to dark—scientists identified them as “light morph” and “dark morph”. Lichen on tree bark provided better camouflage to the light morph so they were less likely to be eaten by predators and therefore survived at higher rates. Pigmentation was an inherited characteristic, so when the survivors reproduced, more of their offspring had light pigmentation.

During the industrial revolution, soot from factories in London covered the trees, killing the light-colored lichen and darkening the bark. When the trees changed, the light morph was no longer camouflaged. The dark morph survived at higher rates and, over several generations, became more common in the population. This change in the frequency of the trait resulted from a change in the allele frequency responsible for pigmentation.

Summary

There are five lines of evidence supporting Darwin’s theory of evolution: fossils, anatomical similarities and differences, patterns of DNA sequences, patterns of amino acid sequences and direct experimentation and observation.

The geologic timeline is organized based on major geologic events and evolutionary milestones.

Radiometric dating is used to determine the age of rocks and organic materials found in rock layers.

A phylogenetic tree branches when the most recent common ancestor lived. The closer two species are on the tree, the more closely they are related.

DNA evidence and the fossil record are used together to determine relationships between species.

Classical classification used similarities in morphology to group organisms. Species with analogous structures were sometimes grouped together in error. Modern phylogenetics uses DNA evidence and morphology to group organisms.

The use of antibiotics to treat Staphylococcus aureus leading to the emergence of MRSA is direct evidence of evolution.

Another example of direct evidence is when the peppered moth population in London changed from mostly light in pigment to mostly dark as a response to an environmental change.

AP Biology Prep Course Unit 7

Evolution: Natural SelectionThis unit explains the mechanism for adaptive evolution—natural selection—and applies this mechanism to various examples in the natural and human-modified world. The content investigates Darwin’s two main observations, which led to the inference that all life experiences a struggle for existence and in turn leads to differential survival and reproduction

OverviewIn this unit, the mechanism of natural selection will be explained and applied to various examples in the natural world.

Conditions for Natural SelectionNatural selection is the main mechanism for evolutionary change and the only one proposed by Charles Darwin. Darwin observed that physical characteristics varied among individuals and populations produced more offspring than could survive. These observations led Darwin to infer that there is a struggle for existence. Individuals best suited to the current environment lived longer and produced more fertile offspring as a result of the struggle for existence. Those individuals with high reproductive success had high fitness, and those individuals who did not survive as long or have as many offspring had lower fitness. This differential survival and reproduction is often referred to as “survival of the fittest.”

Genetic VariationThe idea of genetic variation is quite simple. Organisms contain genes, and one organism’s genes are not the same as another organism’s genes. The more variation among the genes of the members of a population, the better the chance that at least one combination of genes will benefit the species in the future.

Cheetahs, for example, have low genetic variation due to a mass extinction event that left the cheetah population very small. This means that a large percentage of cheetahs have very similar characteristics, including some that are not favorable to fitness, such as kinked tails, which can slow a cheetah down. Not all cheetahs have kinked tails, but the random reduction in genetic variation caused kinked tails to become a common characteristic despite being bad for survival. Although the reduction in cheetah numbers occurred a long time ago, the genetic diversity remains low. Low genetic variation arises when alleles are eliminated from a population that is decreasing in size. Some eliminated alleles are beneficial traits and the mutation to bring back that trait might not occur again.

Sources of Genetic VariationCommon ancestry of living things means that all life came from one original genome. All genetic variation comes from an accumulation of changes to DNA from a variety of sources including sexual reproduction, mutations, duplications and rearrangements of DNA, as well as recombination of DNA in prokaryotes.

Prokaryotes reproduce asexually, but this does not mean DNA is not shared or transferred. Prokaryotes recombine their DNA, which increases genetic variation. Three processes achieve recombination: conjugation, transformation and transduction. During conjugation, two bacteria fuse temporarily and one transfers a plasmid, which is a circle of DNA, to another bacteria. See Figure 2a.

The bacteria are often the same species, but conjugation can occur between species. Transformation is the inclusion of DNA from the surrounding environment. In transformation, a new gene replaces an existing gene. See Figure 2b.

Transduction occurs when a phage (virus) acquires bacterial DNA from one cell and injects it into another cell where it becomes part of the receiver cell's genome. See Figure 2c.

Among sexually reproducing organisms, the reshuffling of genes during meiosis and fertilization is the greatest contribution to genetic variation. Meiosis results in the formation of gametes. Gametes are haploid, meaning they contain one allele for each gene rather than two. During meiosis, a process occurs called crossing over in which homologous chromosomes trade alleles from one homolog to the other. Crossing over greatly decreases the chance that chromosomes in different gametes will be identical. The independent assortment of chromosomes during metaphase I ensures that the homologous chromosomes separate at random. Independent assortment of chromosomes in

humans means that there are 223 (nearly 8.4 million) possible combinations of chromosomes. Add in crossing over, and the chance that two gametes from an individual will be identical is nearly zero.

Mutations also increase genetic diversity. While mutations occur in all types of organisms, the mutation rate is higher in eukaryotes because of sexual reproduction. If a mutation results in a change in the amino acid sequence, often the allele will be different. These changes can increase the possible alleles for various genes and sometimes creates new genes. Mutations can be beneficial, harmful or have no affect at all.

Consider how much each gamete goes through during formation to differentiate it from other gametes: crossing over, possible mutations and independent assortment. Remember, there are over 8.4 million possible combinations for a single human gamete. During sexual reproduction, two gametes combine to form a unique zygote. That zygote’s genome is the combination of the genes in the two gametes. Eventually, the zygote will produce its own gametes and offspring further contributing to genetic variation and diversity.

Overproduction of OffspringThe survival of a species is more important than the survival of an individual. This idea is reinforced over and over again as offspring are produced at higher rates than can survive.

The competition for survival begins at birth. Whether it is a tiny salmon swimming to the ocean or a bald eagle stretching up to get food from its parents, there is serious competition with others of the same species. For example, salmon spawn an average of 3,000 eggs, but only a few survive to adulthood. See Figure 3.

Overproduction of offspring doesn’t necessarily mean that parents have a large number of babies and then let them fend for themselves. Instead, in some cases, overproduction is more of an insurance policy. For some large birds (usually seabirds and birds of prey), rearing more than one offspring is difficult because parents constantly need to fend off predators while providing food to the quickly growing chick. To ensure all that work is worth it, the mother lays two eggs a few days apart. She and her mate may only be able to support one chick and the extra egg is “insurance,” just in case something happens to the first one. If both eggs hatch, the older offspring is stronger and more developed, beating out its younger sibling for food and space. Many times, the older sibling kills its younger sibling by removing it from the nest, an act called siblicide, preventing it from eating or pecking it. Talk about sibling rivalry! If the older sibling happens to have a disadvantage and is not developing properly, the younger one will be the fittest and the older will die. In some species, this is obligate (it always happens) and in other species, it is facultative and

only happens when food is in short supply. Either way, the gene pool is strengthened when the most fit sibling survives.

Struggle for Existence and Differential Survival and ReproductionBased on genetic variation and overproduction of offspring, we can infer that there is a struggle for existence. Because there is competition for limited resources, individuals of a species with favored characteristics will live longer and reproduce more often. This is called differential survival and reproduction. Others will either die before reproducing or will not be as reproductively successful. The environment determines which traits are better, and different environments favor different traits. The Earth has a variety of environments, and each favors particular traits, which leads to diversity of species.

Much of the struggle for existence centers on either getting food or not becoming food. Prey species have evolved many characteristics for evading predators and predators have, in turn, evolved characteristics to overcome the prey’s adaptations. This is often called the evolutionary arms race. Weapons in this race include claws, sharp teeth, strong muscles, armor, spikes, poison, stinging mechanisms, venom, toxic chemicals, and those are just a few of the characteristics used to deter predators! (Of course, many are also used to catch prey.) When an adaptation helps a prey species, in time successful predators evolve to overcome that adaptation. This is called co-evolution. Figure 4 shows the adaptations that help the cheetah hunt and the impala survive.

The classic image of a cheetah chasing down an impala on the African savannah illustrates this evolutionary arms race. Every aspect of a cheetah’s body is made for short, ambush attacks. Spots provide camouflage in the tall grass, so the cheetah can sneak up on the impala. The cheetah’s spine is flexible so its body can act like a spring. Its muscles are enhanced only in areas needed for speed, while the rest of the body is thin. A long tail acts as a rudder, steering the cheetah toward the prey. The rudder action of the tail gives the cheetah an extra advantage if the impala changes direction. The impala loses speed while the cheetah loses little, allowing the cheetah to make its kill. This is just a sampling of the characteristics that make cheetahs successful hunters.

So, what characteristics help the impala survive? The impala’s long gait, aerodynamic body, and eyes on the sides of its head are all characteristics that improve the fitness of this prey species. While the cheetah sprints, the impala has stamina, so if it can wear out the cheetah, it will survive another day. The impala can also jump over 30 feet, which

means it can leap over obstacles the cheetah must go around. While impala are fast, cheetahs are successful hunters more than 50% of the time. Because of this, an impala’s best chance of survival is to stick close to the herd. Being faster than the cheetah is not as important as being faster than another impala. A cheetah will pursue a slower impala over a fast impala. The selective hunting of slower impala ensures the fittest impala survive. An impala’s eyes are on the sides of its head, giving these animals excellent peripheral vision. In a herd, many eyes are on the lookout and often spot the cheetah despite its camouflage. Overall, the survival of an individual impala hinges on that individual having higher fitness than the rest of the herd.

Plants are often prey, so they have adapted many chemical and structural defenses to deter predation and herbivory. Cedar trees have chemical defenses to protect against insect infestation. The bitter taste of many herbs, the nicotine in tobacco plants, the opiates in poppies, and even the smell of fresh cut grass are chemical defenses. Structurally, some plants have thick bark, are made of difficult to eat cellulose, or have spines or thorns. See Figure 5. Plants also distract would-be predators away from important structures by offering up enticing fruit, flowers and nectar. This not only keeps the plant alive, but also helps with successful reproduction and seed dispersal.

There are countless examples of the evolutionary arms race. Think about an example in an ecosystem near you. Consider not only animal interactions, but also interactions between plants, plants and animals, fungi and animals, or fungi and plants. Remember, every trait has been shaped by the environment and most serve important functions in the current ecosystem.

Abiotic factors in the environment also influence the struggle for existence. This means that when ecosystems change, those individuals with characteristics suited to the new conditions will be best equipped and will survive and reproduce at higher rates. For example, in the case of a forest ecosystem, when a forest burns, the abiotic conditions after the fire are different than they were before the fire. Temperature fluctuation is greater, soil nutrients change, the amount of sunlight reaching the ground increases, and humidity is lower. Plants that were not burned by the fire may survive if they have characteristics that allow them to live in this new environment, otherwise other species may come in and take their place. Plants can often overcome these disturbances with seeds that remain dormant until conditions are more favorable. Once the forest ecosystem is changed by a group of species that populate the forest soon after burning, the seeds will germinate and the species will continue. See Figure 6.

Sexual SelectionSexual selection is the selection of mates based on a particular set of traits and/or behaviors. Sexual selection is a unique type of natural selection because the selective pressure comes from within the species rather than from other species or the abiotic conditions of the environment.

There are two types of sexual selection. The first is intrasexual selection, in which members of the same sex compete for mates. This takes many forms, including sparring, territorial

defense and challenges to alpha individuals. Animals that form groups, such as lions and wolves, may only have select individuals that mate. In order to mate, an individual challenges a mating individual. The male lion in a pride mates with several female lions. A male lion may be challenged by a lion that does not have his own pride. Wolves form mating pairs, in which the alpha male and female mate, while others in the pack only mate if resources are available. If the pack is particularly successful, they may have two or three mating pairs. This intrasexual selection generally follows natural selection closely; those with the most beneficial traits are the alphas and mate more than others in the pack.

The second type of sexual selection is intersexual selection, in which individuals of the opposite sex chose a mate. Usually females pick males based on either the appearance or behavior of the male. A clue as to whether or not intersexual selection is a factor is if a species is dimorphic, that is the males and females look different. Many species of birds are dimorphic, indicating sexual selection is a major component of fitness.

In extreme cases, the characteristics favored by the females seem to counter the survival of the male. For instance, male widow birds have tails so long, it hinders their ability to fly. See Figure 7.

Male bowerbirds exhibit specific behaviors to attract a mate. They collect trinkets from all over the forest and decorate a bower that they weave out of grasses, sticks and other materials. When a female is impressed by the decorating, dancing and singing of the male, she mates with him. The bower’s only purpose is as a place of courtship and mating. After mating, the female builds her own nest and raises the young on her own, leaving the male to attract another mate.

Females being choosy about such odd characteristics may seem strange. Darwin himself found these traits to be curious. The leading hypotheses are that the males have other related strengths that are associated with these traits or that surviving the process of impressing a mate indicates overall high fitness. An organism with high fitness will be more likely to reproduce and therefore pass on advantageous traits to the next generation. See Figure 8.

Artificial SelectionHumans have domesticated and bred agricultural species and pets for thousands of years. The selective breeding of individuals to keep desired traits and eliminate undesired traits is artificial selection. For most of human history, phenotype was used to determine which to breed and which to exclude and this is still how most artificial selection occurs. However, DNA analysis allows for artificial selection of genes. Genes can also be inserted to produce a particular trait in an organism. These are genetically modified organisms. Modern techniques have been used to produce crops that are resistant to a variety of diseases and abiotic conditions and to produce medicine such as insulin. Artificial selection, either through selective breeding or genetic modification, has produced an array of domesticated crops and animals.

Summary Darwin’s theory of natural selection is based on two observations (genetic variation

and overproduction of offspring) and two inferences (the struggle for existence and differential survival and reproduction).

The struggle for existence favors some characteristics over others, leading to greater transmission of the genes that code for favored characteristics.

Changes in environmental conditions can affect species’ fitness because different characteristics will be beneficial in the changed environment.

Sexual selection is a specific type of natural selection when the selective pressure comes from within a species rather than from biotic and abiotic factors outside the species.

Artificial selection is the selective breeding or genetic modification of organisms by humans.

AP Biology Prep Course Unit 8Evolution: PopulationsThis unit discusses microevolution in populations and applies Hardy-Weinberg principles. The complicated definition of a species is explored and how species evolve from ancestors is discussed.

OverviewIn this unit you will learn about microevolution, Hardy-Weinberg principles and factors that influence speciation.

Microevolution in PopulationsA species is a group of organisms that have the potential to mate and produce viable offspring. A population is a group of individuals of the same species that regularly interact and interbreed, producing viable offspring. For example, you may find American Robins, Canada Geese and White Oak all in the same ecosystem. Each of these species is a population within that ecosystem. See Figure 1.

The collective genome of the individuals within a population is called the gene pool. These specific alleles are available to be passed to the next generation in the population.

Populations evolve when the ratio of alleles for a trait changes over generations. A change in allele frequency is called microevolution. Microevolution occurs within a population, which means it does not necessarily affect the entire species. Microevolution may result from natural selection (including sexual selection), artificial selection or genetic drift.

Hardy-Weinberg Equilibrium ConditionsIn the early 20th century, a mathematician named Hardy and a physicist named Weinberg both described the gene pool of a population that was not evolving as having allele frequencies that did not change from generation to generation. They determined that stable allele frequencies occurred in populations where all of the following conditions are met:

• Random mating• Extremely large population size• No mutations• No natural selection• No gene flow (i.e. migration)

An entire population will never meet these conditions for all traits, but it will for some traits. The Hardy-Weinberg equilibrium equation is used to examine single-gene traits, one trait at a time, to determine whether or not microevolution is occurring.

Hardy-Weinberg EquationThe definition of evolution in a population is quite simple, but measuring allele frequencies is not. The genome of a population cannot be determined without DNA samples from all members of the population, an arduous task and one that was, until quite recently, impossible. The Hardy-Weinberg equation relates the frequencies of alleles to the number of individuals exhibiting the recessive phenotype—something that is much easier to measure. The frequency of each allele is determined by the following equation:

p2 + 2pq + q2 = 1.00

The table below defines the terms and variables and provides the method for using the equation.

To explain how the Hardy-Weinberg equation is used to track evolution of populations, an example of a gene that is expressed, as three distinct phenotypes will be used.

Different alleles affect the frequency of people who develop sickle cell anemia. If 0.2% of a population has sickle cell anemia, how many individuals carry the allele for the disease?

The pressure from the environment to select in favor of the AS phenotype has changed as mosquito control and management of malaria has improved. The evolution of these traits will lag behind the change in selective pressure because the generation length of humans is long. Traits evolve at different rates due to many factors. The Hardy-Weinberg equation is a tool that tracks the speed of evolution. A closer look at the Hardy-Weinberg conditions shows how evolution happens.

Adaptive Evolution or Chance?When a population deviates from the Hardy-Weinberg conditions, it is either experiencing adaptive evolution or evolution by chance. Of the five Hardy-Weinberg conditions, two apply to adaptive evolution and three apply to evolution by chance. Natural selection and selective mating (sexual selection) both lead to adaptive evolution. Mutations, gene flow and a small population size promote evolution by chance. A population stays in genetic equilibrium when neither adaptive evolution nor chance change the allele frequencies of a trait.

If a genetic change occurs that favors one phenotype, and if the change is beneficial to the survival and reproduction of the species, then the mechanism for evolution is natural selection. Natural selection is a form of adaptive evolution because the change in frequency helps the population adapt to the environmental conditions. Sexual selection is another type of adaptive evolution because it leads to differential survival and reproduction based on particular traits.

Genetic Drift

Large population size is one of the five conditions for maintaining genetic equilibrium. Population size is important to evolution because of probability. Just as the odds of getting heads when a coin is tossed is always 1:2, the odds of “drawing” a particular allele is always based on the ratio of the alleles.

The number of times you toss a coin has an effect on how close the results are to the expected ratio. A coin tossed 100 times might result in more heads by chance. When a coin is tossed 100,000 times, heads will account for 50% and tails will account for 50% because the element of chance is diminished with each toss. When a population size is large, chance will have little impact on the resulting allele ratio for a gene.

However, in small populations, chance can lead to changes in allele frequency, resulting in genetic drift. Genetic drift happens when a population is either isolated from the main population or the population size suddenly declines. A decline in population size may result from a change in the environment caused by a flood, fire, habitat destruction or volcanic eruption, to name a few. Figure 3 shows two different scenarios that both lead to evolution of a population. In both scenarios, a flood has changed the environment.

• In A, a population with mediocre swimming skills attempts to swim to higher ground when their island is flooded. Those that are better swimmers make it to dry land. This is an example of natural selection because the good swimmers survived.

• In B, the population does not swim away and ends up isolated. This is an example of genetic drift because the individuals survived by chance. Those overtaken by the flood die, regardless of fitness.

The founder effect occurs when an isolated population has a different allele frequency from its source population. In an isolated population, rare alleles representing traits detrimental to survival and reproduction may be more common. This causes an overrepresentation of those alleles. For example, the colonization of South Africa by a small population of Dutch Afrikaners led to the overrepresentation of the allele that causes Huntington’s disease. It was by chance alone that some of the settlers had the form of the gene that causes the disease, but because of the small population, the disease was much more common in the founding population. All descendants of this population carry a higher risk for the disease.

A bottleneck effect can occur if there is a sudden decline in population size. The alleles in the remaining population will be different than the original population. The alleles that remain are randomly selected by the sudden environmental event. Some alleles may disappear entirely, while others may be over- or under-represented. Depending on the severity of the bottleneck, this can impact a species’ genetic diversity for generations. See Figure 4.

Changes in Allele Frequencies within a GenerationThe last two Hardy-Weinberg conditions require that there be no mutation and no migration. Mutations and immigration (migration into a population) introduce genetic variation to a population, causing immediate changes to the gene pool. Mutations occur by chance and without regard to fitness. A new mutation may harm, help, or not affect the organism.

The frequency of alleles moving in and out of a population is the population’s rate of gene flow. If migration is frequent, there is high gene flow, if not, there is low gene flow. When two populations have genes flowing between them, the differences in their gene pools decrease and eventually they may become the same population. This slows the development of a new species because it reduces genetic variation between populations.

Gene flow can influence the fitness of a population in different ways depending on the alleles that are introduced or move out. In some cases, an allele that is favored in one environment will have a negative impact on fitness in another environment. When this happens, the effect of natural selection is mitigated by gene flow. Gene flow can also be neutral to fitness, in which case natural selection would be the cause of evolution. If it increases fitness, then the effect of natural selection is amplified.

Analyzing the Evolution of Multi-Gene TraitsRemember, the Hardy-Weinberg equation can only be used with single-gene traits having two alleles. Scientists use different tools to assess the evolution of traits controlled by multiple genes. Most traits result from the interaction of many genes. The phenotypes expressed by these traits can be graphed on a continuum and analyzed to see if the distribution of phenotypes changes predictably over time. Predictable change indicates adaptive evolution.

Three types of selection can be modeled to predict the progressive evolution of a trait. Directional selection occurs when a phenotype at one end of the distribution is

advantageous. Over time the entire graph shifts toward this phenotype. An example is beak length in hummingbirds in environments where flowers are deep. Those with longer beaks are able to eat from all the flowers, therefore the longest beaks are favored. See Figure 5.

The second type is called stabilizing selection in which an intermediate, narrow range of phenotypes is advantageous. In humans, birth weight is a good example of stabilizing selection. Outside of a narrow range, infant mortality rates are much higher, therefore most babies are between 6 and 9 pounds at birth. See Figure 6.

Disruptive selection occurs when phenotypes at both ends of the distribution are favored and intermediate phenotypes are selected against. This leads to two distinct phenotypes in a population. See Figure 7. An example of this is toe pad size in Caribbean anoles. Anoles that spend more time on leaves have large toe pads and those in habitats with sticks have small toe pads.

SpeciationA geographical barrier may cause isolated populations to form new species because gene pools cannot mix due to physical separation. Geographical barriers include mountains, lava flows, rivers, roads, or other physical barriers to interaction. The isolated ecosystems have slight differences, causing natural selection to act upon different traits. Therefore, genetic variability increases to the point where there are clear differences. This type of speciation is the most common and is called allopatric speciation. See Figure 8.

When behavioral or temporal barriers to breeding exist, sympatric speciation can occur. Behavioral isolation occurs when particular courtship rituals aid in mate recognition. Pairs only mate when the courtship ritual is carried out. For example, male blue-footed boobies perform a very specific dance in order to convince a female to mate. Similarly, two species that are closely related but mate at different times of the year, day or under different environmental conditions are considered different species because their genes will never mix. This is called temporal isolation.

Ecological Definition of a SpeciesWhen individuals meet the ecological definition of a species, they have the same role, or niche, in the ecosystem. The sum of the behaviors of members of a population are their niche. It includes what they eat, where they live, what they use to move around and other behavioral characteristics. When a segment of a population begins to behave differently than other members of its population, it may have a different impact in the ecosystem. This is called niche differentiation.

Niche differentiation can result in adaptive radiation—this is when one species evolves into many species to fill available niches in the ecosystem. See Figure 9. When competition is high among members of a species, some individuals may avoid competition by occupying a different niche within the ecosystem. A different niche means different traits are advantageous and selection for these traits will occur. After a large extinction event, adaptive radiation fills the niches left by those extinct species.

Case Study—Spotted Owls and Barred OwlsWhen species are reintroduced to each other after being geographically isolated for a long time, the offspring may be able to reproduce, despite the two being different species. This is the case with the federally threatened spotted owl and the more common barred owl. Historically, the two species were geographically isolated and had adaptations specific to their environment.

The smaller spotted owl is a slow, but agile flier. It darts between trees in a closed-canopy forest. It preys on flying squirrels, wood rats and tree voles and nests in mature trees. The larger and more aggressive barred owl is adapted to the open woodlands found in the eastern parts of the United States. It eats squirrels, chipmunks, mice, voles, birds, amphibians and reptiles. Land conversion from prairie to farmland and urban expansion enabled the barred owl to expand its range west across Canada.

By the 1980s, the barred owls and spotted owls had overlapping ranges. The barred owls outcompeted the spotted owls for resources and are more adapted to second growth forests than the spotted owls. They regularly stole nest sites, competed directly and even preyed upon spotted owls. Most importantly to evolution, the two species started mating, which led to hybridization between the two owls. Some of these hybrids are sterile, meaning the energy expended by their parents to pass on their genes is lost, as the offspring will not reproduce.

The non-native barred owl is winning when it comes to reproduction and survival, even though it is not the environment in which it evolved. This paradox is explained by the fact that a species only gains adaptations if the genes for the trait exist in the gene pool. In this case, spotted owls originally adapted in an environment with ancient trees, plentiful nest sites, and abundant flying squirrels, tree voles and other high-canopy prey. Genes for fast, straight flight to evade predators and long distance hunting were not favored in that environment. Only in the recent past has the environment changed to one that favors the open forest hunters. The spotted owl has also experienced a bottleneck, leaving it without the genetic diversity it might need to adapt to the new conditions and competition.

Summary Microevolution is the change in allele frequency of a gene in a population.

The Hardy-Weinberg principle states that a population is in genetic equilibrium if it has random mating, an extremely large population size, no mutations, no natural selection, and no migration.

When a population is not in genetic equilibrium, it is evolving. The direction and relative amount of allele frequency change can be predicted by analyzing the way in which the five conditions are being violated.

The Hardy-Weinberg equation can be used to determine what the allele frequencies of a population should be based on the frequency of the recessive phenotype.

Evolution of multi-gene traits can be quantified by graphing the phenotypes of the population over many generations to see if the evolution is directional, stabilizing, disruptive or random.

Genetic drift and gene flow often cause evolution in a population that is random and not adaptive. Gene flow can work against adaptive evolution.

Behavioral, temporal and geographic isolation can all lead to reproductive isolation and speciation.

AP Biology Prep Course Unit 9

Interdependence in EcosystemsThis unit defines ecology and explores how ecological interactions impact the distribution and abundance of organisms in all imaginable ecosystems. This unit focuses on how interactions between organisms and their abiotic surroundings, and interactions amongst organisms, impact ecosystems.

Overview

Ecology is the study of interactions between organisms and their environment. Ecologists conduct research to explain how interactions impact the distribution (where they are) and abundance (how many there are) of organisms in all imaginable ecosystems. This unit will focus on how interactions between organisms and their abiotic surroundings, and interactions amongst organisms, impact ecosystems.

Components of an EcosystemAn ecosystem is composed of the organisms and the nonliving environment those organisms interact with in a defined space. The largest of all ecosystems is the biosphere, which includes the Earth and the atmosphere. Localized interactions between abiotic (nonliving) components and biotic (living) components and interactions amongst organisms influence global patterns of species distribution and abundance. For instance, deserts get little rain, have few plants that are clustered around water sources, and are most common at subtropical latitudes. They have a lower biomass, total mass of individuals within a population, than many other ecosystems and have species that are able to thrive in the conditions described above.

ClimateThe abiotic factor that has the largest impact on global biotic patterns is climate. Climate is the average weather pattern for a given location over a long period of time. It includes temperature, humidity, wind, and precipitation. Figure 1 shows a map of annual average temperatures across the Earth.

Climate is influenced by latitude, altitude and continentally. The impact of latitude and sentimentality are both directly related to the uneven distribution of solar energy and the way it interacts with the biosphere. Latitude is a measure of how far north or south a point is on the Earth. The equator is at zero degrees latitude, the North and South Poles are at 90 degrees north and south, respectively. Continentally describes how and why the interiors of continents change temperature quickly, both seasonally and daily, while areas closer to the ocean have more moderate climates. For example, two ecosystems at an equal latitude will have different characteristics if one is near the ocean and the other is towards

the interior of the continent. In Figure 2, this can be seen most clearly when looking at Australia.

Due to its latitude, over the course of a year, the equator will receive much more solar energy than either of the poles. The total amount of solar energy varies on a daily basis as well. The highest concentration of solar energy occurs when the sun is at its highest point in the sky—solar noon—and there is no solar energy between sunset and sunrise. Outside of the tropics, the sun always strikes the surface of the earth at an oblique angle, dispersing the sunlight over a larger area making it less intense. See Figure 3.

Once solar energy reaches Earth’s surface, it interacts differently depending on the type of surface it hits. For example, solar energy interacts with land and water differently. Water is able to absorb solar energy without a substantial temperature change because water has a very high specific heat. Specific heat is the amount of energy needed to raise one gram of a substance by one degree Celsius. Substances with high specific heat require more energy to increase their temperature than those with low specific heat. The unequal heating of the Earth and the Earth’s rotation influence global wind and ocean currents. These currents disperse energy from the equator to other parts of the world, therefore affecting climate patterns.

Regional climates are affected by landforms. For example, the high altitude of a mountain directly correlates to a decrease in temperature. For every 1,000 feet of elevation gain, the temperature drops about 3 °F. These temperature changes affect precipitation and cloud formation around the mountain. Also, the south side of a mountain receives more sun than the north side. Therefore, the south side is warmer and drier, while the north side is cooler and wetter.

Abiotic Factors in Local EcosystemsWhile climate has global and local effects, many other abiotic factors influence species composition and abundance on a local level. Microclimate effects, such as differences in temperature, humidity, and wind in open areas versus adjacent forested areas, impact local species composition. Soil minerals, soil nutrients, slope and soil moisture are other examples of abiotic factors that have a local effect on species composition and abundance in ecosystems.

Ecological HierarchyThe living things in an ecosystem are organized in a hierarchy. At the highest level of this hierarchy are the community of living things in the ecosystem. The community includes all living things, from bacteria in the soil to trees and the animals that inhabit them. Community ecologists study the interactions between species and how they impact the composition of the ecosystem.

A population consists of all the individuals of a particular species. Population ecologists focus on a single species and how its population changes over time. This includes predicting how future changes in the ecosystem might impact the species.

At the bottom of this hierarchy is the organism. The individual organism has a specific impact on its immediate environment. Organismal ecologists examine the particular behaviors, physiology and structure of individuals and how they use the environment to survive and reproduce. The way an organism uses its environment, including what it consumes, where and how it reproduces, and its growth and development, are all part of the organism’s niche.

Interactions Between SpeciesWhen organisms interact they either benefit, are harmed, or are not affected. In this unit, a (+) indicates a benefit, a (–) indicates harm, and a (o) is neutral. An organism is harmed if their ability to survive or reproduce is decreased due to the interaction. An organism benefits if their ability to survive or reproduce is increased due to the interaction. Interactions between species include predation, herbivory, competition, symbiosis and facilitation.

Predation and HerbivoryPredation (+, –) occurs when one organism kills and eats another organism. The predator benefits because eating allows it to survive and be more fertile. The prey is harmed because it dies. Predation is a strong catalyst for natural selection. Prey species have adaptations allowing them to detect predators and evade predation. Predators have their own adaptations allowing them to detect prey and catch them successfully.

Herbivory (+, –) is similar to predation except the plant is not killed. Scientists distinguish between plant predation, in which the plant dies and herbivory, in which only part of the plant is eaten. The herbivore benefits, while the plant is harmed.

SymbiosisSymbiotic relationships occur when two different species live in direct contact with one another. The three types of symbiosis are parasitism, commensalism and mutualism.

Parasitism (+, –) occurs when a parasite lives on or in a host. The parasite uses the host for all their needs—habitat, food, and in many cases to carry out the life cycle. Plasmodia sp. is a parasite that infects humans and causes malaria. While infecting a human, plasmodia use the liver and the blood to reproduce asexually through mitosis.

Some plasmodia form male and female gametes in the blood. When a mosquito bites an infected human, some gametes exit the human. Once in the mosquito, male and female gametes fuse and become a cyst in the mosquito’s stomach lining, producing more of the asexual form of the parasite. The asexual parasites move to the salivary gland of the mosquito where they are injected into the next human they bite. See Figure 5.

Without both humans and mosquitos, plasmodia cannot reproduce and survive. Humans get very sick when infected with plasmodia, as the parasite destroys healthy blood and liver cells. Parasites cause harm to the host, but if they kill the host, they are also harmed. A successful parasite lives with the host for an extended period of time and reproduces without killing the host.

Commensalism (+, o) occurs when one organism benefits but there is no perceived benefit to the other organism. For example, many tall, grasslands birds, such as cattle egret, follow herds of grazing animals and eat invertebrates that are disturbed by the movement of the large animals. The birds obviously benefit by getting food, but there is no effect on the grazing animals.

Mutualism (+, +) occurs when both organisms benefit from the interaction. Mutualistic relationships are quite common because of the evolutionary advantage it creates. Plants and pollinators have a mutualistic relationship in which the plant provides food and the

pollinator spreads pollen ensuring reproductive success. Termites have microbes that digest cellulose, the main component of wood. Humans also have microbes to aid in digestion. In each of these cases, the microbe helps the larger organism obtain nutrients from their food while also eating a meal themselves.

CompetitionCompetition (–, –) harms all individuals involved, but is necessary when resources are scarce. Interspecific competition occurs when organisms of different species compete for a limited resource that is necessary for survival and reproduction. When two species use many of the same resources, their niches overlap. The more overlap, the greater the competition for resources. This usually leads to competitive exclusion, in which one species will eliminate the other from the niche. For example, one species of bird may eat the needles of a pine tree, another may eat the pollen, and another may eat the cones. By utilizing different resources, they reduce competition and all have improved fitness.

Competition also leads to differential survival and reproduction because the individuals of a species that outcompete others live longer and reproduce more often. The immediate impact of competition is negative for all, but the species continually adapts through natural selection.

Intraspecific competition occurs when organisms of the same species compete for limited resources such as territory, mates and food. Plants compete for light, space, soil nutrients and water. This type of competition results in particular behaviors and physical attributes. Competition within a species limits the population size.

FacilitationMany organisms do things to change the environment in ways that help other species inhabit an ecosystem. This is called facilitation and can either benefit both species (+,+) or benefit one species (o, +). In nutrient-depleted soils, some plants, with the help of bacteria, take nitrogen from the air and add it to the soil. Plants that are not able to use nitrogen gas are now able to take hold in the ecosystem because they can obtain these nutrients from the soil. Facilitation by animals may include animals that use abandoned nesting sites from another species. Facilitation is an important factor in succession, the progression of an ecosystem through different dominant plant communities, as the ecosystem recovers from a disturbance.

Ecosystem Stability and DisturbanceThe change in species composition over time in an ecosystem can be predicted with a degree of certainty. When an ecosystem is disturbed, either through natural events or human interference, a series of predictable changes ensues. This type of ecological modeling is possible because of the intricate understanding of the interdependent relationships in the community of species and their access to abiotic resources, such as light and nutrients.

Plants form the living structure of an ecosystem. Their presence changes soil composition, available nutrients, humidity, light availability and temperature. They form the habitat that other organisms, including other plants, need and use. When a disturbance occurs that removes some or all of the major plants in the community, the ecosystem changes. More light reaches the ground and less nutrients enter the soil. Different species that are less limited by nutrients but more limited by light may move in or become more abundant. Animal species may migrate to areas that more closely resemble the ecosystem before the disturbance. Other animals, finding different food sources, may migrate into the disturbed area. In general, an ecosystem that experiences a disturbance such as a flood, fire or deforestation loses diversity and changes species composition. However, disturbance is a natural part of most ecosystems.

Case Study—Fire in Western United States Pine ForestsMany species are adapted to specific types of disturbances common in their ecosystems. The pine forests in the western United States represent an ecosystem that evolved in the presence of frequent fire.

The fire history of the west prior to European Settlement included natural fires and fires set to clear land and move herd animals by Native Americans. The average time between fires was typically 6 to 20 years depending on the microclimate, including frequency of lightning strikes. This fire interval produced park-like forests with large, fire resistant trees and space for animals to walk and forage on an understory of shrubs and small trees. Plant

species adapted to lower nutrient levels, more light, and lower humidity compared to species in forests with less frequent fire.

When European settlement began in the 1800s, the fire regime stayed fairly consistent. However, the age of fire suppression began in the early 1900s. The United States Forest Service employed fire fighters to extinguish every fire they could, manmade or natural. Fire destroyed valuable timber, created ugly burned ecosystems, and sometimes threatened homes and people. In the last 100 years, the frequency of fire declined substantially. While it might seem counterintuitive, the lack of fire in these ecosystems is a disturbance that changes the structure of the ecosystem. Many species had undergone adaptive evolution to survive and thrive in an ecosystem with frequent fire.

These forests are dominated by various pine and sequoia species. These trees have thick bark to provide protection from fire. Some species, such as the lodgepole pine, have cones that are sealed closed. The cones require heat to open and release the seeds. After a fire the understory of grasses, shrubs and seedlings are removed and the seeds germinate easily with little competition for light and nutrients. Other vegetation, such as a common shrub called manzanita, have extensive root systems and store nutrients underground. Although the portion of the plant that is above ground burns, the underground portion survives and regrowth begins quickly. Annual wildflowers thrive on the newly-burned ground and when they die at the end of the season, their biomass is incorporated into the soil. This facilitates the establishment of more plant species as nutrient levels increase.

Frequent fire rarely kills mature trees because there is little buildup of fuel so the fires stay close to the ground. The fire scars at the base of pine trees show their resilience. These trees may have survived fires over hundreds of years.

Pine trees usually need light to remain the dominant trees in the ecosystem. In the absence of fire, pine growth and regeneration is limited by light availability. Other species that are shade tolerant may begin to outcompete the pine and their growth rate may slow. An ecosystem with frequent fire would typically have about 100 trees per acre making up the main canopy. In places where fire has been suppressed, more than 1000 trees per acre is common. These dense forests make it difficult for large birds and mammals to navigate in the ecosystem.

Forests without fire eventually facilitate the growth of shade-tolerant species. These species crowd the forest floor and change the overall structure of the forest. Figure 7 shows how a once open forest becomes crowded and overgrown.

After nearly 100 years of forest suppression, a new fire regime emerged. A buildup of fuels (from understory growth uninhibited by fire to clear debris) coupled with persistent drought caused large, stand-replacing fires. The buildup of fuel allowed the fire to travel from the ground to the tree tops, killing mature trees that had survived frequent ground fires in the past. Fire suppression had changed the ecosystem and caused an instability that led to the replacement of the mature forest with an early succession stage.

This dynamic occurs in all ecosystems. Disturbances change the number of species and the number of individuals of each species on a regular basis. Ecosystems with moderate amounts of disturbance have more species and perform more ecosystem functions. However, when viewed over a long swath of time and with less precision, it is clear that most ecosystems maintain the same overall functions. Pine forests remain pine forests and deserts remain desert. Scientists who study these changes are community or landscape ecologists. They use the tools described below to assess the health and characteristics of ecosystems.

Population DynamicsThe change in population is the population growth rate. To calculate the growth rate:

Any population with a positive growth rate will continue to grow exponentially. See Figure 8a. Exponential growth is interrupted by limiting factors. Limiting factors are biotic and abiotic conditions in the ecosystem that limit the growth of a population. The largest population the ecosystem can sustain over the long run is the carrying capacity.

The growth rate of a population may remain constant for several generations, but will decline to zero as it approaches the carrying capacity. This is called logistic growth. See Figure 8b.

Many of the interactions and abiotic conditions discussed previously contribute to limiting the size of a population. Limiting factors that keep the population near the carrying capacity are called density-dependent limiting factors. Growth rate slows for one of three reasons: birth rate declines, death rate increases or migration out of the population occurs. Examples of density-dependent limiting factors are food availability, light availability, predation and habitat availability.

Graphs of closely associated predator and prey populations show a negative feedback mechanism. As the population of the predator increases, the prey population decreases. Once the prey decreases to a certain level, the number of predators decreases. In this scenario, the carrying capacity is dependent on the population of the other species.

Density independent limiting factors disturb the existing ecosystem and decrease the population quickly. These changes decrease the carrying capacity. For example, a fire may directly kill some organisms, lowering the total population. Additionally, it probably killed the food source for that organism, which decreases the carrying capacity.

Counting Populations to Determine Ecosystem HealthPopulation ecologists determine whether or not a population is healthy by estimating population size. Since policies concerning threatened and endangered species hinge on accurately estimating population size and growth rate, these ecologists have standard methods for counting populations. Some organisms are easier to count than others, such as trees. But a forest is a large place, so density is often used to determine a total number. Population density is the number of organisms per area. For large organisms or those with large territories like trees and mountain lions, organisms per acre is the unit of measure. For smaller organisms or territories, organisms per meter is used. An accurate population count requires a strong understanding of the behavior of individuals within the population.

Ecologists use various statistical analyses to determine the overall diversity of an ecosystem. The statistical treatment is selected based on the characteristics of the ecosystem and the information the ecologist needs. Diversity is a combination of abundance and species richness. Abundance is the total number of individuals in each population. Species richness is the total number of different species in an ecosystem. See Figure 10 for examples. An ecosystem with many individuals, but few species may have lower diversity than an ecosystem with fewer individuals and more species. Diversity is one indication of a healthy ecosystem. A healthy ecosystem is resilient to change and has sustainable population numbers.

Summary Abiotic and biotic factors influence the distribution and abundance of organisms on

a global and local scale. On a global scale, climate has the greatest influence on the distribution and abundance of organisms. On a local scale, interactions between species as well as subtle differences in resource availability and microclimate influence distribution and abundance of organisms.

There are 3 types of symbiotic relationships. Parasitism occurs when the parasite benefits from the interaction and the host is harmed. Commensalism occurs when one organism benefits and the other is not effected. Mutualism occurs when both organisms benefit from the interaction.

Facilitation occurs when one species alters the ecosystem in a way that makes it more hospitable to another species.

The way an organism uses its environment is the organism’s niche. When the niches of organisms overlap, competition for resources increases. One way to reduce competition is to occupy a different niche. This leads to adaptive evolution, as organisms gain adaptations to fit their new niche.

Competition reduces fitness of the organisms involved but increases the overall fitness of the species as those with better adaptations have more reproductive success. Competition can exist between individuals of the same species and among individuals of different species.

A predator consumes a prey species, therefore their populations are related. As the prey population increases, so does the predator population. Subsequent population growth and decline are linked.

A population’s growth rate is determined by the birth rate minus the death rate, plus or minus the migration rate.

The carrying capacity is the maximum number of individuals a population can support over an extended period of time. Carrying capacity is affected by density-dependent limiting factors such as food availability, habitat availability and disease.

When a disturbance, such as a fire or flood, impacts an ecosystem, the types of species and abundance of organisms changes. However, the overall type of ecosystem rarely changes because ecosystems are resilient.

AP Biology Prep Course Unit 10

Ecology: Energy Flow and Nutrient CyclingThis unit reviews the carbon and nitrogen cycles and explores how these elements are essential to life. The carbon cycle and its connection to energy transformation and transfer are discussed in detail. Photosynthesis is also illustrated and reviewed. Additionally, the processes of respiration, decomposition, deposition and combustion are examined, and an interesting case study reviews bioaccumulation and biomagnification in ecosystems.

OverviewThis unit will review the carbon and nitrogen cycles and describe how these elements are essential to life. In addition, this unit will review the connection of energy flow to the carbon cycle and processes of photosynthesis, respiration, combustion and decomposition.

Elemental Components of Living ThingsAll life on Earth is composed of 4 main elements: hydrogen, oxygen, nitrogen and carbon. These four elements make up 96% of the mass of a human—the other 4% consists of trace elements. See Figure 1.

Since water is the most common molecule in the human body and oxygen has a fairly high atomic mass, oxygen makes up more than half of a human’s total mass. Water carries molecules and ions in solution and suspension to all parts of the body and helps maintain homeostasis. Carbon-based macromolecules make up the body’s structure in the form of proteins, carbohydrates, nucleic acids and fats. Carbon is important because it bonds four times, and each bond has the capacity to store a high amount of energy. This makes carbon an ideal molecule for building three-dimensional life that requires energy to be transferred and stored.

Matter Moves in CyclesCarbon and nitrogen move from the environment to living things and back to the environment in nutrient cycles. Other elements, such as phosphorus and calcium, also move within cycles. Hydrogen and oxygen are included in all cycles.

Elements move in cycles because, as described by the law of conservation of mass, matter cannot be created or destroyed. Elements move from one molecule to another as the result of chemical reactions. Each chemical reaction is accompanied by a transfer of energy. By tracing the path of matter, we can also trace energy flow throughout a cycle.

The Nitrogen CycleNitrogen is an important component of proteins and nucleic acids. Earth's atmosphere is about 78% nitrogen gas (N2), however, neither plants nor animals are able to use N2. The nitrogen gas must first be converted to nitrates. Plants are able to take up nitrates with

their roots and convert them to proteins and nucleic acids. Animals then eat the nitrogen-containing compounds.

Nitrogen gas is converted into nitrates by nitrogen-fixing bacteria, which live in the soil and on the roots of specific types of plants. Nitrogen-containing waste and decomposing organic material also contribute nitrogen to the soil. These materials are converted by different bacteria and decomposers to nitrates in a process called nitrification. The plants then absorb the nitrates.

Excess nitrates in the soil are converted back to N2 by the process of denitrification. Some nitrates make their way to ground water or surface water and contribute to algae blooms. In this way, nitrogen can be a pollutant. When too much algae is present, it ultimately starves the water of oxygen, which depletes life in the area.

Figure 2 shows that the nitrogen cycle is in fact two cycles:• Nitrogen from organic matter in the soil is processed and then taken up by plants and then animals who return it to the soil in waste products.• Inorganic nitrogen gas is processed in the soil by nitrogen-fixing bacteria and taken up by plants. It is also returned to the environment by bacteria in a process called denitrification.

The Carbon CycleCarbon dioxide mainly exists in two places on Earth—the atmosphere and the ocean. Near the surface of the ocean, atmospheric carbon dioxide and oceanic carbon dioxide mix. Cold water near the poles dissolves high levels of carbon dioxide that sinks and stays in the deep water, effectively removing it from the carbon cycle. There is 50 times more carbon dioxide in the ocean than in the atmosphere because of these deep-water reserves.

Carbon dioxide is removed from atmospheric and aquatic environments and converted to glucose through photosynthesis by autotrophs. Autotrophs make their own food and include plants, algae and many prokaryotes. These autotrophs then convert the glucose to other types of organic compounds for growth and energy requirements. See Figure 3.

Organic compounds are consumed by heterotrophs, which include animals, fungi and microorganisms. Heterotrophs need to eat or consume, in order to gain energy and obtain necessary nutrients. Heterotrophs that feed on autotrophs are primary consumers. Heterotrophs that eat primary consumers are secondary consumers and so forth. Each time a living thing eats another living thing, atrophic level is added to the food chain. The number of trophic levels in an ecosystem is directly related to the amount of solar energy that is converted to chemical energy during photosynthesis.

When organic material dies or is released as waste, specialized heterotrophs called decomposers break down the material in the same way that consumers break down material—they eat it. Decomposers convert complex organic molecules into molecules that can no longer be used as food in the ecosystem. Fungi, some animals and many microorganisms are decomposers.

A small amount of dead material is not immediately decomposed. Most of this dead material is in the ocean where it sinks to the deep ocean floor and is buried by marine sediment. This process is called deposition. There are very few, if any, decomposers in this environment. The material either becomes fossils or fossil fuels, and its carbon is effectively removed from the carbon cycle until it is burned.

Fossil fuels are organic compounds that have been reduced to hydrocarbons and include oil, natural gas and coal. Since the carbon bonds remain, they have a large amount of potential chemical energy that can be released by adding oxygen and heat. This type of reaction is called a combustion reaction. The combustion of hydrocarbons releases energy, carbon dioxide and other molecules. Until the industrial revolution, fossil fuels were rarely burned. Today, extraction and combustion of fossil fuels is an integral part of the carbon cycle.

All living organisms need energy to maintain homeostasis. This energy is acquired by organisms through consumption, decomposition or photosynthesis. This energy is released through respiration. Respiration almost always leads to a release of carbon dioxide to the environment.

Photosynthesis: The Light ReactionsPhotosynthesis is the process of using light energy to convert water and carbon dioxide to glucose molecules with high chemical potential energy. See Figure 5.

The potential energy stored in glucose originates as light energy from the Sun. It is stored until the plant requires energy to carry out a job such as transferring nutrients from the roots to the rest of the plant or opening and closing stomata to control the intake of carbon dioxide and loss of water.

The cells of a leaf contain a high density of chloroplasts, which is where photosynthesis occurs. Light reaches a plant as photons. Photons from the Sun interact with a series of membranes inside the chloroplasts. These membranes contain pigments that absorb the light at different wavelengths. In fact, a leaf appears green because the chlorophyll transmits and reflects green wavelengths of light while absorbing violet, blue and red wavelengths. See Figure 6.

Photosynthesis functions as a complex process of reactions. In the first part of photosynthesis, light reactions occur in protein-chlorophyll complexes called photosystem II and photosystem I to convert light energy to chemical energy. Follow along in Figure 7 while reading the steps below.

A. When a photon enters a pigment molecule in photosystem II, an electron is elevated to a high-energy state and moves throughout the chlorophyll until it reaches the reaction-center complex within photosystem I.

B. At the same time, a water molecule binds to an enzyme that splits the hydrogen and oxygen to replace the electron that was excited. Oxygen is produced as a product in this reaction and ultimately some of this oxygen will leave the plant and enter the atmosphere.

C. The energized electron is transferred to a primary electron acceptor, where it starts a series of reactions called the electron transport chain. The orange arrows in Figure 7 show the electron transport chain.

D. During this transport, the electrons pass through the cytochrome complex and create a proton (H+) gradient, causing protons to move across the membrane and releasing energy that drives the production of ATP.

E. Meanwhile, an electron is excited by light energy interacting with photosystem I.

F. The excited electron in photosystem I is captured by a primary electron acceptor and transferred along a second electron transport chain (this one is shown in yellow).

G. This creates an electron vacancy in photosystem I, which is promptly filled by the electron arriving from photosystem II.

H. The energized electrons from photosystem I are used by the enzyme NADP reductase to create NADPH.

Photosynthesis: The Calvin CycleNADPH and ATP both have high chemical potential energy as they move to the second part of photosynthesis, referred to as the Calvin Cycle. In the Calvin Cycle, carbon dioxide enters and uses the energy from ATP and the reducing power of NADPH to form sugar. In the process, ATP becomes ADP and NADPH become NADP+. These are cycled back to the first part of photosynthesis, where they are transformed back to ATP and NADPH. Figure 8 shows that water contributes the hydrogen while carbon dioxide provides the remainder of the mass of the glucose molecule. Solar energy continues to be converted to chemical potential energy when photons are absorbed, exciting electrons. Chemical reactions transfer this energy many times until, finally, it is stored in the bonds of glucose molecules.

RespirationNearly all organisms “combust” glucose for energy through the process of respiration. Carbon bonds are broken and when these bonds reform into new molecules, there is a net release of energy. This energy is used by living things to maintain

homeostasis. Without the input of energy, ordered systems become disorganized and cannot maintain homeostasis.

Energy-rich molecules are either produced or consumed by organisms. The organism converts some of these molecules to glucose. Oxygen and glucose are delivered to cells and once inside, move to the mitochondria. The mitochondria provide the surface for respiration, much like the chloroplasts provide the surface for photosynthesis.

Before entering the mitochondria, glucose is broken down into pyruvate by glycolysis. When pyruvate and oxygen enter the mitochondria, an enzyme provides the activation energy to start a cascade of chemical reactions that lead to the production of ATP. Aerobic respiration requires oxygen and creates about 36–38 molecules of ATP. As this ATP is used, energy is released to the environment as heat, a form of light energy.

Anaerobic respiration does not require oxygen and leads to a smaller amount of ATP production, only about two ATP molecules. There are two types of anaerobic respiration, lactic acid fermentation and alcoholic fermentation.

Like aerobic respiration, anaerobic respiration begins with glycolysis. This yields 2 ATP molecules. Alcoholic fermentation uses NADH to convert pyruvate to carbon dioxide and ethanol. The NAD+ is recycled to be used again. Lactic acid fermentation is similar except the product is lactate and no carbon dioxide is produced.

Energy Transfer between Trophic LevelsWhen one organism eats another organism, it consumes the energy that is stored in that organism's carbohydrates, proteins and lipids. However, of all the energy consumed by an organism, on average only about 10% is available to the next organism in the food chain. A graphic representation of this is an energy pyramid. See Figure 9.

The other 90% of energy is not available because it was either transformed to heat as the organism used energy for metabolic processes or was decomposed, which releases heat to the environment and removes the molecules from the food chain.

Bioaccumulation and Biomagnification of ToxinsEnergy-containing macromolecules, such as proteins, fats and carbohydrates, make up the majority of consumption in the food chain. However, minerals and trace elements are also taken up by plants, which are eaten by consumers. Some of these minerals and elements are essential, such as iron, phosphorus and calcium, while others are toxic and either cause harm to the organism directly or cause harm to organisms further up the energy pyramid.

In general, water-soluble toxins are processed by the liver and kidneys where they are detoxified and/or eliminated from the body. However, if the toxins are fat soluble, they are much more difficult to detoxify and often are deposited in fatty tissue. Bioaccumulation is the buildup of toxins in the tissue of an organism.

Persistent toxins remain in the environment long after they are deposited. These harmful toxins are stable, meaning they do not tend to react with other elements. Many are found both in abiotic samples, such as soil, and biotic samples, such as the tissue of fish. Biomagnification occurs when these persistent toxins enter the food chain, and become more concentrated as they move up the food pyramid. The carnivores at the top of the energy pyramid experience the highest load of toxins. See Figure 10.

Examples of persistent toxins are mercury, PCBs (an organic molecule used as a flame retardant and to insulate and cool electrical systems and transformers), and persistent organic pesticides like DDT. These toxins are still found in many ecosystems with high concentrations despite decades-long restrictions and bans on their production and use in the United States and many other countries.

Case Study: Orcas in Puget Sound and PCBsThe Southern Orca population in Puget Sound, along with other orca populations in the Pacific, have some of the highest recorded PCB levels of any animal ever tested. There are both physical and biological factors contributing to the high toxicity of this particular population. For example:• The orcas are year-round residents of Puget Sound.• The Puget Sound does not circulate water very effectively with the Pacific Ocean.• There are many port cities that have had operating industrial areas along the shoreline since before World War II, decades before PCBs were banned. Figure 11 shows the long shoreline of Puget Sound and the connection to the Pacific Ocean via the Strait of Juan de Fuca.

Biologically, this orca population is the fourth-level consumer in the energy pyramid, feeding almost exclusively on salmon. See Figure 12 for an example of a typical Puget Sound food chain with orcas as the top carnivore. Note that the PCBs are not generally introduced by current pollution, but are trapped in sediments, which are carried to Puget Sound, and in the water cycle.

Orcas have a higher percentage of fat than many other animals, so they have a greater capacity to store toxins. PCBs cause immunotoxicity, and they are hormone disruptors. This leads to a high susceptibility to other diseases due to a suppressed immune system and endocrine diseases.

Since 1972, the Southern Orca population has fluctuated from about 65 individuals to 100 individuals. At the end of 2014, the population was 79. Prior to 1972, orcas in Puget Sound were regularly captured and placed in captivity, leading to the small starting population. The historic carrying capacity is estimated at 125. In the past ten years, the population has declined at an average rate of almost 1%, however the population growth rate has fluctuated from a nearly 7.3% decline in 2008 to an increase of 5.7% the following year. See graph at the right. The combination of a small population, bioaccumulation of toxins and an unstable supply of salmon put the Southern Orca population at risk of extinction. This population of Orcas is an endangered species and protected by the Marine Mammal Protection Act, yet there have been no solid signs of recovery.

Summary Living things need energy and nutrients to maintain homeostasis. Energy is

transformed and transferred through an ecosystem via several nutrient cycles.

Nitrogen is essential for construction of proteins and nucleic acids. Only bacteria are able to convert nitrogen gas to nitrates, which plants are able to take up directly. Bacteria also convert excess nitrates back to nitrogen gas.

The carbon cycle is important to the cycling of carbon and transfer of energy. The main processes of the carbon cycle are photosynthesis, respiration, consumption, decomposition, deposition and combustion.

Photosynthesis is a process that uses light energy to convert water and carbon dioxide to glucose molecules. Pigments in chloroplasts absorb light energy, which excites electrons and begins the photosynthesis process.

Respiration processes use energy that has been stored as chemical potential energy. Aerobic respiration is efficient, but requires oxygen. Anaerobic respiration is less efficient, but does not require oxygen. All types of respiration except lactic acid fermentation release carbon dioxide.

As energy is transferred from one trophic level to the next, only about 10% of the energy is passed along. This limits the number of trophic levels in an ecosystem.

Fat-soluble toxins can bioaccumulate in the fatty tissue of organisms. Higher trophic level organisms receive a concentrated amount of these toxins. These toxins persist in the environment and endanger the survival of top-level predators.