Welcome AP Biology teachers

Welcome AP Biology teachers

Chapter 2: Basic Chemistry

Chapter 2, Students need to know…

• basic chemistry: covalent vs. ionic bonds

• Essential elements of life: C, H, O, N, P, S

• What a valence shell is, and why it matters

• Atoms with open valence shells (e.g. C, and O) are going to be reactive

• Basic periodic trends, but focus mainly on the essential elements of life and the “go to” trace elements: K, Na, Ca, Mg, Fe

Important THEME Teach the Skill

• Compound – Two or more elements bonded together resulting

in NEW chemical properties to emerge for the compound.

– This is an example of the Emergent Properties theme. (Fig. 2.2) An example: Water (H20) – a stable liquid and can sometimes be used to out a fire. Hydrogen by itself is a flammable gas; Oxygen by itself is also a flammable gas.

IMPORTANT BIG PICTURE ITEM

– Electrons (These particles carry a negative charge.) (They are located in the “Electron cloud”. The cloud is created because electrons move at the speed of light which creates a blur around the atom.)(The electrons moving, which is called kinetic energy, is why they are associated with energy and batteries. It is potential energy when they are bonded.

• The number of electrons can change. (Atoms with different numbers of electrons than the normal amount for that element are called Ions.)

IMPORTANT

• Energy (represented by the symbol “E”)– Energy comes from the rapid movement of electrons

(e-) normally, but it could be neutrons too.– Potential Energy (PE) – Energy of position. (Usually

refers to electrons “locked” in a chemical bond.)– Kinetic Energy (KE) – Energy of movement. (Usually

refers to electrons that can move freely.)– E levels or e- shells – Where the electrons or E is

located within an atom or molecule.(FIG. 2.7)– Adding energy to electrons makes them move farther

out; losing energy causes them to move inward.

IMPORTANT

– Valence Shell- Where the outer most electrons are located on an atom.

– Valence e- - Refers to the outer most electrons. (These are the most important for chemical bonds and properties.)

– Valence – Refers to the bonding capacity of an atom. (Depends on the number of valence electrons.)

Fig: 2.8

IMPORTANT and Teach the skill

– Covalent Bonds (Fig. 2.11)• This type is the strongest type of chemical bond.

– Results from sharing electrons between elements or molecules to fill BOTH outer shells.

• They always create a molecule. (The size of the molecule may differ though.)

– Two or more atoms together of any kind.• Polar molecules (Fig. 2.12) carry an electrical charge at opposite

poles(poles refers to the “ends” of the molecule) and non-polar molecules do not have an electrical charge

• Electronegativity– Refers to the element’s or molecule’s DESIRE to acquire or release

electrons.– Hydrogen atoms (LEASTelectronegative biological element)(It wants to

RELEASE e-)– Oxygen (MOST electronegative biological element)(It wants to ACQUIRE

e-)

Oxygen is at the end

Important– Ionic Bonds

• These are Fairly strong bonds while dry – but are weak in water so they dissolve into ions.

• These bonds are created by swapping electrons between elements so that each element can fill it’s outer most shell. (Fig. 2.13)

• When dissolved in water Ions are created. (Gatorade is a ion loaded drink.)

– Cations – possess a positive charge because it has more protons than electrons.

– Anions – possess a negative charge because it has more electrons than protons.

– THESE LOVE WATER. (because water is a polar molecule too.)


– Hydrogen Bonds (Fig. 2.15)• Fairly weak bonds. (It is “like” a magnet) (A positive

Hydrogen attracted to a negative “Substance”…USUALLY oxygen.)

• THESE ARE THE MOST IMPORTANT BIOLOGICAL BONDS

Important andTeach the skill

– Van der Waals Interactions• These are temporary bonds. (Usually a fraction of a second.)

(Involves enzymes mostly.)

• These INTERACTIONS are created when electrons clump on one side of an atom making that side temporarily “negative” and the other side “positive” so that charged particles can attach momentarily and then they unclump, because electrons are moving, and the “interaction” disappears because of loss of the charge

AP Biology

Chapter 3: Properties of Water

Chapter 3, students need to know…

• water is a polar molecule• water molecules “stick together” via hydrogen bonds• water has a relatively high specific heat, • Water has a high heat capacity• Why these characteristics of water matter to biological

systems• Water can ionize into H+ and OH- and this is the

chemical basis of the pH scale• The basics of the pH scale (acids vs. bases)• How to describe adhesion and cohesion, • How to identify hydrophobic & hydrophilic molecules.


• Water is a Polar Molecule– Water’s polarity allows for it to make HYDROGEN

bonds easily which helps with nutrient transport.– This polarity makes it possible to conduct

electricity very well. (Remember, electricity is flowing electrons.)

– The polarity allows for a single water molecule to bind to 4 other water molecules at a time. ( Fig. 3.2)

Important and Teach the skill

• Cohesion– This term refers to water molecules binding to other water

molecules.– This property is made possible because of HYDROGEN bonds.– This is important in the Cohesion-Tension Principle that

describes how water moves upward in plants xylem tissues by making water “chains”. (Fig.3.3)

• • Adhesion

– This term refers to water molecules binding to something other than water molecules. (Fig. 3.2)

– This property is made possible because of HYDROGEN bonds.

Cohesion Visual

Important and Teach the Skill

• Surface Tension– This is the linking together of water molecules on

the surface of a body of water. (Fig. 3.4)– This property is made possible because of

HYDROGEN bonds.

Surface Tension Visual

IMPORTANT BIG PICTURE ITEM• Water helps with Temperature Regulation in organisms and on the earth.

– Water can act as a huge heat “piggy” bank. (Such as when the sunlight hits the oceans and other water bodies and the water heats up SLOWLY as it absorbs the light energy.)

– This property is made possible because of HYDROGEN bonds.– It takes tremendous amounts of E to break ALL four hydrogen bonds at once

and turn liquid water to a gas.– This is a important worldly effect as it helps to keep the temperature of earth

stable (the water absorbs the energy of sunlight, so we don’t fry, and then releases that same energy at night, so we don’t freeze… remember that one side of earth is always in the sun and the other side is dark so temperature is stable.)

– Kinetic E terms associated with water.• Heat – This measurement is the total amount of kinetic E in a substance.• Temperature – This measurement is the intensity of all the heat in a substance as the

molecules move. (The faster they move… the hot it gets and the slower they move… the colder it gets.)

IMPORTANT • Specific Heat

– This measurement is the amount of heat required to raise or lower 1g of a substance 1⁰ Celsius.

– The specific heat of water = 1 Calorie = 4.2 Joules. • Water requires a huge amount of E to raise 1 gram of it 1⁰Celcius. (1

gram = 1 cm³)• The HYDROGEN bonds prevent kinetic E from increasing. (Need to

break 4 at a single time!)• Water vs. Steel (Steel has a very low specific heat and that is why it

gets hot QUICKLY.)– Think of it as the ability to RESIST a change in temperature.– The fact that humans and other organism are mostly water,

this keeps us from burning up in the sunlight literally.


• Evaporative Cooling– Putting heat E into water, causing the water to

evaporate and carry the heat E away from the body thus providing a cooling of the organism to occur as the E leaves.

– Wind increases the effect of cooling by carrying the water vapor away from the body. Humidity, water vapor in the air, decreases the effect because water can’t evaporate into the air as it is already full of water vapor.

Evaporative Cooling Demo

Important Terms

• Water is the Universal Solvent– Solvent – Liquid that is doing the dissolving of

another substance.– Solute – Substance being dissolved in the solute.– Solution – Substance possessing equal

distribution of material. (Kool-aid is a good example.)

Important Terms• Hydrophobic “hydro” means water; “phobic”

means fear of– Water cannot attach to the substance because the

substance is non-polar.– The substance “hates” water’s polarity.

• • Hydrophilic “philic” means love of

– Water can attach to the substance because the substance is polar.

– The substance “loves” water’s polarity.•

Important Terms• WET” Chemistry Terminology

– Mole (mol)• Refers to a measurement of molecules that is relative to its

molecular weight. • Avogadro’s Number 6.02 x 10²³

– # of molecules of that particular substance present in a 1 mole.• Find the molecular weight of a molecule using the Periodic

Table and then weigh out that many grams of the substance and that amount is equal to 1 mole. (Sucrose = 342 so I need 342 grams)

– Molarity• Term for telling how many moles of a substance are

dissolved in a solution. (usually water)

AP Biology

Chapter 4:Properties of Carbon


• Carbon is tetravalent, and thus lends itself to a variety of functional molecules.

• Most biologically important molecules are macromolecules

• Macromolecules are polymers comprised of monomers

• Polymers are formed by dehydration synthesis

• Polymers are broken down by hydrolysis

• How to recognize the “Big 6” Functional groups.

– The first three have O, and H in some form

– The other three are stand alones with S, N, or P in the functional group.

– The Essential elements of life are C, H, O, N, P, S…this is not rocket science.


• Carbon’s e- configuration (Figs. 4.3 and 4.4)– Carbon has versatility in four directions because of

its Tetravalence. (Tetra means “four”)– The tetravalence allows carbon to act like an

intersection in the building of an organic molecules.

– Covalent Bonding Capabilities of Carbon• Single Bond between Carbon atoms.(shown as: C-C)• Double Bond between Carbon atoms. (shown as: C=C)• Triple Bond between Carbon atoms. (shown as: C=C)

LE 4-3

MolecularFormula

StructuralFormula

Ball-and-StickModel

Space-FillingModel

Methane

Ethane

Ethene (ethylene)


• Hydrocarbons– Molecules containing mostly Carbon and Hydrogen.– Most hydrocarbons are Energy Sources. (Some

examples are: Fossil fuels, Oils, And Fats)– Hydrocarbons are important parts of cell membranes.

(The tails of phospholipids)(Fig. 5.13 on page 76)– All hydrocarbons are extremely hydrophobic because

the nonpolar molecules. (Hates water’s polarity.)

Carbohydrates

Hydrocarbon tails

Important and Teach the Skill

• Isomers– These are molecules with the same molecular formula but

different molecular structures.– Three types of isomers exist (Fig.4.7)

• Structural Isomers – Same composition but have “different shapes”.

• Geometric Isomers – Change is centered “around a central double bond”.

• Enantiomers – These are “mirror images of each other”, like your hands.

– To types exist: Right orientation (D) and left orientation (L).– They will have very different properties (such as Fig.4.8) and

Thalidomide.• Example of Emergent Properties and Structure = Function themes.

LE 4-7

Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane.

Geometric isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon.

cis isomer: The two Xsare on the same side.

trans isomer: The two Xsare on opposite sides.

L isomer D isomer

Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers are designated the L and D isomers from the Latin for left and right (levo and dextro). Enantiomers cannot be superimposed on each other.

Ryan’s Objectives

• Discuss the importance of carbon, the “big 6” functional groups, monomers vs. polymers and dehydration synthesis vs. hydrolysis (notice the importance of water here)

IMPORTANT BIG PICTURE ITEM• Functional Groups Associated with Organic Molecules (Fig.4.9 and 4.10)

– These are the sites of most organic molecules chemical reactions or properties. (They have a function to do.)

– Example of Structure = Function theme. – Hydroxyl s (-OH)

• This group allows molecules to act as an alcohol or polar molecule.• Name usually ends with “ol”.

– Carbonyls (Only has one double bonded oxygen.) (It takes ONE stroke to make a lower case “n”.)

• Aldehydes (A is at one end of the alphabet.)(Carbonyl is located on the end of the molecule.)• Ketones (K is in the middle of the alphabet.)(Carbonyl is located in the middle of the molecule.)

– Carboxyl (Has two oxygens…one double bonded and one singled.)(It takes TWO strokes to make an “x”)

• These molecules can act as an acid by losing a Hydrogen atom and can also possibly polar too.– Amine (Contains Nitrogen)

• Can act as bases by picking up free H+.– Sulfhydrls (Contains Sulfur)

• Sulfur can make Di-Sulfide bridges for “pockets” in protein formation .(Fig. 5.20 on Pg. 83)– Phosphate ( Contains Phosphorus)

• These molecules are usually involved in E Transfers. (ATP) Also acts like an Anion.(negative)

LE 4-10ab

STRUCTURE

NAME OF COMPOUNDS

Ketones if the carbonyl group iswithin a carbon skeleton

EXAMPLE

Acetone, the simplest ketone

A ketone and an aldehyde maybe structural isomers withdifferent properties, as is the casefor acetone and propanal.

Aldehydes if the carbonyl group isat the end of the carbon skeleton

Acetone, the simplest ketone

Propanal, an aldehyde

FUNCTIONAL PROPERTIES

LE 4-10ac

STRUCTURE

NAME OF COMPOUNDS

Carboxylic acids, or organic acids

EXAMPLE

Has acidic properties because it isa source of hydrogen ions.

Acetic acid, which gives vinegarits sour taste

FUNCTIONAL PROPERTIES

The covalent bond betweenoxygen and hydrogen is so polarthat hydrogen ions (H+) tend todissociate reversibly; for example,

Acetic acid Acetate ion

In cells, found in the ionic form,which is called a carboxylate group.

AP Biology

Chapter 5: Macromolecules

IMPORTANT and Teach the Skill

• Macromolecules – “Macro” means “large”– Polymers “poly” means many; “mer” means unit.

• These are formed from individual units called monomers “Building Blocks”.• Monomers are linked together by covalent bonds. Organisms need these to

stay intact so the strongest type of bond is used.• These are another example of the theme: Structure = Function.

– Macromolecules are formed by Dehydration or Condensation Reactions. (Fig. 5.2)

• Hydroxyl and Hydrogen must be aligned properly to produce water.• This orientation of molecules and making of a bond requires E.• Enzymes help speed up the rate of the reaction.

– Macromolecules are broken apart into individual monomers by Hydrolysis reaction. “lysis” means to split.

• This process Releases E in the bond breakage.• The process needs water (hydroxyl and hydrogen) to fill the open bonds on

the monomers. • Enzymes speed up the rate of the reaction here too.


• This is a monster chapter. I divide it up into the energy molecules and the structural molecules.

• Part 1: Carbohydrates:– CH2O are primarily energy and structure

molecules– Glucose is the “king of the monosacchrides”– Recognize the structure and know the function of

the polysaccharides…• Amylose, Glycogen, Cellulose, and Chitin

– How the strucutre of these molecules relates to their function

Carbohydrates:IMPORTANT

– The chemical composition is: Carbon = Oxygen; 2x as many hydrogen also present.

– The names usually end with “ose”. Such as Fructose, Glucose, Sucrose.

– These are primary E sources for cells.

CarbohydratesSee the Carbonyls and Hydroxides?


• Part 2: Lipids• Lipids are a diverse set of molecules, all of

which are hydrophobic• The difference between saturated and

unsaturated fats• How to recognize a steroid• That chloresterol is similar to a steroid• Phospholipids are ambiphatic molecules, and

they are the primary component of cell membranes

Lipids: IMPORTANT– These macromolecules are fats, oils, waxes, and steroids.– Most lipids are hydrophobic molecules. “Hydro” means

“water”; “phobic” means “fear of”.– Lipids are mainly composed of Hydrocarbons (All the

Hydrogen means lipids have 2x The E of Carbs.)– Two Main parts (Fig.5.11)

• Fatty Acid (Hydrocarbon)(Number of Carbons will be a multiple of 2 if it is made by living cells)

• 3 Carbon Glycerol molecule (alcohol) to hold the whole molecule together.

• Lipids use a covalent bond called an Ester Linkage to hold the fatty acid and glycerol together.

• An Ester linkage is a Carboxyl of the Fatty Acid paired with a hydroxyl of the glycerol molecule

LE 5-11b

Ester linkage

Fat molecule (triacylglycerol)

IMPORTANT

• Steroids, Hormones, and Cholesterol– A steroid has 4 carbon rings with the top ring looking like a

house. – What makes them different are the attached functional

groups. These functional groups help determine the function of the steroid.

Steroid Structure


• Part 4a: Proteins:• Proteins may be the most important of the

macromolecules• Proteins are usually pictured as purple images in

text books• Proteins have a variety of structural and

biochemical roles in cells.• Perhaps the most important roles of proteins

include enzymes, channel proteins and proton pumps, communication devices across the cell membrane and structural components of cells.

Proteins:Important• Proteins (A. K.A. Polypeptides) and Enzymes

(Enzymes are a TYPE of protein.)– Proteins make up greater than 50% of an organisms

dry weight.– This is another important example of the theme:

Structure = Function. (These are very large 3-D Molecules.)

– The monomer “building blocks” are Amino Acids (There are 20different Amino Acids that can be involved in making proteins. Proteins and enzymes usually have hundreds of Amino acids in their structure.)

Important– Amino Acids have 4 different parts to them:

• Carboxyl end (COOH) – This part acts as the acid because it can give off the hydrogen.

• Amine end (NH2) – The end can act as a base by accepting a third hydrogen.• Alpha (α) Carbon – This is the central Carbon that holds the whole molecule

together.• R group (This is the most important part as it gives each amino acid its

distinctly different property. Notice all 20 amino acids have a different R group.) (Fig. 5.17)

– Individual Amino Acids (monomers) are bonded together by a peptide bond. An amine end of one amino acid is positioned to combine with a hydroxyl of the Carboxyl of the second amino acid. The open bonds left behind by removing to make water allows for a bond between the carbon and nitrogen to be created. When we put many amino acids together, we get a POLYPEPTIDE or protein.

LE 5-UN78

Aminogroup

Carboxylgroup

carbon

IMPORTANT BIG PICTURE ITEM– Arrangement and Quantity of Amino acids affect the

structure and function of that protein or enzyme. (Structure = Function) (Fig. 5.20)

• Primary Structure (Represented by the symbol - 1’ )– This refers to the sequence of bonded Amino Acids. THINK

“SEQUENCE” for Primary structure.– Fredrick Sanger (in 1948) discovered the first protein Amino Acid

sequence. It was for insulin.– Primary Sequence is REALLY IMPORTANT; just look at the

difference between Sickle-Cell Disease and normal red blood cells. Just changing the SIXTH amino acid in the primary sequence creates this horrible disease. The easy way to remember that it is the SIXTH amino acid that changed, remember the number of the devil 666. Bad number = bad disease. (Fig. 5.21)

Fig: 5.20 – Insulin 1’ sequence


• Secondary Structure (2’ )– HYDROGEN bonds allow for overlapping and coiling to occur in

the “folding” of the protein into that 3-D shape. All proteins must be “folded” in order to work. THINK “FOLDS AND COILS” for secondary structure.

– Coiling – Is referred to as an Alpha (α) helix.– Overlapping – Is referred to as a Beta (β) pleat sheets.

• Tertiary Structure (3’ ) (“ Tert” means “third”)– Di-sulfide bridges form Hydrophobic “pockets” to keep some

Amino Acids away from water. It keeps the hydrophobic ones away from water.

– To make the Di-Sulfide bridge the Amino Acid Cystein is needed.

• THINK “DI-SULFIDE POCKETS” for Tertiary structure.

2’ structure

3’ Structure


• Part 3: Nucleic Acids

• That nucleic acids exist and they will be the focus of an entire unit later this fall!

Nucleic Acids: IMPORTANT• Nucleic Acids

– Monomers are called Nucleotides– Polymers are called DNA or RNA- It depends on the 5

Carbon sugar present in the monomer.– These are the source of genes and hereditary

information primarily.– Two Types (Fig. 5.26)

• DNA – This polymer is the “Master Million Dollar Blueprint”.– It is kept “safe” in the nucleus. (Nucleus is like a vault to keep the

DNA in.)• RNA – This polymer is like a “cheap 10 cent copy” of the

“Master Million Dollar Blueprint”. It is disposable/recyclable. It makes messenger RNA and other RNA molecules.

Important– Pyrimidines ( C, T,U )

• Big name small molecule. (These have 1 Carbon ring in the Nitrogen base.)

• “Counting steps Takes you Up the Pyramid” is the easy way to remember them.

– Purines ( A, G,)• Small name big molecule. (These have 2 Carbon rings in the

Nitrogen base.)• “Alabama is Purely Greater than Auburn” or “Auburn is Purely

Greater than Alabama” is an easy way to remember. It just depends on who you like more.

– It is Always a pyrimidine paired with a purine.– Individual nucleotides joined by a Phosphodiester bond.

The phosphate of one nucleotide is joined with the 5 Carbon Sugar of the previous nucleotide.

Fig: 5.26

IMPORTANT BIG PICTURE ITEM– THE SEQUENCE DETERMINES WHAT PROTEIN OR

ENZYME IS MADE• Structure = Function and Emergent Properties• That is why it is the “BLUEPRINT”.

• • Genes and Evolution

– The more Nucleotide sequence “genes” in common; the more closely related the organisms are.

– The fewer Nucleotide sequence “genes” in common: the more distantly related they are.

AP BIOLOGY

Chapter 8:Metabolism and Enzymes

Chapters 5 & 8, students need to know…

• Part 4b:Proteins Continued• How to recognize primary through quaternary structure • The bonds that hold each level of organization together• Enzymes are the chemical gate keepers of a cell’s metabolism• Enzymes are substrate specific• Enzymes have an active site, a place where substrates are “worked on”• Enzymes merely speed up reactions, they do not add energy to a

system• Enzymes are not consumed by the reactions they facilitate, therefore a

little enzyme goes a long way• Enzymes, like all proteins, are influenced by environmental conditions

like temperature, pH, and salinity. All enzymes have an optimal set of environmental conditions

• Enzymes traditionally end in “ase”, and their name describes their function.

• They will encounter dozens of enzymes over the course of AP Biology.

IMPORTANT BIG PICTURE ITEM• Metabolism

– The sum of all the chemical reactions occurring in an organism.– The collective process has two separate phases.

• Catabolism – This refers to the breaking down of a molecule.– This process releases “potential” E found in the chemical bond between

monomers.– This is an exergonic reaction because it releases heat to the environment– Think Catastrophe; breaking up things.

• Anabolism –This is the assembly of molecules.– This process requires “Kinetic” E to position molecules in away so as to create

a chemical bond between monomers.– This is an endergonic reaction because it absorbs energy from the

environment.– Think Anabolic steroids; these BUILD muscle.

• This is a great example of E Coupling – two different processes united by common energy

IMPORTANT BIG PICTURE ITEM• Thermodynamics

– The study of Heat E (Thermo) and its properties (dynamics).– First Law of Thermodynamics (Also called the Principle of the

Conservation of E)• E cannot be created nor destroyed ONLY transformed or transferred.

– Second Law of Thermodynamics• Every E transfer increases the entropy of the universe.

– Entropy- means disorder; unable to do work because it is in a LOW state of order

• Sunlight(high quality E) going in and heat (low quality E)coming out; it can’t do work

• Conception to birth to death is how life relates to second law– You are at your most organized state as a single cell; as you “progress” you go

move toward a state of entropy (death).

•

Important

• Free E (represented as “G”)( Fig. 8.6)– It is referred to as “free” because E is available to

perform work. (Mainly making ATP or GTP in a cell.)– G=H-TS (This is the formula for calculating Free E.)

• G- Free E (This amount goes from positive to negative as catabolism of food occurs.)

• H- Total E in the system. (Starts large but becomes smaller as food is broken down.)

• T- Temperature constant (Measured in Kelvin, ⁰C +273.)• S- Amount of Entropy (Starts at 0 but becomes larger as the

reaction continues to produce heat and the highly organized food molecules are broken apart more and more.)


– If ΔG is negative, then there is E available “free” to perform work. (It is Spontaneous.)(It is Exergonic.)

• This is the result of Cellular Respiration and Digestion. (Catabolic processes release free E.)

– If ΔG is positive, then there is E that is not available because it is “locked up” and can NOT perform work. (It is Non-Spontaneous.)(It is Endergonic.)

• Photosynthesis is a good example (Anabolic processes store free E.)

Important• ATP (Adenosine Tri-Phosphate)(Fig: 8.8)

– Made from Ribose sugar and the nitrogen base Adenine.– Has 3 NEGATIVE phosphates linked together which makes it

HIGHLY unstable like a “COMPRESSED SPRING”. Unstable, means it has the capacity do perform work remember.

– ATP converting to ADP has a ΔG = -13J ; ADP being converted to ATP has a ΔG = 13J (The energy needed to make this bond comes from the “free” e in our food as it is broken down.)(ADP is recycled back to ATP.)

• D. Phosphorylation (Fig: 8.11)• The attaching of an unstable phosphorus ion to another molecule to

make it unstable and thereby able to perform work. (Take the phosphorus off and it quits working.)

•

Potential Energy vs. Kinetic Energy

Ryan’s Objectives

• 3) Teach the essential role of enzymes as biological catalysts.How? Perform AP Lab 2: Enzyme Catalysis. Options include: the College Board’s published AP Lab 2, using probe ware and Oxygen or pressure sensors, or using Hudson Alpha’s cholinesterase lab

IMPORTANT• Enzymes

– These molecules are Biological Catalysts.• Proteins that speed up and control the rate of a chemical reaction.

• THEY ARE RECYCLED; THEY ARE NOT CONSUMED BY THE REACTION.

• Enzymes are Selective in what they will work with. We used to say they had a “lock and key fit” (old term); we now say it “fits like a glove or has an induced fit”. (new term)

• This is like putting on a latex glove… it stretches to conform to the shape of your hand.

• Enzyme names usually end with “ase”.•

IMPORTANT BIG PICTURE ITEM• Free E of Activation (Fig: 8.15)• This refers to the Free E used to start a chemical reaction in

motion. (Essentially is the energy for getting the molecules moving and positioned so that it is possible to combine or be torn apart.)

• The energy of activation is lowered by the action of enzymes. (Enzymes reduce by GRABBING the molecule and positioning it correctly… we don’t have to WAIT for nature to do it.)

• Enzymes also replace the need for heat in most chemical reactions (remember heat can make molecules move faster) so that organisms don’t burn up during metabolism

LE 8-15

Course ofreactionwithoutenzyme

EA

without enzyme

G is unaffectedby enzyme

Progress of the reaction

Free

ene

rgy

EA withenzymeis lower

Course ofreactionwith enzyme

Reactants

Products

IMPORTANT BIG PICTURE ITEM• Factors that can affect enzymes ability to work optimally.

(“optimal” means “best” or “Fastest”)• Temperature – freeze/cold (cold things don’t move quickly)

or Heat causing it to Denature (melt).• pH of the environment• Salt concentrations• The Optimal Conditions for most human enzymes:

• 98.6˚F (35 - 40⁰C)• pH usually between 6 – 8 (The human body’s pH of blood is an

average of 7.4.)• Remember, this is an unstable (dynamic) environment. There is an

upper limit and a lower limit for enzymes. Beyond the limits, bad things begin to happen. So it is basically, trying to stay between the limits. The limits of “life”.


• Inhibitors• The name implies that these molecules negatively affect an

enzymes ability to work optimally. These slow down or stop the rate of the chemical reaction.

• Two types of Inhibitors exist, based on the location of the enzyme that is affected: (Fig: 8.19)

• Competitive- These molecules compete for the active site. (This is because of similar shape.)

– These molecules slow down the reaction rate. (These molecules will be removed.)

• Non-competitive –These molecules attach somewhere other than the active site causing the shape of the active site to change so the substrate can’t fit into it.

– These molecules cause the reaction to stop completely. (These molecules may affect the enzyme permanently or maybe temporarily in the case of an Allosteric connection.)

LE 8-19Substrate

Active site

Enzyme

Competitiveinhibitor

Normal binding

Competitive inhibition

Noncompetitive inhibitor

Noncompetitive inhibition

A substrate canbind normally to the

active site of anenzyme.

A competitiveinhibitor mimics the

substrate, competingfor the active site.

A noncompetitiveinhibitor binds to the

enzyme away from theactive site, altering the

conformation of theenzyme so that its

active site no longerfunctions.


• Feedback Inhibition (Fig: 8.21)– A product IN EXCESS shuts down the reaction that

is taking place at an earlier point in the pathway.– Prevents “waste” of precious materials and

energy by not making more of what is not needed at that time.

LE 8-21

Active siteavailable

Initial substrate(threonine)

Threoninein active site

Enzyme 1(threoninedeaminase)

Enzyme 2

Intermediate A

Isoleucineused up bycell

Feedbackinhibition Active site of

enzyme 1 can’tbindtheoninepathway off

Isoleucinebinds toallostericsite

Enzyme 3

Intermediate B

Enzyme 4

Intermediate C

Enzyme 5

Intermediate D

End product(isoleucine)

Documents

Welcome AP Biology teachers