AP Biology

AP Biology

AP Biology

Enzymes

Chapter 8.4, 8.5

AP Biology

Activation energy§ Breaking down large molecules

requires an initial input of energyu activation energyu large biomolecules are stableu must absorb energy to break bonds

energycellulose CO2 + H2O + heat

AP Biology

Too much activation energy for life§ Activation energy

u amount of energy needed to destabilize the bonds of a molecule

u moves the reaction over an “energy hill”

Not a match!That’s too much energy to expose

living cells to!

glucose

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Reducing Activation EnergyCatalysts

Pheeew…that takes a lot

less energy!

reactant

product

uncatalyzed reaction

catalyzed reaction

NEW activation energy

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Catalysts§ Reduce the amount of energy to start a

reaction§ Cells use ENZYMES to reduce

activation energy

DG

Call in the ENZYMES!

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QUESTION 1:How do enzymes speed up chemical reactions?

AP Biology

Enzymes § Biological catalysts

u proteins (& RNA)u facilitate chemical reactions

§ increase rate of reaction without being consumed§ reduce activation energy§ don’t change free energy (DG) released or required

u required for most biological reactionsu highly specific

§ thousands of different enzymes in cellsu control reactions of life

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AP Biology

Enzyme Vocabularysubstrate

§ reactant which binds to enzyme§ enzyme-substrate complex: temporary association

product§ end result of reaction

active site§ enzyme’s catalytic site; substrate fits into active site

substrate

enzyme

productsactive site

“transition state”

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Properties of Enzymes§ Reaction specific

u each enzyme works with a specific substrate § chemical fit between active site & substrate

forming H bonds, ionic bonds§ Not consumed in reaction

u single enzyme molecule can catalyze thousands or more reactions per second§ enzymes unaffected by the reaction (reusable)

§ Affected by cellular conditionsu any condition that affects protein structure

§ temperature, pH, salinity

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Naming Conventions§ Enzymes named for reaction they catalyze

u sucrase breaks down sucroseu proteases break down proteinsu lipases break

down lipidsu DNA polymerase builds DNA

§ adds nucleotides to DNA strand

u pepsin breaks down proteins (polypeptides)

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QUESTION 2:Use slides 3 – 6 to give FOUR WORDS that describe enzymes.

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Lock and Key model§ Simplistic model of enzyme action

u substrate fits into 3-D structure of enzyme’ active site§ H bonds between substrate & enzyme

u like “key fits into lock”

In biology…Size

doesn’t matter…Shape matters!

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AP Biology

Induced Fit model§ More accurate model of enzyme action

u 3-D structure of enzyme fits substrateu substrate binding cause enzyme to

change shape leading to a tighter fit § “conformational change”§ bring chemical groups in position to catalyze

reaction

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QUESTION 3:What is the difference between the lock and key model and the induced fit model? Which model is more accurate?

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How do enzymes lower Ea?§ Variety of mechanisms to lower activation

energy & speed up reaction1) In synthesis, active site orients substrates

in correct position for reactionw enzyme brings substrate closer together

2) In digestion, active site puts stress on bonds that must be broken, making it easier to separate molecules

3) Providing a favorable microenvironment(ex: pH)

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Got any Questions?!

AP Biology 2007-008

Factors that Affect Enzymes

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Factors Affecting Enzyme Function§ Enzyme concentration§ Substrate concentration§ Temperature § pH§ Salinity§ Activators§ Inhibitors

catalase

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Enzyme concentration

enzyme concentration

reac

tion

rate

What’shappening here?!

QUESTION 4:IN YOUR OWN WORDS,describe what this graph is showingin a complete sentence.

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Factors affecting enzyme function § Enzyme concentration

u as ­ enzyme = ­ reaction rate§ more enzymes = more frequently collide with

substrate u reaction rate levels off

§ substrate becomes limiting factor§ not all enzyme molecules can find substrate

enzyme concentration

reac

tion

rate

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AP Biology

Substrate concentration

substrate concentration

reac

tion

rate

What’shappening here?!

QUESTION 5:IN YOUR OWN WORDS,describe what this graph is showingin a complete sentence.

AP Biology

Factors affecting enzyme function

substrate concentration

reac

tion

rate

§ Substrate concentration u as ­ substrate = ­ reaction rate

§ more substrate = more frequently collide with enzyme

u reaction rate levels off§ all enzymes have active site engaged§ enzyme is saturated§ maximum rate of reaction

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AP Biology

37°

Temperature

temperature

reac

tion

rate

What’shappening here?!

QUESTION 6:IN YOUR OWN WORDS,describe what this graph is showingin a complete sentence.

AP Biology

Factors affecting enzyme function§ Temperature

u Optimum T°§ greatest number of molecular collisions§ human enzymes = 35°- 40°C (body temp = 37°C)

u Heat: increase beyond optimum T°§ increased energy level of molecules disrupts

bonds in enzyme & between enzyme & substratew H, ionic = weak bonds

§ denaturation = protein loses 3D shape (3° structure)u Cold: decrease below optimum T°

§ molecules move slower§ decreased collisions between enzyme & substrate

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Enzymes and temperature§ Different enzymes function in different

organisms in different environments

37°Ctemperature

reac

tion

rate

70°C

human enzymehot spring

bacteria enzyme

(158°F)

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How do ectotherms do it?

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7

pH

pH

reac

tion

rate

20 1 3 4 5 6 8 9 10

pepsin trypsin

What’shappening here?!

11 12 13 14

pepsin

trypsin

QUESTION 7:IN YOUR OWN WORDS,describe what this graph is showingin a complete sentence.

AP Biology

Factors affecting enzyme function§ pH

u changes in pH§ adds or remove H+

§ disrupts bonds, disrupts 3D shape w disrupts attractions between charged amino acidsw affects 2° & 3° structurew denatures protein

u optimal pH?§ most human enzymes = pH 6-8

w depends on localized conditionsw pepsin (stomach) = pH 2-3w trypsin (small intestines) = pH 8

720 1 3 4 5 6 8 9 10 11

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AP Biology

Salinity

salt concentration

reac

tion

rate

What’shappening here?!

QUESTION 8:IN YOUR OWN WORDS,describe what this graph is showingin a complete sentence.

AP Biology

Factors affecting enzyme function§ Salt concentration

u changes in salinity§ adds or removes cations (+) & anions (–)§ disrupts bonds, disrupts 3D shape

w disrupts attractions between charged amino acidsw affect 2° & 3° structurew denatures protein

u enzymes intolerant of extreme salinity§ Dead Sea is called dead for a reason!

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QUESTION 9:What does the following words mean in everyday language?- “regulate”/”regulation”- “activate”- “inhibit”- “competitive”- “irreversible”- “feedback”

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Compounds which help enzymes§ Activators

u cofactors§ non-protein, small inorganic

compounds & ionsw Mg, K, Ca, Zn, Fe, Cuw bound within enzyme molecule

u coenzymes§ non-protein, organic molecules

w bind temporarily or permanently toenzyme near active site

§ many vitaminsw NAD (niacin; B3)w FAD (riboflavin; B2)w Coenzyme A

Mg inchlorophyll

Fe inhemoglobin

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QUESTION 10:Compare and contrast cofactorsand coenzymes.

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Compounds which regulate enzymes§ Inhibitors

u molecules that reduce enzyme activity

u competitive inhibitionu noncompetitive inhibition

(both could be irreversible)

u feedback inhibition

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Competitive Inhibitor § Inhibitor & substrate “compete” for active site

u penicillinblocks enzyme bacteria use to build cell walls

u disulfiram (Antabuse)treats chronic alcoholism§ blocks enzyme that

breaks down alcohol § severe hangover & vomiting

5-10 minutes after drinking§ Overcome by increasing substrate

concentrationu saturate solution with substrate

so it out-competes inhibitor for active site on enzyme

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Non-Competitive Inhibitor § Inhibitor binds to site other than active site

u allosteric inhibitor binds to allosteric siteu causes enzyme to change shape

§ conformational change§ active site is no longer functional binding site

w keeps enzyme inactiveu some anti-cancer drugs

inhibit enzymes involved in DNA synthesis § stop DNA production§ stop division of more cancer cells

u cyanide poisoningirreversible inhibitor of Cytochrome C, an enzyme in cellular respiration§ stops production of ATP

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QUESTION 11:What is the difference between a competitive inhibitor and a non-competitive (allosteric) inhibitor?

AP Biology

Irreversible Inhibition§ Inhibitor (either competitive or

noncompetitive) permanently binds to enzymeu competitor

§ permanently binds to active siteu allosteric (non-competitor)

§ permanently binds to allosteric site§ permanently changes shape of enzyme§ nerve gas, sarin, many insecticides

(malathion, parathion…)w cholinesterase inhibitors - doesn’t breakdown

the neurotransmitter, acetylcholine

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Allosteric regulation§ Conformational changes by regulatory

molecules u inhibitors

§ keeps enzyme in inactive formu activators

§ keeps enzyme in active form

Conformational changes Allosteric regulation

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Metabolic pathways

A ® B ® C ® D ® E ® F ® Genzyme

1

®enzyme

2® enzyme

3

®

enzyme4

® enzyme5

® enzyme6

®

§ Chemical reactions of life are organized in pathwaysu divide chemical reaction

into many small steps§ artifact of evolution§ ­ efficiency

w intermediate branching points § ­ control = regulation

A ® B ® C ® D ® E ® F ® Genzyme

®

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Efficiency§ Organized groups of enzymes

u enzymes are embedded in membrane and arranged sequentially

§ Link endergonic & exergonic reactionsWhoa!

All that going onin those littlemitochondria!

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AP Biology allosteric inhibitor of enzyme 1

Feedback Inhibition§ Regulation & coordination of production

u product is used by next step in pathwayu final product is inhibitor of earlier step

§ allosteric inhibitor of earlier enzyme§ feedback inhibition

u no unnecessary accumulation of product

A ® B ® C ® D ® E ® F ® Genzyme

1

® enzyme2

® enzyme3

® enzyme4

® enzyme5

® enzyme6

®X

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AP Biology

Feedback inhibition§ Example

u synthesis of amino acid, isoleucine from amino acid, threonine

u isoleucine becomes the allosteric inhibitor of the first step in the pathway§ as product

accumulates it collides with enzyme more often than substrate does

threonine

isoleucine

AP Biology

Don’t be inhibited!Ask Questions!

QUESTION 12:Write down questions, vocabulary,or concepts that you are unclear about. Be prepared to share with me (Ms. Lin)so that we can go over it as a class!

Ask now or forever hold your peace!!!!!!!!!

AP Biology

Cooperativity § Substrate acts as an activator

u substrate causes conformational change in enzyme§ induced fit

u favors binding of substrate at 2nd siteu makes enzyme more active & effective

§ hemoglobin

Hemoglobin§ 4 polypeptide chains§ can bind 4 O2;§ 1st O2 binds § now easier for other

3 O2 to bind