Human Biochemistry [Option B]

B7: Enzymes

Objectives 7.1 – 7.7

Devin Vitello, Jess Plaskon, Erica Falvey, Ms. McLaughlin, Samantha Giffen, Sam Huddleston,

Alex Sanfilippo

Objective B.7.1

Describe the characteristics of biological catalysts (enzymes).

Devin Vitello

Basic Characteristics of EnzymesCatalystsSpeed up biological reactions by providing an alternate pathway for the reaction to occurLowers activation energy of reactionTypically contain several hundred amino acidsType of globular proteins

Single or multiple chainsWater soluble

3D shape is called conformationConformation – determined by interactions

between all its R groups and is essential for function

Tertiary and quaternary structure is critical to function

Well-defined tertiary structure makes them globular proteins and soluble in water

Some enzymes have more than one polypeptide so they also have a quaternary structure

Basic Characteristics of Enzymes (cont’d)

Contain an active site Active site – area on enzyme where the substrate

attaches Can be affected by pH and temperature Remains unchanged by reaction

Specific to a substrateExist in cytoplasm of cellsControl activity of cells at the molecular levelSome proteins need co-factors

Co-factors – non-protein molecules that bind for activity

Inorganic co-factors could be metal ionsOrganic co-factors called coenzymes and could be vitamins

Substrate Specificity

Only a particular substrate will bind to the active site of the enzyme to initiate the reactionLow specificity:Enzyme only binds to one specific

substrateHigh specificity:Enzyme binds to several related

substrates

Low Specificity

High Specificity

Enzyme 1

Enzyme 2

Substrate A

Substrate A

Substrate B

Substrate C

Objective B.7.2

Compare inorganic catalysts and biological catalysts (enzymes).

Jess Plaskon

Enzymes and Inorganic Catalysts

Not all catalysts are enzymes but all enzymes are catalystsBoth:

Increase rate of reaction Cannot initiate a reaction Provide alternate pathway Decrease activation energy Have no change in their composition Create a product Can be used repeatedly

Differences between Inorganic Catalysts and Enzymes

Inorganic Catalysts Enzymes~have varied structure and can be

simple metal ions to complex molecules

~all are proteins except ribozymes which

are RNA~much less specific ~ highly specific structure

~ most donÕt show reactant saturation ~ reach a maximum reaction rate with respect to substrate concentration

(saturation)~work as homogeneous and

heterogeneous (same or different phases)

~ homogeneous (enzymes and reactants

are both aqueous)~ increase reaction rate by only a fraction of the increase effected by

enzymes

~ increase reaction rates by 103 to 106

~usually not regulated by other

chemicals (like inhibitors or cofactors)

~subject to inhibitors and activators

(cofactors)~usually not sensitive to pH or temp ~sensitive to pH and temperature

~ often work well at high temp. and pressure

~ usually work best under a narrow range of conditions (optimal)

~ low molecular weight ~ high molecular weight

Objective B.7.3

Describe the relationship between substrate concentration and enzyme activity.

Erica Falvey

B.7.3 Describe the relationship between substrate concentration and enzyme activity.

• As concentration increases, so does activity (to a point)• Since an enzyme can only process a certain quantity of

substrate at once, the rate of reaction will eventually plateau– This occurs when all enzymes are saturated with substrate– Ultimately, this rate depends on how quickly the enzymes can

process the substrates

B.7.3 Describe the relationship between substrate concentration and enzyme activity.

A graph showing the effect of substrate concentration on enzymatic activity

• At low substrate concentrations, rate of reaction is proportional to substrate concentration

• As substrate concentration increases, the rate decreases and is no longer proportional (as some active sites are occupied)

• At high substrate concentrations, the rate is constant and independent of substrate concentration – The enzyme is saturated with substrate at this point

B.7.3 Describe the relationship between substrate concentration and enzyme activity.

Objective B.7.4

Determine Vmax

and the value of the Michaelis constant (K

m) by graphical means and explain its

significance.

Ms. McLaughlin

Objective B.7.5

Describe the mechanism of enzyme action, including enzyme substrate complex, active site,

and induced fit model.

Samantha Giffen

Enzyme Characteristics

Basic mechanism by which enzymes catalyze a reaction starts with the binding of a substrate(s) to an active site

Binding of the substrate causes changes in the distribution of electrons in the chemical bonds of the substrate, ultimately leading to the reaction that forms the products

The enzyme and the substrate form a temporary binding to form the enzyme-substrate complex

Induced Fit Theory

Substrate is available to go into an active site, but it is not an exact fit

Active site of the enzyme changes shape to give a better fit

– Note: Substrate does NOT change, active site does Enzyme-Substrate Complex then forms

– No chemical bonds are formed between the enzyme and active site

Catalyzed reaction takes place Product(s) is released and enzyme returns to its original

shape

Enzyme Substrate Complex The enzyme is usually much bigger than the substrate The binding in the complex depends on the R groups of

the amino acids in the active site and can include hydrophobic interactions, dipole-dipole interactions, hydrogen bonds, and ionic attractions

The binding puts a strain on the substrate molecule, so facilitates the breaking and forming of bonds

Once the substrate has reacted, it no longer fits in the active site so it detaches

The enzyme is released unchanged and is able to catalyze another reaction

Main IdeaEnzyme + Substrate → Enzyme Substrate Complex → Enzyme + Product

All the reactions can be summarized using E for enzyme, S for substrate, and P for product:

E+S E-S E-P E+P*All the reactions are equilibrium reactions so are reversible depending on the

conditions.

Enzyme Specificity

Absolute- enzyme will only bind to one substrate Group specific- enzyme will only react with

substrates with similar functional groups, side chains, or positions on a chain

Bond specific- enzyme will only react with a specific chemical bond

Enzyme Specificity

The specificity of an enzyme depends on its tertiary and quaternary structure

The part of the enzyme that reacts with the substrate is the active site

Active site is specific to certain molecules Groove or pocket in the enzyme where the substrate will

bind Not necessarily rigid

Can alter its shape to allow for a better fit (induced fit theory)

Review Questions

What is an enzyme-substrate complex and what is it used for?

What is the purpose of an active site and how does it work?

What is the induced fit model?

References

Neuss, G. (2007). Chemistry. Oxford, NY: Oxford University Press.

Ophardt, C.E. (2003). Mechanism of enzyme action. Retrieved from http://www.elmhurst.edu/~chm/vchembook/571lockkey.html

Objective B.7.6

Compare competitive inhibition and non-competitive inhibition.

Sam Huddleston

The Basics

In equilibrium, an enzyme binds to a substrate in order to form an enzyme-substrate complexThe enzyme-substrate complex can dissociate or irreversibly convert the substrate to a productEnzyme inhibition is a common goal for the pharmaceutical industry All inhibitors cause the substrate to react at a lower rate than without the inhibitor

Competitive Inhibition

Competitive inhibitors bind at the active site of the enzymes to form an enzyme-inhibitor complexThe inhibitor blocks the active site, and the substrate cannot bind until the inhibitor detaches

Competitive Inhibition

Because the inhibitor and substrate compete for the same site, raising the substrate concentration can eventually overcome the inhibitor, and Vmax can be achieved

Although Vmax can be achieved, a competitive inhibitor raises Km, indicating that the attraction of the enzyme for the substrate is lower in the presence of the inhibitorThe effect of a competitive inhibitor in a Lineweaver-Burk plot is both to move the x-intercept and increase the slope

Non-competitive Inhibition

Non-competitive inhibitors bind at an allosteric site on the enzyme and leave the active site unblockedWhen the inhibitor binds, the shape of the active site is changed so it cannot bind the substrate.

Non-competitive Inhibition

In a pure non-competitive system, the substrate has an equal attraction for both the enzyme-inhibitor complex and the enzymeIn a pure non-competitive system, the Km value is unchanged while the Vmax is loweredPure non-competitive inhibitors are virtually unknown

Examples of Non-competitive Inhibition

Metal ions (ex. Lead, mercury, silver, copper)CyanidePenicillin blocks an enzyme in bacteriaAnti-cancer drugs block cell division in tumors

Remember!Enzyme inhibition isn’t always a bad thingAt times, it’s necessary to control the activity of enzymes (especially in our bodies)Our bodies will induce “negative feedback”

Possible Review Questions (?)

What is the main difference between competitive and non-competitive inhibition? Which one is competitive, and which one is non-competitive in the following picture:

Which one is this?Which one is this?

My Source

Teipel, J. W.; Hill, R. L. J.(1968) Biol. Chem. 243, 5679. Retrieved from: http://www.chm.davidson.edu/erstevens/Lineweaver/Lineweaver.html

Objective B.7.7

State and explain the effects of heavy-metal ions, temperature changes, and pH changes on enzyme

activity.

Alex Sanfilippo

Heavy MetalsCommon Poisonous Heavy Metals:

- Lead, Copper, Mercury, Silver

Non-competitive inhibitors Prevent enzyme from functioning properly Change shape of enzyme and active site Do not interact with the enzyme at the active site

React with sulfhydral (-SH) groups Found in cysteine -SH -S(Metal)

• Interaction between enzyme and inhibitor interferes with tertiary structure and side chains Enzyme and substrate cannot bind because of shape change

Increase in temperature gives particles involved in reactions more energy More reactants can reach activation energy Increases rate of enzyme catalyzed

reactions

Optimum Temperature Temperature at which rate of

enzymatic reactions are the greatest

Excessive raise in temperature Enzymes denature

H-bonds break Disrupts tertiary structure

This leads to irreversible damage

• Low temperature can deactivate an enzyme- But the damage is usually reversible

Temperature Change

Temperature Change and Enzyme Activity in the Body

Optimum Temperature of Enzymes Usually at core body temperature (37oC)

Enzymes denature at excessively high temperatures

Tertiary structure is disrupted permanently Note: Covalent bonds are not broken –

That’s what happens during digestionLow temperature deactivates enzymesSo, any change of core body temperature of 2+ degrees (e.g. fever, hypothermia, etc.) can be fatal

Optimal pH Rate of enzyme catalyzed reaction reaches its maximum Depends on pKa and pKb of R groups of amino acids

Especially at the active site

For example: Pepsin’s optimal pH is 2

Acidic environment Stomach

Trypsin’s optimal pH is 8 More alkaline environment in the intestines

pH change Interferes with acidic and basic molecules in protein side chains Alters

tertiary structure Tertiary structure is disrupted Enzyme and substrate can’t bind

pH Change

Sources

Neuss, Geoffrey (2007). IB study guides: Chemistry. New York: Oxford University Press.

The End!

Any Questions?