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 Enzymes Catalysts Speed up biological reactions by providing an alternate pathway for the reaction to occur Lowers activation energy of reaction Typically contain several hundred amino acids Type of globular proteins Single or multiple chains Water soluble 3D shape is called conformation Conformation – 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 substrate Exist in cytoplasm of cells Control activity of cells at the molecular level Some proteins need co-factors Co-factors – non-protein molecules that bind for activity Inorganic co-factors could be metal ions Organic 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 reaction Low specificity: Enzyme only binds to one specific substrate High specificity: Enzyme binds to several related substrates Low Specificity High Specificity Enzyme 1 Enzyme 2 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 catalysts Both: 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

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 V max 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 Idea Enzyme + 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

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 complex The enzyme-substrate complex can dissociate or irreversibly convert the substrate to a product Enzyme 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 complex The 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 V max can be achieved Although V max can be achieved, a competitive inhibitor raises K m, indicating that the attraction of the enzyme for the substrate is lower in the presence of the inhibitor The 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 unblocked When 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 enzyme In a pure non-competitive system, the K m value is unchanged while the V max is lowered Pure non-competitive inhibitors are virtually unknown

Examples of Non-competitive Inhibition Metal ions (ex. Lead, mercury, silver, copper) Cyanide Penicillin  blocks an enzyme in bacteria Anti-cancer drugs  block cell division in tumors

Remember! Enzyme inhibition isn’t always a bad thing At 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?

My Source Teipel, J. W.; Hill, R. L. J.(1968) Biol. Chem. 243, Retrieved from: Lineweaver.html 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 Metals Common 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 (37 o C) Enzymes denature at excessively high temperatures Tertiary structure is disrupted permanently Note: Covalent bonds are not broken – That’s what happens during digestion Low temperature deactivates enzymes So, 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 pK a and pK b 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!

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