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Enzymes: A Molecular Perspective

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1 Enzymes: A Molecular Perspective
Shuchismita Dutta, Ph.D.

2 Learning Objectives Introduction to Enzymes Enzyme action Enzyme regulation

3 Learning Objectives Introduction to Enzymes Enzyme action Enzyme regulation

4 Enzymes Structure and Composition Functions Most enzymes are proteins
Some enzymes are RNAs Enzyme function (catalysis) is facilitated by specific amino acids or groups in the molecule along with ions, cofactors etc. Catalyzes specific reaction Reusable molecule Substrate(s) + Enz Product(s) + Enz Starch Amylase Salivary and Pancreatic Amylase enzymes digest starch

5 Enzymes Are Chemical Catalysts
Speed up Reaction rate Sometimes by million fold Lower energy barrier for Reaction Temporarily stabilizes interaction between substrates Forms Transition state complexes Helps form Product(s)

6 Amylase Digests Starch
Amylase (enzyme) Site of substrate cleavage Zn Learn more about Amylase structure and function at Cl Part of starch molecule (substrate) Active site residues Glu 233, Asp 197, Asp 300

7 Learning Objectives Introduction to Enzymes Enzyme action Enzyme regulation

8 Enzyme Action Models Lock and Key Induced fit Emil Fischer (1894)
Active site rigid, substrate(s) fit(s) precisely into enzyme active site Daniel Koshland (1959) Binding of substrate(s) changes conformations of substrate(s) and enzyme Lock and Key Model Induced Fit

9 Hexokinase: Induced Fit Model
Hexokinase without glucose (open) Hexokinase with glucose (closed) Hexokinase (HK) transfers a phosphate from ATP to glucose (forms glucose 6-phosphate) Catalyzes first step in glycolysis Shaped like a clamp - big groove in one side HK structure without glucose (open); with glucose (closed) Learn more about Hexokinase and other enzyme action at

10 Residues for peptide bond cleavage in all Serine Protease enzymes
Catalytic Mechanism Residues in catalytic site conserved in enzyme families (e.g. Serine Proteases) Residues for peptide bond cleavage in all Serine Protease enzymes Serine Histidine Aspartate Learn more about Serine Proteases at Trypsin Chymotrypsin Elastase

11 Substrate Specificity
Property Trypsin Chymotrypsin Elastase Enzyme cuts after positive amino acids bulky amino acids small uncharged amino acids Substrate has Lysine, Arginine Phenylalanine, Tryptophan Alanine Enzyme specificity pocket has Aspartate Serine Valine, Threonine Active site: Histidine Serine Specificity pocket residues PDB ID:2ptn PDB ID:2cha PDB ID:3est

12 Coenzymes Work together with enzyme
Small molecules, bound to enzymes to play critical roles May act as carrier of specific atoms or groups Are altered during enzyme reactions Are recycled and may take part in many different reactions. Nicotinamide adenine dinucleotide (NAD+) carries electrons in oxidation-reduction reactions can accept a hydrogen ion (H+) and two electrons (e-) to form NADH NADH can donate electrons to a second substrate, re-forming NAD+ Learn more about Glyceraldehyde-3-phosphate dehydrogenase and other glycolytic enzymes at Glyceraldehyde-3-Phosphate Dehydrogenase active site with bound NAD+

13 Learning Objectives Introduction to Enzymes Enzyme action Enzyme regulation

14 Allosteric Regulation
Binding of a small molecule outside the catalytic site Regulator binding alters overall shape and interactions of enzyme Binding may specifically activate or inhibit enzyme activity

15 Pyruvate Kinase: Allosteric Activation
Pyruvate kinase makes ATP only when needed Composed of four flexible subunits arranged as a diamond shape Inhibited by ATP and amino acids Activated by Fructose-1,6-Bisphosphate into flexed shape. Inactive Enzyme Active Enzyme Learn more about Pyruvate Kinase at Catlytic Sites Regulatory Sites

16 Enzyme Inhibition Why? How?
To prevent excessive function within cells/organism How? Portion of Enzyme or another protein blocks access to enzyme active site Pancreatic Trypsin Inhibitor ensures that any traces of active Trypsin are inactivated when not necessary Trypsinogen: has extra piece of protein chain to cover active site and keep it inactive Learn more about Trypsin and its inhibition at

17 Enzyme Inhibitors as Drugs
HIV-1 Protease bound to substrate peptide HIV Protease inhibitors as Drugs: Substrate-like or other molecules bind to protease active site  block HIV-1 protease function (viral maturation) Learn more about Trypsin at Indinavir Saquinavir Ritonavir Nelfinavir

18 Introduction to Enzymes Enzyme action
Summary Introduction to Enzymes Enzymes and Catalysis Enzyme action Enzyme Action models Catalytic mechanisms, specificity and coenzymes Enzyme regulation Allosteric Regulation Inhibition and Drugs

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