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The Catalytic constant, kcat

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Catalytic efficiency, kcat/Km

The Vmax of an enzyme catalyzed reaction is 4.77 mM/s in the presence of 9 µM of enzyme. What is the turnover number for the enzyme?

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rate constant of the reaction when the enzyme is saturated with substrate ([ES] ~ [E]T and Vinit ~ Vmax) kcat = k2 = Vmax / [E]T kcat: Number of catalytic cycle per unit of time (turnover number). the number of times each enzyme site converts substrate to product per unit time.

Enzyme effectiveness as a catalyst depends on: – The efficiency of the enzyme to bind its substrate (KM) – The rapidity at which it converts substrate to products (kcat). – The kcat /KM ratio, where kcat is the catalytic constant for the conversion of substrate into product, and KM is the Michaelis constant, has been widely used as a measure of enzyme performance

Two-substrate Reactions

Sequential Kinetic Mechanism

both substrates must bind to the enzyme before any products are made and released

Ping-Pong Kinetic Mechanism also called a double-displacement reaction, is characterized by the change of the enzyme into an intermediate form when the first substrate to product reaction occurs. It is important to note the term intermediate indicating that this form is only temporary. At the end of the reaction the enzyme MUST be found in its original form.

Enzyme Inhibition

Competitive Inhibition

An inhibitor that resembles the normal substrate binds to the enzyme, usually at the active site, and prevents the substrate from binding.

Uncompetitive Inhibition

takes place when an enzyme inhibitor binds only to the complex formed between the enzyme and the substrate (the E-S complex).

Mixed Inhibition

the inhibitor may bind to the enzyme whether or not the enzyme has already bound the substrate but has a greater affinity for one state or the other.

How is Transition State Stabilization Achieved?

– acid-base catalysis: give and take protons – covalent catalysis: transient covalent bond is formed between enzyme and substrate – metal ion catalysis: use redox cofactors, pKa shifters – electrostatic catalysis: preferential interactions with TS •

Acid-base catalysis: depends on donation and acceptance of protons (proton transfer reactions). The catalytic rate is pH-dependent.

General Acid-Base Catalysis

General acid-base catalysis involves a molecule besides water that acts as a proton donor or acceptor during the enzymatic reaction. ... General acid-base catalysis is involved in a majority of enzymatic reactions, wherein the side chains of various amino acids act as general acids or general basis. Specific acid–base catalysis means specifically, –OH or H+ accelerates the reaction. ... Therefore, the rate of the reaction is dependent on the buffer concentration, as well as the appropriate protonation state. Specific vs General Acid-base Catalysis

General acid-base catalysis involves a molecule besides water that acts as a proton donor or acceptor during the enzymatic reaction Specific acid–base catalysis means specifically, –OH or H+ accelerates the reaction Metal Ion Catalysis

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Covalent catalysis

Metal ions provide a high concentration of positive charge that is useful in binding small molecules Alkaline metals (Na+, K+, Mg2+, Ca2+) Transition metals (Zn2+, Fe2+, Cu2+) –

Nucleophilic attack by the enzyme on electrophilic group on the substrate leads to the formation of a covalent bond. – Nucleophiles: Electron-rich atom (e.g. O, N, S) – Electrophiles: Electron-deficient center (e.g. C=O) – Nucleophilic side chain forms an unstable covalent bond with an

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electrophilic group For example, serine group uses serine as nucleophile for attack.

Covalent Catalysis: Chemical Example

Covalent Catalysis: In Enzymes

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Proteases and peptidases – chymotrypsin, elastase, subtilisin – reactive serine nucleophile Some aldehyde dehydrogenase – glyceraldehyde-3phosphate dehydrogenase – reactive thiolate nucleophile Aldolases and decarboxylases – amine nucleophile Dehalogenases – carboxylate nucleophile NH

HO

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O S

O

N

The Serine Proteases

O

N

O N

O

N

O

Serine proteases are enzymes that cleave peptide bonds in proteins, in which serine serves as the nucleophilic amino acid at the active site. They are found ubiquitously in both eukaryotes and prokaryotes. Serine proteases fall into two broad categories based on their structure: chymotrypsin-like or subtilisin-like Specificity of Serine Proteases is Determined by the Substrate Binding Pocket

The substrate residue N-‐terminal to the cleavage site (P1) largely determines the specificity of serine proteases. P1 binds S1, which is called the specificity pocket; its interactions were found early on to be a major determinant of the substrate specificity for trypsin, chymotrypsin and elastase. Mechanism of action of chymotrypsin

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The critical amino acids in the active site of chymotrypsin are Ser 195 and His 57. Involves acid/base catalysis and covalent catalysis.

Mechanism of action and kinetics. In vivo, chymotrypsin is a proteolytic enzyme (serine protease) acting in the digestive systems of many organisms. ... The main substrates of chymotrypsin are peptide bonds in which the amino acid N-terminal to the bond is a tryptophan, tyrosine, phenylalanine, or leucine. chymotrypsin (kī´mōtrĬp´sĬn), proteolytic, or protein-digesting, enzyme active in the mammalian intestinal tract. It catalyzes the hydrolysis of proteins, degrading them into smaller molecules called peptides. Peptides are further split into free amino acids. Serine protease mechanism

Lipids

Biological Functions of Lipids

The functions of lipids include storing energy, signaling, and acting as structural components of cell membranes. Classification of Lipids

Fatty Acids

Function: Building Blocks for all classes of lipids Always have carboxylic acid head group, always given position 1 Conformation of Fatty Acids

saturated lipids pack tightly together Unsaturated, no free rotation around bond, cannot pack as tight

Melting Point and Double Bonds

Hydrophobic interactions between saturated lipid molecules Glycerolipids Triacylglycerols (fats and oils)

Function: Primary storage of lipids Condensation reaction Waxes

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Function: Metabolic fuel Protection Waterproofing Lotions Long chain alcohol is backbone not glycerol Glycerophospholipids

Function: Cell membranes

Sphingolipids

• Function: Cell membranes Sphingosine backbone, has alcohol and amine functional group, amide bond

Sterols and Cholesterol

Function: Building Block No fatty acids, steroid nucleus, no free rotation, rigid planar structure, non-polar chain with polar head Physiological Role of Sterols

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• • • Steroid Hormones

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Membranes

Cholesterol and related sterols are present in the membranes of most eukaryotic cells. – Modulate fluidity and permeability – Thicken the plasma membrane – Most bacteria lack sterols Mammals obtain cholesterol from food and synthesize it de novo in the liver Cholesterol, bound to proteins, is transported to tissues via blood vessels – Cholesterol in low-density lipoproteins tends to deposit and clog arteries Many hormones are derivatives of sterols Steroids are oxidized derivatives of sterols Steroids have the sterol nucleus, but lack the alkyl chain found in cholesterol. This makes them more polar than cholesterol. Steroid hormones are synthesized in gonads and adrenal glands from cholesterol They are carried through the body in the blood stream, usually attached to carrier proteins Many of the steroid hormones are male and female sex hormones

Functions of Membranes

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• • Common Features of Membranes

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Define the boundaries of the cell Allow import and export • Selective import of nutrients (e.g. lactose) • Selective export of waste and toxins (e.g. antibiotics) Retain metabolites and ions within the cell Sense external signals and transmit information into the cell Provide compartmentalization within the cell • separate energy-producing reactions from energy-consuming ones • keep proteolytic enzymes away from important cellular proteins Produce and transmit nerve signals Store energy as a proton gradient and support synthesis of ATP Sheet-like flexible structure, 30-100 Å (3-10 nm) thick Main structure is composed of two leaflets of lipids (bilayer) Form spontaneously in aqueous solution and are stabilized by non-covalent forces, esp. hydrophobic effect Protein molecules span the lipid bilayer Asymmetric • Some lipids are found preferably “inside” • Some lipids are found preferably “outside” • Carbohydrate moieties are always outside the cell

Membrane Bilayer

Polar head group exposed to aqueous environment Glycolipids Sphingolipids Sterols Composition of the Membrane Bilayer

Fluid Mosaic Model of Membranes

Application question about type of protein and location Membrane Dynamics: Lateral Diffusion

Functions of Proteins in Membranes

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Types of Membrane Proteins

Receptors: detecting signals from outside • Light (opsin) • Hormones (insulin receptor) • Neurotransmitters (acetylcholine receptor) • Pheromones (taste and smell receptors) Channels, gates, pumps • Nutrients (maltoporin) • Ions (K-channel) • Neurotransmitters (serotonin reuptake protein) Enzymes • Lipid biosynthesis (some acyltransferases) • ATP synthesis (F0F1 ATPase/ATP synthase)

Transport across membranes

Acts like lactase or transporter-how does it work Model for Glucose Transport

What happens to km in conformational change? larger km release of glucose Model for Glucose Transport

Classes of Transport

A uniporter is an integral membrane protein that transports a single type of substrate species (charged or uncharged) across a cell membrane. It may use either facilitated diffusion and transport along a diffusion gradient or transport against one with an active transport process A symporter is an integral membrane protein that is involved in the transport of many differing types of molecules across the cell membrane. The symporter works in the plasma membrane and molecules are transported across the cell membrane at the same time, and is, therefore, a type of cotransporter. An antiporter (also called exchanger or counter-transporter) is a cotransporter and integral membrane protein involved in secondary active transport of two or more different molecules or ions across a phospholipid membrane such as the plasma membrane in opposite directions. Cotransport is the name of a process in which two substances are simultaneously transported across a membrane by one protein, or protein complex which does not have ATPase activity. Different types of co-transport. Lactose Permease

Lactose permease is a membrane protein which is a member of the major facilitator superfamily. Lactose permease can be classified as a symporter, which uses the proton gradient towards the cell to transport β-galactosides such as lactose in the same direction

into the cell....