Enzymes

Enzymes are catalysts that drive reaction rates forward. Most, but not all, are made up of amino acid chains called proteins that accelerate the rate of reactions in chemical systems. Their functionality depends on how

proteins are folded,what they bind to, and what they react with. For protein-based catalysts, amino acid polarization lies at the core of catalytic activity.

Introduction

In chemistry, a catalyst is a chemical that drives a reaction forward. Catalysts lower the activation energy, which is the amount of energy required for reactants to form products (See Figure 1).  Catalysts also lower the kinetic barrier, which is needed to drive a reaction forward and backward. A certain amount of energy contained in molecules is needed when the two of them react together to form a product. If the two molecules do not have enough energy to react, then no product is produced.  By lowering the activation energy, a catalyst allows molecules to gain enough energy to go over the barrier and form products.

Figure 1: Compare the red curve with the blue curve. Which hill would you want to climb over? This figure shows the decrease in activation energy and kintetic barrier in a reaction where there is a catalyst, or enzyme (red curve). Extracted from Dr. Delmar Larsen's Lecture 22 on 5/24/10.

Catalysts raises both rates of the forward and backwards reaction (K_f to denote the rate of the forward reaction and K_b to denote the rate of the backward reaction). Exergonic forward reactions convert reactants to products, while endergonic backward reactions convert products to reactants. Usually, it takes more energy, measured in Gibbs energy, to convert products to reactants. Recall that the difference in energy between products and reactants is measured as ΔG (Gibbs energy). It is very important to note that catalysts do not change G, they simply affect the speed of reaction. Catalysts are very beneficial in biological systems because they drive individual reactions forward. Our bodies are a vast combination of redox reactions. Heat may drive a reaction forward. For example, when you catch a fever, your body raises its temperature to drive reactions forward in your body, dissipating energy in the form of heat. Note that the body raises its temperature to drive reactions forward. This extra energy drives your immune system forward to get rid of the germs faster. Oftentimes, life does not want whole systems to be driven forward; instead, merely wanting to produce a little extra product or a small amount of excess reactant of one reaction. It would be a waste of energy to constantly have our body hotter than needed, and we would probably die much faster. That is why our body invented reaction specific catalysts. These reaction specific catalysts are what are needed to keep our body alive. In this section, we will talk about the chemistry of inorganic and organic biological catalysts, also called enzymes, and how their composition is evaluated in medicine.

Figure 2

Amino Acids and Polarity

What makes an amino acid polar or nonpolar? Which leads to affecting its hydrophobicity or hydrophilic characteristics? This is the basic structure of an amino acid:

Figure 3

Notice that the basic structure always carries an amine group (NH₂), and a carboxyl functional group (CO₂H). The general formula for an amino acid is H₂NCHRCOOH, which denotes what order the hydrogen and carbon atoms are bonded. All 20 amino acids have this same general structure. What makes them different is the R-linked side chain. Images of the 20 different amino acids.

Amino acids differ in their electronegativity in R groups, and hence their hydrophobicity. The side chains denote if an amino acid is:

1. Basic and polar 
2. Acidic and polar 
3. Neutral non-polar
4. Neutral polar

Recall that the more electronegative an R side chain is compared with its amine and carboxyl, the more polar the amino acid. In general, side chains with hydrocarbon alkyl groups (C_nH_n), or benzene rings are non-polar. Examples: phenylalinine, Leucine, Isoleucine  The number of alkyl groups affects polarity. The more C_nH_n groups, the more nonpolar. 

So, what makes an amino acid more polar?

• Acids, amides, amines, and alcohols make an amino acid more polar.
• Acids 
• Amides (the Rs can be Hydrogens in their respective prime locations)
• Amines
• Nitrogen may bond with up to four hydrogens in an organic compound to be called an amine. The most common amines are ammonia (NH₃), and NH2)
• Alcohols (carbon-hydrogen chains with OH groups attached to the ends)

What makes an amino acid basic?

• An amine functional group. (Note that amino acids with amides on the side chain do NOT produce a basic amino acid)

What makes an amino acid acidic?

• Usually, carboxylic acid (COOH) groups attached to R side chains make an amino acid acidic.

Enzyme and Substrate Chemistry 

Enzyme and Substrate Chemistry can be described biologically. Enzymes provide the particular substrate with an active site, which forms an enzyme-substrate complex, necessary for its catalyst and formation of products.

 

In the Figure 4 above, the particular substrate fits in the enzyme as a key fits into a lock. Extracted from Casiday and Frey Chemical-Kinetics Experiment.

The Rate of an Enzyme-Substrate reaction is proportionally related to the concentrations of both, the enzyme and substrate. As the concentration of either decreases or increases, so does the reaction rate. However, there are certain exceptions to this rule of proportionality. The reaction rate disregards or is independent of the concentration of the substrate when it is very high. Thus, rate of reaction for an enzyme-catalyzed reactions with a high substrate  concentration follows a zero rate equation: Rate of Reaction=K. In terms of a normal proportional reaction rate to concentration level, the rate equation is considered at a first order: Rate of Reaction=k[S].

Note: [S] is the concentration of substrate.

     

                 Figure Above:Zero Order Reaction             Figure Above:First Order Reaction
 

CoEnzymes & CoFactors

Kinetics of Enzyme-Substrate Chemistry

Homogeneous Catalysts

Homogeneous catalysts interact with the reactants in the same phase (i.e: turning a substrate into a product in a faster rate). Those homogeneous catalysts do not change their current states unlike heterogeneous states. By states we mean the phase state which means either solid, liquid, or gas. If homogeneous catalysts are solid they will remain solid after the reaction is completed and the same for liquid and gas homogeneous catalysts. Although many biological enzymes are heterogeneous, there are some homogeneous enzymes that remain in their same state after the reaction like immunoassay (EIA).

Heterogeneous Catalysts

Heterogeneous catalysts are catalysts that speed up the rate of reactions by allowing them to occur on a solid surface. An examples of a heterogeneous catalyst is a clay DNA polymer scaffolding, where DNA's individual purines and pyrimidines link together on a clay surface to allow more secure bonding to occur. 

The Basics

Enzymes are made up of many amino acids that react with substrates in biological chemistry. Enzymes are there to drive the rates of reactions forward in our bodies. Without them, products would not form quickly enough for our body to actually process the energy that we need. The basic reaction for any enzyme-substrate complex is this:

Step 1: E+S <--> ES

The enzyme-substrate complex bound together is an intermediate in a reaction, denoted by [ES].

Step 2: ES <--> E+P

Where P stands for products, E for enzyme, and S for substrate.   

The rate determining step for an enzyme-substrate reaction is always the second step, where [ES] is converted into product. The reason for this is because once the enzyme does its job, it is free again to do more work. Once an enzyme can do more work after conversion, a reaction can go faster. 

The rates of enzyme-substrate reactions go between first order and second order. At first, a reaction will be first order, because it will depend on the amount of substrate added. When the maximum amount of active sites are consumed, the rate of an enzyme-substrate reaction maximizes, becoming a zero order reaction, where the rate of reaction is constant. A zero-order reaction is typically denoted graphically by an asymptote which indicates the rate limit of reaction. When an enzyme-substrate reaction tends toward zero order, the only way to make a reaction speed up is to add more enzyme, and therefore more active sites. If more enzyme is added to a zero order maximized reaction, the reaction will go back to first order, until either all active sites are taken once again, or all substrate is converted into product, leaving an excess of empty active sites. 

The rate of production of product depends on the velocity (V) of a reaction. In order of any enzyme-substrate reaction to go forward, the rate of product formation (or decomposition of ES) must equal the rate of formation of ES. If ES only forms and does not decompose into product, then the enzyme is not working. Enzymes that do not work are discussed later, and may be a result of faulty RNA translation from DNA, which causes the active site on an enzyme to be malformed.

Because the total concentration of enzyme can never be accurately measured, biochemists like to use E₀ to denote the sum of unbound enzyme versus bound enzyme ES. A convenient constant to use when relating the rates of the forward versus reverse reactions of enzyme chemistry is K_M. One may get this constant by dividing the rates of formation of unbound E (k_-1 and k₂) to the bound ES (k₁). 

K_M=k_-1+k₂/k1

Where k_-1 is ES to E+S, k₂ is ES --> E+P, and k₁ is E+S -->ES.

Note that this constant is always changing due to fluctuations in the rates of the forward and reverse reactions due to concentrations of enzyme or substrate. The equation for velocity can then be understood.

V=k₂[E₀][S]/K_M+[S]

If [S] is low, then the value of K_M will be large, and the reaction rate will depend on the concentration of substrate. This reaction will be a first order reaction because there is enough enzyme to drive the reaction forward at a fairly quick rate. 

K_M>>[S]

If the concentration of substrate is high and all of the active sites are taken, K_M will be sufficiently less than [S] and the reaction will tend toward its maximum rate. More enzyme will need to be added to drive this reaction faster, and the reaction will become zero order and attain an asymptote. 

K_M<<[S] 

Thermodynamics

The thermodynamics of a biological reaction are crucial. Your body temperature stays at a constant 97.5 to 98.8 degrees Fahrenheit. This is due to the fact that if the body raises above that temperature it can cause certain proteins to denature in your body. A lowering of this range will cause reactions to slow down, which also may cause you to die. However, slight changes above this set homeostasis can drive all reactions forward in your body, causing you to burn more energy, which escapes partially in the form of heat. This is why when you have a fever, your mother or father may have felt your forehead to see if you were warmer than usual.

Active Site Chemistry  

Active sites are the parts of enzymes that are substrate-specific. In other words, certain enzymes will only bind to certain substrates because of a lock-key like site on the surface of the enzyme. We will be taking a look at a very common enzyme family called serine protease for an example of how active site chemistry works. The serine protease family is an important enzyme for digestion, blood clotting, and fertilization. They are also the enzymes that catalyse peptide bond cleavage by attacking the carbonyl bond. Serine proteases are most famous for their specificity for substrates. They contain disulphide linkages (S--S) to keep their shape. Charged side chains are found on the outside of the enzyme, interacting with the solvent unless involved in catalysis. 

Let us use an enzyme called trypsin in the serine protease family. Trypsin's active site has two domains, with the active site between the two. At the center of each domain is a barrel structure. Polar regions of the structure are well hydrated. Trypsin's active site contains the amino acid sequence Asp 102, His 57, Ser 195 (Aspartic Acid, Histidine, and Serine respectively). The numbers correspond with the actual sequence and position of the amino acids. These amino acids are found on loop regions of the two domains, and represent the charge relay system for the active site. The specificity pocket is also found in the loops of the two domains. These two domains of barrel structures are important because they provide a scaffold where the specific amino acid bonds can interact to form the substrate-specific active site. The connection between domains is less tight at the active site and may allow more rigid movements within the domains that may contribute to catalysis. These rigid body movements are a fundamental part of enzyme catalysis. We still have much to research on serine proteases, as not much is understood about their crucial chemistry.

The Reaction of Trypsin

His 57 and Asp 102 are supposed to fix the Ser 195 in a state capable of reacting with the incoming peptide chain, and also to stabilize any intermediate formed during catalysis. His 57 acts as a strong base, abstracting the alcoholic proton of Ser 195 and moves it to the amine leaving group. The negative end of Asp 102 cancels out the positive charge developed by His 57 during the transition state. Then, the hydrolysis (adding of H₂O) of the acyl-enzyme  releases the product.  (On this link, do not pay attention to the actual reaction, just pay attention to the highlighted intermediate of acyl-enzyme. This reaction is an protease inhibitor.)

The actual reaction mechanism. And another...
These catalysts drive the reaction forward 1,000,000 times faster than one without a catalyst.

Problems:

1) What is a catalyst?

A catalyst is a compound that speeds up a reaction.

2) What is an enzyme?

An enzyme is a biological catalyst that speeds up reactions and interactions between molecules in biological systems.

3) What is the name of reactants that enter a substrate to form products at a faster rate?

The name of the reactants that enter a substrate to form products at a faster time are called substrates.

4) In which place on the enzyme does the substrate bind (to that enzyme, specifically) to give us products at a faster rate?

The name of the place on which the substrate binds is the active site of the enzyme.

• the Alkali Metals: , especially pay attention to how sodium, potassium, lithium and hydrogen react. In biological systems, you need to know this because sodium channels catalyze and direct neurological activity. Potassium balance is important because its levels depend on sodium and muscular reactions. Lithium is used as a psychotropic drug for bipolar patients. Hydrogen bonding is very important in living organisms and is very prominent in the universe. 
  
• the Alkaline Earth Metals: Calcium is very important to catalyze muscle twitch reactions.
• the The Carbon Family: You will need to know about carbon in Organic Chemistry. 
• the Oxygen Family: Oxygen acts as a catalyst for every reaction in our aerobic respiration. It also acts as a strong free radical. 
  
• The Effect of Temperature on Reaction Rates 

From reading this chapter, you should have an idea of how important temperature is on reaction rates and how it does and does not relate to catalysis: Kinetics and Temperature dependence of reaction rates