Enzymes

=**Enzymes (HL) - By Eun Ji Song and Jeff Dryden**=

__**Vocabulary:**__
 * ** Enzyme (biological catalyst): **** Globular Protein that increases the rate of a biochemical reactions by lowering the activation energy threshold **
 * ** Active Site **** : The site on the surface of an enzyme which binds to the substrate molecule **
 * ** Substrate **** : the reactants **
 * ** Specificity: **** the idea that an enzyme only works with a particular substrate. The active site is specifically shaped for a particular substrate **
 * ** Co-factor **** : a substance held to the protein by other bonds (e.g. Ca2+) **
 * ** Co-enzyme: **** Non-protein organic molecules (e.g. vitamins) **
 * ** Denaturation : structural change in a protein that results in loss of its biological ****properties**

__**Characteristics of Enzymes**__:
 * Most proteins are enzymes
 * Act as catalysts for biochemical reactions in our body
 * Each enzyme is highly specific for a particular reaction
 * Enzymes are incredibly efficient, being able to increase the rate of reaction by more than one hundred million times.
 * Enzyme's activity depends on its tertiary or quaternary structures
 * Properties and positions of the R-group at the active site determine which substrates will bind to the enzymes
 * Some enzymes do not bind to substrates unless their active sites do not contain additional ions or molecules
 * Most enzymes end with //-ase// (e.g. amylase)
 * Lowers activation energy of products
 * Increases rate of biochemical reactions

__**How enzyme works:**__
 * Enzymes have __active sites__ (as mentioned before)
 * This is the part of the molecule that has the right shape and functional groups to bind to __the substrate__
 * An enzyme-catalyzed reaction takes a different 'route'
 * The enzyme and the substrate form a __reaction intermediate__
 * This concept can be illustrated through the "lock and key" model in the following:



__ **Relationship between substra** ____ **te concentration and enzyme activity:** __


 * Low concentrations: Linear Relationship
 * Enzymes have more active sites than substrate molecules (active sites>substrates) --> Therefore there will be a linear increase in rate
 * As concentration increases, the rate will diminish because more active sites are being used up (active sites < substrates)
 * Eventually, the point of saturation is reached when the rate will not increase any further because all actives sites are occupied

__**Vmax and the value of the Michaelis consta****nt** **(Km):**__


 * ** Vmax **: Maximum rate of reaction at the point of saturation (horizontal asymptote)
 * Only way to increase Vmax is to increase the concentration of substrate
 * ** Km **: Substrate concentration when rate is at 1/2 of Vmax
 * Representation of how readily substrate-binding occurs
 * Km will always by the same for a particular enzyme.
 * Indicates whether or not a particular enzyme requires high of low concentration to catalyze a reaction efficiently.
 * At low substrate concentrations the rate of reaction is proportional to the concentration of the substrate.
 * However, at higher concentrations the rate reaches a maximum known as Vmax
 * Km indicates whether enzyme functions efficiently at low substrate concentrations or whether high substrate concentrations are necessary for efficient catalysis

__**Active Site and Induced Fit Theory of Enzyme Catalysis:**__
 * **Cluster of chemical groupings formed as part of the enzyme's folding patterns.**
 * **When enzymes and substrates combine, they change shape for a better fit --- known as the induced fit theory**
 * **Induced Fit Theory of Enzyme Catalysis:**

1) Enzyme: -Substrate (triangle+square) can go into pocket of active site but not an exact fit

2) Enzyme-Substrate Complex: -Active site changes shape to give an exact fit

3) Enzyme-Product Complex: -Catalyzed reaction takes place

4) Enzyme and Products -Products ( Square and Triangle separately) released and enzyme reverts to original shape

 __ *If you need better understanding of the difference please refer to the following Youtube video* __ media type="custom" key="24793628"
 * __ Competitive Inhibition and Non-competitive Inhibition: __**
 * ** Competitive Inhibitors ** : **Compounds that are similar in shape to the substrate. They bind to the active site to prevent substrate.**
 * Vmax = same
 * But Km increases (indicating that substrate cannot bind as well in the presence of this inhibitor)
 * When concentration of substrates increases, the effect of the inhibitors decreases
 * ** Non-competitive Inhibitors: ** **They bind to enzyme at location different from the active site. They do not affect the enzyme-substrate binding. And they also increase the activation energy.**
 * Vmax = decreases
 * But Km remains the same
 * When concentration of substrate increases, the effect of inhibitors does **NOT** change
 * Important to note that there isn't any competition between the inhibitors and the substrates therefore increasing the concentration of the substrate won't help
 * By binding to another site, the noncompetitive inhibitor controls the shape of the active site that it prevents substrates from binding.

__**Effects of Temperature, pH and Heavy Metal Ions on Enzyme Activity:**__

Graph:
 * ** Effect of Temperature : **
 * Increases in Temperature will increase the Rate of Enzyme-catalyzed Reactions as more reactants reach activation energy
 * However, if the temperature is too high (higher than the temperature), the hydrogen bonds will break, causing the enzyme to denature
 * They normally function at body temperature of 37 Celsius

Graph:
 * ** Effect of pH: **
 * Enzymes are electrically charged because R-groups may ionize when they dissolve in water
 * Change in pH interferes with acidic and basic molecules on the side chain, altering the tertiary structure
 * Each enzyme has its optimum pH, at which the rate is maximum. So enzymes will only function at given pH
 * Most enzymes function best at pH of around 7 (neutral)
 * ** Effect of Heavy Ions: **
 * Heavy ions act as non-competitive inhibitors by with sulfhydral groups (turning **S**H group --> -**S**Metal). This will interfere with the tertiary structure and the side chains

__**I****B** **Practice Questions:**__ **Source: (** [] )

__** Question 1 **__ Enzymes are proteins that can catalyze the reactions of some molecules in living matter.

(a) The action of enzyme is //specific//. Outline what is meant by the term specific and explain how an enzyme works. (You may use the symbols E for enzyme, S for substrate and P for product.) [4]

(b) Enzyme-catalyzed reactions are sometimes slowed down by inhibitors. The following graph represents the rate of an enzyme-catalyzed reaction at different substrate concentrations. (i) Explain how a non-competitive inhibitor would slow down such a reaction and draw a line on the graph to show its effect. [3] (ii) State the effect of a non-competitive inhibitor on the values of [2]
 * Vmax_____
 * __Km_______

__Outline how enzymes catalyze reactions [7 marks]__
 * Question 2 **

__Explain the effect of pH and temperature (using graphs) on enzyme activity [6 marks]__
 * Question 3 **

__Explain the effect of a competitive inhibitor on enzyme activity [6 marks]__
 * Question 4 **


 * Work Cited:**__

"B. Human Biochemistry." Human Biochemistry. N.p., 9 May 2011. Web. 02 Jan. 2014. . "Biochemistry." Ms. Wiseman's I.B. Chemistry:. N.p., n.d. Web. 02 Jan. 2014. . "Brent Cornell." 3.6 Enzymes. N.p., n.d. Web. 02 Jan. 2014. . "Enzymes." Chemistry for Biologists. N.p., n.d. Web. 02 Jan. 2014. . Hodgkinson, Wayne. "Competitive and Non-competitive Inhibition.mp4." YouTube. YouTube, 14 Jan. 2012. Web. 02 Jan. 2014. . "Option C - Human Biochemistry (HL)." IB Chemistry Syllabus and Notes. N.p., n.d. Web. 02 Jan. 2014. . "Proteins and Enzymes." BBC News. BBC, n.d. Web. 2 Jan. 2014. .