Biochemistry Study Guide Exam 2 

What is it called when products are being made as quickly as reactants?

In this study guide you will know more about enzymes and their basic concepts; catalytic  reactions and characteristics and Regulation.  

Enzymes: are biological catalysts (which speed up reaction). The enzymes can speed up  reactions to 1012. Here are some important characteristics about enzymes. Increase the rate of  reaction

∙ Do not alter the equilibrium constant  

∙ Lower the activation energy If you want to learn more check out What are the 2 rules where we are to walk one towards another?

∙ Are not changed nor consumed in the reaction (means they appear the same as the  reactants and the products)

∙ Are pH and temperature sensitive and has optimal activity at certain ph ranges ∙ Do not affect the overall delta G of the reaction  

What do we commonly call coenzymes and cofactors?

We also discuss several other topics like What is the state of hammurabi?

∙ And they are very SPECIFIC

∙ Protein and RNA molecules are enzymes.  If you want to learn more check out What does exponential growth mean?

Cofactors are small molecules or metal ions that help aid in catalysis. There are two cofactors  which are:

1. Coenzymes: Binds to electron with intermolecular forces (vitamins)

2. Prosthetic groups: which binds to electrons covalently

Halo-enzymes: are enzymes with a cofactor 

Apo-Enzymes: are enzymes without a cofactor

Next we will list 6 different reactions that Enzymes undergo and participate in.  

1. Oxidorerductase/ Dehydrogenases: is the transfer of electrons between biological  molecules. They often have electron carriers such as NAD+ or NADP+. The electron  donor is usually the reductant and the electron acceptor is known as the oxidant.  

How do you find kcat from km and vmax?

∙ Enzymes with dehydrogenase or reductase in their names are usually  oxidoreductases. Enzymes with oxygen is the final electron acceptor and often  included oxidase in their names 

2. Transferases: Catalyze the movement of a function group from one molecule to  another. Most transferases are straightforward; remember that Kinases are members of  this class and that they usually aid in the transfer of a phosphate group (Generally from  ATP TO ANOTHER MOLECULE).  We also discuss several other topics like What are the reasons of changes in attitudes?

3. Hydrolases: catalyze the breaking of a compound into two molecules using the addition  of water. They are usually named for their function. For example: Lipases breaks down  lipids, phosphatase cleaves a phosphate group and peptidases break down proteins. On  the exam and you are stuck. Think for a moment and break the word down, it would be  easy to then spot this reaction.

4. Lyases: Catalyze the cleavage of a single molecule into two products, this reaction do  not need redox or water. Also this reaction can make two molecules into one. Therefore  making or breaking molecules to create a product. This is also called a synthases  reaction.  

5. Isomerases: Is the rearrangement of bonds within a molecule. This reaction creates an  isomer. -> No need to continue with that definition 

6. Ligases: Makes covalent bonds with energy extracted from ATP. This is the BIGGER  reaction versus Lyases. Meaning, that larger molecules that needs synthesis or addition  will participate in LIGASES however smaller molecules will participate in lyase.  We also discuss several other topics like What is done by congress for federal courts?

The next concept is knowing how enzyme acts:  

Substrate: is the molecule that an enzyme act on. Or the ENZYME SUBSTRATE COMPLEX.  The Active Site: Is the location within the enzyme where the substrate is held during the rxn.  

∙ The active site is the main reason why teachers and students say that enzymes  are specific! It is mainly because this site dictates which molecule or group of  molecules interact with the enzyme, in order to know they must “fit”.  

Two theories to describe this phenomenon:  

1. Lock and Key theory: Suggest that the enzyme active site (lock) is already in the  appropriate confirmation for the substrate (key) to bind. I suggest googling pics of this  theory to understand what I mean by this concept. Its straight forward I promise!

2. Induced Fit Model: Picture this! You have a very nice foam bed, it has memory foam and  everything. You decided to take a nap and you become very comfortable and relaxed  because your bed have taken up your shape. Meaning that it curves in all the right  places. Where am I getting at you may say. In this theory the foam bed is the enzyme  and you are the substrate. Which means that the enzyme will take up the shape of the  substrate thus binding together to become HAPPY AND RELAXED. Because you and the  bind have become comfortable (INDUCED ALSO KNOW AS THE TRANSITION STATE) you  both realize that you can react together to make a single product which equals: A rested  person. BED+HUMAN BEING ????BIND TO SLEEP (TRANSITION STATE/ INDUCED FIT)=  Rested Person! We also discuss several other topics like What are the reasons that make you buy a product?

Kinetics of Enzymes: This is one of the most important concepts. This will mention the  Michaelis-Menten Equation and the Line weaver –Burk Plots.  

Vmax: is the theoretical number that an enzyme is working at maximum velocity (but the  enzyme will never reach maximum). 

Km: Is the substrate at ½ Vmax. It is a measure of the affinity of the enzyme for its substrate.  (Higher the Km the lower affinity; the number must be small).

Kcat: Measures the steady state conditions. Kcat= K2. This element will give you product/sec  and we want big #.  

Kcat/Km: Catalytic efficiency basically how good enzymes are doing its job. This element needs  a big number.  

Know the Double reciprocal plot: Please look up the plots for this.

Michaelis- Menten Equation: 

This equation describes the rate of the reaction, v, depends on the concentration of both the  enzyme [E] and the substrate [S] which forms product [P]. ES complexes form at a rate K1. The  ES complex can either dissociate at a rate K2.  

The velocity of the enzyme to substrate concentration is in this equation: V= Vmax [S]/Km+ [S] ∙ The Km is the Michaelis constant and is often used to compare enzymes.  Lineweaver- Burk Plots 

Is a double reciprocal graph. This plot is useful when determining the type of inhibition that an  enzyme is experiencing because Vmax and Km can be compared without estimation.  

Regulation of Enzymes and Other Functions 

Regulation of Enzyme Activity is subject to inhibition and activation.  

Feedback regulation: is when enzymes are regulated by intermediates that precede the enzyme  in the pathway (feed-forward regulation).  

∙ Feedback inhibition or Negative Feedback: Is when there is enough product  given, the reaction cuts off rather than creating more. This is also maintaining  homeostasis. In this process the product may bind to the active site of an  enzyme or multiple enzymes therefore inhibiting enzymes to do their work.  

Reversible inhibition: There are four types: competitive, noncompetitive, mixed and  uncompetitive.  

1. Competitive: Inhibitor will bind to the same place as the substrate in the active site. In  order to stop this you will need to add more substrate which increases the Km but keep  the Vmax the same.  

2. Noncompetitive: Is the opposite of the competitive; which means the inhibitor binds to  a different place than substrate. This also results when the inhibitor with equal affinity  to enzyme and ES complex. Vmax is decreased and Km is constant.

3. Mixed: Is when the inhibitor binds unequally. Vmax is decreased and Km is increased or  decreased depending on the inhibitors affinity for ES complex.  

4. Uncompetitive: results when the inhibitor binds only with ES complex Km and Vmax  both decrease. However this is not natural.  

Irreversible inhibition: alters the enzyme so the active site is not available. Sequential Mechanism: Is when reactants or substrates bind then products are in results

∙ Ordered: is a particular order of the reaction

∙ Random: Means that is in a random order. Doesn’t matter what which substrate  gets products.  

∙ Double Displacement: where substrate A binds and gets a product A and then  substrate B binds and gets product B.

Be sure to review Acid/Base Catalysis.  

Lastly, be sure to know the different Proteases such as serine proteases: like chymotrypsin.  Lastly, regulatory enzymes can experience activation

∙ Allosteric: are sites that can be occupied by activators which increase affinity or  turnover

∙ Phosphorylation (covalent phosphate) or glycosylation (covalent carbohydrate) thus this  will alter the activity of the enzymes.  

∙ Zymogens: is an inactive enzyme.  

Have Fun Studying.