Lecture 8-10 - Enzymes

Question 1

What is the general formula for an enzyme reaction?

Answer 1

E + S = ES = E + P

Question 2

Define kcat related to uncatalyzed and catalyzed enzymatic reactions.

Answer 2

Kun is regarded as the uncatalyzed rate (Slow/Small as hell)
Kcat is the Catalyzed Rate, or the speed with an enzyme (hopefully a lot faster/higher)
(Both of these are usually “per second”)

The enzymatic rate enhancement is calculated with (Kun/Kcat)
However, the enzymatic efficiency is usually defined using Kcat.

Question 3

What is one of the most famous/fastest examples of a biochemical enzyme

Answer 3

Carbonic Anhydrase: Helps convert CO2 into HCO3- for transport throughout bloodstream, and also helps maintain pH.

Uncatalyzed rate is about 0.13. Catalyzed rate is about 10^6.

Question 4

One more time now…

Define the two Free energy formulas

Answer 4

deltaG = deltaGstandard + RTln([B]/[A])

And deltaGstandard = -RT*ln(Keq)

Question 5

At what phase during the enzymatic reaction is the free energy at it’s highest?

Answer 5

During the transition state. Enzyme binds to substrate to create a transition state with high free energy and increases the need to quickly drop into a product state.

Question 6

Define LeChatlier’s principle and Coupled Reactions

Answer 6

LeChatlier’s principle, or the mass energy principle, states that you can push a reaction’s equilibrium more towards the product side by adding more substrate/reactants, and/or decreasing the amount of product.

Coupled reactions are best described with ATP, where the free-energy released from catalyzing said ATP is used to drive endergonic reactions.

Question 7

What are the two major types of biochemical reactions found?

Answer 7

Oxidation-Reduction Reactions - Electron donor will reduce the electron acceptor. And the donor will be oxidized by the acceptor.

Acid-Base Reactions - Weak acid dissociates in water, releasing a proton and its conjugate base, or weak base combines with protons in water, forming its conjugate acid. Not much work is done with strong acids or bases.

Question 8

Give the full bicarbonate formula used to maintain pH

Answer 8

(H+) + (HCO3-) ->

Question 9

Blood is maintained at a slightly basic pH of about 7.4.

Describe Acidosis 2 disorders associated with each.

Answer 9

Acidosis (pH is too low)

• Respiratory acidosis: Hypoventilation increases CO2 (changing the equilibrium to more protons) (Reaction goes to the left).
• Metabolic acidosis: Addition of a strong acid (lactate, ketones) increases protons, or loss of bicarbonate base increases acidity of the body and lowers pH. (Often occurs during diarrhea)

Question 10

Describe Alkalosis and give 2 examples:

Answer 10

(pH is too high)
Respiratory Alkalosis - hyperventilation releases CO2 too quickly and pushes the reaction too far to the right (lower [H+] = higher pH
Metabolic Alkalosis - Addition of a strong base (ingesting antacids), or loss of acid (vomiting)

Question 11

List and briefly describe the 6 Enzyme Classes

Answer 11

1. Oxoreductases - transfers electrons (oxo/red reaction)
2. Transferase - Transports a Functional Group between molecules
3. Isomerases - Rearrange Isomerize Molecules
4. Lyases/Synthases - Add or remove molecules to or from a pi bond
5. Ligases/Synthetases - Forms Organic Bonds with the hydrolyzing of ATP
6. Hydrolases - Cleaves bonds by adding water

Question 12

Describe the environment of the active site

What does chymotrypsin and trypsin do again?

Answer 12

Active site contains a unique microenvironment, usually void of water, and controls the proper shape, pH and polarity for substrate binding and chemical reactivity
Chymotrypsin - Serine protease that breaks peptide bonds on the C-terminus of aromatic bonds
Trypsin - Does the same, but on the Carboxyl side of lysine and arginine.

Question 13

Describe the catalytic triad

Answer 13

This is the “key” to serine protease function.
The setup is Asp, His, Ser. Asp steals a proton from His, so His steals a proton from Ser, which converts it into a basic (alkoxide) ion. This allows it to become the peptide hydrolyzer it’s known as.

Question 14

What are two factors that effect enzymatic effectivity

Answer 14

Enzymes require optimal temperature and pH. In many cases, that ideal temperature is about 37 degrees celsius. Any lower and the enzyme has reduced efficiency, but too high and the enzyme begins to denature from the heat.
pH extremes can alter the ionic charges on an enzyme which changes it’s shape and potentially makes it useless.

Question 15

What are some necessary factors in Metals when used as cofactors?

Answer 15

• Positively charged
• Stable coordination of active site groups
• Contribute to chemical reactivity
• Ex. Zinc activates H 2 O to fom OHnucleophile

Question 16

What are important aspects of coenzymes?

Answer 16

• Coenzymes are small organic molecules often derived from vitamins
• When bound tightly, called a prosthetic group

Question 17

What is the relationship between the Velocity of a reaction and it’s rate constant

Answer 17

V = k[A]

Question 18

What is on the Y-axis and X-axis of the Michaelis Menton graph. What is Km defined as (Michaelis Constant)

Answer 18

Y-axis is substrate Velocity (Should reach a limit Vmax after enough time)
X-axis is Substrate Concentration (Can indefinitely go up to prove a point)

The point at which the [S] reaches a point on the MM chart where V = (Vmax/2) is the michaelis constant.

Question 19

What is the official Michaelis Menton Equation?

What is represented by [E]T?

Answer 19

Velocity = (Vmax * [S]) / ([S] + Km)

The turnover rate (Kcat), is the number of products an enzyme molecule can produce in one unit of time. [E]T represents the concentration of active sites within a solution…I think.

Question 20

What are the parameters of a Lineweaver Burke Plot?

Answer 20

Easiest way to remember this one is to take the reciprocal of the previous MM formula.
Y-axis = (1/V)
X- Axis = (1/[S])
X-Intercept = (-1/Km)
Y-Intercept = (1/Vmax)
Slope = (Km / Vmax)

Question 21

Describe an allosteric enzyme

Answer 21

These enzymes, which don’t obey the standard MM plot have multiple subunits and active sites, therefore have more “requirements” and “restrictions.” These enzymes can also be inhibited by changing their conformation using another cofactor or substrate or etc…

Question 22

What is a common coenzyme/metal for alcohol dehydrogenase?

Answer 22

NAD+/Zn, NAD+ allows specific enzyme to bind to ethanol for conversion into acetaldehyde. Zn allows enzyme to be positioned this enzyme correctly

Random Note: Lyases (Synthases) almost always form double bonds
And Chymotrypsin is an example of a hydrolase.

Question 23

Give an example of an oxidoreductase?

Answer 23

Alcohol Dehydrogenase (ADH) - Uses NAD+ as a coenzyme to convert alcohol into aldehydes (NAD+ can also be used to further convert said aldehyde to acetic acid, but a different enzyme is needed)

Question 24

Give an example of a transferase

Answer 24

Kinases - Add phosphorous groups to proteins (Very often contain tyrosine, serine, and threonine)

Question 25

Give an example of a hydrolase

Answer 25

Chymotrypsin is one example, as are any enzymes that cleave polysaccharides, such as sucrase. And lactase.

Question 26

What is a lyase?

Answer 26

Any enzyme that adds or removes molecular groups to create a double bond. I’m not clear on how extensive that is, but it could include major cleavage of a protein as long as it forms a double bond in the end.

An example includes Aldolase, which is involved in the second step of glycolysis

Question 27

Give an example of an isomerase

Answer 27

Triose Phosphate Isomerase - Don’t honestly know much about this one, but it requires a reducing portion and an oxidizing portion to properly conform the substrate.

Question 28

Give an example of a ligase?

Answer 28

Most obvious answer is DNA ligase. Joins DNA strands together.
Frequently requires ATP

Question 29

Describe what happens in a sequential reaction?

Double Displacement Reaction?

Answer 29

• During this type of reaction, (this case is conditional to when two or more substrates make two or more products) all substrates must first bind to the enzyme. Only then are products released.
• In a double-displacement reaction, it’s a bit more complicated where one of the products is released before the second substrate is added.

Question 30

Name the 3 types of enzyme inhibitors

Answer 30

Competitive - Binds to the enzyme Instead of the substrate
Noncompetitive - Binds to the enzyme allosterically and changes it’s conformation, blocking the substrate from binding
Uncompetitive -