Fundamentals of Biochemical Reactions

Question 1

What is metabolism?

Answer 1

A series of biochemical reactions that can be either metabolic or anabolic in nature to harness energy from biomolecules.

Question 2

The concept of Delta G and how to apply it.

Answer 2

G is the free energy change

g=0 Rxn is at equillibrium
g>0 rxn is NON-spontaneous (energonic)
g<0 rxn is spontaneous (exergonic)

Question 3

What is Keq?

Answer 3

Keq is the ratio of the products/reactants within an equation

Question 4

What is the relationship between Keq and Go’

Answer 4

Go’=-RTLnK

Keq is directly proportional to Go’

When:
Keq=1 Go’= 0 Reaction is at Eq (no change)

Keq>1 Go’<0 Reaction is Spontaneous (rxn will proceed to the right)

Keq<1 Go’>0 Reaction is NOT SPONTANEOUS
(Will proceed to the left)

Question 5

What are the Reaction Drivers? How can you make a reaction go in the direction you want?

Answer 5

a.) Mass Action–> Based on Le Chatelier’s Principle, you can make the reaction go in the direction that you want by altering reaction kinetics
- If reaction is NOT SPONTANEOUS and pushes
to left, you can push it to the right by removing
product or adding reactants.

b.) Input of Energy/ Energy Coupling
- endergonic rxns coupled with exergonic
reactions to make the former happen
**THE FINAL DELTA G of sum of rxns will
determine the fate of the reaction coupling
mechanism

Question 6

List the type of reactions and give examples of each.

Answer 6

1.) Addition/ Elimination Rxn
Addition Rxn–> adding a product to a double bond
Elimination Rxn–> removing a product to form a double
bond

2. ) Substitution Rxn–> a SN1 or SN2 rxn that uses a nucleophile to attack an electrophile to create a substitution.
3. ) Rearrangements–> shift of a functional group on a molecule via isomerase/ mutase
4. ) Oxidation/Reduction–> a reaction that causes electrons to be transferred from one molecule to another
5. ) Acid-Base Rxn–> involves molecules that donate protons and accept protons

Question 7

What is the body’s buffering system? What type of rxn is this an example of?

Answer 7

The buffering system is an example of an acid-Base rxn.

HC03- +H+ –> H2CO3–> H20 + C02

Question 8

What is the normal physiological PH of the body’s buffering system?

Answer 8

pH= 7.37- 7.43

Question 9

What are enzymes? What do they do?

Answer 9

Enzymes are biological catalysts that increase the reaction rate.

Bind to substrates and convert them into products by lowering the activation energy (Ea)

Question 10

What are some examples of oxidoreductases?

Answer 10

Dehydrogenases
Oxidases
Peroxidases
Reductases
Monooxygenases
Dioxygenases

Question 11

Lock and Key Hypothesis vs. Induced Fit Hypothesis

Answer 11

Lock and Key Hypothesis- substrate fits enzyme like a perfect fit like a key to a lock

Induced Fit Hypothesis- substrate binds to enzyme and causes conformational changes

Question 12

What is the difference between a cofactor and a coenzyme?

Answer 12

Cofactors are not organic molecules

Coenzymes are organic molecules

**Both play a functional role in aiding an enzyme perform its duties in making reactions occur.

Question 13

Example of Coenzymes

Answer 13

FAD, FMN, Heme (not just Fe BRO!!!!!), NAD+, Lipoic Acid, Panthoneic Acid, Pyroddoxil Phosphate, THF, Thiamine Pyrophosphate

Question 14

Examples of Cofactors

Answer 14

Cu, Fe, Mg, Se, Zn

Question 15

How does the H+/K+ ATPase pump work in the STOMACH?

Answer 15

H+/K+ ATPase uses ATP to push H+ into the stomach to combine with Cl- –> HCL

HCl acid is good because the acidity will activate pepsinogen–> pepsin for protein digestion!

Question 16

What are some of the common proton pump inhibitors that work on the H+/K+ ATPase Pump?

Answer 16

Omeprazole, Lansoprazole, Esmoprazole

-all the “prazoles”

Question 17

What is the rate of an enzymatic reaction based on?

Answer 17

[substrate]
affinity of the enzyme (Km)
Velocity (v, Vmax)

Question 18

What are the different types of Enzyme Inhibition?

Answer 18

Competitive Inhibition–> Vmax the same, Km increased
-How to Overcome: Increase [SUBSTRATE]

NON-Competitive Inhibition–> binds to the E and ES complex at site other than substrate binding which results in DECREASED [Vmax], SAME [Km]

***Uncompetitive Inhibition–> only binds to ES complex; results in DECREASE of BOTH Vmax & Km

Question 19

What are examples of Competitive Inhibitors?

Answer 19

Malonate
Sulfanilamide
Methotrexate

Question 20

What are Chelating agents and how are they used?

Answer 20

Chelating agents are agents that bind more strongly to a poison than its affinity for another substrate.

-Example–> Pb and Ca-EDTA

Question 21

What does it mean when an enzyme is inactive or irreversibly inactive?**

COVALENT MODIFICATION

Answer 21

It means the enzyme has lost its function irreversibly from destruction or covalent modification of key functional groups that were important for the enzyme to function.

-Km unchanged, Vmax DECREASED (SIMILAR TO NON-COMPETITIVE INHIBITION)

Question 22

What is an irreversible enzyme inactivation similar to in terms of competitive, noncompetitive, and uncompetitive rxns?

COVALENT MODIFICATION

Answer 22

Very similar to noncompetitive inhibition because just like an irreversible reaction:

-the Km is unchanged, Vmax is DECREASED

Question 23

Examples of Irreversible Inhibitors

Answer 23

Pb
Organophosphates
Aspirin
Cyanide
Sulfide

Question 24

Allosteric Enzymes are modified through covalent or non-covalent interactions? And what are activators vs. inhibitors?

Answer 24

Allosteric inhibitors bind via NON-COVALENT interactions.
Activators–> INCREASE activity
Inhibitors–> DECREASE activity

Question 25

Allosteric Enzymes are modified through covalent or non-covalent interactions? And what are activators vs. inhibitors?

Answer 25

Allosteric inhibitors bind via NON-COVALENT interactions.
Activators–> INCREASE activity
Inhibitors–> DECREASE activity

Question 26

What type of graph do you use for allosteric enzymes?

Answer 26

You use a sigmoidal graph where:

(+) activator –> shift to left
(-) inhibitor –> shift to the right

Question 27

What are isozymes?

Answer 27

Enzymes that have same function, but different AA sequences

ex: CK-MB, AST, LDH

Question 28

What are proenzymes/zymogens?

Answer 28

Proenzymes/Zymogens are inactive forms of the enzyme that have to be activated via cleavage

Ex: pepsinogen, chymotripsinogen