Chapter 1 Amino Acids, Peptides, and Proteins

Question 1

Why are peptide bonds rigid, in terms of their rotation?

Answer 1

Peptide bonds are rigid because they are a part of the carboxylic group and partake in resonance, thus there is partial double bond characteristics - thus the rigidity

Question 2

What are the 6 categories of enzymes?

Answer 2

Oxidoreducatses
Transferases 
Hydrolases
Lyases
Isomerases
Ligases

Question 3

Oxidoreductases

Answer 3

This classification of enzymes catalyze reactions that require the transfer of electrons

Question 4

Transferases

Answer 4

These transfer functional groups from one molecule to another - like a kinase which transfers phosphate groups from one protein to another

Question 5

Hydrolases

Answer 5

Hydrolases separates molecules and in doing so removes a water molecule

Question 6

Lyases

Answer 6

This classification of enzymes catalyze the cleavage of (or synthesis of) two molecules, not requiring water or electron transfer

Question 7

Isomerase

Answer 7

This classification of enzyme transfers functional groups from one part of a molecule to another part of the same molecule

Question 8

Ligase

Answer 8

Ligases are a classification of enzymes that typically catalyze synthesis reactions that involve two large, similar molecules (like DNA)

Question 9

Coenzymes and cofactors

Answer 9

Coenzymes and cofactors are groups that are required for enzyme function and are typically smaller and assist the enzyme by protonation/deprotonation/ionization.

Question 10

Prosthetic group

Answer 10

A prosthetic group is a coenzyme or cofactors that is tightly bound to the enzyme

Question 11

Cofactors

Answer 11

Cofactors are typically inorganic minerals that need to be taken in through diet

Question 12

Coenzymes

Answer 12

Coenzymes are typically organic molecules like vitamins or vitamin derivatives

Question 13

What does the Michaelis-Menton equation describe in a reaction with an enzyme?

Answer 13

Typically this equation describes that the reaction is dependent on both the concentration of the substrate and enzyme.

Question 14

What is Km?

Answer 14

Km is the concentration at which half the enzyme’s active sites are full

Question 15

Vmax

Answer 15

The maximum velocity that an enzyme will go; the only way to increase this now is to add more machines - add more enzyme

Question 16

Competitive inhibition

Answer 16

A type of inhibition of an enzyme whereby an inhibitor binds directly to the active site, thus the only way to overcome this is to increase the substrate

Question 17

Noncompetitive inhibition

Answer 17

A type of enzyme inhibition where an inhibitor uses a different site of the enzyme, coined the allosteric site. The only way to overcome this is to increase the amount of enzyme - increasing the substrate won’t work because the enzyme has changed conformation when the inhibitor is bound.

Noncompetitive inhibitors bind EQUALLY WELL to both the enzyme without its substrate and an enzyme with its substrate.

Question 18

Uncompetitive inhibition

Answer 18

A type of enzyme inhibition whereby the inhibitor binds only to the enzyme-substrate complex. So, this decreases Km (increasing affinity) but lowers Vmax because there’s less enzyme producing product. Thus, the lines are parallel with or inhibitor on a plot.

Question 19

Zymogens

Answer 19

Zymogens are inactive forms of enzymes that are only activated upon activation (say, an allosteric site or removal of a molecule blocking the active site)