Enzymes

Question 1

What is an enzyme?

Answer 1

A specific protein that speeds up the rate of a reaction by lowering the activation energy of a reaction.

• They are not changed or consumed in the reaction
• are sensitive to temperature and pH
• do not affect equilibrium
• do not change thermodynamic parameters (G, S, H)

Question 2

What is the structure of an enzyme?

Answer 2

• scaffolded for support and position the active site

- then the active site has a binding site and a catalytic site

Question 3

Catalytic site

Answer 3

Part of enzyme that is very specific and where the reaction is catalyzed

Question 4

Binding site

Answer 4

Where the substrate interacts with enzyme through intermolecular interactions
Positions the substrate so it is properly in the catalytic site

Question 5

Substrate

Answer 5

What is being changed by the enzyme

Question 6

Ligand

Answer 6

Any Substance enzyme interacts with - encompasses both substrate and regulatory molecules

Question 7

Orthosteric Regulatory Elements

Answer 7

Interact with enzyme at its active site

Question 8

Allosteric Regulatory Elements

Answer 8

Bind/interact with enzyme at some other place, other than the active site

Question 9

Induced fit model

Answer 9

Enzyme and substrate affect each other

-initial binding undergoes conformational shifts that allow closer binding and more efficient catalyst

Question 10

Lock and key

Answer 10

Substrate fits into enzyme like a key to a lock - perfect fit with no changes in structure to get a better fit
This is inadequate to explain enzymes interactions with their substrates

Question 11

Oxidoreductases

Answer 11

Catalyze oxidation/reduction reactions

Ex: alcohol dehydrogenase, superoxide dismutase

Question 12

Transferases

Answer 12

Transfer fictional group between molecules
Ex: aspartame transaminase
Creatine kinase
DNA polymerase

Question 13

Hydrolases

Answer 13

Catalyze hydrolysis
Ex: angiotensin converting enzyme
Pancreatic lipase
Lactase

Question 14

Isomerases

Answer 14

Catalyze isomerization

Ex: Ribose-5-phosphate isomerase

Question 15

Ligases

Answer 15

Join molecules together with covalent bonds
Ex: aminoacyl tRNA synthetase
Glutamine synthetase
Pyruvate carboxylase

Question 16

Kinase

Answer 16

Adds a phosphate group to a molecule (phosphorylates

Question 17

Phosphatase

Answer 17

Removes a phosphate

Question 18

Name the different types of enzyme regulation

Answer 18

Negative feedback
Positive feedback
Feed forward regulation
Cooperativity

Question 19

Negative feedback

Answer 19

Downstream products inhibit the pathways to the products
Stimulus —> sensor —> control —> effector
If you have negative inhibition of an enzyme, the products of the reaction end up inhibiting the enzyme upstream in the pathway

Question 20

Positive feedback

Answer 20

Downstream products amplifies initial stages of a reaction

Question 21

Feed forward regulation

Answer 21

Products at an earlier step in the pathway regulate the enzyme

Question 22

Cooperativity

Answer 22

Where the binding of one substate makes it easier to bind the next
Characterized by a sigmodal curve

Question 23

Hill coefficient

Answer 23

Expresses the degree of cooperativity of an enzyme or protein
>1 is positively cooperative
<1 is negatively cooperative
=1 non-cooperative

Question 24

What is the vmax?

Answer 24

The maximum rate of reaction

When X is fully saturated and rate of reaction can’t increase

Question 25

What is Km

Answer 25

Concentration of the substate that corresponds to 1/2 vmax | Can be used to measure the affinity and enzyme has for a substrate

Question 26

Michaelis-menten plot

Answer 26

Reaction rate on y axis Substrate concentration on x axis 1/2 vmax = rate where substrate conc = km

Question 27

Lineweaver-Burk plot

Answer 27

``` Double-reciprocal transformation of Mich-Men, 1/v is on the y 1/Conc. of substate is on the x axis Y intercept = 1/vmax X intercept = -1/km ```

Question 28

Competitive inhibitors

Answer 28

Bind at active site Increase Km Vmax stays the same You can out compete them with more substrate

Question 29

Non competitive inhibitor

Answer 29

Bind allosterically Lower Vmax Km stays same

Question 30

Uncompetitive inhibitor

Answer 30

Prevent enzyme from letting go of substate Vmax decreases Km decreases

Question 31

Mixed inhibition

Answer 31

Inhibitor binds at the allosteric site or binds the enzyme substrate complex Vmax is always decreased Km depends on if the mixed prefers binding the free enzyme or if it prefers the complex Km increases if it prefers free Km decreases if it prefer complex

Question 32

Glycosytion

Answer 32

Form of regulating/modifying enzymes by adding carbohydrate moieties

Question 33

Zymogens

Answer 33

Aka proenzymes | Enzymes that need to be cleaved to be active

Question 34

Cofactors

Answer 34

Chemical compounds that help enzyme carry out its biological function Ex: Mg2+, cu2+, coenzymes (if it’s a cofactor that acts in an enzyme), vitamins

Question 35

Prosthetic groups

Answer 35

When a coenzyme is very tightly bonded to its enzyme | Ex: heme

Question 36

Holoenzyme

Answer 36

Enzyme together with its coenzyme and/or metal

Question 37

Apoenzyme

Answer 37

Enzyme without the coenzymes needed for to function

Question 38

Primary Structure

Answer 38

amino acids held together by covalent bonds (the peptide bonds holding each one together). These are strong, hard to break, so primary structure resilient

Question 39

Secondary Structure

Answer 39

formed by hydrogen bonds between the amine and carboxylic acid groups of the amino acid backbone ex: alpha helices, beta sheets

Question 40

Tertiary Structure

Answer 40

formed by hydrogen bonding and interactions between the side chains of the amino acids to form a 3D structure environment plays role in how the side chains will behave ex: hydrophobic side chains moving the protein so they are enclosed by hydrophilic proteins when in an aqueous environment -oxidizing environments that cause formation of disulfide bonds -reducing environments (often by a reagent, such as 2-mercaptoethanol) to break those bonds disulfide bridges contribute heavily to tertiary structure b/c covalent ex: hydrogen bonding, van der waals, disulfide bridges, salt bridges

Question 41

Quaternary Structure

Answer 41

At least two subunits (full tertiary structure of a protein = 1 subunit) coming together via intramolecular bonds

Question 42

Common Denaturing Agents

Answer 42

temperature high and low pH extremes (this would interfere with charges, or break disulfide bridges if reducing environment) once you remove the denaturing conditions, proteins are able to fold/reassemble again

Question 43

What breaks primary structures?

Answer 43

proteases | these target specific amino acid residues