Properties of proteins

Question 1

What can cause a protein to denature? (4)

Answer 1

1.) Strong acids or bases, or reducing agents: Add or remove hydrogens
2.) Organic solvents, detergents: Disrupt hydrophobic, polar and charged interactions
3.) Salts: Disrupt polar and charged interactions
4.) Heavy metal ions

Question 2

What 2 groups can a heavy metal bind with to denature it by changing its shape?

Answer 2

1.) negatively charged groups
2.) sulfhydryl (SH)

Question 3

Enzymes are an example of what type of protein?

Answer 3

Globular

Question 4

Enzymes speed up a reaction by lowering the ___________ of the reaction with out changing the ____________ nor ___________.

Answer 4

activation energy/standard free energy/equilibrium

Question 5

________ is the minimal amount of energy needed to make/break the bonds necessary for a reaction to occur.

Answer 5

Activation energy

Question 6

True or false.
Activation energy is sometimes defined as the amount of energy needed to reach the transition state.

Answer 6

True

Question 7

The _____________ is the highest energy configuration formed when changing from reactants to products.

Answer 7

transition state

Question 8

The transition state is (transient/constant) and (isolated/not isolated).

Answer 8

transient/not isolated

Question 9

The activation energy is (increased/lowered) in the catalyzed reaction.

The overall standard free energy of the equation is (lowered, increased, not changed)

Answer 9

lowered/not changed

Question 10

The active site is formed by precise (primary/secondary/tertiary/quaternary) structure of a protein

Answer 10

quaternary

Question 11

Do amino acids in the active site participate in substrate binding and catalysis?

Answer 11

Yes

Question 12

Once inside the active site, the substrate binds the enzyme forming an __________________ complex.

Answer 12

enzyme-substrate (ES)

Question 13

In the __________ model, binding of substrate is thought to induce a conformational change in shape of the enzyme.

Answer 13

induced fit model

Question 14

What are the mechanisms of an enzyme, once it has bound to the active site?

Answer 14

1.) electrostatic interactions to form between S and E
2.) ensures correct positioning of catalytic groups in the enzyme

Question 15

In what 2 ways do catalytic groups speed up reactions?

Answer 15

1.) acid-base catalysis
2.) covalent catalysis

Question 16

In _____________ mechanism, the addition or removal of a proton can make a substrate more reactive.

Answer 16

Acid-base catabolism
(The side chains of certain amino acids can add or remove H+’s by acting as general acids or bases)

Question 17

Acid- base effects:
When there are no catalysis, the reaction is slow, it is fast with either acid catalysis or base catalysis, with BOTH acid and base catalyses, it is (the fastest/the slowest).

Answer 17

fastest

Question 18

In ________________ enzyme mechanism, a nucleophilic side group in the enzyme active site forms a temporary covalent bond with the substrate

Answer 18

covalent catalysis

Question 19

What are 2 common nucleophilic side groups of AA?

Answer 19

Asp and Glu (R- COO-)
Ser (R-OH) and Cys (R-SH)

Serine and Cystein are only weakly nucleophilic, but their nucleophilicity is enhanced by the presence of other amino acids that can remove the H*

Question 20

Cofactors are typically _____ cations.

Answer 20

metal (mg2+, Zn2+)

Question 21

What is magnesium’s role in several glycolytic enzymes involving ATP?

Answer 21

helps position the ATP in the enzyme active site

helps to stabilize the negative changes on the ATP

Question 22

What are coenzymes typically derived from?

Answer 22

vitamins

Question 23

In what 3 ways can cofactors and coenzymes speed up reactions?

Answer 23

1.) Can help position the substrate in the active site of the enzyme
2.) Can stabilize negative charges on the substrate or the TS to make it easier for a nucleophilic attack to occur
3.) Can accept/donate electrons in redox reactions

Question 24

The optimal temperature for an enzyme is usually (higher than, lesser than, equal to) the organism.

Answer 24

Equal to

Question 25

Changing the pH (can/cannot) change the protonation state of the enzyme and/or the substrate

Answer 25

Can

Question 26

What types of bonds between E and S would potentially be disrupted by a change in pH? (2)

Answer 26

1.) H-bonds
If an H is removed, no H-bond can be formed
If an H is added, an H-bond might form that is not usually formed.
2.) Electrostatic interactions
Adding an H can turn COO- into COOH
Removing an H can turn NH3+ into NH2

Question 27

What is the function of a lysosome?

Answer 27

Main site of intracellular enzymatic degradation for a wide range of molecules

Question 28

What 4 main ways can enzymatic activity be controlled?

Answer 28

1. Genetic
2. Covalent modification
3. Allosteric regulation
4. Compartmentalization

Question 29

True or false.
Enzymes transcription can be induced OR repressed based on the needs of a cell.

Answer 29

True

Question 30

Which type of enzyme regulation, Involves altering the structure of an enzyme (or “proenzyme”) by making or breaking bonds

Answer 30

Covalent modification. (making or breaking covalent bonds)

Question 31

The main regulated enzyme in glycogenesis is (activated/ de-activated) by phosphorylation while the main enzyme in glycogenolysis is (activated/deactivated) by phosphorylation.

Answer 31

deactivated/ activated

Question 32

Phosphorylation is catalyzed initially by the same enzyme____________.

Answer 32

protein kinase A (PKA)

Question 33

Which type of enzyme regulation involves cleavage of peptide bonds in proenzymes or zymogens and
ensures the enzyme is not used until it is in the correct location and until it is needed

Answer 33

covalent modification

Question 34

Phosphofructokinase-1 is (inhibited/activated) allosterically by high levels of ATP

Answer 34

inhibited

Question 35

Phosphofructokinase-1 in (activated/inhibited) allosterically by high levels of AMP

Answer 35

activated

Question 36

Compartmentalization of enzymes via membrane-bound organelles allows for regulation by: (2)

Answer 36

1. Separation of enzymes from opposing pathways into different cellular compartments, and selective transportation of substrates
2. Creation of unique microenvironments (ex. pH levels)