topic 4: Enzymes

Question 1

What are most enzymes?

Answer 1

Most enzymes are proteins, and proteins are polymers of amino acids.

Question 2

What are amino acids?

Answer 2

Chemical compounds made up of amino (NH2-) group, carboxyl (COOH-) group and a differing R-group (different amino = different side chain). They use covalent bonds.

Question 3

How are amino acids polymerized?

Answer 3

They are linked by peptide bonds through dehydration synthesis (forming through removal of H2O).

Question 4

What are peptide bonds?

Answer 4

When the carboxyl group of one amino acid is linked to the amino group of the second amino acid (usually C-N).

Question 5

Key differences in R-groups?

Answer 5

Some are polar (hydrophilic) and some are non-polar (hydrophobic). REMEMBER that amino acids can be non-polar despite having amino and carboxyl group.

Question 6

Hydrophobic vs Hydrophilic R-groups?

Answer 6

Hydrophobic on inside of membrane bilayer (with tail) + have MOSTLY non-polar bonds in R-group (C-H mostly or S-S… . Hydrophilic have polar bonds (NH3, OH…) or can even have charges (+/- compound).

Question 7

Peptide vs polypeptide vs protein

Answer 7

Peptide is 2-10 row of amino acids and a polypeptide is around 50 chain of amino acids. Protein differs by being a long polypeptide (>50) which has a FUNCTIONAL 3D SHAPE. Formation

Question 8

What are the levels of protein structure?

Answer 8

Primary (sequence/raw polypeptide), Secondary (folds/helices), Tertiary (3d arrangement), and Quaternary (multiple tertiary, not all have).

Question 9

What are the start and end of a polypeptide chain?

Answer 9

The N-terminus and C-terminus aren’t connected to anything.

Question 10

Where are new Amino Acids added?

Answer 10

To the C-terminus from carboxyl group of last Amino Acid. ?

Question 11

How is Helix (a-helix) shape created?

Answer 11

Through HB bond pattern- when O (carboxyl) and H (amino) from Aa1 and Aa4 (4 residues apart) repeatedly interact.

Question 12

What is the b-strand?

Answer 12

The sheet part of the secondary protein structure, where stretched segments of polypeptide chain are arranged adjacently by hydrogen bonds. More likely to be anti-parallel.

Question 13

When does a protein attain function?

Answer 13

At its 3rd structure where R-groups interact in 3d arrangement.

Question 14

Same 4th?

Answer 14

Homo not hetero.

Question 15

What is key thing in protein structure (besides raw sequence)?

Answer 15

The ARRANGEMENT of that sequence is just as important. Team does not equal Tame, even though same letters present.

Question 16

Why do we need enzymes?

Answer 16

Biological reactions are extremely slow. When bonds of reactants are stable, external E must be inputed- or the reaction made easier. Enzymes are biological catalysts.

Question 17

Energy required to set off reaction?

Answer 17

Activation Energy. This is what enzymes lower to increase rate of reaction.

Question 18

State where old bonds breaking and new ones starting to form?

Answer 18

Transition State- highest potential E.

Question 19

What remains the same even with enzymes?

Answer 19

deltaG- the (free) energy of the reactants/products is the same.

Question 20

What are some ways to increase the rate of chemical reaction?

Answer 20

1. Increase the temperature (more collisions + colliding with more E). 2. Add a catalyst to lower Ea. 3. Manipulate the concentration of reactants and products (more collisions + lechatelier (visualize)).

Question 21

How do enzymes decrease activation energy?

Answer 21

They make it more likely for products to interact and collide at proper orientation. They have activation site, a region where Enzyme-subtrate complex is created and interaction lowers Ea.

Question 22

Specific ways for enzymes to decrease activation energy?

Answer 22

The ES complex changes conformation of enzyme, creating an INDUCED FIT. The induced fit is shaped for the transition state where bonds of substrate rearranged- lowering Ea. The enzyme forces the subtrate into its transition state.

Question 23

What happens after products are created in enzyme?

Answer 23

They are released and enzyme goes back to original conformation.

Question 24

Different ways of forcing transition state?

Answer 24

Bringing reactants closer, polarizing, distort substrate molecules, ect.

Question 25

Different ways of forcing transition state?

Answer 25

Bringing reactants closer, polarizing (making bonds unstable), distort substrate molecules, ect.

Question 26

When are enzymes used as energy coupling devices?

Answer 26

When the free energy change (deltaG) is positive, enzymes need to catalyze multiple reactions at the same time.

Question 27

How do enzymes work as E coupling devices?

Answer 27

They can transfer the energy released from one reaction to another reaction that requires E to complete it. They do this by becoming phosphorylated or being reduced. P to enzyme to Product

Question 28

What does enzyme kinetics depend on and how do cells control?

Answer 28

Concentration of enzyme and substrate. Cells control this through enzyme activators/inhibitors.

Question 29

What peaks?

Answer 29

Saturation leads to stagnation (max rate), but if enough substrate, additional enzyme will always increase speed.

Question 30

What is denaturation?

Answer 30

Loss of protein structure = less functional (or completely). Reversible or permanent. Can also be due to heat (body conditions best). Different enzymes (in different body parts) have different preferences.

Question 31

What is enzyme inactivity?

Answer 31

Lowering rate of reaction. Can be due to denaturation or inhibition. Reversable vs permanent

Question 32

Reversible Competitive Inhibitor?

Answer 32

Similar structure to substrate- competes to fill active site and lower enzyme activity. Concentration of inhibitor vs substrate determines rate of reaction.

Question 33

Reversible non-comptetitive inhibitor?

Answer 33

NOT chemically similar to subtrate. Binds to allosteric binding site and makes enzyme have low affinity for substrate. High concentrations of substrate DO NOT outcompete this.

Question 34

What are regulatory (allosteric enzymes)?

Answer 34

All biochem pathways include regulatory enzymes that control rate of ENTIRE PATHWAY. Binds to enzyme to change shape to more active form= allosteric activator

Question 35

Feedback inhibition?

Answer 35

When the final product of a biochem pathway is an allosteric inhibitor and it blocks an enzyme early in the pathway.