Lecture 1

Question 1

iterated

Answer 1

repeated

- biomolecules in metabolism are typically not iterated, as DNA and proteins are

Question 2

metabolite

Answer 2

intermediate in a metabolic pathway

Question 3

Metabolic pathway-

Answer 3

f

Question 4

catabolism-

Answer 4

the breakdown of biomolecules into smaller molecules for energy

Question 5

anabolism-

Answer 5

the building up of larger biomolecules from smaller ones, requires energy

Question 6

Metabolome/Metabolomics-

Answer 6

e

Question 7

functional group-

Answer 7

a

Question 8

L-amino acid-

Answer 8

a

Question 9

peptide bond-

Answer 9

s

Question 10

C-terminus and N-terminus-

Answer 10

s

Question 11

alpha helix-

Answer 11

e

Question 12

beta sheet-

Answer 12

d

Question 13

primary, secondary, tertiary, quaternary structure-

Answer 13

s

Question 14

cofactor//

Answer 14

• Help enzyme perform its function and are required for it to be able to perform its function
• Can be either small molecules (coenzymes) or metal ions that have to associate with the enzyme for the enzyme to work
• Usually derived from vitamins

Question 15

prosthetic group//

Answer 15

A tightly bound cofactor

Question 16

enzyme//

Answer 16

• Biological catalyst
• Typically a protein but not always; can also be RNA
• They speed up reactions by lowering the activation energy by providing a different pathway (and different transition state) for the reaction to take
• They do NOT make non spontaneous reactions spontaneous; they affect kinetics, not thermodynamics
• Do not get altered as a result of a chemical reaction
• They can, and do, change shape, etc, but they always regenerate their original form at the end of the reaction, so it is like they were never altered
• They form complexes with substrates
• Only operate under specific physiological conditions, or else we get the whole “change protonation/functional group state, change structure, change function”
• Produce product in high yield
• Most can be regulated
• Many use cofactors for activity
• They increase the rates of both the forward AND reverse reactions
• Enzymes do NOT affect the final amount of product formed, only the rate at which it is formed (ex. it will take 1 second to make 100 molecules of something instead of 1 hour)
• Enzymes do NOT affect the final ratio of products to reactants (hence why the rate of both the forward and reverse reactions must increase)
• BIG IDEA: Enzymes accelerate the attainment of equilibria but do not shift their positions, i.e. do not affect the actual equilibrium positions.

Question 17

active site//

Answer 17

• The part of the enzyme the substrate binds to
• Is a three dimensional cleft of crevice in the enzyme and only takes up a small volume of the enzyme
• Contains residues that are directly involved in making and breaking bonds in the substrate
• The formation of the enzyme-substrate complex is the first step in enzymatic catalysis, and it occurs at the active site
• The active site is a unique microenvironment that is different from the environment outside the enzyme
• the active site sometimes excludes water by having hydrophobic residues there
• Sometimes water is needed in the substrate-enzyme interaction, however, so it is allowed in the active site, it really all depends on the enzyme and substrate

Question 18

reaction coordinate diagram//

Answer 18

A one dimensional graph that represents the progress of a reaction plotted against the free energy of all the components.

Question 19

activation energy //

Answer 19

ΔG^‡

Energy difference between reactant and transition state

Question 20

transition state//

Answer 20

‡
Corresponding to a “hill” on a reaction coordinate chart; it is the high energy structure between the reactant and product that needs to be formed for the reaction to occur

Question 21

catalytic mechanisms-

Answer 21

d

Question 22

entropy reduction//

Answer 22

General: They provide different pathways (mechanisms) for a reaction to take place that have a lower activation energy and a transition state with lower free energy so more molecules can reach that threshold
Typically do so by stabilizing the transition state/introducing a new transition state that is lower
energy
- The free energy of the substrate isn’t changed, but now that the free energy of the transition state is lower, more molecules of the substrate have sufficient energy to overcome that barrier
Specific:
- They can hold one of the molecules in place in the correct orientation that it needs to be in to increase the chance of a constructive collision occurring (playing with orientation)
- Can also make the other molecule be more attracted to it (the enzyme) so it has a higher chance of colliding
Actual definition?: energy, called “binding energy” is released when multiple weak interactions form between an enzyme and its substrate. This energy can only be maximized with the correct pairing of an enzyme and its substrate, with the correct alignment of weak interactions

Question 23

acid-base catalysis-

Answer 23

s

Question 24

metal ion catalysis-

Answer 24

s

Question 25

covalent intermediate-

Answer 25

s

Question 26

substrate//

Answer 26

The molecule the enzyme acts upon.

Question 27

product-

Answer 27

The resulting product after a substrate-enzyme interaction, or in other words, the substrate after it has been modified/altered by the enzyme.

Question 28

Practice amino acids

Answer 28

done

Question 29

f

Answer 29

d

Question 30

specificity/selectivity

Answer 30

h