Enzymes and Proteins

Question 1

Metabolism

Answer 1

All the chemical reactions that occur in the cell

Question 2

Catabolism

Answer 2

Breakdown
Energy yielding
Generate raw materials

Question 3

Anabolism

Answer 3

Building macromolecules

Question 4

2nd law of thermodynamics

Answer 4

Energy is lost as heat (entropy)

Question 5

Free energy (G)

Answer 5

Energy in a molecule that can be used to do work
Spontaneous reaction: negative delta G
Reaction with positive delta G can be coupled to a reaction with negative delta G
Net free-energy change for the pair of coupled reactions is less than 0

Question 6

Activation energy

Answer 6

Minimum amount of energy needed in a collision between 2 molecules that will result in a reaction

Question 7

Enzymes

Answer 7

Molecules that lower activation energy: catalyze reaction
Hold substrates in proper orientation and bring them together
Can be reused (aren’t used up in reaction)
Changes only rate (not delta G)
Proteins or RNA
Highly specific
Can be coupled to other enzymatic reactions (free energy from 1 reaction can be used to power less favorable reaction)
Changes conformation when binding to substrate

Question 8

Active site

Answer 8

Pocket or groove formed by amino acids where substrates bind

Question 9

Oxioreductases

Answer 9

Enzymes

Redox reactions

Question 10

Transferases

Answer 10

Enzymes
Transfer of functional groups from one molecule to another
Kinases

Question 11

Hydrolases

Answer 11

Enzymes
Hydrolytic cleavage of molecule at C-O, C-N, or C-C bonds
Nucleases, proteases, amylases

Question 12

Lyases

Answer 12

Enzymes

Break or form double bonds

Question 13

Isomerases

Answer 13

Enzymes

Movement of a functional group within a molecule

Question 14

Ligases

Answer 14

Enzymes
Joining 2 molecules together
Create new C-C, C-N, C-O, or C-S bonds using ATP

Question 15

Michaelis-Menten equation

Answer 15

V= (Vmax * substrate conc.)/ (Km + substrate conc.)
Vmax= maximum velocity
Km= substrate conc. at 1/2 Vmax

Question 16

Lineweaver-Burk plot

Answer 16

Determine Vmax and Km
Double reciprocal plot
y-intercept: 1/Vmax
x-intercept: 1/Km

Question 17

Competitive inhibition

Answer 17

Inhibitor binds to enzyme’s active site
Substrate can’t bind
Enzyme’s activity is limited

Question 18

Noncompetitive inhibition

Answer 18

Inhibitor and substrate bind to different sites
Binding of inhibitor distorts enzyme
Likelihood of substrate binding is lowered

Question 19

Feedback inhibition

Answer 19

Product of pathway inhibits an early enzyme in the pathway

Question 20

Allosteric regulation

Answer 20

Regulation of an enzyme with a molecule that is not its substrate or product
Inhibition: inhibitor stabilizes enzyme in low-affinity form, resulting in little or no activity
Activation: activator stabilizes enzyme in high-affinity form, resulting in enzyme activity

Question 21

Irreversible inhibitors

Answer 21

Binds covalently to enzyme

Question 22

Reversible inhibitors

Answer 22

Can bind to enzyme and then dissociate

Question 23

Roles of proteins

Answer 23

Enzymes
Structures
Transport (in and out of cell)
Scaffold-localizing
Transcription
Motor: move things around cytoskeleton
Storage: albumin (egg)

Question 24

Forms of proteins

Answer 24

Alpha helix
Beta sheet
Chemical interactions between side chains determine folding

Question 25

Primary structure

Answer 25

Composition of amino acids in a polypeptide chain

Question 26

Secondary structure

Answer 26

Structures formed by backbone | Alpha helices and beta sheets

Question 27

Tertiary structure

Answer 27

Structures formed by side chain interaction and secondary structure interactions

Question 28

Quaternary structure

Answer 28

Interactions between multiple polypeptide chains

Question 29

Protein binding

Answer 29

``` Binding sites created by protein folding Substrate binds weakly to R components Distortion of bonds Enzyme accepts or donates electrons Stabilizes "unstable" bonds ```

Question 30

Electrophoresis

Answer 30

Run proteins through electrical field: proteins separate based on charge and size

Question 31

Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE)

Answer 31

Gel matrix: polyacrylamide Buffer Denaturing agents Anionic detergent (SDS) to provide negative charge

Question 32

Things to do following SDS-PAGE

Answer 32

Transfer proteins to paper membrane and probe for specific proteins Western blotting: antibody binds to protein, labeled secondary antibodies bind to antibody Elute proteins off of gel and identify via mass spectrometry Detect enzymatic reactions of gel: use non-denaturing gel, enzymatic activity can be detected within the gel by staining substrate