lecture 8

Question 1

negative regulator

Answer 1

proteins can have negative feedback inhibition

-when you make too much of something, it will be inhibited
-inhibiting activity of the enzyme will inhibit the pathway
(ex. lysine, methionine, threonine)

Question 2

ligand

Answer 2

any substance bound by a protein

Question 3

protein-ligand interactions are dictated by

Answer 3

noncovalent interactions

Question 4

binding site

Answer 4

region of protein that associated with a ligand

Question 5

what dictates the specificity of the binding sites

Answer 5

specific interactions between the binding site amino acids and the ligand

Question 6

Y shaped molecule composed of two heavy chains and two light chains

Answer 6

antibodies

Question 7

antibodies bind very specifically to

Answer 7

a target molecule called and antigen

Question 8

antibodies contain two

Answer 8

antigen binding sites where the amino acid sequence is highly variable

Question 9

how many different possible antibodies are there?

Answer 9

billions

Question 10

Antibodies function

Answer 10

important for fighting infections

laboratory tool: molecule identification, quantification and localization

Question 11

Enzymes (E)

Answer 11

biological catalysts that speed up the rate of the reaction

Question 12

Enzymes bind to — forming an —

Answer 12

substrates (S)
enzyme-substrate complex (ES)

Question 13

after the reaction has proceeded, the enzyme will be in contact with the product as an —- and will eventually release a —

Answer 13

enzyme-product complex (EP)

product (P)

Question 14

Active site

Answer 14

the region of an enzyme that binds and catalyzes the substrate

Question 15

only a few amino acid residues in the active site participate in catalysis
–> why are enzymes so large then?

Answer 15

to provide a folding framework for the active site– precisely aligns the active site residues.

optimizes binding energy in the transition state

Question 16

Activation energy

Answer 16

the energy needed to go from the ground state to transition state

Question 17

transition state

Answer 17

the maximum energy species formed on the reaction coordinate

Question 18

3 ways that enzymes lower the activation energy

Answer 18

1. aligns substrates in a favourable orientation
2. rearranges the electron distribution
3. physically strains the substrate to induce a reaction

Question 19

lysozome

Answer 19

enzyme that breaks polysaccharide chains that form cell walls in bacteria

Question 20

lysozome function

Answer 20

-performs hydrolysis rxn
-helps rxn overcome the activation energy

Question 21

Enzyme active sites
–> what type of amino acids would you expect to find there?

Answer 21

polar or charged amino acids are more likely to be found in the active site

(more energetically favourable)

Question 22

enzyme names generally end in…

Answer 22

“ase”

Question 23

protease

Answer 23

cuts protein

Question 24

hydrolase

Answer 24

cuts hydrogens off

Question 25

many protons rely on small nonprotein molecules to perform particular functions

give two examples

Answer 25

Retinal: binds to the protein rhodopsin. retinal changes shape when the photon is absorbed

Heme: binds to the protein hemoglobin and allows reversible binding of oxygen

Question 26

enzymes are not always

Answer 26

active

(this would not be efficient!)

Question 27

Regulating protein activity

Answer 27

-regulation of gene expression

-regulation of protein degredation

-confining protein to specific compartments

-regulating protein activity directly

Question 28

Feedback inhibition

Answer 28

the end product of a chain of enzymatic reactions reduces the activity of an enzyme earlier in the pathway

Question 29

feedback inhibition effects are

Answer 29

almost instantaneous and the effects can be rapidly reversed if product levels fall

Question 30

preventing an enzyme from acting is a form of

Answer 30

negative regulation

Question 31

positive regulation

Answer 31

enzyme activity is stimulated

Question 32

feedback inhibition can have multiple

Answer 32

points of control

ex. biosynthesis of amino acids

Question 33

allosteric proteins

Answer 33

proteins that can exist in multiple conformations depending on the binding of a molecule to a site other than a catalytic site

Question 34

allosteric proteins: ADP and ATP example

Answer 34

ADP levels increase as ATP levels decrease which signals the need for additional oxidation of sugars

(this is an example of allosterically regulated enzyme that is positively regulated by ADP)

Question 35

protein phosphorylation

Answer 35

attaching phosphate groups to proteins is a very common method of regulating its activity

-target proteins become active via kinase, creates covalent bonds

Question 36

3 characteristics of protein phosphorylation

Answer 36

-may cause conformational changes
-reversible
-involves the enzyme-catalyzed transfer of the terminal phosphate of ATP to the hydroxyl group of serine, threonine or tyrosine

Question 37

protein kinase

Answer 37

enzyme that catalyzes the addition of a phosphate

Question 38

protein phosphatase

Answer 38

enzyme that catalyzes the removal of a phosphate

–> phosphorylating can either activate or inhibit protein activity

Question 39

phosphorylation can also create

Answer 39

docking

Question 40

docking (in protein phosphorylation): 2 functions

Answer 40

• important for intracellular signalling proteins

-binding of a signal causes phosphorylation of tyrosine residues which allows other proteins to bind

Question 41

examples of covalent modifications that can be done in the cell

Answer 41

-addition of an acetyl group
-attaching (poly) ubiquitin
-addition of fatty acids

many proteins will have multiple covalent modifications

Question 42

GTP binding proteins

Answer 42

-for some proteins, the phosphate is transferred from GTP (guanosine triphosphate) instead of ATP

-can be turned “on” and “off”
“on”= bound to GTP
“off”= bound to GDP
reversible process.
GTP-binding proteins can affect the activity of other proteins.

Question 43

motor proteins

Answer 43

generate forces responsible for muscle contractions and most eukaryotic cell movement

Question 44

what is the “problem” for motor proteins?

Answer 44

if the movements are easily reversible, the proteins will move back and forth and not get anywhere!!

Question 45

what is the “solution” for motor proteins?

Answer 45

the steps involved in the movement are (basically) irreversible.
A way to do this is to couple one of the conformational changes to the hydrolysis of ATP.

Question 46

Protein machines

Answer 46

proteins often work in tandem with other proteins to function as a large multiprotein complex

Question 47

hydrolysis of nucleoside triphosphates drives what (protein machines)

Answer 47

drives an ordered series of conformational changes in individual subunits which affects the entire complex

ex. DNA replication