E.4 Protein function and intro to enzymes

Question 1

name the different protein complexes in increasing order

Answer 1

monomer, dimer, trimer, tetramer, multimer

Question 2

what are the two types of dimers?

Answer 2

homodimer (two identical monomers) and heterodimer (two different monomers)

Question 3

what is a dimer and trimer?

Answer 3

dimer- complex made up of two protein monomers
trimer- complex formed from three molecules of a monomer

Question 4

what is a tetramer and multimer?

Answer 4

tetramer- a protein made up of four subunits that are identical or similar
multimer- a protein molecule made up of two or more polypeptide chains, or monomers, that are linked together by covalent or non-covalent bonds

Question 5

Haemoglobin function?

Answer 5

transports oxygen in the blood- erythrocytes. It is tetrameric (tetramer).

Question 6

Myoglobin function?

Answer 6

stores oxygen in muscles- skeletal and cardiac

Question 7

myoglobin is monomeric, what does that mean?

Answer 7

a molecule that can react with other monomer molecules to form a larger polymer chain

Question 8

structure of myoglobin?

Answer 8

single polypeptide chain of 153 amino acids folded forming 8 alpha helixes

Question 9

structure of haemoglobin?

Answer 9

4 polypeptide chains- 2 alpha chains of 141 amino acids, 2 beta chains of 146 amino acids; each chain folds to form 8 alpha helixes

Question 10

similarities between structure of haemoglobin and myoglobin?

Answer 10

-both have haem prosthetic group- protoporphyrin IX, with central Fe2+ atom. This is where oxygen binds.
-3D structure of polypeptide chains are very similar

Question 11

Describe the bonding of oxygen to haemoglobin

Answer 11

cooperative: binding to one subunit causes a conformational change from a tense (T) to relaxed state (R) and increases ease of binding of oxygen to the other subunits – this is called allostery; Haemoglobin is an allosteric protein (protein which changes shape due to binding)

Question 12

Does myoglobin or haemoglobin have a higher affinity for binding with oxygen?

Answer 12

Myoglobin as haemoglobin binds oxygen in the lungs and releases it in the capillaries and to myoglobin in the muscle for storage.

Question 13

Describe the conformational change when oxygen binds to the haem group in haemoglobin

Answer 13

-oxygen binding pulls the Fe2+ into the haem plane (without oxygen, Fe2+ is out of plane)
-oxygen binding also pulls histidine F8 ligand and F helix.

Question 14

How does haemoglobin lower its affinity for oxygen when blood enters the tissues? (bohr effect)

Answer 14

-CO2 produced by metabolism in tissues is converted into carbonic acid catalysed by carbonic anhydrase
-dissociation of carbonic acid produces protons which react with amino acids in haemoglobin causing conformational changes that promote the release of oxygen

Question 15

what are the different functions of proteins?

Answer 15

-structural proteins for cytoskeleton
-transport and store molecules
-enzymes catalyse biochemical reactions
-membrane transport proteins for ions and molecules
-regulatory and signalling proteins to control activities of other proteins and coordinate cellular responses
-motor proteins move intracellular complexes

Question 16

are all enzymes proteins?

Answer 16

most but some are RNA (e.g peptidyl transferase involved in protein synthesis on ribosomes)

Question 17

Describe enzymes

Answer 17

-lower the energy of the transition state of a chemical reaction
-works under physiological conditions
-highly specifics
-active site can use functional groups, coenzymes or metal ions

Question 18

what is a transition state?

Answer 18

an unstable chemical form, part- way between substrate and product. It has the highest free energy in reaction pathway

Question 19

What is Gibbs free energy of activation?

Answer 19

difference in free energy between the substrate and transition state. triangleG‡

Question 20

How does an enzyme increase rate of reaction?

Answer 20

stabilises the transition state and lowers gibbs free energy of activation
(Entropy, Orientation, Distortion, Solvation)

Question 21

Describe the Michaelis-Menten kinetics or saturation kinetics model

Answer 21

-Initial substrate, [S] and enzyme [E] concentrations are known
-all these sites may be occupied by substrates - the enzyme is saturated
-A plot of V against [S] gives a hyperbolic curve

Question 22

Describe saturation kinetics

Answer 22

-Enzyme combines with substrate to form enzyme- substrate complex
-The E-S complex can dissociate again to form E+S OR form E and the product P

Question 23

what is Vmax and Km?

Answer 23

Vmax = the maximum reaction rate (represents when reaction is saturated, all in E-S state)
Km= substrate concentration where V= Vmax/ 2

Question 24

describe the michaelis- menten equation?

Answer 24

V0 = Vmax [S] /Km +[S]
-At low [S], a doubling of [S] will lead to a doubling of initial velocity V0 - linearly proportional

Question 25

the lower the Km…

Answer 25

the higher the affinity of the enzyme for the substrate

Question 26

Describe the Lineweaver-Burk plots (to linearize Michaelis-Menten)

Answer 26

-The reciprocal of both sides of the Michaelis-Menten equation generates an equation that has the form of straight line (y = mx + c)
-y=I/V0; m=Km/Vmax; x=1/[S]; c=1/Vmax
(more info on one note)

Question 27

what are the varied ways in which an enzyme lowers activation energy and achieves transition state intermediates

Answer 27

-Acid –Base (proton donation/abstraction)
* Temporary covalent bond formation
* Redox effects
* Electrostatic effects
* Orientation/proximity effects and straining effects.

Question 28

what are cofactors

Answer 28

non-protein molecules that are required for a reaction to take place in addition to the enzyme and substrate. can be organic or inorganic.

Question 29

what are coenzymes

Answer 29

cofactors that bind loosely and are chemically altered by the enzyme. They are recycled for participating in the same reaction

Question 30

what is a apoenzyme

Answer 30

enzyme without cofactor

Question 31

what is holoenzyme

Answer 31

enzyme with cofactor

Question 32

where do we get our cofactors?

Answer 32

minerals and vitamins

Question 33

what ways can enzyme activity be regulated?

Answer 33

-competitive inhibition (reversible or irreversible)
-covalent modification
-allosteric regulation
-Rate slows as product accumulates
-Rate depends on substrate availability
-Genetic controls - induction and repression of the enzyme
-Zymogens, isozymes and modulator proteins may play a role

Question 34

Explain covalent modification as a way of regulating enzyme activity

Answer 34

-chemical modification of amino acid residues which can lead to an increase or decrease of enzyme activity
-common type of normal cellular regulation
-some drugs work this way

Question 35

Describe allosteric regulation of enzyme activity

Answer 35

-non covalent binding away from active site which causes conformational change leading to increase or decrease of enzyme activity

Question 36

why are enzymes common drug targets?

Answer 36

they affect large numbers of substrate molecules; small changes in enzyme activity leads to large change in product concentration

Question 37

what is used to treat HIV/AIDS

Answer 37

Anti-retroviral protease inhibitors

Question 38

what do statins do

Answer 38

inhibit enzymes involved in cholestrol metabolism

Question 39

what do non-steroidal anti-inflammatory drugs (NSAIDs) do?

Answer 39

modulate pain and inflammation by inhibiting cyclooxygenases

Question 40

what do antibiotics do

Answer 40

block enzymes involved in assembling the bacterial cell wall

Question 41

how are potential drug targets identified

Answer 41

• By studying the mechanism of action of existing drugs
• By studying the differences between diseased and normal cells or organisms
• By finding mutations that make normal cells like disease cells or the other way around