Biochemistry- Enzymes

Front 1

Enzyme- substrate, the reaction:

Back 1

Enzyme+ Substrate--> Enzyme- substrate complex--> Enzyme product complex= Enzyme + product

Front 2

Function and properties of enzymes:

Back 2

1. Increase the rate of chemical reactions
2. Decrease the activation energy of the reaction
3. Reduce the time to reach reaction equilibrium
4. Are not consumed nor changed by the reaction

Front 3

Enzymes do NOT:

Back 3

1. Change the ΔG of the reaction
2. Change the equilibrium position of the reaction

Front 4

Transition state:

Back 4

A structure on the substrate that is acted on by the active site, where the bonds are not like those in the substrate or product. The state in which bonds can be rearranged from substrates to products.

Front 5

Structure of enzymes:

Back 5

Most are proteins, contains aminoacids in the active site which have binding properties.

Front 6

Whats a Ligand?

Back 6

A signal triggering molecule that binds to a site on a protein altering the conformation of the protein (Enzyme). Ligands can be: substrates, activators, inhibitors and neurotransmitters.

Front 7

What kind of bonds are there between ligands and the binding site on a protein?

Back 7

Weak non- covalent bonds such as: Ionic bonds, Hydrogen bonds, Van der waals forces and intermolecular forcers.

Front 8

Characteristics of enzymes:

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1. Intracellular enzymes
2. Extracellular enzymes
3. Simple enzymes
4. Complex enzymes

Front 9

Simple enzymes:

Back 9

Only protein structure

Front 10

Complex enzymes:

Back 10

Protein structure + cofactor

Front 11

Cofactor:

Back 11

Nonprotein compounds:
1. Inorganic elements: Zn, Mn, Mg, Fe, Cu
2. Organic molecules: Coenzyme, prosthetic group

Front 12

Coenzyme:

Back 12

A organic cofactor slightly bound to the enzyme and that undergoes a chemical change and then are released. E.g: NAD(P), FAD, coenzyme Q

Front 13

Prosthetic group:

Back 13

A organic cofactor that are tightly bound to the enzyme and remain associated during the reaction. E.g: heme

Front 14

Apoenzyme:

Back 14

An inactivated protein part of an enzyme.

Front 15

Holoenzyme:

Back 15

Activated whole enzyme containing both protein part and cofactor

Front 16

NADH

Back 16

Nicotinamide adenine dinucleotide

Front 17

FADH2

Back 17

Flavin adenine dinucleotide

Front 18

NADP

Back 18

Nicotinamide adenine dinucleotide phosphate

Front 19

Precursor of FAD:

Back 19

Riboflavin= vit b12

Front 20

Precursor of pyridoxin in PALP (pyridoxal phosphate):

Back 20

vitamin B1

Front 21

Precursor of tetrahydrofolate (THF):

Back 21

Folic acid

Front 22

Cofactors of lysases:

Back 22

Pyridoxal phosphate (PALP) (decarboxylases)

Front 23

Cofactors of ligases:

Back 23

ATP, biotin (vitamin H, carboxylases)

Front 24

Oxidoreductases function:

Back 24

Catalyze oxidation- reduction reactions

Front 25

Transferases function:

Back 25

Catalyze transfer of C-, N- or P- containing groups

Front 26

Hydrolases function:

Back 26

Catalyze cleavage of bonds by adding of water

Front 27

Lysases function:

Back 27

Catalyze the non hydrolytic or oxidative cleavage of C-C, C-S and certain C-N bonds

Front 28

Isomerases function:

Back 28

Catalyze racemization of optical or geometrical isomers. (intramolecular changes)

Front 29

Ligases function:

Back 29

Catalyze formation of bonds between carbon and O, S, N coupled to hydrolysis of high energy phosphates

Front 30

Isoenzymes:

Back 30

Enzyme variants that catalyze the same kind of reactions but have different structural and physical properties.

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Isoenzymes properties:

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1. Produced by different genes (true isozymes)
2. Or have different posttranslational modifications (isoforms)
3. Located in different compartments of the cells and different tissues of the body
4. Can be oligomers of various subunits

Front 32

How many major classes of enzymes are there?

Back 32

6

Front 33

Oxidoreductases: (8)

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1. Dehydrogenase
2. Reductase
3. Oxidase
4. Peroxidase
5. Oxygenase
6. Hydroxylase
7. Desaturase (desauturation of bonds)
8. Alkohol dehydrogenase

Front 34

Transferases:

Back 34

1. Grouptransferases (aminotransferases)
2. Kinase (phosphotransferase)
3. Phosphorylase
3. Transketolase/ transaldolase

Front 35

Hydrolases: (8)

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1. Esterase
2. Phosphatase
3. Phosphodiesterase
4. Nuclease
5. Peptidase
6. Protease
7. Glucosidase
8. alpha- amylase

Front 36

Ligases:

Back 36

A+B + ATP--> A-B + ADP+ Pi
1. Polymerases
2. Synthease
3. Carboxylase

Front 37

Formula for initial reaction velocity:

Back 37

Vo= Vmax (S)/ Km (S)

Front 38

What is the Michelis constant (Km)?

Back 38

It corresponds to the substrate concentration at which velocity is half of maximum velocity.

Front 39

When is Km low?

Back 39

When an enzyme has a high affinity to its substrate because then you need a lower concentration to reach half of Vmax. If the affinity is low Km will be higher because you need a higher concentration to reach half of Vmax

Front 40

Allosteric enzymes show a sigmoid curve, why?

Back 40

Because of the conformational change to a higher functional state increases the rate of the reaction

Front 41

Concentration of substrate vs. enzyme?

Back 41

Enzyme consentration is much lower then substrate concentration. Rate of reaction is directly dependent on enzyme concentration.

Front 42

Will increased substrate concentration increase reaction rate?

Back 42

Yes until the point where all active sites are saturated

Front 43

Factors that influence enzyme activity:

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1. pH (pepsin:2, trypsin: 8)
2. Temperature
3. Affinity to substrate
4. Inhibition

Front 44

Irreversible inhibition:

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Covalent bonds between protein enzyme and metal ion. E.g HCN inactivates iron containing enzymes by covalently binding to Fe2+ in heme. Blocks cellular resp. by cytochrome oxidase.

Front 45

Competitive inhibition (reversible):

Back 45

Competes with the substrate on binding to the active site, is not changed by the enzyme. Vmax is not changed. Km is elevated. (Need more (S) to reach the same enzyme activity because substrate affinity is decreased. Increasing (S) will decrease inhibition.

Front 46

Non- competitive inhibitor:

Back 46

- Binds to another place on the enzyme then the active site.
- It has equal affinity to the free enzyme as to the enzyme- substrate complex. - - Km is unchanged but Vmax is decreased.
- Inhibition is not reversed by increasing substrate concentration
- Only reversible if inhibitor is NOT bound by covalent bonds

Front 47

Uncompetitive (anticompetitive) inhibition:

Back 47

Inhibitor binds only to the enzyme- substrate complex. Both Vmax and Km are decreased.

Front 48

Zymogen:

Back 48

Inactive proenzyme that must be cleaved by regulatory proteases to become active, or must be activated by phosphorylation

Front 49

Enzyme regulation:

Back 49

1. Allosteric regulation
2. Covalent modification
a) Phosphorylation/dephosphorylation
b) Limited proteolysis (regulation of cleavage of zymogens)

Front 50

Allosteric modification:

Back 50

Modification of enzymes in two different conformations:
1. Taut (T) conformation: Have a great affinity for inhibitors
2. Relaxed (R) conformation: Have a greater affinity for activators and substrates.

Allosteric enzymes can be monomeric or oligomeric

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Inhibition by products as intermediates:

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1. Feedback regulation
2. Cross- regulation
3 Feedforward regulation

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1 katal=

Back 52

1 mole of substrate transformed per 1 sec

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1IU=

Back 53

1 micromole substrate transformed per 1 minute

Front 54

ATL and its significance to acute viral hepatitis;

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Physiological activity of ALT in blood: <-- 0.73 microkat/L
Pathological: 50x higher activity