ENZYMES

Question 1

What are catabolic pathways?

Answer 1

Involves the breakdown of complex molecules into simpler ones and typically release energy.
-Energy stored in the bonds of complex molecules, such as glucose and fats, is released in catabolic pathways.

Question 2

What are anabolic pathways?

Answer 2

Involves the synthesis of large molecules from smaller building blocks of molecules

Question 3

What is the definition of enzymes?

Answer 3

Enzymes are protein catalysts that increase the rate of a biological reaction by lowering the energy of activation

• Catalyzes nearly all the chemical reactions taking place in the body
• Have unique 3D shapes called active sites that fit the shapes of reactants, called substrates

Question 4

What is the enzyme active site?

Answer 4

A region that fits the shape of substrate molecules

• Complementary
• Amino acid side chains align to bind the substrate through H-bonding, salt bridges, hydrophobic interactions and van der waals
• Products are released when the reaction is completed

Question 5

What is the lock and key hypothesis?

Answer 5

• The active site has a rigid shape
• Only substrates with the matching shape can fit
• Substrate=the key
• Active site=the lock

Question 6

What is the induced-fit model of enzymatic action?

Answer 6

• The active site is flexible
• Shape of the enzyme, active site and substrate adjusts to maximise the fit which improves catalysis
• There is greater range of substrate specificity
• Some active sites can fit more than one enzyme

Question 7

What are carboxypeptidases?

Answer 7

Protease enzymes that hydrolyzes a peptide bond at the carboxy-terminal end of a protein or peptide

Question 8

What is the definition of substrate specificity?

Answer 8

Certain enzymes bind to the certain substrates only

• Enzymes have varying degrees of specificity
• ABSOLUTE: Catalyzes one type of reaction for a single substrate (urease catalyzes only the hydrolysis of urea)
• GROUP: Catalyzes one type of reaction for similar substrates (Hexokinase adds a phosphate group to hexoses)
• LINKAGE: Catalyzes one type of reaction for a specific type of bond *Chymotrypsin catalyzes the hydrolysis of peptide bonds)

Question 9

Principles of enzyme nomenclature

Answer 9

1. The name identifies the reacting substance, usually ending in “ase”
2. The name also describes the function (eg. oxidases catalyzes oxidation reactions)
3. Common names are used for the same functional group (eg. digestive enzymes like pepsin and trypsin)
4. Some names describe the substrate and the function (eg. alcohol dehydrogenase oxidises ethanol)

Question 10

What are cofactors?

Answer 10

A cofactor is a non-protein chemical that assists with a biological chemical reaction.

• The catalytic activity of many enzymes depends on the presence of cofactors
• Can be considered “helper molecules”
• Classified depending on how tightly they bind to an enzyme
• APOENZYME: Enzyme lacking co-factor (inactive)
• HOLOENZYME: Enzyme with cofactor (active)

Question 11

Differences between tightly and loosely bound cofactors

Answer 11

TIGHTLY BOUND:

• Act as activators or inhibitors
• Prosthetic groups are usually small inorganic ions, mostly metal ions (Cu, Mg, Mn, Fe, Zn, Ni)

LOOSELY BOUND:

• Transfers electrons
• Forms of breaks covalent bonds
• Transfers a group

Question 12

What are coenzymes?

Answer 12

When cofactors bind, they are known as coenzymes

• Small non protein molecules
• Modified during a reaction
• -Eg. NAD+/NADH, coA, Vitamin C, folic acid, B6-pyridoxal phosphate)

Question 13

What is Heme?

Answer 13

A common enzyme cofactor

• Porphyrin ring containing iron (prosthetic group)
• Present as a cofactor in many enzymes involved in oxidation reactions
• Eg. Hemoglobin which contains 4 heme groups combined to 4 oxygens

Question 14

What is the role of NAD?

Answer 14

Nicotinamide adenine dinucleotide is a coenzyme central to metabolism
-Eg. Provides the hydrogen required for lactate in anaerobic glycolysis (pyruvate to lactate, NADH oxidized to NAD+)

Question 15

Role of vitamins in enzymology

Answer 15

Precursors of cofactors and coenzymes

• Vitamins are a required micronutrient that the organism cannot synthesize adequate quantities of for normal health
• Eg. Pellagra (B3 deficient), BeriBeri (B1 deficient), Scurvy (Vitamin C deficient), Neural tube defect/anemia (Folic acid deficient)

Question 16

What are the 6 major classes of enzymes?

Answer 16

1. Oxidoreductases: oxidation-reduction reactions
2. Transferases: transfers groups of atoms eg. kinases transfer phosphates
3. Hydrolysis: break down
4. Lyases: addition of atoms
5. Isomerases: Rearrangement of atoms
6. Ligases: Uses ATP to combine molecules

Question 17

What are proenzymes?

Answer 17

A biologically inactive substance which is metabolized into an enzyme

• AKA zymogen
• Inactive proenzyme is proteolytically cleaves in order for it to be converted to its active form
• Non-reversible reaction
• Digestive, blood clotting, complement and developmental enzymes

Question 18

What is the role of trypsin?

Answer 18

The common activator of all the pancreatic proenzymes

• Prevents digestive enzymes from digesting the cells that they are produced in
• Synthesized in the pancreas

Question 19

What is chymotrypsinogen?

Answer 19

An inactive precursor (zymogen) of chymotrypsin, a digestive enzyme which breaks proteins down into smaller peptides.

• synthesized in the pancreas
• stored in membrane bound granules, acinar cells
• signal stimulates release to duodenum
• single polypeptide chain of 245 amino acid residues
• requires activation in the lumen to produce an active enzyme
• cleaves peptide bonds containing aromatic amino acids

Question 20

What is the process of chymotrypsinogen activation?

Answer 20

It is two step activation process

• cleaved between Arg-15 and Ile-16 by trypsin to generate two peptides
• pi-chymotrypsin is active and acts on other pi-chymotrypsin molecules
• two dipeptides removed to generate the final active enzyme: alpha-chymotrypsin

Question 21

What are the 2 dipeptides removed to generate active chymotrypsinogen?

Answer 21

Amino acid 14/15 and 147/148

Question 22

Principles of enzyme kinetics

Answer 22

1. When a substrate (S) fits properly in an active site, an enzyme-substrate complex (ES) is formed
2. Within the active site of the ES complex, the reaction occurs to convert substrate to product (P)
3. The products are then released, allowing another substrate molecule to bind the enzyme

Question 23

Parameters of enzyme kinetics

Answer 23

• temperature
• PH
• enzyme conc
• substrate conc
• Michaelis-Menten constant (determines how fast a reaction occurs)

Question 24

How does temperature affect enzyme activity?

Answer 24

Enzymes are the most active at an optimum temperature, usually 37 degrees

• little activity at low temp
• activity is also lost at too high temps as denaturation occurs

Question 25

How does PH affect enzyme activity?

Answer 25

Optimum PH is different for all groups -amino acids with acidic or basic side-chains have the appropriate charges for functional enzyme activity when the PH is optimum -activity is lost at low or high pH as tertiary structure is disrupted the optimum pH for a given enzyme is normally the pH where it is required to act

Question 26

How does enzyme concentration affect enzyme activity?

Answer 26

The rate of the reaction increases as enzyme concentration increases - at high enzyme conc, more enzymes are available to catalyze the reaction (more reactions can occur at once) - there is linear relationship between reaction rate and enzyme concentration

Question 27

How does substrate concentration affect enzyme activity?

Answer 27

Maximum activity occurs when the enzyme is saturated (when all enzymes are binding to a substrate) -the relationship between reaction rate and substrate conc is exponential and asymptotes (levels off) when the enzyme is saturated

Question 28

What is Km?

Answer 28

The rate of reaction when the enzyme is saturated with substrate is the maximum rate of reaction, Vmax - This is usually expressed as the Km (Michaelis constant) of the enzyme, an inverse measure of affinity - For practical purposes, Km is the concentration of substrate which permits the enzyme to achieve half Vmax

Question 29

Why is Km physiologically important?

Answer 29

The Km of an enzyme, relative to the concentration of its substrate under normal conditions permits prediction of whether or not the rate of formation of product will be affected by the availability of substrate. -Eg. Some individuals are more sensitive to ethanol, fash flushing and tachycardia after ingesting small amounts of alcohol

Question 30

What does having HIGH Km mean?

Answer 30

The enzyme has low affinity for its substrate and requires a greater conc of substrate to achieve the maximum rate of reaction

Question 31

What are enzyme inhibitors?

Answer 31

Molecules that causes a loss of enzyme activity | -prevents substrates from fitting into the active site of the enzyme

Question 32

What are two types of inhibitors?

Answer 32

1. Competitive inhibitors - structure similar to the substrate - competes with the substrate for the active site - can be irreversible or reversible - if irreversible, it remains chemically bound so another enzymatic reaction cannot occur - if reversible, as the conc of the substrate increases, the inhibitor will be displaced from the active site 2. Non-competitive feedback inhibition - an inhibitor molecule binds to the enzyme at a location other than the active site (an allosteric site) - the substrate can still bind to the enzyme, but the inhibitor changes the shape of the enzyme so it is no longer in optimal position to catalyze the reaction

Question 33

What are isoenzymes?

Answer 33

Different forms of an enzyme (using different forms of exons in the same gene) the catalyzes the same reaction in different tissues of the body - different gene products and different kinetic properties - minor variations in the amino acid sequences of the subunits of their quaternary structure - permits the fine tuning if metabolism - Eg. lactate dehydrogenase (LDH), which converts lactate to pyruvate, consists of 5 isoenzymes, H form (heart), M form (muscle) and the functional enzyme is a tetramer of different combinations of H and M

Question 34

How are enzymes used for diagnosis?

Answer 34

The levels of diagnostic enzymes in the blood can be used to determine the amount of damage in specific tissue - Elevated LDH and Aspartate transaminase (AST) levels can be used to diagnose tissue damage or liver disease (hepatitis, cirrhosis) - Elevated creatinine kinase levels can be used to indicate heart attacks - Elevated alkaline phosphatase can be used to indicate liver (carcinoma) or bone disease (rickets) - Elevated amylase, cholinesterase lipase (LPS) can be used to indicate pancreatic disease - Elevated acid phosphatase (ACP) can be used to indicate prostate carcinoma