enzymes as catalysts

Question 1

properties of enzymes

1. what do enzymes provide for the reaction?
2. types?
3. define the quickly changing practice of enzymes in chemical reaction

Answer 1

Properties of enzymes

1. speed, specificity and regulatory control
2. types:Proteins, RNA(ribozymes)
3. increase the rate of reaction by lowering the energy of activation.
   
   1. Turnover number-number of substrate molecules converted to product per enzyme molecule per second

Question 2

What are the general components of an enzyme. Describe the parts

Answer 2

holoenzyme (active) = apoenzyme (unactive) + cofactor

1. cofactor is the nonprotein component of the enzyme
   
   1. loosely-bound -coenzymes=small organic molecules
      
      1. ​cosubstrates-transiently associate with the enzyme
   2. tightly(permanently) bound-prosthetic group

Question 3

give three reasons for compartamentalization of enzymes

Answer 3

1. isolate
   
   1. isolation of the reaction, substrate or product from other competing reactions.
2. provide favorable enviornment
   
   1. manipulate the pH
3. organize
   
   1. organize the enzymes into purposful pathways

Question 4

Glucokinase and hexokinase have similar functions. Describe similarities and differences

Answer 4

they are isozymes-different enzymes that catalyzed the same reaction. Can be found in different organs.

1. glucokinase-liver and high Km
2. hexokinase-in most cells and low Km

this varying of Km levels allows the processing of glucose as it varies in concentration through out the day and locations of cells.

Question 5

digestive enzymes are secreted into the enviornment but must meet required conditions. Why?

Answer 5

proenzymes/zymogens -inactive form of enzyme

1. activated by
   
   1. cleaving amino acid group
   2. introduction to pH->conforms to active shape…
2. examples
   
   1. protease
   2. proteins in coagulation cascade

Question 6

describe the active site of an enzyme and a substrate. What type of interactions are usually seen here?

Answer 6

E + S <-> ES <-> E + P

active site binds substrate and form ES complex.

1. aka transition state complex- unstable high-energy complex
   
   1. decomposes to P and E
2. substrate binds via
   
   1. hydrophobic
   2. electrostatic
   3. hyrophobic

Question 7

list, define and give examples of the 6 major classes of enzymes. classification is based on the reaction they catalyze.

Answer 7

1. oxioreductase-redox reactions
2. transferase-transfer groups with CNP
3. hydrolase- using water to break bonds
4. lyases-cleaves C-C, C-N, C-S
5. isomerase- racemization
6. ligases-joins group,

Question 8

How can drugs affect enzymatic function

Answer 8

drugs can inhibit an enzymatic reaction by stopping the TSC from forming.

1. binding of specific drug to active site

Inhibitors- are compounds that decrease the rate of reaction

1. mechanisms based inhibitors- mimic or participate in intermediate step of reaction
   
   1. transition state analogous
      
      1. penicillin
         
         1. ​forms a covlent bond with the active-site serine of glycopeptidyl transferase
      2. allopurinol
         
         1. ​is an irreversible or “suicide” inhibitor of xanthine oxidase that decreases urate production and is used in treatment of gout.
      3. organophosphorus toxins
         
         1. ​nerve gas, forms covalent intermediate with acetylcholine esterase
      4. aspirin
         
         1. ​covalently acetylates active site of cycloxygenase which is a key enzyme in prostglandin synthesis.

Question 9

Describe the mechanism of chymotrypsin

Answer 9

chymotrypsin is a serine endopeptidase. cleaves carbon side of hydrophobic amino acids

1. produced by pancrease as the precursor chymotrypsinogen
2. activated by trypsin in duodenum

catlytic triad- operates by proximity and orientation

• SHD

Question 10

what are two ways functional groups in active sites are used in catalysis

Answer 10

1. AA residues
   
   1. serine proteases
      
      1. trypsin
      2. chymotrypsin
   2. gastric protease pepsin has aspartate in the active site and most active at pH 1.5-2.0
2. cofactors
   
   1. coenzymes
      
      1. heme: hemeblobin and cytochromes
   2. prosthetic group: metal ions= Fe2+, Mg2+, ZN2+

Question 11

Vitamin deficiency can lead to disease manifestation. what are two reasons someone would generate vitamin deficiency?

Answer 11

coenzymes are usually produced from vitamins

1. functional vitamin deficiency
   
   1. inhibition of coenzyme synthesis
   2. failure in transport system
      
      1. B12 deficiency due to failure of intracellular transport of B12 by transcobalamin-2
2. dietary vitamin deficiency
   
   1. lack in the diet
   2. lack of absorption

Question 12

discuss examples of activation-transfer and the mechanism in the following diseases

1. Beriberi
2. parathesia
3. sideroblastic anemia

Answer 12

activation-transfer = coenzymes form covalent bond with sibstrate

1. beriberi results from a B1 deficieny-thiamine definciency
   
   1. b1 is used for decarboxylation reaction in pyruvate dehydrogenase and alphaketoglutarate dehydrogenase
   2. symptoms
      
      1. fatigue, red dots on body, wet/dry, wernicke-korsakofs syndrome
2. B5 deficieny leads to parathesia
   
   1. sympotoms
      
      1. brunining, chilling in hand
3. sideroblastic anemia results foms when B6-PLP forms covalent intermediate causing transamination.-pyrodoxine deficinency
   
   1. symptoms
      
      1. B6=first step in hemeglobin generation
   2. cause
      
      1. alcohol-dietary lose of pyridoxine
      2. lead poinsoning
      3. Cu2+ deficiency
   3. 1.

Question 13

what is the function and disease manifestation from Oxidation-reduction coenzyme deficiencies via alcoholism?

Answer 13

oxidation-reduction coenzymes= coenzymes do NOT form covalent bond with substrate

1. involved in reactions catalyzed by oxioreductases, which transfer hydrogen atoms. They donate or accept electrons.
   
   1. nad+
   2. fad
2. example
   
   1. ​alcohol dehydrogenase-catalyzes oxidation of EtOH
      
      1. active as a dimer
      2. active site contains a Zn2+ along with S + H
      3. requirs NAD+ which is reduced during oxidation
      4. acetaldehyde is a product of ethanol oxidation
         
         1. highly reactive and toxic
         2. associated with chronic alcoholism
         3. converted via actaldehyde dehydrogenase
      5. problem
         
         1. as EtOH is oxidized in the liver, NAD+ gets reduced to NADH.
         2. NADH is an inhibitor of alcohol dehydrogenase, as a competative inhibitor
         3. as the ratio of NADH/NAD+ increase so does the livers ability to clear EtOH from the blood
         4. the processing of alcohol is limited to the regeneration of NAD+ in the liver.

Question 14

what are the functions of metal ions in catalytic reactions? give examples in phosphate, ATP, alcohol dehydrogenase and carbonic anhydrase

Answer 14

metal ions assist in substrate binding

they can accept and donate electrons

they participate in coenzyme binding to enzyme

1. phsohpate groups require Mg2+ to bind to enzyme
2. ATP is bound through to the enzyme through the TSC stability of Mg2+
3. alcohol dehydrogenase and carbonic anhydrase have a Zn2+ in their active site, which assist in the stability of the TSC

Question 15

how do hevy metals lead act as toxins and manifest symptoms of disease?

Answer 15

heavy metals cause tight binding of metals to functional groups

1. Hg, Pb, Al and Fe act through nonspecific binding at high doses
   
   1. Hg
      
      1. often binds to many SH groups of enzymes
      2. inactivation of antioxidant radicals through binding to Selenium
   2. Pb
      
      1. inhibits by replacing normal functional metal in enzyme, changing the affinity and operation
      2. toxicity is seen to replace Ca2+ in calmodulin and protein kinase C
   3. Al
      
      1. interferes with Fe transport binding to transferrin and albumin, leading to anemia
   4. Fe
      
      1. leads to liver failure in high concentrations
      2. children are the most affected of this toxicity

Question 16

List three medical uses for inhibitors and breif explanation

1. chemotherapy
2. metabolic control
3. natural poisons

Answer 16

1. chemotherapy
   
   1. slidenafil-inhibits cGMP phosphodiesterase type 5
   2. methotrexate is structurally similar to folic acid
      
      1. killing rapidly dividing cells(tumor and WBC)
2. metabolic onctrol -allosteric or substrate inhibition and activation
   
   1. phosphofructokinase- inhibited by high [ATP]
   2. found in the TCA cycle
3. natural poisons -secondary metabolites, peptides or proteins
   
   1. alpha amanitin- inhibts RNA synthase

Question 17

define the type of inhibition of a antibacterial against that stops the formation of the peptydoglacan layer of bacteria.

Answer 17

mechanism based inhibitor bind more tighly to the transition state analog than the substrate product.

1. penicicllin
   
   1. forms a covalent bond witht he active-site (S) of glycopeptidyl transferase
      
      1. this inactivates the enzyme

Question 18

Jerry is a diabetic with gout. what medication can he be given and what is it form of inhibition?

Answer 18

1. mechanism based inhibitor bind more tighly to the transition state analog than the substrate product.
   
   1. allopurinol
      
      1. irreversible inhibitor of xanthine oxidase
         
         1. normal function is to decrease urate production
         2. hypoxanthine is excreted in the urine
      2. used
         
         1. treatment of gout

Question 19

WW2 soldiers were exposed to nerve gas and died shortly after exposure. describr the inhibitory mechanism

Answer 19

nerve gas is made from organophosphorus toxins

1. form covalent intermediate with ACh-esterase
   
   1. the covalent intermediate cannot be hydrolyzed by water
2. this leads to an the ACh being left in the synaptic cleft
3. treatment
   
   1. medication that binds ACh receptor

Question 20

define a mechanism based inhibition

Answer 20

1. inhibitors
   
   1. compunds that decrease the rate of enzymatic reaction
   2. types
      
      1. mechanism-based
         
         1. mimic or participate in intermediate step of reaction

Question 21

Describe the differences between covalent and transition-state inhibitors

Answer 21

mechanism based inhibitors-mimic or participate in intermediate step of reaction

covalent-

1. function
   
   1. do not recognize the TSC but covalently bond to the active site
2. examples
   
   1. sarin gas
   2. aspirin

transition state inhibitors-

1. function
   
   1. resemble the transition state of the the catalytic reaction, blocking the active site
2. examples
   
   1. penicillin
   2. allopurinol

Question 22

after experiencing a horrible hangover, from last nights halloween party, Jim decided to take a Bayer pill. What is the medication and its mechanism of inhibition?

Answer 22

aspirin

1. covalently acetylates active site of cyclooxygenase (COX)
   
   1. ​COX= key enzyme in prostaglandin synthesis
2. COX-1
   
   1. covalent bond permanently inhibits
3. COX-2
   
   1. changes substrate specificity of COX-2, which is an inducible form of the enzyme