Topic 6 - Enzymes Flashcards Preview

Biochem 153A > Topic 6 - Enzymes > Flashcards

Flashcards in Topic 6 - Enzymes Deck (18):
1

Spontaneous Reactions

  • all are thermodynamically or energetically favorable
  • all reactions of enzymes are spontaneous
  • enzyme does not change free energy of substrate of product
  • enzyme does not affect whether rxn is thermodynamically favorable, will merely catalyze it

2

Properties of Enzymes

  1. Catalysts: Not used up in the reaction (Regenerated)
  2. Biological catalysts have higher reaction rates than chemical catalysts
  3. Mild reaction conditions: normal pH & temperature, occur within biologically appropriate conditions
  4. Greater rxn specificity: an enzyme can be very specific for its substrate (glucokinase can only phosphorylate glucose) or not very specific (hexokinase can phosphorylate glucose, frucotose, and mannose)
  5. Capacity for regulation: enzyme activity can be increased/decreased via covalent modification (irreversible or reversible) or non-covalent modification (allosteric/regulatory enzymes)

 

 

3

Enzyme Classes 

(6)

1. Oxidoreductases

2. Transferases

3. Isomerases

4. Hydrolases

5. Lyases

6. Ligases

4

Q image thumb

1. Oxidoreductase: The transfer of electrons

  • Catalyze redox reactions - thus requires an electron acceptor and electron donor
  • Ex:
  • COMMON NAME: lactate dehydrogenase
  • SYSTEMATIC NAME: electron donor:acceptor + oxidoreductase - lactate:NAD+ oxidoreductase 
  • electrons from lactate are transferred to NAD+ (as hydride ion, a hydrogen with an extra electron) --> NAD+ becomes NADH.
  • Reduction = loss of hydrogens. (NOTE: it is NOT protonation b/c NAD is not picking up a proton, it is picking up a hydride ion).

5

Q image thumb

2. Transferase: Transfer of functional groups from one molecule to another: involves 2 molecules and a functional group such as an amino group of phosphyl group. It is NOT just the addition of a functional group.

  • Subgroups: Kinases - transfer phosphate groups from ATP to substrate
  • Ex:
  • COMMON NAME: phosphofructokinase (PFK)
  • SYSTEMATIC NAME: molecule + kinase - fructose-6-phosphate kinase
  • phosphofructokinase transfers a phosphate from ATP to the substrate

6

Q image thumb

3. Isomerase: INTRAmolecular rearrangement

  • Ex: 
  • COMMON NAME: triose phosphate isomerase
  • SYSTEMATIC NAME: substrate + isomerase - dihydroxyacetonephosphate isomerase

 

7

Q image thumb

4. Hydrolase: Single bond cleavage via addition of H2O OR bond formation via the removal of H2O

  • Ex: 
  • SYSTEMATIC NAME: compound to be cleaved + hydrolase - peptide hydrolase (peptidase) - break peptide bond by adding water, make peptide bond by removing water
  • Note: peptide bond = bond between carbonyl group and amino group of aa

8

Q image thumb

5. Lyase: Group elimination to form a double bond

  • NOTE: POE - Eliminate the other options first, because this is usually difficult to identify !
  • NOTE: May be confused with hydrolase, but there is no conversion to double bond like with lyase
  • Ex:
  • COMMON NAME: enolase
  • SYSTEMATIC NAME: 2-phosphoglycerate lyase

 

9

Q image thumb

6. Ligase: bond formation coupled to ATP hydrolysis

  • NOTE: do not confuse with transferases
  • Ex: 
  • COMMON NAME: pyruvate carboxylase
  • SYSTEMATIC NAME:  molecule:molecule + ligase - pyruvate:carbon dioxide ligase

10

Enzymes & Transition State

  • determines rate of reaction
  • magnitude of change in free energy/Ea (activation energy)
  • enyzmes decrease Ea by stabilizing the transition state
  • BAD: if enzyme binds to substrate perfectly and interacts with it - results in a very stable enzyme-substrate complex - lowers energy and increases Ea
  • NEED: enzyme that perfectly binds the transition state; interactions that stabilize TS lower the energy of TS --> decreases Ea
  • catalysts: stabilize TS --> lower energy of TS
  • enzyme catalysis: 2 step process - substrate must bind to enzyme & E-S complex catalyzes conversion

11

Enzymes: Binding Sites

(Properties)

  • Active Site: Substrate Binding Site + Catalytic Site
  • Regulatory Site: a second binding site for other molecules other than the substrate; it is separate from the active site. Binding by regulatory molecule affects the active site - alters the efficiency of catalysis, and/or improves or inhibits catalysis
  • Both active & regulatory site should be complementary to the ligand that they are trying to bind
  • Three dimensional space; Occupies small part of enzyme volume; Clefts or crevices - where the substrate binds
  • Ligands (substrate or effector) are bound by multiple weak interactions
  • Specificity from precise arrangement of atoms in active site: correct orientation and complementarity to size, shape, and charge/polarity to favorably bind the ligand
  • Geometric (physical) complementarity
  • Electronic (chemical) complementarity
  • Charge and polarity

12

Enzyme-Substrate Complex

  • active site of enzyme will have same shape as substrate: same size and shape, as well as complementarity, such as +charge to interact with - charges, electron acceptor interacting with electron donor, etc.

13

Stereospecificity leads to Substrate specificity

Explanation for the specificity of the enzyme to its substrate

Explanation for why citrate always becomes R-isocitrate: because of specificity of substrate binding. Only 3 out of the 4 attachments can interact with the enzyme, and will interact in a specific way/orientation to always give R-isocitrate.

Enzymes vary in geometric specificity: Alcohol dehydrogenase can catalyze the oxidation of 3 different alcohols,  but prefers ethanol > methanol > isopropanol. Ethanol fits best, methanol is smaller but can still react with the pocket, and isopropanol is bigger but can still react.

14

Trypsin

 

Q image thumb

cleaves after long +charged side chains: has a long groove with a negative charge to stabilize +charge of aa

15

Chymotrypsin

 

Q image thumb

has large, hydrophobic pocket to accommodate rings of large, aromatic side chains

16

How do we identify and characterize active sites?

  • Using model substrates (which are similar to the desired substrate) and competitive inhibitors to determine structure (size, shape, charges) of active sites.
  • Can therefore identify amino acids of enzymes that are involved in binding & catalysis

17

Model Substrate: Chymotrypsin - What is required for binding & catalysis?

Model substrates will be similar to the actual substrate, but different in a few regions to assess the importance of these regions in the enzyme - will the enzyme still function after these regions have been changed?

1. Do we need the whole peptide chain? NO: the amino acid can still be modified at the N or C-terminus, or have an additional amino group, and still be considered a good substrate b/c chymotrypsin can still cleave the peptide bond

2. Do we need the a-amino group? NO: when a-amino group is gone, the peptide is still be a good substrate. Only alpha-Carbon, carbonyl, and peptide is required for binding & catalysis. The amino group at the end is not required either, as long as it is an electronegative atom, chymotrypsin can still cleave the bond

3. Does R group have to be Phenyalanine, Tyrosine, or Tryptophan? NO: as long as R group is relatively bulky and generally hydrophobic, it will bind to the pocket

Conclusion: Chymotrypsin recognizes a bulky hydrophobic group attached to a “peptide bond” (a carbonyl attached to an electronegative atom) - this is all that is required for binding

18

Competitive Inhibitors: Arginase

Competitive Inhibitors: Compounds that compete with the substrate for binding; they bind in the active site but enzymes cannot use them as substrates - they inhibit catalysis

Assay to see if it is an inhibitor: run an enzyme assay with normal substrate & include inhibitor --> is there decreased activity?

Arginine is cleaved into ornithine & urea; Arginase will bind to compounds that look similar to arginine --> must have 3 charges and a relatively long chain in between the alpha-carbon and the charge at the end of the R-group