Celular metabolism and enzymes

Question 1

Describe the structure of proteins

Answer 1

• Primary: polypeptide chain, sequence amino acids linked by strong covalent peptide bonds
• Secondary: alpha helix/beta sheet. stabilised by weak hydrogen bonds
• Tertiary: protein fold over, polar chains outside, hydrophobic chains inside. Weak hydrogen bonds, stronger ionic bonds between +ve and -ve charged amino acids, hydrophobic interactions and covalent disulphide bond linkages.
• Quaternary: multiple proteins chains together.

Question 2

Enzyme function:

Oxidoreductases

Transferases

Hydrolases

Lyases

Isomerases

Ligases

Answer 2

• Oxidoreductases = oxidation-reduction reactions
• Transferases = Transfer of C-, N-, or P- containing groups
• Hydrolases = Cleavage of bonds by addition of water
• Lyases = Cleavage of C-C, C-S and certain C-N bonds
• Isomerases = Racemization of optical or geometric isomers
• Ligases = Formation of bonds between carbon and O, S, N coupled to hydrolysis of high-energy phosphates

Question 3

What are enzymes?

Draw the free energy diagram

Answer 3

• Protein catalysts
• increase rate of chemical reactions without being changed in the process
• lower the activation energy assoicated with an uncatalysed reaction
• specialised area called active site
• highly specific
• lock and key model/induced fit

Free energy diagram:

energy profile determines rate of reaction.

Uncatalysed; activation energy required is high. Energy supplied by kinetic energy of molecules

Enzymes lower activation enery, promote transition state.

Free energy of the overall reaction is unchanged delta G

Question 4

What are co-factors/co-enzymes?

Answer 4

• enzymes can work on their own or require presence of other factors/molecules

1. metal ion -co factors
   
   1. mg2+ hexokinase
   2. Zn2+ carbonic anhydrase
   3. Fe2+ cytochrome oxidase
2. organic melecules (co-enzymes)
   
   1. coenzyme A - acyl group reactions
   2. coenzyme B12 - alkyl group reactions

Question 5

What is the effect of temperature on enzymes?

Answer 5

Increasing kinetic energy (temperature increase) generally increases reaction rates. However, enzymes can denature at higher temperatures, thereby reducing their activity.

Gut enzymes are pH sensitive as the organism will have evolved enzymes that work at a specific pH in the alimentary system. Hydrogen ion changes can affect the charge of amino acids at the active site, as well as altering the general structure of the protein structure.

Question 6

What is the effect of pH on enzymes?

Answer 6

Gut enzymes are pH sensitive as the organism will have evolved enzymes that work at a specific pH in the alimentary system. Hydrogen ion changes can affect the charge of amino acids at the active site, as well as altering the general structure of the protein structure.

Question 7

Enzyme kinetics:

Draw the hyperbolic velocity/substrate graph

Answer 7

dotted line is if no enzyme present

curve represents hyperbolic function as described by Michaelis Menton equation

Km = the substrae dose at which the reaction velocity of half the maximal value (Vmax)

Question 8

Michaelis Menton

Answer 8

Michaelis and Menton proposed the following reaction model to explain the observed kinetics for enzymes:

S = Substrate

P = Product

E = Enzyme

ES = Enzyme substrate complex

k1, k-1, k2 are rate constants

Equation:

V₀= V_Max [S] / K_m + [S]

V₀ = initial reactio velocity

V_Max = maximum velocity

K_m = Michaelis constant K_-1 +K₂/ K₁

S = substrate concentration

Question 9

Lineweaver–Burke plot

Answer 9

V0= VMax [S] / Km + [S]

Rearranged:

1/V₀ = K_m/V_Max[S] + 1/V_Max

Follows function y=mx+c

Question 10

Km changes

Answer 10

Blue enzyme has a low Km and therefore the substrate has a higher affinity for this enzyme.

Red enzyme has a higher Km than enzyme 1, and therefore the substrate has a lower affinity for this enzyme.

Green enzyme has the same Km but a lower Vmax than enzyme 1.

At low substrate concentration, the enzyme kinetics are first order i.e. the rate of reaction is proportional to the amount of substrate present

At high concentrations the reaction velocity is constant i.e. zero order kinetics apply.

Question 11

Competative inhibitor

Answer 11

• bind reversible to enzyme
• usually binds at active site
• binding at distant site -> conformational change
• reversibly prevent substrate binding to the enzyme
• can be overcome by increasing the substrate concentration
• increases Km
• V_Max unaffected
• increase slope in Lineweaver-burke graph

Question 12

Non-competative inhibitor

Answer 12

• binding of substrate to enxyme unafected
• bind covelently to enzyme causing permanent conformational change
• catalytic activity reduced
• net effect similar to reduced amount active enzyme present
• K_m same
• V_Max redcued