Exam 3 Biochem

Oxidoreductases

Catalyzes oxidation-reduction reactions

Transferases

Catalyzes transfer of functional groups

Hydrolases

Catalyzes Hydrolysis reactions

Lyases

Catalyzes group elimination by breaking a covalent bond without water or oxidation (often to form double bonds)

Isomerases

Catalyzes isomerization reactions

Ligases

Catalyzes bond formation couples with ATP hydrolysis

Translocases

Catalyzes solute transport through membranes

What kind of enzyme catalyzes this reaction?

Transferase

What kind of enzyme catalyzes this reaction?

Lyase

What kind of enzyme catalyzes this reaction?

Isomerase

What kind of enzyme catalyzes this reaction?

Oxidoreductase

Activation Energy

Energy barrier to achieve the transition state

Transition State

The highest point of free energy that a reaction needs in order to form products

What does a reaction require in order to overcome repulsions to come together to make products?

Free Energy (x-axis)

Is this a spontaneous reaction?

Yup

Is this a spontaneous reaction?

Nah

Cofactors

Needed to catalyze reactions that functional groups in Aas cant catalyze by themselves (redox reactions)

Coenzymes

Organic Cofactors

Cosubstrates

Coenzymes that are loosely bound and transiently interact with enzyme and substrate

Prosthetic Group

Coenzyme that is a permanently bound group that interacts with substrate

Acid-Base Catalysis

Reaction mechanism where a catalyst donates/accepts a proton during the reaction (facilitating proton transfer)

What Amino Acid side chains can participate in acid-base catalysis?

Histidine, Aspartate, Glutamate, Lysine, Arginine, Cysteine, and Tyrosine

What do all the Amino Acid side chains that can participate in acid-base catalysis have in common?

they all contain ionizable functional groups

ionizable function groups

functional groups (on amino acids) that can gain or lose a proton based on the pH levels

Covalent Catalysis

Where a covalent bond forms between the catalyst and the substrate during formation of the transition state; uses nucleophiles and electrophiles to form new bonds

What Amino Acid side chains can participate in covalent catalysis?

Serine, Tyrosine, Cysteine, Lysine, and Histidine

What do all the Amino Acid side chains that can participate in acid-base catalysis have in common?

They can all act as nucleophiles

Nucleophile

Chemical molecule that donates an electron pair to form a chemical bond with an electrophile

Electrophile

Chemical molecule that forms bonds with nucleophiles by accepting an electron pair

What is the catalytic triad of chymotrypsin?

His 57, Ser 195, and Asp 102

What is the role of His 57 in the catalytic triad?

being a base catalyst that takes a proton (H+) from Ser 195

What is the role of Ser 195 in the catalytic triad?

being a covalent catalyst that attacks peptide bonds of substrates

What is the role of Asp 102 in the catalytic triad?

stabilizes positively charged His 57 after it takes H+ from Ser 195

Catalytic triad

Interacts through H-bonding in active site

Oxyanion Hole

Negative oxyanion in chymotrypsin active site that is stabilized by two hydrogen bonds with chymotrypsin peptide backbone; H-bond only form with transition states

Velocity (v)

Progress of the reaction that’s measured by the appearance of product/disappearance of substrate over time (usually in mM/s)

Initial velocity (v0)

When [S] is low, v is linear. more [S] = faster rate

Maximal Velocity (Vmax)

When [S] is high, V plateaus. more [S] = same rate. Enzyme becomes saturated

Non-molecular (0th order) kinetics

When a reaction has a velocity (rate) independent of [S]

Unimolecular (1st order) kinetics

When a reaction has velocity (rate) dependent on concentration of a single substrate

Bimolecular (2nd order) kinetics

When a reaction has velocity (rate) dependent on concentration of two substrates

When does Michaelis-Menten Equation Apply?

When [S] is much greater than [E]

Km

Constant that combines the three rate constants; A measure of an enzyme’s affinity for a substrate

What does a small Km signify?

Enzyme has high substrate affinity; more effective at lower substrate concentrations

What does a large Km signify?

Enzyme has a lower substrate affinity; less effective at lower substrate concentrations

What is Kcat?

The turnover number; the rate constant of the reaction when the enzyme is saturated with substrate; is the number of catalytic cycles that each enzyme undergoes per unit of time

What are the three types of Reversible Inhibitors?

Competitive, Non-competitive, and Uncompetitive

Competitive Inhibitor

Compete with substrate to bind to active site

What effect do Competitive Inhibitors have on Km and Vmax?

Increases Km and has no effect on Vmax

Uncompetitive Inhibition

Inhibitor does not interfere with substrate binding, but prevents reaction from completing and forming product

What effect do Uncompetitive Inhibitors have on Km and Vmax?

Km and Vmax both decrease proportionately

Noncompetitive Inhibition

Binds to a site other than the active site before or after the substrate binds

What effect do Noncompetitive Inhibitors have on Km and Vmax?

Km stays the same, and Vmax decreases

What type of Inhibition does this graph belong to? (Blue = normal Red = w/ Inhibitor)?

Noncompetitive

What type of Inhibition does this graph belong to? (Blue = normal Red = w/ Inhibitor)?

Competitive

What type of Inhibition does this graph belong to? (Blue = normal Red = w/ Inhibitor)?

Uncompetitive

What’s the difference between Saturated and Unsaturated Fatty Acids?

Saturated Fatty Acids have all C single bonds, while Unsaturated Fatty Acids have at least one C double bond

What’s the system for naming fatty acids (that we use)?

Counting carbons starting at the carboxylic acid, and then counting which carbon the double bond started at (# carbons : # double bonds (Delta) carbon position)

Name this Fatty Acid

18:0

Name this Fatty Acid

18:1 (Delta)^9

Name this Fatty Acid

18:2 (Delta)^9,12

How to identify a Omega-3 Fatty Acid?

If the last double bond is 3 carbons away (counting the start) from the end of the fatty acid

How to identify an Omega-6 Fatty Acid?

If the last double bond is 6 carbons away (counting the start) from the end of the fatty acid