Proteins and Amino Acids Flashcards
How are ligands attracted to certain enzyme’s active sites?
By the size, charge, shape, hydrophilicity or hydrophobicity.
Cooperative binding
When bind affects the affinity of the next binding.
The degree of cooperative binding by looking at the hill coefficient.
n > 1, positive cooperativity
n<1, negative cooperativity
n=1, enzyme doesn’t exhibit cooperativity
What two models exist about cooperative binding?
MWC model - Enzymes exist in R and T states in equilibrium. When there is more ligand it shifts to more R states if more inhibitors it shifts to more T states.
Sequential model - When the ligand binds it causes a conformational in the enzyme which increases the affinity for the next ligand.
Identify the following enzyme categories
- Oxidoreductases - catalyze redox reactions. ( ie. dehydrogenases)
- Transferases - transfer functional group from one compound to another ( ie. kinases- phosphorolayte)
-Hydrolases - catalyze reaction that use water to cleave bond ( ie. kinases) - lyases- breaks bonds w/o use of ATP or water ( ie. synthases- break bond and create a pi bond as result)
- isomerases - catalyze formation of isomers.
- ligases - combine bonds ( ie. synthetases- create bonds using ATP as energy).
What happens to an enzymatic reaction when we add an enzyme and when we don’t?
With catalysts as we add more substrate it will reach a point of saturation in which more substrate doesnt change the maximum velocity. Without catalysts the rate will continue to increase.
What two theories exist regarding ligands binding to enzymes?
The induced fit model - enzyme’s active site changes shape to fit the substrate ( more accepted model).
Lock and key - the enzyme’s active site and substrate fit like a “ key”
Cofactors ( coenzymes)
small molecules that are attached to active site of enzyme and helps carry out it’s function.
- Apoenzyme - enzymes that doesn’t have it’s cofactor.
- Holoenzyme - enzymes that does have it’s cofactor.
Michealis- Menten equation
Describes the kinetics of enzyme driven reactions.
Describe the variables involved in enzyme kinetics.
- Km
- Kcat/Km
- Kcat ( K2)
- Km- michealis- menten constant. Its the substrate concentration when enzymes are operating at 1/2 Vmax. Measures affinity with an inverse relationship.
- Kcat/Km - The catalytic effeciency. Higher the value the more effecient it is.
- Kcat- turnover rate of enzyme substrate complex to enzyme and product.
What does the lineweaver- burk plot tell us?
It tells us what type of inhibitor we have by looking at the changes in Vmax and Km.
Negative feedback regulation
When the product of an enzyme works back on enzymes further back in the pathway and inhibit it.
Competitive inhibitors
Inhibitor binds to free enzyme to the active site. Characterized by an increase in Km but with a constant Vmax. Can be outcompeted by adding more substrate.
Noncompetitive inhibitors
Inhibitor binds to free enzyme and enzyme substrate complex with equal affinities Characterized by a decrease in Vmax and a constant Km.
Mixed inhibitors
Inhibitors bind to free enzyme and enzyme substrate complex with different affinities. When bind to free enzyme you get an increase in Km but a decrease in Vmax. With binding to enzyme substrate complex you get a decrease in Km and Vmax.
Uncompetitive inhibitors
inhibitor binds enzyme substrate complex and decreases both Km and Vmax.
Kd
The dissociation constant and measures affinity. Inverse relationship to affinity.
Irreversible inhibitors
An inhibitor that irreversibly binds to enzyme. Doesn’t get removed by adding more substrate only by making new enzyme.
Allosteric sites ( allosteric activators v. allosteric inhibitors)
sites other than active site where inhibitor or substrate can bind,
- allosteric activator- binding causing conformational change that allows active sites to be more avaliable.
- allosteric inhibitor- binding that decreases substrate’s affinity to active site.
Phosphorolaytion or dephosphorolaytion
adding phosphate group or removing phosphate group
Glycosylation
Adding carbohydrate group to protein
Zymogens
Enzymes are inactivated by a group in the active site until it’s removed.
Motifs
proteins that arranged in a repetitive secondary structure.
Collagen v. Elastin v. Keratins v. Actin v. Tublin
- Collagen - tri helical motif that plays a role in structurally supporting the EC matric.
- Elastin - responsible for stretch in EC matrix.
- Keratins - Primarily serves to mechanically support hair and nails but all epithelial cells.
- Actin - makes up myofibrils and microfilaments and has a positive and negative end by which proteins can travel unidirectionality.
- Tublin - makes up microtubules which is important for cell structure, seperation of chromosomes during mitosis, and intracellular transport via kinesin and dynein.
Kinesins and Dyneins
Kinesins bring proteins down the positive end of microtubules while dyneins bring proteins toward the negative end.
