Explain promoters and enzzymes.
Promoters bind to very specific sequences within the promoter. If we affect sequences in oriniterm we affect the binding of proteins or whether it is n or off
At promoter, what happens.
different proteins accumulate
- many involve direct contact of DNA
- Everything is replicated
Mutations cant what?
tell the difference between exons and introns. They just cause mutations. If within exons, the Km and Vmax can be affected, altering amino acid associated with active site--> reaction mechanism is affected or the binding affinity of substrate is affected
cells can use this for regulation.
Evolutionarily speaking, the gene for an enzyme existed--> gene replicated--> if it mutated, different variations of the gene arise--> same function of enzyme withdifferent structure
Explain the lactate dehydrogenase example.
lactate dehydrogenase coverts pyruvate to lactate
Circles are the M version and squares are the H version.
As a fetus, the circles are more occupied, whcih represent a lower affinity for pyruvate, because the fetus gets oxygen from mom. As they get older (even when still in the womb and preparing for birth), signals in the womb cause change to squares to signal that the environment will change. The squares have a better affinity for pyrute and works better under aerobic conditions
What is a cascade?
when you take a little tiny signal and amplify it
What are some modifications of protein activity?
we're inside cells; a captive supply of ATP allows a phosphate group to be added to or removed from Ser, Thr, and Tyr. After conformation of prootein--> can turn it on
Explain the phosphorylation process.
Take the -OH group, bring in ATP, pop off the gamma phosphoryl group and add it to protein--> phosphorylation (done by glycogen phosphorylase)
Use protein phosphatase to remove it
Explain phosphorylation in terms of proteins and phosphates.
Free energy increases and is highest when the protein is not phosphorylated; ATP has all three phosphates
Protein-P has higher energy than just protein (net loss of energy between ATP and ADP; there is loewr energy in ADP, but protein now has a higher free energy associated with it (when the phosphate is attached)
Protein and free phosphate have lowest energy
What is cAMP?
second messenger and helps transmit signal from membrane to cytoplasm; produced by adenylyl cyclase; taking ATP and making cAMP
Protein kinase A?
four olypeptide chains (2 catalytic and 2 regulatory);
- key aspect lies in the regulatory subunits and has two features that can regulate PKA
- 1) binding sites for cAMP
- 2) ???
PKA is a what?
serine, threonine kinase; it finds specific serine and threonines that are in the sequence: Arg-ARg-x-S/T-Z, where x is the small and Z is the large hydrohphobic one
Binding site for cAMP
camp incerases, it readily diffuses and binds to regulatory site--> conformational change--> causes regulatory subunit to let go of catalytic subunit
What is the sequence in PKA called?
consensus sequence, which is a generic term to describe any protien sequecne that you find over and over again doing the same thing
What does an inhibitor do?
provides a pseudosubstrate.
It replaces Ser/ Thr with another amino acid; so, everything binds, but no reaction is catalyzed because the alanine (or replacement amino acid) replaces the Ser/Thr). Can't get phosphorylated because there is no Ser/ Threonine
In proteolytic activation, what is not an option?
What are some examples of this?
digestive and blood clotting
Explain the process in summary.
Zymogens are secreted into the intestine; we don't want tem active within cells; so, they are packaged into membrane bound vesicles in proenzyme force. Signal comes--> granules fuse to membrane and zymogens are released, but must be activated.
Proenzyme versus zymogen.
- proenzyme: inactive form of an enzmye
- zymogen: inactive form of a protein
Explain activation of chymotrypsin.
it exists as a 245 amino acid protein
there is cleavage between the 15th and 16th protein to create pi-chymotrypsin, which acts on other pi-chymotrypsins to cleave into three polypeptide chains, which is the functional one
Explain the conformational change of chymotrypsin.
it comes right after the first cut. Isoleucine is originally on the surface, but goes inside the protein once cut. It also has a positively charged amino termnus that attracts Asp 194
Movement of one drags the whole chain with it, producing a hydrophobic pocket that makes the active site and positions the catalytic triad so that they function properly
Explain activation of zymogens for the stomach?
in the stomach, they must all be activated, but are not all active int eh cell.
Enteropeptidase activates trypsin, which is the master protease, activating all the proteases and itself.
Proteins can begin doing what to each other? To prevent this, what happens?
digesting each other
inhibitors are released with the enzymes
has a lysine residue to fit into the active site
when it binds, its half life is long--> stays bound for a long times and inactivates the enzyme--> doesn't function
Amount released is proportional to the amount of __.
enzyme released (irreversible inhibitor)
has a random conformation and is found in tissues that regularly change shape
target of elastase: released to desgrade damaged elastin and remodel
What does elastin have?
has an inhibitor- alpha antiproteinase to inhibit it
When will the inhibitor not work?
when there is a mutation in the inhibitor gene and change in charge
proactively damaged by smoking (oxidation reaction prevents binding of inhibitor on elastase, whcih goes crazy, digesting elastin) Body replaces it with collagen
what are clots?
Platelets embedded in a mesh of cross-linked fibrin
Reasons for clot:
- stop bleeding
- temp. shield over wound surface
- matrix through which new cells repair the wound [scaffolding matrix]
Two pathways that lead to a clot that differ by teh __.
sources o damage
intrinsic: exposure to an unnatural surface; broken skin
extrinsic: blunt forced trauma
What are the clots done by?
thrombin and fibrin
prothrombin adn fibrinogen are the precursors
It is a __ and keeps the response __.
three pairs of polypeptide chains
present in blood in high concentrations (3 mg/ml)
What is the key to fibrinogen?
- 1) stays soluble
- 2) stays monomers (not polymers)
What is not important? They just need a lot of negative charges to __
- help keep them soluble
- help them repel each other to prevent polymerization
Once activated, there is a __ at either end to __.
- binding site
- allow activation
Thrombin does what?
Those polymerized molecule are cross linked by __
activates fibrinopeptides, allowing polymers to form: FIBRIN!
transglutaminase: glutamine and lysine
How does cross linking occur?
- a serine protease
- starts at 582 amino acid zymogens
- 2 cuts for activation
- --> short polypeptide and long polypeptide held by ionic bonds, no disulfide bonds
Other domains on thrombin.
Gla: has alot of glutamic acid; post-translational modification
Purpose of domains of thrombin
since thrombin needs to get to the site, platelets participate
prothrombin arrives at a wound site riding on platelets
The glutamate residues get __.
Enzymes that do this require __.
modified to carboxyglutamate
Vitamin K as a cofactor
What hapens if Ca can't bind?
can't bind to prothrombin, it can't attach to plate membrane
__ and __ anchors self in platelets.
As platelets accumulate, what happens?
athe protein is there adn is modified, activated, leading to clot formation
Clot forms causing __.
small signal--> large signal
Cut cross links to __.
- Another protease: __
Responsible for what?
release from surface of new skin
cutting links to release scabs
Structure of thrombin
serine protease domain
A clot has __--> attracts __, which is cleaved-? activates it--> clot breaks free.