What occurs in the ribosomes tunnel?
A peptide bond is formed between two amino acids
Is energy required when catalysis occurs in the tunnel?
NO
What sites do amino acids move through the ribosome (in order)?
Remember, APE (but read right to left) A site P site E site
In which direction do ribosomes read an mRNA strand?
5’ –> 3’
What are the two DNA strands called, and which one is used to make mRNA?
Coding strand and Template Strand, and the Template Strand is use when making mRNA
What is unique to RNA Polymerase as compared to DNA Polymerase?
It unwinds DNA. It adds new bases and proofreads in the same active sight. This is called back-tracking
How do you calculate delta G (Free Energy of Activation)?
(Free Energy of the Transition State) - (Free Energy of the Substrate)
What is the equation for the the reaction velocity?
V=k[S1][S2]
What is the equation for the the reaction rate constant?
k=[S]CTe^-(deltaG**/(RT))
What are the stop codons?
UAA
UGA
UAG
What are the Eukaryotic ribosome subunits called?
How does synthetase work?
It binds tRNA with its correct amino acid.
There is an editing site that checks for the correct aa
It requires the cleavage of 2 high-energy phosphate bonds to operate
What stops DNA replication?
What binds the beta subunit of the RNA pol complex?
Rifampicin (R…P=RNA Pol)
What does Puromycin do?
(Remember “P” for Protein)
Stops growing protein by binding in the A site of ribosome
What does Cycloheximide do?
Think -hex-=6
Binds 60S subunit, inhibits peptide bond formation
What does Erythromycin do?
(Think “E” is the 5th letter of the alphabet)
Binds the 50S subunit and inhibits translocation
What does Tetracycline do?
(Tetra=4??? PSYC, its actually 3)
Binds 30S subunit and inhibits aa-tRNA binding
What does Ricin do?
Cytotoxic
B subunit binds surface carbs and facilitates cell entry
A** subunit (A for in_A_**ctivates)
N-glycoside hydrolase inactivates ribosomes
What is the OTHLIL accronym used for?
Oxireductase
Transferase
Hydrolase
Lyase
Isomerase
Ligase
What does Oxireductase do?
Transfers electrons
What do spliceosomes (ssDNA) do?
Cut out the introns in mRNA, and ligate the exons back together
Which enzyme has a specificity pocket for non-polar/aromatic side chains?
Chymotrypsin
Which enzyme has a specificity pocket for cationic side chains?
Which enzyme has a specificity pocket for small side chains?
Why is metallic mercury toxic?
It has a high affinity for Cysteine side chains (sulfhydryl group)
What does Rifampicin?
(Think “R”NA “P”olymerse)
Inhibits RNA Polymerase
Which enzyme chymotrypsin or carboxypeptidase A is allosteric?
Carboxypeptidase A
What is an allosteric enzyme?
Allosteric enzymes are enzymes that change their conformational ensemble upon binding of an effector, which results in an apparent change in binding affinity at a different ligand binding site.
Which enzyme, chymostrypsin or carboxypeptidase A has an acyl-enzyme intermediate?
Chymotrypsin
How does competitive inhibition change the V vs [S] curve?
Vmax remains unchanged, but the curve shifts to the right
How does non-competitive inhibition change the V vs [S] curve?
Vmax is REDUCED and the V vs [S] curve shifts down
In order to maintain V, what needs to happen to [S] in competitive inhibition?
[S] needs to increase