The pyranose form of glucose dominates (>99%) at equilibrium in aqueous solution

TLS Online TPP Program

#Id: 5887

#Unit 3. Fundamental Processes

Only when a correct base pair is formed are the 3’-OH of the primer and the a-phosphate of the incoming nucleoside triphosphate in the optimum position for catalysis to occur.

TLS Online TPP Program

#Id: 5888

#Unit 3. Fundamental Processes

Incorrect base pairing leads to dramatically lower rates of nucleotide addition as a result of a catalytically unfavorable alignment of these substrates. This is an example of kinetic proofreading, in which an enzyme favors catalysis using one of several possible substrates by dramatically increasing the rate of bond formation only when the correct substrate is present. 

TLS Online TPP Program

#Id: 5889

#Unit 3. Fundamental Processes

DNA polymerases show an impressive ability to distinguish between ribonucleoside and deoxyribonucleoside triphosphates (rNTPs 10 and 1 dNTPs)

TLS Online TPP Program

#Id: 5890

#Unit 3. Fundamental Processes

In DNA polymerase, the nucleotide-binding pocket cannot accommodate a 2’-OH on the in-coming nucleotide. This space is occupied by two amino acids that make van der Waals contacts with the sugar ring. Changing these amino acids to other amino acids with 

TLS Online TPP Program

#Id: 5891

#Unit 3. Fundamental Processes

DNA binds in a large cleft composed of three domains. The “palm” domain has important conserved sequence motifs that provide the catalytic active site. The “fingers” are involved in positioning the template correctly at the active site. The “thumb” binds the DNA as it exits the enzyme, and is important in processivity.

TLS Online TPP Program

#Id: 5892

#Unit 3. Fundamental Processes

DNA polymerases fall into five families based on sequence homologies; the palm is well conserved among them, but the thumb and fingers provide analogous secondary structure elements from different sequences.