int to biochem prelab week 14

Name the following three, circled bonds in the structure of the DNA

1. Phosphodiester bond

2. Hydrogen bond

3. N-glycosidic

Name the following purine and pyrimidine bases and draw the hydrogen bonds that form between them

Name the following purine and pyrimidine bases and draw the hydrogen bonds that form between them

Explain briefly why we can say that bacterial DNA replication is semi conservative

When bacterial DNA replication occurs, each strand serves as a template strand; one strand of the replicated double strands is the original strand and the other is the newly synthesized strand

Explain briefly why we can say that bacterial DNA replication is semi discontinuous

The leading strand is synthesized continuously as a single strand, while the lagging strand is synthesized discontinuously as Okazaki fragments

Name three enzymes of bacterial DNA replication that cleave phosphodiester bonds between deoxyribonucleotides

• DNA polymerase I

• DNA polymerase II

• DNA polymerase III

Name that enzyme of bacterial DNA replication which a) creates phosphodiester bonds between ribonucleotides, b) cleaves phosphodiester bonds between ribonucleotides

a) primase

b) DNA polymerase I

Name those enzymes of bacterial DNA replication that cleave hydrogen bonds

Helicase enzyme

Name those four enzymes of bacterial DNA replication that create/seal phosphodiester bonds between deoxyribonucleotides

• DNA polymerase I

• DNA polymerase II

• DNA polymerase III

• DNA ligase

Which structural change of bacterial DNA will the formation and movement of the replication bubble lead to? Which enzyme of replication can correct this structural change?

Structural change : supercoil

Enzyme : topoisomerase II (and/or topoisomerase I)

Which newly synthesized DNA strand is formed by Okazaki fragments, and which enzymes are required for their synthesis?

Strand:

lagging strand

Enzymes:

Helicase

Primase

DNA polymerase III

DNA polymerase I

DNA ligase

Name and give the function of those enzymes that are required to join the Okazaki fragments

• DNA polymerase I: removal of RNA primers while leaving the nick

• DNA ligase: sealing of the nick by recreating the broken phosphodiester bond

Which enzyme of bacterial DNA replication removed the primers? Why is primer removal necessary?

• enzyme: DNA polymerase I

• why: the primer is RNA and must be replaced with DNA

Name and explain that characteristic based on which DNA polymerase III ( and not DNA polymerase I or II) is considered the main polymerase of bacterial DNA replication.

DNA polymerase III has the highest processivity, which is the average number of nucleotides added before the DNA polymerase dissociates

Name the three bacterial DNA polymerases and underline those which play a role in DNA replication

• DNA polymerase I

• DNA polymerase II

• DNA polymerase III

explain briefly how bacterial DNA polymerase III will correct the incorporation of a non complementary nucleotide during bacterial replication?

DNA polymerase III removes a non- complementary nucleotide from the newly synthesized DNA strand by 3’ —> 5’ exonuclease activity and adds the correct complementary nucleotide by 5’—> 3’ polymerization activity

What is the role of the following enzymatic activities of DNA polymerase I during bacterial DNA replication? a) 3’-5’ exonuclease activity, b) 5’-3’ exonuclease activity

a) proofreading

b) removal of RNA primers

What is the difference between the mechanism of action of endonuclease and exonuclease?

• endonuclease hydrolyze phosphodiester bonds at specific internal sites in a nuclei acid strand or molecule, reducing it to smaller and smaller fragments

• exonuclease hydrolyze nucleic acids one by one from one end of the molecule by cleaving phosphodiester bonds either in 3’-5’ or 5’-3’ direction on one strand

What does a mismatch in the structure of the DNA mean and how does it affect the formation of secondary interactions between the deoxyribonucleotides?

meaning: occasional incorporation of incorrect nucleotides, leading to a non complementary base pairing

how: inappropriate hydrogen bonds between deoxyribonucleotides cause deformation in the structure of the DNA

What is the role of the DNA methylation in the process of bacterial mismatch repair?

Name the bacterial DNA methylase enzyme

role: promotion of the mismatch repair on the unmethylated strand by distinguishing between the newly synthesized DNA strand and the parent DNA strand

name: Dam methylase

Name those proteins that defect and localize the DNA alterations in the following bacterial repair processes, a) mismatch repair, b) base-excision repair, c) nucleotide-excision repair

a) Mut L and Mut S

b) DNA glycosylase

c) ABC exinuclease

Name the proteins that function as endonucleases in the following bacterial DNA repair processes. a) mismatch repair, b) base-excision repair, c) nucleotide-excision repair

a) Mut H

b) AP endonuclease

c) ABC exinuclease

Name the proteins that function as exonuclease in the following bacterial repair processes. a) base-excision repair, b) nucleotide-excision repair

a) DNA polymerase I

b) None because DNA Helicase removes a DNA fragment containing the damage, and there is no need for exonuclease action

Give the function of the following proteins of bacterial DNA repair processes. a) DNA photolyase, b) O6- methylguanine DNA methyltransferase, c) AlkB

a) correction of pyrimidine dimmer caused by exposure to UV light

b) correction of methylated nucleotides by removing the methyl group at O6 site of guanine

c) direct repair of alkylated bases