Bio 107 Exam 3 Ch 14

In the Frederick Griffith Experiment, why did the mixture of heat-killed virulent and live non virulent strains of pathogen kill the mouse?

The heat-killed virulent and live non-virulent strains of S. pneumoniae killed the mouse since the heat-killed virulent exchanged DNA with the non-virulent strain. This transfer of virulence is called transformation

In the Hershey and chase experiment, how was it concluded that DNA is the genetic material?

Bacteriophage DNA was label with radioactive phosphorus (32P), and bacteriophage protein was labelled with radioactive sulfur. (Bacteriophages are only made of DNA and protein). Phages are grow to be radioactive, they infected bacteria, and then the phage coat was separated via blending centrifugation. The radioactivity was tracked, and the radioactivity was in the pellet of DNA which shows that the bacteriophage DNA entered the bacteria and was able to produce more bacteriophages.

Overall structure of DNA

a 5-carbon sugar, a phosphate group (5’), a nitrogenous base (A,T,G,C), and a free hydroxyl group —OH (3’).

What’s on the on the 5’ C in DNA?

A phosphate group

What’s on the 3’ C in DNA?

Free hydroxyl group

What’s on the 2’ C in DNA?

H in DNA, and OH in RNA

What is a phosphodiester bond?

A bond between adjacent nucleotides, they’re formed by the phosphate group of one nucleotide and the 3’ OH of the next nucleotide. These chains have a 5’ to 3’ orientation

What are Chargaff’s rules?

He determined that there’s always an equal proportion of 2-ringed purines (A and G) and single-ringed pyrimidines (C and T). Amount of A = amount of G, and amount of C = amount of G.

Structure of a single strand of DNA

Phosphodiester BB, made of repeating sugar and phosphate units joined by phosphodiester bonds. A single strand extends in a 5’ to 3’ direction. Each phosphodiester strand has inherent polarity based on orientation of sugar-phosphate BB. One end terminates in 3’OH, and one end terminates in 5’ PO4.

What is the difference between major and minor groove?

In a double helix there are two grooves, major and minor. The major groove occurs when bbs are far apart, and minor is when they’re close.

What are the models of DNA Replication?

Conservative model, semiconservative, and dispersive model

Conservative model

Both strands of parental DNA remain intact; new DNA copies consist of all new molecules

Semiconservative model

Daughter strands each consist of one parental strand and one new strand

Dispersive model

New DNA is dispersed throughout each strand of both daughter molecules after replication

How did Meselson stahl conclude replication is semi conservative? What does it mean for replication to be semi conservative?

This was determined by combining two stands of DNA, one was lighter and one was heavier. The heavy DNA was replicated with the light DNA, so if it was conservative and both bands were made, we’d see a prominent heavy band (bottom) and light band (top). If it was semiconservative, then there’d be a band in the middle, and a light band. Lastly, if it was dispersive then there’d be multiple bands. In the second round there were two bands, with one of them being in the middle, which shows that it wasn’t just heavy DNA or light DNA being made, and that light DNA is still present since it is the template for the heavy DNA’s replication.

What does DNA polymerase do?

DNA polymerase is used to synthesize new strands of DNA. They can add nucleotides to growing DNA strands, can cut DNA internally (endonucleases), or remove nucleotides from end of DNA (exonucleases)

What are the three polymerases in E. coli?

Pol 1, Pol 2, and Pol 3

What does DNA polymerase 1 do?

Acts on lagging strand to remove primers and replace them with DNA?

What does DNA polymerase 2 do?

Involved in DNA repair processes

What does DNA polymerase 3 do?

Helps with most gene/chromosomal replication. Extends leading-strand, it lets the polymerase stay attached with a beta subunit (sliding clamp).

Why does E. coli have 3 DNA polymerases?

All 3 have 3’ to 5’ exonuclease activity (proofreading), and DNA Pol 1 has 5’ to 3’ exonuclease activity (removes RNA primers)

Endonuclease

Cut DNA internally

Exonuclease

Remove nucleotides from end of DNA

Telomeres

Specialized structures found on the ends of eukaryotic chromosomes. They’re composed of specific repeat sequences, they protect ends of chromosomes from nucleases and maintain the integrity of linear chromosomes. 

What is the purpose of topoisomerase?

It’s an enzyme that prevents supercoiling. Supercoiling happens when torsional strain caused by the unwinding of DNA leads to the twisting of helix. 

Replication fork

The partial opening of the helix formed where double stranded DNA is being unwound.

DNA gyrase

Same thing as topoisomerase, prevents supercoiling. DNA gyrase can unlink two copies.

What does Pol 1 do in a replication fork?

It gets rid of primers used to replicate the lagging strand

DNA ligase

Joins Okazaki fragments to form complete strands

DNA primase

Makes RNA primer for Okazaki fragments

Why is one strand of DNA replicated continuously, and the other is discontinuous?

DNA is translated from 5’ to 3’, and when a strand is split, the added strand must be antiparallel. If there’s a 3’ to 5’ strand, then the complementary strand must be 5’ to 3’, but it can only translate to the extent where the strand is open, so a primer must be added to act as a starting point for translation to occur. 

Mismatch repair (MMR)

Removes incorrect bases incorporated during DNA replication. Replaces with the correct base by copying the template strand. To distinguish between the newly synthesized strand the strand is unmethylated for a brief window to get MMR identify the strands.

Photorepair

Specific repair mechanism, thymine dimers caused by UV light where adjacent thymines become covalently linked together. A photolyase absorbs light in visible range, and this energy is used to cleave those thymine dimers.

Excision repair

Non specific repair. Damaged regions are removed and replaced by DNA synthesis. First there’s recognition of damage, removal of the damaged region, resynthesized using the information on the undamaged strand as a template. In E. coli these proteins are encoded by uvr-A, -B and -C to carry out this repair.