Biochemistry Video 3
Terms
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- What are the names of the histone proteins? (5)
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H1
H2A
H2B
H3
H4 - What is the charge of histone proteins, why is this important?
- They are positively charged. Most proteins are negatively charged
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Which two amino acids carry positive charges?
Why is this significant? -
Arginine and Lysine
Histone proteins are thus made of an abundance of arginine and lysine amino acids - what is a nucleosome?
- DNA donut composed of histone proteins at the core with a DNA "shoelace" surrounding the histone proteins
- How many histones are found in a nucleosome and what are these histones?
- There are 8 total histones in the nucleosome. There are two copies of H2A, H2B, H3, and H4
- What happens to DNA missing hte H1 protein?
- That DNA is sensitive to nucleases
- What is the width of DNA without H1?
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10nm
it is refered to as the "10nm FIBER" - What is DNA packaged with proteins known as?
- chromatin
- What is chromatin with a 10nm width known as?
- euchromatin, also loosely packaged chromatin
- What is significant about euchromatin?
- it is sensitive to nucleases and lacking the H1 histone
- What is the role of H1?
- it condenses the nucleosomes tightly together
- What is chromatin with H1 known as?
- heterochromatin
- What is the significance of heterochromatin?
- it is not sensitive to nucleases
- What is the width of heterochromatin?
- 30 nm
- Where in the DNA is replication started?
- Specific sequence known as the origin of replication
- What is the initial produce of DNA replication in a eukaryote?
- Sister chromatids
- Where are the sister chromatids connected?
- centromere
- What is required for DNA polymerase to start DNA replication?
- RNA primer
- When a mismatch of a base is made during the DNA replication, what is needed to correct this problem?
- 3' Exonuclease
- What molecule actually performs the 3'exoclease?
- 3' exonuclease is a property of all DNA polymerases
- What is used to make an RNA strand and how is this different from the replicatoin of DNA?
- RNA polymerase is needed and this is different from the DNA replicatoin because RNA polymerase does not need an RNA primer
- Compare the proofreading of DNA vs. RNA?
- DNA replication is a HIGH-FIDELITY process and thus mismatched bases are corrected, while RNA synthesis is a LOW FIDELITY process and thus mismatched bases are not corrected
- What molecule recognized the origin of replication in bacteria?
- DNA A protein
- What molecule denatures the DNA to expose the bases for replication in bacteria?
- helicase
- In bacteria, what inhibits the single strands from recombining after they have been separated by helicase?
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SSB
Single strand binding proteins - What are the two functions of SSBs?
- To inhibit the parent strand from reannealing and the protect the single strand DNA from nuclease enzymes
- After the strands have been separated and stabilized, what happens before DNA replication can take place and what molecule causes this?
- PRIMASE (RNA polymerase) must first add the RNA primer the the DNA polymerase to continue from
- What is the DNA polymerase, in bacteria, that does most of the DNA replication
- DNA polymerase 3
- What is the name of the fragments of DNA synethesized on the lagging strand?
- Okazaki Fragments
- In bacteria, after the DNA has been reeplicated, what are the final modification made to the newly synthesized strand?
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DNA polymerase 1's 5' Exonuclease activity will remove the RNA primers and, because it is a DNA polymerase it will replace the RNA with DNA.
After the RNA has been replaced with DNA the DNA segments must be connected. This is done by DNA ligase - What are the differences between replication in prokaryotic vs. eukaryotic cells
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Prokaryotes:
DNA A protein recognizes origin of replication.
Eukaryotes: unknown recognition of origin of replication
Synthesis of DNA -
Prokaryotes:
DNA polymerase III does both the leading and lagging strand
Eukaryotes:
Leading strand - DNA polymerase delta
Lagging strand - DNA polymerase alpha
Removal of RNA primers:
Prokaryote - DNA polymerase I (5'exonuclease)
Eukaryote - Unknown
Replacement of RNA with DNA:
Prokaryote - DNA polymerase I
Eukaryote - Unknown
Synthesis of telomeres:
Prokaryotes - Not necessary because there are no telemeres
Eukaryotes - Telomerase - What enzyme removes the positive supercoils ahead of advanceing replication forks?
- DNA topoisomerase II
- What is the difference between DNA ligase in prokaryotes and eukaryotes?
- In prokaryotes, DNA ligase requires NAD. In eukaryotes, DNA ligase requires ATP.
- In prokaryotes, what is DNA topoisomerase II often known as?
- DNA gyrase
- What antibiotics inhibit DNA gyrase?
- quinolones and fluoroquinolones