DNA packaging L03

List three functions of supercoiling

1. Supercoiling compacts the DNA so that it can be packaged into the cell. 2. Negative supercoiling promotes strand separation (eg. DNA replication). 3. Positive supercoiling is introduced during DNA replication and transcription and must be corrected. Positive supercoiling makes DNA strand separation more difficult.

What is the size range of the 5 histone proteins

11-16kDA

Name and describe the other three steps of DNA packaging

300nm - Extended section of chromosomes 700nm - Condensed section of chromosomes 1400nm - formation of metaphase chromosome

Describe the formation of the 30nm packaging

30nm packaging is formed from the association of nucleosomes (with each other). This structure results from interactions between adjacent histone H1 proteins.

As DNA is wrapped round the core octamer of nucleosome it develops

A single negative supercoil

Explain the term supercoiling in prokaryotes

Addition of turns being introduced into a circular DNA double helix

Briefly explain the histone code

Additional histone modifications alter the interaction of the DNA and the histone tails. This can include methylation, phosphorylation and ubiquitination.

What is the content of chromosomes

Chromatin

Name the enzymes responsible for supercoiling in prokaryote

DNA gyrase and Topoisomerase I

How does DNA gyrase act

DNA gyrase makes a covalent linkage to both strands of one DNA helix and making a double stranded break. The second DNA helix is passed through the break. The break is resealed and the enzyme dissociates. This reaction requires ATP hydrolysis.

Describe a nucleoid bacteria structure

DNA is attached to a protein core from which approximately 50 supercoiled DNA loops radiate outwards.

List the steps involved in heterochromatin formation

DNA methyl transferase (Dnmt3) methylates both strands of the DNA Methylcytosinebinding protein (binds to methylcytosines) MeCP2. Recruits Histone Deacteylase (HDAC1) (remove acetyl group from aa residue on the histone).

What causes heterochromatin formation What enzyme catalyses this process

DNA methylation Methyl group is added to cytosine to form 5'methyl cytosine. Methylation silences genes. DNA methyl transferase

What drug interferes with the heterochromatin formation process and what is its mechanism of action

Decitabine (5-aza-2'-deoxycytidine) It causes DNA hypomethylation and increased transcription

Name and described the two types of chromatin identified based on chromosome staining

Euchromatin-decondensed and transcriptionally active Heterochromatin-condensed and transcriptionally inactive

Which proteins associates with these enzymes and what is it's equivalent in eukaryotes

HU proteins Histone protein

The DNA in the nucleus of eukaryote somatic cells is packaged by

Histones

Why is DNA attracted to histone

Histones are positively charged proteins because they contain Lysine and Arginine.

The drug ciprofloxacin that is used in the treatment of urinary tract and respiratory infections results in bacteria cell death by which of the following mechanisms

Inhibits DNA gyrase

Name the function of ciprofloxacin

It inhibits DNA Gyrase stopping replication in bacteria because DNA Gyrase helps relieve positive supercoiling.

What is chromatin

It is the complex of DNA and chromosomal proteins.

How does acetylation comes into play in heterochromatin formation and euchromatin formation

Lysine residue with acetyl group. When lysine is acetylated it has a neutral charge. If HDAC catalyses this reaction, lysine would have a +ve charge, the DNA would be more attracted to the histone and wrap around it more tightly. HATs would add acetyl to lysine causing it to be neutrally charged. The DNA would not be attracted to histone and would become loss forming Euchromatin

What stage is DNA most highly condensed

Metaphase

Where does histone modification occur

Modifications occur on the amino acid residues found in the exposed tails of the histones.

Why is it that supercoiling can not be relieved by simply rotating the DNA double stranded helix

Most DNA molecules do not contain a freely rotating end as DNA molecules in the cell are often associated and bound to various matrix or scaffold proteins

What is the component of 10nm packaging

Nucleosomes and the linker DNA and histone H1

Name the types of supercoiling and how do they differ from each other

Postive and negative Negative supercoiling promotes strand separation (eg. DNA replication). Positive supercoiling is introduced during DNA replication and transcription and must be corrected. Positive supercoilingis introduced ahead of the protein and negative supercoilingis introduced behind the protein.

Is Topoisomerase I present in prokaryotes or eukaryotes

Present in both

Differentiate between a relaxed DNA and a supercoiled DNA

Relaxed DNA doesn't have additions of turns to it's helix while supercoiled does. Supercoiled DNA is packaged and therefore reduced in size compared to a relaxed DNA.

DNA in all eukaryote is tightly bound to histones name the exception to this role

Sperm - Protamines

What puts an end to Topoisomerase I reactions

Spontaneous re-formation of the phosphodiester bond regenerates both the DNA helix and the DNA topoisomerase

List two ways in which supercoiling can be introduced

Supercoiling can be introduced by the action of gyrase or topoisomerase enzymes and by the action of enzymes and proteins involved in DNA replication and transcription.

What is bead on string and what is it's diameter

The first level of packaging 10nm

Describe the nucleosome structure

The nucleosome core is composed of two molecules each of H2A, H2B, H3 and H4 histone proteins. It also has H1 protein which holds the structure together

Why is the Topoisomerase I reaction reversible

The original phosphodiester bond energy is stored in the phosphotyrosine linkage

Describe the protein core of the nucleoid of a bacteria

The protein core contains DNA gyrase, topoisomerase I and packaging proteins such as the HU protein.

The total mass of histone is equal to

The total mass of DNA

What activates DNA gyrase

This enzyme is activated when two double helices cross over each other.

How can supercoiling be corrected

This supercoilingmust be corrected by DNA gyrase and Topoisomerase I.

What is the difference between DNA gyrase and Topoisomerase II

Topoisomerase II is the name of DNA gyrase for Eukaryote

What class of Topoisomerase is DNA gyrase

Two

Name the packaging protein in prokaryote and eukaryote

https://mega.nz/#F!kQ1QGRDS!tY_l2kgHylRJ16JKfm6h3A

What is the function of Topoisomerase I

transiently forms a single covalent bond with the DNA and breaking a phosphodiesterbonds; this allows free rotation of the DNA around the covalent backbone bonds.