Case of the Week 5 Flashcards
Why is DNA made of deoxyribose
It is extremely stable and at the same time it allows for some changes (plasticity)
Easy to copy, easy to access or silence as different genes are required at different times of the cell cycle and lastly it can store an infinite variety of information (meaning content)
Which one is double stranded/single stranded generally
DNA/RNA comes in both double and single stranded
Spacing in DNA
- 4 A between base pairs
10. 5 base pairs between turns
DNA structure?
How it is achieved in humans
The DNA structure has to be compact so it can fit inside the cells but it also has to be accessible. In the humans this is achieved by a protein-DNA complex called Chromatin
Euchromatin and heterochromatin
Euchromatin – light staining (open chromatin), genes are actively expressed
Heterochromatin – dark staining, repetitive, it is compact. It is of 2 types: constitutive (contains repeats such as telomeres telomeres (chromosome ends) and centromeres (chromosome centers). Facultative is the part that has the developmental genes that have been silenced in specialized cells
Methylation of DNA
Methylation of DNA is very specific.
Know how to identify the CPG pair (it is methylated on both sides)
Methylation has a regulatory role. It represents 1% of all the basis.
Is DNA methylation reversible
DNA methylation is silencing of those genes and it is essentially irreversible (as demethylation involves identify the methyl group, modifying it, removing it and then repairing the DNA).
It continues to spread along the DNA polymer, adding methyl groups to cysteines unless it is stopped by specialized proteins.
Significance of DNA methylation
DNA methylation is important in many scenarios like inactivation of one of the X chromosomes in female. Also this is how cells develop constitutive heterochromatin and methylation is also important in suppression of oncogenes (cancer causing genes).
How is DNA packaged
Know how the DNA molecule is packaged. DNA double helix structure is packaged in histones (each histone contains 200 bps). It is called a nucleosome fiber (remember the structure of beads on a strong model). Then this structure is wrapped around in solenoid form.
Histones
Chromatin has 2 of each of these proteins: H2A, H2B, H3 and H4
Histone 1 assists in higher order packing, it seals the entry and exit point.
Histone proteins are rich in lysines and arginines so they can interact with the negatively charged phosphate backbone of DNA. These histones have globular structure with tails that get modified. The R groups of these amino acids towards the end get modified and this is what controls the access of DNA (transcription of DNA).
Important concepts about histones
There are what we can call small modifications that include – acetylation, methylation, phosphorylation – whereas there are large modifications such as ubiquitylation, sumoylation and ADP-ribosylation.
These modifications regulate gene transcription as these lead to opening or closing of the chromatin structure. For example:
Acetylation is pro-transcriptional – leads to loosening of histones, enabling access to DNA
Methylation of arginine and lysine depends, it can be pro-trnascriptional or it can hinder transcription by tightening the DNA-hisotne complex at specific intervals.
It is important to know that these modifications are dynamic whereas methylation of DNA is irreversible more or less.
There are specific groups of modifications that mark active and inactive genes.
Details about lysine acetylation
This is done by the enzyme Acetyl transferase (which borrows the acetyl group from Acetyle CoA) wheras the deacetylation (the reverse reaction) is done by Histidine deacetylase. The lysine has acetyle group added to its charged NH3 group
Epigenetics
Epigenetics: information in DNA that is not stored in the nucleotides but it is still inherited.
These are imprinting methods (like modifications) that are passed on (the way the DNA histone complex is modified). However some modifications such as histone modifications are not passed on to the offspring (they can be passed on to daughter cell when the cell divides but it is not passed on sexually).
Epigenetic silencing of a gene
It is silenced by the methylation of that gene on the DNA.
When is DNA most compact
DNA is most compact during metaphase, the phase right before cell division (sort of).
Kinds of repeats on DNA
Half of our DNA is just repeats.
There are interspersed repeats that are repeats that are spread out whereas as there are tandem repeats that are all in a row. Then there also segmental repeats.
What are transposons
Transposons are jumping DNA that can be transcribed into RNAs and then they can go back to the DNAs at a different location.
4 main classes of interspersed repeats
- LINEs – 20% of our genome – Long Interspersed Nuclear Elements – these are transposons (or retrotransposons), LINE 1 is 17% of the DNA, a fraction of it is capable of either moving or facilitating moving of other retrotransposons.
- SINEs – Short Interspersed Nuclear Elements – these are inactive of moving but their movement can be facilitated by active transposons. These are also called Alu repeats.
- Retrovirus like elements - 8% - these are called Human Endogenous Retroviruses (HERVs). These are transpositionally inactive.
- DNA Transposons Fossils – 3% - these are also transpositionally inactive
Tandem repeats
- Satellite DNA – These are alpha DNA or alphoid DNA that lie in the centromers of all DNA, these are also repeat units, account for 3 to 7% of our DNA
- Minisatellite DNA – also called VNTRs (variable nucleotide repeats), used for DNA fingerprinting
- Microsatellite DNA – also used for DNA fingerprinting, clusters are short.
Segmental Duplications
These are bigger regions with more than 90% of the identity present more than once on the genome. Duplications can be of the same or multiple chromosomes. These contribute to genomic rearrangements via crossing over in meiosis. These are about 5% of the human genome.
Significance of DNA repeats
- Used in forensics for paternity or maternal testing
- These are the driver of evolution (such as LINE, SINE) as transposons are the source of insertional mutations
- They facilitate recombination events
- They have important roles in gene regulation
Number of bps and protein coding genes
3.2*10^9 bps and 21,000 protein coding genes
What gets least damaged in the sun?
The answer is exons for the first one since they constitute the smallest part of the human genome.
What does the drug do for actinic kerotosis
DNA probably incorporates it as it is made of deoxyribose.
This molecule causes strain breaks, it is mutagenic, so it will damage the DNA and the cell will not be able to repair its DNA and it would have to undergo apoptosis. The cancer cells are affected more than the normal cells as they undergo replication more often (normal cells will also be affected but to a less extent).
