Case of the Week 5

Question 1

Why is DNA made of deoxyribose

Answer 1

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)

Question 2

Which one is double stranded/single stranded generally

Answer 2

DNA/RNA comes in both double and single stranded

Question 3

Spacing in DNA

Answer 3

3. 4 A between base pairs

10. 5 base pairs between turns

Question 4

DNA structure?

How it is achieved in humans

Answer 4

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

Question 5

Euchromatin and heterochromatin

Answer 5

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

Question 6

Methylation of DNA

Answer 6

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.

Question 7

Is DNA methylation reversible

Answer 7

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.

Question 8

Significance of DNA methylation

Answer 8

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).

Question 9

How is DNA packaged

Answer 9

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.

Question 10

Histones

Answer 10

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).

Question 11

Important concepts about histones

Answer 11

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.

Question 12

Details about lysine acetylation

Answer 12

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

Question 13

Epigenetics

Answer 13

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).

Question 14

Epigenetic silencing of a gene

Answer 14

It is silenced by the methylation of that gene on the DNA.

Question 15

When is DNA most compact

Answer 15

DNA is most compact during metaphase, the phase right before cell division (sort of).

Question 16

Kinds of repeats on DNA

Answer 16

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.

Question 17

What are transposons

Answer 17

Transposons are jumping DNA that can be transcribed into RNAs and then they can go back to the DNAs at a different location.

Question 18

4 main classes of interspersed repeats

Answer 18

1. 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.
2. 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.
3. Retrovirus like elements - 8% - these are called Human Endogenous Retroviruses (HERVs). These are transpositionally inactive.
4. DNA Transposons Fossils – 3% - these are also transpositionally inactive

Question 19

Tandem repeats

Answer 19

1. 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
2. Minisatellite DNA – also called VNTRs (variable nucleotide repeats), used for DNA fingerprinting
3. Microsatellite DNA – also used for DNA fingerprinting, clusters are short.

Question 20

Segmental Duplications

Answer 20

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.

Question 21

Significance of DNA repeats

Answer 21

1. Used in forensics for paternity or maternal testing
2. These are the driver of evolution (such as LINE, SINE) as transposons are the source of insertional mutations
3. They facilitate recombination events
4. They have important roles in gene regulation

Question 22

Number of bps and protein coding genes

Answer 22

3.2*10^9 bps and 21,000 protein coding genes

Question 23

What gets least damaged in the sun?

Answer 23

The answer is exons for the first one since they constitute the smallest part of the human genome.

Question 24

What does the drug do for actinic kerotosis

Answer 24

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).

Question 25

FSHD

Answer 25

Know this for FSHD (facioscapulohumeral muscle dystrophy). Unaffected people have a 100 of these repeats whereas the FSHD patient have only 20 of these repeats, so they have lost a lot of the repeats. Their DNA at the end is less methylated so the genes at the end like DUX4C are expressed which somehow causes muscle wasting and muscle cell atrophy.

The loss of the repeats does not get recognized by the DNA methylation machinery so these repeats are not methylated and hence the genes at the end are expressed.

Question 26

How does LINEs and SINEs move in the DNA

Answer 26

LINE, undergoes transcription, becomes RNA, undergoes reverse transcription, becomes DNA, undergoes reintegration, becomes part of the DNA

Question 27

Effects of LINE and Alu methylation on the survival rates of patients with cancer

Answer 27

The figures in the lecture showed that as the methylation of LINE elements decrease, patients had a higher probability of dying from cancer, the cancer would become more and more aggressive.
To state this in other words, patients with less LINE methylation had a higher risk of dying from cancer. No change in Alu methylation was observed.
One mechanism can be that genes are being expressed that shouldn’t be expressed.
Another mechanism can be that LINES are being over expressed, they are jumping around too much, they either are killing the expression of a gene or activating the expression of a gene.
There are different extents of methylation in different forms of cancer.

Question 28

Familial Hypercholestrolinemia

Answer 28

Liver can’t breakdown the LDL, high amounts of LDL in blood. There is a mutation for LDL cholesterol receptor in the LDLR gene. Lack of functional receptors leads to no uptake of LDL in liver.
There is rearrangement going on. It doesn’t have to do with methylation but it has to do with recombination.

These two parts of the DNA are similar and undergo non-allelic homologous recombination.
DNA rearrangement is the most common cause of this disease in patients.

The drug prescribed for this disease increases histone acetylation. This drug works by inhibiting histone deacetylase, so more acetylation increases the expression of genes, including apoptosis genes which leads to the cell dying.

Question 29

Genetic mosaicism

Answer 29

Having more than 1 set of genome in an individual

Question 30

Where does DNA methylation occur

Answer 30

At the GC pair (on both sides)