Genes and Disease

Question 1

How common are rare genetic diseases?

Answer 1

There are around 6,000 rare genetic diseases
Each has a prevalence of 5/10,000 people
Combined they effect 260 to 450 million people

Question 2

What is the most common type of genetic disorder mutation?

Answer 2

45% of disorders are autosomal recessive
32% are autosomal dominant
10% are sex linked.

Question 3

How many and in what ways to genetic disorders tend to affect children?

Answer 3

83% of rare genetic disorders affect the child
Almost 90% of which affect the nervous system

Question 4

What is the progress with the human genome project?

Answer 4

Cost £2 billion and 13 years to complete, sequences the whole genome in 2003.
By 2018, sequenced 100,000 genomes.

Question 5

What is a gene?

Answer 5

A functional unit of DNA, that composes of transcribed regions and regulatory sequences.
Directs the production of polypeptides or RNA (not always mRNA).

Question 6

What is the idea of the central dogma refering to the transfer of information?

Answer 6

Information flows from DNA to RNA to proteins in humans.

Question 7

Give an overview of the functional elements of genes.

Answer 7

1-2% of the human genome is protein coding
The encylopedia of DNA elements is looking into the remaining 99-98%.
Most of our DNA is transcribed into non-protein forming RNAs which perform useful functions.

Question 8

What type of RNA might non-protein coding gene produce?

Answer 8

Regulatory RNA
Long non-coding RNA (LncRNA)
miRNA
siRNA

Question 9

Describe the structure of a human gene.

Answer 9

5’
promotor region
5’ UTR or untranslated region
Transcription state site indicated by a start codon
Then a sequence of introns (removed during splicing) and exons.
Poly A signal
Termination codon
3’ UTR region

Question 10

Where might eukaryotic gene expression be controlled?

Answer 10

Transcriptional control
(premRNA stage)
RNA processing control
(mRNA stage)
RNA transport and localisation control
mRNA degregation
Translation control
Protein activity control

Question 11

What is alternative splicing and why is it important in protein production?

Answer 11

When exons from the same gene are joined together in different combinations, often caused by differences in the splicing process.
Creates different tertiary structure proteins,
Creates a wide range of protein functions from the same gene.

Question 12

What is the RNAi pathway?

Answer 12

THe process by which RNAi is produced.
In the nucleus double stranded RNA is proced by DROSHA (RNAase enzyme) resulting is shorter dsRNA.
In the cytoplasms the shorter dsRNA is cleaved into smaller fragments by a second RNAase enzyme.
dsRNA associated with a protein complex, stands unwind and one strand in neglected.
The remaining strand in the portein-RNA complex binds to complementary mRNA.
The attaches protein complex inhibits the translation of the associated mRNA sequence through mRNA cleavage.

Question 13

Why is RNAi important?

Answer 13

Found in all eukoryotes except fungi –. ancient evolutionary origin
Defends against pathogens mainly viruses by stopping protein production
Protects against transposins and other insertional elements
Indicates that gene expression rather than encoding genes themselves is important to evolving complex organisms.

Question 14

What is the key difference between miRNA and siRNA?

Answer 14

siRNA has a more specif target mRNA molecule
miRNA has a wider target options

Question 15

What is meant by the degenerative nature in DNA?
Why is this important when considering the location of substitution mutations in a triplet codon?

Answer 15

Degenerate - two different triplet codon may code for the same amino acid
A susbtitution eralier (base 1) in the triplet codon is more likley to change the resulting amino acid
A substituion laater in the triplet codon (base 2 or 3) is less likley to change the resulting amino acid.
Changing the resulting amino acid is more likely to have a phenotypic effect.

Question 16

What are the different types of point mutations?

Answer 16

Substitution
Deletion
inversion

Question 17

What are the different types of block mutations?

Answer 17

Duplication
Inversion (reversed order)
Deletion
Insertion (moved from one to the other - no exchange)
Translocation (exchange)

Question 18

What is a missense mutation?
Why is it important in genetic disease?

Answer 18

A change in the triplet codon due to a single base substitution that results in a different amino acid.
May create a functional or non-functional protein.
Depends of the biochemical similarity between the original and the new AA

Question 19

What is a conservative substitution mutation?

Answer 19

When the resulting changed amino acid is similar biochemically to the original, so the function of the protein is less impacted, this has a smaller effect phenotypically.

Question 20

What is a silent mutation and why is it important clinically?

Answer 20

Is a genetic alteration in which a single base pair substitution in the protein coding portion of a gene does not change the resulting amino acid.
Most likley to occur in the third base of the triplet codon
However, it may affect mRNA splicing or stability to still change protein function

Question 21

What is a nonsense mutation and why is it important in genetic disease?

Answer 21

A single base pair substitution in a protein coding gene results in a premature stop codon, this results in a truncated protein.
This is often non or less functional

Question 22

What is a nonstop mutation?

Answer 22

When the stop codon is removed and transcription occurs past the normal range resulting in an elongated protein that may be non or less functional.

Question 23

What is meant by a frameshift mutation?

Answer 23

Often an addition or a deletion mutation in which multiple triplet codons are changed.

Question 24

What is Hurler syndrome?

Answer 24

An autosomal recessive disease
A type of lysosomal storage disease.
Is also known as severe MPS1
Causes by a deficient IDUA enzyme, a lysosomal enzyme
Dermatan and heparan sulfate (GAGs) accumulate within the cell (including within the lysosome) within tissues or organs
Causes developmental delay, corneal clouding, skeletal, respiratory and cardiac abnormalities.
Often have thickend lips, flat bridge in nose and prominent foreheads.

Question 25

What is Duchenes Muscular Dystrophy?

Answer 25

Autosomal recessvie condition
Progressive muscle weakness and atrophy of skeletal muscle
Mutation is dystrophen, that links the cytoskeleton to the ECM.
Binds to cytoskeletal F-actin by the N-terminus, and the protein complex in the sarcolemme by the c-terminus
Affects plasma membrane intergrity and intracellular Ca2+ concentration, affects mitochondria.

Question 26

What is Hunters Syndrome?

Answer 26

MPS 2
A lysosomal storage disease caused by a lack of IDS enzyme
Heparan and dermatan sulfate accumulate as they are not degraded

Question 27

What is the relationship between Hunters and Herlers syndrome?

Answer 27

Both are lysosomal storage diseases.
The different enzymes involved in both conditions IDS and IDUA are both required to degrade GAGs

Question 28

What are lysosomal storage diseases?

Answer 28

A group of over 70 diseases that are characterised by lysosomal dysfunction which are inherited as autosomal recessvie traits.
Affect 1 in 5,000 live births
Typically presents in infancy and childhood.
Most have a progressive neurodegenerative clincal course.
The enzyme effected varies by the disease
When not functional catabolism is not regualted and causes the accumulation of macromolecules in lysosomes.
All diseases are a spectrum

Question 29

What are the different therapies available for Lysosomal Storage Disorders?

Answer 29

Therapies are mostly based on enzyme replacement.
Includes small-molecule therapies, substrate reduction, chaperone therapies, gene therapy, genetic editing and stem cell transplanatation.

Question 30

What is meant by enzyme replacement therapy?

Answer 30

A recombinant enzyme is administered to replace the mutated faulty one, often only successful in mild cases.

Question 31

What is substrate reduction therapy for LSD?

Answer 31

Administration of a small molecule that inhibits enzymes in the biosynthetic pathway of the accumulated substances.
Prevent GAG synthesis.

Question 32

What is gene therapy?

Answer 32

Infection of a patients cell with a virus that expresses a functional enzyme or co-factor (non protein that is required for an enzymes function).
The introduction of new genes inti a cell

Question 33

What is chaperone therapy in treatment for genetic conditions?

Answer 33

In cases a mutation prevents the protein from folding correctly, chaperone proteins can assist the folding process

Question 34

What are the different types of stem cell transplants that should be availbale to LSD patients?

Answer 34

Allogenic bone marrow transplant
Hematopoetic stem cell transplant
Mesenchymal stem cell transplant
Transplanted cells produce the required protein.

Question 35

What are the three different genome editing approaches?

Answer 35

rAAV
Zinc Fingers
CRISP

Question 36

Give an overview of how rAAV works.

Answer 36

Adeno Associated Virus
High precision but a low through out
Can be used at any locus or cell tropism
Well validated. KI focus
INjects a single stranded DNA into nucleus which is incorporated into genome by cross over events by the homologous recombinant process.

Question 37

Give an overview of Zinc FIngers.

Answer 37

Medium precision and through out put
Good genome coverage
Well validated, KO focus
Plamsid coding for Enzymes with a DNA binding and DNA cleavage domain.
ZFN causes double stranded DNA break, the natural repair mechanism allows for gene knock out and gene knock in/

Question 38

Give an overview of CRISPR.

Answer 38

Is a new therapy but has high potential
Capable of multi gene targeting
Simple RNA-directed cleavage
Combined with AAV method.
The Casp protein associated with a guide RNA which binds to a specific DNA region adjacent to the target site.
Casp causes unwinding of the DNA helix, remaining guide RNA will bind to a specific DNA sequence
If matched Casp causes a double stranded break around this sequence.
DNA repair mechanisms are used to cause the wanted outcome.

Question 39

Give a description of a basic gene structure.

Answer 39

The start of a gene contains a promotor region, for binding of transcription factors
Then a 5’ UTR region
Followed by an intitiation codon and a random pattern on introns and exons
There will be a Poly A signal to generate a poly A tail at the three prime end
Followed by a termination codon and a 3’ UTR region.

Question 40

What are the different directions that DNA is read in semi-conservative replication and transcription?
Then what direction is mRNA read during translation

Answer 40

During semiconservative replication the leading strand is read in a 3’ to 5’ direction
In transcription DNA is read in a 5’ to 3’ direction
mRNA is read in a 5’ to 3’ direction

Question 41

What is an intronic microRNA?

Answer 41

Coding sequence is found within the intron region of the target gene. Spliced out during the transcription process.
Hence shares the same promotor region as the target gene.