Difficult Questions! Flashcards
How is DNA packaged?
DNA winds around histone proteins, forming nucleosomes
Nucleosomes are organised into solenoids (tightly packed helix)
Solenoids fold into loops
Define intragenic
Introns within genes
Define intergenic
Non coding regions between genes
MtDNA
- Structure
- How many genes?
Double stranded
Circular
37 genes
When is genetic variation introduced during meiosis?
Crossing over - Prophase I
Independent assortment - Metaphase I
Give an example of a genetic disorder caused by meiosis going wrong
Downs Syndrome is trisomy of chromosome 21
Occurs when chromosomes do not split evenly during meosis I or meosis II
What is checked during G1/S phase?
Is the environment favourable?
Presence of growth factors?
Is there enough nutrients?
What is checked during G2/M phase?
Is all DNA replicated?
Is all DNA damage repaired?
What is checked during the checkpoint within M phase?
Are all chromosomes attached to the mitotic spindle?
What can be some detrimental consequences of apoptosis?
Uncontrolled apoptosis can lead to Alzheimers (degeneration of neurons) and Parkinsons (loss of dopinamergic neurons)
Features of a cancer syndrome
Inherited autosomal dominantly
Predisposes to cancer
Much more likely to cause early onset cancer
What is Li-fraumeni syndrome?
-increases risk of
Cancer syndrome
Inherited mutation in one allele for the p53 gene
Increased risk of osteosarcoma, breast cancer, leukaemia etc
What is hereditary breast-ovarian cancer syndrome?
- genes mutated
- role of genes
- increases risk of
Mutations in BRCA1 or BRCA2 genes, which are DNA repair genes, involved in repairing double stranded breaks
DNA damage is not repaired correctly, leading to faster accumulation of mutations
Predisposes to breast, ovarian, fallopian tube carcinoma and prostate cancer in men
How can cancer syndromes be tested for?
Take a sample of body fluid or tissue (blood, saliva, amniotic fluid)
Use NGS to determine DNA sequence of mutation
Or use PCR to look for a specific mutation
What is familial adenomatous polyposis?
- what happens during
- age of onset
Autosomal dominant cancer syndrome
Many polyps form in the epithelium of the large intestine
Start benign, may transform into malignant cancer if left untreated
Usually adult onset
What are the 3 types of familial adenomatous polyposis?
FAP
Attenuated FAP
Autosomal recessive FAP
What is the mechanism behind FAP?
Mutation in APC gene leads to total loss of function. APC combines with axin and a kinase to form part of the beta-catenin destruction complex in the Wnt signalling pathway. Beta-catenin is a transcription factor for cell proliferation.
93% will develop cancer by age 50
What is the mechanism behind attenuated FAP?
A mutation in the APC gene that leads to production of an attenuated APC protein. Still functional but has impaired function.
What is autosomal recessive FAP?
Mutation in the MUTYH gene. Has much milder effects, and required a mutation to be inherited from both parents
What are the 4 main cyclins that control the cell cycle (in order of when their concentrations peak)
Cyclin D - present throughout cycle
Cyclin E - peaks at G1/S
Cyclin A - peaks in G2
Cyclin B - peaks at G2/M
Name 4 tumour suppressor genes
Retinoblastoma
p53
BRCA1/BRCA2
APC
Name 3 proto-oncogenes
Myc/c-Myc
HER-2
MDM2
What does Myc do?
- what is it
- involved in
- activity enhanced by
Myc is a transcription factor involved in many functions (cell proliferation, apoptosis, cellular transformation)
Involved in Wnt, Hedgehog and MAPK signalling pathways
Enhanced by HIF-2a which is active in hypoxic conditions e.g. in the centre of tumours
What is HER-2?
-what does it stand for?
Human Epidermal growth factor Receptor Tyrosine kinase receptor Over expression causes dimerisation when no ligand bound Initiates MAPK and JAK/STAT pathways Has role in development of breast cancer
What is MDM2?
In normoxic conditions, MDM2 ubiquitylates p53 to mark it for degradation
Mutations in MDM2 lead to constitutive cell proliferation
Describe the process of the MAPK cascade
- Ligand binds receptor
- Dimerisation, trans auto phosphorylation
- Recruit SH2 domain of Grb2
- Brings SOS
- Activates Ras
- Activates MAP3K….to MAPK
- Phosphorylates Myc
What is the function of the dishevelled protein?
Inhibits the kinase in the beta-catenin destruction complex
What is cellular senescence?
and what is it caused by
Cells lose their ability to divide due to ageing
Due to telomere shortening
Detected as DNA damage, which activates p53
What is hyperplasia?
Enlargement of an organ or tissue to to increased rate in cell proliferation
What is dysplasia?
Presence of abnormal cell types within a tissue
May be a pre-indication of cancer
What is metaplasia?
The change of one type of differentiated cell into another
What is neoplasia?
The presence of a new growth of tissue, due to abnormal cell proliferation
Give two examples of genes that beta-catenin transcribes
Cyclin D
Myc
What is a polymorphism?
An allele variant that is present in more than 1% of the population
What is a variant?
Any loci that has more than one possible allele within the entire population, even if in less than 1%
Features of mendelian inheritance
- The gene has two copies (maternal and paternal)
- The copies of the gene separate into two gametes
- The copies of the gene segregate independently
Example of an autosomal dominant condition
- onset
- what is it caused by
- what does it do
- symptoms
Huntington’s Disease
Middle age onset
Rare
Trinucleotide repeat in Huntingtin gene
Mutant protein becomes elongated, sticky, doesn’t fold correctly, aggregates within cells
Damages brain cells
Causes decline of motor abilities and cognitive abilities
How can a loss of function mutation ever be dominant?
Haploinsufficiency
One correctly functioning allele is not enough to maintain normal function
Example of an autosomal recessive condition
- what is it
- symptoms
Phenylketonuria
No production of phenylalanine hydroxylase, so build up of phenylalanine, which is toxic
Causes learning difficulties and epilepsy
Example of an X-linked recessive condition
- what is it
- what causes it
- symptoms
Duchenne Muscular Dystrophy
Progressive neuromuscular disorder
Mutation in gene for dystrophin - links muscle cell cytoskeleton to extracellular matrix
Causes muscle weakness and wasting
Features of an X-linked dominant condition
Usually only found in females, as it is usually lethal in males so they do not survive
Example of an X-linked dominant condition
Rett Syndrome
Mutation in gene involved in transcriptional silencing of methylated DNA (epigenetics)
Causes delayed development, autism, lack of speech, lack of ability to walk
What does hemizygous mean?
One copy of a chromosome
e.g. males are hemizygous for the X chromosome
Name 5 examples of non-mendelian inheritance
De novo mutations Mitochondrial inheritance Mosaicism Epigenetics Trinucleotide repeat disorders
What is mosaicism?
-how can it occur
The mutation is not present in every genetically related cell
Can occur if a mutation occurs during early mitosis of a zygote
e.g. If it occurs during the first division, 50% of all cells will be affected
What is germline mosaicism vs somatic mosaicism?
Germline mosaicism = a mutation in the germline cells means that some gamtes carry the mutation and some don’t. Disease may occur in child and siblings
Somatic mosaicism = mutation arises post-fertilisation
What is mitochondrial inheritance?
-what effects severity of it and explain this term
Mitochondria come from the ovum, so are inherited maternally
Severity depends on if there is heteroplasmy or not - the presence of more than one type of organelle genome (e.g. mitochondrial genome) in a cell
What causes trinucleotide repeat disorders?
Happens as a result of slippage during mitosis
Example of a disease that shows anticipation
Huntington’s disease
What are epigenetics?
A modification of gene expression that is heritable
Caused by DNA methylation, histone modifications, non-coding RNAs
Example of a disease caused by epigenetics
Prader-Willi Syndrome
Paternal inheritance
What is genomic imprinting?
Type of epigenetic mechanism
The pattern of gene expression depends on which parents pattern you inherit
What is MODY?
- stands for
- inheritance pattern
- monogenic/polygenic?
- main symptom
Maturity Onset Diabetes of the Young Inherited form of diabetes Autosomal dominant Monogenic Not related to Type 1 or Type 2 No production of insulin OR beta cells don't release their insulin
5 features of MODY that mean it could be mistaken for type 1 diabetes
Early onset - usually before age 25
Usually normal body weight (BMI under 25)
Causes hyperglycaemia
Insulin dependent
Genetic component - may have family history
What mutations can be the cause of MODY?
Single mutation in hepatocyte nuclear factor genes (HNF1a/1b/4a) which express GLUT1 and GLUT2 transporters
Or in glucokinase gene (GCK) that codes for pancreatic glucose sensor
Or NEUROD1, IPF1
What is the most common mutation cause for MODY?
Single base pair insertion in HNF1a
Leads to a premature stop codon
The RNA produced is subject to nonsense-mediated-decay
Leads to haploinsufficiency of HNF1a
What is the best treatment for MODY?
Sulphonylureas
K+ channel blockers, cause depolarisation of beta cells so they are more easily activated and release insulin
What is the other type of monogenic diabetes?
- what is it
- what is the cause of this?
Neonatal diabetes
Occurs in first 6 months of life
May be permanent or transient
Caused by mutations in the K+ channels on beta cell
Two ways of testing for gene presence?
Molecular diagnostics = gene sequencing
Biochemical diagnostics = assay for protein presence/activity
What are 4 methods of screening foetuses for genetic disorders?
Amniocentesis
Chorionic villus sampling
Ultrasound
cell free fetal DNA
Example of when NMD is detrimental
In CF, some mutations result in a truncated protein that NMD decays
However
What are the 3 RNA surveillance mechanisms?
Nonsense mediated decay
Non-stop mediated decay
No-go decay
What proteins regulate nonsense mediated decay?
UPF1, UPF2, UPF3
Which mRNA transcripts undergo nonsense mediated decay?
Transcripts with a premature termination codon that is at least 50 or more nucleotides upstream of the final exon-exon junction
How is nonsense mediated decay initiated?
Where exons have been spliced together, exon junction complexes form
RNA removes these as it is translating
When reaching a PTC, if there a more EJCs down stream, NMD happens
What is the process of NMD?
EJCs consist of UPF2/3
UPF1 is assembled at the site of termination translation
UPF1 is phosphorylated by UPF2/3
Initiates degradation of the transcript
What transcripts are degraded by non-stop mediated decay?
Degrades mRNA that lacks a stop codon
Ski7 mediated or non-ski7 mediated
What transcripts are degraded by no-go mediated decay?
Degradation of mRNA transcripts on which the ribosome has stalled, for example due to formation of a secondary structure
How do glucose in the blood lead to insulin release?
Glucose uptaken into pancreatic beta cells by GLUT2 transporters Metabolised by glucokinase, produces ATP ATP dependent K+ channels close Depolarisation VOCCs open Exocytosis of insulin vesicles
What happens when there is low amounts of glucose in the blood?
Pancreatic alpha cells secrete glucagon
Glucagon increases glycogenolysis
Hepatocytes release glucose into blood
6 points where gene regulation can occur
Chromatin structure Transcription initiation mRNA processing mRNA export Translation initiation mRNA decay
How is chromatin made into heterochromatin or euchromatin?
Histone modifications
Acetylation = turns gene on
Methylation = turns genes off
Where does methylation usually happen?
On a cytosine adjacent to a guanine
Known as CpG island
How is transcription initiated?
TFIID = TBP + 11TAFs
TBP binds TATA Box
Recruits and positions RNA Pol
Forms pre initiation complex
What are the two functions of insulators?
Chromatin boundary - prevents the spread of heterochromatin
Suppress the activity of enhancers
(Bind insulator proteins)
How are genes regulated by mRNA processing?
5’ Cap and PolyA tail protect from endonucleases
Alternative splicing
5’ Cap allows nuclear export
How is constitutive splicing carried out? Name proteins
U1 binds 5' splice site U2 binds branch point U4/5/6 binds in between Branch point attacks 5' splice site Intron lost as lariat
What happens during Poly adenylation?
- PolyA site (AAUAAA) recognised by cleavage and polyA specificity factor (CPSF)
- Cleavage factors CF1 and CF2 make cute
- Cleavage stimulation factor (CstF) promotes cleavage
- PolyA tail added by polyadenylate polymerase
- PolyA binding proteins PAB1 and PAB2 regulate mRNA stability
What happens during RNA export?
RNA exits through nuclear pore
RNA transport proteins hnRNP, p15 and TAP
Sequences in 3’UTR tell transcript where to go
What is mRNA turnover?
The rate at which mRNA is degraded intracellularly
What shape does mRNA take after transcription and why?
Circular
Cap binding protein interacts with polyA binding protein
How is RNA stability regulated?
RNA Binding Proteins
AU Rich elements cause degradation
C rich elements bind alphaCP proteins, causing stabilisation
How do small RNAs regulate gene expression?
About 20 nucleotides long
Recognise sequences in the 3’ UTR
Bind to and blocks ribosome binding site
Define heritability
-scale
The degree of variation in a phenotypic trait that can be explained by genetic variation
Scale of 0-1
Measure of VARIATION
How can the heritability of a trait be determined?
Heritability Studies
Parent-Offspring Correlations
