EMS Flashcards
What is a nucleosome?
200 base pairs of double stranded DNA wrapped around a histone core octamer
Describe the mitochondrial genome
Circular, cytoplasmic material inherited via oocyte cytoplasm
What its satellite DNA?
Large blocks of repetitive sequence heterochromatin, tenderly repeated sequences with possible polymorphic blocks
- alphoid DNA 171bp repeat unit required for centromere assembly
What are interspersed repeats?
Alu repeats
- Scattered around the genome, individual copies at many locations
- Short interspaced nuclear element
- Dispersed into retro transposition
What is a de novo mutation?
A new mutation which has occurred during gametogenesis - parents are not affected and do not have the mutation in their somatic tissue
What is anticipation?
Symptoms of a genetic disorder becoming more severe as the gene is passed on through each generation
What is Mocaicism?
A new mutation occurrence post-zygotically
- distribution of mutant cells is unpredictable and could involve lethal mutations if non-mosaic
Describe Sanger sequencing
- Use PCR as a template DNA in the reaction
- Template DNA, nucleotides and polymerase to reaction (+primer)
- Add dye terminator nucleotides (ddNTPs) to terminate the sequence reaction labelled with fluorescent dyes
- cycle through denaturing, annealing and extension 35 times
- DNA will be different lengths due to random incorporation of terminator bases and separate as they leave the capillary based on their size
- Excited with a laser and each dye gives off a different signal which can be collected and decoded
Describe next generation sequencing
- Clonal sequencing machines which sheer the DNA wanted and make small clones using PCR onto a flow cell
- Similar to Sanger
- Sequencing reads are small (150bp)
Describe whole exome sequencing
- Generate an exam library - sheer genomic DNA, amplify, tag, hybridise it with a library of probes matching axons in the genome
- have small magnetic bead on the end so we can pull out the sequences that have hybridised
- Go into standard ilumino ex gen sequencing to produce the sequencing reads
Describe comparative genome Hybridisation (aCGH)
- Standard reference DNA and patient DNA
- Cut and label with patient DNA green fluorescent dye and reference DNA with red dye
- Hybridise it to an array - lots of probes and expand genome
- if equal red and green = yellow
- can see different quantities of DNA but not where it is in the genome
What is the dosage effect?
Copy number variation, CNV - loss usually worse phenotype than gain
Types:
- Aneuploidy, polyploidy
- Chromosome structure - deletion/duplication
- Mosaicism
What is the position effect?
Gene in a new chromosomal environment functions inappropriately - unmasking of a recessive disorder
What are the three viable trisomy’s?
Trisomy 13 - patau syndrome
- microcephaly, holoprosencephaly, cleating, polydactyly
Trisomy 18 - Edward’s Syndrome
- microcephaly, growth retardation, rocker-bottom feet, clenched hands and cardiac abnormalities
Trisomy 21 - Down’s syndrome
- Aneuploidy, resulting from meiotic errors, strong maternal age effect, little or no paternal effect
Describe Polyploidy
- Errors at fertilisation, most usually triploidy
- Parental origin effect
Describe reciprocal translocation?
- Breaks and exchanges of chromosomes
- Stem from meiotic errors in segregation and can produced unbalance gametes
- Pachytene cross
Describe Robertson Translocation
- Whole arm fusion
- Acrocentrics - short arm loss
- No phenotype, reproductive risk
- Full genetic makeup just 45 chromosomes not 46
What are 4 types of normal genetic variations?
- Single nucleotide polymorphisms
- INDEL’s - insertion or deletion of one or more nucleotides
- SNP + INDEL’s - target site for nuclease enzymes - restriction fragment length polymorphisms RELPs
- CNVs - large indwells change copy number of sequence greater than 100 nucleotides in length
Describe allelic heterogeneity
Different pathogenic variants in a single gene leading to multiple different phenotypes
Describe a point mutation
Mutation that effects a single nucleotide
- most common cause of disease
Describe variant consequences
Protein effect: - No effect - Exchange for reference amino acid for alternate - Null effect - complete absence of the genes protein product People Effect: - No effect - Contribution to individual variation - Cause of mendelian disease - Contribution to normal disease
Describe missense mutation
- DNA change
- Incorporation of different amino acid at that position substitution
- effect on protein depends on the degree of difference between the reference and substituted amino acids
- Conservative - substitution within the same group
- Non-conservative - amino acid substitution to one in a different group
Describe Null Variants
- Nonsense
- Frameshift
- Canonical splice site variants - occur at the boundary of an exon and intron impacting splicing
- Loss of start codon
- Single exon or multiexon deletion
Describe Atheroma
intimal lesion that protrudes into vessel wall
- Raised lesion with soft core of lipid (Mainly cholesterol and cholesterol esters) covered by a fibrous cap
Commonly affected vessels:
Bifurcations, abdominal aorta, coronary arteries, popliteal arteries, carotid arteries, circle of wills
Describe atherosclerosis formation
Starts with damage or injury to the inner layer of an artery
- Development of a chronic inflammatory response of the arterial wall to endothelial injury
- Lesion progression through interactions of modified lipoproteins, monocyte-derived macrophages, T-lymphocytes and normal cell constituent of artery wall
- Fatty Streak - earliest lesion in atherosclerosis composed of lipid filled foamy macrophages - begins as multiple flat yellow spots and begin to form in adolescence
- Intermediate lesion
- Atheroma
- Fibroatheroma
- Complicated lesion
Describe a thrombus
- Solid mass of blood constituents formed within the vascular system in vivo
- Commonly superimposed on atheroma
- Venous thrombosis commonly caused by stasis
Describe Virchow’s triad
Endothelial Damage
Hypercoagulability - Heredity (Factor V Leiden, prothrombin G2021OA, Protein C and S deficiency) or acquired
Stasis
Describe an embolus
A mass of material in the vascular system able to become lodged in the vessel and block its lumen
- Most derived from thrombi
What is ischaemia and Hypoxia?
Ischaemia = interruption of blood flow to cells and tissues reducing oxygen supply
Hypoxia - when the oxygen supply to tissues is impaired
ischaemia always results in hypoxia
Describe the mechanisms of ischaemic cell injury
- Decreased oxidative phosphorylation
- Switch to anaerobic respiration
- Failure of Na pump
- Membrane damage and leakage of intracellular proteins - enzymatic digestion of cell
- Failure of Ca pump
- Decreased protein synthesis
Describe detection of ischaemic cell injury
Increased lactate
Creatine kinase, troponins - cardiac muscle damage
Transaminases, alk phosphate - liver damage
What are the 6 causes of ischaemia?
- Vascular occlusion
- Vasospasm
- Vascular Damage
- Extrinsic compression
- Mechanical interruption
- Hypoperfusion
What are the 5 factors for ischaemia outcome dependence?
- The nature of the blood supply - alternative?
- The duration of ischaemia
- The rate of vascular occlusion
- Tissue vulnerability - brain takes 3-4 mins for irreversible damage, heart takes 20-30mins
- The blood oxygen content
Describe necrosis and the two types
Coagulative - denaturation, basic outline of cell is preserved but DNA and internal material is lost - eosinophilic ghost cells
Liquifactive - enzyme digestion from inside out
What are the types of shock?
Hypovolaemic - haemorrhage and non-haemorrhagic
Cardiogenic - myopathic, arrhythmia related, mechanical, extra-cardiac
Distributive - anaphylactic, septic, TSS, neurogenic
Obstructive
Symptoms of peripheral Arterial Disease
- Hairloss of legs and feet
- Numbness or weakness in the legs
- Brittle slow growing toenails
- Ulcers on feet and legs - non-healing
- Skin colour changes
- Shiny skin
- Painful numb limb
- Wounds and ulcers
- Gangrene
What is ischaemic heart disease and its syndromes? (4)
Cardiac muscle dysfunction due to inadequate blood supply to the myocardium Syndromes: Angina pectoris Acute coronary syndrome Sudden cardiac death Chronic ischaemic heart disease
Describe MI gross morphology
< 24h - normal
1-2 days - pale, oedematous, myocyte necrosis, neutrophils
3-4 days - yellow with haemorrhage edge, myocyte necrosis, macrophages
1-3 weeks - red-grey to grey-white, pale, thin, granulation tissue then fibrosis
3-6 weeks - dense fibrous scar
Describe NSTEMI (Subendocardial MI)
- Can infarct without any acute coronary occlusion
- Normally relatively poorly perfused
- Need for oxygen cannot be met
What are the blood markers for cardiac myocyte damage (Cardiac enzymes) (5)
Troponins T&I
- detectable 2-3 hours after, peaks at 12-48 hours - detectable for 7 days post MI
Creatine Kinase MB - 2-3 hours after, peaks 10-24 hours and detectable up to 3 days
Myoglobin - peak at 2 hours and also released from damaged skeletal muscle
Lactate Dehydrogenase Isoenzyme 1 - peaks at 3 days detectable to 14 days
Aspartate Transaminase - also present in liver so less useful for cardiac damage
Describe MI Treatment
- M.O.N.A - Morphine, oxygen, nitrates and aspirin
- Reperfusion
- Ace-1, anti platelets and anticoagulation
- Anti-arrhythmics, beta-blockers
- Statins
What are some complications of MI?
- Arrhythmias, ventricular fibrillation
- Sudden death
- Myocardial rupture
- Cardiac mural thrombus and emboli
- Pericarditis
Describe familial hypercholesterolaemia
- Mutation in genes involved in cholesterol metabolism
- LDL receptor gene
- Apolipoprotein B
Describe left and right sided heart failure
Left - problems with pumping of blood outside the main circulation
Right - problems coming from the central circulation and pumping into the lungs
Describe Alzheimers disease and the two dominant genes
- Familial clustering 3 to 10 relative risk to second sibling
- Two genes dominant for Alzheimers - PSEN1 and PSEN2
- 95% multifactorial
- Most implicated because of heart disease gene APOE which has three alleles
E2 - protective effect
E3 - low risk
E4 - increased risk to 90% - Mean age of consent decreases with increased risk from 84 to 68
Describe Linkage disequilibrium
- Most disease bearing chromosomes in populations are descended from a few ancestral chromosomes
- Can detect association <2-3 cM
- Careful selection of control groups in GWAS
What are the causes of cell death? (6)
Hypoxia Physical agents - temperature, trauma, radiation Chemical agents Immunologic agents Genetic rearrangements Nutritional imbalance
What are the types of cell injury?
Reversible
- cell swelling, pallor, hydropic change, vacuolar degenerations
Irreversible
- mitochondrial swelling, lysosomes swells, damage to membranes and leakage of enzymes
Ischaemic Reperfusion Injury
- New damage on repercussion mediated by free oxygen radicals
What are the factors determining the outcome of injury?
- Ability of cells to replicate
- Ability to rebuild complicit architectural structures
Describe labile cell populations
- High normal turnover
- Active stem cell population
- Excellent regenerative capacity
Describe stable quiescent cell populations
- Low physiological turnover
Turnover can massively increase if needed - Good regenerative capacity
Describe the permanent cell populations
- No physiological turnover
- long life cells
No regenerative capacity
Describe organisation of cells (scar formation)
- The repair of specialised tissue by formation if a fibrous scar
- basic stereotyped pathological process
- Production of granulation tissue - acting as a scaffold of fibrin and removal of dead tissue by phagocytosis
- Granulation tissue contracts and accumulates collagen forming a scar - type 1 + 3
- organisation is a common consequence of pneumonia and infarction
Organised area = firm and puckered
Describe healing by first and second intention
First - Clean surgical wounds - Good haemeostasis - Edges opposed with sutures or staples Second - Wound edges are not opposed - Extensive loss of tissue - More florid granulation tissue reaction - More extensive scaring