Genetics Flashcards
What are chromosomes?
Thread like structures containing DNA and protein ball
DNA wound around proteins eg histones
What is the structure of DNA?
2 strands paired in an antiparalele fashion. Read in the 5’ –>3’ direction.
Sugar phosphate backbone is 2-deoxyribose
C1- base
C3- phosphate group
C5- another phosphate group
What elements does DNA contain?
Nitrogen, Carbon, Hydrogen, Oxygen and phosphorus
When are chromosomes visable?
When the cell is about to divide
How many copies of each chromosome in a diploid cell?
2 except X and Y
What is intaphase?
The period in which the cell is not dividing?
What happens in G1 and G2 phase?
G1 proteins from which organelles are synthesised are produced
G2 organeels grow and divide and energy stores increase
Mitosis is divided into 4 stages. WHat are these and what happens during each phase?
Prophase = chromosomes become visable and the nuclear membrane dissolves Metaphase = Chromosomes arrange themselves along the equator and centriole produce spindal fibres Anaphase = Chromatids migrate to opposite poles of the cell Telophase = Nuclear envolope reforms and the chromatids become indistinct
What are centrioles and spindal fibres made from?
Centrioles are tubular proteins and spindal fibres are microtubules
How long does the human cell cycle take and what proportion is interphase?
24 hours
90%
During DNA replication, DNA can be damaged in a number of ways. What are these and what diseases can they cause?
DNA strand break =>BRCA 1/2 or RAD51
Chemical crosslinking => xeroderma pigmentosa
Mismatched base => Lynch syndrome
What is meiosis?
When 1 parent cell produces 4 hapliod daughter cells
What happens during meiosis 1?
Homologous chromosomes pair up and the chromatids wrap around each other so crossing over occurs.
Harmologous pairs are separated such that one chromosome from each pair goes to each of the daughter cells
What happens during meiosis 2?
Chromatids move apart and 4 hapliod cells are produced with 23 chromosomes (1 copy of the genome) in each
How is genetic variation produced in meiosis?
Independent segregation (genes segregate indeendantly even if they are on the same chromosome) of harmologous chromosomes Recombination of harmologous chromosomes by crossing over
What determines the amount of protein produced by a cell?
Rate of transcription
Rate of splicing
Half life of mRNA (how long it spends in the cell)
Rate of processing of a polypeptide
How are proteins modified?
Post translational modification
Variation: What causes sequence variations with a gene?
Changes in the promoter sequence
Changes in the exon sequence
Variation: What causes sequence changes in the DNA between genes?
Single neucleotide polymorphisms
Larger deletions/duplications
What is a polymorphism?
Any variation in the human genome that does not cause a disease in its own right. It may predispose an individual to a common disease.
What percentage of the genome is coding?
2-3% of the genome is exons
What are the roles of introns?
Regulation of genes
Insulating genes from promotors
Provide substrate to expand the genome
What is a mutation?
Any heritable change in the human genome
What is a disease causing mutation?
A heritable change in the human genome that causes a genetic disorder
Mutation is common. How many genetic variations do you have that your parents d not have?
60-120. Every cell in the body has mutations caused by mitosis
What is PCR?
Polymerase chain reaction. Allows small sections of DNA (100-10000bp) to be amplified
How many base pairs usually gives a unique sequence?
16bp
What is required for PCR?
DNA fragment to be copied
DNA polymerase (thermostable) to join neucleotides together
Primers- short sequences of neucleotides that have a set of bases complementary to those at the end of a DNA fragment
Nucleotides- contain each of the 4 bases of DNA
Thermocycler- machine that varies temperature precisely over a period of time
Give an example of a thermostable DNA polymerase which is used in PCR?
Taq polymerase
What are the 3 stages of PCR and temperatures?
1) Separation of DNA strands: 95 degrees
2) Annealing of primers: 55 degrees
3) Synthesis of DNA: 72 degrees (optimum temp for DNA polymerase)
What happens when primers anneal and why is it important?
Primers anneal to complementary bases at one end of a DNA fragment which prevents the strands rejoining. Gives DNA polymerase somewhere to start as it can only add bases to an existing chain
If one allele has a mutation why is PCR useful?
You amplify the gene and get a defined difference between the volumes of mutated DNA and normal DNA so mutations are easier to spot
To identify a mutation what must be done following PCR?
Sequencing of the gene using sangar sequencing or gel electrophoresis. If there is variation in the strands you see overlap where 2 different bases are present
What is the result of a promoter mutation?
No/reduced transcription => no/reduced protein
What is the result of a mutation where the splice consensu is altered (Skip and exon)?
mRNA decay and an abnormal or absent protein
What is the result of a mutation that results in a base change that forms a stop codon?
A nonsense mutation. mRNA decay and a short or absent protein
What is the result of a mutation that results in a base chage that alters the amino acid sequence?
Missense mutation and a different protein produced
What is a triply expansion mutation?
Replication of a trinucleotide
What are the 2 types of insertion/deletion mutations?
IN frame or OUT of frame mutation
What is a de novo mutation?
A new mutation which occurs in gametogenesis
What is a genetic mosaic?
The presence of 2 or more populations of cells with different genotypes
Who is a genetic mosaic?
Everyone!
What are the 4 steps to next generation sequencing?
1) Extract gDNA
2) gDNA is fragmented into a library of small segments that are each sequenced in parallel
3) Individual sequence reads are reassembled by aligning to a reference genome
4) The whole genome sequence is derived from the consensus of combined reads
What is implied by a different base in half the reads of NGS?
Half the reads contain a varient allele- either a polymorphism or a disease causing mutation
What are the advantages and disadvantages of NGS?
+ Can identify abnormalities across a whole genome
- You have over 3 million polymorphisms but if you have a disease causing mutation it will only be one
Any change in DNA could be one of 3 things. What are they?
1) Polymorphism
2) disease causing mutation
3) Varient of unknown significance
How is a chromosome regognised?
Banding pattern with specific stains, length and position of the centromere
What is an acrocentric chromosome?
Chromosome without a p arm or a very short p arm
What are the different parts of a chromosome?
Telomere - one at each end
Centromere in the middle
q arm- bottom long arm
p arm- top short arm
What does the P arm of a chromosome code for?
tRNA and ribosomal genes
What is a balanced chromosomal rearrangement?
All the chromosomal material is present- no more or less
What is an unbalanced chromosomal rearrangement?
Extra or missing chromosomal material (usually 1 or 3 copies
Chromosomal imbalance leads to developmental disorder
What is aneuploidy?
A whole extra or missing chromosome
What is translocation?
Rearrangement of chromosomes
What is a robertsonian translocation?
two acrocentric chromosomes stuck end to end eg R(14:21)
What is cytogenetics?
How chromosomes relate to cell behaviour
Common chromosomal diseases: Trisomy 21?
Downs syndrome
Common chromosomal diseases: Trisomy 18?
Edwards syndrome
Common chromosomal diseases: 45X?
Turners syndrome
Common chromosomal diseases: 47XXX?
Triple X
Why is triple X generally well tolerated?
X inactivation
Common chromosomal diseases: 47XXY?
Klinefelter syndrome
Common chromosomal diseases: 22q11?
Digeorge syndrome (deletion of part of chromosome 22
What is the result of an unbalanced reciprocal translocation?
Miscarriage or a child with severe developmental delay
What is a reciprocal translocation?
A type of chromosome rearrangement involving the exchange of chromosome segments between two chromosomes that do not belong to the same pair of chromosomes.
Why is a large reciprocal translocation considered better than a small one?
More miscarriages but less developmental disorders
What is a monosomy?
Having a diploid chromosome compliment where one chromosome lacks a harmologus partner (deletion and leads to unbalanced chromosomes and developmental disorders.
A parent can be normal with a reciprocal translocation. Why is it then a risk for reproduction?
Some zygotes will not have normal or balanced chromosome compliments (50% will have an unbalanced rearrangement)
What is FISH and when is it used?
Fluorescent in situ hybridisation
Used for chromosome changes smaller than 5 million bp as they are too small to see down a microscope
How does FISH work?
Light up small sections of chromosome- used in clinical pathology
Targets a specific region.
You need to have an idea of the chromosome where the mutation may be as you cannot light up the whole genome
What is FISH commonly used to identify?
DiGeorge syndrome
HER2 protein expression
What is aCGH?
Array comparative genomic hybridisation
What are the advantages and disadvantages of aCGH?
- Only detect if the chromosome is unbalanced and many polymorphisms are detected
+ Most frequently used genetic test as it looks at the volume of DNA
What is somatic mosaicism?
Somatic cells of the body are of more than one genotype because cells acquire mutaions as they divide but mutations are only passed on if they occur in gametes
How could a chromosome change cause cancer?
Activate an oncogene or delete a tumour suppressor gene
How does the philadelphia chromosome cause cancer?
Translocation of chromosome 22 causing leukeamias
If you have HER2 amplification what targeted treatment can be given?
Monoclonal antibody = trastuzamab
If you have the Philadelphia chromosome what targeted treatment can be given?
Tyrosine kinase inhibaor = Imatinib
What is penetrance?
The likelihood of having a disease if you have a gene mutation. 100% means you will always get the disease if you have the mutation
What is a mendelian disorder?
A disease which is predominantly caused by a change in a single gene. High penetrance
What are the 4 types of mendelian disorders?
Autosomal dominant, autosomal recessive, X linked and Mitochondrial
Common genetic disease mutations: FGFR 3?
Achondroplasia
How is a miscarriage represented on a pedigree drawing?
triangle (unfilled)
How is parents related represented on a pedigree drawing?
Double line
What are the characteristics of autosomal dominant disorders?
One faulty copy causes the disease 100% penetrance Disease seen in all generations Severity can be variable Males and females equally effected
What is genetic heterogeneity?
The same disease may be caused by mutations in one of several genes
Is it possible for different mutations within the same gene to cause the same disease?
Yes, Think CF
Whatnare the characteristics of an autosomal recessive condition?
2 faulty copies are needed to have the disease
Often just one generation is affected
Increased likelihood in consanguineuous families
What is a consanguineuous marriage?
Marriage between 2 cousins or closer
What are the characteristics of X linked disorders?
Mutation on the X chromosome
More males affected
Females carry the mutation but do not show the majority of features of the disease
Why do female carriers of X linked diseases show minor but not major features of a disease?
X inactivation- only one X chromosome is active and producing gene product. Early in embryonic development 1 chromosome is switched off which is a random process (different in each cell)
Why is X inactivation important?
Provide gene dosage compensation in females
What happens if X inactivation doesn’t occur in females?
Some genes in the pseudoautosomal region can escape inactivation.
The XIST gene at Xq13 is essential for X inactivation and methylation is a mechanism of X inactivation
What is a copy number varient?
Extra of missing stretches of DNA
Highly prevalent in the genome and >1500 CNV known
Can de deletions or duplications
What is a multifactorial disease?
A disease which is brought about by the environment and genetics. Low penitrence and high environmental contribution. Single neucleotide polymorphisms which may predispose to a conditions.
3 million SNP in each individual when complared to the standard reference sequence
Twin studies: What percentage f DNA is shared by monzygotic and dizygotic twins?
100% monozygotic
50% Dizygotic
How do you know if a polymorphism contributes to a disease?
Is the SNP more common in those with the disease than without it
What type of disease is cancer?
A disease of somatic mosaicism. Largely caused by post zyygotic mutations
Why does the risk of cancer increase with age?
More cell divisions = greater chance of de novo mutation
Which genes promote cancer and which genes prevent cancer?
Promote = DNA damage, growth factors, oncogenes Prevent = DNA repair, tumour suppressor genes
What is the role of drug metabolism genes in cancer?
The genes produce proteins that metabolise carcinogens.
Do cancer genes have the same genome to that of the person?
No
What are driver mutations?
Mutations that drive carcinogenisis (1-10 needed for cancer)
Can be point mutations or chromosome abnormalities
What are passenger mutations?
Incidental mutations which occur because the tumour is unstable
Cancers develop genomic instability. What is this?
Cells with a high level of mutability
Cancers tend to have a variable penitrance. What does this mean?
Not everyone with the mutation will have the disease
What is the 2 hit hypothesis for rare inherited cancers?
2 copies of a gene are needed to develop cancer.
If you inherit one mutated gene you have a much greater chance of gaining an acquired somatic mutation
=> Autosomal dominant patterns of cancer
The two hit hypothesis mainly effects what type of gene mutations?
Tumour suppressor genes (retinoblastoma)
Mutations in DNA repair pathways (nucleotide excision repair gene)
How can oncogenes be activated to cause cancer?
1) Duplication of the gene
2) Activation of the gene promoter
3) Change in amino acid sequence => active protein configuration
BRAF mutations are found in which cancer and what treatment can be given?
Why are relapses almost invariable
Melanoma- activate the KRAS pathway
Vemurafenib will inhibit this activation.
Cells will adapt to find new ways to activate the pathway
HER2 amplification is found in which cancer and what treatment can be given?
Breast cancer
Trastuzumab (Herceptin)
The philadelphia chromosome is found in what type of cancers and what treatment can be given?
Leukaemia- translocation of bcr gene to ABL gene
Imatinib (inhibator of ABL oncogenes)
What is risk in association with genetics and cancer?
Function of the constitutional genotype and environment
What is behaviour in association with genetics and cancer?
A function of the somatic mutation
How common is breast cancer?
1 in 10 women in lifetime
If you have a BRCA1 gene what is your lifetime risk of breast and ovarian cancer?
80%
What is the BRCA gene?
DNA strand repair gene
How can the risk of breast cancer be modified?
Screening = breast exams and mammograms
Hormonal manipulation = tamoxifen
Surgical intervention = mastectomy/ oophrectomy
