Cell Biology Theme 4

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  • Created by: Splodge97
  • Created on: 14-05-17 18:58
What is genomics?
Global study of genes and how they interact with the genome
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What is proteomics?
Global genome-wide study of the structure, function, activity and regulation of an organism's proteins
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What are metagenomes?
Genomes of many types of bacteria taken from swabbing a biofilm
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Describe sanger sequencing
Single-stranded DNA fragments placed in tubes with DNA polymerase, primers, free nucleotides and one type of terminator nucleotide; creates many different length strands which are analysed by gel electrophoresis.
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Describe next generation sequencing
Single-stranded DNA fragments placed into a tube wiith DNA polymerase, primers, free nucleotides and four different terminator nucleotides labelled differently; as the terminator nucleotides bind an image is taken (later images pieced together)
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What is bioinformatics?
Extraction of useful information from gene sequences by predicting where genes/regulatory sequences occur. Undergone by analysing variation between populations/species and monitoring molecular evolution.
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What are open reading frames?
Long DNA sequences starting with TAC (produces AUG on mRNA) that stretch for at least 100bp before a stop codon is present; high likelihood they will be genes
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What is ORF noise?
Large introns which may be mistaken for open reading frames
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How are open reading frames identified?
By splice sites, regulatory sequences and codon bias (organisms have a codon preference for certain amino acids)
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Why does the presence of mRNA (expression sequence tags) not guarantee expression?
mRNA degradation, protein degradation and protein activation control may prevent expression
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What is RNAseq?
Sequencing RNA from a gene and comparing it to mRNA in a cell to see if its expressed. Gives better indication of introns/extragenic sequences than using reverse transcriptase but a lack of proof reading with RNA polymerase means mistakes likely.
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What is homology?
Alignment of a sequenced genome with that of a different species to identify homologous genes (which can be modified in the model organism to identify their function)
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What is copy number variation?
Interspecies human variation which occurs due to the loss/gain of long stretches of DNA
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What are nucleotide repeat polymorphisms?
Polymorphisms resulting from different individuals having a different sumber of tandem repeats
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What is antigenic drift?
When HA and NA antigens on viruses change due to mutations caused by the lack of proof-reading of RNA polymerase
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What is antigenic shift?
Reassortment occuring when host cells are infected by two different strains of bacteria (generating novel strains which possess antigens of both original strains)
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What is epigenetics?
Enduring changes in DNA expression which don't involve changes in the DNA sequence (i.e. modifications to DNA expression rather than the genome itself)
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Give examples of epigenetics
DNA methylation at CG islands in introns (prevents RNA polymerase binding), histone modification and regulatory RNA's
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What is functional genomics?
Sequence of steps to gain information from the genome (through bioinformatics) which may be applied to proteomics
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What is the transcriptome?
Set of all messenger RNA's in one cell/a population of cells which can be used to identify if genes are expressed/rapid changes in DNA expression (more effective in comparison to detection via protein expression)
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What is necessary to perform RNAseq?
Cells must be lysed and buffers used to isolate their mRNA; a poly-T primer must then be added to the poly-A tail of the mRNA to allow reverse transcriptase to bind
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Describe in situ hybridisation
Use of enzyme/fluorophore labelled probes to identify DNA in a tissue (which has has its DNA hybridised)
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What are microarrays?
When thousands of DNA probes thought to be complementary to genes in a sample are stuck to the bottom of wells; labelled cDNA then added and washing occurs (the brighter the colour of a well the more that gene is present)
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What technique can separate denatured proteins by mass?
2D gel electrophoresis - SDS must be added so all equally negative
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Describe high performance liquid chromatography
Separates proteins - passed through small tube under high pressure containing non-polar silica molecules with hydrocarbons attached (stationary phase) and a polar solvent (mobile phase). More polar proteins attracted to mobile phase so leave faster.
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How are fragments produced for use in mass spectrometry?
Digested by enzymes with known restriction sites/restriction endonucleases (usually trypsin)
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How can the 3D structure of proteins be analysed?
X-ray crystallography (if crystallised) or NMR spectroscopy (if not crystallised)
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Why is it difficult for a protein's 3D structure to be gained from its AA sequence?
Doesn't account for proteolytic cleavage (formation of AA's/small polypeptides by proteases), folding, combination (with other proteins), chemical modifications, disulphide bond formation or intein splicing (removal of AA's, like starting methionine)
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What are biomarkers?
Molecules expressed in the lead up to a disease
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What are prognostic biomarkers?
Biomarkers allowing identification of a disease's progression
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What are predictive biomarkers?
Biomarkers indicating how a pateint has responded to treatment/how toxic a drug has been to a patient
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What is empirical medicine?
Development of drugs which work on a large proportion of the population
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What is stratified medicine?
Drugs made to affect only a group of people with a specific disease
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What is individualised medicine?
Drugs tailored to an individual by monitoring their reaction to it (tailoring the type and dose to them specifically)
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What is targeted medicine?
Drugs developed by a process of pharmacogenomics (global study of the impact of drugs on the genome); it caters to rarer diseases
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What is pharmacokinetics?
In targeted medicine, when the genetics of metabolism are studied by looking at the movement of drugs in the body
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What is the role of CYP450's and UGT's?
Enzymes which break down drugs in the body
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What is pharmacodynamics?
In targeted medicine, when the genetics of disease are studied by looking at the effects of drugs and the mechanism of their action
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What is herceptin?
A monoclonal antibody prescribed to patients with breast cancer that express an amplification of the ERBB2 gene (which encodes HER2/neu, a receptor tyrosine kinase which stimulates the divsion of cancer cells in increased numbers)
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What is personalised medicine?
Medicine encompassing specific treatment plans and investigating drugs through N-of-1 trials (effects monitored in one pateint)
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How would you look for a specific mutation in a specific gene?
Pyrosequencing (where addition of dNTP's to single strands releases pyrophosphate, converted to ATP to produce a flash of chemiluminescence which differs for each nucleotide)
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How would you look for any mutation in a specific gene?
Sanger sequencing
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How would you look for any mutation in any gene?
Next generation sequencing
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What is gene augmentation?
Where - in somatic gene therapy - gene expression increased by adding the gene into diseased cells
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What is gene mutation correction?
Where - in somatic gene therapy - enzymes are used to excise a defective allele which was producing a harmful gene product (normal allele can operate to produce the normal phenotype)
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What is gene expression inhibition?
Where - in somatic gene therapy - siRNA/ribozymes/antisense oligonucleotides degrade mRNA coding for a harmful gene product
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What are antisense oligonucleotides?
Synthetic deoxynucleotide polymers with chemically modified nucleotides complimentary to mRNA sequences (so their binding prevents translation of the mRNA by RNA polymerase)
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How can diseased cells be killed via somatic gene therapy?
Incorporation of a toxic gene so they initiate an immune response or a prodrug metabolising gene which causes them to produce a toxic product
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What is transduction (in somatic gene therapy)?
Delivery of genes via viral vectors; highly efficient but new genes may be placed in existing ones/may cause infection
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What is transfection (in somatic gene therapy)?
Delivery of genes via non-viral vectors (naked DNA, liposomes and DNA nanoparticles); no risk of integration into genome/infection but less effective
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Why is the ex-vivo technique preferable in somatic gene therapy?
Cells are removed and then vector added before culturing then re-injection of cells expressing desired modifiction; this allows greater control than injecting the vector directly (the in-vivo technique)
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Card 2

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What is proteomics?

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Global genome-wide study of the structure, function, activity and regulation of an organism's proteins

Card 3

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What are metagenomes?

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Card 4

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Describe sanger sequencing

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Card 5

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Describe next generation sequencing

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