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MIC2011
Theme 2
| Question | Answer |
|---|---|
| define genome | the complete set of genes/genetic material present in a cell or organism |
| define haploid | one set of chromsomes |
| define diploid | two sets of chromosomes |
| define genotype | specific set of genes of an organism |
| define phenotype | collection of observable characteristics |
| summary of DNA | deoxyribonucleic acid - storage molecules for genetic instructions to carry out metabolism and reproduction 4 DNA based AGCT |
| summary of RNA | ribonucleic acid - expressed the information in DNA |
| structure of DNA | - solved in 1953 - two complementary strands forming a double helix - bases on the inside, sugar-phosphate backbone on the outside - major groove and minor groove |
| bases of DNA | purine (adenine, guanine) - two rings pyrimidine (cytosine, thymine) - one ring uracil and thymine differ by one methyl group |
| sugars in RNA and DNA | RNA - ribose DNA - deoxyribose phosphate esterfied to sugar carbon |
| nucleotides | nuclei acids is a polymer of 3 components: - nitrogenous base - ribose/ deoxyribose sugar - phosphate phosphodiester bonds connect individual nucleotides -- the phosphate ester bond connect C3 (3') of one sugar with C5 (5') of another sugar |
| base pairing in DNA | adeenine and thymine - 2 hydrogen bonds guanine and cytosine - 3 hydrogen bonds |
| prokaryotic genomics | refers to the science, sequencing, mapping, analysing and comparing genomes. - quick and affordable; annotating and analyzing genome sequences is now the limiting step |
| main steps of genomic | sequencing -> mapping -> assembly -> annotation |
| analysing genome sequence | limiting factor of genomics - annotation = assigning regions likely to encode proteins (open reading frames), identifying horizontally-aquired DNA phylogenetics = comparing sequences of key genes to determine evolutionary relationships |
| analysing genome sequences p2 | function predictions = predicting the characteristics of the organsims based on the genes it contain (e.g. capsule, flagella, specific metabolic genes) |
| what is in a prokaryote genome | strong correlation between genome size and number of genes gene = DNA that encodes a protein or RNA molecules majority of the genome is dedicated to protein-coding gene sequences around 1% encodes tRNA and rRNA regulatory sequences |
| genetic material in prokaryotes | chromosome, plasmid, prophage, transposable elements (transposons) |
| chromosome in prokaryotes | - Location of most of the genetic material -Encode essential functions (DNA replication, translation, central metabolism, etc) -Replication is coordinated with cell cyle, each daughter cell gets one copy - single, circular chromosome |
| plasmids in prokaryotes | - small, extrachromosomal DNA molecules - replicate independently of the chromosome - usually circular |
| prophage in prokaryotes | - a bacterial virus genome that has integrated into the chromosome - replicated along the chromosome, until they excise and sart generating functional virus particle again |
| transposable elements (transposons) | - 'jumping gene' - move around the genome and mix things up as they go |
| mobilome | entire set of mobile genetic elements in a genome made up of plasmids, prophage and transposons important drivers of genetic variation |
| two types of genome | core genome and pan genome |
| core genome | set of genes shared by all strains of a given species |
| pan genome | all the genes that are found in a species, including those only represent in some strains. many important bacteria have large pan genomes that encode useful accessory functions pangenome deals with presence- absence gene, not allelic variation |
| why is the pangenome important | many bacteria have large pan genomes that encodes useful accessory functions - E. coli is an example. ability to cause dysentery, meningitis, UTIs, etc all due to pangenome genes such as Shiga toxin, kps cluster (encodes capsule) |
| why is the pangenome important p2 | PAI = pathogenicity island - regions of horizontally-acquired genes on the chromsome are often called 'islands' |
| gene organisation | Prokaryote genomes have relatively little noncoding DNA - Introns are rare - Gene are often organised into contiguous transcribed functional clusters each of these is called an operon - Genes in a operon are co-regulated |
| gene organisation - How does this compare with eukaryotes | In comparison with eukaryotes, prokaryotes have: Different structures for genetic material Smaller genomes Higher proportion of protein-coding sequences Simple gene structures (no introns) More horizontally-acquired DNA |
| summary week 6 - prokaryote genomes | - Prokaryotes usually ave single, circular chromsomse which encodes essential functions - Plasmids are small extrachromosomal DNA molecules that replicate independently |
| summary week 6 p2 - prokaryote genomes | - Tranposons and phages are additional mobile DNA structures, that can be located in the chromosome or on plasmids - The pangenome is the collective gene set of an entire species, including those that are only found in a few strains |
| summary week 6 p3 - prokaryote genomes | - Pangenome genes can dramatically change the function and pathogenic potential of an organism |
| sequencing | sequence reads |
| mapping | map them to reference to another genome sequence |
| assembly | assembled to another genome without other gaps |
| annotation | annotate where the functional regions are |
Created by:
redshre
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