Term
| What type of organism uses single stranded RNA? |
|
Definition
| HIV, flu, Ebola, Polio, Measles |
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Term
| What sort of organism uses double stranded RNA? |
|
Definition
| Blue tongue virus and rotavirus |
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Term
| What sort of organism uses single stranded DNA |
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Definition
| M13, X174, sea water viruses |
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Term
| What type of viruses use double stranded viruses |
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Definition
| Herpes, smallpox, T4, lambda |
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Term
| What is an RNA nucleotide made of |
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Definition
| Phosphate, ribose sugar, and a base |
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Term
| Two types of bonds found in nucelic acids |
|
Definition
| phospho-diester and glycosidic |
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Term
|
Definition
| double helix. why the fuck would you not just say double helix. goddamn it william |
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Term
| Evidence RNA came before DNA |
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Definition
| DNA precursors are made from RNA precursors, two different thymidylate synthetases that methylate dUMP in many organisms suggests T evolved twice |
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Term
| What does ribonucleotide reductase do |
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Definition
| makes DNA precursors from RNA precursors |
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Term
| wHY IS dna MORE STABLE THAN rna |
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Definition
| Presence of 2'OH group in ribose sugar makes RNA alkali labile, DNA has thymine instead of uracil, allowing cytidine instability to be repaired, does not fall apart when nicke, complementarity allows copies to be made, phospho-diester backbone protects from aqueous phase |
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Term
| Cytosine deamination is a what reaction |
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Definition
|
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Term
| What enzyme is used for removing Uracil in DNA |
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Definition
|
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Term
| What is base excision repair? |
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Definition
| Repairing the uracil product of cytosine deamination, also removes oxidized and alkylated bases, after removing the damaged base, AP endonuclease opens the side of the DNA the damaged base. what happens next depends on if it is a long or short patch |
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Term
|
Definition
| polymerase displaces previous bases, flap enonuclease and ligase seal new bases |
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Term
|
Definition
|
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Term
|
Definition
| Cytidine deamination gene, encodes for seven cytidine deaminases, some of which edit transfecting DNA, such as HPV, so operates as an antiviral |
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Term
| Three sorts of double helixes |
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Definition
| A-DNA, right handed used in RNA-DNA duplexes and dsRNA, B-DNA, used by ds DNA and right handed, Z DNA, left handed, formed by alternating purines and pyrimidines, biological function unproven |
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Term
| Two ways double helixes are stabilized |
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Definition
| Hydrogen bonds and hydrophobic stacking interactions, stronger at high salt concentration |
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Term
| Hydrophobic stacking interactions |
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Definition
| Van-der-waals forces between stacks of the same base |
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Term
|
Definition
| increase in absorbance(optical density of a material |
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Term
| Why do strands with high amounts of GC content have higher melting temperatures |
|
Definition
|
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Term
|
Definition
| A process used to fractionate DNA into different repeat classes. The faster it cools, the more repeated it is. Also known as Cot analysis |
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Term
|
Definition
| Bind to and recognise sequences via binding to the major groove |
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Term
| Cytidine deaminases are important for |
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Definition
| RNA editing, innate immunity to retroviruses and transpoable elements, adaptive immunity, protection from cancer |
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Term
| Two forms of ApoB proteins |
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Definition
| ApoB100, synthesized in liver, lipoprotein assembly and LDL receptor, transports lipids from liver to tissues, ApoB48 synthesized in small intestine, lipoprotein assembly domain only, required for synthesis of cylmicrons by gut |
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Term
|
Definition
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Term
| How do APOBEC proteins aid against viruses |
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Definition
| APOBEC3 targets viruses in already infected T cells with ubiquitin, so they are degraded, are also incorporated into new viral molecules, and when in a susceptible T cell they inhibit reverse transcriptase, and mutate the virus in an attempt to prevent it from working |
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Term
| Activation induced deaminase |
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Definition
| AID, needed for production of high affinity IgG and class switching(changing a B cells antibody production type) |
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Term
| How do APOBEC proteins increase immunospecificity |
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Definition
| cytidine deamination increases mutation rates by a faction of 1 million, B cells that are mutation called centrocytes, produce antibodies with a range of affinity, FDCs present antigens, ones with highest affinity bind, and and remove antigens, highest affinity survives and gives antibodies to t cells, low affinity B cells undergo apoptosis, over several generations means high affinity |
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Term
| What lead to APOBEC creation |
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Definition
|
|
Term
| Issues with cytosine deamination |
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Definition
| generates URacil, if methylated cytosine is deaminated thymine is produced, which is often not recognised as a mutation |
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Term
|
Definition
| a heritable change in phenotype that does not involve a change in DNA sequence |
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Term
|
Definition
| study of cells using a microscope |
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Term
|
Definition
| study of genetics by looking at them |
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Term
| To look at individual genes use |
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Definition
|
|
Term
| To look at copy number changes use |
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Definition
|
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Term
| Chromosomes are classified by which features |
|
Definition
| location of centromere, size and banding patterns |
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Term
|
Definition
| Near centromere and telomere, silenced genes, high AT content, stains darker |
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Term
|
Definition
| Less condensed, gene expressing, High GC content, stains lighter |
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Term
|
Definition
| p is shorter, q is longer |
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|
Term
| Four types of chromosomes |
|
Definition
Telocentric - no p arm, centromere on end
Acro-centric, very small p arm
Submetacentric p arm slightly smaller than q
Metacentric, p and q same length |
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|
Term
|
Definition
| Obtain any cell but a red blood cell, arrest in metaphase, spread out and identify staining, normally after g staining |
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Term
|
Definition
| complete extra set of chromosomes, cannot survive to birth |
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Term
| Robertsonian translocation |
|
Definition
| two q arms of different chromosomes come together and the p arms are lost |
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Term
|
Definition
| two different chromosomes exchange parts - often no effect |
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Term
|
Definition
| have two identical arms, two qs or two ps |
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Term
|
Definition
| non-disjunction occurs in both mothers and fathers gametes, two copies of one chromosome from one parent |
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Term
|
Definition
| Heart problems, learning difficulties, cleft palate, immune deficiencies 22q11.2 deletion |
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Term
|
Definition
| culture white blood cells, arrest in metaphase with colcemed, swell in hypotonic medium, fix in methanol: acetic acid: 3:1, cells swell and spill chromosomes, allow methanol and acetic acid to evaporate, incubate with trypsin, stain with giemsa |
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Term
|
Definition
| specifically staining centromeric regions |
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Term
|
Definition
| collection of microscopic DNA probeseach probe occupies a spot, when fluorescently labeled target sequences bind, can see level of activity for that area |
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Term
|
Definition
| Chromosome shattering, followed by attempted repair with some regions lost, can result in cancer |
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Term
| Characteristics of chromothripsis |
|
Definition
| lots of rearrangements, low copy number states, regions where heterozygosity is preserved |
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Term
|
Definition
| trisomy 13, microcephaly, eye defects, musculoskeletal and urogenital defects, heart defects 80% die iwthin ifrst year |
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Term
|
Definition
| X0, 45 chromosomes, ADD, broad chestm cardiac malformations, sterile |
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Term
|
Definition
| Klinefelter, male breasts, tall small testes, low iq |
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Term
| tests for karyotype abnormality |
|
Definition
| Amniocentesis, chorionic villus sampling, analysis of maternal plasma DNA - cffDNA |
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Term
|
Definition
| study of cells using a microscope |
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Term
| Polyploidy ressults in agriculture |
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Definition
|
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Term
|
Definition
| replication of the nuclear genome in the absence of cell division, |
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Term
|
Definition
| cell avoids mitosis completely |
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Term
|
Definition
| endoreplication where cell completes some parts of mitosis, but aborts before it finishes |
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Term
| Polyploidy advs and disadvs |
|
Definition
Increased size, long term genetic novelty
possible sterility |
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|
Term
| Extrachromosomal gene amplification |
|
Definition
| doesnt affect genome or germ line, massively increased rates of RNA synthesis |
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Term
| Intrachromosomal gene amplification |
|
Definition
| Creates dead-end cells with massively increased rates of RNA synthesis |
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Term
| Neutrel Indel Model shows |
|
Definition
| repeats are not subject to selection |
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Term
| Why are genomes with circular chromosomes small? |
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Definition
| They do not grow, so non-functional DNA is removed by selection, they are unstable |
|
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Term
| Why is sister chromatid exchange so dangerous for circular chromosomes |
|
Definition
| They can form a bridge, which leads to breakage, followed by fusion of the two chromatids |
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Term
| BFBs can occur on linear chromosomes if |
|
Definition
|
|
Term
| Theories for explanation of extra genomic DNA |
|
Definition
| Selfish DNA, Bulk DNA, Metabolic cost, competition, power of natural selection |
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|
Term
| Consequences of linear genome |
|
Definition
| need telomeres, and repeated sequences are common |
|
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Term
|
Definition
| Micro and mini satellites, satellites, tri-nucleotide repeats, telomeres, tandemly rep[eated families, clustered families |
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Term
|
Definition
| used to create early linkage maps, repeat CA for a few hundred bps |
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Term
|
Definition
| 5-100bp, near telomeres, contain a core of GGCAGGAXG, early use as DNA fingerprinting reagents, |
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Term
|
Definition
| CENTROMERES THAT FUNCTION OVER REGIONS OF THE GENOME THAT DO NOT USUALLY FUNCTION AS CENTROMERES |
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Term
|
Definition
| A set of homologous genes within an organism |
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Term
| Why is extra DNA a mutational liability? |
|
Definition
| Mutations in the normally silent DNA can form binding sites or promoters and influence gene transmission |
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Term
| Sequence duplication is important because? |
|
Definition
| it allows the evolution of new genes without the loss of old ones, may be responsible for what some have termed genetic redundancy, often a source of polymorphism due to variation in the number of repeats, important mutational mechanism |
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|
Term
|
Definition
|
|
Term
|
Definition
| through an RNA intermediate |
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|
Term
| Excisive transposons vs replicative |
|
Definition
| excisive move place, replicative replicate |
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|
Term
| Genetic consequences of transposable elements |
|
Definition
| can disrupt a gene by moving into it, can promote re-arrangements |
|
|
Term
| Basic minimal insertion sequence structure |
|
Definition
| simple transposon, ends inverted repeats surrounding tnp (transposase gene) |
|
|
Term
| Two ways in which excisive transposons spread |
|
Definition
| jump in front of replication fork, or jump in G2 and use sister for repair |
|
|
Term
|
Definition
| have terminal repeats but no transposase |
|
|
Term
|
Definition
| a process using transposons as vectors |
|
|
Term
| How can transposon tagging and sequencing allow us to determine gene function at a genome wide scale |
|
Definition
| Make a population of miroorganisms with as many genes as possible disrupted. Sequence transposons. To know what genes are needed for what, see which populations can do a certain thing, then sequence them and see which genes are knocked out. These genes arent needed for the thing. |
|
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Term
|
Definition
| a special class of bacterial tranposable elements in which two IS (insertion sequence) elements flank a selectable marker |
|
|
Term
| tHE ltr IN ltr RETROTRANSPOSONS STANDS FOR |
|
Definition
| LONG TERMINAL REPEAT. Again, william, just spell the words out. You only need to do it once. It takes like a second. |
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|
Term
| Life cycle of an LTR transposon |
|
Definition
| Transcription, translation, VLP (virus like particle) formation and reverse transcriptase, integration |
|
|
Term
| Important non-LTR retrotransposons proteins |
|
Definition
ORF1-NA binding protein
ORF2-Endonuclease, reverse transcriptase
UTR untranslated region |
|
|
Term
|
Definition
| Long interspersed nucleotide elements, l1 elements that can move |
|
|
Term
|
Definition
| Short interspersed nucleotide lements, use LINE machinery to move, non-autonomous |
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|
Term
| What makes heterochromatin consitutive> |
|
Definition
| Its is permanent, close to centromeres and telomeres, froms chromocentres, is genetically incative, and inactivates nearby regions |
|
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Term
|
Definition
| highly repeated strands of DNA that protect the end of the chromosomes |
|
|
Term
| Why are ciliates useful for studying telomeres |
|
Definition
| they have two nuclei, one big, one small |
|
|
Term
| What is the telomeric repeat |
|
Definition
|
|
Term
| When tetrahymena telomeres are put in yeast, |
|
Definition
| yeast telomeres grow on the end |
|
|
Term
|
Definition
| synthesizes new repeats to add to telomeres, using its own RNA component |
|
|
Term
|
Definition
| Telomerase reverse transcriptase |
|
|
Term
|
Definition
| its a catalytic subunit of telomerase, short piece on RNA that requires a 3' end as a primer, and synthesizes from 5' to 3', synthesizes one repeat then repositions itself |
|
|
Term
|
Definition
|
|
Term
|
Definition
| Alternative lengtheining of telomeres, 10% of human cancer cells, active recombination between telomeres and physical association |
|
|
Term
|
Definition
| A protein that william decided to ask a question about, and then explain, cos hes a douche, that protects telomeres from DNA repair, regulates telomerase activity and forms T loops |
|
|
Term
| which proteins are required for T loop formation |
|
Definition
|
|
Term
|
Definition
| inhibits damage response and aids formation of T loops |
|
|
Term
| POT1 what does it stand for and do |
|
Definition
| Protection of telomeres 1, protects the ends signal through ATR, regulates telomerase |
|
|
Term
| What does NERDI stand for |
|
Definition
| nuclear envelope rupturing during interphase |
|
|
Term
|
Definition
| generates ssDNA in bridges and promotes bridge resolution, is a DNAase |
|
|
Term
| Inhibition of telomerase has been suggested to, the issues with this are |
|
Definition
| treat cancer, take time to act, damage stem cells, increased chromosome instability, emergence of resistant cells using ALT pathway |
|
|
Term
| Human telomere syndromes - childhood onset |
|
Definition
| dyskeratoisis congenita, hoyeraal-hreidarsson syndrome, revesz syndrome, coats plus syndrome |
|
|
Term
| Human telomere syndromes- adult onset |
|
Definition
| Idiopathic pulmonery fibrosis, aplastic anaemia |
|
|
Term
|
Definition
| skin hympermuation oral leukoplakia, nail dystrophy, marrow failure, pulmonary fibrosis, cancer |
|
|
Term
| Hoyeraal-hreidarsson syndrome |
|
Definition
| developmental delay, immunodeficiency, cerebral hypoplasia, bone marrow abnormalities |
|
|
Term
|
Definition
| bilateral exudate retinopathey and bone marrow failure |
|
|
Term
|
Definition
| bilateral exudate retinopathy and bone marrow failure |
|
|
Term
| Idiopathic pulmonary fibrosis |
|
Definition
| autosomal dominant adult onset |
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