Flashcards
Molecular Evolution and Systematics
Cards in this deck (112)
- 1Define nomenclatureProcess of naming organisms
- 2Define classificationAssignment of organisms to specific groups (taxa)
- 3Define taxonomyStudy + process of nomenclature and classification
- 4Define phylogeneticsStudy of evolutionary relationships between taxa
- 5Define systematicsOverall goal of combining taxonomy and phylogenetics
- 6What is DNA barcoding?Attempt to use 1/a few genes/gene fragments to identify species
- 7What is metabarcoding?Where all/most of individuals in diverse communities are identified
- 8Reliable barcoding depends heavily on high quality ____a____ identification of material deposited on the database. Also requires high quality ___b___ sequenced correctly.a - taxonomic
b - specimen - 9Wales have led the field of DNA barcoding with the project aiming to........barcode all flowering plants and conifers (98% at least)
- 10When do the International Barcode of Life (IBOL) aim to have sequenced all life on Earth?2045
- 11What do recent studies suggest as the origin of eukaryote cells?within an archaeal domain of life
- 12What is the name of the Archaea with the most eukaryotic-like genes?Lokiarchaeota
- 13Who propose the "Eocyte Tree"?Williams et al., 2012
- 14A change in perception suggests that eukaryote genomes are ___a___ of many lateral gene transfer events, probably from _____b_____ of food (bacteria).a - chimeras
b - phagocytosis - 15Brusatte et al., 2015 "Brids evolved from dinosaurs and therefore are dinosaurs, in the same way that ___a___ are a type of ___b___".a - humans
b - mammal - 16When were virtually all modern birds (Neoaves) in existence by?50 Mya
- 17True or False? Dinosaurs evolved before feathers.False - Feathers evolved before dinosaurs
- 18What is classed as ancient DNA?>75 years and up to a few thousand years old.
Upper limit = ~100,000 years due to natural DNA breakdown - 19What did the de-extinction programme of E. quagga, established in 1987, produce?virtually identical morphotypes to original quagga.
- 20What did phylogenetic analysis of preserved E. quagga DNA show?That E. quagga is a subspecies of plain zebras.
- 21What properties of DNA make it a good information-storing molecule?- Durable, double-stranded polymer
- Orientated strands (3' and 5')
- Genetic coding = sequence of the 4 nucleotide bases
- Complementary base pairing - 22What bonds are form the backbone of DNA?phosphodiester bonds
- 23If you have more A and G nucleotides in one strand, what can you call the complementary strand + why?The 'light strand' as it will have less A + G bases (double-ringed purines) due to complementary base pairing
- 24How many hydrogen bonds can be found between G + C?3
- 25How many hydrogen bonds can be found between A + T?2
- 26What is standard base pairing also called?Watson-Crick pairing
- 27During DNA replication, what are added in a complementary form to the template strand?Nucleoside triphosphates (NTPs)
- 28In DNA replication and RNA synthesis (e.g. transcription), which 'end' is always created first?The 5' end. Complementary bases are added to the 3' end of the template strand.
- 29How does DNA polymerase catalyse the addition of complementary bases to nucleotides on the template strand?It strips off 2 phosphates from NTPs and bonds between base pairs form (1 phosphate used in bonding of sugar-phosphate backbone)
- 30DNA replication is semi-conservative. What does this mean?Each strand acts as a template for a new double helix (so DNA generates daughter DNA molecules that are exact copies of the original DNA)
- 31Does DNA polymerase catalyse (a) phosphodiester bond formation between NTPs and the sugar-phosphate backbone or (b) hydrogen bonds between bases?(a)
- 32In transcription, why is the non-template strand called the 'coding strand' even though its not translated?As the mRNA synthesised from the template DNA strand has a sequence that is identical to the non-template strand.
- 33What do ribosomes catalyse?Binding of tRNA to mRNA
- 34Where in nature are there slight differences in tRNA coding of amino acids?In different taxa and between nuclear + plastids (mitochondrial + chloroplasts) DNA
- 35In how many cases does the standard tRNA code work?~90%
- 36What is meant by amino acid binding/genetic code being 'degenerate'?Diff mRNA codons can code for the same amino acid.
Non-specificity in the 3rd base of anticodons, allowing them to bind to different mRNA codons, e.g CUC + CUU bind to the same leucine-binding tRNA anticodon (GAG). - 37What is the central dogma?DNA -> mRNA -> protein
- 38Name some other pathways that go beyond the central dogma.- Protein -> DNA that doesn't occur in nature
- DNA + RNA replication
- Reverse transcription - 39What is the main vehicle for reverse transcription?Retrotransposons
- 40Where did retrotransposons arise from and where are they found?Elements incorporated into the genome that arose through viruses
- 41What do retrotransposons use to replicate RNA?RNA-dependent RNA polymerases (RdRp's)
- 42What are RNA-dependent RNA polymerases used for in eukaryotes?Gene silencing/interference + micro RNA (miRNA) replication
- 43How many proteinogenic (protein-coding) amino acids are there? + How many are found in humans?22, 20 of which are found in humans
- 44True or False? Some amino acids are more closely related to each other than others.True - for example some are large, +ve, -ve, etc.
- 45What is the impact of a non-synonymous mutation dependent on?How closely related the new amino was to the original one (i.e. how functionally different it is)
- 46What is the primary protein structure?Amino acid sequence
- 47What is the secondary protein structure?- Alpha helices + Beta-pleated sheets
- Dependent on primary structure - 48What is the tertiary structure of a protein?Overall relationships between different motifs (distinctive sequences). E.g. how an alpha helix may or may not interact with a beta-pleated sheet.
- 49What is the quaternary structure of a protein?Many polypeptides interacting + binding to form whole protein (usually requires chaperones to form correctly).
- 50What does protein structure ultimately depend on?Primary structure of a protein
- 51_a_ and _b_ protein structures form spontaneously but _c_ and _d_ protein structures vary in the cell, depending on how they were produced and how they where ____e____ into the right structure.a - primary
b - secondary
c - tertiary
d - quaternary
e - chaperoned - 52Give an example of proteins that aren't intrinsically structured.Glycoproteins - may attach variable-length oligosaccharide side chains onto the protein core, depending on the cell environment.
- 53True or False All mutations are equal.False - There are variable and non-variable regions on proteins, depending on how severely the regions affect the structure and function of the protein if mutated.
- 54What will happen to a mutation if it is severe to protein function?It will be removed from the population
- 55How much of the human genome is made up of protein-coding DNA?Only ~2-3%
- 56Why is sequence data better for phylogenetic reconstruction than morphological characteristics?- DNA + AA strictly heritable
- Sequence data is unambiguous + precisely measured
- Molecular characters evolve at a more regular rate and so better at showing relationships between taxa
- Sequence data more open to stat analysis
- Easier to verify homology of diff genes
- Some molecular data are robust measures of long-term evolutionary divergence
- More molecular characters than morphological ones - 57What does "sense" mean?The way you read it ('sense' of direction)
- 58What is the minimum primer length?~15 bases
- 59What are the 3 PCR steps and what temperature are they carried out at?1) Denaturing -> 94-96 degrees
2) Annealing -> ~45-55 degrees
3) Elongation -> 75-80 degrees - 60What occurs in the 'denaturing' phase of PCR?H bonds break + DNA 'unzips'
- 61What occurs in the 'annealing' phase of PCR?Primers bind to separated strands
- 62What occurs in the 'elongation' phase of PCR?DNA polymerase (Taq) catalyses the addition + bonding of NTPs to the 3' end of primers to create new amplicons (DNA strands)
- 63Why is the 'annealing' step of PCR specific in temperature?As temperature during this step needs to be hot enough to break however many G-C bonds there are, but also be cool enough so primers can bond
- 64What would happen if the temperature was too low in the annealing step of PCR?The whole DNA would re-anneal
- 65Apart form the complementary DNA sequence, what else can primers bind to during the annealing stage of PCR?Other primers to form primer dimers
- 66What is the first (+ last) part of sequence data and what do you need to do with this?Primer sequences, these need to be trimmed
- 67When do terminated dsDNA products begin to accumulate exponentially in PCR?After 3rd cycle
- 68If the reading frame for protein-coding regions is incorrect, what will it contain by chance?'Stop' codons
- 69What are the main genes that aren't protein-coding?Ones coding for functional RNA (transcribed into RNA but not translated into protein)
- 70What is the main function of functional RNA?Mainly control gene expression
- 71Why can functional RNA be useful markers of distant genetic relatedness?As they're typically highly conserved through evolution, as failure of these controlling molecules will normally be fatal.
- 72What are some examples of non-coding parts of protein-coding genes?- "Flanking regions" -> not transcribed but control initiation (e.g TATA box), tempo, timing and tissue-specificity of transcription
- Some sections of primary transcript aren't translated but control form + function of mRNA
- Introns in eukaryotes - 73What are "Flanking regions" AKA?"Promoters"
- 74What % of the human genome consists of exons?Only ~1.5%
- 75What AA does the initiation/start codon code for in eukaryotes?Methionine
- 76What were introns originally perceived as?- 'Junk DNA'
- Remnants of protein domains that had become inactivated, or retrovirus that had become inactivated but not eliminated - 77What was shown in some cases when introns were removed, suggesting some regulatory control?Proteins shown not to be expressed or over-expressed
- 78When can some introns be expressed and what does this allow?Under certain cellular conditions, allowing modification of expressed protein structure and function
- 79What are some examples of DNA that isn't transcribed?- Regions involved in promotion, suppression, coregulators of protein expression + DNA replication
- "Pseudogenes" -> non-functional coding regions that have a gene product that is inactive/non-functional due to mutations
- "Telomeres" + "Centromeres" (structural DNA elements) - 80What are "Telomeres"?Structural DNA elements that stabilise chromosome structure + prevent erosion at the end of the chromosome
- 81What are "Centromeres"?Structural DNA elements that provide attachment points for spindle machinery during cellular division
- 82What % of genes in humans overlap?~3%
- 83What is the major way of classifying mutations?Based on length of the sequence affected (point + segmental)
- 84When do point mutations usually occur?During DNA replication - when bases are replaced by unusual structural forms that pair with non-standard bases
- 85What are the two forms of point mutations?Synonymous (same AA coded) + Non-synonymous (different AA coded)
- 86What are the two types of synonymous point mutations?Silent -> Same AA
Noisy -> Same AA but coding sequence also used as attachment point for regulatory proteins - 87What are the three types of non-synonymous mutations?Missense -> AA to different AA
Nonsense -> AA to STOP codon
Sense -> STOP to AA - 88What must occur for a mutation to become fixed in a population?Needs to be passed to offspring and enough individuals in the population need to have it
- 89What % of random point mutations are expected to be missense?71%
- 90There is an increased chance of a synonymous mutation (_a_%) in the 3rd base of a triplet codon due to ____b____ in the genetic code.a - 69
b - redundancy - 91Point mutations that occur frequently can cause problems in sequencing but can also be useful........markers of variation
- 92What are point mutations called?Single Nucleotide Polymorphisms (SNPs)
- 93What diseases can SNPs cause?Sickle cell anaemia, Beta - thalassemia, cystic fibrosis, etc.
- 94What are the three types of segmental mutations?- Recombinations
- Indels
- Inversions - 95When do recombination segmental mutations usually occur?From chromosomal cross-over in cell division + insertion of retroviral sequences (retroviral sequences and retrotransposons)
- 96Double-strand breaks (DSBs) that allow recombination usually occur in........hotspots in intergenic (between genes) regions or possibly in a coding sequence
- 97Why are insertion/deletion mutations called indels?As normally don't know which was the ancestral state
- 98Where are indels fatal?In coding regions (2/3 cause frameshifts)
- 99What do indels cause in terms of chromosomes?Unequal crossing-over
- 100When can inversion mutations occur?Via intra-chromosomal crossing-over
- 101__a__ mutations = random + chronic __b__ mutations = sporadic + more profound effects on evolutiona - point
b - segmental - 102What are the arguments for saying mutations are not random?- Some sites mutate more due to different forms of bases occuring
- Transitions (purine -> purine) more likely
- Missense more likely than synonymous (except at 3rd base of a codon)
- Vary among taxa, gender, dev stage, + in relation to mutagens exposure - 103What is the arguments for saying mutations are random?- Advantageous and disadvantageous or benign mutations are all equally likely to occur
- 104in the 1930s, who synthesised (a) Natural Selection and (b) Genetics?(a) Darwin
(b) Mendel - 105How was the idea of 'lots of genetic variation within species' proven in the Mid 60s + Who by?Via protein electrophoresis methods, mainly by Lewontin et al
- 106What is the main question from the 60s onwards regards genetic diversity?What controls the high levels of genetic diersity?
- 107There was a major divide in the 70s and 80s regards evolutionary theory. What was it regarding?The relative importance of random genetic drift vs natural selection
- 108____A____ believe that gene substitutions occur as a result of _____B____ selection, where an allele predominates only if it improves ____c____.a - Selectionists
b - positive
c - fitness - 109How do Selectionists believe polymorphic alleles arise?Via balancing selection, e.g. variable environments favour different alleles (sickle cell anaemia)
- 110What is Balancing Selection?Selective processes by which different alleles are kept in the gene pool of a population at frequencies above that of gene mutation.
- 111What are Polymorphic Alleles?2+ alleles that occupy the same gene's locus
- 112In contrast to the Selectionist view, what did Kimura (1968) propose?The "Neutral Evolution Theory", where genetic drift was the main factor causing evolutionary change, not selection.
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- Flashcards on Molecular Evolution and Systematics, created by George B-T on 14/04/2022.
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