Chapter 7 Lec 1 + Lec 2 Flashcards
Comparative genomics (28 cards)
When did life originate on earth? And what was this 1st cellular life form?
About 3.5 BYA(Billion years ago)
Prokaryotes
True/false
Eukaryotes emerged two billion years later to prokaryotes?
True
What is the reason of prokaryotes and eukaryotes sharing enough residual similarities?
Because they have a common ancestor.
What is the result of the great diversity of living forms?
Divergence
What does sequence analysis do and in higher organisms.
It gives the most unambiguous evidence for the relationships among species.
For higher organisms, sequence analysis + classical tools (e.g. comparative anatomy, palaeontology and embryology) usually give a consistent picture.
Why is it more difficult when classifying microorganisms?
(1)Because it is less obvious how to select the features on which to classify them, (2) extensive lateral gene transfer threatens evolutionary tree entirely.
Discuss the general approaches to comparative of different species.
1) we compare genomes in a way that illuminates the relationship between humans and other species (already we’ve done human vs human-HapMap project; gene variations within populations, i.e.cancer genomics)
Who and when proposed the concept of classification?
Carl Linnaeus in the 18th century
Carl Linnaeus classification involved describing living organisms based on a hierarchical system of seven levels, name them and most living organisms are described using popular system that follows binomial description.
1) kingdom
2) phylum
3) class
4) order
5) family
6) genus
7) species
Genus and species
For macroscopic organisms, the Linnaean classification is reinterpretable as a______.which is”a set___________species”. Species are______; _____of biological thought.
Phylogenetic tree
A set of ancestor-decscent relationships between species.
Fundamentally discrete, cornerstone
Genome sequences provide the most ____,____and ____approach to definition of species. Sequence rule____,but jostle (push) for power with ________in classification of plants and animals.
General, detailed and consistent
Microbial taxonomy, traditional morphological methods
Briefly explain the concept of DNA barcoding.
This field try’s to identify species using short DNA region that occurs either in the nuclear DNA, mtDNA or cpDNA(for plants). These DNA regions are selected based on their ease of usability and other factors.
Name old vs new methods of bacterial classification.
Morphology (cell size+shape)
Biochemistry (cell staining, carbon +nitrogen sources, fermentation products)
Physiology (growth temp, range and optimum, osmotic tolerance)
Immunological cross-reactivity( especially infectious species)
True/false
Before sequencing, hybridization of DNA from two different bacteria was not a criterion for similarity- occured only if base sequence similarity is <80%.
False
Was a criterion, similarity is >80%
Following Carl Woese variations in 16S ribosomal RNA(rRNA) and other sequences which are?
If 16S rRNA sequences differ by 2.5-3% then simply different species, that’s becoz such difference corresponds to <70% similarity in overall genome sequence.
Looking at the taxonomy based on sequences, which sequences have illuminated relationships between species,both for ____and ____.
Protein, RNA and DNA sequences
Macroscopic organisms and microbes
The sequences have clarified some relationships but have exposed others as simplistic. Major results include the following:
1) All life on earth has enough general similarity to show that all life forms had a common origin. Evidence for this came from:
◇ universality of basic chemical structures of DNA, RNA and proteins
◇ universality of general biological roles
◇ near-universality of the genetic code
2) On the basis of 16S rRNAs, Carl Woese divided living things into bacteria, archaea and eukarya.
◇ while archaea and bacteria are both unicellular organisms that lack nuclei, at the molecular level archaea are somewhat more closely related to eukarya than to bacteria.
◇ recently discovered Lokiarchaeum (complex prokaryote) - bridges gap between archaea and eukaryotes; contains ~175 eukarya genes.
◇ it is also likely that the archaea are the closest living organisms to the root of the tree of life.
How do genomes help us?
They help us understand ourselves as individuals and our relationships with all other organisms that exist in life.
To make archive or make progress with how our genomes help us,we must integrate several data streams, including:
1) genome seq
2) RNA and protein expression patterns
3) the spatial organization of individuals macromolecules, their complexes, organelles, entire cells, tissues and bodies.
4) regulatory networks, the internal structure and logic of adaptive control systems.
What was S.E Luria’s suggestion?
His suggestion was that to determine common features of all life one should not try to survey everything, but,rather,identify the organism most different from us and see what we have in common with it.
Combining S.E Luria’s suggestion with a complementary idea: mention the two types of questions this combination also implies.
To take the most closely related organisms and identify the differences.
How do human genome and E.coli genome express our common heritage?
How do genomes that are over 96% identical create the differences between humans and chimpanzees?(4%difference)
With regards to genome sizes the term C-value has been used to refer to:
The amount of DNA in a haploid cell, that is, a gamete; the letter C refers to the constancy of the amount of DNA per cell in a species.
What are the general correlation between complexity of organism and amount of DNA per cell.
The more complex the organism the more DNA per cell. Vice versa.
Prokaryotes have less DNA per cell than eukaryotes.
Among eukaryotes, yeast has less than mammals.
Provide the deviations of C-value paradox, these are organisms with less complexity and more DNA per cell.
1) amoeba dubia genome is 200 times larger than the human genome.
2) marbled lungfish (Protopterus aethiopicus), a closer relative, is 43 times as large as humans.
3) clivia genome is about 6 times larger than humans (DNA in pg=genome size in bp/0.978×10^9bp.
Pg=picograms ×10^-12 g
