Chapter 7 Lec 1 + Lec 2

Question 1

When did life originate on earth? And what was this 1st cellular life form?

Answer 1

About 3.5 BYA(Billion years ago)

Prokaryotes

Question 2

True/false

Eukaryotes emerged two billion years later to prokaryotes?

Answer 2

True

Question 3

What is the reason of prokaryotes and eukaryotes sharing enough residual similarities?

Answer 3

Because they have a common ancestor.

Question 4

What is the result of the great diversity of living forms?

Answer 4

Divergence

Question 5

What does sequence analysis do and in higher organisms.

Answer 5

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.

Question 6

Why is it more difficult when classifying microorganisms?

Answer 6

(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.

Question 7

Discuss the general approaches to comparative of different species.

Answer 7

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)

Question 8

Who and when proposed the concept of classification?

Answer 8

Carl Linnaeus in the 18th century

Question 9

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.

Answer 9

1) kingdom
2) phylum
3) class
4) order
5) family
6) genus
7) species

Genus and species

Question 10

For macroscopic organisms, the Linnaean classification is reinterpretable as a______.which is”a set___________species”. Species are______; _____of biological thought.

Answer 10

Phylogenetic tree

A set of ancestor-decscent relationships between species.

Fundamentally discrete, cornerstone

Question 11

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.

Answer 11

General, detailed and consistent

Microbial taxonomy, traditional morphological methods

Question 12

Briefly explain the concept of DNA barcoding.

Answer 12

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.

Question 13

Name old vs new methods of bacterial classification.

Answer 13

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)

Question 14

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%.

Answer 14

False

Was a criterion, similarity is >80%

Question 15

Following Carl Woese variations in 16S ribosomal RNA(rRNA) and other sequences which are?

Answer 15

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.

Question 16

Looking at the taxonomy based on sequences, which sequences have illuminated relationships between species,both for ____and ____.

Answer 16

Protein, RNA and DNA sequences

Macroscopic organisms and microbes

Question 17

The sequences have clarified some relationships but have exposed others as simplistic. Major results include the following:

Answer 17

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.

Question 18

How do genomes help us?

Answer 18

They help us understand ourselves as individuals and our relationships with all other organisms that exist in life.

Question 19

To make archive or make progress with how our genomes help us,we must integrate several data streams, including:

Answer 19

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.

Question 20

What was S.E Luria’s suggestion?

Answer 20

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.

Question 21

Combining S.E Luria’s suggestion with a complementary idea: mention the two types of questions this combination also implies.

Answer 21

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)

Question 22

With regards to genome sizes the term C-value has been used to refer to:

Answer 22

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.

Question 23

What are the general correlation between complexity of organism and amount of DNA per cell.

Answer 23

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.

Question 24

Provide the deviations of C-value paradox, these are organisms with less complexity and more DNA per cell.

Answer 24

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

Question 25

Why do we get different amounts of DNA?

Answer 25

1)Because most of the human genome does not encode proteins or RNA.
•regions of genomes without known function are often called ‘junk DNA’
•however, unknown function does not mean no function
•Also, not all regions are transcriptionally inert/inactive- some, encode novel types of RNA molecules, mostly involved in regulatory processes.

2)further, amount of space between Gene’s affect the rate of crossing over(as well as recombination) and thereby,rates of evolution.

• large amount of repetitive sequence between our genes enhance recombination rates by promoting homologous recombination
• change in gene sequences allude to evolution taking place; rate of evolutionary change is a characteristic of a species that is certainly subject to selective pressure.
• features of the genome that affect rate of evolution cannot be dismissed entirely as junk
• overall, different amounts of DNA in genomes provide different ‘theatres ‘ for evolutionary play

Question 26

If genome size per se does not single out humans from other species, what about numbers of genes? Again there is general correlation between complexity of organism and est. numbers of genes.

Answer 26

• viral genomes encode only a few proteins (i.e.contain a few genes)
• prokaryotes genomes contain 100s or 1000s of genes.
• yeast has almost 6000 genes, fewer than twice as many as E.coli
• metazoa (e.g.animals,plants,etc) have tens of 1000s of genes

Question 27

However, within groups of related organisms, including vertebrates, there is no simple correlation between apparent complexity of an organism, or even genome size, and numbers of genes.

Answer 27

• pufferfish and humans, seem to have roughly the same number of genes (~23K),but differ by almost an order of magnitude in genome size(365 Mbp vs 3289 Mbp)
• surprisingly, C.elegans (100 Mbp,19000 genes) appears to have more genes than the fruit fly(122 Mbp,13000 genes)

Question 28

Why has it been difficult to get accurate gene number of complexity vs genome organization?

Answer 28

Gene definition; alternative splicing; RNA editing; antibodies ( DNA-level splicing)