Chapter 17 Study Guide

We will focus on only a few key concepts from this chapter. You should already be familiar with many of these concepts from other courses.

1. It is believed that the first organisms appeared on Earth around 3.8 billion years ago. What evidence do each of the following for this occurrence?
• Stromatolites

-the earliest forms of lfe for which we have clear fossil evidence
-a bulbous mass of sedimentary layers of limestone accreted by microbes over years
-within the outer layers, microbes grow as a microbial mat (sort of like a biofilm)
-outer laters of mat contain oxygenic phototrips that exude bubbles of oxygen
-a few mm below surface, red light supports bacteria photolyzing H2S to sulfate which is then reduced by lowe layers of sulface reducing bacteria

-fossils formed as layers of phototropic microbial communities grew and died their form filled in by calcium carbonate or silica
-accepted to date as eatly as 3.4 Gyr ago
-too deformed to reveal the detailed structure of cells and the biological origin of such fossils is questioned by some researchers

-mainly in isolated pools whose high salt concentration exclude predators

• Microfossils
-the most convincing evidence for ealy microbial life is the visua appearance of microfossils which are microscopic fossils in which minerals have precipitated and filled in the form of ancient microbial cells
-dated bythe age of the rock formation in which they are found, which is based on evidence like radisotope decay
-convincing oned need to sho the 3-d patterns of cells that cannot be ascribed to abiotic causes
-earliest convincing ones are from 2.0 Gyr

• isotope ratios
-may serve as a biosignature if the ratio between certain isotopes of a given element is altered by biological activity
-enzymiatic rxns are so selective for their substrate that their rates may differ for molecules containing different isotopes ex: carbob fixing enzyme rubisco fixes CO2 conting C12 rather than C13, the C12 is eventually converted to calcium carbonate → shows lower C13 contenr than CO2 deposited by abiotic processes
-fractional difference

• biosignatures

-a chemical indictor of life
-have been found that are earlier than oldest dossils
-siginificance is limited because it is hard to rule out nonbiogenic explanations

2. View the animation “Phylogenetic trees” to refresh your memory about cladograms. These trees make the assumption that the rate of nucleotide change is constant. For each of the following explain why this is not always true.
• sequences that code for functional genes change slower
• genes in rapidly replicating organisms change faster
• different environments result in different selective pressur

-functional sequences change slower→ why?
-functinal sequences: code for structures: ribosomes→ differ because theyre more important and the organism can’t survive if they change

-selective pressure: genes that provide desireable genes

phylogenetic tree: estimates the relative amounts of evolutionary divergence between the sequences
-if divergence rate over time or mutation rate is the same for all sequences compared, then divergence data can be used to infer the length of time since two species shared a common ancestor

-Maximum Parsimony: evolutionary distances are computed for all pairs of taxa based on the numbers of nucleotide or amino acid substitution between them - a proposed common ancestor is reconstructed, all possible trees comparing relative time of divergence from the common ancestor are computed -the best fit tree is the one with the fewest mutations to fit the fata

Maximum Liklihood: for each possible tree, the likelihood that such a tree would have produced the observed DNA sequences
-the probability of given mutations is based on complex statisrical calculations -require large amouns of computation but obtain the most info from the data

3. Compare the three domains of life. Traditionally trees of life have shown the Domain Bacteria branching off first (Figure 17.21), then the Arachea branching off later from the lineage leading to the Domain Eukarya. Use the information summarized in Table 17.2 to explain the evidence that supports this hypothesis.

-archaea are roughly as distant from bacteria as eukaryotes
-thee domans → Woese

-root of the tree: compare a pair of homologous genes wth one organims, homologs that diverged from a common ancestral gene and acquired distant functions

-most phylogenetic data so far indicate a root between Bacteria and the common ancestor of Archaea and Eukarya -thus Bacteria diverged before Archaea and Eukarya diverged from each other

-All domains have distinctive traits absent of scarce in the other two

Eukaryotes: have nucleus and complex membranous organelles
-mitrochondira and chloroplasts which evolved from internalized baceria
-bacteria and archaea have no nucleus and have relatively simple intracellular membranes -size is limited by diffusion across the cell membrane with occasionall exceptions
-the larger size and complexity of eukaryotic cells generally require the most high-powered sources of energy such as aerobic respiration and oxygenetic photosynthesis although some protists conduct fermentation
-prokaryores have a wider range of metabolic alternatives
-eukaryotic plans and animals have attained a degree of multicellular complexity unknnw in the prokaryotic domains

-eukarya have traits with archaea that distinguish them from bacteria -core information machinery of eukayores more closely resembles that of archaea -share closely related components of the centra DNA-RNA protein machine RNA polymerase, ribosomes and transcription factors -even hallmarks of eukayrotes like intragenic introns, the splicing machinery and the RNA interference regulatory complexes are found in archaea

-eukaryotes also share fundamental structures with bacteria that differ from those in archaea
-archaea have unique cell membrane components including ether-linked membrane lipids (deep-branching bacterial species)
-only domain archaea have species that can grow in the most extreme environments -temp above 110 or below -20 pH below 1
-archaea also have complete absence of archael pathogens of animals or plants

-although they are three distinct groups, there is gene flow unaccounted for by monophyletic descent

4. Horizontal gene transfer is now believed to be relatively common. How does this affect the reliability of phylogenetic trees? Are all genes transferred horizontally at the same rate? Why or why not?

-horizontal gene transfer is the acquisition of a piece of DNA from another cell
-DNA is transferred horizontally by plasmids, transposable elemtns and bacteriophages as well as through transpormation (bacteria and archaea)

-transfer events are rare (one in a million generations) but over time the number accumulates

-evidenceL DNA sequence whose GC/AT ratio differs from the rest of the genome

-does not occur at the same rate between more closely related taxa, transfer occurs even faster -rapid gene exchange allows pathogens to avoid the host immune system by expressing novel proteins not recognized by host antibodies

--eukaryotic genomes have many genes acquired from bacteria: most from the endosymbiotic ancestors of their mitochondria and chloroplats
-the content of their noncoding intergenic sequences and introns dervices largely from ancient viruses and retrotransposons

-the redrawn tree of life to shoe how phylogeny combines horizontal and vertical transfer

two types of genes evlve differently
-informational genes specify products essential for transcription and translation of information rich macromolecules -products include RNA polymerase, ribosomal RNAs and elongation factors
-informational genes need to interact directly in complex ways with large numbers of cellular components → thus capacity for horizontal transfer is limited

-operational genes are those whose products govern metabolism, stress resppnse and pathogeniity -function with relative interdependence from other cell components → undergo horiztonal transder more easily than do informational genes -also tend to meet conditional needs dependent on the availability of nutrients and other environmental conditions, whereas informational gene products have functions essential to cell growth under every condition

5. Why does the biological species definition commonly used for eukaryotes not work for prokaryotes? What is the definition of a bacterial species?

-eukaryotes: a species is defined by the principle that members of different species do not normally interbeed with each other -the failure to interbreed is the traditional property defining species
-bacteria and archaea interbreed asexually though, so interbreeding is not a basis for classification
-microbes transfer genes horizontally between distantly related clades
-scientists hoped that a quantitiative measure of divergence could provide a basis for defining species of asexually reproducing microbes - -but some organisms the genomes of different strains that cause the same disease differ by as much as 7%, in other cases strains of microbes with nearly identical genomes can cause completely different diseases
-phylogeny and ecology are both important
-phylogeny: a species is a group of individuals that share relatedness of a key set of house keeping genes: informational genes like ribosomal and transcriptional components -genes should all be orthologs (common function and origin) ; not paralogs (which diverged from a common ancestor but now differ in function) ecology: a species sould include individuals that share common traits and an ecological niche or ecotype ; shared traits include cell shape and nutriotnal requirements and there should be a common habitat and life history working definition of species: DNA hybridization > 70%:: when DNA from two genomes is denatured and mixed together the strands reanneal to form hybrid heix; if the propotion of hybridization is 70% or greater, the two organisms are usually the same species
SSU rRNA similarity > 97%: two organisms with 97% or greated similarity in SSU rRNA sequence are considered to share a genus –high percent due to the high conservation of rRNA sequence compared to other genes
-average nucleotide identity of orthologs > 95%: if whole genomes are available and nnotated we can define all orthologus genes shared by a pair of strains, two strains have > 95% of greater ANI for these genes = same species