Evolution
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| Biochemistry | chemistry that deals with the chemical compounds and processes occurring in organisms
deals with the structure and function of cellular components such as proteins, carbohydrates, lipids, nucleic acids and other biochemicals
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| Metabolome | all the small molecule components of living cells
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| RUBISCO | enzyme that fixes CO2 during photosynthesis
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| methanogens | live off CO2 and H2 by producing methane
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| What isotope of carbon is preferred by living organisms (in carbon fixation)? | C12
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| methanogens second carbon fixation mechanism | reductive carboxylation of acetyl-CoA to pyruvate by pyruvate: ferredoxin oxidoreductase as part of reductive TCA cycle
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| isotope effect | preference of lighter isotope of carbon common in enzymatic reactions
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| How do we tell the difference between organic matter and carbon from non-biological material? | Organic material has a carbon isotope ratio the reflects depletion of heavier isotopes; non-biological carbon material has a different ratio
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| Graphite | contains loght carbon signature and therefore must be derived from living cells
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| First evidence for life on Earth | Graphite from Greenland-3.85 billion years ago (challenged)
nearby rocks determine genuinely 3.78 billion years ago
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| Fossil Stromatolites | 3.43 billion year old photosynthetic (earliest not oxygenic) bacterial mats that look similar to modern day stromatolites that are still growing (show same types of layers)
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| Photosystem I | -anoxygenic (no oxygen byproduct)
-gets electrons from source besides water
-electrons possibly from ferrous ion (Fe2+)
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| Oxidation of ferrous ion in photosystem I | -forms ferric ion (Fe3+)
-ferric reacts with water to form Fe(OH)3
-precipitates over time, dehydrates to form hematite (Fe2O3)
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| Hematite | Fe2O3
-major form of iron in BIF
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| BIF | banded iron formations found all over the globe from 3.7-1.8 billion years ago
-indirect evidence for life from 3.7 billion years on (world-wide oxidation of the iron was caused by living organisms)
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| Ferrous ion | Fe2+
-abundant in early oceans
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| Ferric ion | Fe3+
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| Photosystem II | oxygen reacts directly with ferrous ion to form hematite
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| Great oxygen event | GOE
appearance of oxygen in the atmosphere
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| What may have caused the great oxygen event? | global glaciation caused by the evolution of cyanobacteria with photosystem II producing oxygen and depleting methane (green house gas) from the atmosphere
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| Steranes | Biomarker molecules made by eukaryotes need O2: evidence 2.7 billion years ago
-doesn't make sense bc O2 showed up 2.4 billion years ago
--steranes were newer and made their way down
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| What does the presence of oxygen coincide with? | photosynthesis 2.4 billion years ago
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| Hopanes | biomarker molecules made by bacteria
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| Microfossil evidence | earliest candidates 3.3, 3.46, and 3.49 billion years ago
cyanobacterial microfossils- 2.7
eukaryotic- rare until 850 million years ago
Large colonial organisms with growth in O2= 2.1 billion years ago
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| DNA/RNA | -nucleic acid informational molecule (all living organisms have one or the other)
-encodes information to make living cell
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| How are nucleic acids coded? | triplet code
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| Ribosome | complex machinery that interprets nucleic code into proteins, common among all living things
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| What is the evidence for all living things to have a common ancestor? | All living things have ribosomes and nucleic acid molecules
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| What is used as a universal sequence that is used to make the tree of life? | 16s ribosomal RNA
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| Carl Woese | made first rRNA trees and named a new branch Archaebacteria
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| Theories on Archaebacteria | 1. novel group of organisms, equally different from bacteria and eukaryotes
2. younger bacterial branch derived from gram-positive actinobacteria and sisters to eukaryotes
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| Root of tree of life theories | 1. Cavalier-Smith
2. Koonin
3. Valas and Bourne
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| Cavalier-Smith | root between chlorobacteria and other gram negatives (negibacteria), archaea and eukaryotes evolved from gram-positive actinobacteria
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| Koonin | root lies between Archaea and bacteria; network analysis supports
points out flaw in Cavalier-Smith (called for rapid evolution in archaea which is not true)
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| Valas and Bourne | archaea evolved from gram positive bacilli
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| What is the latest argument for the root of the tree of life? | root between two equally ancient prokaryotic groups: archaea are not much younger and not derived from actinobacteria
Not eukarya because they are derived from others
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| 3 domains of life | archaea, bacteria, eukaryotes
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| ribonucleotide reductase | Enzyme required to make DNA nucleotides starting from RNA nucleotides
-unusual free radical mechanism
-all three classes of ribonucleotide reductase descended from common ancestor- DNA last to evolve
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| Of the three biomolecules, which evolved last? | DNA
-there was a time when only RNA and protein existed
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| What was the first evidence that RNA had enzymatic activity? | RNA splices introns out of itself without proteins (type I or II introns are self splicing)
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| the RNA world | life without DNA or protein
- complete DNA to RNA to protein apparatus was not needed
- protein enzymes not needed early (everything catalytic can be done by RNA)
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| Ribosome | formation of peptide bonds is catalyzed by the RNA part of the ribosome, not the protein part
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| messenger RNA | key ingredient in information transfer
-many viruses use RNA as the main informational macromolecule
-RNA preceded DNA as first info macromolecule
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| SRP | signal recognition particle
-contains essential 7SL RNA
-derived from ancient ribosomal large subunit, bound to membrane
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| Sec system | binds SRP
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| RNAase P | protein RNA complex needed for maturation of the 5'end of tRNAs
-RNA and protein subunit
-in bacteria, RNA is responsible for enzymatic activity (protein enhances 20 fold)
-eukaryotes- have RNAase P and RNAase MRP
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| snRNAs | small nucleolar RNAs
needed to process mRNA for export to cytosol by removing type II introns (enzymatic activity of splicing)
-evolved from from group II introns
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| tRNAs | predate protein synthesis
-anticodon loop later evolutionary development
some have specific catalytic roles
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| tRNA in heme biosynthesis in plants | formation of delta aminolevulinate
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| AA-tRNAs | amino acid donors in bacterial peptidoglycan syntheses and in formation of Ala-phophatidyl glycerol and Lys-phosphatidyl glycerol in bacteria
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| Ser-tRNA | used in pathway to make valinomycin
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| Ribozymes | -have few useful structures to catalyze reactions and need many coenzymes to add necessary functionality
-bind coenzymes more readily if contain nucleotides that H bond with the RNA nucleotides
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| Coenzymes | -many contain ribose and not deoxyribose
-nucleotide part does not participate in reactions
-helps protein recognize and bind coenzyme
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| ATP | major energy currency of the cell
-ribose containing nucleotide
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| Telomerase | ribonucleoprotein complex that restores the ends of eukaryotic linear chromosomes
*only in eurkaryotes: probably not an RNA world relic
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| LUCA | last universal common ancestor
core gene set- 669 genes
prokaryote with a cell wall and lipid bilayer, incorporating membrane proteins, probably used electron transport (electron acceptor was Fe3+ or sulfur compound) and proton pump for ATP synthesis
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| LUCA contd. | ability to make many coenzymes and other special molecules (heme, flavins, iron sulfur centers)
DNA to RNA to protein
DNA and RNA polymerase present
protein export machinery: cell wall
lipid synthesis: ester-linked lipids
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| LUCA contd. contd. | biochemical pathways for purines, pyrimidines, 20 AA
unsure about photosynthesis
-older than 3.5 billion years=no photosynthesis
-stromalites suggest photosynthesis
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| What are the two proposals on how eukaryotes evolved? | endosymbiosis and direct evolution model from a bacteria with only one membrane (gram positive) and loss of murein cell wall
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| What gave rise to gram positive bacteria? (endosymbiosis theory) | Gram negative bacterium with 2 phospholipid bilayer membranes and murein and peptidoglycan cell wall between them with photosystem I only. Photosystem II evolved and outer leaflet of outer membrane is replaced with LPS (need transport system across)
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| Argument against endosymbiosis | merging of an archaea and proteobacterial cell is hard to imagine because both have cell walls
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| How did gram positive give rise to archaea and bacteria? (endosymbiosis theory) | Loss of cell wall and cell sruface is modified to incorporate Asn-linked glycoproteins. This cell evolves sterol biosynthesis and phosphatidyl inositol
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| Archaea line(endosymbiosis theory) | adapt to hot environments by changing their membrane lipids from acyl ester-linked phospholipids to ether-linked isoprenoid lipids
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| Eukaryotic line (endosymbiosis theory) | evolves cytoskeleton with actin and tubulin and a nucleus and internal membranes form. cell becomes phagocytic and forms endosymbiosisis with an alpha proteobacterium that becomes mitochondrion; all eukaryotes descend from this cell
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| New: Negibacteria endosymbiosis theory | gram negative bacteria may be the result of endosymbiosis of an Actinobacterium and a Clostridium (two bacteria with single lipid membrane)
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| Evidence for negibacteria endosymbiosis theory | -inner membrane of gram negative looks like only membrane of other bacteria
-contains photosynthetic membrane proteins, ion pumps, transporters and flagella
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| Peptidoglycan cell wall evidence for negibacteria endosymbiosis theory | peptidoglycan cell wall is outside of the gram positive bacteria, and outside of the inner membrane of gram negatives
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| Unikonts | eukaryotes that descended from a cell with one flagellum
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| bikonts | eukaryotes that descended from a cell with 2 flagellum
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| What are the six major supergroups in eukaryotes? | 2 unikonts: Opisthokonts and Amoebozoa
4 bikonts: Plants, chromalveolates, Rhizaria, and excavates
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| Opisthokonts | animals and fungi
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| Amoebozoa example | Dictyostelium
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| Examples of Chromalveolates | malaria, diatoms, paramecium
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| Rhizaria example | foraminifera
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| Examples of Excavates | trypanosomes, euglena, giardia
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| What is the major goal of evolutionary biology? | decide relationships between 6 supergroups and understand the evolution of eukaryotes
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| What are the POSSIBLE 3 megagoups of eukaryotes? | unikonts, bikonts, excavates (will probably join the other bikinis)
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| Where does Cavalier-Smith propose the root of eukaryotes is? | between Euglenozoa and other eukaryotes
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| Why use a small number of genes to produce a tree? | Many species do not have many sequences
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| Phylogenomics | intersection of evolution and genomics
-comparison of whole genomes
-higher signal to noise ratios in phylogenetic trees
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| GenBank | store DNA sequence data; replace protein sequencing
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| FASTP | sequence comparison program
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| Orthologs | genes descended directly from a common ancestral gene by speciation and usually have the same function
-identified by BLAST hits
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| COGs | group of orthologous genes from at least three different genomes that are not closely related
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| KOGs | equivalent group of orthologous genes found in eukaryotes
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Created by:
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