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Lecure 1- Nelson


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
Metabolome all the small molecule components of living cells
RUBISCO enzyme that fixes CO2 during photosynthesis
methanogens live off CO2 and H2 by producing methane
What isotope of carbon is preferred by living organisms (in carbon fixation)? C12
methanogens second carbon fixation mechanism reductive carboxylation of acetyl-CoA to pyruvate by pyruvate: ferredoxin oxidoreductase as part of reductive TCA cycle
isotope effect preference of lighter isotope of carbon common in enzymatic reactions
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
Graphite contains loght carbon signature and therefore must be derived from living cells
First evidence for life on Earth Graphite from Greenland-3.85 billion years ago (challenged) nearby rocks determine genuinely 3.78 billion years ago
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)
Photosystem I -anoxygenic (no oxygen byproduct) -gets electrons from source besides water -electrons possibly from ferrous ion (Fe2+)
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)
Hematite Fe2O3 -major form of iron in BIF
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)
Ferrous ion Fe2+ -abundant in early oceans
Ferric ion Fe3+
Photosystem II oxygen reacts directly with ferrous ion to form hematite
Great oxygen event GOE appearance of oxygen in the atmosphere
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
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
What does the presence of oxygen coincide with? photosynthesis 2.4 billion years ago
Hopanes biomarker molecules made by bacteria
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
DNA/RNA -nucleic acid informational molecule (all living organisms have one or the other) -encodes information to make living cell
How are nucleic acids coded? triplet code
Ribosome complex machinery that interprets nucleic code into proteins, common among all living things
What is the evidence for all living things to have a common ancestor? All living things have ribosomes and nucleic acid molecules
What is used as a universal sequence that is used to make the tree of life? 16s ribosomal RNA
Carl Woese made first rRNA trees and named a new branch Archaebacteria
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
Root of tree of life theories 1. Cavalier-Smith 2. Koonin 3. Valas and Bourne
Cavalier-Smith root between chlorobacteria and other gram negatives (negibacteria), archaea and eukaryotes evolved from gram-positive actinobacteria
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)
Valas and Bourne archaea evolved from gram positive bacilli
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
3 domains of life archaea, bacteria, eukaryotes
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
Of the three biomolecules, which evolved last? DNA -there was a time when only RNA and protein existed
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)
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)
Ribosome formation of peptide bonds is catalyzed by the RNA part of the ribosome, not the protein part
messenger RNA key ingredient in information transfer -many viruses use RNA as the main informational macromolecule -RNA preceded DNA as first info macromolecule
SRP signal recognition particle -contains essential 7SL RNA -derived from ancient ribosomal large subunit, bound to membrane
Sec system binds SRP
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
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
tRNAs predate protein synthesis -anticodon loop later evolutionary development some have specific catalytic roles
tRNA in heme biosynthesis in plants formation of delta aminolevulinate
AA-tRNAs amino acid donors in bacterial peptidoglycan syntheses and in formation of Ala-phophatidyl glycerol and Lys-phosphatidyl glycerol in bacteria
Ser-tRNA used in pathway to make valinomycin
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
Coenzymes -many contain ribose and not deoxyribose -nucleotide part does not participate in reactions -helps protein recognize and bind coenzyme
ATP major energy currency of the cell -ribose containing nucleotide
Telomerase ribonucleoprotein complex that restores the ends of eukaryotic linear chromosomes *only in eurkaryotes: probably not an RNA world relic
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
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
LUCA contd. contd. biochemical pathways for purines, pyrimidines, 20 AA unsure about photosynthesis -older than 3.5 billion years=no photosynthesis -stromalites suggest photosynthesis
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
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)
Argument against endosymbiosis merging of an archaea and proteobacterial cell is hard to imagine because both have cell walls
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
Archaea line(endosymbiosis theory) adapt to hot environments by changing their membrane lipids from acyl ester-linked phospholipids to ether-linked isoprenoid lipids
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
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)
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
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
Unikonts eukaryotes that descended from a cell with one flagellum
bikonts eukaryotes that descended from a cell with 2 flagellum
What are the six major supergroups in eukaryotes? 2 unikonts: Opisthokonts and Amoebozoa 4 bikonts: Plants, chromalveolates, Rhizaria, and excavates
Opisthokonts animals and fungi
Amoebozoa example Dictyostelium
Examples of Chromalveolates malaria, diatoms, paramecium
Rhizaria example foraminifera
Examples of Excavates trypanosomes, euglena, giardia
What is the major goal of evolutionary biology? decide relationships between 6 supergroups and understand the evolution of eukaryotes
What are the POSSIBLE 3 megagoups of eukaryotes? unikonts, bikonts, excavates (will probably join the other bikinis)
Where does Cavalier-Smith propose the root of eukaryotes is? between Euglenozoa and other eukaryotes
Why use a small number of genes to produce a tree? Many species do not have many sequences
Phylogenomics intersection of evolution and genomics -comparison of whole genomes -higher signal to noise ratios in phylogenetic trees
GenBank store DNA sequence data; replace protein sequencing
FASTP sequence comparison program
Orthologs genes descended directly from a common ancestral gene by speciation and usually have the same function -identified by BLAST hits
COGs group of orthologous genes from at least three different genomes that are not closely related
KOGs equivalent group of orthologous genes found in eukaryotes
Created by: Vanaleigh

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