Exam 1 Material Flashcards
When did the Earth form?
About 4.5 billion years ago
When did life arise?
About 3.6 billion years ago
Hadean Eon (4.6-3.8 bya)
-Origins of cellular life
-formation of the Earth
-formation of earth’s crust and oceans
Archaean Eon (3.8-2.5 bya)
-Divergence of bacteria and Archaea
-Origins of an oxygen is photosynthesis
-Origins of Cyanobacteria and oxygen is photosynthesis
Proterozoic Eon (2.5 bya - 542 Mya)
-Start of the Great Oxidation Event
-Ozone Shield forming
-Evidence for multicellular eukaryotes
-Start of Cambrian explosion
Phanerozoic Eon
-Origins of the first animals
-extinction of dinosaurs
What kind of metabolism used by some archaea may be a remnant of early form of chemiosmosis?
FeS-based
Fossil evidence places evolution of Cyanobacteria and oxygen in photosynthesis to how long ago?
About 3 billion years ago
Where are fossilized remains found?
Stromatolites and sedimentary rocks
What are stromatolites?
layered rocks formed by incorporation of mineral sediments into microbial mat
What is likely the site for the origin of life on Earth?
Deep-sea hydrothermal vents
RNA can perform diverse functions including:
-Backbone of essential molecules (ex: ATP, NADH, coenzyme A)
-Bind small molecules (ex: nucleotides, amino acids)
-Catalyze some biochemical reactions
-Template for own synthesis
-Catalyze protein synthesis
What were the events from 4.3-3.8 BYA that fell under the category of “Precellular Life”?
RNA world
- catalytic RNA
- Self-replicating RNA
Protein Synthesis
- RNA-templated translation
DNA
- Replication
- Transcription
What does LUCA stand for?
Last universal common ancestor
What is the difference between a prokaryotic and eukaryotic cell?
Prokaryotic: lack a true membrane-delimited nucleus
Eukaryotic: have a membrane-enclosed nucleus, are more complex morphologically, and are usually larger than prokaryotic cells
Describe the following shape: Spirillum
Thin wavy noodle. Looks like a less curly version of my hair after it has been In braids
Describe the following shape: Spirochete
Like Megan’s curls. Wavy at the two ends, but it is super curly in the middle
Describe the following shape: Anabaena (a Cyanobacterium)
A chain of large ovals connected like paper dolls
Describe the following shape: Large Bacillus
A big oval rock
Describe the following shape: Escherichia coil
Shaped like an oval pill
Describe the following shape: Staphylococcus
Perfect circle
Describe the following shape: Rickettsia
Oval pill that is smaller than staphylococcus. Super small
Prokaryotes
Bacteria and Archaea
-no organelles (membrane-enclosed structures), no nucleus
Eukaryotes
Plants, animals, algae, protozoa, fungi
-contain organelles
-DNA enclosed in a membrane-bound nucleus
-mitochondria and chloroplasts
The simplest and smallest “organisms” are:
Mycoplasmas
what is Mycoplasma genitalium?
A Gram-Positive (purple) bacterium with. 580 kbp genome with 470 defined coding regions
Some microbes are not unicellular. Provide a few examples
Nonstop: a photosynthetic bacterium that forms filaments
Neurospora crassa: filamentous fungus that forms hyphae
Not all microbes are small. Provide a few examples:
-Armillaria ostoyae
-bridgeoporus nobilissimus
What is natural classification?
Arranges organisms into groups whose members share many characteristics (based on anatomical characteristics)
What does the natural classification fail to provide?
Information of evolutionary relatedness
Taxonomy
-Identify and name difference organisms
-Define groups based on relatedness among the different organisms (morphological and molecular relatedness)
Binomial system of nomenclature
They are assigned 2 names:
-Genus name: italicized and capitalized
-species epithet: italicized but not capitalized
Can be abbreviated after first use
Phylogenetic classification is usually based on:
Direct comparison of genetic material
The direct comparison of genetic material for phylogenetic classification was more feasible after
Woese and Fox proposed using rRNA nucleotide sequences to assess evolutionary relatedness of organisms
How did Woese and Fx determine that all living organisms belong to one of 3 domains?
Using the nucleotide sequence of the small ribosomal RNAs (SSU rRNAs)
Orthologs
The same function and originate from a single ancestral gene in a common ancestor
Paralogs
Evolved to have difference functions resulting from gene duplication
Phylogenetic analyze typically focus on
Orthologs
Sequence alignment adds gaps to establish
Positional homology
Limitations o phylogenetic trees
-Can be difficult to choose true tree if several fit data well
-bootstrapping can deal with uncertainty ; indicated percentage of tie a node is supported by data
-homoplasy (convergent evolution) complicates tree construction when similar sequence positions result from recurrent mutation instead of inheritance
Horizontal gene transfer
The transfer of genes from one genome to another through mechanisms such as transposable elements, plasmid exchange, viral activity, and perhaps fusions of different organisms
Metagenomics
Direct DNA sequencing of microbial communities
Cell size: Bacteria (E. Coli)
About 0.7-1.4 um diameter, about 2.-4 um length, and about 0.5-5 um^3 in volume
Yeast (S. cerevisiiae)
3-6 um diameter, about 20-160 um^3 in volume
Mammalian cell volume
100-10,000 um^3; HeLa cell 500-5000 um^3
Plasma Membrane
Selectively permeable barrier, mechanical boundary of cell, nutrient and waste transport, location of many metabolic processes (respiration, photosynthesis), detection of environmental cues for chemotaxis
Gas vacuole
Buoyancy for floating in aquatic environments
Ribosomes are primarily responsible for
Protein synthesis
Inlcusions function
Storage of carbon, phosphate, and other substances
Nucleoid
Localization of genetic material (DNA)
Periplasmic space
In gram-negative (pink) bacteria, contains hydrologic enzymes and binding proteins for nutrient recessing and uptake; in gram-positive bacteria (purple) and archaea cells, may be smaller or absent
Cell wall function
Provides shape and protection from osmotic stress
Capsules and slime layers
Resistance to phagocytosis, adherence to surfaces; rare in the Archaea
Fimbriae and pill
Attachment to surfaces, bacterial conjugation and transformation, twitching and gliding motility
Flagella
Swimming motility
Endospore characteristic
Survival under harsh environmental conditions; only observes in bacteria
what shape is coccus?
Spherical
what shape is bacillus?
Rod or cylinder
What shape is coccobacillus?
Short round rod
What shape is Vibrio?
Curved rod
what shape is Spirillum ?
More rigid spiral shape
What shape is Spirochete?
More flexible spiral shape
What is mycelium?
Network of long, multicellular filaments
What are pleomorphic?
Organisms that are variable in shape
What is Treponema pallidum?
Spirochete that causes syphilis
The arrangement of cells depends on…
Plane of division
Division along a single plane may result in
Pairs or chains of cells
An example of paired cells
Diplococci (ex: neisseria gonorrhoeae)
Example of chained cells
Streptococci (ex: species of streptococcus)
Division along two or three perpendicular planes forms
Cubical pockets
Division along several random planes form
Clusters
functions of plasma membrane
-separation of cell from its environment
-selectively permeable barrier
-location of metabolic processes
-Detection of and response to molecules in the environment
What molecules diffuse freely through hth plasma membrane? Which are blocked from unrestricted passage?
Freely: H2O, O2, CO2, N2
Blocked: rage molecules, charged molecules, H+, sugars, amino acids
Transport systems aid in movement of these molecules
What aids in the movement of lblocked molecule transport through the plasma membrane?
Membrane proteins (provide specificity)
peripheral proteins
Loosely associated with the membrane and relatively easily removed
-can be “stripped” from intact membrane
Integral Proteins
Embedded within the membrane and not easily removed
-typically required membrane disruption, for example: by treatment with detergent
Unlike eukaryotes, bacterial membranes do not contain sterols. They do contain…
Hopanoids, sterol-like molecules (five ring, not four ring)
Hopanoids fulfill the same function as steroids in making memories
More fluid
Archaea membranes are composed of
Unique lipids
- lipid is branched-chain, not straight-chains
- lipids are connected to glycerol by ether linkage, not ester linkage
** Some have monolayer structure instead of bilayer
Squalene and tetrahydrosqualene are examples of:
Archaeal lipids
Biosynthetic cytoskeletons play roles in:
cell division, cell shape determination, and protein localization
Homologs of all 3 eukaryotic cytoskeletal elements have been identified in prokaryotes
FtsZ, MreB, Crescentin
what is FtsZ?
functional equivalent of eukaryotic tubulin
- required for cell division
- localized to the center
- makes a circular filament
- scaffolding for other cell division proteins
What is MreB?
functional equivalent of eukaryotic actin
- helix under the plasma membrane
- archaea appear to lack an MreB-like molecule
What is Crescentin?
intermediate filament-like protein
what forms highly dynamic filaments and interacts with proteins involved in cell division or cell shape, maintenance, respectively
bacterial tubulin-like protein FtsZ and actin-like MreB proteins
What was the first known protein to form a ring at midcell and recruits further cell division proteins to form the divide that ultimately drives formation of the division septum
FtsZ
What forms helical filaments underneath the cell membrane and are involved in maintenance of cell shape; possibly directing locations of cell wall synthesis; may also play a role in chromosome segregation
MreB
what intermediate filament-like protein that is essential for cell curvature in C. crescents and forms a filamentous structure at the short axis of the cells
Crescentin
actin-like straight filaments; positions magnetosomes (special organelles) in a straight-line underneath the cell membrane
MamK
have additional distinct filamentous cytoskeletal elements, the function of which is still unclear
spirochetes
Cytoplasmic matrix
substance in which nucleic, ribosomes, and inclusion bodies are suspended in an aqueous environment
