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Department
Biology
Course
BIO1130
Professor
Jon Houseman
Semester
Fall

Description
EONS: Archean  Occurred from 3800 to 2500 mya  The time duration in which the first life was seen on Earth (not chemical evolution)  Special Archea Bacteria and anaerobic Eubacteria are seen that can harness energy by breaking inorganic matter. Proterozoic  Occurred 2500 to 543 mya  Saw the rise of Eukaryotic cells Phanerozoic  Started 543 mya and continues to now.  Multicellular organisms appear and dominate QUALITIES OF LIFE: Self-Replicating  Life from life with a genetic program Metabolizing  Capturing, processing and releasing chemical energy (food) Self-regulating  To be able to maintain an internal environment different from the external  To be able to balance the internal environment in a certain range (homeostasis) Reproducing  Creating another life from a living organism Evolving  Adapting and changing to the environment by generations. Responding  Sensing and interacting with the surrounding world. Growth  Increasing in size. BACTERIA (MORPHOLOGY): (Eu)bacteria  Formerly heavily relied on morphology for classification (size, shape, mobility)  Currently classed in a chemical/genetic manner since many species share same morphs. Nucleoid Region  Nucleoid region of the bacteria contains the genetic material  Bacterial DNA is circular  Bacillus Bacteria  Rod shaped bacteria  Generally large, gram positive, spore bearing, and forms colonies in chains.  Some of them have a flagella for mobility  E.g. bacillus anthracis causes anthrax Coccal Bacteria  Coccus bacteria are spherical  Can occur singly, in pairs, or in groups in cubicle packets/grape-like clusters  Generally non-motile (w/o flagella or cilia) and do not form spores  E.g. staphylococci and streptococci have pathogenic species. Spirochete  These are non-rigid and spiral shaped. Bacteria  Generally, they are gram negative, anaerobic and feed on dead organic matter.  Very common in sewers and polluted water; e.g. Treponema Spirillum  Spirilla are rigid and spiral shaped Bacteria  Generally, they are gram negative, aerobic and highly motile containing a flagella. 1 BACTERIA (CELL STRUCTURE):  In spite of the variation, they typically have a generic structure:  DNA is large and circular, found in a nucleoid region of the cell, with no nuclear envelope Ribosomes  Protein/rRNA structures that synthesizes protein from mRNA, in process of translation  They are very different in eukaryotes, bacteria, and Archea Cell Wall  Made up of peptidoglycan (exclusive to bacteria), meshwork of sugars and peptides.  (in plants cell walls are cellulose-based; in fungi, cell walls are chitin-based) Periplasm  Space in between 2 phospholipid bilayers of the gram negative cells.  Contains many proteins that serve diverse functions (antibiotic resistance, ETC, and other enzymes) Peptidoglycan  Made of peptides and organic sugars.  Reacts with the Gram’s stain positively; thus, gram-positive bacteria have outer peptidoglycan layer. Capsule  Thick rigid gelatinous layer completely surrounding the cell wall of some bacteria  Protective function by making the bacteria harder to ingest by phagocytes Gram positive  Bacteria that are gram pos react to Gram’s stain, and contain thick peptidoglycan layer  Their cell boundary consists of: o Cytoplasm | Plasma Memb. | Peptidoglycan | (Capsule) | Extracellular  They retain the first dye, appearing blue-black  See slide 36 and 37 Gram negative  Acetone-alcohol washes out the violet dye, making the smear look red.  This is because their peptidoglycan layer is not as easily accessible  Their cell boundary consists of: o Cytoplasm | Plasma Memb. | Peptidoglycan | outer memb. | Capsule | Extracellular  Gram neg. bacteria are generally vectors for diseases. Bacterial  Strictly a prokaryotic motor, as it evolved in a different manner than that of eukaryotes. Flagella  Is an example of a biological motor  Bacteria pump the protons into the region outside the memb. similar to ETC on mitos.  The proton pump opening is in the motor; as proton moves through it, the protein changes shape, and ratchet against the motor, which starts/spins the flagellum Flagellar hook  Sharp bend just outside the cell surface (base of filament) allows axis of helix to point directly away from the cell Flagellar motor  Motor that turns in response of a proton going down the bearing.  This is what turns the filament, producing propulsion.  This is thought to be a precursor to ATP synthase commonly found in mitochondria. CELL WALL TYPES: Cellulose:  Organic compound made of polysaccharides, found in the cell walls of mainly plants & algae Chitin:  Long polymer composed of a derivative of N-containing glucose  Typically found in cell walls of fungi, exoskeletons of arthropods and radula of molluscs. Peptidoglycan:  Polymer of sugars/amino acids that form the cell wall of bacteria (but not archea)  Gram + bacteria have a thicker peptidoglycan layer than the gram – bacteria.  Its role is to provide structural strength to counteract osmotic pressure, but doesn’t have bacteria its shape.   2 BACTERIA (REPRODUCTION): Binary Fission  Simple reproduction process in which the cell cleaves close to the middle as it finishes up DNA replication.  As the cell separates, each genome copy is anchored at the plasma membrane.  Bacteria can only reproduce asexually, since they have no genetic recombination/segregation mechanics.  In this form of reproduction, variation only comes about from mutation Circular  Piece of genome that is circular in shape, and as a result does not need telomeres. Genome  It is found mostly in the nucleoid region of bacteria and prokaryotes.  This genome is copied as a result of binary fission. Daughter Cell  A parent cell divides into 2 daughter cells; each with a copy of the parental genome Mutation  A random change of nucleotide sequence in the genome that can potentially cause it and all its derivative cells to be different in appearance or function from normal. Conjugation  Transfer of genetic material between 2 bacterial cells by direct cell to cell contact  Typically, plasmids are used in genetic material transfer.  Conjugation plays a huge role in bacterial variation and bacterial genome diversity Pilli  Filamentous projection on a bacterial cell used for adhering to other bacteria  Can bring the bacteria towards what the Pilli Bridge is attached to.  Also significant as it is the bridge by which plasmids are transferred in conjugation. Plasmid  Fragments of circular DNA found in the cytosol of the bacteria.  Plasmids have to ability to merge with the circular DNA in the nucleoid region.  In this case, during conjugation, the entire genome up to the plasmid copy is transferred to the recipient gene; the bacteria will express genes that are not native to it. + -  For conjugation to occur, the 2 bacterium do not have to the same species. + F and F  Bacterium that can provide plasmid copies to other bacterium are known as F cells.  F cells copy and transfer the plasmid genes to F cells; those without that gene. Transformation  The ability of bacteria to uptake free DNA from the extracellular and incorporate it into its own genetic material.  Transformation allows bacteria to uptake the DNA and tests them for beneficiality.  This process began 2.8 bya, and increases variation within bacteria.  If the uptake is successful (e.g. allows them to metabolize new things, or produce certain proteins), then it will survive and pass it on to its future derivatives.  If the DNA is deleterious (i.e. poisonous to the bacteria), then it will kill itself, or it will store it in a separate membrane as toxins for predators.  This is possible since the genetic material is universal to all life; species aren’t a factor.  They can only pick up DNA from the same domain, so it can’t take stuff up from fish/humans naturally. Horizontal Gene  Any process by which an organism incorporates genetic material from another organism Transfer without being its offspring.  This includes Transformation, Transduction and Conjugation. Transduction  Transduction is a very rare method to increase variation.  Bacteriophages hijack the living bacterial cells to replicate their genes.  After they replicate, they burst the cell in a lytic process and release the next gen. virus.  The bacterial genome is destroyed/digested in the process.  In extremely rare cases, some bacterial genome survive and is locked in the viral capsid  Then this virus containing bacterial genome will transfer it to other bacteria, increasing its variation. There is also a potential for the viral DNA to combine with the bacterial DNA Bacteriophage  Viruses that invade bacteria and use them as their host. They insert their genetic material into that of bacteria, essentially taking over its central control.  Host produces everything that is needed to make new viruses, their genes and capsid.  If bacterial genes survive, they also move into a capsid for transduction to occur. 3 Pathogen  Infectious biological agent (bacteria, viruses, prions, virions, and funi) Penicillin  Anti-microbial agent (antibiotic) derived by penicillium fungi  First drug that was effective against many bacterial strains since it inhibits a specific enzyme (DD-transpeptidase) which links peptidoglycans together, causing it to lyse. Antibiotic  Antibiotics are a chemical (natural or synthetic) that kills/inhibits growth of bacteria and Resistance micro-organisms, usually by destroying the cell wall or interfering with its metabolism.  Antibiotic resistance occurs when a micro-organism contains a gene (plasmid) that can negate the effects of the antibiotic. METABOLIC PROCESSES Redox Pairs:  An electron donor and its corresponding oxidized form (e.g. NADH and NAD+) Oxidation:  Increase of charge as a species loses one or more electrons. Reduction  Reduction of charge by gaining one or more electrons. Cellular  *stepwise oxidation vs. direct burning/combustion. Respiration:  Process by which glucose is oxidized for a gradual transfer of energy from glucose to the cell  Glucose is split into 2 3C molecules during glycolysis and moves to the Kreb’s cycle  Role of O 2s to accept free electrons and combine them with H to make water. Anaerobic:  These are organisms that live/thrive without requiring oxygen.  Many other metabolic processes are used to acquire energy, like fermentation of glucose  Mainly comprised of bacteria; humans are capable of anaerobic for only short time periods  ATP yield is significantly lower than aerobic, but process is 2.5x faster. Fermentation:  Anaerobic process by which energy is produced by the oxidation of an organic compound (glucose) by using electron acceptors without the use of Oxygen.  Product of fermentation is ethanol and CO in2yeast.  Crucial process in anaerobic resp. as it allows for the regeneration of NAD+ by accepting electrons from NADH  In humans, fermentation produces lactic acid, where pyruvate acid is reduced by NADH. Aerobic:  Aerobic organisms live and thrive in oxygenated environments  These guys require oxygen to oxidize glucose in the cellular resp.  Animals, fungi, and some bacteria adopt aerobic resp. methods.  Multicellular organisms must overcome problems associated with a large V to SA ratio  One way to deal with this to create body cavities to increase SA (e.g. lungs) Electron Donor:  Chemicals that donates an electron to another chemical; a.ka. reducing agent Electron Receptor:  Chemicals that accept a free electron; a.k.a. oxidizing agent Electron Transport  Organic process in which an electron is moved from highly reducing products of the citric Chain: cycle (NADH and FADH2) down a chain of enzymes/proteins inside of a plasma membrane to a highly oxidizing dioxygen. When this high energy moves across the proteins/enzymes, protons are pumped out of the inner space, to be used for ATP synthase.  The proton gradient across the membrane makes protons more likely to enter the memb.  As the Hydrogen moves in through ATP synthase, ATP is generated. The H then combines with Oxygen, the final electron acceptor to make water. This process is 40% efficient. Proton Gradient  Occurs when there is a greater concentration of protons on one side of a membrane compared to the other. This increases the tendency for the protons to diffuse through. ATP Synthase  Important enzyme which provides energy to the cell by ATP synthesis.  Imbedded in phospholipid bilayer and has 2 subunits: top one rotates when a proton passes it, creating energy required to bind a phosphate to an ADP molecule.  There is evidence that it originated from mechanism that powers bacterial flagella. 4 ADAPTATIONS: Autotroph:  Organism that produce complex C molecules (organics) from inorganic CO 2  They are capable of producing their own food and organic building blocks.  Includes plants and algaes, and reduce atmospheric CO in 2he process.  They receive energy from inorganic sources such as sunlight Photo trophs  One of the only 2 metabolic pathway (other is chemoorganoheterotroph) that moved on to multicellular life.  They make their own organic compound by reducing inorganic CO using2solar energy.  These include plants and algae. Chemo organo  An organism that uses organic compounds as their source of energy. trophs  This includes all animals and fungi and most heterotrophs (chemolithotrophs are exception as they use inorganic compounds as energy)  Organic chemicals that are used for energy include glucose, lipids and acetates. Chemo litho  An organism that uses an inorganic electron donor to acquire its energy trophs  The compound is oxidized to remove a high energy electron which ultimately produces ATP  E.g. Nitrifying bacteria (uses NH3to make NO a3d an electron) and Iron bacteria (Fe to make electrons)  In aerobic bacteria, the electron acceptor can be oxygen  Plays an important role in withering rocks to establish an ecosystem Heterotrophic:  Organisms that consume their C compounds from other organisms  Includes all carnivores (single and multi-cells); they move to consume prey Photo  Organisms that use light for energy but must acquire their C source from elsewhere heterotrophs  Source includes other organisms or the environment as they can’t use CO 2  E.g. heliobacteria. Chemo organo  One of the only 2 metabolic pathways (other being phototrophs) that moved to heterotrophs multicellular life.  Organisms that acquire their energy through breaking of C bonds in organic substances, which originated from another organism (as food)  These are predominantly animals and fungi. Chemo litho  Organisms that use inorganic substances to produce ATP, but must acquire their C sources hetero trophs from another organism (e.g. colourless sulphur bacteria) Lithotrophs  Any organism that use inorganic substrates and transforms them into their reducing form for biosynthesis or used in aerobic/anaerobic respiration to oxidize the NADH to NAD+  Exclusively seen in prokaryotes (bacteria and archea)  E.g. Nitrobacters, Acidithiobacillus, Ferrooxidans (using Iron) DOMAINS: Prokaryotes:  Includes all unicellular organisms that lack a nucleus  This includes archea, bacteria, as well as cyanobacteria.  One of the longest living domains on Earth and also the first ones to arrive; most diverse. Archea Bacteria:  Single cell organisms that resembles a bacteria, but is different due to their genome  They arose in the Archean Eon, and have survived to this day in extreme conditions.  They have a very unique metabolic pathway, to be able to use Sulphur compounds for food. Extremophiles:  Property of Archea bacteria to be able to live in extreme conditions  They have not changed for bya’s, and have thought to have lived through mass extinctions  Part of reason why they are so resistant: highly branched, rigid plasma memb. doesn’t break easily 5 Thermophiles:  Archea that can withstand high temperatures (45 to 122ºC)  Typically found in hot springs and hydrothermal vents. E.g. Thermos Aquatis Methanogens:  Archea that produce CH as4a metabolic by product, from living in non-oxygenated areas  E.g. methanoberibacter Smithii, found in human guts to help digestion of polysaccharides. Halophiles:  Extremophillic archea that can surive and thrive in very high salinity  E.g. halobacterium halobium. (Eu)bacteria:  Single celled organisms that are fairly uniform in morphology since developed 3.8 bya  they are the most abundant and varied organism on Earth  They do not contain double membrane organelles inside their cytoplasm. Cyanobacteria:  The first phototrophs on Earth, the first organisms to convert light and inorganic CO i2to usable organic matter (food or structural components)  Also responsible for oxidation of minerals in ocean, O r2ch atmosphere and ozone layer.  A.k.a blue-green algae, that are primitive ancestor of plants and eukaryote algae. Photosynthesis:  Process by which light is converted into energy that cells use to make food/building blocks  This is achieved by the use of photosynthetic pigments to capture photons of light.  Takes inorganic CO a2d water as the reactants to produce glucose and O . 2 Stromatolite:  Layers of sedimentary rock made by biofilms secreted by cyanobacteria.  One forms a layer, and when it dies, another one forms a lay on top of it.  Provides some of the most ancient records of life on Earth. Monera:  One of the 5 kingdoms in the Linnaean classification system  Includes unicellular organisms without a nucleus.  Includes the domain of bacteria and archea, but exludes cyanobacteria (its plantae) Nitrogen  Very important role of diazotroph bacteria. Fixation:  They are the only living creatures that can integrate atmospheric N into organic compounds 2  This N containing organics makes it way to plants and the rest of the ecosystem. Living Fossils:  The fact that some of the living bacteria resemble bacteria found in fossils bya’s old.  We can study the anatomy of these “living fossils” to speculate the origins of bacterial cells. Eukarya:  Domain consisting of all eukaryote organisms including protists, fungi, animals and plants. Eukaryotes  An organism with genetic material contained within a distinct nucleus. 6 PROTEROZOIC EON Proterozoic:  Started about 2.5 bya and ended about 542 mya.  This eon saw the rise of the eukaryotes and protists. ENDOSYMBIOSIS AND ORIGINS OF THE NUCLEAR ENVELOPE Nuclear  Memb. that surrounds and protects the genetic material of the cell. Envelope:  Origins lie in the invagination of the plasma memb of the cell, creating a membrane around DNA  Provides a customized area in which genetic material occur at maximum efficiency.  Separates events like DNA replication and transcription from the rest of the cell. Endomembrane  Refers to the different membranes that are suspended in the cytoplasm within eukaryotes. System:  They are membranes that divide structural or functional units of the cell (organelles)  Structures of the endomembrane system include nuclear envelope, rER, sER, golgi, etc.  Plays an important role in transport, protection, and selective permeability. Histone  Proteins found in the nuclei of eukaryote cells, used in DNA packaging. Proteins:  They are used to package DNA, making it more compact and easier to store.  They are highly alkaline, and combine easily with nucleic acid  Endosymbiosis:  Process by which smaller bacteria entered a bigger bac
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