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Archean Keywords.doc

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Biology
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BIO1130
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Jon Houseman

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Archean Keywords Aerobic The term aerobic means 'requiring oxygen'. Aerobic organisms require oxygen to perform life processes and use oxygen to survive and grow. Aerobic organisms appear at the end of the Archean and dominate the Proterozoic eon. Aerobic forms, including the cyanobacteria, transform the planet into an oxygen rich aerobic environment which we find ourselves in today. In cellular respiration, aerobic respiration uses oxygen and generates large amounts of ATP. Anaerobic The term anaerobic means 'without oxygen', as opposed to the term aerobic. Anaerobic organisms do not require oxygen to perform life processes and survive and grow without oxygen; in fact, oxygen is seen as toxic toward anaerobic organisms. Anaerobic organisms dominate most of the Archean eon. Anaerobic respiration is a form of respiration using electron acceptors other than oxygen. Although oxygen is not used as the final electron acceptor, the process still uses a respiratory electron transport chain; it is respiration without oxygen. Antibiotic resistance Antibiotic resistance is a type of drug resistance where a microorganism is able to survive exposure to an antibiotic. While a spontaneous or induced genetic mutation in bacteria may confer resistance to antimicrobial drugs, genes that confer resistance can be transferred between bacteria in a horizontal fashion by conjugation, transduction, or transformation. Thus a gene for antibiotic resistance which had evolved via natural selection may be shared. Evolutionary stress such as exposure to antibiotics then selects for the antibiotic resistant trait. Many antibiotic resistant genes are encoded on plasmids, facilitating their transfer. Darwinian natural selection has played a major rule in modern antibiotic resistance. Antibiotics kill of bacteria, but the bacteria that survive are able to pass on their antibiotic resisting characteristics. Almost all major diseases have developed resistance to modern chemicals used to control its spread. Archaea Archea, also known as extremophiles, are single-celled prokaryotes and were extremely abundant during the Archaean eon. The Archaea are a group of bacteria that can withstand extreme conditions. Thermophiles are able to withstand extreme temperatures (normally very hot temperatures would cause enzymes to denature and very cold temperatures would cause ice crystals to form and puncture the cell membrane), halophiles live in extremely saline conditions, and methanogens produce methane. They have a unique lipid composition of the plasma membrane and have unique metabolic pathways that allow us to remediate under certain circumstances (i.e.: cleaning up toxic elements in the environment) ATP synthetase (synthase) ATP synthase is an important enzyme that provides energy for the cell to use through the synthesis of ATP. Energy is often in the form of H+ moving down an electrochemical gradient. This proton pump couples the energetically favourable transport of protons across a membrane to form ATP. In the motor in the base of a bacterial flagellum, ATP is hydrolized, creating protons which drives the process. Protons are pumped across the periplasm through the plasma membrane and they build up in high concentrations which have the potential to do work. In the motor, as protons pass through the ATP synthase, the energy creates a conformational change which ends up causing the flagellum to spin. Autotroph Autotrophs are the produces in the world. Autotrophs are organisms that produce complex organic compounds from simple inorganic molecules (using energy from light or inorganic chemical reactions). The opposite of an autotroph is a heterotroph which uses pre-existing organic carbon-carbon bonds. Plants are autotrophs. Bacillus bacteria Bacteria were previously named based on size, shape, and mobility. The bacilli bacteria are notable for their rod shaped morphology. Bacteria (Eubacteria) Bacteria (eubacteria) are simple, microscopic organisms and can be considered one of the earliest forms of lie. Bacteria are 1 of the 3 domains of life. They are basically a bag of cytoplasm surrounded by a phospholipid plasma membrane; there is no compartmentalization in bacteria. The plasma membrane is surrounded by a cell wall made of non-living materials (peptidoglycan layer and the outer membrane) which ensures the integrity of the cell due to osmotic factors. Ribosomes and a nucleoid area can be found inside the cytoplasm and the nucleoid area is made up of a single, circular DNA material with no membrane (the DNA is dense in the nucleoid area). The cytoplasm surrounds the ribosomes and nuclear material that is contained in a nucleoid made of packed chromosomes which stabilizes the DNA strand. There are no internal organelles. Bacteria also contain a circular plasmid. Bacteria reproduce asexually via horizontal gene transfer (i.e.: conjugation, transduction, transformation) and have many diverse forms of metabolism to capture energy. Bacterial movement involves a unique spinning flagellum. Bacterial flagellum The bacterial flagellum is unique to bacteria. It is made up of 20 proteins and contains 3 major components. The flagellum is a spinning, propeller-like structure. It is made up of one type of protein and that is polymerized. The hook ties the flagellum to the motor. The base contains the motor. The base is made up of rings which embed the motor into the membrane. The rings create a bearing (a hole in the plasma membrane so the hook can spin with little resistance). Lipophilic sites anchor the protein into the membrane. The motor that is found in the base creates the flagellar movement. ATP is hydrolized, creating protons which drive the process. Protons are pumped across the periplasm through the plasma membrane and they build up in high concentrations, which give them the potential to do work. The protons cross the ATP synthase and the energy created causes a conformational change in the motor proteins which moves the central rotor. A switch protein can change whether the motor is spinning clockwise or counter clockwise. Gram positive bacteria pumps protons into space below peptidoglycan and outer portion of the inner membrane in the cell wall, while gram negative bacteria pumps protons right into periplasm. Bacteriophage A bacteriophage is a virus that takes over the bacterial cell and kills them during the lytic phase of its life cycle. Bacteriophage are involved in bacterial reproduction via transduction. A bacteriophage injects its DNA into a bacteria and the DNA of the virus destroys the bacterial genome to get building blocks to build its own DNA. The virus particles contain the genome that it created and the DNA of the host bacteria. The virus takes over the host cells' replication, transcription, and translation and uses it to replicate its own genome and produce the proteins of the viral casing that is encoded in the viral genome. The new bacteria that is attacked by the virus incorporates the DNA of the first bacteria. Bacteriophage are useful in keeping bacterium levels from rising significantly. Binary fission Binary fission is a form of horizontal gene transfer and asexual reproduction in bacteria. It involves the parent cell splitting in half (fissures) to produce 2 cells. Nuclear materials duplicate and the circular genome attaches at one spot at the cell membrane and allocates itself to one of the divided (daughter) cells when the cell undergoes division. Variation is transmitted when mutation occurs during DNA replication or when DNA is misrepaired during the life of the cell. Capsule The outer surface of bacteria is covered by a form of mucilaginous outer capsule that is equivalent to the glycocalyx. The capsule is believed to play an important role for adhesion to substrates and as a defence against bacteriophages and phagocytosis by protists or the immune system of another organism. It is made up of hydrocarbons and is not a universal characteristic. Cellular respiration Cellular respiration is the set of the metabolic reactions and processes that take place in the cells of organisms to convert biochemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products. The reactions involved in respiration are catabolic reactions that involve the redox reaction (oxidation of one molecule and the reduction of another). Respiration is one of the key ways a cell gains useful energy to fuel cellular reformations. Nutrients commonly used by animal and plant cells in respiration include sugar, amino acids and fatty acids, and a common oxidizing agent (electron acceptor) is molecular oxygen. Bacteria and archaea can also be lithotrophs and these organisms may respire using a broad range of inorganic molecules as electron donors and acceptors, such as sulfur, metal ions, methane or hydrogen. Organisms that use oxygen as a final electron acceptor in respiration are described as aerobic, while those that do not are referred to as anaerobic Cellulose Cellulose is the most common organic compound on Earth. In organisms with a cell wall, the wall consists of simple monomers strung together to form fibres that give the cell wall its strength and rigidity. In plants glucose molecules are strung together to form cellulose. Cellulose is relatively hard to digest. Chemolithoheterotroph In the naming system of the different types of metabolisms in organisms, the first part of the name refers to where the energy comes from and the second part of the name refers to where the carbon source comes from. Chemolithohetertrophs use minerals (i.e.: nitrate or nitrite from iron) that are ionically charged as the source of high energy electrons used for energy transfer and use existing organic compounds with the C-C bonds. Chemolithotrophs In the naming system of the different types of metabolisms in organisms, the first part of the name refers to where the energy comes from and the second part of the name refers to where the carbon source comes from. Chemolithotrophs use minerals (i.e.: nitrate or nitrite from iron) that are ionically charged as the source of high energy electrons used for energy transfer and use CO2 as the source of their carbon. Chemoorganoheterotrophs In the naming system of the different types of metabolisms in organisms, the first part of the name refers to where the energy comes from and the second part of the name refers to where the carbon source comes from. Chemoorganoheterotrophs use high energy organic bonds (the energy released when the bonds are broken) as the source of their high energy electrons used for energy transfer and use existing, organic compounds with the C-C bonds as the source of their carbon. Chemoorganotrophs In the naming system of the different types of metabolisms in organisms, the first part of the name refers to where the energy comes from and the second part of the name refers to where the carbon source comes from. Chemoorganotrophs use high energy organic bonds (the energy released when the bonds are broken) as the source of their high energy electrons used for energy transfer and CO2 as their source of carbon. Chitin In organisms with a cell wall, the wall consists of simple monomers strung together to form fibres that give the cell wall its strength and rigidity. N-acetyl-glucosamine monomers form the chitin of the fungal cell wall. Circular genome There are no chromosomes in bacteria and instead the genome consists of a one circular piece of double stranded DNA, or in a few cases a linear piece, that loops, folds and supercoils on itself to form a compact structure suspended in the cytoplasm. The genome is the structure that carries the genetic information during bacterial reproduction. Coccal bacteria Bacteria were previously named based on size, shape, and mobility. Coccal bacteria are notable for their round shaped morphology. Conjugation Conjugation is a form of horizontal gene transfer. Conjugation occurs when a F-positive bacteria interacts with a F-negative bacteria. The F factor is contained in the plasmid and is the mechanism by which the plasmid drives the bacterial cell to fuse with another bacterial cell and swap DNA. First, a cytoplasmic bridge forms when pilli attach and fuse and this pulls the bacteria together, allowing cytoplasm to flow in between. The plasmid in the F-positve bacteria replicates and sends a single strand of DNA into the other bacterium through the cytoplasmic bridge and a double stranded duplication is created in the cell. The complementary strand is produced and the bacterial cell now contains a plasmid that may include genes for antibiotic resistance or unique metabolic pathways. Some plasmids stop replicating and put itself into the genome of host bacteria after crossing over to the host. Cyanobacteria The Archean Eon is the age of the bacteria and it starts with anaerobic forms and finishes with the aerobic forms including cyanobacteria that collectively transform the planet to the oxygen rich aerobic environment we know today. Cyanobacteria figure out how to capture energy from light and develop a metabolic pathway to use CO2 and the splitting of water molecules to build organic carbon. They are the first photoautotrophs. They are submersed in the waters and harness the electrons from photons that penetrate the water. Oxygen (as a by-product) starts to build up in high concentrations in the water and begin to react with minerals in the rock (creating rust). Oxygen is released into the atmosphere when the water becomes saturated with oxygen. Atmospheric oxygen forms ozone which filters UV light (that previously caused thymine dimers) and allows organisms to move up on land. Cyanobacteria are still around and are considered living fossils. Daughter cell Either of the two cells formed when a cell undergoes cell division. Daughter cells are genetically identical to the parent cell because they contain the same number and type of chromosomes. Electron donor A chemical entity that donates it's electrons to another compound during processes like cellular respiration. The electron donor is said to be oxidized and is known as the reducing agent. Electron receptor A chemical entity that accepts electrons transferred to it from another compound. The electron receptor is said to be reduced and is known as the oxidizing agent. Electron transport chain The electron transport chain involves high energy electrons that are combined in a redox pair, where the electron is passed between two compounds, allowing energy to be harnessed. A series of redox reactions is used to pump protons in the space between the inner and outer mitochondrial membranes. An electron transport chain (ETC) couples electron transfer between an electron donor (such as NADH) and an electron acceptor (such as O2) with the transfer of H+ ions (protons) across a membrane. The resulting electrochemical proton gradient is used to generate chemical energy in the form of adenosine triphosphate (ATP). Electron transport chains are the cellular mechanisms used for extracting energy from sunlight in photosynthesis and also from redox reactions, such as the oxidation of sugars (respiration). Eukaryota Eukaryotes are 1 of the 3 domains of life. The term comes from the Latin 'eu' meaning true and 'karyote' meaning seed, referring to the nucleus. The eukaryote contains complex structures within its membrane. A eukaryote is an organism whose cells contain complex structures enclosed within the membrane. Extremophiles Extremophiles deal with Archaean organisms. Extremophiles are bacteria that can withstand extreme conditions. For example, thermophiles have the ability to withstand high temp
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