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MCB 3020
Exam 2
| Term | Definition |
|---|---|
| cell | provides spatial arrangement in which the biochemical reactions of maintenance and synthesis can occur |
| compartmentalization | permits the establishment of a particular biochemical in a specific area where specialized reactions can occur; may protect certain essential structures from being hydrolyzed by enzymes |
| coccus | spherical |
| bacillus | cylindrical |
| spirillum | rod twists or spirals |
| spirochete | long, helically coiled |
| vibrio | half moon |
| diplococcus | divide in 1 plane and stay together for 1 division; pairs |
| streptococcus | divide in one plane and remain together for many divisions; chains |
| staphyloccus | divide in many planes and remain attached; like bunch of grapes |
| tetracoccus | 1 plane and 1 perpendicular plane |
| sarcinae | like tetra and plane cross sections behind; cuboidal packets |
| cell size | the rate at which nutrients and waste products move in and out of cell is generally inversely proportional because they are a function of the amount of membrane surface area available in comparison to volume |
| surface area to volume ratio | the larger the surface area to volume area, the more easily nutrients can move into the cell; small cells have more surface area and thus more effective transporters. |
| viruses | nucleic acid (DNA or RNA, not both) and a protein coat called capsid (made up of capsomeres); outside of the host cell they are unable to reproduce and are non-living (obligate intracellular parasites); no cell membrane. |
| viroids | single stranded circular RNA that forms a seemingly double stranded structure (able to exist outside host cell); no cell membrane; interferes with regulatory RNA in plants not animals; no protein coding. |
| prions | small, infectious polypeptides that are misfolded proteins that can cause the normal forms of the protein to convert into the misfolded form; no cell membrane. |
| cytoplasmic membrane | thin structure that completely surrounds the cell and consists of phospholipids and proteins; highly selective; 6-8nm wide; separates cell from environment; phospholipid bilayer; enables cell to concentrate metabolites and excrete waste |
| phospholipid | consist of hydrophobic fatty acids esterifeid to glycerol; removal of water between alcohol group on glycerol and carboxyl group of fatty acid |
| anhydride | high energy bond |
| ester | low energy bond |
| peripheral proteins | not embedded but associated with membrane surface; some easily removed with changes in ph, ionic strength; typically on surface and some may be bound to integral proteins; some have been shown to have a lipid tail that anchors them to cell membrane |
| n-terminus (amino terminus) | by convention, left side of the molecule |
| c-terminus (carboxyl terminus) | by convention, right side of the molecule. |
| integral proteins | tightly bound and full embedded in membrane; surfaces exposed on both the inside and outside of cell; must have hydrophobic external surfaces that make close contact with bilayer; not easily removed; |
| ampipathic | have both hydrophobic and hydrophilic regions. |
| fluid mosaic model | proteins and phospholipids have a lot of freedom to move about; roughly the viscosity of motor oil; allows for conformation changes in proteins; |
| permeability barrier of the cell membrane | prevents leakage and functions as a gateway for transport in/outl; passive movement of polar/charged/large solutes does not occur readily; some nonpolar/fat soluble substances may enter/exit by dissolving in lipid phase and diffusing through. |
| protein anchor of the cell membrane | site of many proteins involved in transport; bioenergetics; signaling & chemotaxis |
| energy conservation of the cell membrane | site of the generation and use of the proton motive force |
| sterols | eukaryotes have 5-25% sterols(rigid planar molecules that stabilizes the membrane's structure and makes it less flexible) in their membranes that are usually absent in prokaryotes (exception: mycoplasma). |
| hopanoids | (similar to sterols) are present in the membranes of many bacteria and play a role similar to that of sterols in eukaryotic cells. |
| archaea lipids | instead of ester bonds in bacteria/eukarya lipids, archaea have ether bonds between glycerol and their hydrophobic side chains; lack fatty acids but have side chains of repeating units of 5C hydrocarbons; |
| Woese's discovery | it was 16S ribosomal RNA sequence differences that led Woese to discover Archaea as a new domain distinct from bacteria/eukarya |
| glycerol diether | archaea lipid; produces the lipid bilayer; phytanyl |
| diglycerol tetraether | archaea lipid; produces the lipid monolayer; extremely resistant to heat denaturation; found in hyperthermophiles; biphytanyl; |
| carrier mediated transport | saturable sometimes even at low solute concentration; high specificity; So + C -> [CS]o -> [CS]i -> Si +C |
| rate of solute entry | y axis: Solute inside x axis: time |
| simple diffusion | passive transport; non-saturable; driven by concentration gradient |
| facilitated diffusion | passive transport; facilitated by a carrier; saturation at high concentrations of solute (specificity for solute); driven by concentration gradient |
| simple active | active transport; ion gradients/proton motive force |
| ABC (atp-binding cassette) system | active transport; energy from atp; periplasmic binding protein; high affinity for substrate; membrane-spanning proteins: carrier or transmembrane protein that serves as a channel; g+ lack true periplasm |
| group translocation | active transport; chemical modification of solute as it is transported across the membrane; modification uses energy; driven by PEP; |
| membrane spanning proteins | 12 alpha-helices that wind back and forth through membrane to form a channel through which solute enters cells; protein conformation changes upon solute binding and this shuttles it across the membrane |
| uniporter membrane transport protein | transport a molecule in a unidirectional fashion across a membrane. |
| symporter membrane transport protein | transport a substance along with another substance frequently a proton (H+); also called cotransporters |
| antiporter membrane transport protein | transport a substance across the membrane in one direction while at the same time transporting a second substance in the opposite direction |
| Enz I and HPr | nonspeicifc components of phosphotransferase system (sugar transport) that if mutated cause the inability to transport any of the 3 main types of sugar |
| macromolecule transport | some exported through or inserted into cell membrane by translocases; example: Sec (secretory) system |
| Sec (secretory) system | involve 7 proteins to transport macromolecules; proteins transported are synthesized as presecretory proteins called preproteins that have a signal peptide at n-terminus recognized by Sec; chaperon proteins bind to signal and prevent conformation changes |
| cell wall | protects cell from osmotic pressure and prevents cell lysis; confers shape and rigidity to cell |
| gram + | one thick layer of peptidoglycan; amino acid of DAP is linked to carboxyl group of terminal D-alanine by peptide bond; has more crosslinks; most cocci have lysine instead of DAP |
| gram - | two layers (thin peptidoglycan and LPS); cross-linkage occurs by way of a peptide interbridge |
| peptidoglycan | a rigid layer composed of two sugar derivatives (beta 1-4 glycosidic bond) and a small group of amino acids and either lysine or DAP. gram + 90%; gram - 10%; 50nm wide cables |
| Archaea/Eukarya | the sugar n-acetylmuramic acid and the amino acid diaminopimelic acid are never found in the cell walls |
| teichoic acids | acidic polysaccharides that enter the peptidoglycan layer; polyalcohols connected by phosphate esters and usually have other sugars and D-alanine attached; negatively charged partially responsible for - charge on g+ surface |
| lipoteichoic acids | teichoic acids covalently linked to membrane lipids |
| lysozyme | can destroy the peptidoglycan layer by breaking the beta 1,4-glycosidic bonds between n-acetylgucosamine and n-acetylmuramic acid |
| protoplast | microbial cells that are devoid of their cell walls |
| protoplast experiment | in dilute solution, breakdown of cell wall releases the protoplast, but then immediately lyses. in isotonic solution, water does not enter the protoplast and therefore does not lyse. |
| gram + treated with lysozyme | produces protoplast in isotonic environment |
| gram - treated with lysozyme | produces a spheroplast which is similar to protoplast but has residual wall attached. |
| pseudomurein | similar to the peptidoglycan; found in some archaea cell walls; backbone is composed of alternating repeats of N-AcGlu and N-acetylalosaminuronic acid; glycosidic bonds are beta 1,3 NOT 1,4 |
| archaea s layer | consist of protein or glycoprotein; typically have hexagonal symmetry that provides protection from osmotic lysis; naturally resistant to penicillin or lysozyme; doesn't let large in or out |
| penicillin (and other beta-lactam ring antibiotics) | inhibits the formation of cross linkings of peptidoglycan by binding to transpeptidase enzymes that catalyze cross-links; more effective towards gram + |
| lipopolysaccharide layer (LPS) | gram - only; this second lipid bilayer contains polysaccharides and phospholipids which are linked in the outer membrane to form lipopolysaccharide structures; distinct from the cytoplasmic membrane but still a part of the cell wall; heat resistant |
| lipid A | gram - only; inner component of LPS that is endotoxic and actually embedded in the phospholipid portion. |
| endotoxins | takes really high concentrations of gram - bacteria to produce fever, decrease in blood pressure, activation of inflammation and coagulation of blood. |
| porins | transmembrane proteins that consist of three identical subunits: water filled channels; allow entry/exit for low-molecular weight hydrophilic substances |
| capsule | excreted slimy polysaccharide or protein organized in a tight matrix like an envelop around a cell |
| slime layer | excreted slimy polysaccharide or protein organized in a more diffuse and easily deformed |
| surface polysaccharides | attachment of microbes to solid surfaces; pathogens first bind to surface components on human tissues; nonpathogenic bind to surfaces in nature forming biofilm; encapsulated pathogens are harder to engulf and destroy; make cells resistant to desiccation |
| fimbriae | shorter than flagella and more numerous |
| pili | similar to fimbriae but typically longer and only 1 or a few on cell surface that serves the purpose of conjugation and adhesion of pathogens to specific host tissue; receptors for some viruses |
| conjugation | genetic transfer mediated by cell to cell contact; F+ x F- (recipient) -> F- becomes F+ |
| poly-beta-hydroxbutyric acid granules | b-hydroxybutyrate molecules joined by ester bonds |
| inorganic phosphate | stored in the form of granules of polyphosphate; degrade later for synthesis of nucleotides or phospholipids |
| H2S | often oxidized to sulfur to produce sulfur globules stored in periplasm |
| magnetosomes | intracellular particles of Fe3O4 that impart a magnetic dipole on cell which orients cell in a particular direction with regard to Earth's magnetic field lines |
| gas vesicles | confer buoyancy on cells; arranged in bundles; made up of two proteins: GvpA (97%) and GvpC |
| (free) endospores | resistant to heat, drying, disinfectants, acid, and radiation; can remain dormant for extremely long periods of time; bacteria are found most commonly in the soil; core of dipicolinic acid |
| dipicolinic acid (DPA) | causes dehydration by binding free water and therefore slowing down reactions resulting in a longer "shelf life"; gets between DNA bases and stabilizes DNA to prevent denaturation |
| small acid-soluble proteins (SAPS) | functions as C & E source for outgrowth of a new vegetative cell from endospore during germination; bind to DNA in core and protect DNA from damage by UV radiation & drying; changes molecular structure of DNA from B to A form (A is more resistant/compact) |
| monotrichous | single flagella at one end |
| lophotrichous | bundle (tuft) flagella at one end |
| amphitrichous | bundle (tuft) of flagella at bond ends |
| peritrichous | flagella around the cell |
| L ring of the basal body (flagella) | located in the LPS of gram negative |
| P ring of the basal body (flagella) | located in the peptidoglycan layer of gram negative |
| MS ring of the basal body (flagella) | located in the cytoplasmic membrane of gram negative |
| C ring of the basal body (flagella) | located in the cytoplasmic membrane of gram negative |
| mot protein of the basal body (flagella) | provide the torque for the flagella to rotate; located in cytoplasmic membrane |
| fli protein of the basal body (flagella) | provide the direction for the flagella to rotate (clockwise or counterclockwise); located in cytoplasmic membrane; proton motive force provides the energy |
| gliding | considerably slower than propulsion by flagella but still provides a means of moving about; requires that the cells be in contact with a solid surface; may excrete slime |
| twitching motitility | uses pili extension and retraction |
| catabolic reactions | energy releasing (exergonic) |
| anabolic reactions | energy requiring (endergonic) |
| CHONPS | close to 95% dry weight of cell; major components of macromolecules |
| carbon | 50% of a cell's dry weight; many prokaryotes require this |
| nitrogren | comes in two forms: organic and inorganic with the bulk being in the inorganic form. |
| obligate aerobes | can only extract energy from compounds in the presence of oxygen |
| obligate anaerobes | can only extract energy in the absence of oxygen |
| facultative anaerobes | can extract energy in the presence or absence of oxygen |
| facultative aerobes | can extract energy in the presence or absence of oxygen but grow better when in the presence of oxygen |
| Gibbs free energy (G) | energy released that is available to do work; if negative, reaction will release energy and therefore exergonic; if positive, reaction requires energy and therefore endergonic; says nothing about rate |
| enzymes | highly specific; combines with the substrate at the active site forming an enzyme-substrate complex by forming weak bonds. as the reaction proceeds, the product is released and the enzyme returns to its original form. |
| prosthetic groups of enzymes | bind tightly to enzyme; typically bind permanently by covalent bonds |
| coenzymes | loosely bound to enzymes; single coenzyme molecule may associate with a number of different enzymes |
| oxidation | removal of electrons from a substance |
| reduction | addition of electrons to a substance |
| reduction potentionals | written as reduction half reactions; standard conditions are at pH=7; more negative donates electrons to the more positive; more positive - more negative; |
| electron tower | the farther the electrons drop from a donor before they are caught by an acceptor, the greater the amount of energy released. |
| faraday's constant | 23 kcal/volt used in the formula: G=-nFE |
| catabolism (fueling): phase 1 | degradative metabolism, exergonic, oxidative, G=-, spontaneous |
| anabolism (biosynthesis, polymerization, assembly): phase 2-4 | biosynthetic metabolism, endergonic, reductive, G=+ |
| fueling - phase 1 | provides: energy (from oxidation of energy source in a complete redox reaction), C skeleton (12 intermediates [3 central pathways: EM, Krebb's, Pentose]), reducing power. |
| biosynthesis - phase 2 | uses the C skeletons to make subunits of macromolecules;12 key precursor metabolites that produce the correct #'d C skeletons: 20 amino acids, 4 Rnucleotides, 4 Dribonucleotides, monosacc, n-acetylglucosamine, n-acetylmuramic acid, fatty acids, glycerol |
| polymerization - phase 3 | consist of the directed, sequential linkage of activated molecules into long (branched?) chains; polymerization of building blocks into proteins, dna, rna, and glyco occur inside the cell where their assembly into LPS, capsule, murein are outside of cell |
| assembly - phase 4 | involve the chemical modification of macromolecules, their transport to prespecified locations in the cell, and their association to form cellular strucutres |
| high-energy phosphate bonds | in living organisms, chemical energy released in redox reactions is conserved in these bonds; function as the energy source to drive energy-requiring reactions in the cell |
| phosphate groups | are attached via oxygen atoms by ester or anhydride bonds; NOT all phosphate bonds are high-energy bonds |
| substrate level phosphorylation (SLP) | direct synthesis of ATP or other high energy phosphate in a direct chemical (metabolic) reaction |
| oxidative phosphorylation (OP) | electron transport mediated synthesis of ATP. mechanism involves mitchell's chemiosmosis and generation of proton motive force |
| electron transport chain | the presence of a series of membrane associated electron carries arranged in order of more positive E0'; the generation of a H+ motive force as a result of charge separation across the membrane, acidic (out), and alkaline (in); alternatio of e only and e+ |
| fermentation | involves glucose oxidation to pyruvate and the donation of hydrogens from NADH+ plus H+ to pyruvate or a derivative of it; uses 2 atp to start; only 2 net atp produced by two slp steps; rate is fast; no oxygen; no atp from op; em pathway |
| bacterial respiration | 4 moles of NADH and 1 mole of FADH2 are produced per pyruvate; since there are 2 pyruvates per starting glucose, this produces 30 net atp; when the two slp atp are added and the nadh goes to e transport to produce 6 more; making a total of 38 atp per cell |
| atp synthase | catalyst for conversion of proton motive force into atp; |
| anaerobic respiration | biological oxidation in which the terminal electron acceptor is usually inorganic molecule (external) other than oxygen(nitrate, sulfate, or carbon dioxide); uses oxidative phosphorylation for atp synthesis; |
Created by:
JacobGant
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