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Med micro
Exam 2
| Question | Answer |
|---|---|
| Microbial nutrition | all living organisms require a constant influx of certain substances from their habitat...for example, need C, H, O, P, K, N, Ca, Fe, Na, Cl, Mg, and other elements.... |
| essential nutrient | any substance that an organism must have |
| Macronutrients | required in relatively large quantities and play principal roles in cell structures and metabolism |
| Micronutrients | also called trace elements, are present in much smaller amounts and are involved in enzyme function and maintenance of protein structure...includes manganese, zinc, and nickel |
| the main determinant of a microbe's nutritional type | source of carbon and energy |
| Carbon source | can an organism use CO2 for its carbon source or does it have to obtain its carbon in an organic form |
| Energy source | can an organism utilize sunlight asa source of energy (photosynthesis) or does it gain energy from chemical compounds |
| Autotrophs | an organism that can use CO2 as its carbon source, are not nutritionally dependent on any other living things |
| Heterotrophs | an organism that must obtain its carbon in an organic form |
| Phototrophs | an organism that can utilize energy captured from sunlight |
| Chemotrophs | an organism that can gain its energy from organic chemical compounds |
| Photoautotrophs | an autotroph that uses light as its energy source |
| Chemoautotrophs | an autotroph that obtains their energy from chemical compounds |
| Photoheterotrophs | heterotrophs that use light as an energy source |
| Chemoheterotrophs | heterotrophs that use preformed chemical compounds for both energy and carbon |
| Microorganisms must be able to take in necessary nutrients and expel waste | transport of substances occurs across the cell membrane, a structure specialized for this role....specialized membrane proteins for transport of different molecule |
| diffusion | molecules move in a gradient from an area of higher to lower density or concentration...the driving force is the natural tendency of molecules to be in constant random motion....becomes faster as the temperature increases |
| limits of simple diffusion | movement of solutes by simple diffusion is limited to small non polar molecules like oxygen or lipid soluble molecules that can pass through the membrane |
| osmosis | when there is a concentration gradient of larger molecules that are blocked but the cell membrane , water can move across the membrane to equilibriate the concentrations .....the water moves to equilibriate |
| Hypotonic conditions | the solute concentration of the external environment is lower than the cell's internal environment....water moves into cell, cell can burst |
| Hypertonic conditions | the solute concentration of the external environment is higher than the cell's internal environment....water moves out of cell, cell can shrivel |
| Isotonic conditions | environment is equal in solute concentration to the cell's internal concentration...no net change in cell water levels |
| facilitated diffusion | there is an associated protein transport that allows diffusion but goes with the gradient so is still passive |
| active transport | requires the presence of specific membrane spanning proteins and often needs an input of energy...goes against the gradient |
| endocytosis | an energy-using process by which cells absorb molecules, particles, or even other cells by engulfing them...cells can encapsulate and engulf large particles |
| microbial cells cannot control their temperature and take on the ambient temperature of their natural environment | they cannot regulate their own temperature...have an optimal range for temperatures for the growth of a certain species |
| cardinal temperatures | the small range of temperatures which promotes the fastest rate of growth and metabolism in a certain species of microbe |
| Psychrophiles | have an optimal growth below 15ºC and generally cannot grow above 20º C many are found in deep water |
| Psychotrophs | have a slightly higher optimal temperature than the psychrophiles...they are a problem in low temperature food spoilage |
| Mesophiles | comprise the majority of medically significant microorganisms....optimal temperatures fall in the range of 20ºC and 40ºC.....most human pathogens are mesophiles |
| Thermophiles | microbes that grow optimally at temperatures greater than 45º C.....in soil and water associated with volcanic activity, in compost piles, and in habitats directly exposed to the sun |
| Extreme thermophiles | grow between 80º C and 121º C |
| Oxygen | an important respiratory gas, but also a powerful oxidizing agent...can be toxic |
| Obligate aerobes | use gaseous oxygen in their metabolism and possess the enzymes needed to process toxic oxygen substances |
| Obligate anaerobes | do not use oxygen in respiration and lack the enzymes needed for processing toxic oxygen and will die in its presence |
| Facultative anaerobes | do not require oxygen for metabolism, but will use it and do prefer it when it is present |
| Aerotolerant anaerobes | do not use oxygen but can tolerate its presence |
| most bacteria grow best at a narrow pH range | near neutrality, 6.5-7.5 pH |
| Acidophiles | some bacteria that can grow in conditions where the pH level is as low as 1 |
| Alkalinophiles | prefer high pH and live in hot pools/soils that contain high levels of basic minerals....like the sulfur pits |
| most organisms cannot grow in a high solute environment.... | water in the cell will leave the cell through osmosis if the environment is too salty |
| Extreme halophiles | microbes that require high salt conditions for growth....found in the Great Salt Lake and the Dead Sea |
| Facultative halophiles | do not require high salt concentrations to live, but can still tolerate hight salt conditions up to 90% |
| barophiles | can live under high pressure and will often die under normal conditions |
| microbes live in shared habitats which give rise to complex and fascinating associations | interactions can be beneficial, harmful, or have no particular effect |
| Symbiosis | a situation where two organisms live together in a close partnership |
| mutualism | when organisms Iive in an obligatory but mutually beneficial relationship |
| Commensalism | where only one partner is benefitted and the other is neither benefitted not harmed |
| parasitism | a relationship in which the host organism provides the parasitic microbe with nutrients and a habitat...the host organism is typically harmed to some extent |
| Synergism | a relationship between two free-living organisms that benefits them but is not necessary for their survival...they participate together to do something that couldn't do on their own |
| binary fission | the method of bacterial reproduction....asexual reproduction and cell division used by all prokaryotes |
| bacterial growth | refers to increase in bacterial population size, not the size of individual cells |
| generation time | the time required for a cell to divide (population of bacteria to double) |
| faster generation time for pathogens | means it has a shorter incubation time (how long it takes to start feeling the symptoms) |
| a population of bacteria does not maintain its potential growth rate and does not double endlessly | populations typically display a pattern of growth called a growth curve |
| four stages of the growth curve | lag, log, stationary, death |
| lag phase | a short time after the bacterial cells are placed into a fresh medium....the cells do not immediately reproduce and very little change in population is apparent. Bacteria need time to adjust to a new environment |
| log phase (growth> death) | when the bacterial cells have adjusted, the cells begin to divide and enter a period of growth....cellular reproduction is most active and the generation time becomes constant..as long as the cells have adequate nutrients and the environment is stable |
| stationary phase (growth = death) | the growth rate will slow and the population number will stabilize as microbial death balances new growth (exhaustion of nutrients, accumulation of waste products, and harmful changes in pH can start the stationary phase) |
| death phase (growth < death) | a bacterial population will enter the death phase when the number of deaths begins to exceed the number of new cells formed |
| metabolism | the sum of all chemical reactions that occur within living organisms |
| catabolism | the breakdown of complex organic compounds into simpler ones....typically release energy (are exergonic)------digestion, like glycolysis |
| anabolism | the building of complex organic molecules from simpler ones....typically require energy (are endergonic) ----biosynthesis like Photosynthesis |
| ATP | adenosine triphosphate...the energy currency inside all cells, provides the energy needed for all cellular work |
| ATP coupling | anabolic reactions can be coupled to ATP breakdown...ATP stores the energy from catabolic reactions and releases it top drive anabolic reactions and perform cellular work |
| redox reactions | oxidation (the removal of electrons from a molecule) releases energy....a proton is removed in the form of a hydrogen.....the reduction of a molecule (replacing the H) requires energy |
| Activation energy | the energy required for a reaction to take place |
| reaction rate | depends on the number of reactant molecules at or above the activation energy level....can be affected by temperature |
| Enzymes | act as a biological catalyst....are very specific and act on only 1 substrate, increase the probability of a reaction to occur, can be used many times |
| active site | tue area of the enzyme that interacts with the substrate...the enzyme will bind and orient the substrate in the way that increases the potential of the reaction |
| enzyme-substrate complex | the formation of the enzyme-substrate complex effectively lowers the activation energy of the reaction |
| Most enzymes are proteins | there is a small category of enzyme that are RNA |
| Simple enzymes | consist of protein alone |
| Conjugated enzymes | contain protein and non-protein molecules( additional elements used to aid in their actions---cofactors etc.) |
| Cofactors | if the additional molecule used by the enzyme is metal or inorganic molecule |
| Coenzymes | if the additional molecule used by the enzyme is an organic molecule |
| Constitutive enzymes | always present and in relatively constant amounts |
| Regulated enzymes | the levels are tightly controlled, being either turned on or off in response to changes in concentration of the substrate |
| Enzymes have an optimal temperature for their function | too cold, molecules move too slow for reaction to proceed too hot, the enzyme will denature (lose shape and function) |
| Enzymes have an optimal pH range for their function | raising or lowering the pH will lower enzymatic activity |
| substate concentration also effects enzyme activity | enzyme activity increases as the substrate concentration approaches saturation |
| a sequence of enzymatically catalyzed reactions | called a metabolic pathway...used to extract energy from organic compounds and store it in a form of chemical energy |
| metabolic pathways | let organisms release the energy from compounds step by step (a little at a time) so that less energy is wasted as heat. |
| types of metabolic pathways | linear (glycolysis) circular (CAC) branched-divergent and convergent |
| enzymes are controlled by inhibitors | gives tight regulation by stopping at one step (enzyme) in a metabolic pathway |
| non-competitive inhibitors (allosteric inhibition) | interact with another part of the enzyme that is not the active site (the allosteric site)....causes binding site to change shape, active site can no longer bind substrate |
| competitive inhibitors | work to compete with the substrate for the active site......competitive inhibitor have similar size, shape, and chemical structure as the natural substrate |
| Feedback inhibition | a type of inhibition used to prevent overproduction of a particular substance that would waste chemical resources.....the end product of a pathway can inhibit the enzymes of the first steps in the pathway....stop the pathway because enough is made |
| Glucose | main energy source for basically all types of organisms |
| Cellular respiration | the harvesting of energy from the breakdown of food molecules |
| main stages of energy harvest by cellular respiration | glycolysis---kreb's cycle---electron transport chain (oxidative phosphorylation) |
| glycolysis | the oxidation of a glucose (6C) molecule into two pyruvate (3C) molecules....a process that occurs in the majority of living cells (10 step process) |
| net gain of ATP from glycolysis alone | 4 are made, two get used....2 ATP is net gain per glucose molecule |
| Anaerobic cellular respiration | glycolysis is an anaerobic cellular respiration process...no Oxygen is needed in this process |
| the Kreb's Cycle | a series of biochemical reactions in which the large amount of potential energy stored in pyruvate is released step by step (2 acetyl-coAs go into the cycle from the 2 pyruvates) |
| Net gain from the CAC | 2 ATP, 6 NADH, and 2 FADH2, and 4 CO2.....from one glucose molecule |
| converting pyruvate to acetyl-CoA | releases 2 CO2 and 2 NADH |
| the ETC | the last stage of cellular respiration (oxidative phosphorylation) energy is produced by the electron carriers FADH2 and NADH.... energy is passed form one carrier to the next, using energy to pump proteins outside the cell |
| proton gradient | proton pumping creates a gradient where more protons are found on the outside of the membrane than the inside...the "down-hill" run of the protons back into the cell reestablishes equilibrium and is used to drive ATP synthesis |
| enzyme of ATP synthesis | ATP synthase....Hydrogen channel propels the phosphorylation of ADP to ATP |
| the final electron acceptor | Oxygen....picks up the electrons transferred from NADH and FADH2...also grabs protons to create H2O harmless to body |
| 1 NADH makes... | 3 ATP |
| 1 FADH2 makes | 2 ATP |
| total ATP made in prokaryotic cellular respiration from one glucose molecule | 38 ATP |
| in eukaryotic cells.....total ATP | less than 38 since there is energy required in transport through mitochondrial membranes etc.... is around 36 ATP |
| Aerobic respiration | a series of pathways that convert glucose to CO2 and allows the cell to recover significant amounts of energy (includes Glycolysis, Kreb's Cycle, and ETC) ...relies on O as final electron acceptor |
| Anaerobic respiration | uses the same three pathways but doe not use O as the final electron acceptor....instead uses NO3, SO4, CO3, or other compounds are the final electron acceptors |
| Fermentation | an alternate usage of the pyruvic acid created in glycolysis...does not go through Kreb's cycle or the ETC.....is needed to replenish NAD+ for glycolysis |
| reasons to undergo fermentation | some organisms have to since they are anaerobic, but some will just when O is scarce.......pyruvic acid gets converted into many different end products depending on the organism, |
| Lactic Acid Fermentation | the two molecules of NADH made in glycolysis are oxidized to NAD+ and pyruvic acid is reduced to lactic acid.....this ends the pathway |
| organisms that do lactic acid fermentation | used to make yogurt, sauerkraut, pickles, etc... |
| Alcohol fermentation | the two molecules of pyruvic acid are converted into two molecules of acetaldehyde, 2 molecules of CO2 are released....the NADH then reduces the acetaldehyde to ethanol....converts NADH to NAD+ |
| organisms that do alcohol fermentation | yeasts and many bacteria....can provide the alcohol in alcoholic beverages and the CO2 made by yeasts cause bread to rise |
| lipida and proteins | can also be used as energy sources in the cell....as they are broken down, some of their parts will enter at different stages of Glycolysis and the Kreb's cycle |
| Glycerol from lipids | can be converted into G3P....glycolysis |
| Fatty acids | can be converted into Acetyl co-A....kreb's cycle |
| Genetics | the study of inheritance or heredity of living things |
| four things included in genetics | 1) transmission of biological traits from parents to offspring 2) expression and variation of these traits 3) the structure and form of the genetic material 4) how this material changes |
| genome | the entire genetic material of an organism, includes chromosomal DNA but also plasmids, and mitochondrial/chloroplastic DNA |
| there is lots of variety in number of genes by organism | viruses can have 4-5 genes, E. coli has 4,288 genes on one chromosome, Human has 25,000 genes on 46 chromosomes |
| Chromosome | a discrete cellular structure composed of a neatly packaged DNA molecule (located in the nucleus of Eukaryotic cells |
| most bacteria have one circular chromosome | many bacteria can have several circular chromosomes and a few have linear chromosomes |
| Gene | a segment of DNA that contains the necessary code to make a protein or RNA molecule |
| Genotype | the unique allelic mixture present in an organism's genome, an organism's hereditary material |
| Phenotype | the expression of the genotype as visible features and traits |
| Nucleotide | the basic unit of DNA, made of a phosphate, a deoxyribose sugar, and a nitrogenous base |
| linkage between nucleotides | covalently linked together to form the sugar-phosphate backbone....bases exposed to H bond to its compliment |
| pairing of bases | not random, depends on ability to form H bonds G---C and T--A |
| antiparallel nature of double stranded DNA | one strand runs 5´ to 3´and the other is 3´to 5´ |
| DNA must be replicated in bacterial division | the one chromosome of the bacteria is duplicated, one copy of the chromosome ends up in each of the two daughter bacterial cells |
| DNA replication | the process of duplicating DNA...one parental molecule is turned into two daughter molecules....can take up to 30 cellular proteins |
| Semi-conservative replication | each daughter molecule will have one old strand and one new strand....be the same as the parent molecule in composition |
| Beginning replication | at the origin of replication, an AT rich zone....replication then proceeds in two opposite directions till it meets up with itself at the termination site |
| Steps of replication (1-3) | 1) DNA gyrase unwinds helix 2) helicases bind to unwound DNA and break H bonds...get two separate strands with bases exposed 3) single stranded binding proteins keep two strands apart |
| Steps of replication (4-6) | 4) DNA polymerase synthesizes two new strands of DNA using old DNA as template (made 5´to 3´) 5) the replication fork moves along the DNA .....old DNA strand rewinds with a newly made DNA strand 6) replication forks meet at termination site |
| at the end of replication | DNA ligases complete the synthesis and separate the two circular daughter molecules |
| the replication fork moves along the parental DNA but DNA can only be synthesized in the 5´ to 3´ direction | DNA on the leading strand is made continually but DNA on the lagging strand has to be made in pieces....Okazaki fragments |
| Gyrase and helices | relax and unwind the DNA |
| Single stranded binding proteins | bind to the single stranded DNA to keep it from re-annealing |
| DNA polymerase | synthesizes the DNA |
| DNA ligase | seals the gaps between the Okazaki fragments |
| transcription and translation | the code in DNA is first used to synthesize mRNA by transcription and then translated into proteins by translation |
| transcription is 1 to 1 | 1 DNA base counts as 1 RNA base |
| translation is 3 to 1 | 3 RNA bases counts as 1 codon...1 amino acid |
| Initiation | RNA polymerase recognizes a segment of the DNA called the promoter region |
| Elongation | an mRNA molecule is assembled by the addition of nucleotides that are complementary to the DNA template |
| Termination | the RNA polymerase recognizes another DNA code that signals the separation and release of the mRNA transcript |
| Translation | a cell "reads" the mRNA and uses it to build proteins |
| mRNA...messenger | a copy of the gene in the DNA that carries the sequence that will dictate the eventual amino acid sequence of the protein |
| tRNA....transfer | serves as an adaptor molecule that converts RNA language into protein language |
| rRNA..ribosomal | helps make up the overall structure of a ribosome, the large, complex molecule used for making the protein |
| codons | groups of three nucleotides, each coding for a specific amino acid, gets read by the ribosome |
| there are 64 possible codons | 61 code for an amino acid, three do not...they are stop codons (nonsense) |
| the start codon | AUG...codes for methionine always |
| the stop codons | UAG, UAA, UGA |
| the ribosome binds to the mRNA starting at the AUG start site | the ribosome uses tRNAs with specific amino acids that recognize specific codons that code for the related amino acid |
| each tRNA... | as an anticodon (sequence of three bases that is complementary to the codon) that allows it to base pair with its associated codon |
| the tRNAs bring in the proper amino acids | these amino acids get lined up and peptide bonded...polypeptide bond results |
| end of translation | ends when one of three stop codons on the mRNA are reached....the ribosome is separated from the mRNA and the peptide is released |
| genes can be highly regulated | about 20-40% of genes for proteins are regulated so they are only present when needed....this saves energy! |
| Repression | the regulatory mechanism that inhibits gene expression and decreases the synthesis of proteins...mediated by repressors |
| repressors | block the ability of RNA polymerase to initiate transcription of repressed genes |
| Induction | the process that turns on the transcription of a gene or genes...mediated by inducers |
| inducers | a substance that works to induce transcription of a gene |
| mutation | a change in the base sequence of DNA....can have drastic effects to the protein made, make it not function |
| mutations are rare (spontaneous mutations) | occur at very low rates...once in every ten to the ninth replicated base pairs...DNA polymerase has an editing ability as well |
| point mutations | include the addition, deletion, or substitution of single bases |
| base substitution | the most common type of mutation...a single base in the DNA sequence is replaced with a different base (the incorrect one) |
| when a DNA sequence that codes for a protein gets a base substitution mutation... | the mRNA transcribed will carry an incorrect base at that position......can have many effects (Silent, nonsense, missense) |
| Silent mutation | the amino acid code is not disrupted...the changed base in the RNA codes for the same amino acid |
| missense mutation | an incorrect amino acid is inserted in the position of the mutation....can be conservative (a similarly structured amino acid) or nonconservative (Awidely different amino acid) |
| nonsense mutation | the base substitution cause the creation of a premature stop codon.....there is no amino acid put in... |
| Frame shift mutation | occurs when one or a few nucleotide pair are deleted or inserted in the DNA....causes a shift in reading frame and every amino acid downstream changes.... |
| result of frameshift mutations | a long stretch of altered amino acids...the production of an inactive protein |
| mutagens | agents in the environment such as certain chemicals and radiation that can ring about mutations |
| UV light can be a mutagen | UV light can cause the formation of harmful covalent bonds between certain bases (adjacent thymines in DNA can cross link...thymine dimer, can cause serious damage or death to the cell) |
| Nucleoside analogs are mutagens | these mutagens are chemicals that are structurally similar to normal bases but have slightly altered base-pairing properties.....if they are incorporated into DNA, they cause mistakes to be made in base pairing during replication |
| bacteria have special gene transfer | they can pass on genetic information to other microbes of the same generation...horizontal gene transfer |
| recombinant | the recipient cell that incorporates donor DNA into its own DNA is called a recombinant |
| horizontal gene transfer | the transfer of genetic material between microbes of the same generation |
| Transformation | genes are transferred from one bacterium to another as "naked" DNA the bacteria picks up fragments of free DNA that has been released from another dead cell |
| Conjugation | involves the specific action of a specific plasmid called an F factor...has a gene that codes for the synthesis of sex pili, F factor plasmid is replicated and a copy is transferred from the donor to a recipient |
| the use of pili in conjugation | a projection from the donor's cell surface contacts the recipient and helps bring the two cells into direct contact and allows the DNA to be transmitted into the recipient |
| Hfr (high frequency of combination) cells | plasmids are usually separate from the host genome, but sometimes the F factor can be incorporated into the chromosome of the F+ cell....recombination events can lead to the transfer of chromosomal DNA in addition to the F factor |
| conjugation with a Hfr cell | the recipient cell may get the F factor along with some chromosomal DNA from the host |
| Transduction | bacterial DNA is transferred from a donor cell to a recipient cell by way of a virus...bacterial DNA can get incorporated into new viral particles being produced ... gets transferred to a new bacteria when the virus are released and inject into new cell |
| bacteriophages are the mailmen of transduction | the phages that contains bacterial DNA can infect a new cell and donor DNA is injected into the recipient and new genes may be transferred |
Created by:
Gracie Cook
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