Biol 251 Chapter 6 & 8

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  1. Psychrophiles
    • Cold loving
    • Different kind of lipids in their membrane structure - more unsaturated fats
    • Cold shock protein (choperones) which response to cold stress, protein stay folding in form of ice crystal face;anti frozen mechanism
    • Optimum growth at 15 degree Celsius; highly sensitive to higher temperature
    • Most cannot survive at room temperature
    • These microbes developed adaptation to survive different environment
  2. Psychrotrophs
    • Optimum temperature 20 - 30 degree Celsius, grow well in refrigerator cause food spoilage;milk, juice, cheese
    • Reproduction rate decrease at the low temperature - slow degrade food
    • Listeria is pathogenic bacteria found on ready to eat meat or hot dog - immune compromise or older, pregnant women need to avoid
    • Grow continuously in refrigerator - fever, stiff neck, confusion, vomitting
  3. Mesophiles
    • Optimal growth at 25 - 40 degree Celsius - most common type of microbes
    • Organisms that have adapted to live in the body of animal usually have an optimal temperature close to that of their host (37 degree Celsius)
  4. Thermophiles
    • Heat loving
    • Motility;in high temperature molecules move frequently
    • Plasma membrane structure - saturate fat
    • Heat shock protein (choperones) keep protein from denature - stay folding
    • Optimal 50 - 60 degree Celsius; hot water tap sunlit soil, thermal waters, hot springs
    • Thermophiles are not considered public health problems
    • Endospore formed by thermophilic bacteria are usually heat resistant - canned food
  5. Hyperthermophiles or extreme thermophiles
    • Bactria that grow at temperatures over 80 degree Celsius - thermal vent, volcanic hot springs
    • Pressure (autoclave) allows hotter & adaptation makes hyperthermophiles live in hot temperature
    • Immense pressure in the ocean depths prevents water from boiling at temperatures will above 100 degree Celsius
  6. How do bacteria reproduce?
    • Binary fission 
    • Budding
    • Filaments
    • Fragments
  7. Binary Fission process
    • Cell elongates and DNA replicates
    • Cell wall and plasma membrane begin to constrict
    • Cross-wall forms
    • Completely separating the two DNA copies
    • Cells separates
  8. Budding
    • Pinch off
    • They form a small initial outgrowth (a bud) that enlarges until it's size approaches that of the parent cell, and them it separates
  9. Fliaments
    Some filamentous bacteria (certain actinomycetes) reproduce by producing chains of conididspores (an asexual spore) carried externally at the tips of the filaments
  10. Fregments
    Few filamentous species simply fragment and the fragments initiate the growth of new cells
  11. List the phases of growth
    • Lag phase
    • Log phase
    • Stationary phase
    • Death phase
  12. Lag phase
    • The number of cells changes very little because the cells o not immediately reproduce in a new medium
    • This period of little of no cell division is called Lag phase and it can last for 1 hour or several days
    • During this time, however, the cells are not dormant
  13. Log phase
    • Cells begin to divide and enter a period of growth, or logarithmic increase, called the log phase or exponential growth phase
    • Cellular reproduction is most active during this period, and generation time (intervals during which the population doubles) reaches a constant minimum
    • The log phase is the time when cells are most active metabolically
  14. Stationary phase
    • The growth rate slows, the number of microbial death balanes the number of new cells and population stabilize 
    • This period of equilibrium is called he stationary phase - cause exponential growth to stop
  15. Death phase or logarithmic decline phase
    The number of death eventually exceeds the number of new cells formed, and the population enters the death phase or logarithmic decline phase
  16. What is cause of exponential growth to stop?
    • Exhaustion of nutrients
    • Accumulation of waste products
    • Harmful changes in pH
  17. What are the chemical requirements for growth?
    • Carbon
    • Nitrogen
    • Sulfur
    • Phosphorus
    • Trace element
    • Oxygen
    • Organic growth factors
  18. Carbon
    • Structural back bone or organic molecules
    • Chemotroph use organic as energy- sugar, lipids, proteins
    • Authotroph use CO2 as energy source
    • All micro molecule meed carbon - life must have carbon
    • Chemoheterotroph; derive organic materials from the surroundings (protein, carbon, lipids)
    • 50% of dry weight is carbon
  19. Nitrogen
    • Component of protein (amino group), DNA and RNA (nucleotide), and ATP
    • Protein synthesis requires considerable amount of nitrogen as well as some sulfur
    • Nitrogen makes up about 14% of the dry weight
    • Organics use nitrogen primarily to form the amino group of amino acid of protein
    • Most bacteria decompose protein material from nitrogen source
    • Some bacteria use NH4+, NO3- for organic material
    • Some bacteria use N2 (gaseous nitrogen) directly from atmosphere - nitrogen fixation
    • Nitrogen can break down their own or from surroundings
    • Without nitrogen, organism an not have DNA or proteins
  20. Sulfur
    • Used to synthesis sulfur - containing amino acids and vitamins; Thiamine & Biotin
    • Most bacteria compose proteins for the sulfur source - important natural source of sulfur include sulfate ion, hydrogen sulfide and sulfur containing amino acid
    • Cystein - sulfur containing amino acid; break down protein tho get sulfur or from surroundings
  21. Phosphorus
    • Phosphorus is essential for the synthesis of nucleic acid (DNA, RNA) and phospholipids of cell membranes
    • Also found in energy bond of ATP
    • Microbes derive phosphorus from phosphate ions
  22. Trace Elements
    • Microbes require very small amount of other mineral elements ( inorganic - no carbon bond); iron, copper, molybdenum, and zinc
    • Most are essential for the function of certain enzymes - usually as cofactors
  23. Oxygen
    • Obligate aerobes
    • Facultative anaerobes
    • Obligated anaerobes
    • Aerotolerant anaerobes
    • Microaerophiles
  24. Obligated aerobes
    • Only aerobic growth; oxygen required
    • Growth occurs only where high concentrations of oxygen have diffused into the medium
    • Presence of enzymes catalase and superoxide dismutase (SOD) allows toxic forms of oxygen to be neutralized; can use oxygen
  25. Facultative anaerobes
    • Both aerobic and anaerobic growth; greater growth in presence of oxygen
    • Growth is best when oxygen is presented, but occurs through tube
    • Presence of enzymes catalase and SOD allows toxic forms of oxygen to be neutralized; can use oxygen
    • Ability to continue growing in absence of oxygen 
    • Facultative anaerobes can use oxygen when it is present but they are also able to continue growth by using fermentation or anaerobic respiration when oxygen is not available
  26. Obligated anaerobes
    • Only anaerobic growth; growth ceases(stop) in presence of oxygen
    • Growth occurs only where there is no oxygen
    • Lacks enzymes to neutralize harmful forms of oxygen; cannot tolerate oxygen
    • Bacteria that are unable to use molecular oxygen for energy yielding reaction, infect most of them are harmed by oxygen
  27. Aerotolerent anareobes
    • Only anaerobic growth; but growth continue in presence of oxygen
    • Growth occurs evenly; oxygen has no effect Presence of one enzyme, SOD allows harmful forms of oxygen to be partially neutralized; tolerate oxygen
    • Cannot use oxygen  for growth but they tolerate it fairly well
    • Many of the aerotlerant bacteria characteristically ferment carbohydrates to lactic acid
    • Aerotlerant anaerobes can tolerate oxygen because they posses SOD or an equivalent system that neutralizes the toxic forms of oxygen
  28. Microaerophiles
    • Only aerobic growth; oxygen required in low concentration
    • Growth occurs only where a low concentration of oxygen has diffused into medium
    • Produce lethal amounts of toxic forms of oxygen if exposed to normal atmospheric oxygen
    • They are aerobes; they do require oxygen, however, they grow only in oxygen concentrations lower than those in air
    • Limited tolerance is due to their sensitivity to superoxide radicals and peroxides, which they produce in lethal concentrations under oxygen-rich conditions
  29. Toxic forms of oxygen
    • Singlet oxygen (O2-) - normal molecular oxygen O2 that has been boosted into higher energy state and extremely reactive
    • Superoxide radicals or superoxide anions - In the presene of oxygen, obligated anaerobes also appear to form some superoxide radicals which are so toxic to cellular components that all organisms attempting to grow in atmospheric oxygen must produce an enzyme, superoxide dismutase (SOD) to neutralize them.
  30. Characteristics of prokaryotes in replication,
    • Single point of origin
    • Replication process both directions
    • Operons are clusters of structural gen (more than one gene) with a single promoter
    • The end of promoter is called operator which controls the transcription of the genes
  31. Characteristics of prokaryotes in transcription
    • Happens in cytoplasm
    • 3-20 proteins involved (RNA polymerase and sigma factors)
    • More than one gene on a mRNA (operon)
    • Do not go through RNA processing; no splicing
  32. Characteristics of prokaryotes in translation
    • Happens in cytosole
    • Can begin before transcription has finished
    • One gene become one protein
    • 70s ribosomes (30s+50s)
  33. Characteristics of eukaryotes in replication
    • Multiple points of origin
    • Replication process in both directions from each points
    • Split genes
    • Eukaryotic structural gene has a single promoter and contains intron; control elements that one not part of the gene control the transcription of the gene
  34. Characteristics of eukaryotes in transcription
    • Happens in the nucleus
    • 1000-2000 proteins involved (RNA polymerase and transcription factors)
    • Only 1 gene on a mRNA
    • Go through RNA processing; cut introns out, splice exons together
  35. Characteristics of eukaryotes in translation
    • Happens in cytosole
    • Can only begin once transcription has finished and mRNA is transported to cytosol
    • One gene can become several different proteins due to RNA splicing
    • 80s ribosomes (40s+60s)
  36. Mutation
    Permanent changes in the base sequence of DNA (chromosome)
  37. What are two types of mutations that change the DNA sequence?
    • Point mutation (Base substitution) - Result from the deletion, insertion or substitution of a single mucleotide
    • Chromosomal mutation - result fro the extensive changes in DNA structure; deletions, insertions trans-locations of large sequences of nucleotides
  38. What are mutations that changes DAN sequence?
    • Spontaneous mutation
    • Induced mutation
    • Silent mutations
    • Nonsense mutation
    • Missense mutation
    • Frame shift mutation
  39. Spontaneous mutation
    • Permanent changes in genetic code without the influence of external forces, just because cellular processes are imperfect
    • Base substitutions and frame-shift mutations may occur spontaneously because of occasional mistakes make during DAN replication. 
    • These spontaneously mutations apparently occur in the absence of any mutations causing agent
  40. Induced
    Permanent changes in genetic code caused by an outside force (mutagen)
  41. Silent mutations
    • Do not change the amino acid sequence
    • The change in DNA base sequence causes no change in the activity of the product encoded by the gene
  42. Nonsense mutaion
    • Change the amino acid sequence stopping the translation too soon
    • By creating nonsense codon (stop) in the middle of an mRNA molecule, some base substitutions effectively prevent the synthesis of complete functional protein - no protein made
  43. Missense mutation
    Change the amino acid by 1 sequence of amino acid
  44. Frame shift mutation
    • Change the amino acid sequence form that point onward
    • Base-pair mutations, there are also changes in DNA called frame-shift mutations in which one or a few nucleotide pairs are deleted or inserted in the DAN 
    • Stopping the translation can cause
  45. How does transformation work?
    • Transformation - genes are transferred fro one bacteria to another as "naked" DNA in solution
    • Same bacteria, perhaps after death and cell lysis, release their DNA into the environment. Other bateria can then encounter the DNA, and depending on the particular species and growth conditions, take up fragments of DAN and integrated them into their own chromosomes by recombination protein called Aec A binds to cell's DNA
  46. Process of transformation
    • Living encapsulated bacteria injected mouse - died - colony of encapsulated bacteria isolated
    • Living nonencapsulated bacteria injected mouse - healthy - few colony of nonencapsulated isolated
    • Heat-killed bacteria injected into mouse - Healthy - no colony were isolated
    • Living nonencapuslated and heat-killed encapsulated bacteria injected- mouse died- colonies of encapsulated bacteria were isolated
  47. Mechanism of genetic transformation in bacteria
    • Recipient cell takes up donor DNA
    • Donor DNA aligns with complementary bases
    • Recombination occurs between donor DNA and recipient DAN - genetically transformed cell
  48. Conjugation
    • Plasmid transferred from one bacterium to another.
    • Requires cell-to-cell contact via sex pili
    • Donor cells carry plasmids (F factor) and are called F+ factor cells
    • Hfr cells contain F factor on the chromosome
    • Another mechanism by which genetic material is transferred form one bacterium to another is known was conjugation.
    • Conjugation is mediated by one kind of plasmid, a circular piece of DNA that replicates independently form the cell's chromosome
  49. How conjugation work?
    • When F factor (a plasmid) is transferred from donor (F+) cell to recipient (F-) cell, F- cell is converted to a F+ cell
    • When F factor becomes integrated into chromosome of an F+ cell, it makes the cell a high fragments of recombination (Hfr)cell
    • When Hfr donor passes a portion of its chromosome into a F- recipient, a recombinant of F- cell results
  50. Conjugation differ form transformation in two major ways
    • Conjugation requires direct cell-to-cell contact
    • The conjugation cells must generally be of opposite mating type; donor cells must carry plasmid, and recipient cells usually do not
  51. Gram negative bacteria conjugation
    In gram-negative bacteria, the plasmid carries genes hat code for the synthesis of sex pili, projections from the donor's cell surface that contact the recipient and help bring the two cells into direct contact
  52. Gram positive bacteria conjugation
    • Gram-positive bacteria cells produce sticky surface molecules that cause cells to come into direct contact with each other.
    • In the process of conjugation the plasmid is replicated during the transfer of a single stranded copy of the palsmid DNA to the recipient
  53. F factor (fertility factor)
    • First plasmid observed to  be transferred between cells during conjugation
    • Donors carrying F factors (F+ cells) transfer the plasmid to recipient(F- cell), which become F+ cells as a result
    • The F factor is a conjugation plasmid that carries genes for sex pili and for the transfer of the plasmid to another cell. Although plasmids are usually dispensable, under certain conditions genes carried by plasmids can be crucial to the survival and growth of the cell
  54. Hfr cell (Highly fragment recombination)
    • In some cells carrying F factors, the factor integrates into the chromosome, converting the F+ cells to an Hfr cell
    • Conjugation with an Hfr cell, an F- cell may acquire new versions of chromosomal genes ( just as in transformation) However, it remains an F- cell because it did not receive a complete F factor during conjugation
  55. How do bacteriophages contribute to the transfer of genetic material?
  56. Transduction
    • A thridmechanism of genetic transfer between bacteria is transduction
    • In this process, bacterial DNA is transferred form a donor cell to a recipient cell inside a virus that infects bacteria called a Bacteriophage, or phage
    • To understand how transduction works, we will consider the life cycle of one type of transducting phage of E. coli; this phage carries out generalized transduction
    • All genes contains within a bacterium infected by a generalized transduction phage are equally likely to be packaged in a phage coat and transferred
    • In another type of transduction called specialized transduction only certain bacterial genes are transferred
  57. Transduction in bacteria
    • DNA is transferred form a donor cell to recipient via a bacteriophage
    • Generalized transduction - random bacterial DNA is packaged inside a phage and transferred to recipient cell
    • Specialized transduction - specific bacterial genes are packaged inside a phage and transferred to a recipient cell
  58. Transduction by bacteriophage
    • Generalized transduction
    • A phage infects the donor bacterial cell
    • Phage DNA and proteins are made and the bacterial chromosome is broken into pieces
    • Occasionally during phage assembly, pieces of bacterial DNA are packaged n a phage capsid
    • Then the donor cell lysis and release phage particles containing bacterial DNA
    • A phage carrying bacterial DNA infects a new host cell, the recipient cell
    • Recombination can occur, producing a recombinant cell with a genotype different from both the donor and recipient cells
  59. What are plasmids and what are some of their capabilities?
    • Plasmid are self-replicating, gene containing circular pieces of DNA
    • 1 to 5% the size of a bacterial chromosome
    • Often code for proteins that enhance the pathogenicity of a bacterium
    • Conjugation plasmid - carries genes for sex pili and transfer of the plasmid
    • Dissimilation plasmids - encode catabolism of unusual compounds
  60. R factor (resistant factor)
    • Encoded antibiotic resistant
    • Resistance factors are palsmids that have significant medical importance
    • R factors carry genes that confer upon their host cell resistance to antibiotics heavy metals, or cellular toxins
    • Many R factors contain two groups of genes Resistant transfer factor (RTF). r-determinant
    • R factors present very serious problems for treating infectious disease with antibiotics
  61. Dissimilation plasmid
    • Code for enzymes that trigger the catabolism of certain unusual sugars and hydrocarbons
    • Such specialized capability permit the survival of those microorganisms in very diverse and challenging environments
    • Other plasmids code for proteins that enhance the pathogenicity of a bacterium. the train of E. coli that causes infant diarrhea and traveler's diarrhea carries palsmids that code for toxin production and for bacterial attachment to intestinal cells
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Biol 251 Chapter 6 & 8
2016-05-08 11:55:27
Microbial genetics growth

Biol 251 Chapter 6 & 8
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