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Physiology Exam 1

Chapter 1
Physiology---the study of biological function--of how the body works, from cell to tissue, tissue to organ, organ to system and of how the organism as a whole accomplishes particular tasks essential for life.

• The study of the mechanical, physical, and biochemical functions of living organisms.
• The study of how cells, tissues, and organs function.
• Dealing with cause-and-effect sequences.
• Knowledge of physiological mechanisms is deduced from date obtained experimentally.

Pathophysiology-----concerned with the functions of diseased or injured body systems and is based on knowledge of how normal systems function, which is the focus of the physiology.

Comparative physiology----the physiology of invertebrates and of different vertebrate groups. Animals including humans are more alike than they are different. It is concerned with the physiology of animals other than humans and shares much information with human physiology.

Three essential characteristics of scientific method

1. It is assumed that the subject under study can ultimately be explained in terms we can understand.
2. Descriptions and explanations are honestly based on observations of the natural world and can be changed as warranted by new observation.
3. Humility谦卑, or willingness to accept the fact that we could be wrong is an important characteristic of the scientific method. The scientist must be willing to change his or her theories when warranted by the weight of the evidence.

What is "vitalism" or "vital spirit"-------Vitalism is the metaphysical 纯粹哲学的, 超自然的doctrine that living organism possess a non-physical inner force or energy that gives them the property of life. It belives that the laws of physics and chemistry alone cannot explain life functions and processes. One example of which is Qi gong It is now replaced by physiology.

What are the advantages of four chambered heart?

• The heart performs two main functions — pumping blood to the lungs (pulmonary circulation), and pumping blood around the body (systemic circulation). The four-chambered heart is the most efficient design because it separates the pulmonary and systemic circulations — there is no mixing of oxygenated blood from the lungs with deoxygenated blood from the body.
• This separation also confers another advantage — the ability to grow to much larger sizes than animals with incomplete separation of pulmonary and systemic circulation (e.g. lizards, with three-chambered hearts). Large animals need high pressures from the systemic left ventrical to pump blood around the body, and such pressures would rupture the delicate tissues in the lungs if the pulmonary system were not separate. In the four-chambered heart, the right ventrical is much smaller and provides the correct pressure to send blood to the lungs.

Theory-----A proved hypothesis. 1) Cell theory: all life starts with a cell. Human(sperm and egg). 2) Evolution.

Teleology----- the philosophical study of design, purpose, directive principle, or finality in nature or huam creations. It is the doctrin of final purpose. All things designed with a purpose in mind and we can trace the path of evolution to the small.

Steps of scientific method

1. Observation: first thing to start out of curiosity. can be visual or mental observation.
2. Study/Experiment: to gether date
3. Analyze date
4. Form a hypothesis: an educated guess of how things work, an attempy to explain how things work.
5. Test hypothesis: design experiment.
6. Modify hypothesis
7. Repeat over and over
8. "Good" hypothesis
9. Publish paper and date on scientific journal.
10. Peer review
11. Theory

Homeostasis----- the constancy坚定不移 of internal environment.

Negative feedback loops

1. Sensor must be able to detect deviations from a set point. A set point for body temperature, blood glucose concentration, the tension on a tendon.
3. When a sensor detects a deviation from a particular set point, it must relay this information to an integrating center which receives information from many different sensor. The integrating center is often a particular region of brain or spinal cord, or a group of cells in an endocrine gland.
5. The relative strengths of different sensory inputs are weighed in the integrating center, which responds by either increasing or decreasing the activity of particular effector( generally muscle or glands) . A direct opposite of what happened.

Antagonistic反对的 effector:

posted by C-T @ 5:11 PM 0 comments

Final Exam 1

History

Robert Hooke (1665)

• Microscophia
• "cella"---cell
  

Anton van Leeuwenhoek

• Dutch dry goods merchant
• 1632-1723
• Famous for animalcules
• He drew what he saw. structural details of protozoa, fungi and microscopic algae.
  
• Report to the Royal Society
• Single lense microscope, enlarges the specimen mount 300 times.
• Observation and experimentation--are sornerstone of all science today.
  

Louis Pasteur

• Ended spontaneous generation controversy (1861)
• Chemist: two different types of tartaric acid crytals.
• Science should have pratical use.
  
• Pasteurization: a pratical solution to sour wine problem.
• Germ theory: microorganisms are responsible for infectious disease.( swan-neck flask experiment)
  
• Reported anthrac bacillus is temperature sensitive. Anthrax spores from the soil and suggested diseaed animals should be buried and burned deeply in the soil.
  
• Vaccinated sheep against anthrax by suspending the bacteria in mild acidic medium and remain undisturbed for a longer peroid.
  
• Diphtheria vaccine 1894
• Rabbi vaccine.
• péine disease of silkworms was caused by a protozoan parasite
• Confirmed water is a way of transmission.
• Won Nobel prize 1905 because of tuberlosis.

Robert Koch( 1843-1910)

• Linked microbes to disease.
• Proved germ theory. Koch's Postulates and are still used to establish the link between a particular microorganism and a particular disease:(mice and anthrax experiment)
  
• The microorganisms must be present in every case of the disease but absent from healthy individuals
• The suspected microorganisms must be isolated and grown in pure culture
• The same disease must result when the isolated microorganism is inoculated into a healthy host
• The same microorganism must be isolated again from the diseased host
• Pure culture on petri dish.

Edward Jenner (1749-1823)-----first vaccination.

Joseph Lister (1827-1912)-----Listerine. Aseptic surgery designed to prevent microorganisms from entering wounds; his patients had fewer postoperative infections, thereby providing indirect evidence that microorganisms were the causal agents of human disease; his published findings (1867) transformed the practice of surgery

Hans Christian Gram (1843-1938)-----Gram stain.

Richard Petri ----- Petri dish

Alexander Fleming----- Discovered antibiotic activity Penicillium notatum.

Rebecca Lancefiel----- studies strptococcal antigens, M protein. Classification of streptococcal hemolytic groups.

The Conflict over Spontaneous Generation

1. The proponents of the concept of spontaneous generation claimed that living organisms could develop from nonliving or decomposing matter
2. Francesco Redi (1626-1697) challenged this concept by showing that maggots on decaying meat came from fly eggs deposited on the meat, and not from the meat itself. It is the first disrupte the SG using experimentation.
   
3. John Needham (1713-1781) showed that mutton broth boiled in flasks and then sealed could still develop microorganisms, which supported the theory of spontaneous generation
4. Lazzaro Spallanzani (1729-1799) showed that flasks sealed and then boiled had no growth of microorganisms, and he proposed that air carried germs to the culture medium; he also commented that external air might be needed to support the growth of animals already in the medium; the latter concept was appealing to supporters of spontaneous generation
5. Louis Pasteur (1822-1895) trapped airborne organisms in cotton; he also heated the necks of flasks, drawing them out into long curves, sterilized the media, and left the flasks open to the air; no growth was observed because dust particles carrying organisms did not reach the medium, instead they were trapped in the neck of the flask; if the necks were broken, dust would settle and the organisms would grow; in this way Pasteur disproved the theory of spontaneous generation

Early Epidemiology and Disease

• Girolamo Francastoro---"Contagion is an infection"
• Ignaz Semmelweis-----Hand washing in chlorine water.
  
• John Snow-----Cholera and the Broad Street water pump.
  

The Trail to DNA

• Edward Griffith -----demonstrated the phenomenon of transformation: nonvirulent bacteria could become virulent when live, nonvirulent bacteria were mixed with dead, virulent bacteria
• Avery, MacLeod, McCarty-----1) demonstrated that the transforming principle 2)DNA is the genetic material in cells.
  
• Erwin Chargaff------1:1 ratio of pyrimidine and purine bases
• Hershey and Chase-----DNA enters cells. showed that for the T2 bacteriophage, only the DNA was needed for infectivity; therefore, they proved that DNA was the genetic material
• Rosalind Franklin-----X-ray image of DNA, important in determining structure of DNA., Maurice Wilkins
• James Watson, Francis Crick-----Determined structure of DNA; Central Dogma

Kingdom and characteristics of prokaryotic and eukaryotic

Five Kingdoms of living things:

1. Monera (Bacteria and cyanobacteria-----Prokaryotic-----E. coli)
   
2. Protista (Unicellular algar, Protozoa----- Eukaryotic unicellular organims-----slime molds, euglenoids, algae, and protozoans)
3. Fungi (Mold, Yeast, Mushroom-----Eukaryotic "multicellular organisms"-----sac fungi, club fungi, yeasts, and molds)
4. Plantae (Mosses, Flowering plants, Green Algar, Brown Algae, Red algae, Golden Algae-----Eukaryotic "multicellular organisms")
5. Animalia (Starfish, Vetebrates, Roundworms, Flatworms, Molluscs, Insect, Segmented worms, Jellyfish, Sponges-----Eukaryotic "multicellular organisms")

Three Domains:

1. The Archaea (archaebacteria)
2. The Bacteria (eubacteria)
3. The Eukarya (eukaryotes)

Characteristics of prokaryotic cells(Archaea, Bacteria)

• Overview of Prokaryotic Cell Structure
• Size, shape, and arrangement
• Procaryotes come in a variety of shapes including spheres (cocci), rods (bacilli), ovals (coccobacilli), curved rods (vibrios), rigid helices (spirilla), and flexible helices (spirochetes)
• During the reproductive process, some cells remain attached to each other to form chains, clusters, square planar configurations (tetrads), or cubic configurations (sarcinae)
• prokaryotic generally smaller than most eucaryotic cells
• Procaryotic cells contain internal structures, not all structures are found in every genus; procaryotes are morphologically distinct from eucaryotic cells and have fewer internal structures.
• Cell membrane.
• The plasma membrane of bacteria consists of a phospholipid bilayer and most bacterial membranes lack sterols.
• Many archaeal membranes have a monolayer instead of a bilayer.
• The Cytoplasmic Matrix
• lacking a true cytoskeleton, the cytoplasmic matrix of bacteria does have a cytoskeleton-like system of proteins
• Inclusion Bodies---Many inclusion bodies are granules of organic or inorganic material that are stockpiled by the cell for future use; some are not bounded by a membrane, but others are enclosed by a single-layered membrane. Gas vacuoles are a type of inclusion body found in cyanobacteria and some other aquatic forms; they provide buoyancy for these organisms and keep them at or near the surface of their aqueous habitat.
• Ribosomes-----synthesis of cellular proteins. Procaryotic ribosomes are similar in structure to, but smaller than, eucaryotic ribosomes.
• The Nucleoid-----an irregularly shaped region in which the chromosome of the procaryote is found.
  
• a single circular chromosome( looped and coiled extensively), though some have more than one chromosome or have one or more linear chromosomes
• The nucleoid is not bounded by a membrane, but it is sometimes found to be associated with the plasma membrane or with mesosomes.
• plasmids are usually small, closed circular DNA molecules. They can exist and replicate independently of the bacterial chromosome. They are not required for bacterial growth and reproduction, but they may carry genes that give the bacterium a selective advantage (e.g., drug resistance, enhanced metabolic activities, etc.
• Cell Wall-----a rigid structure, outside the plasma membrane, it provides the characteristic shapes of the various procaryotes and protects them from osmotic lysis
• The cell walls of most bacteria contain peptidoglycan.
• archaea lacks peptidoglycan and instead are composed of proteins, glycoptoteins, or polysaccharides.
• Gram-positive cell walls-consist of a thick layer of peptidoglycan and large amounts of teichoic acids.
• Gram-negative cell walls, thin layer of peptidoglycan surrounded by an outer membrane composed of lipids, lipoproteins, and a large molecule known as lipopolysaccharide (LPS)--lipid A. LPS can play a role and protectiveact as an endotoxin causing some of the symptoms characteristic of gram-negative bacterial infections; there are no teichoic acids in gram-negative cell walls.
• Components External to the Cell Wall.
• Capsules, slime layers and S layers.
• Capsules and slime layers (also known as glycocalyx) are layers of polysaccharides lying outside the cell wall. a) from phagocytosis, desiccation, viral infection, and hydrophobic toxic materials such as detergents; b) protect the bacteriaaid bacterial attachment to surfaces and gliding motility.
• S layers are regularly structured layers of protein or glycoprotein observed in both bacteria and archaea, the only structure outside the plasma membrane; they protect against ion and pH fluctuations, osmotic stress, hydrolytic enzymes, or the predacious bacterium Bdellovibrio.
• Pili and fimbriae-----short, thin, hairlike appendages that mediate bacterial attachment to surfaces (fimbriae) or to other bacteria during sexual mating (pili)
• Flagella and motility-----Counterclockwise rotation causes forward motion (called a run). Clockwise rotation disrupts forward motion (resulting in a tumble)
• The Bacterial Endospore----- a) a special, resistant, dormant structure formed by some bacteria, which enables them to resist harsh environmental conditions. b) Endospore formation (sporulation) normally commences when growth ceases because of lack of nutrients;

Comparison between Prokaryote and Eukaryote

1. Eucaryotes have a membrane-delimited nucleus and many complex membrane-bound organelles, each of which perform a separate function for the cell
2. Procaryotes lack a membrane-delimited nucleus and internal membrane-bound organelles; they are functionally simpler and do not undergo mitosis, meiosis, endocytosis, and other complex activities performed by many eucaryotes
3. the same basic chemical composition, the same genetic code, and the same basic metabolic processes.

Microscopy

Magnification-----mafnigication of objective lens X magnification of the ocular.

Resolution-----the smallest distance at which one points are seen separate.

Numerical Aperture-----Maximum cone of light thtat enters the objective.

Microscope types

• Light Microscope

• Brightfield Microscope-----1) direct light path 2) used for stained samples 3) student microscope
• Dark field Microscope-----1) light path partially blocked 2)used for unstained samples
• Phase contrast Microscope-----1) enhances the contrast between intracellular structures that have slight differences in refractive index 2) good for unstained living cells
• Differential Interference Contrast(DIC) Microscope-----1) similar to the phase-contrast microscope except that two beams of light are used to form brightly colored, three-dimensional images of living, unstained specimens 2) use polarized light
• Fluorescent Microscope-----1) use UV light for illumination 2) requires labeled sample 3) used in clinical diagnosis.
  
• Confocal Microscope-----1) use laser and pinhole aperture 2) scans specimen along x/y and z zxes 3) higher resolution that other light microscope because out-of-focus light rays are suppressed
• 
  
• Electron Microscope
• Transmission Electron Microscope-----1) electrons scatter when they pass through thin sections of a specimen 2) produce an image of the internal structures of the organism 3) TEM has a resolution about 1,000 times better than that of the light microscope 4) requires heavy metal stain (OsO4)
• Scanning Electron Microscope----- 1) electrons reflected from the surface of a specimen to produce a three-dimensional image of its surface features 2) sample is often sputter-coated with gold.
  

Preparation and Staining of Specimens

1. Fixation refers to the process by which internal and external structures are preserved and fixed in position and by which the organism is killed and firmly attached to the microscope slide
1. Heat fixing----- is normally used for bacteria; this preserves overall morphology but not internal structures
2. Chemical fixing----- is used to protect fine cellular substructure and the morphology of larger, more delicate microorganisms
2. Dyes and simple staining -----are used to make internal and external structures of the cell more visible by increasing the contrast with the background
3. Differential staining----- is used to divide bacteria into separate groups based on their different reactions to an identical staining procedure
1. Gram staining is the most widely used differential staining procedure because it divides bacterial species into two roughly equal groups-gram positive and gram negative
1. The smear is first stained with crystal violet, which stains all cells purple
2. Iodine is used as a mordant to increase the interaction between the cells and the dye
3. Ethanol or acetone is used to decolorize; this is the differential step because gram-positive bacteria retain the crystal violet whereas gram-negative bacteria lose the crystal violet and become colorless
4. Safranin is then added as a counterstain to turn the gram-negative bacteria pink while leaving the gram-positive bacteria purple
2. Acid-fast staining is a differential staining procedure that can be used to identify two medically important species of bacteria-Mycobacterium tuberculosis, the causative agent of tuberculosis, and Mycobacterium leprae, the causative agent of leprosy
4. Staining specific structures
1. Negative staining is widely used to visualize diffuse capsules surrounding the bacteria; those capsules are unstained by the procedure and appear colorless against a stained background
2. Spore staining is a double staining technique by which bacterial endospores are left one color and the vegetative cell a different color
3. Flagella staining is a procedure in which mordants are applied to increase the thickness of flagella to make them easier to see after staining

Microbial Grwoth Curve

1. Population growth is usually analyzed in a closed system called a batch culture; it is usually plotted as the logarithm of cell number versus the incubation time
2. Lag phase-----the period of apparent inactivity in which the cells are adapting to a new environment and preparing for reproductive growth, usually by synthesizing new cell components; it varies considerably in length depending upon the condition of the microorganisms and the nature of the medium
3. Exponential (log) phase-----the period in which the organisms are growing at the maximal rate possible given their genetic potential, the nature of the medium, and the conditions under which they are growing; the population is most uniform in terms of chemical and physical properties during this period
4. Stationary phase-the period in which the number of viable microorganisms remains constant either because metabolically active cells stop reproducing or because the reproductive rate is balanced by the rate of cell death
1. Microbial populations enter stationary phase for several reasons including nutrient limitation, toxic waste accumulation, and possibly cell density
2. Responses to starvation conditions are of practical importance for medical and industrial microbiology; these responses include morphological changes and changes in gene expression and physiology
5. Death phase-the period in which the cells are dying at an exponential rate.

Microbial metabolism

• Glycolysis-----Breakdown of Glucose to Pyruvate
• The 6-carbon sugar stage glucose is phosphorylated twice to yield fructose 1,6-bisphosphate; this requires the expenditure of two molecules of ATP
• The 3-carbon sugar stage cleaves fructose 1,6-bisphosphate into two 3-carbon molecules, which are each processed to pyruvate; two molecules of ATP are produced by substrate-level phosphorylation from each of the 3-carbon molecules for a net yield of two molecules of ATP; 2 molecules of NADH are also produced per glucose molecule
• Krebs cycle
• Pyruvate can be degraded to carbon dioxide after first being converted to acetyl CoA; this reaction is accompanied by the loss of one carbon atom as carbon dioxide
• Acetyl-CoA reacts with oxaloacetate (a 4-carbon molecule) to produce a 6-carbon molecule, which is subsequently broken down to two molecules of carbon dioxide, regenerating the oxaloacetate; during this process.
  
• ATP is produced by substrate-level phosphorylation
• Three molecules of NADH and one molecule of FADH2 are produced
• Electron Transport
• The mitochondrial electron transport chain uses a series of electron carriers to transfer electrons from NADH and FADH2 to O2.
• Electron carriers are located within the inner membrane of the mitochondrion
• During oxidative phosphorylation, three ATP molecules may be synthesized when a pair of electrons passes from NADH to O2; two ATP molecules may be synthesized when electrons from FADH2 pass to O2.
  
• bacterial electron transport chains are located in the plasma membrane
• Fermentation
• Fermentation-a process in which an organism oxidizes the NADH produced by one of the pathways above by using pyruvate or one of its derivatives as an electron and hydrogen acceptor; thus the process involves the use of an endogenous electron acceptor.
• Alcoholic fermentations produce ethanol and CO2. (yeast)
• Lactic acid fermentations produce lactic acid (lactate) (S. Latis)
• Anaerobic Respiration
• Uses molecules other than oxygen as terminal electron acceptors; the most commonly used alternative electron acceptors are nitrate, sulfate, and CO2.
• Dissimilatory nitrate reduction occurs when nitrate is used as the terminal electron acceptor; if the nitrate is reduced to nitrogen gas, the process is called denitrification.
• Anaerobic respiration is not as efficient in ATP synthesis as aerobic respiration because the alternative electron acceptors do not have as positive a reduction potential as O2; despite this, anaerobic respiration is useful because it is more efficient than fermentation.

Bacteria Genetics

Central Dogma------DNA makes RNA makes proteins.

1. Replication in E. coli :
1. Replication starts at the origin of replication of the DNA loop.
2. The enzyme opens the DNA molecule at the origin of replication, and two V-shaped replicating forks result. 1) leading strand: sunthesized continuously and DNa polymerase adds nucleotides. 2) lagging strand: synthesized discontinuously, Okazaki fragments. RNA prime, DNA ligase binds fragments.
3. DNA synthesis continues along the two replication forks of the two DNA strands. On both strands, the new DNA lengthens as nucleotides are added to the open ends.
   
4. As synthesis nears completion, the inner chromosome moves to a position outside the outer chromosome and prepares to separate.
5. Following separation, two chromosomes now exist. A semiconservative method of DNA replication.
   
2. Transcription
1. DNA template makes messager RNA by RNA polymerase.
2. Nucleic acid to nucleic acid
3. The RNA product is complementary to the DNA template
4. An adenine nucleotide in the DNA template directs the incorporation of a uracil nucleotide in the RNA; otherwise, the base pair rules are the same as for DNA replication
5. Three types of RNA are produced by transcription
1. mRNA carries the message that directs the synthesis of proteins
2. tRNA carries amino acids during protein synthesis
3. rRNA molecules are components of the ribosomes
3. Translation
1. The process takes place at the ribosome, where the mRNA molecule meets tRNA molecules bound to their appropriate amino acids.
   
2. mRNA codons are used to make protein.
1. Chain initiation: translation began with the addition of the tRNA whose anticodon recogizes the start codon AUG. The first amino acid was MET.
   
2. Chain elongation: the second tRNA is inserted into the ribosome. Hydrogen bonds between the codon and anticodon bases temporarily hold the tRNA in position, while an enzyme attaches aminos together to form a chain.
   
3. Chain termination: the process of adding tRNAs and transferring the elongating polypeptide to the entering amino acid continues until the ribosome reaches a stop codon (UAG, UGA, UAA) Releasing factor binds where the tRNA would normally bind.
   

Bacterial Conjugation

• The transfer of genetic information via direct cell-cell contact; this process is mediated by fertility factors (F plasmids)
• F+ ¥ F- mating
• In E. coli and other gram-negative bacteria, an F plasmid moves from the donor (F+) to a recipient (F-) while being replicated by the rolling circle mechanism
• The displaced strand is transferred via a sex pilus and then copied to produce double-stranded DNA; the donor retains the other parental DNA strand and its complement; thus the recipient becomes F+ and the donor remains F+
• Chromosomal genes are not transferred.
• Hfr conjugation
• F plasmid integration into the host chromosome results in an Hfr strain of bacteria
• The mechanics of conjugation of Hfr strains are similar to those of F+ strains
• The initial break for rolling-circle replication is at the integrated plasmidís origin of transfer site
1. Part of the plasmid is transferred first
2. Chromosomal genes are transferred next
3. The rest of the plasmid is transferred last
• Complete transfer of the chromosome takes approximately 100 minutes, but the conjugation bridge does not usually last that long; therefore, the entire F factor is not usually transferred, and the recipient remains F-.

DNA Transformation

• Transformation-a naked dead DNA molecule from the environment is taken up by the cell and incorporated into its chromosome in some heritable form.
• A competent cell is one that is capable of taking up DNA and therefore acting as a recipient; only a limited number of species are naturally competent; the mechanics of the natural transformation process differ from species to species
• Species that are not normally competent (such as E. coli) can be made competent by calcium chloride treatment or other methods, which makes the cells more permeable to DNA

Transduction

• Transduction-transfer of bacterial genes by viruses (bacteriophages); occurs as the result of the reproductive cycle of the virus
1. Lytic cycle-a viral reproductive cycle that ends in lysis of the host cell; viruses that use this cycle are called virulent bacteriophages
2. Lysogeny-a reproductive cycle that involves maintenance of the viral genome (prophage) within the host cell (usually integrated into the host cellís chromosome), without immediate lysis of the host; with each round of cell division, the prophage is replicated and inherited by daughter cells; bacteriophages reproducing by this mechanism are called temperate phages; certain stimuli (e.g., UV radiation) can trigger the switch form lysogeny to the lytic cycle.
• Generalized transduction-any part of the bacterial genome can be transferred; occurs during the lytic cycle of virulent and temperate bacteriophages
1. The phage degrades host chromosome into randomly sized fragments
2. During assembly, fragments of host DNA of the appropriate size can be mistakenly packaged into a phage head (generalized transducing particle)
3. When the next host is infected, the bacterial genes are injected and a merozygote is formed
1. Preservation of the transferred genes requires their integration into the host chromosome
2. Much of the transferred DNA does not integrate into the host chromosome, but is often able to survive and be expressed; the host is called an abortive transductant
• Specialized (restricted) transduction
1. Transfer of only specific portions of the bacterial genome; carried out only by temperate phages that have integrated their DNA into the host chromosome at a specific site in the chromosome
1. The integrated prophage is sometimes excised incorrectly and contains portions of the bacterial DNA that was adjacent to the phageís integration site on the chromosome
2. The excised phage genome is defective because some of its own genes have been replaced by bacterial genes; therefore, the bacteriophage cannot reproduce
3. When the next host is infected, the donor bacterial genes are injected, leading to the formation of a merozygote

The Polymerase Chain Reaction (PCR)

1. PCR is used to synthesize large quantities of a DNA fragment without cloning it
2. Synthetic DNA molecules with sequences identical to those flanking the target sequence are used as primers for DNA synthesis; replication is carried out in successive cycles using a heat-stable DNA polymerase
3. Since its initial discovery, PCR has been automated and improved (e.g., new procedures allow RNA to be used as a template to produce and amplify complementary DNA)
4. PCR has proven valuable in molecular biology, medicine (e.g., PCR-based diagnostic tests) and in biotechnology (e.g., use of DNA fingerprinting in forensic science)

Restriction Enzyme

• an enzyme that cuts double-stranded DNA. The enzyme makes two incisions, one through each of the phosphate backbones of the double helix without damaging the bases.
• The restriction enzyme EcoRI is used to open the first plasmid. The plasmid then exists as a linear strand of DNA.
  
• The smae restriction enzyme is used to open the second plasmid. The plasmids are unrelated bu they have identical recognition sites for the enzyme, and therefore, the bases at the "sticky ends" are identical in the two plasmids. The second loop also forms a linear strand.
  
• The two strands are brought together, and the exposed ends join with each other. The nitrgenous bases form weak hydrogen bonds with their complementary baes.
  
• To permanently secure the "backbone" of the molecule, DNA ligase is used. This enzyme joins the deoxyribose molecules to the phosphate groups.
  
• As the other ends join, mediated by DNa ligase, a single large plasmid forms. This type of union is the basis for synthetic genetic recombinations.
  

Fungi----eucaryotic, spore-bearing organisms with absorptive metabolism and no chlorophyll; reproduce sexually and asexually

• 1. are eukaryotic;
  2. have a rigid cell wall;
  3. are chemoheterotrophs (require organic compounds for both carbon and energy sources);
  4. obtain their nutrients by absorption;
  5. obtain nutrients as saprophytes (live off of decaying matter) or as parasites (live off of living matter).
• Heterotrophic, absorptive
• Grow best at 25 degree; mildly acidid enviorment,
  

Mold

• Mold Morphology
• a. Molds are multinucleated, filamentous fungi composed of hyphae. A hypha is a branching tubular structure approximately 2-10 µm in diameter which is usually divided into cell-like units by crosswalls called septa. The total mass of hyphae is termed a mycelium . The portion of the mycelium that anchors the mold and absorbs nutrients is called the vegetative mycelium , composed of vegetative hyphae; the portion that produces asexual reproductive spores is the aerial mycelium, composed of aerial hyphae.
• b. Molds have typical eukaryotic structures .
• c. Molds have a cell wall usually composed of chitin, sometimes cellulose, and occasionally both.
• d. Molds are obligate aerobes .
• e. Molds grow by elongation at apical tips of their hyphae and thus are able to penetrate the surfaces on which they begin growing
• Reproduction of Mold
• Asexual reprodcution
• 1. conidiospores (conidia) -----Spores borne externally on an aerial hypha called a conidiophore. Penicillium and of Aspergillus;
• 2. sporangiospores .------Spores borne in a sac or sporangium on an aerial hypha called a sporangiophore . Rhizopus; .
• 3. arthrospores ----- spores produced by fragmentation of a vegetative hypha
  
• Sexual reproduction: by sexual spores such as ascospores and zygospores but this is not common.

Yeast

• Yeast Morphology

• a. Yeast (def) are unicellular fungi which usually appear as oval cells 1-5 µm wide by 5-30 µm long.

  b. They have typical eukaryotic structures).

  c. They have a thick polysaccharide cell wall.

  d. They are facultative anaerobes .

  e. The yeast Candida is said to be dimorphic in that it can grow as an oval, budding yeast, but under certain culture conditions may also produce filaments called hyphae similar to molds . The hyphae help the yeast to invade deeper tissues after it colonizes the epithelium. Asexual spores called blastospores develop in clusters along the hyphae, often at the points of branching. Under certain growth conditions, thick-walled survival spores called chlamydospores may also form at the tips or as a part of the hyphae.

• Reproduction of yeasts
• Yeasts reproduce asexually by a process called budding . A bud is formed on the outer surface of the parent cell as the nucleus divides. One nucleus migrates into the elongating bud. Cell wall material forms between the bud and the parent cell and the bud breaks away.
  
• b. A few yeasts, such as Candida albicans, also produce clusters of asexual reproductive spores called blastospores and thick-walled survival spores called chlamydospores.
• c. Yeasts can also reproduce sexually by means of sexual spores called ascospores which result from the fusion of the nuclei from two cells followed by meiosis). Sexual reproduction is much less common than asexual reproduction but does allow for genetic recombination .

Classification of Fungi

• Zygomycota-zygomycetes
• Most are saprophytes; a few are plant and animal parasites
• Coenocytic hyphae (no crosswalls), with many haploid nuclei
• Asexual reproduction leads to the formation of sporangiospores
• Sexual reproduction leads to the formation of zygospores; these are tough, thick-walled zygotes that can remain dormant when the environment is too harsh for growth
• Representative member: Rhizopus stolonifer (commonly known as bread mold, but also grows on fruits and vegetables)
• Zygomycetes are used in the production of foods, anesthetics, coloring agents, and other useful products
• Ascomycota-ascomycetes
• cause food spoilage, a number of plant diseases (e.g., powdery mildew, chestnut blight, ergot,and Dutch elm disease)
• Include many types of yeast, edible morels, and truffles, as well as the pink bread mold Neurospora crassa
• Mycelia are septate
• Produce conidiospores when reproducing asexually
• Ascospores (haploid spores located in a sac called an ascus) are formed when reproducing sexually
• Thousands of asci may be packed together in a cup-shaped ascocarp
• Basidiomycota-basidiomycetes (club fungi)
• Includes smuts, jelly fungi, rusts, shelf fungi, stinkhorns, puffballs, toadstools, mushrooms, and bird's nest fungi
• Basidia are produced at the tips of the hyphae, in which the basidiospores will develop
• Basidiospores are held in fruiting bodies called basidiocarps
• Usefulness-many basidomycetes are decomposers; some mushrooms serve as food (some are poisonous); one is the causative agent of cryptococcosis; and some are plant pathogens.
• Deuteromycota-deuteromycetes (commonly called Fungi Imperfecti)
• This is a classical division grouping together fungi that lack a sexual reproductive phase or fungi for which a sexual reproductive phase has not been observed;
  
• Most are terrestrial; a few are freshwater or marine organisms; most are saprophytes or plant parasites; some are parasitic on other fungi
• Human impact
  1. Some are human parasites (e.g., causing ringworm, athlete's foot, histoplasmosis)
  2. Some are used industrially to produce antibiotics, cheese, soy sauce, and other products
  3. Some produce substances that are highly toxic and carcinogenic to animals (e.g., aflatoxin and trichothecenes)
• Chytridiomycota-chytrids (simplest of true fungi)
• Terrestrial and aquatic fungi that reproduce asexually by forming motile zoospores
• Microscopic in size; may consist of single cells, a small multinucleate mass, or a true mycelium
• Reproduce asexually or sexually
• Some saprophytic; others are parasites of algae, other true fungi, and plants
• Oomycota-Oomycete
• Egg fungi, water molds

Animalia

Flatworm

• Phylum---Platyhelminthes
• Falttened bodies that are slender and leaf-like, long and ribbon-like.
  
• Bilateral symmetry
• Mutilcellular.
• No respiratory or circulatory structures, lack digestive tracts
• gut consists of a sac with a single opening.
• Complext reproductive system--female and male.
  

Three class of flatworm

1. Turbellaria---including freeliving flatworms aht do not cause disease.
   
2. Trematoda---include fluke--leaflike worms. 1) complex life cycle include encysted egg stage and temporary larval forms. 2) sucker devices present to hold fast to parasite host. 3) two host exist: an intermediate
   
3. Cestoda---consists of tape worms.
   

Roundworm

• Phylum---Aschelminthes
• The asc--sca refers to a digestive tract set apart from the internal muscles in a sac-like arrangement. The sac is a tubular intestine open at the mouth and anus so food can move in one direction.
• More evolutional than flatworm.
• Separate sexes
• Nematodes----because they are thread-like.
  

Water and soild

Water Microbes Habitates

• Littoral zone海滨的, 沿海的---Shoreline, full of nurients, sunlights.
• Limnetic zone淡水的---Offshore surface, open water, plenty of sunlight, few nutrients.
  
• Profundal zone---Deep water, offshore, no plant life.
• Benthic zone---Bottom, anaerobic, no light.

Water purification

1. Sendimentation step沉淀
1. Leaves, particles of sand and gravel, and other materials from the soil are removed in large reserviors or settling tanks.
2. Chemicals such as aluminum sulfate Al 2 (SO 4 ) 3 or iron sulfate FeSO₄are dropped as a powder onto water and they form jelly-like masses of coagulated material called flocs.
3. The flocs fall through the water and cling to organic particles and microorganisms, dragging a major portion to the bottom sediment in the process of flocculation.
2. Filtration
1. Slow sand filter---for smaller-scale operations. containing fine particles of sand several feet deep. A layer of microorganism (Schmutzdecke Layer)within the sand as a supplementary filter.
   
2. Rapid sand filter---contains coarser 粗糙的 particles of gravel. No Schmutzdecke Layer.Used in municipal water systems.
   
3. Chlorination
1. Chlorine Cl gas is added to the water. Chlorine is an active oxidizing agent that reacts with any organic matter in water. It is important to continue adding chlorine until a residue is present.
2. Under that condition, most remining microorganims die within 30 minutes.

Waster water treatment: 1) water is separated from the waste 2) the solid matter is broken down by microorganisms to cimple compounds for reture to the soild and water.

• Homes
• waste is emptied into underground cesspools 化粪池. Water passes into the soild through the bottom and pores of the cesspool, while solid waster accumulates on the bottoms of the cesspool. Microorganisms, anaerobic bacteria digest the solid matter into soluable products that enter the soild and enrich it.
• Septic tank---an enclosed concrete box that collects waster from the house. Organic matter accumulates on the bottom of the tank, while water rises to the outlet pipe and flows to a distribution box. The water is then separated into pipes that empty into the soils.
• Small towns
• Small town collect sewage into oxidation lagoons.
• Then the sewage is left undisturbed for up to three months.
  
• Aerobic bacteria digest organic matter in the water, anaerobic organisms break down sedimented material.
• the waste may be totally converted to simple salts. Then the bacteria die and water clarifies, the pond may be emptied into a nearby river or stream.
• Municipalities
  
• Pretreatment --- invovles grit and insoluble waster removal.
  
• Primary treatment---war sewage is piped into huge open tanks for organix waste (sludge)removal. Sludge is passed into sludge tanks for further treatment. Flocculating material are added to the raw sewage to drag microorganisms to the bottom.
  
• Secondary treatment---1) liquid phase---aeration of the water portion to enzourage arobic growth of microorganisms which digest organic matter. The water then is passed through a clarifier and filter to remove the microorganisms and remaining organic matter, after which it flows into river or stream. 2) solid phase---in the sludge tankd, microbial growth is encouraged by aerobic and anaerobic process. In the aerobic process, compressed air is forced into the sludge, and the suspended particles form gelatinous masses thrive on the organic matter. The anaerobic method of sludge digestion, sewage is held in the tank for 30 days while the sludge ferments. Gas produced can be value to chemical industries. And dried actiated sludge may be used as fertilizer.
  
• Tertiary treatment---purifing the water. Sedimentation is followed by filtration and chlorination. after which the water is placed back into circulation and make available to consumers.

MPN---Most probable number----Fecal Coliform/Fecal Streptococcus ratio

CHNOPS

• Carbon cycle----Influenced by microorganismsPhotosynthesis represents the major method for incorporatingcarbon dioxide to organic matter, and cellular respiration accounts for its return to the atmosphere. Microorganisms are crucial to all decay in soil and ocean sediments. Photosynthesis fixes CO2 to build glucose nad respiration recyle glucose into CO2, water and ATP.
• H and O---Hydrogen and oxygen recycles with other elements, water recycled as part of photosynthesis respiration.
  
• Nitrogen cycle
• Ammonification---Microbes convert decay and waster products to ammonia.Amino acids to NH3 and pyruvic acid.
  
• Nitrification---Changes ammonia to more useful forms: nitrates used by plants for protein synthesis. Ammonia to nitrite to nitrate.
  
• Denitrification(nitrate reduction)-----Nitrate--Nitrite---Nitrous oxide--Nitrogen gas. (Pseudomonas, Thiobacillus, E. coli. Bacillus)
  
• Nitrogen fixation---N2---NH3( Rhiobium infect legumes.
• Phosphorus cycle---Phophate PO4- required for DNA, RNA, ATP, Teichoic acid.
  
• Sources of phophate---dead organisms, in oceans. sediments of ancient seas.
  
• Sulfur cycle---Needed for use as anenergy source. For synthesis of amino acids cysteine, methoinine. Thiobacillus, Beggiatoa involves.v So4--H2S

Food intoxication and food infection

• Food intoxication -----are diseases in which bacterial toxins, or poisons are ingested in food or water.
• Food infection -----are disease in which live bacteria in fod and water are ingested and grow in the body.
  

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