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Exam 2-Scott
Microbial Metabolism, Growth, Reproduction
106
Microbiology
Undergraduate 1
10/10/2012

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Term
Selective Media
Definition
Inhibits growth of one bacteria over another. EG: McConkey is selective for gram negative and Mannitol Salt is selective for gram positive
Term
Enrichment Media
Definition
All bacteria types can grow but only one will outgrow all the rest because of nutrients. EG: blood agar, fastidious microorganisms
Term
Differential Media
Definition
Distinguish one microorganism type from another growing on the same media. McConkey is differential for lactose fermentation and mannitol salt agar is differential for mannitol fermentation
Term
Obligate anaerobe
Definition
Microorganisms that live and grow in the absence of molecular oxygen. They gather at the bottom of the test tube to avoid oxygen. They do not have enzymes, and lack an electron transport chain. That is why we can't use oxygen to ...? These form endospores and are also thermophiles
Term
Facultative anaerobe
Definition
These are not obligate. The anaerobe does not need oxygen to grow. Lack of oxygen does not hurt them. they can be found all along the test tube. They are adapting to variations. Have both enzymes (superoxide dismutase and catalase). Eg; E. coli and S. aureus
Term
Microaerophile
Definition
Require oxygen but at a low concentration. So they will gather towards upper end of test tube, but not at bottom. Have little enzymes. Eg: Heliobacter Pylori - also a neutrophile and makes an enzyme called Urease which changes the pH from 3 to 7 so it can survive in the stomach. Causes ulcer.
Term
Obligate aerobe
Definition
Oxygen-needing bacteria. Gather at the top of test tube in order to absorb max amount of O2. Has enzymes. Survival depends on their ability to detoxify O2 and successful gene expression. Eg: Bordetella Pertussis (whooping cough).
Term
Aerotolerant Bacteria
Definition
Are not affected at all by oxygen. The are evenly spread along the test tube. They only contain the enzyme superoxide dismutase (SOD) Use Peroxidase to break down peroxide and superoxide.
Term
Describe the natural antioxidants in our bodies
Definition
1. Superoxide dismutase (SOD) - removes the free radical from oxygen making o2 and H2O2 (hydrogen peroxide). (or the reverse?)
2. Catalase - Hurns H2O2 into O2 and H2O so now it can safely go into the body.
Term
Hemolysins
Definition
Enzymes that break down red blood cells. Red blood cells carry oxygen.
Term
Lag phase of growth curve
Definition
Early phase of bacteria population grown during which no signs of growth occur as bacteria are adjusting to their environment.
Term
Log phase of growth curve
Definition
maximum rate of cell division during which growth is geometric in rate of increase. Also called exponential growth
Term
Death phase of growth curve
Definition
End of the cell growth due to lack of nutrition, depletion of environment, accumulation of wastes. Population of cells begins to die. More cells are dying than dividing.
Term
Stationary phase
Definition
survival mode, balance is equal between cells dividing and cells dying
Term
CFU - Colony-forming unit
Definition
A measure of viable bacterial numbers. Unlike direct microscopic counts where all cells, dead and living, are counted, CFU measures viable cells. Results are given as CFU/ml for liquids, CFU/g for solids
Term
Gene
Definition
The fundamental unit of heredity responsible for a given trait in an organism. A site on a chromosome that provides information for a certain cell function. A specific segment of DNA that contains the necessary code to make a protein or RNA molecule.
Term
Genotype
Definition
Genetic makeup of an organism. The genotype is ultimately responsible for an organism's phenotype, or expressed characteristics.
Term
Phenotype
Definition
The observable characteristics of an organism produced by the interaction between its genetic potential (genotype) and the environment.
Term
Chromosome
Definition
The tightly coiled bodies in cells that are the primary site of genes.
Term
Nucleotide
Definition
The basic structural unit of DNA and RNA; each nucleotide consists of a phosphate, a sugar (ribose in RNA, deoxyribose in DNA), and a nitrogeneous base such as adenine, guanine, cytosine, thymine (DNA), or uracil (RNA).
Term
Semiconservatism
Definition
In DNA replication, the synthesis of paired daughter strands, each retaining a parent strand template. DNA copies itself just before cellular division by this process. Semiconservatism replication means that each "old" DNA strand is the template upon which each "new" strand is synthesized.
Term
mRNA
Definition
Carries the message of DNA to the ribosome. Contains *codons*: a sequence of base pairs that code for an amino acid. Eg: AUG - you use the codon to determine the name of the amino acid.
Term
tRNA
Definition
Adapter molecule to transfer RNA. Adapts the genetic code based on the base sequence of mRNA anticodon. Eg: AUG-UAC brings the amino acid from the cytoplasm into the ribosome.
Term
rRNA
Definition
Not clear what it does but it is thought to synthesize ribosomes. A single-stranded transcript that is a copy of part of the DNA template.
Term
DNA Polymerase
Definition
Adds new nucleotides to a new strand of DNA modeled after an old strand of DNA. It is also for proofreading. Note that the nucleotides are not stable because DNA ligase has not been applied yet.
Term
RNA Polymerase
Definition
Enzyme process that translates the code of DNA to RNA
Term
DNA Ligase
Definition
seals in nucleotides (composed of a phosphate, nitrogenous base, and a sugar) after DNA Ligase is applied the nucleotides are stable
Term
DNA Gyrase
Definition
located in Bacteria cells only.

"supercoiling" DNA
Term
Molecular Genetics
Definition
When a message of DNA is turned into a protein. "Gene Expression"
Term
DNA Replication
Definition
The semiconservative mechanisms that ensure precise duplication of the parent DNA strands. DNA fingerprinting.
Term
Transcription
Definition
mRNA synthesis: the procss to which a strand of RNA is produced against a DNA template.
Term
Translation
Definition
Protein synthesis; the process of decoding the messenger RNA code into a polypeptide.
Term
DNA ---> DNA
Definition
Replication
Term
DNA ---> RNA
Definition
Transcription
Term
RNA --- > Proteins
Definition
Translation. Proteins are the functional products of DNA because they carry out the instructions of DNA.
Term
Mutation
Definition
A Change in DNA sequence. Mutations can benefit the microbe, but in most cases it does not.
Term
Frameshift mutation
Definition
Addition or deletion of one or more bases

CGC GGT --- > CGC
Term
Base Substitution or Point Mutation
Definition
One base is substituted for another base. CCT --- > CTT
Term
Induced Mutations
Definition
Happen all the time. They result from exposure to known mutagens:

1. Chemicals
2. Radiation
Term
Spontaneous mutations
Definition
Spontaneous mutations are very rare. Change in DNA arising from errors in replication, when there is an absence of an environmental agent.
Term
Gene Expression: What are 3 ways to express a gene?
Definition
Constitutive
Induction
Repression
Term
Constitutive
Definition
Set of genes that's constantly on
Term
Induction
Definition
Set of genes that's turned on, so this means they are initially off. These are genes we don't need.
EG: Cancer cells
Term
Lactose Operon -- Induction
Definition
Turned on in the absence of glucose, does not make lactose, makes 3 enzymes that convert lactose to glucose. The repressor -- allosteric protein -- is what is causing the operon to be off. The lactose binds to the allosteric site causing the active site to change shape. So then the repressor comes off, allowing RNA polymerase to bind to the promoter and initiate transcription.
Term
Secondary Messengers
Definition
Secondary messengers tell the lactose operon whether or not it is needed.
Term
Tryptophan Operon - Repression
Definition
Makes tryptophan. When the conc. of tryptophan meets the max. threshold, Tryptophan binds to the allosteric site acting as a coil(?) repressor. The repressor protein changes shape and the conc of trypt goes down and the operon is turned off.
Term
Types of Gene Transfer -- All-natural mutations
Definition
Conjugation
Transduction
Transformation
Term
Conjugation -- Gene transfer between 2 organisms by a pilus
Definition
A pilus can only be formed by the F-plasmid (F+) which contains genetic information. F stands for fertility. An F+ donor cell and a F-recipient (F-) both contain a host cell genome. The F plasmid (F+) cell makes a copy of itself by DNA polymerase, ligase, helicase, gyrase, and semiconservatism which moves it over to the F-cell. When the F-plasmid moves over then it is no longer a recipient cell but a donor cell (F plasmid) survival of the species?
Term
Transduction -- Gene Transfer between bacteria cells through a bacteriophage
Definition
The virus, containing nucleic acid, enters cell A's genome and leaves with genes from cell A and enters into cell B. Cell A is destroyed. So the virus now contains nucleic acid and cell A's genes. When it goes into cell B it leaves behind part of c ell
Term
Tranformation
Definition
The uptake of naked DNA by another bacterial cell. In a host cell genome, inside of a bacteria cell, DNA comes out in fragments from the cell bursting. To make the cell burst it has to go under change in water availability (hypotonic) or temperature, or PH. This is how the DNA comes out of the cell. Then another bacteria cell can bring in one of the DNA fragments.
Term
Classical Biotechnology
Definition
Use living organisms to produce useful products to solve a problem. "invivo" testing - using a rat or some type of animal
Term
Modern Biotechnology
Definition
Use biological molecules to produce useful products or solve a problem. "Invitro" testing -- using a test tube with bacteria cells or human cells.
Term
Genetic Engineering
Definition
More specific terms of biotechnology. Manipulate the genes of an organism. Recombinant DNA technology.
Term
Recombinant DNA technology
Definition
Cutting and combining genes from 2 different organism. It involves modification of an organism's genome. Used to create genetically modified food that may have increased nutritional properties, be easier to grow, or may even vaccinate the person eating it against a host of diseases.
Term
Tools of the Trade for Recombinant DNA technology
Definition
1. Restriction Enzymes -- enzymes that recognize and cut DNA sequences. They learn things from bacteria cells.
2. Plasmids. Genest that can make bacteria resistant to antibiotics and can express genes from foreign organisms. 1. F-plasmid. 2. R-Plasmid, R-Resistance. Carry antibiotic resistance and are self-replicating.
3. DNA Ligase - seals in the gene.
Term
Transposons
Definition
Act Like Plasmids, mobile genetic elements -- "jumping Genes". They can jump from one plasmid or host cell genome in a DNA unit to the other and replicate itself. This causes instability in the cell.
Term
Contributions to Biotechnology
Definition
1. Gene Library -cloned DNA stored in yeast, viruses, or bacteria.
2. Polymerase Chain Reaction (PCR)-amplify DNA.
3.DNA Fingerprinting - analyze DNA/associated with replication, forensics, paternity testing, diagnostics
4. Medicines
5. Vaccines
6. Human Genome Project
Term
Examples of Aerotolerant bacteria
Definition
Lactobaccillus - Yoghurt
Acidophilus - Makes lactic acid to keep urogenital tract low PH.
Both of these are good bacteria cells that keep you from getting a yeast infection.
Term
Aseptic Technique
Definition
Methods of handling microbial cultures, and patient specimens in a way that prevents infection of the handler and others who may be exposed.
Term
Operon
Definition
Cluster of genes that regulate metabolism by controlling mRNA production.
1. Promoter - where RNA polymerase binds to start transcription. DNA sequence.
2. Operator -- a repressor binds to block transcription. On/Off switch. DNA sequence
3. Structural Genes -- encode for a set of enzymes.
Term
Bacteriostatic
Definition
Any process or agent that inhibits bacterial growth
Term
Bactericidal
Definition
Killing bacteria cells
Term
Asepsis
Definition
A safe level free of viable pathogenic microorganisms but is not sterile. You still may see microbial growth including endospores.
Term
Sterilization
Definition
Any process that completely removes or destroys all viable microorganisms, including viruses, from an object or habitat. Endospores are the indicators if something is sterile or aseptic. All sterile techniques are bactericidal.
Term
Moist Heat
Definition
Heat can be under pressure or not. Heat that is under pressure is steam and is sterile, killing endospores. Example is a Crock Pot. Heat that is not under pressure is boiling. Boiling is a bactericidal, aseptic technique -- does not kill endospores.
Term
Dry Heat
Definition
Sterile. Example: when we flame the loop in lab.
Term
Cold Heat
Definition
bacteristatic and aseptic
Term
Mesophiles
Definition
Grow at intermediate temperatures, warm loving. 37 degrees C. Eg: staph. aureus.
Term
Psychrophiles
Definition
Cold-loving bacteria, thrive at low temperatures (0-20 degrees C.)
Term
Thermophiles
Definition
Hot loving, 60 degrees C. or higher. Endospore forming bacteria. Obligate anaerobes.
Term
PH affecting microbial growth
Definition
Bactericidal and aseptic, because endospores can survive in too basic or too acidic condition.
• Acidophile --likes pH3
• Neutrophle -- likes pH7(our bodies)
• Alkalophile -- likes pH9
Term
Water availability affecting Microbial Growth
Definition
Cells are drying. Cells like an isotonic environment. Cells are bacteristatic but over time it becomes bactericidal and aseptic. It takes a while to kill the cells because of the water.
Term
Halophile
Definition
likes a hypertonic environment (salt-loving) Eg: staph aureus
Term
Radiation affecting Microbial Growth
Definition
UV Radiation and Gamma Radiation
Term
Explain UV Radiation
Definition
Starts bactericidal, but over time it becomes sterile. UV rays don't penetrate through clothes or plastic. Becomes sterile by Thymine Dimers -- fuse 2 thymine together, this blocks DNA Polymerase from reading it so the UV light can now destroy the cell.
Term
Explain Gamma Radiation
Definition
Sterile Technique. Can go through clothes, plastic. They form free radicals.
Term
Filtration.
Definition
Sterile technique that doesn't interfere with any cellular structures or processes and is mechanically removing bacterial cells from a solution. Once a solution goes through the filter it becomes sterile.
Term
Size of Filter Unit Pores
Definition
.01um for bacteria and viruses
.10um for bacteria and viruses
.22um for bacteria but not viruses
.45um for some bacteria but mainly dirt
Term
Chemical Factors of Microbial Growth
Definition
Interfere with proteins and the plasma membrane. (mode of action)
•Alcohol
•Halogens
Term
Describe the alcohol factor of microbial growth
Definition
bacteriostatic and aseptic. 70% alcohol is more effective than 100% alcohol because the water content in the 70% helps it be absorbed faster.
Term
Bleach
Definition
Halogen that is aseptic and bactericidal. If it is used properly it is a sterile technique that interferes with DNA.
Term
Iodine
Definition
Halogen that is bactericidal and aseptic
Term
Phenols/Phenotics
Definition
Halogens that are bactericidal and aseptic.
Eg. LIsterine/Lysol/Triclosan
Term
Surfactants
Definition
Halogens that are bacteristatic and aseptic.
Eg. Hand Soap
Term
Heavy Metals
Definition
Halogens that are antiseptic, bactericidal, and antimicrobial (nickel, silver, mercury)
Term
What are the physical factors of microbial growth?
Definition
Temperature, pH, water availability, radiation
Term
How is DNA, mRNA, and fRNA made?
Definition
DNA -- 5' - 3'
-- 3' - 5'
mRNA 5' - 3', so the 3' - 5' from DNA is what we have to use because it is the opposite.
tRNA -- 3' - 5' because it is the opposite of mRNA
Term
Example of Facultative Anaerobe?
Definition
E. Coli and Staph. Aureus
Term
Example of Microaerophile?
Definition
Heliobacter Pylori
Term
Example of Obligate Aerobe?
Definition
Bordetella Pertussis
Term
Where does transcription occur in Prokaryotic and Eukaryotic Cells?
Definition
Transcription of DNA to RNA occurs in the nucleus of Eukaryotic cells and the nucleoid of Prokaryotic cells.
Term
Where does Translation occur in Prokaryotic and Eukaryotic Cells?
Definition
In the ribosomes.
Term
Direct bacteria cell counts
Definition
Using the eye to see bacteria. Also uses an instrument like a coulter counter. As cells pass through this device, they trigger an electronic sensor that tallies their numbers.
Term
Indirect bacteria cell counts
Definition
1. Metabolism - looking at by-products. Co2 and ATP are measured.
2. Dry weight - wet solution
3. Turbidity - cloudiness in the test tube.
Term
Describe a mass spectrophotometer
Definition
Used to measure indirect bacteria cells turbidity. You place a testtube in a slot where light is coming through. The light bounces off anything solid. We get the Optimal Density from this.
Term
Inaccuracy of coulter counter and spectrophotometer
Definition
There is no distinction between dead and live cells
Term
Name examples of Obligate Anaerobes
Definition
Clostridium Perfringens -- gangrene
Clostridium tetini -- tetanus
Clostridium botulinum -- botulism
Term
What is the AMPr gene?
Definition
Ampicillin resistance gene
Term
Recombination in bacteria depends in part on the fact that bacteria contains...
Definition
Extrachromosomal DNA - Plasmids -- interchanging genes
Term
What is a Functional Product?
Definition
Fu
Term
What are the essential elements?
Definition
Carbon, Hydrogen, Oxygen, Phosphorus, Nitrogen, Sulfur, Iron.
All living things require these elements.
Term
Growth Factors -- Organic Nutrients
Definition
Only required for fastidious organisms (organisms that require special nutritional or environmental conditions for growth). Eg: nisseria gonorrhea -- needs amino acids.
1.Amino acids. 2. Purines. 3. Pyrimidines.
Term
What is the advantage of using Agar?
Definition
Agar is a polysaccharide. It is heat stable meaning it can be heated up and it still works. Nutrients have to be placed in the agar.
Term
What are the 2 categories of Agar?
Definition
• Complex media - used in lab. We don't know or care the exact chemical composition.
• Chemically-defined agar (more expensive, unnecessary unless you're doing research, looking for particular stuff to grow or isolate)
Term
Trace Elements, Inorganic?
Definition
Micronutrients (Zinc, copper, Magnesium) that occur in small amounts and are involved in enzyme function and maintenance of protein structure. They are non-fastidious organisms (meaning they don't require special nutritional or environmental conditions for growth.
Term
Repression
Definition
Set of genes that are turned off. We need these genes, they are always on. They are controlled by a repressor. The repressor is not bound to the operator (so it is on) so we have to make the repressor bind to the operator to turn it off.
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