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185 Cards in this Set
- Front
- Back
What is the cell theory of life?
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Concept developed by Schwann. All organisms are composed of cells.
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What is pasteurization?
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Exposing food to enough heat to destroy microorganisms without affecting quality.
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What is the germ theory of disease?
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Disease is caused by microorganisms. Lister.
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What are Koch's postulates?
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1. MO is found in diseased animals but not healthy animals.
2. MO can be grown in pure culture. 3. Healthy animals are made sick by the MO. 4. You can re-isolate the MO from these animals. |
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What did Tyndall do?
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Helped dispel the idea of spontaneous generation. Invented tyndallization (which destroys MOs with pressure).
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About how many bacteria in the oral cavity?
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2 x 10^7
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A bacterial ribosome is defined as__S. What two subunits does it have?
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70
Subunits: 50S and 30S |
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Prokarya are defined by what they do not have, namely ____. This is why Pace thinks the term is outdated.
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nuclei
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Bacteria ribosomal RNA is defined as ___S.
What two subunits does it have? |
16
subunits: 23S and 5S |
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What are the three domains? Which two have the closest evolutionary origin?
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Eukarya, Archaea, and Bacteria
E and A are closest in origin |
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What RNA is used to classify bacteria? Which section is variable?
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the 16S rRNA. The middle is variable.
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Eubacteria lack ___ in cell membranes.
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sterols
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Which organelles are thought to have evolved from bacteria?
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mitochondria and chloroplasts (endosymbiotic theory)
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What kinds of lipids are in bacteria?
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only simple phospholipids
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What kinds of ribosomes do eukaryotes have?
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80S (and some 70S from ribosomes)
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Do eukaryotes or prokaryotes display colinearity? What is it?
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Prokaryotes do. Means number of amino acids is proportional to the nucleotides. (Eukaryotes have introns)
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Do viruses translate/transcribe RNA or DNA?
Do they have lipids? |
No.; It is POSSIBLE for them to have a lipid coat, but this is not a biological membrane.
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Why aren't bacteria giant?
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Once the volume to surface area ratio gets too high, it is difficult for a cell to function.
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Do bacteria have ribosomes? Do viruses?
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Bacteria have ribosomes (70S) and viruses don't.
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Do bacteria have DNA/RNA? Do viruses?
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Bacteria have both. Viruses have one or the other, but never both.
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Four basic steps of the Gram stain.
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1. Crystal violet
2. Iodine (fixing in +) 3. acetone/alcohol (washing from -) 4. safranin |
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What's the difference between classification and taxonomy?
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taxonomy is the study of classification
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What did Carl Linnaeus start?
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the binomial system of nomenclature
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After performing the Ziehl-Neelson stain, the acid-fast bacteria are stained ____.
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RED
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The biggest acid-fast genus is ____. Species of this genus cause what two major diseases?
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Mycobacterium
leprosy and tuberculosis |
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Almost all Gram + cocci n the oral cavity are ___.
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Streptococcus
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Almost all Gram - spirochetes in the oral cavity are ___.
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Treponema (all spirochetes in general are Gram -)
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Almost all Gram - cocci in the oral cavity are ____.
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Veillonella
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A star shaped colony indicates ____.
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Aggregatibacter actinomycetemcomitans
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Gram - rods with a black/brown colony from the oral cavity are usually one of what two things?
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Bacteroides species or Porphyromonas gingivalis
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Does Aggregatibacter actinomycetemcomitans have catalse? How can you tell?
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It does have catalase! It bubbles when you add hydrogen peroxide.
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Why are Bacteroides black in colonies?
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melanin
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What is notable about Serratia marcesens?
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It is blood red in culture because of a pigment called prodigiosin.
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What are some ways to identify bacteria by products?
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1. their products of fermentation
2. their acid profiles 3. their fatty acid profiles 4. their protein profiles 5. their antigen profiles |
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What are biotypes?
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classifications based on fermentation reactions
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What are serotypes?
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classifications based on immunospecific reactions (antigen/antibody)
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How does neutral red work?
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If the bacteria ferments lactose, the lactate will neutralize the red color. (this is a "biotype")
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What are two typical tests for serotype?
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ELISA. Adding fluorescent antibodies to a bacteria and seeing if they fluoresce.
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Steps in ELISA.
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1. antigens added
2. first antibody added 3. second antibody (attached to a dye) is added |
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What is API?
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Automated phenotypic identification. Strips that you inject your bacteria into and then incubate. Pretty neat.
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What's the difference between Gram negative and Gram positive bacteria?
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Negative have a smaller PG layer. They also have an outer membrane.
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On a Gram - bacteria, the ___ is between the inner membrane and the outer membrane.
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periplasmic space
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Why are bacterial membranes described as tripartate?
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With the electron microscope, there are three layers.
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What kind of bacteria have enclosing membranes?
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acid-fast (I'm not sure why I made this question and I don't know what it means, but I'm leaving it in case I find out)
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What is unique about the genus Mycoplasma?
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It lacks PG. It can absorb sterols into its membrane. In these ways, they're like eukaryotes. (MYCOPLASM /= MYCOBACTERIA)
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What are the three parts of PG?
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1. Glycan backbone (NAG and NAM)
2. tetrapeptide side chain 3. amino acid cross-links |
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What is NAM? NAG?
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N-acetyl muranic acid (found only in bacteria). N-acetyl glucosamine
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How are NAG and NAM linked?
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beta-1,4 disaccharide linkages
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What are the conformations of the aas in the tetrapeptide side-chain? What does it end in?
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Usually L, then D, then L/D, then D. It always ends in D-alanine.
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Does the tetrapeptide chain attach to NAG or NAM?
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NAM
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The cross bridge of PG connects what to what?
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D-alanine (position 4), to an amino acid in position 3 on a different glycan backbone.
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What is the amino acid in position 3 in the tetrapeptide chain? What's unique about it.
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Usually D,L-diaminopimelic acid. It's unique because it's diamino, dicarboxy, allowing it to make 3 peptide bonds, which makes crosslinking possible.
Abbreviation: meso-DAP |
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What doesn't the D-alanine in position 4 have to be diamino dicarboxy?
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It only has to make two peptide bonds. Think about it.
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What's the difference between the structure of PG in Gram - and +?
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Gram - has less cross-linking. In Gram +, all the NAMs are linked.
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What happens to a eukaryotic cell under hypertonic conditions? Hypotonic?
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hypertonic: plasmolysis
hypotonic: cytolysis |
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What structural feature most explains bacteria's ability to live in weird places?
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The cell wall. Keeps them from lysing/shrinking. It's also resistant to detergent and heat.
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Where does lysozyme cut the cell wall?
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It cleaves between NAG and NAM. (Many host cell defenses target PG)
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What is the major surface polymer of (all and only) Gram positive bacteria?
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Lipoteichoic acid (LTA)
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The hydrophilic portion of LTA is composed of alternating phosphates and one of what two sugars?
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glycerol or ribitol
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What is the major surface polymer of (all and only) Gram - bacteria?
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LPS (lipopolysaccharide, aka endotoxin)
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What are the three parts of LPS.
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1. Lipid A (in membrane)
2. Core polysaccharide (short. maybe 4-5 sugars) 3. O-polysaccharide (aka O-antigen) |
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What is the composition of the O-antigen?
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It's got about 4 sugars that repeat many times.
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Why is the O-polysaccharide helpful for serotyping?
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The repeating sugars vary from bacteria to bacteria, so the antigens that respond to each one will be different.
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Describe Lipid A.
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Two phosphorylated NAGS with FAs attached. Lipid A is the TOXIC PORTION of LPS.
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LTA attaches to the ___ and passes out through ___.
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cytoplasmic membrane; PG
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LPS attaches to the ____.
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outer membrane
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How does LPS create an asymmetrical membrane?
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The outer leaflet of the outer membrane is composed mainly of the FAs and sugars of lipid A, while the inner leaflet of the outer membrane is generic phospholipid.
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What's the structure of a porin? What's the biggest thing that can get through it?
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It's a trimer. A pentasaccharide can get through it.
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Like Gram positive bacteria, ____ have a cytoplasmic membrane and PG, but no outer membrane.
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acid-fast bacteria
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What is the most important surface compound of acid-fast bacteria? Describe it.
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Mycolic acid. It's large and very waxy and excludes water. It makes growth difficult.
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A shiny, glistening colony might indicate the presence of what?
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A thick glycocalyx
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Falgella are composed of ___, while pili are composed of ____.
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flagellin; pilin
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What are the protein surface appendages?
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flagella and pili
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Flagella are used for ____, while pili are used for ____.
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motility; adhesion (including mating)
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E. coli has a single flagellum. These are called ___.
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polar flagella
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When bacteria have more than one flagellum, they are called ____.
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peritrichous flagella
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How does a bacteria change direction?
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The flagellum (or flagella bundle) changes its direction of rotation.
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What kinds of bacteria have axial filaments? What are they?
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Spirochetes. Axial filaments are flagella that give spirochetes their corkscrew movement.
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O-polysaccharide is sometimes called ____, and flagella are sometimes called ____. Capsules are sometimes called____.
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O-antigen; H-antigen; K-antigen
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Why do obligate anaerobes die in the presence of O2?
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They cannot eliminate superoxide anions. They don't have the enzyme superoxide dismutase.
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Autotrophs do not require what?
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organic carbon. They use only CO2 (e.g. blue-green).
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What do superoxide anions do?
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they inhibit DNA (OK. Not sure, but I think they bind the two strands of DNA together...?)
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Heterotrophs require ____.
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an organic source of carbon
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Bacteria that grow at high temperature are called? Medium temp? Cold temp?
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High: thermophiles
Medium: mesophiles Cold: psychrophiles |
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What is heterotrophic CO2 fixation?
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The use of inorganic carbon for growth by heterotrophs (~5-10%)
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How does glycerol get through the cytoplasmic membrane?
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diffusion (this is rare and only for small molecules)
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How do glucose, fructose, and sucrose get through the cytoplasmic membrane?
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the phosphotransferase system (PTS)
[active transport] |
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What are the two kinds of passive transport across the cytoplasmic membrane?
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simple diffusion or facilitated diffusion (as through a permease)
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Describe active transport by a permease.
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The permease goes through a conformation change. Once the molecule is inside, it is phosphorylated by ATP (usually), so it can't get out.
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Superoxide anions are broken down by _____ into _____, which can further be broken down by ___ or _____.
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superoxide dismutase; hydrogen peroxide; catalase; peroxidase
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How does sugar get through the 3 layers of the Gram - bacteria?
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facilitated diffusion through outer membranes, can pass through PG, and is actively transported across the cytoplasmic membrane.
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What is the permease for glucose?
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Enzyme IIGlu
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Unlike other active transport systems, the PTS system uses ___ for phosphorylation instead of ATP.
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PEP
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____ takes the phosphate from PEP and puts it on ___. (re: PTS)
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Enzyme I; HPr (histadine-rich protein
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HPr brings phosphate to ___, which brings it to ___, which transfers it to the sugar as it enters.
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Enzyme II; Enzyme III
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In the PTS, sucrose binds to ____ on the cell membrane. Unlike glucose, sucrose does not have an ____.
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Enzyme IIScr; Enzyme III
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What are the soluble cytoplasmic components of the PTS? Which enzymes are in the membrane?
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HPr and Enzyme I. Enzyme IIs are in the membrane.
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What is the name for the bacterial glycolytic pathway?
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The Embden-Meyerhoff-Parnas (EMP) pathway
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The EMP breaks glucose down to ___.
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pyruvic acid
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What are the three general stages of the EMP?
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1. phosphorylation
2. splitting 3. redox |
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What are the products of EMP?
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Net 2 ATP, 2 NADH, 2 pyruvic acid
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If glucose-6-P enters the PPP instead of the EMP, it will be converted first to 6-phosphogluconolactone, and ultimately will become building blocks for ___.
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nucleic acids
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What are the products of the pentose phosphate pathway?
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1 net ATP, 1 NADH, 2 NADPH, a C4 product
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Anaerobic bacteria (and facultative bacteria) will take pyruvate and make what?
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alcohol, acid, and CO2
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Aerobes (and facultative bacteria) take pyruvate and make what?
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carboxylic acid intermediates and ATP
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What process is coupled to the reduction of pyruvate to lactate (C3)?
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the oxidation of NADH back to NAD+
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During alcoholic fermentation, pyruvate is generally converted to ___, with ___ as an intermediate.
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ethanol (C2); acetaldehyde (C2)
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What kinds of bacteria are homolactic and heterolactic?
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Both Streptococcus and Lactobacilli can be both
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(Re: fermentation) Fusobacterium produce ____. Veillonella produce ____.
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butyric acid; propionic acid
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Do aerobic bacteria use the TCA cycle?
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Yes, but it's modified. It's not complete. They don't have all the enzymes.
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What are the main products of TCA?
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NADH2 and intermediates for amino acid biosynthesis
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In bacteria the ETC is in the ____. Protons are pumped ___ the cell. As protons rush back ___, they create energy.
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cytoplasmic membrane; out of; in
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What is the chemiosmotic hypothesis?
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The idea that the proton gradient across the membrane allows ATP synthesis
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What TCA enzyme is notably inactivated in anaerobic conditions?
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a-ketoglutarate oxidase (which typically converts it to succinyl-CoA)
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Do facultative bacteria completely stop TCA in the absence of O2?
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No. It still makes some of the intermediates. It uses different enzymes.
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During heterotrophic CO2 fixation, where is the carbon used?
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It is used to make oxaloacetate from pyruvate for TCA. (NB: ATP is generated from CO2 fixation.)
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What is horizontal (lateral) gene transfer?
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Gene transfer from one MO to another. (No sex, no children.)
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What are the consequences of lateral gene transfer?
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Genetic plasticity allow MOs to evade host defenses and acquire resistance to antimicrobial agents.
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What are the three types of mobile genetic elements?
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1. plasmids
2. transposons 3. bacteriophages |
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Little circles of DNA that are separate from the bacterial chromosome are called ____.
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plasmids
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What is the "copy number" of a plasmid?
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It determines the number of copies of the plasmid that the bacteria will make.
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What are bacteriocins?
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Plasmids that code for proteins that kill other bacteria.
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What is an F-factor?
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A plasmid that codes for the sex pilus (fertility factor).
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What is a colicin?
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A type of bacteriocin coded by a plasmid that is toxic to E. coli.
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What's the main difference between a plasmid and a transposon?
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Plasmids are circular. Transposons are linear. (NB: both are dsDNA)
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What is on the ends of the transposon?
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inverted repeats
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The RNA or DNA of a bacteriophage is always contained in a ______.
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protein coat
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On a bacteriophage, there may be a ____ between the tail and the tail fibers. There may be a ____ between the head and the core.
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base plate; collar
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What is a capsomere?
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the protein coat on the genetic material of a bacteriophage
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What are Bradley groups?
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Different kinds of bacteriophages based on DNA/RNA, ds/ss, tail/no tail, long tail/short tail, etc.
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What are the three mechanisms of lateral gene transfer?
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1. transformation (naked dsDNA)
2. conjugation (plasmid or transposon) 3. transduction (bacteriophage) |
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What are R strains and S strains?
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R = rough, no capsule
S= smooth, capsule |
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In Griffith's experiments, why could inactive S strain make the R strain toxic?
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Because of transformation. Naked dsDNA from the lysed S strain incorporated into the R strain, inducing it to form capsule.
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What is the competence factor?
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A protein made by the cell that binds to other cells at high cell concentration. It turns on autolysin. (Re: transformation)
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What does autolysin do?
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It makes the membrane more permeable. (Re: transformation)
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What does nuclease do? (Re: transformation)
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It sits on the cell surface near pores and DNA-binding protein.
It degrades one strand of the dsDNA that enters the cell. |
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What is competence-specific protein?
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It coats the ssDNA made by the nuclease in protein, allowing it to enter the cell and incorporate into the chromosome during transformation.
(NB: both DNA and the membrane are negative, so the protein allows the DNA to get through the membrane) |
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What are the two cell types involved in conjugation?
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F+ donor cell (caries the F plasmid) and F- recipient cell (no F factor)
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What happens when the F+ attaches to the F-?
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The F pilus acts as a bridge and makes a copy of its plasmid for the F- cell.
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What is an Hfr cell?
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A high frequency recombinant cell. It's a cell that has incorporated a plasmid into its chromosome during conjugation.
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What is an F' cell?
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It is an cell that has received a plasmid during conjugation that has extra DNA in it from the Hfr.
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What is the last piece of DNA to pass to from the Hfr to the F-?
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The F gene, which is the incorporated plasmid.
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What are the two types of phages?
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virulent and temperate
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Virulent phages ___ the cell.
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lyse
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Virulent phages go through the ___ cycle. Temperate phages go through the ____ cycle.
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lytic; lysogenic
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Why is it called the lysogenic cycle?
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The prophage DNA is carried silently, but always has the potential to become lytic given the right stimulus.
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What is a good example of feed forward activation in S. mutans?
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When sucrose is found in excess, G6P activates pyruvate kinase. F16BP activates lactate dehydrogenase. T3P inactivates pyruvate formate lyase.
The overall effect is homolactic fermentation (the strongest acid). |
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1. Pyruvate kinase
2. lactate dehydrogenase 3. pyruvate formate lyase |
1. PEP to pyruvate
2. pyruvate to lactate 3. pyruvate to other stuff (heterlactic fermentation) |
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What does beta-glactosidase do?
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Breaks lactose into galactose and glucose
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What enzyme allows lactose to get into the cell?
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galactoside permease
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The lactose operon is an example of ___ and ___ control.
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negative; local
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What is the regulatory gene of the lactose operon?
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lacI. It makes the repressor, which is always expressed in the absence of lactose.
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What is the inducer of the lactose operon?
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lactose. It changes the conformation of the repressor, so it can no longer block the operator.
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What happens when the repressor is not bound to the operator (in negative control)
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It allows lacY, lacZ, and lacA to be transcribed. (These make galactoside permease, b-galactosidase, and transacetylase, which are needed for lactose catabolism.)
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What's the main difference with positive control?
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The inactivated repressor binds at a different region of the operon to induce transcription.
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What are the four stages of the bacterial growth cycle?
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1. Lag
2. Log 3. Stationary 4. Death |
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Antibiotics made by...
1. fungi 2. Gram + 3. Gram - |
1. beta-lactam
2. aminoglycoside 3. quinolone |
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What is MIC?
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minimal inhibitory concentration required to inhibit bacterial growth
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What are the four mechanisms of action of antibiotics we looked at?
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1. inhibit cell wall synthesis
2. disrupt cell membrane 3. inhibit nucleic acid synthesis/replication 4. inhibit protein synthesis |
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The second part of PG is a tetrapeptide, but when it is being synthesized, it's actually a ____, with the 4th and 5th aas being ____.
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pentapeptide; D-alanine
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What does D-cycloserine do?
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(1) Inhibits formation of the D-alanine-D-alanine bond in the pentapeptide.
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What antimicrobials prevent PG precursors from getting out of the cell?
|
(1) vancomycin prevents transport across cell membrane.
(1) bacitracin prevents Carrier Lipid PP from dephosphoylating so it can't be recycled |
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What does penicillin do?
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(1) prevents cleaving of the second D-alanine. Cross-links cannot be formed.
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Penicillin is a close analog of ___.
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D-alanyl-D-alanine
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What are the two families of antimicrobials that disrupt cell membranes (2)?
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a. polymyxins (for prokaryotic cells)
b. polyenes (interact with sterols -for eukaryotic cells, e.g. yeast) |
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What are the four families of antibiotics that inhibit DNA replication/synthesis (3)?
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1. quinolones
2. metronidazole 3. rifamycins 4. sulfonamides |
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What do quinolones do?
|
(3) Inhibit DNA replication
|
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What do metronidazoles do?
|
(3) Produce superoxide anion radicals to inhibit DNA replication.
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What do rifamycins do?
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(3) Inhibit DNA transcription by inhibiting RNA polymerase
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What do sulfonamides do?
|
(3) block folic acid synthesis, which is needed for NA synthesis
|
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Which antibiotics inhibit protein synthesis by inhibiting 30S (4)?
|
a. kanamycin
b. tetracycline c. spectinomycin 4. streptomycin |
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Which antibiotics inhibit protein synthesis by binding to the 50S (4)?
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a. chloramphenicol
b. erythromycin 3. clindamycin 4. lincomycin |
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Ethambuton, isoniazid, and pyrazinamide are all what?
|
Antiobiotics effective against acid-fast bacteria.
|
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What are the four general mechanisms of antibiotic resistance?
|
1.Decrease cell permeability
2. Mutation to alter target site 3. Acquire gene to pump out antibiotics 4. Acquire genes to kill antibiotics |
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Mutations in transpeptidase might cause ____ resistance.
|
penicillin
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Mutations in PG structure might cause ____ resistance.
|
vancomycin
|
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How might bacteria become resistant to tetracyclin?
|
A ribosome protection gene or a tetracyline pump.
|
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What's the last line of defense against MRSA?
|
vancomycin
|
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Mutated DNA gyrase would cause resistance to ___.
|
quinolone
|
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Which enzyme destroys penicillin?
|
beta-lactamase
|
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Over time, pneumococci have become resistant to ____.
|
penicillin G
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Over time, both meningococci and gonorrhea have become resistant to _____. The antibiotic of choice for gonorrhea is now ____.
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sulfonamides; quinolones
|
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Enteric bacteria are often treated with ____, but many are becoming resistant.
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tetracycline
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Regarding operons, ____ genes are always expressed and code for the ____.
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constitutive; repressor
|
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What is catabolite repression?
|
In the presence of glucose, genes that code for metabolic intermediates are repressed.
With a lack of glucose, the PTS activates cAMP, which activates these genes. This is an example of global control of several operons. |