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Microbio > Exam 2 Super Review > Flashcards

Exam 2 Super Review Flashcards

1
Q

i. Media: Sim tube (inoculate in a straight light)
ii. Reagent: None added
iii. Results
1. Tube is cloudy if mobile
2. Black means positive for H2S (the microbe is anaerobic)

A

Motility/H2S Test

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2
Q

a. Media: Starch agar (Tan)
b. Reagent Added: Iodine
c. Results for Positive Test: Clear halo

A

Starch Hydrolysis

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3
Q
  1. Starch is hydrolyzed in to maltose, glucose and dextrins by
A

Amylase

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4
Q

a. Media: Milk Agar (white)
b. Reagent Added: none
c. Results for Positive Test: Clear halo

A

Casein hydrolysis

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5
Q
  1. Fat, hydrolyzed into fatty acids and glycerol
A

lipase

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6
Q

a. Media: DNA agar (aqua green compared to Spirit)
b. Reagent Added: none
c. Results for Positive Test: Clear Halo

A

DNA hydrolysis

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7
Q
  1. Hydrolyzed nucleotides
A

DNAse

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8
Q

a. Media: Tryptophan Broth (in to test tube)
b. Reagent Added: Kovacs’ Solution (testing for presence of indole)
c. Results for Positive Test: Red/pink layer on top of the test tube

A

Tryptophan hydrolysis

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9
Q
  1. An amino acid, hydrolyzed into indole, pyruvic acid and ammonia by
A

tryptophanase

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10
Q

a. Media: Urea Broth
b. Reagent Added: None
c. Results for Positive Test: Turns from yellow to pink (response to high pH)

A

Urea hydrolysis

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11
Q
  1. Hydrolyzed into ammonia and carbon dioxide by
A

urease

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12
Q

a. Media: Bile Esculin Slant
b. Reagent Added: None
c. Results for Positive Test: Turns black

A

Esculin hydrollysis

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13
Q
  1. Hydrolyzed into glucose, esculatin and ferric citrate (dark brown salt) by
A

esculinase

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14
Q
  1. Media: Durham Fermentation Tube
  2. Reagent Added:
  3. Results: Yellow = acid; +/- for gas (see inverted tube)
A

Sugar Fermentation

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15
Q
  1. Media: MRVP Broth
  2. Reagent Added: 5 drops of Methyl Red
  3. Results: Red if pH 5
A

Mixed Acid Fermentation

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16
Q
  1. Media: Citrate Slant
  2. Reagent Added:
  3. Results: From green to intense blue
A

Citrate Utilization

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17
Q

a. Citrate used during the kreb’s cycle
b. Suggests that they engage in some form of cellular respiration if they can ingest citrate
2. Media: Citrate Slant

A

Citrate Utilization

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18
Q
  1. Media: Nutrient Agar Tube
  2. Reagent Added: Drop/o Oxidase on swab
  3. Results: from Red=> Blue/Black
A

Oxidase Test

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19
Q

a. Bacteria’s ability to has electron transport system

b. Suggests bacteria be engage in aerobic cellular respiration

A

Oxidase Test

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20
Q
  1. Media: nitrate broth
  2. Reagent Added: 5 drops of nitrate A+B
  3. Results: Red = presence of nitrite
A

Nitrate Reduction

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21
Q

a. Nitrate provides oxygen for cells that engage in anaerobic cellular respiration
b. Red means anaerobic cellular respiration, since nitrate  nitrite in cellular respiration

A

Nitrate Reduction

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22
Q
  1. Media: MRVP
  2. Reagent Added: VPA 15 drops, VPB 5 drops to 1 mL broth “Barritt’s reagent” tests for acetoin, precursor to alcohol fermentation product
  3. Results: Red after 10 min
A

Alcohol Fermentation

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23
Q
  1. Media: Slant Agar
  2. Reagent Added: Catalase (Hydrogen Peroxide)
  3. Results: Bubbles or not
A

Catalase

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24
Q

a. Bubbling indicates oxygen production, confirms the presence of catalase
b. Catalase is needed to survive in the presence of oxygen

A

Catalase

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25
Q
  1. plasmid
  2. codes for beta-lactamase
  3. and beta-galactosidase
A

PGal

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26
Q

a. test if transformed, put on agar with ampicillin

b. will enter media, inactivate ampicillin, normal sensitive can grow

A

beta lactamase

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27
Q

a. put e coli on agar enrihched with sugars galactosides

b. exoenzyme will enter media, hydrolyze sugars, turn blue

A

beta galactosidase

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28
Q

xii. =the natural process by which some bacteria can increase their genetic variability

A

Transformation

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29
Q
  1. Being able to acquire naked DNA from the environment around
A

Competent

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30
Q

i. Put bacteria on the plate
ii. Incubate on ice for 10 minutes
iii. Remove and incubate in 42 degrees hot water bath for 90 seconds
iv. Return tubes to ice water bath for 1 minute
v. Add recovery broth to the tubes
vi. Incubate in 37 degree water bath for 30 minutes
vii. Inoculate controls.
viii. Make E. Coli competent try to transform competent cells from white, ampicillin sensitive bacterium to a blue ampicillin resistant bacterium.
ix. Mix E coli with plasmid pGal

A

Transformation

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31
Q
  1. Streptococcus pyogenes
  2. Staphylococcus aureus
  3. Clear halo forms
  4. All the RBC’s and hemoglobin have been destroyed
A

Beta hemolysis

Alcohol on Bacterial Growth

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32
Q
  1. Halo generated, not clear
  2. Billiverdin
    a. Prouct of hemoglobin hydrolysis
A

Alpha Hemolysis

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33
Q

Do not generate a halo

A

Gamma hydrolysis

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34
Q

i. Chemically defined media

ii. We know every component and how much of that component is in the media

A

Synthetic

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35
Q

i. Infusions and extracts
ii. We use this in class a lot
iii. Secretions of ground up animal/plant stuff
iv. We don’t know the exact amount of each component beause we just kind of throw stuff in there.
v. Most commonly used media

A

Non Synthetic

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36
Q

a. Liquid medium containing beef extract and peptone

A

Nutrient Broth

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37
Q

a. Solid media containing beef extract, peptone, and agar

A

Nutrient Agar

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38
Q

i. Media that prevents the growth of one type of bacteria without inhibiting the growth of another type

A

Selective

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39
Q

i. Media Select for G-

ii. Inhibit G+

A

EMB and Hektoen

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40
Q

i. Selects for halophiles

A

SM 110

MSA Mannitol Salt agar

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41
Q

i. The way the organism grows on or its effect on a media helps tell the bacteria apart

A

Differential

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42
Q

i. Media Changes colors of bacteria

A

ChromAgar

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43
Q

a. EMB
b. Blood agar
c. ChromAgar
d. MSA
e. Columbia CNA

A

Examples of Differential Media

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44
Q

i. Additivevs are included to promote growth of fastidious bacteria
1. Ex:
a. TSA
b. Blood agar

A

Enriched media

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45
Q

good for propagating large numbers of organisms as well as for testing

A

Liquid media

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46
Q

shows surface growth patterns

i. Convenient for “pure culturing” organisms

A

Solid media

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47
Q
  1. Just the protein alone
  2. Has Apoenzyme core
  3. Cofactors
  4. Coenzymes
A

Simple Enzyme Structure

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48
Q

a. The protein portion

b. Contains the active site

A

Apoenzyme core

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49
Q

a. Non protein portions chemical compound that is bound tightly to an enzyme and is required for catalysis.
i. Metallic
1. Fe
2. Cu
3. Mg

A

Cofactors

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50
Q

a. Organic materials, non protein molecule that carries chemical grous between enzymes
b. vitamins

A

Coenzymes

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51
Q

i. They increase the rate of chemical reactions by lower the energy of activation.

A

Enzymes

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52
Q

ii. Only catalyze energy releasing reactions (net reaction must yield energy)

A

Enzymes

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53
Q

i. = a molecule with a shape complementary to the enzyme’s active site that, when it interacts with the enzyme, is changed by the enzyme

A

Substrate

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54
Q

ii. It binds to an active site.

A

Substrate

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55
Q
  1. Enzymes that do their job intracellularly (inside the cell)
A

Endoenzymes

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56
Q
  1. Enzymes that are secreted and do their jobs outside of the cell (extracellularly)
A

Exoenzymes

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57
Q
  1. Enzymes that are produced in response to the presence of a particular substrate
A

Induced Enzymes

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58
Q
  1. Only produced when the need is there; Turned on with changes in substrate concentration
A

Induced Enzymes

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59
Q
  1. Need is always there

2. Enzymes that are always produced

A

Constitutive Enzyme

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60
Q
  1. Enzymes that are not produced when the product of the enzyme pathway is present
A

Repressible

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61
Q
  1. Turned off in response to the substrate concentration
A

Repressible

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62
Q

vi. Their names are typically given based on their substrate and/or the reaction they complete

A

Enzymes

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63
Q

i. = Condensation Reactions
ii. When larger molecules are synthesized from building blocks by removing water
1. Ex: proteins from amino acids

A

Dehydration synthesis

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64
Q

i. When large molecules are split apart (digested) by adding water

A

Hydrolysis

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65
Q

i. When a molecule loses electrons/hydrogens (OIL RIG)

A

Oxidation

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66
Q

i. When a molecule gains electrons

1. Ex: during photosynthesis. CO2 is reduced to glucose C6H12O6

A

Reduction

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67
Q

i. When a phosphate is added to a molecule

1. Ex: Photosynthesis: When chlorophyll used in conversion of ADP –> ATP

A

Phosphorylation

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68
Q

i. Occurs when the final product, of an enzyme pathway, blocks further enzyme activity
ii. The product reacts with an allosteric site
iii. The shape of the enzyme’s active site is changed; and product production ceases.

A

Feedback Inhibition

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69
Q

i. An inhibitor molecule resembles the enzyme’s normal substrate and competes with the substrate for the active site.

A

Competitive Inhibition

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70
Q

i. Resemble and compete with PABA for a bacterial enzyme’s active site
ii. Is normally converted to the vitamin folic acid, by microbial enzymes.

A

Sulfa Drugs

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71
Q

adenine and guanine

A

Purines

Two rings

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72
Q

Cytosine and Thymine

A

Pyrimidines

One ring

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73
Q

i. 1 of the 4 nitrogenous bases
ii. Deoxyribose: a 5 carbon sugar
iii. A single phosphate group

A

Components of nucleotides

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74
Q

i. Sides of the DNA ladder consist of deoxyribose molecules alternating with phosphate molecules
ii. Rungs (steps) of the ladder are made by nitrogenous bonds
1. A binds to a T/U (D/R NA)
2. C binds to a G

A

Arrangement of nucleotides

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75
Q

three base sequence that codes for an amino acid or a control system

A

codon

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76
Q

a sequence of codons between a start and stop codon that codes for a protein/RNA

A

gene

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77
Q

a cluster of genes (primarily in prokarya) that operate as a unit, e.g., genes for enzymes of the same biosynthetic pathway.

A

operon

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78
Q

one DNA molecule

A

chromosome

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79
Q

the sum total of all the chromosomal DNA in the cell

A

genome

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80
Q

Composed of promoter site and operator site

A

Controlling site of operon

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81
Q

attachment for RNA Polymerase

A

promoter site

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82
Q

serves as attachment for repressor protein

A

operator site

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83
Q

a. Includes structural gene that codes for a repressor protein

A

Regulatory Operon

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84
Q

b. Includes a promoter site that serves as an attachment for RNA polymerase

A

Regulatory Operon for Repressor Protein

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85
Q

c. Has no operator site (no repressor protein for the repressor protein ha!)

A

Regulatory Operon for Repressor Protein

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86
Q
  1. The substrate binds to the repressor protein
  2. The repressor protein changes shape and has less affinity for operator site
  3. Now RNA polymerase can attach to promoter region; transcribe the structural genes into mRNA
A

Inducible enzymes

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87
Q
  1. If the substrate is absent, the repressor protein is in the wrong shape to bind/block the operator site
  2. Enzymes are produced
  3. Product is produced
  4. The produce forms a complex with repressor protein
  5. The product-repressor complex fits the operator site and blocks RNA polymerase
  6. – no more transcription.
A

Repressible enzymes

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88
Q

a. DNA supercoiling is relaxed by
a. DNA helix unwinds and unzips
b. Synthesis of complementary strands

A

DNA replication steps

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89
Q

i. Topoisomerase in eukarya

ii. DNA gyrase in prokarya

A

DNA supercoiling relaxed by

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90
Q

i. Starts at a single “origin of replication” in prokaryotes
1. Unzips in both directions
ii. (Multiple origins in Eukarya)
iii. Both catalyzed by helicase

A

dna helix unwinds and unzips

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91
Q

i. Each strand of DNA acts as a template for the arrangement of complement nucleotides
1. Remember A to T and C to G

A

complementary strands

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92
Q

builds RNA primer that’s necessary to start the complementary strand

A

RNA Polymerase

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93
Q
  1. Takes over after the primer is built
  2. Catalyzes the addition of DNA nucleotides to the growing DNA molecule
    a. Archaea have a special DNA polymerase
    i. Used in PCR
A

DNA Polymerase

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94
Q
  1. The fragments are ultimately attached to one another via an enzyme called a ligase
  2. DNA Pol can only add to a strand on its 3’ end, meaning it “writes” from 5’ to 3’
    a. Has to then read a strand from 3’ to 5’
A

DNA replication is continuous on the 3’ strand and discontinuous on the 5’ strand

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95
Q
  1. Unzips the DNA helix
A

Helicase

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96
Q
  1. Synthesizes an RNA Primer
A

Primase/RNA Polymerase

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97
Q
  1. Adding bases to the new DNA chain

2. Proofreads the chain for mistakes

A

DNA Polymerase III

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98
Q
  1. Removes RNA primer
  2. Closes gaps
  3. Repairs mismatches
A

DNA Poly I

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99
Q
  1. Final binding of nicks in DNA during synthesis and repair
A

Ligase

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100
Q
  1. Supercoiling
A

Gyrase

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101
Q

i. Source: synthetic agents
ii. Effect: block DNA gyrase (the enzyme responsible for relaxing the DNA supercoiling prior to the unwinding of a DNA strand)
1. Prevents relaxation of the DNA

A

a. Naladixic acid and ciprofloxacin

Interfere with DNA Replication

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102
Q

i. Source: synthetic nucleotide mimic that has a base similar to guanine
ii. Target: DNA Polymerase
iii. Effect: Competitive inhibition of DNA synthesis
iv. Microbe affected:
1. Genital Herpes
2. Chickenpox
3. Shingles
v. Toxicity
1. Brain seizures
2. Confusion and skin rash

A

Interfere with DNA Replication

Acyclovir

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103
Q

i. = Azidothymidine (and related synthetic drugs)
ii. Source:
1. Synthetic thymine analogue
a. Mimics thymine nucleosides
iii. Target:
1. Reverse transcriptase
a. (has a lesser affinity for DNA Polymerase)
iv. Effect:
1. Competitively inhibits the transcription of HIV RNA into HIV DNA
v. Microbe Affected
1. Retroviruses (like HIV – the AIDS virus)
vi. Toxicity
1. Causes anemia and immunosuppression
a. Inhibits mitochondrial DNA replication

A

Interfere with DNA Replication

AZT

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104
Q

are antiviral drugs that are analogs of purines and pyrmidines (nucleoside mimics)

A

AZT and Acyclovir

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105
Q

how to make mRNA

A

transcription

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106
Q

i. DNA untwists and unzips to expose the codons
ii. RNA polymerase attaches to promoter site on one of the DNA strands
1. Specifically the template strand, which is the strand from which mRNA can be generated continuously
iii. Complementary RNA nucleotides are attached sequentially until a “stop” codon is reached
iv. There are no introns to remove in prokaryotes and finished mRNA may represent more than one protein
v. Completed m-RNA

A

Transcription

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107
Q

fold introns, remove them and splice remaining exons together.

A

Spliceosomes

Eukaryotes

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108
Q

a. mRNA Sent out of the nucleus into the cytoplasm where it will encounter 80s ribosomes

A

Eukaryotes

Completed mRNA

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109
Q

can be translating the same m-RNA at the same time

A

Polyribosomes

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110
Q

i. Happens as the the m-RNA is being

A

70s ribosomes find and attach to mRNA

Prokaryotes

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111
Q

v. There are no introns to remove in prokaryotes and finished mRNA may represent more than one protein

A

fact.

112
Q
  1. A transfer RNA (tRNA) with an appropriate complementary anticodon and carrying an activated amino acid attaches at the start codon
A

Translation

113
Q
  1. Begins when 30s ribosome subunit binds to the start codon (AUG) on the m-RNA
A

Initiation

Translation

114
Q
  1. the transcript RNA
  2. Consists of a single chain (half a ladder) of nucleotides
    a. Has the same bases as DNA except Thymine replaced by uracil
    b. Uses the sugar ribose instead of deoxyribose
A

mRNA

115
Q
  1. derived from a large precursor RNA molecule that is split into not only ribosomal RNA, but also transfer RNA
  2. Combines with protein to form the 50s and 30s subunits of ribosomes
A

rRNA

116
Q
  1. made from a number of different precursor RNA molecules
  2. consists of about 80 nucleotides with one exposed codon
    a. this is called the anti-codon
  3. is the “decoder” molecule
    a. transports ATP activated amino acids to the appropriate, complementary codon on the mRNA.
    b. Responsible for the translation of the mRNA code into an actualy amino acid sequence
A

tRNA

117
Q
  1. Can be doing transcription/translation at the same time
  2. Do not have introns and exons
  3. Finished mRNA may represent more than one protein
A

Prokaryotes

118
Q
  1. Have removal of introns via spliceosomes

2. Transcription and translation are different times and location (nucleus vs. cytoplasm)

A

Eukaryotes

119
Q

a. E
i. Linear chromosomes
b. B
i. 1 circular
c. A
i. 1 circular

A

DNA

120
Q

a. E
i. histones
b. B
i. none
c. A
i. Histone like

A

Histones

121
Q

i. Introns in m-RNA
ii. Operons rare
iii. Topoisomerase (relaxes the supercoiling)
iv. Replicates through mitosis

A

E

122
Q

i. no introns in m-RNA
ii. Operons
iii. DNA gyrase relaxes the supercoiling
iv. Binary fission for replication

A

B

123
Q

i. No introns in mRNA
ii. DNA gyrase for relaxing the supercoiling
iii. Has Unique DNA Polymerase that tolerates extreme temperatures

A

A

124
Q

i. M-RNA processing in the nucleus

ii. Transcription is separate from translation

A

E

125
Q

i. One class has only one type of RNA polymerase; the other has >1
ii. No m-RNA processing
iii. Transcription and Translation happen at the same time.

A

B+A

126
Q

a method for rapidly generating identical strands of DNA

A

Polymerase Chain Reaction

127
Q

b. Heating a DNA strand of 94 degrees C for 30 seconds,

i. causes the DNA to unwind and unzip

A

PCR

128
Q

c. Cooling the DNA to 50 degrees C

i. will allow primers to attach to the two separate DNA strands

A

PCR

129
Q

d. Raising the temperature to 72 degrees C for 2 minutes and providing DNA polymerase
i. promotes the synthesis of complementary strands

A

PCR

130
Q

i. Provide the unique heat resistant DNA Polymerase used for this

A

Archaea

PCR

131
Q

a. Involve environmental mutagens
i. Viruses
ii. UV radiation
1. Dimers are the most common mutations
iii. Compounds foreign to the cell

A

Induced mutation

132
Q

a. Involve DNA Replication errors

A

Spontaneous Mutation

133
Q

a. When, within a codon, one nucleotide is replaced by another with a different base
b. If the new codon codes for the same amino acid as the original codon, no change in he protein coded by the gene will occur
c. If the substitution results in a code for a different amino acid, the resultant protein may be defective
i. Hemoglobin in sickle cell anemia differs from normal hemoglobin by one aino acid

A

Point mutation

Base Substitution

134
Q

a. Due to insertions or deletions of nucleotides
b. Can result in changing all the codons that follow the insertion or deletiono
c. Change the encoded protein COMPLETELY

A

Point mutation

Frameshift

135
Q
  1. Found naturally in sunlight
  2. Wavelengths of 40nm-390nm
  3. Causes the redistribution of electrons and protons in thymines and cytosine, making them highly reactive
    a. Bonding of adjacent thymines and/or cytosines creates dimers, which distort the DNA
    b. Interferes with DNA replication and transcription
    c. Most common mutation***
A

Non Selective Agents that Damage DNA

UV light

136
Q

a. Create hyperactive ions which react with nucleotides causing the release of bases and the breakage of the DNA
b. Create free radicals
i. Highly reactive molecular fragments that have an unpaired electron; attack DNA
c. Have high penetration, but sterilization is often not possible because of negative effects on the media
d. Kill salmonella and E. coli in food products
e. can be used to sterilize plastic equipment and pharmaceutical products, as well as preventing food spoilage

A

Non Selective Agents that Damage DNA
Ionizing radiation
Gamma rays

137
Q

a. Can create free radicals that attack DNA

b. Have considerable energy and penetration

A

Non Selective Agents that Damage DNA
Ionizing Radiation
x rays

138
Q
  1. Increase the penetration power of water

2. Are either anionic (negatively charged) or cationic (positively charged)

A

Non Selective Agents that Damage DNA

Soaps and detergents

139
Q

i. Usually bad

A

mutations

140
Q

ii. Discovered by Barbara McClintock in 1948.

A

Other sources of genetic variation

transposons

141
Q

i. Special DNA segment that have the capability of moving from one location in the genome to another – “jumping genes.”
ii. Discovered by Barbara McClintock in 1948.
iii. Causes the rearrangement of the genetic material
iv. Can move from one chromosome site to another, from a chromosome to a plasmid, or from a plasmid to a chromosome.
v. May be beneficial or harmful
vi. Thought atht 45% of our genome could be from these.
vii. A “jumping gene” that can “jump” between chromosomes or plasmids
viii. Enters the host genome via the enzyme transposase generating recombinant DNA (DNA generated from two or more sources)

A

Other sources of genetic variation

transposons

142
Q

a. Where plasmids are transferred via a mating bridge involving sex pili in G- cells
i. attaches to a receptor on a target cell retracts, pulling the cells together

A

Other sources of genetic variation

conjugation

143
Q
  1. Plasmids are…
    a. G+ cells gain intimate contact and exchange DNA through a conjugation bridge
    b. donor transfers a copy of plasmid through pilus
A

Other sources of genetic variation

conjugation

144
Q

a. A copy of the chromosome can begin the passage to a second cell via mating/conjugation bridges
b. The passage is usually interrupted and the chromosomes breaks such that only a partial transfer occurs
c. Transferred chromosomal DNA can integrate itself into the new cell’s genome, creating recombinant DNA

A

Other sources of genetic variation
conjugation
involving chromosomes

145
Q
  1. Conjugation can be accelerated when the cells are exposed to environmental stress
A

Other sources of genetic variation
conjugation
truth

146
Q
  1. = the transfer of genes from one bacterium to another via a virus=bacteriophage
A

Other sources of genetic variation

transduction

147
Q

a. Some viruses can infect several species and even genera

A

Other sources of genetic variation

148
Q

a. Random fragments of disintegrating host DNA are picked up by the phage during assembly
i. Any gene can be transmitted this way
b. The bacterial genome breaks into fragments and some of the newly forming viruses pick up a bacterial DNA fragment instead of viral DNA
c. Bacterial DNA is then injected into another bacteria

A

Other sources of genetic variation

Generalized Transduction

149
Q

a. A highly specific part of the host genome is regularly incorporated into this virus
b. Viral DNA is integrated into a bacterial genome at one specific site
i. =lysogenized
c. The virus excises itself along with the neighboring bacterial DNA
i. A restricted group of bacterial genes are transferred to new host cell, instead of a random fragment.

A

Other sources of genetic variation

Specialized transduction

150
Q

b. Viral DNA is integrated into a bacterial genome at one specific site

A

Other sources of genetic variation
transduction
=lysogenized

151
Q
  1. Chromosome fragments from a lysed cell are accepted by a recipient cell; the genetic code of the DNA fragment is acquired by the recipient
    a. Donor and recipient cells can be unrelated
    b. Useful tool in recombinant DNA technology
A

Other sources of genetic variation

Transformation

152
Q
  1. Where Naked DNA is taken up by bacteria and recombines with the main bacterial genome
A

Other sources of genetic variation

Transformation

153
Q

the term used when eukarya take up naked DNA

A

Other sources of genetic variation

Transfection

154
Q

a. For bacteria, competency can occur for a short time during the log phase of growth
b. Is facilitated by a competence factor that can be released into the medium by the bacterial cells or displayed as a surface protein that binds to the DNA

A

Cells must be competent in order to take up naked DNA

155
Q

i. Live strain w/ capsule killed rat
ii. Heat killed strain/w capsule rat survives
iii. Live strain, no capsule rat lives
iv. Live no capsule + dead capsule = dead rat
1. Both strains are found in dead rat LIVING with isolated

A

Griffith’s work
Transformation
Streptococcous Pneumoniae

156
Q
  1. When genes from a cell are transferred to another existing cell
    a. i.e. when genes from a bacterium are transferred to a neighboring bacterium
A

Other sources of genetic variation

Lateral Gene Transfer

157
Q

is when genes are passed to two daughter cells that result from mitosis or binary fission

A

Other sources of genetic variation

Vertical Gene Transfer

158
Q
  1. Conjugation, transduction, and transformation (transfection)
A

Other sources of genetic variation

all result in lateral gene transfer

159
Q
  1. About 80% of microbe genes have been laterally transferred at some point in their history.
  2. Bacterial speciation is more driven by LGT than from mutations. Pretty cool!
A
  1. About 80% of microbe genes have been laterally transferred at some point in their history.
  2. Bacterial speciation is more driven by LGT than from mutations. Pretty cool!
160
Q

i. =the intentional removal of genetic material from one organism and combining it with that of a different organism
ii. Bacteria picks up plasmid by trransformation

A

Recombinant DNA Technology

161
Q
  1. Objective is CLONING, which requires that the desired donor gene be selected, excised by restriction endonucleases, and isolated
  2. The gene is inserted into a vector (plasmid, virus) that will insert the DNA into a cloning host
  3. Cloning host is usually bacterium or yeast that can replicate the gene and translate it into a protein product.
A

Recombinant DNA Technology

162
Q

A gene source

i. A vector = what you use to transfer the gene to the bacteria
ii. A cell in which the recombinant can proliferate =clone

A

Genetic Engineering

requirements

163
Q
  1. The gene must include a start codon, a stop codon, AND a controlling site
  2. Gene product must not be toxic to a host cell
A

Genetic Engineering

gene source

164
Q
  1. DNA into which the desired gene is spliced so the gene can be inserted into a host cell
    a. Since host cells won’t usually accept a foreign gene all by itself
A

Genetic Engineering

vector

165
Q
  1. bacterial and yeast plasmids as well as viral DNA are often used
    a. must be able to replicate
    b. must have a gene that allows selection of the DNA that is recombinant
    i. usually two genes for antibiotic resistance
A

Genetic Engineering

vector

166
Q

= viruses, have the natural ability to inject their DNA into bacterial hosts through transduction

A

Genetic Engineering

= bacteriophages

167
Q

iii. A cell in which the recombinant can proliferate

A

Genetic Engineering

=clone

168
Q

i. Construction of the recombinant DNA
ii. Introduction of the recombinant into the host cell via a vector
iii. Selection of a host cell with a recombinant DNA
iv. Cloning and expression of the gene involves

A

Steps in Genetic Engineering

169
Q

a. Bind DNA (DNA in the vector as well as well as DNA in the gene source) and uct it in one or more places at specific sites
i. Each species or strain of bacteria has a specific restriction endonuclease that normally breaks down foreign DNA

A

Steps in Genetic Engineering
i. Construction of the recombinant DNA
Restriction endonucleases

170
Q

a. Cuts DNA so it has staggered ends (sticky ends)

b. is used to prepare DNA so a gene can be spliced in to generate recombinant DNA

A

Steps in Genetic Engineering
i. Construction of the recombinant DNA
Restriction endonuclease

171
Q

is used as a vector to carry and incorporate genes into mammalian cells

A

Steps in Genetic Engineering
ii. Introduction of the recombinant into the host cell via a vector
viral genome

172
Q

a. are the most common techniques for delivering “naked DNA” to new hosts
b. The host cells need to be made competent
c. Eukaryotic plant cells can be transfected (infected by the new recombinant DNA) by the gram negative bacteria Agrobacterium tumefaciens

A

Steps in Genetic Engineering
ii. Introduction of the recombinant into the host cell via a vector
Transformation of bacterial cells
Transfection of eukaryotic cells

173
Q
  1. Are usually made competent via exposure to chloride salts solutions and temperature extremes or via electroporation
    a. Cells are exposed to pulses of electrical fields that open small pores in cell membranes
  2. Plasmids are used as vectors to transform bacteria
A

Steps in Genetic Engineering
ii. Introduction of the recombinant into the host cell via a vector

Truth.

174
Q
  1. The vector, with the gene of interest, needs to include two genes for antibiotic resistance
A

Steps in Genetic Engineering

iii. Selection of a host cell with a recombinant DNA

175
Q
  1. The host cells are plated on a media that contains the 2 antibiotics
A

Steps in Genetic Engineering

iii. Selection of a host cell with a recombinant DNA

176
Q
  1. Cells with appropriate antibiotic resistance, that is, resistance to 1 of the antibiotics (and therefore has the gene of interest) can be identified
A

Steps in Genetic Engineering

iii. Selection of a host cell with a recombinant DNA

177
Q
  1. Harvesting the resistant cells that contain the recombinant (gene of interest)
  2. Allowing the cells to multiply (gene amplification)
A

Steps in Genetic Engineering

iv. Cloning and expression of the gene involves

178
Q

Significance of Genetic Engineering

  1. Factor VIII
    a. For hemophilia
  2. Growth hormone and insulin
  3. The gene for normal hemoglobin
  4. The gene for normal chloride ion channels
    a. Cystic fibrosis
  5. Interleukin II (Bubble Boy) for the treatment of SCID (Severe Combined Immunodeficiency)
A

i. Genetically engineer human proteins and cells to correct hereditary diseases

179
Q

Significance of Genetic Engineering

  1. Alpha interferon for treatment of Hairy Cell Leukemia
  2. Vaccines
    a. Hepatitis B (HBV)
    i. The gene for a viral surface protein is inserted into a yeast plasmid
A

Genetically engineered drugs

180
Q

Significance of Genetic Engineering

= use of an organism’s biochemical and metabolic pathways for industrial production

A

Biotechnology

181
Q

Significance of Genetic Engineering

i. Gene for herbicide resistance
ii. Bacteria transformed
iii. Transfection of plant cells
iv. 99% of corn, soy, and cotton are genetically engineered.

A

eukaryotic plants can be transfected by the G- bacteria, Agrobacterium Tumefaciens, plant pathogens

182
Q

Significance of Genetic Engineering

i. Correct or repair a faulty gene in humans

A

gene therapy

183
Q

Significance of Genetic Engineering

a. Normal gene cloned in vectors, tissue removed from the patient

A

ex vivo

184
Q

Significance of Genetic Engineering

a. Naked DNA or vector is directly introduced to the patients tissue

A

in vivo gene therapy

185
Q
  1. Glycolysis
    ii. Incomplete oxidation of glucose/carbs in the absence of oxygen
    iii. Yields small amount of ATP
  2. But less competition in areas w/o oxygen
    iv. Formation of acid, gas, and other products by action f various bacteria on pyruvic acid
    v. Glycolysis
  3. Organic compounds are the final electron acceptors
    vi. Products include
  4. Swiss cheese with CO2
    a. Makes the holes
A

Fermentation

186
Q

i. Glycolysis
ii. Kreb’s cycle
iii. Respiratory chain
iv. Yields about 28ATP

A

Aerobic Respiration

187
Q

i. Glycolysis
ii. Kreb’s cycle
iii. Respiratory chain
1. Molecular Oxygen is NOT the final electron acceptor
2. Has oxygen containing ions but not free oxygen
3. Nitrate (NO3) and nitrite (NO2-)
iv. Yields fewer ATP (~20)

A

Anaerobic Respiration

188
Q
  1. O2-
  2. Superoxide
  3. Free radical
A

i. All organisms exposed to oxygen produce the toxic molecule

189
Q

ii. Obligate aerobes plus facultative and microaerobes have enzyme which converts O2- into

A

hydrogen peroxide

190
Q

a. Breaks O2- into hydrogen peroxide

A

Superoxide dismutase

191
Q

a. Breaks hydrogen peroxide into H2O and O2

A

Catalase

192
Q

i. Anaerobic and can be independent of the sun
ii. Can occur in extreme temperatures and pressures
iii. H2 oxidised to form sugar
iv. Sulfur compounds are oxidized to form sugar
v. Rocks are oxidized to form sugar

A

chemosynthesis

193
Q
  1. Methane as byproduct
  2. Found in variety of ecological niches
    a. Seqage slude
    b. Marine and lake sediments
    c. Geothermal springs
    d. Deep sea hydrothermal vents
    e. Animal intestines (cow farts)
    f. Archaea photosynthesis
A

Methanogens

194
Q

i. Archaea
1. Bacteriorhodopsin
ii. Only produces ATP
iii. No Calvin Benson Cycle – no sugar
iv. No ETC

A

Archaea photosynthesis

195
Q

Light dependent reactions

A

Oxygenic photosynthesis

196
Q
  1. Light
    a. Cyclic Phosphorylation
    i. ATP
  2. +CO2
  3. Calvin Benson Cycle (light indp)
  4. Sugar
    b. +H2O + NADP
    i. Non Cyclic Phosphorylation
  5. ATP/NADPH/O2
    a. Calvin Benson Cycle Sugar/H2O/RuBP
A

Oxygenic photosynthesis

ight dependent reactions

197
Q

i. Done by green and purple sulfur bacteria
ii. Uses the pigment bacteriochlorphyll
iii. Uses hydrogen sulfide or hydrogen gas for replacement electrons
iv. No O2 released

A

Anoxygenic photosynthesis

198
Q

i. Breakdown of Glucose to pyruvic acid
ii. For one glucose,
1. 2 ATP IN, 4 ATP out = net 2ATP gain
2. 2 NADH (for electron transport chain)
3. 2 pyruvic acid

A

Glycolysis

199
Q

i. Pyruvic acid  Acetyl CoA before begins this
ii. Processes pyruvic acid and generates
iii. 3 CO2 molecules
iv. NADH and FADH2 generated
v. ATP
vi. Makes 6 NADH, 2FADH2 (per glucose; goes to ETC)
vii. Makes 2 ATP and 6CO2 (per glucose)

A

Kreb’s cycle

200
Q

i. Final processing of electrons and hydrogen and the major generator of ATP
ii. Chain of redox carriers that receives electrons from reduced carriers (NADH and FADH2)
iii. Shuttles electrons down the chain
1. Energy released
2. Subsequently captured
iv. Used by ATP synthase complexes to produce ATP
1. Oxidative phosphorylation
v. Accepts electrons from NADH and FADH
vi. Generates energy through sequential redox reactions called “oxidative phosphorylation”
vii. It’s a total of 10 NADH and 2FADH2/glucose give electrons and hydrogens to the ETS
1. Electrons pass along a group of coenzymes
2. Hydrogens pumped to to exterior of the cell membrane, creating a gradient
viii. NADH  3 ATP
ix. 1 FADH2  2 ATP

A

Electron Transport System

+ Phosphorylation

201
Q
  1. Algae and Plants

a. Chlorophyll a and b

A

Oxygenic photosynthesis pigment

202
Q
  1. Cyanobacteria
    a. Phycobiliprotein
    b. Chlorophyll a and b Sometimes
A

photosynthesis pigment
bacteria
oxygenic photosynthesis

203
Q

a. Bacteriochlorophyll

A

photosynthesis pigment
bacteria
anoxygenic photosynthesis

204
Q

i. Archaea
1. Bacteriorhodopsin
ii. Only produces ATP
iii. No Calvin Benson Cycle – no sugar
iv. No ETC

A

photosynthesis pigment

Archaea photsynthesis

205
Q

i. The ultimate source of all the chemical energy in cells comes from the sun
1. 6CO2 + 6 H2O –light glucose (C6H12O6)+6O2

A

Photosynthesis in general

206
Q
  1. Electron released from pigment returns to its original photosystem (photosystem 1) via the ETS
  2. Only generates ATP
A

Cyclic photophosphorylation

207
Q
  1. If electrons lost from PS1 are picked up by a molecule of NADP
  2. The electrons are released from chlorophyll in PSII
    a. Used to replace those lost by chlorophyll in PS 1
    b. Are delivered to PS1 via ETS that generates ATP
  3. H2O provides final replacement electrons (and O2)

a. Photolysis of H2O with loss of flectrons to PSII
b. PSII powerful oxidizing agent, removes electrons from hydrogens in water
i. Electrons are used to replace electrons lost form chlorophyll in PS II
ii. ATPs generated in ETC
iii. H+ are used for the reduction of NADP- to NADPH
4. Generates ATP and NADPH to go to the Calvin Benson cycle

A

noncyclic photophosphorylation

208
Q

i. Light independent

1. Uses ATP and NAPH to fix CO2 and convert it to glucose

A

Calvin Benson cycle

209
Q
  1. Must obtain carbon in an organic form made by other living organisms
    a. Proteins
    b. Carbohydrates
    c. Lipids
    d. Nucleic acids
A

Carbon Source

Heterotroph

210
Q
  1. =self feeder
  2. An organism that uses Co2, an inorganic gas, as it’s carbon source
  3. Not nutritionally dependent on other things
  4. Makes its own sugars
A

Carbon source

Autotroph

211
Q
  1. Gains its energy from chemical compounds

a. Glycolysis and breaking down glucose

A

Energy source

chemotroph

212
Q
  1. Gain energy through photosynthesis
A

Energy source

phototroph

213
Q
  1. Don’t use light so have to each other things as a source of nutrients
  2. Have organic compounds as its carbon source
  3. Differ based on their final electron acceptor
A

Chemoheterotrophs

214
Q

Chemoheterotrophs

i. All animals
ii. Most fungi
iii. Protozoa
iv. Bacteria

A

Chemoheterotrophs

O2 electron acceptor

215
Q

Chemoheterotrophs

i. Separated by
ii. Inorganic compounds
1. Like Clostridium
iii. Organic compounds
1. Fermentation of Streptococcus for instance

A

Chemoheterotrophs

No O2 electron source

216
Q
  1. The ones that do chemosynthesis
  2. Energy source chemicals
  3. Carbon source CO2
  4. Archaea and Bacteria
A

Chemoautotrophs

217
Q
  1. Light as energy source
  2. Organic compounds for C source
    a. Green and purple, nonsulfur bacteria
    b. Archaea
A

Photoheterotrophs

218
Q
  1. Light energy source
  2. Co2 carbon sourc
  3. Use H2O to reduce CO2?
A

Photoautotrophs

219
Q

Photoautotrophs

i. Oxygenic photosynthesis
1. Plants/algae
2. cyanobacteria

A

Photoautotrophs

Use H2O to reduce CO2

220
Q

Photoautotrophs

i. Anoxygenic photosynthesis
1. Green purple sulfur bacteria

A

Photoautotrophs

Do not use H2O to reduce CO2

221
Q
  1. Lowest temperature that permits a microbe’s growth and metabolism
A

Minimum temperature

222
Q
  1. Highest termperature that permits a microbe’s growth and metabolism
A

Maximum temperature

223
Q
  1. Promotes the fastest rate of growth and metabolism
A

Optimum temperature

224
Q

i. Optimum temperature
1. 15 degrees C
2. Capable of growth of 0 degrees C Refrigerator spoilage

A

psychrophile

225
Q

i. Optimum temperature 20-40degrees

ii. Most human pathogens

A

mesophile

226
Q

i. Optimum temperature greater than 45 degrees

ii. compost

A

Thermophile

227
Q

i. A mesophile that can grow at 0 degrees

ii. Cause for disease and spoilage

A

Psychrotolerant

228
Q

i. Greater than 80 degrees

ii. Includes Extremophiles (which are happy <0 degrees C)

A

Hyperthermophiles

229
Q

80 degrees C

A

Extremophiles

230
Q

i. Cannot grow without oxygen

ii. Can utilize oxygen and detoxify it

A

Obligate aerobe

231
Q

i. Utilizes oxygen but can also grow in its absence
1. Staphylococcus
2. E. Coli

A

Facultative Anaerobe

232
Q

i. Requires ony a small amount of oxygen

ii. Helicobacter species

A

Microaerobes

233
Q

i. Lacks the enzymes to detoxify oxygen so cannot survive in an oxygen environment

A

Obligate Anaerobe

234
Q

i. All organisms exposed to oxygen produce the toxic molecule
1. O2-
2. Superoxide
3. Free radical

A

truth

235
Q

i. Oxygen level at which organism switches from aerobic to anaerobic metabolism

A

Pasteur Point

236
Q

ell environment results in cellular dehydration and plasmolysis with protein precipitation

A

High solute concentration

237
Q

a cell’s environment result in water entering the cell such that cells may lyse

A

Low solute concentration

238
Q
  1. Require an environment with high concentration of organic molecule
  2. Sugar
A

osmophiles

239
Q
  1. Do not require high concentration of solute but can tolerate it when it occurs
A

osmotolerant

240
Q
  1. Require environment with high salt concentrations to stabilize their membranes
A

halophiles

241
Q
  1. Parent cell enlarges, duplicates its chromosomes, and forms a central transverse septum dividing the cell into two daughter cells.
A

binary fission

242
Q

a. = Time required to complete fission cycle (one parent  two daughter cells

A

generation time for bacteria

243
Q

i. “flat” period of adjustment
ii. Enlargement
iii. Little growth
1. Cells are increasing in cell mass

A

Lag phase

244
Q

i. Period of maximum growth
ii. Continues as long as cells have adequate nutrients and a favorable environment
iii. Proportional to the rate of energy metabolism
iv. Very susceptible to antibiotics and other chemicals at this point.

A

Log phase

Exponential Growth phase

245
Q

i. Rate of cell growth = rate of cell death
ii. Caused by depleted nutrients and O2,
iii. Caused by excretion of organic acids and pollutants
iv. Cells in survival mode, making defensive proteins

A

Stationary Phase

246
Q

i. As limiting factors intensify, cells die exponentially

ii. Remain are those most resistant and endospores

A

Death Phase

247
Q

i. Most simple
ii. Turbidity = degree of cloudiness
1. Reflects the relative population size

A

Turbidometry

248
Q

i. Dilutions and plating allow plate to have accurate counting of plates
ii. Remember the dilutions and you can multiply that and see how many colonies were in the original sample

A

Plate count

249
Q
  1. Reduce the number of pathogens off inanimate objects

reduces number of microbes

A

Disinfectant

250
Q
  1. To reduce or inhibit microbes on living tissue

reduces number of microbes

A

Antiseptic

251
Q
  1. Removes or kills all microbes

a. They are incapable of reproducing

A

Eliminates microbes

252
Q

You sterilize PLUS remove all microbial toxins

A

Decontaminations

253
Q

i. Inhibits bacteria

A

Bacteriostatic

254
Q

Kills bacteria

A

Bacteriocide

255
Q

Kills fungi

A

Fungicide

256
Q

Kills microbes

A

Germicide

257
Q

Destroys bacterial or fungal spores

A

Sporicide

258
Q

i. Sterilizes

ii. Like what we do to inoculating loop and inoculating needle

A

Dry heat

oven and incineration

259
Q
  1. Sterilizes if spores are not present
A

Boiling

260
Q
  1. Sterilizes if spores are present
A

Tyndallization

261
Q
  1. Pressure cooker
  2. Results in temperatures about boiling
  3. Good penetration
  4. The most practical and dependable
  5. Sterilizes, DOES NOT CONTAMINATE
A

Autoclave

262
Q
  1. Does not sterilize
  2. Used to eliminate pathogens from food products
    a. Usually beverages like milk
  3. Controlled heat BELOW boiling (72 degrees for milk) for 15 seconds
  4. Media that are concentrated or contain fats and sweeteners require higher temperature
    a. Skim milk vs. cream
A

Pasteurization

263
Q

i. Shortest time required to kill all microbes in a suspension at a given temperature.

A

Thermal Death Time

264
Q

i. The lowest temperature at which microbes are killed in 10 minutes

A

Thermal Death Point

265
Q

i. Bacteria are added to tubes with different dilutions of a chemical agent and then incubated
ii. Identify agents that prevent growth at the great dilution
iii. Minimal inhibitory concentrations
1. Serial dilution of the agent plus
a. A suspension of the organism
2. = the tube with the lowest amount of agent that is without visible growth

A

Dilution tests

266
Q

i. Filter paper method
ii. Look for a clear area around the paper disks soaked in a given agent.
1. This is where bacteria growth has been inhibited
iii. The media used in determining sensitivity should be comparable to tissue fluids of the body
iv. Staphylococcus Aureus is the usual test organism
v. Can’t tell if the organisms are dead or inhibited
vi. Various agents diffuse through agar at differet rates

A

Sensitivity Discs

267
Q

i. Occasionally acquired during spontaneous mutation in critical chromosomal genes
ii. OR
iii. Acquisition of new genes or sets of genes via transfer from another species.
1. Originates from resistance factors (plasmids) encoded with drug resistance, transposons
iv. Survival when there was a high concentration of antibiotics

A

How resistance of genes are spread

268
Q

a. ajor contributors to resistance
i. Hospitals (immunosuppressed, sick, old)
ii. Daycare centers (immature immune systems, high exposure)
iii. Antibiotic use in livestock
iv. Third world countries (no controls on use, war, and poverty)
v. First world countries
1. Given unnecessarily
2. Instructions not followed
3. Antibiotics in products

A

Where do humans most often encounter resistant microbes?

269
Q

Immunocompromised
Kids
Health care workers

A

who’s at risK?

270
Q

a. Produce enzymes that activate antibiotics
b. Prevent antibiotics from reaching the target
c. Alter antibiotic targets
d. Change the enzyme’s pathway
e. Note that resistance tends to increase with time
f. Humans pool antibiotics from trillions of bacteria

A

Major resistance strategies by microbes

271
Q

ii. Actual results are the same when treating livestock with antibiotics such that we can acquire resistant bacteria from animal products. Body flora of livestock represent the 3rd major reservoir of genes for antibiotic resistance.
iii. The more effective a treatment is at eradicating a susceptible population fof bacteria, the more it will promote the development and spread of resistant bacterial populations.

A

Successful Antibiotic treatment

272
Q

i. The sensitive bacterial pathogen and benign normal body flora are both killed by the antibiotic
1. The “shield” that normal body flora provide against new pathogens entering the body is weakened
2. Resistant normal body flora
a. Will flourish without competition and create super infections
i. E.g. Clostridium difficile
b. Surviving resistant normal body flora act as a reservoir for resistance genes that can be transferred to antibiotic sensitive pathogens

A

Successful antibiotic trreatment

273
Q

i. Surviving resistant pathogens may replicate leading to a renewal of the disease
ii. The antibiotic fails
1. The disease is now harder to treat
2. Re-emergence of disease and an increase in untreatable infections
iii. Wrong antibiotic given or wrong dosage
iv. Instructions not followed

A

Unsuccessful antibiotic treatment

274
Q

i. Hospitals (immunosuppressed, sick, old)
ii. Daycare centers (immature immune systems, high exposure)
iii. Antibiotic use in livestock
iv. Third world countries (no controls on use, war, and poverty)
v. First world countries
1. Given unnecessarily
2. Instructions not followed
3. Antibiotics in products

A

Major contributions to resistance

275
Q

i. Increased health costs
ii. Re-emergence of disease
iii. Loss of work
iv. Higher death rates
v. Increased side effects

A

Consequences of antibiotic resistance

276
Q

a. Use less antibiotics!
b. Practice prevention
c. Reduce exposure in hospitals and daycares
d. Survey diseases and resistance
e. Eliminate vectors that spread disease
f. Educate people (and doctors) on the proper use of antibiotics

A

Best strategy to reduce number of resistance bacterial populations

277
Q

a. Because resistance is on a plasmid, it slows replication rate.
b. Would be a disadvantage in an environment without anti biotics
c. Allows the sensitive bacteria to outgrow and outcompete the resistant ones
d. Loss of plasmids becomes favored (plasmids not copied, unevenly distributed to daughter cells).
e. Resistance still maintained but on a lower level.

A

Explain why resistant bacteria are disadvantaged when antibiotic use is discontinued.

Microbio (14 decks)

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