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Exam 2 Flashcards

1
Q

Heterotroph

A

Use organic molecules as carbon sources

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2
Q

Autotrophs

A

Use carbon dioxide as their sole or principal carbon source

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3
Q

Phototrophs

A

Use light (energy source)

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4
Q

Chemotrophs

A

Energy from oxidation of chemical compounds (energy source)

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5
Q

Lithotrophs

A

reduced inorganic substances (electron source)

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6
Q

Organotrophs

A

extracts electrons from reduced organic compounds
(electron source)

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7
Q

What would it mean for an organism
to be a photolithoautotroph?

A
  • Gets energy from light
  • Gets electrons from inorganic minerals
  • Gets carbon from CO2
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8
Q

Photoorganoheterotroph

A
  • Gets energy from light
  • Gets electrons from organic minerals
  • Gets carbon from Organic carbon
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9
Q

Chemolithoautotroph

A
  • Gets energy from inorganic chemicals
  • Gets electrons from inorganic minerals
  • Gets carbon from CO2
  • Certain bacteria & Archaea
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10
Q

Chemoorganoheterotroph

A
  • Gets energy from organic chemicals
  • Gets electrons from organic minerals
  • Gets carbon from organic carbon
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11
Q

Respiration

A
  • Chemoorgantrophic pathway
  • Uses electron transport chain
  • Aerobic respiration
  • Anaerobic respiration
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12
Q

Aerobic respiration

A

Final electron acceptor is oxygen

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13
Q

Anaerobic respiration

A

Final electron acceptor is different oxidized molecule such as NO-3 , SO2- , or Fe3+

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14
Q

Fermentation

A
  • Chemoorganotrophic pathway
  • No Electron Transport Chain, substrate-level phosphorylation only
  • Electron acceptor is an intermediate of the pathway used to oxidize the organic energy source
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15
Q

Amphibolic pathway

A

Embden Meyerhof pathway can “run in reverse” to convert 2 pyruvate molecules back into a glucose molecule

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16
Q

Embden-Meyerhof Pathway

A
  • Starts with glucose
  • Net yield: 2 ATP, 2 NADH, 2 pyruvate
  • Amphibolic pathway
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17
Q

Entner-Doudoroff Pathway

A
  • Used by Gram negative bacteria
  • Replaces the 6-carbon phase of the Embden-Meyerhof pathway
  • Net yield per glucose molecule: 1 ATP, 1 NADPH, 1NADH
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18
Q

Pentose-Phosphate Pathway

A
  • Can operate at the same time as glycolytic pathway or Entner-Doudoroff pathway
  • Can be aerobic or anaerobic
  • Amphibolic pathway, but does not make ATP
  • More of an anabolic role (ribose 5-phosphate builds precursors for amino acids, nucleic acids)
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19
Q

Bacterial Electron Transport Chain: Flexible

A
  • Electron carriers can be replaced or different terminal oxidases may be used
  • Located in plasma membrane
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20
Q

Bacterial Electron Transport Chain: Branched

A

Electrons may enter the chain at several points and leave through several terminal oxidases

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21
Q

Bacterial Electron Transport Chain: Shorter

A

Fewer protons transported across the membrane and therefore less energy

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22
Q

Dissimilatory nitrate reduction (card 1)

A

-Use of nitrate as terminal electron acceptor
- making it unavailable to cell for assimilation or uptake

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23
Q

Denitrification

A

Reduction of nitrate to nitrogen gas (N2)

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24
Q

Anaerobic Respiration (more details)

A
  • Same electron transport chain, but oxygen free
  • dissimilatory nitrate reduction
  • denitrification
  • yields less ATP bc molecules are less electronegative than O2
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25
Q

Fermentation (more details)

A
  • Simpler, produces less ATP than respiration
    1. does NOT involve electron transport chain
    2. Pyruvate or other derivatgive is final e- acceptor
    3. Oxygen not needed
    4. Substrate-level phosphorylation of ATP only
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26
Q

Lactic acid fermentation

A
  • Reduction of pyruvate to lactate (lactic acid)
  • Used by many species of Lactobacillus
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27
Q

Alcoholic fermentation

A
  • Reduction of pyruvate to acetaldehyde
  • then alcohol thru enzyme called alchol dehydrogenase
  • Used by yeasts
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28
Q

Mixed acid fermentation

A
  • Excretion of a mixture of acids (that is, acetic, lactic, succinic and formic acids)
  • Ex. E.Coli
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29
Q

Butanediol fermentation

A
  • Butanediol is the end product
  • Some ethanol, lactic acid and formate are also made
  • Ex. Klebsiella, Enterobacter sp.
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30
Q

What’s the difference between
photosynthesis and phototrophy?

A

Photosynthetic organisms use light energy to ultimately make sugar, while phototrophic organisms may only convert light energy to chemical energy (ATP)

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31
Q

Chlorophyll

A

Used by cyanobacteria to do oxygenic phososynthesis

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32
Q

Bacteriochlorophyll a,b

A

Found in purple&green bacteria, anoxygenic photosynthesis

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33
Q

Bacteriorhodopsin

A

Used by halophilic archaea to capture light energy and use it to fuel proton pump (chemical energy)

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34
Q

Anabolic reactions in microbes

A
  1. Cell wall (peptidoglycan)
  2. Amino acids (enzymes, ribosomes)
  3. Nucleic acids (reproduction/repair)
  4. Lipids (membranes, LPS)
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35
Q

Bactoprenol

A

transports NAG-NAM-pentapeptide units across the cell membrane

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36
Q

Carbohydrate Synthesis

A
  • Complex process
  • Bactoprenol; key target for antibiotics
  • cross links are formed by transpeptidation
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37
Q

Synthesis of Amino acids

A
  • many precursor metabolites are used as starting substrates for synthesis of amino acids
  • carbon skeleton is remodeled
  • amino group and sometimes sulfur are added
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38
Q

Steps of synthesis of amino acids

A
  1. Inorganic nitrogen assimilation
  2. sulfur assimilation
  3. Amino acid biosynthetic pathways
  4. Anaplerotic reactions
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39
Q

Transaminases

A

Nitrogen can be transferred to other carbon skeletons by this

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40
Q

Assimilatory Nitrate Reduction

A
  • Used by bacteria to reduce nitrate to ammonia
  • then incorporate it into an organic form
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41
Q

Nitrogen Fixation

A
  • Reduction of nitrogen (N2) to ammonia (NH3)
  • catalyzed by nitrogenase
  • found only in a few bacteria and archaea
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42
Q

Sulfur assimilation

A
  • Sulfur needed for: synthesis of amino acids and synthesis of several coenzymes
  • Sulfur obtained from: either external sources or intracellular amino acid reserves and inorganic sulfate
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43
Q

Amino acid biosynthetic pathways

A
  • used in the synthesis of multiple amino acids
  • A single precursor metabolite can give rise to several amino acids
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44
Q

Anaplerotic reactions

A
  • regeneration of intermediate molecules
  • carbon skeletons used for: biomass & extract energy from carbon-carbon bonds
  • citric acid cycle intermediates are used
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45
Q

Lipid Synthesis

A
  • Necessary for all membranes
  • most bacterial and eukaryal lipids contain fatty acids
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46
Q

Lipopolysaccharide synthesis

A
  • important component of gram negative bacterial outer membrane structure
  • combines lipid and carbohydrate anabolic pathways: Lipid A (core branch) & O-antigen (branch)
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47
Q

What cellular structures are unique to bacteria?

A

Peptidoglycan cell walls, 70s ribosomes

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48
Q

Which type of bacterial fermentation is used in the dairy industry?

A

Lactic acid fermentation

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49
Q

Which phototrophic pigment molecule is found in archaea?

A

Bacteriorhodopsin

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50
Q

Name some terminal electron acceptors in anaerobic respiration

A

Nitrate, sulfate, iron

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51
Q

Biocide

A

Antimicrobial agents that control microorganisms

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52
Q

Sterilization

A

Process in which all living entites are destroyed or removed from an object
- sterilant is the chemical agent

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53
Q

Disinfection

A

Killing, inhibition, or removal of disease causing microorganisms

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54
Q

Sanitization

A

reduction of microbial population to levels deemed safe by public health standards

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55
Q

Antisepsis

A

destruction of microbes on living tissue

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56
Q

Antiseptics

A

Chemical agents applied to tissue to kill or inhibit growth

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57
Q

Depth filter

A

fibrous materials that have been bonded into a think layer filled with narrow channels

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58
Q

Membrane filter

A

Porous membranes with defined pore sizes that remove microorganisms

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59
Q

High-efficiency particulate air (HEPA) filters

A
  • used in laminar flow safety cabinets
  • exclude 99.97% of particles
  • Covid-19 showed this filter to be effective
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60
Q

Moist heat

A
  • destroys viruses, fungi, and bacteria by degrading nucleic acids, denaturing proteins and disrupting cell membranes
  • boiling will not destroy endospores and does not sterilize
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61
Q

autoclave

A
  • device used to steam sterilization
  • above 100C (15 psi)
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62
Q

pasteurization

A
  • controlled heating at temperatures below boiling
  • process does not sterilize, but does kill pathogens and slows spoilage
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63
Q

Ultraviolet radiation

A
  • 260nm wavelength most lethal
  • causes thymine dimers preventing replication and transcription
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64
Q

chemotherapy

A

application of chemicals to kill microorganisms

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65
Q

Cidal agents

A
  • agent that kills
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66
Q

Static agents

A
  • agents that inhibit growth
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67
Q

Phenolics

A
  • denature proteins, disrupt cell membranes
  • used in hospital settings
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68
Q

Halogens

A
  • Iodine, oxidizes cell components and proteins
  • Used as a skin antiseptic
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69
Q

Chlorine

A
  • Oxidizes cellular components, destroys vegetative bacteria and fungi
  • bleach
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70
Q

Metals

A
  • inactive proteins, only copper and silver used
  • copper sulfate treats algal blooms in lakes
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71
Q

Quaternary ammonium compounds

A
  • Detergents that have broad spectrum antimicrobial activity
  • effective disinfectants, but cannot kill endospores
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72
Q

Broad-spectrum antibiotics

A

kills a wide variety of bacteria

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73
Q

Narrow-spectrum antibiotics

A

specifically kill one or a few kinds of bacteria

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74
Q

Penicillins

A
  • inhibit peptidoglycan synthesis
  • Ex. penicillin, amoxicllin
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75
Q

Cephalosporins

A
  • inhibit peptidoglycan synthesis but broader spectrum than pencillins and cephalosporins
  • used to treat severe infections
  • Ex. imipenem, meropenem
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76
Q

Glycopeptides

A
  • inhibit the synthesis of peptidoglycan by binding to amino acids in the cell wall
  • Ex. Vancomycin (“drug of last resort)
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77
Q

Aminoglycosides

A
  • Block the A site of the ribosomes so no new amino acids can be added
  • Ex. Streptomycin, neomycin kanamycin
  • inhibit the small (30s) subunit
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78
Q

Tetracyclines

A
  • prevent tRNAs from binding to ribosomes
  • Ex. minocycline, doxycycline
  • inhibit small (30s) subunit
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79
Q

Macrolides

A
  • bind to 50s subunit, preventing ribosomes assembly
  • Ex. Z-pak, erythomycin
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80
Q

Lincosamides

A
  • Bind 50s subunit
  • Ex. Clindamycin, lincomycin
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81
Q

Fluoroquinolones

A
  • target protein of the bacterial replication machinery (gyrase and topoisomerase) blocking DNA pol III
  • Ex. Ciprofloxacin, levofloxacin
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82
Q

Folate synthesis inhibition

A
  • requires folate (Vitamin B9) to complete DNA replication
  • sulfonamides compete w other intermediates in pathways that produce folate, inhibiting synthesis
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83
Q

Kirby-bauer method

A
  • disks with antibiotic at known concentration placed onto inoculated plate
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84
Q

Zone of inhibition

A

Clearance area in a kirby-bauer method

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85
Q

E-test

A
  • strip with a gradient of antibiotics is placed on inoculated plate
  • where ellipse intersects the scale shows the dosage at which bacteria is susceptible
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86
Q

Methicillin-resistant staphylococcus aureus (MRSA)

A

responsible for many cases of post surgical sepsis and death

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87
Q

Clostridium difficile (C-diff)

A
  • causes extreme diarrhea which can be fatal
  • difficult to treat because spores remain resistant and can germinate, causing relapse
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88
Q

reverse transcriptase inhibitors

A
  • used to treat HIV and AIDS
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89
Q

Amphotericin B

A
  • binds to ergosterol (similar to cholesterol), dissolves cell membrane
  • anti-fungal drug
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90
Q

Azoles

A
  • block synthesis of ergosterol
  • anti-fungal drug
  • Ex. ketaconazole
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91
Q

Anti-malarial drugs

A
  • chloroquine, lariam, artimisin used in combination to destroy malaria infected red blood cells
  • resistance growing across the world
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92
Q

Anti-giardia drugs

A
  • Metronidazole
  • effective against Trichomonas vaginalis
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93
Q

Overcoming drug resistance

A
  1. Tighter controls over use of antibiotics in animal feed
  2. Limiting over-prescription of antibiotics to patients
  3. Combination therapies (multiple drugs)
  4. targeted biological therapy
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94
Q

Phages

A

viruses that prey on bacteria

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95
Q

Reproductive strategies

A
  • reproduce by binary fission
  • reproduce by forming a bud or multiple fission
  • must replicate and segregate the genome prior to division
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96
Q

Bacterial cell cycle

A
  1. period of growth after the cell is born
  2. chromosome replication and partitioning
  3. Cytokinesis, during which a septum and daughter cells are formed
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97
Q

FtsZ

A

Protein that establishes divison site at mid-cell, defines plane of division

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98
Q

Peptidoglycan synthesis

A
  • plays a role in determine cell shape
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99
Q

Coccus (shape)

A
  • peptidoglycan forms at central septum
  • FtsZ localization placement involved
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100
Q

Elongasome

A

rod complex

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101
Q

MreB

A

protein scaffold on cytoplasmic face of cell membrane

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102
Q

Crescentin

A

protein that localizes asymmetrically, giving rise to vibrio shape

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103
Q

Bacterial growth

A
  • referred to as population growth rather than growth of individual cells
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104
Q

Batch culture

A

incubated in a closed vessel with a single batch of medium

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105
Q

Lag Phase

A
  • bacterial growth curve
  • cell synthesizing new components
  • replenish spent materials
  • Adapt to new medium or conditions
  • eventually, cells replicate DNA, increase in mass, divide
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106
Q

Exponential phase

A
  • bacterial growth curve
  • rate of growth and division is constant and maximal
  • population is uniform
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107
Q

Stationary Phase

A
  • bacterial growth curve
  • closed system, growth ceases
  • viable cells remains constant
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108
Q

reasoning for stationary phase

A
  1. Nutrient limitation
  2. limited oxygen availability
  3. toxic waste accumulation
  4. carrying capacity reached
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109
Q

Death phase

A
  • bacterial growth curve
  • number of viable cells declines exponentially
  • nutrient deprivation and build up of waste causes harm
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110
Q

Long-term stationary phase

A
  • bacterial growth curve
  • bacterial population continually evolves
  • process marked by successive waves of genetically distinct variants
  • natural selection occurs within a single culture
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111
Q

extremophiles

A

Grow under harsh conditions that would kill most other organisms

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112
Q

Halophiles

A
  • require NaCl at a concentration > 0.2 M
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113
Q

Extreme halphiles

A
  • require salt concentrations 3M-6.2 M
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114
Q

Salt in halophiles

A
  • accumulate K and Cl in cytoplasm
  • proteins need high salt levels
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115
Q

Salt out halophiles

A
  • keep salt ions outside of cell
  • synthesizes compatible solutes that do not interfere with growth
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116
Q

Acidophiles

A
  • growth best between pH 0-5.5
  • pump protons (H+0
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117
Q

Alkaliphiles

A
  • growth best between pH 8-11.5
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118
Q

Psychrohiles

A

0 to 20C

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119
Q

Psychrotrophs

A

0 to 35C

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120
Q

Mesophiles

A

20 to 45C

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121
Q

Thermophiles

A

45 to 85C

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122
Q

Hyperthermophiles

A

85 to 100C

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123
Q

Adapting to temperature

A
  • protein structure stabilized by a variety of means
    1. more H bonds
    2. more proline, less flexible peptides
    3. Chaperones aid in folding
  • membranes stabilized by variety of means
    1. more saturated, more branched, higher molecule weight
    2. ether linkages, resistant to hydrolysis
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124
Q

obligate aerobe

A

requires O2

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125
Q

Obligate anaerobe

A

usually killed in presence of O2

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126
Q

Microaerophile

A

requires 2-10% O2

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127
Q

Facultative anaerobes

A

doesn’t require O2 but grow better in its presence

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128
Q

Aerotolerant anaerobes

A

grow with or without O2

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129
Q

Reactive oxygen species (ROS)

A
  • oxygen reduced
  • superoxide radical
  • hydrogen peroxide (H2O20
  • hydroxyl radical
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130
Q

Aerobes produce protective enzymes

A
  • Superoxide dismutase (SOD)
  • Catalase
  • Peroxidase
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131
Q

Biofilms

A
  • Slime enclosed communities of microbes
  • ubiquitous in nature in water
  • can be formed on any conditioned surface
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132
Q

Extracellular polymeric substance (EPS)

A
  • microbes reversibly attach to conditioned surface and release polysaccharides, proteins and DNA
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133
Q

Emergent properties

A

the whole system is greater than the sum of its individual parts

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134
Q

Quorum sensing

A
  • bacterial cells communicate via small molecules that diffuse the environment
  • number of microbes must be present and participating
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135
Q

Culture medium

A

Solid or liquid mixture of nutrients and other compounds

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136
Q

defined/synthetic medium

A

each ingredient can be defined with a chemical formula

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137
Q

Complex media

A

Contain some ingredients of nonspecific chemical composition

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138
Q

Supportive media

A
  • sustain growth of many microorganisms
  • trypic soy brother and agar
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139
Q

Enriched media

A
  • supportive media supplemented with special nutrients
  • blood agar
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140
Q

selective media

A
  • allow the growth of particular microorganisms, while inhibiting the growth of others
  • gram negative bacteria grows on bile salts, gram positive bacteria cannot
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141
Q

Differential media

A
  • distinguish among different groups of microbes and permit identification of microbes
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142
Q

replication fork

A

where DNA is unwound

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143
Q

Replicon

A

portion of the genome that contains an origin and is replicated as a unit

144
Q

Bidirectional replication

A

comes from a single origin

145
Q

Replisome

A
  • 12 proteins involved in replication
  • two replisomes move in either direction away from the origin
146
Q

Helicase

A

ring encircles DNA, disrupts H-bonds and provides force to move the replisome

147
Q

template

A

directs synthesis of complementary strand

148
Q

Primer

A

DNA or RNA strand

149
Q

dNTPS

A

deoxynucleotide triphospahtes

150
Q

Single-stranded DNA binding proteins

A

Coat single stranded DNA to protect it from damage

151
Q

Topoisomerases

A

Relieve twist generated by rapid unwinding of double helix, prevents supercoiling

152
Q

Primase

A

synthesizes short complementary strands of RNA primers

153
Q

Okazaki fragements

A
  • Lagging strand is synthesized in short fragments
  • joined by DNA ligase
154
Q

Catenanes

A

form when topoisomerase break and rejoin DNA strands to ease supercoiling

155
Q

recombinase

A

catalyze an intramolecular crossover that separates 2 chromosomes

156
Q

Promoter

A

located at the start of the gene

157
Q

Leader

A

transcribed into mRNA but is not translated into amino acids

158
Q

Shine-Dalgarno sequence

A

important for translation initiation

159
Q

Coding region

A
  • begins with DNA sequence 3’ - TAC - 5’
  • produced codon AUG
  • ends w stop codon, followed by trailer sequence
160
Q

Trailer sequence

A

prepares RNA polymerase for terminator sequence

161
Q

Point mutation

A

protein-coding genes can affect protein structure
types:
1. silent (codes for same amino acid)
2. Missense (codes for different amino acid)
3. Nonsense (insert STOP codon)
4. Frameshift 9changes reading framed)

162
Q

Tautomerization mutation

A
  • nitrogenous base of nucleotide shifts to tautomeric form allowing for unique base pairing
  • “C” - A
  • “T” - G
163
Q

Transition mutations

A

lead to stable alteration of nucleotide sequence

164
Q

Transversion mutations

A

when a purine is substituted for a pyrimidine, causing steric problems

165
Q

Proofreading

A
  • correction of errors in base pairing made during DNA replication
  • errors corrected by DNA polymerase
166
Q

Mismatch repair

A
  • mismatch correction enzyme scans newly synthesized DNA for mismatched pairs
  • mismatched pairs removed and replaced by DNA polymerase
167
Q

Excision repair

A
  • corrects damage that distorts the DNA double helix
  • Nucleotide excision pair
  • base excision repair
168
Q

recombinational repair

A
  • corrects DNA that has both bases of a pair missing or damaged
169
Q

RecA

A
  • aligns damaged DNA to the second copy of the genome
  • acts a protease, destroying LexA, to increase production of excision repair enzymes
170
Q

Vertical Gene transfer

A
  • in eukaryotes, sexual reproduction is accompanied by genetic recombination
  • by binary fission
171
Q

Horizontal gene transfer (HGT)

A
  • bacteria and archaea doesn’t reproduce sexually
  • gene from one independent, mature organism to another
  • antibiotic resistance gene
172
Q

Conjuagtion

A
  • DNA transferred from a donor cell
  • similar to sexual reproduction, but lacks crossing over and fertilization
173
Q

Transformation

A
  • DNA acquired directly from environment
  • “naked” plasmids
174
Q

Transduction

A

DNA transported in a bacteriophage

175
Q

Fate of DNA in recipient cell

A
  1. integration
  2. separate existence of DNA
  3. Remain in cytoplasm
  4. degradation
176
Q

integration

A

donor DNA pairs with recipient DNA and recombine

177
Q

Separate existence of DNA

A

DNA persists separate from recipient chromosome if donor DNA is able to replicate

178
Q

Degradation

A

Led by CRISPR/Cas, preventing the formation of a recombinant cell

179
Q

transposition

A

genetic elements move within and between genomes via this

180
Q

transposable elements

A

jumping genes

181
Q

Insertion sequences

A
  • simplest transposable elements
  • short sequence of DNA
182
Q

Conjugation Plasmids

A
  • Small, double stranded DNA molecules
  • can exist independently from host chromosome
  • have own replication origins, replicate autonomously, and are stably inherited
  • direct formation of sex pilus
183
Q

transduction

A
  • occurs during lytic cycle
  • during virion assembly, genomes mix
  • once DNA is in recipient cell, it’s incorporated into chromosome
184
Q

Immunity genes

A

Resistance genes that exist in nature to protect antibiotic producing microbes from their own antibiotics

185
Q

resistance genes can be found on…

A
  1. Bacterial chromosomes
  2. Plasmids
  3. Transposons
  4. other mobile genetic elements
186
Q

R (resistance) plasmid

A
  • can be transferred to other cells by horizontal gene transfer
  • genes code for enzymes that destroy or modify drugs
187
Q

Transcription

A

-DNA-> mRNA
-3 types of RNA are produced: tRNA, rRNA and mRNA

188
Q

Operons

A
  • cluster of genes that are transcribed together to give a single messenger RNA (mRNA) molecule, which encodes multiple proteins
  • not common in eukaryotes (monocistronic)
189
Q

polycistronic mRNAs

A

transcription yields mRNA consisting of a leader, one coding region, a spacer and a second coding region

190
Q

sigma factor

A

Has no catalytic activity but helps the core enzyme recognize the start of genes

191
Q

RNA polymerase holoenzyme

A

core enzyme + sigma factor
- only the holoenzyme can begin transcription

192
Q

Transcription cycle in bacteria

A
  1. Sigma factor directs the RNA polymerase core enzyme to the -35 sequence
  2. RNA polymerase denatures a short stretch of DNA at the -10 region, forming an open complex that is stabilized by sigma
  3. RNA polymerase core synthesis RNA, and sigma dissociates from the core after about 12 ribonucleotides have been linked. Trancription enters the elongation phase
  4. Elongation continues until a terminator is encountered. RNA polymerase ceases trancription and the RNA is released
193
Q

Transcription Elongation

A
  • creating the mRNA
  • after binding, RNA polymerase unwinds DNA
  • ATP, GTP, CTP and UTP incorporated into RNA complementary to DNA template
  • RNA synthesis proceeds in a 5’ - 3’ direction
194
Q

Transcription bubble

A
  • Moves with the polymerase as it synthesizes mRNA
  • within the bubble a temporary RNA:DNA. A hybrid is formed
195
Q

Transcription termination mechanisms

A
  1. Intrinsic termination
  2. Rho factor-dependent
196
Q

Translation in bacteria

A
  • RNA–> Protein
  • decoding mRNA and covalently linking amino acids together to form a polypeptide
  • direction of synthesis N terminal –> C terminal
  • ribosome = site of translation
197
Q

A (acceptor) site

A

receives tRNA carrying amino acid

198
Q

P (peptidyl) site

A

holds tRNA attached to growing polypeptide

199
Q

E (exit) site

A

empty tRNA leaves ribosome

200
Q

16s rRNA

A
  • needed for initiation of translation
  • binds to shine-dalgarno sequence (ribosome binding site)
  • binds to 3’ CCA end of aminoacyl-tRNA
201
Q

23s rRNA

A

ribozyme that catalyzes peptide bond formation

202
Q

Initiation of protein synthesis

A
  1. N-formylmethionine tRNA bacterial initiator tRNA … archaea and eukaryotes use methionine- tRNA
  2. 30s initiation complex… initiator tRNA, mRNA and the 30s ribosomal subunit
  3. Two initiation factors are involved.. require for formation of the initiation complex, GTP catalyzes energy use for these
203
Q

Elongation of polypeptide

A
  1. Aminoacyl-tRNA binding
  2. Transpeptidation reaction
  3. Translocation
204
Q

Nonsense (stop) codons

A
  • aid in recognition of stop codons
  • No tRNA for a stop codon, so the ribosome halts
205
Q

Polyribosome

A

complex of mRNA with several ribosomes

206
Q

Chaperones

A
  • proteins that help other proteins fold
  • present in all domains of life
207
Q

Trigger factor

A
  • helps fold many cytoplasmic proteins
  • masks hydrophobic regions so they don’t interact with each other prematurely, or with other proteins
  • Also helps proline cis/trans isomerization
208
Q

Sec system

A

general secretion pathway

209
Q

Tat system

A

-secretes only folded proteins
- moves across plasma membrane
- proteins must completely fold in the cytoplasm

210
Q

YidC

A

folding and translocation plasma membrane proteins

211
Q

Translocation

A

Movement of proteins from cytoplasm to or across the plasma membrane

212
Q

Secretion

A

movement of proteins from the cytoplasm to external environment

213
Q

Sec Dependent pathway

A

translocates unfolded proteins across plasma membrane

214
Q

Signal peptide

A

N-terminal sequence that directs peptide to specific route

215
Q

Signal recognition particle

A

Protein RNA complex translating ribosomes to identify hydrophobic peptides

216
Q

Inducer

A

small effector molecule that stimulates gene expression

217
Q

Inducible genes

A
  • genes that encode inducible enzymes
  • required only when their substrate is available
218
Q

Corepressor

A

small effector molecule

219
Q

Repressible genes

A

Genes for enzymes involved in biosynthetic pathways

220
Q

Regulation of transcription (negative control)

A
  • repressor protein
  • binding operator inhibts transcription initiation by blocking RNA polymerase from binding
221
Q

Regulation of transcription (positive control)

A
  • activator protein
  • binding to activator binding sites upstream of promoter encourages RNA polymerase to bind
222
Q

Inducible Operon

A
  • normally off
  • when lactose is present, repressor is removed
223
Q

tryp operon

A
  • functions in the absence of tryptophan
  • when trp present, it acts as corepressor
224
Q

Riboswitches

A

contain effector binding element in the long reader RNA

225
Q

Small (sRNAs)

A
  • noncoding (ncRNAs)
  • doesn’t function as mRNA, TRNA or rRNA
226
Q

Antisense RNAs

A
  • complementary to mRNA and function by base pairing
  • may inhibit or enhance translation
  • some require a chaperone to promote interaction with complementary sequences
227
Q

Global regulatory systems

A
  • affect many genes, operons, and pathways simultaneously
  • important for bacteria… responds rapid to wide variety of changing conditions
228
Q

sensor kinase

A

spans the plasma membrane so a part is exposed to extracellular environment, while other part is in cytoplasm

229
Q

Two component signal transduction

A
  • sensor kinase
  • phosphorylates itself, then transfer phosphate to response regulator
230
Q

Phosphorelay systems

A
  • when phosphoryl groups are transferred to many proteins through a complex system
231
Q

Alternate sigma factors

A

immediately change expression of many genes as they direct RNA polymerase to specific subsets of bacterial promoters

232
Q

Sanger sequencing

A
  • DNA synthesis continues until a ddNTP, rather than a dNTP, is added to the growing chain
  • without a 3’ - OH group, synthesis stops
  • results in a collection of DNA fragments of varying lengths, each ending in the same ddNTP
233
Q

Massively parallel sequencing techniques

A

thousands of identical DNA fragments are sequenced simultaneously

234
Q

Whole genome sequencing

A
  1. library construction - generates clones of portions of genome
  2. random sequencing - determines sequences of genome fragments in vector
  3. Fragment alignment and gap closure: computer analysis joins to form contig
  4. editing: proofreading ensures all reads of the same sequence are identical
235
Q

Metagenomics

A
  • study of microbial genomes based on DNA extracted directly from the environment
  • used to learn more about diversity and metabolic potential of microbial communities
236
Q

Genome annotation

A

bioinformatics combines biology, mathematics, computer science and statistics to convert raw nucleotide data into the location and potential functions of genes

237
Q

-Omics

238
Q

Metatranscriptomics

A
  • extraction of RNA directly from the environment, followed by sequencing and comparison to known sequences
  • can identify active microbes
239
Q

Proteomics

A
  • collection of proteins that an organism produces
  • provides information about genome function not available from genomics or mRNA studies
240
Q

Core genome

A

set of genes found in all membranes of a species

241
Q

Pan-genome

A

every gene in a strain of a species

242
Q

Genetic engineering

A

modification of the genetic code of a living organism

243
Q

Recombinant DNA

A

DNA molecules with segments origination from different organisms

244
Q

DNA cloning

A

Use of enzymes and bacterial cells to modify and amplify DNA

245
Q

Biotechnology

A

Use of organisms to produce useful products

246
Q

Restriction endonucleases

A

recognize and cleave specific DNA sequences

247
Q

Restriction enzymes

A
  • cuts both strands at complementary sequence
  • produce sticky ends (overhangs) or blunt ends in DNA target
248
Q

Origin of replication

A

allows independent replication

249
Q

Selectable marker

A

gene on the plasmid helps survive under certain conditions

250
Q

Multicloning site

A

cluster of restriction sites

251
Q

PCR

A
  • enables gene amplification
  • rapid synthesis of billions of copies of a specific DNA fragment
  • oligonucleotide primers
252
Q

oligonucleotides primers

A

single-stranded DNA molecules, between 15 and 30 nucleotides long

253
Q

Reverse transcriptase PCR

A
  • synthesizes double-stranded DNA from RNA template
  • constructs complementary DNA (cDNA)
254
Q

CRISPR-Cas 9

A
  • used for altering genomes in living organisms
  • direct modification of genomic DNA in any crll into which DNA can be introduced and expressed
  • Cas 9 is endonuclease that cuts both strands of target DNA
255
Q

Pathogens

A
  • disease causing microbes
  • must overcome surface barriers and antimicrobial activity
256
Q

Immune system

A
  • composed of widely distributed proteins, cells, tissues, and organs
  • neutralize or destroy foreign substances
257
Q

Immunity

A
  • ability of host to resist infection or disease
258
Q

Immunology

A

study of immune responses and how they protect the host

259
Q

Innate immunity

A
  • first line of defense
  • offers resistance to any microbe or foreign material
  • includes general mechanisms such as skin, mucus, and antimicrobial chemicals
260
Q

Adaptive immune response

A
  • activated by cells and chemicals of innate immunity
  • tailored to a particular foreign agent
  • has “memory” - effectiveness increases on repeated exposure to foreign agent
261
Q

Skin (mechanical defense)

A
  • mechanical barrier to microbial invasion
  • skin microbiota prevent colonization of pathogens
262
Q

Keratinocytes

A

cells in outer layer

263
Q

Mucous membranes

A
  • form a protective covering that resists penetration and traps microbial invaders
264
Q

Cell types

A
  1. Epithelial cells
  2. Goblet cells- produce mucus
  3. paneth cells- secrete antimicrobial peptides
265
Q

Respiratory system

A
  • microbes >10 um usually are trapped by hairs and cilia lining the nasal cavity
  • Microbes <10 um pass through the nasal cavity and are trapped in mucociliary escalator
266
Q

lysozyme

A

Hydrolyzes bond of bacterial cell wall (tears)

267
Q

Lactoferrin

A

Sequesters iron, reducing its availability for microbes, limiting their ability to multiply (breastmilk)

268
Q

Bacteriocins

A

Toxic peptides produced by normal microbiota, kill closely related species

269
Q

Chemical defense: major activities

A
  1. stimulate an inflammatory response by helping to recruit white blood cells
  2. lysing microbial cell membranes
  3. Promoting phagocytosis of microbial invaders
270
Q

Cytokines

A
  1. regulators of innate immunity
  2. regulators of adaptive immunity
  3. Stimulators of hematopoiesis
271
Q

Chemokines

A

stimulate cell migration

272
Q

Interleukins

A

Produced by one white blood cell, act on another

273
Q

Interferons

A

regulatory cytokines produced in response to infection

274
Q

Colony stimulating factors

A

Stimulate growth and differentiation of immature white blood cells in bone marrow

275
Q

Tumor necrosis factor

A

stimulate an inflammatory response

276
Q

leukocytes

A
  • White blood cells in the immune system
  • originate from hematopoietic precursor stem cells
277
Q

Cells on the immune system

A
  1. Mast cells
  2. granulocytes
  3. monocytes, macrophages, and dendritic cells
  4. innate lymphoid cells
278
Q

Mast cells

A
  • inflammatory
  • not phagocytic
  • role in allergic responses
  • similar to basophils
279
Q

Granulocytes

A
  • irregularly shaped nuclei with 2 to 5 lobes
  • cytoplasm has granules with reactive substances that kill microbes
  • 3 types: basophils, eosinophils, neutrophils
280
Q

Eosinophils (granulocyte)

A
  • worm and fungal infections
  • allergy
  • inflammatory reactions
281
Q

Basophils (granulocytes)

A
  • inflammatory events
  • allergies
282
Q

neutrophils (granulocytes)

A
  • blood phagocytes
  • active engulfers and killers of bacteria
283
Q

Monocytes

A
  • produced in bone marrow and enter the blood
  • after 8 hrs, they migrate into tissues and mature into macrophages
  • elevated in acute illness stage
284
Q

Macrophages

A
  • larger than monocytes
  • highly phagocytic
  • serve as sentinel cells
285
Q

Dendritic cells

A
  • antigen presenting
  • long cellular projections
  • present in skin and mucous membranes
  • programmed to detect and phagocytose pathogens
286
Q

Antigen presenting

A

display foreign antigens on their surfaces to share vital information with lymphocytes to stimulate an adaptive immune response

287
Q

Antibody dependent cell mediated cytotoxicity

A

when non-self proteins are generated and detected

288
Q

B cells

A

Bone Marrow

289
Q

T cells

290
Q

Primary organs and tissues

A

hematopoietic stem cells differentiate into immune cells

291
Q

Secondary organ and tissues

A

where lymphocytes are activated by antigen interaction

292
Q

thymus

A
  • primary lymphoid organ
  • precursor cells move, enter from bone marrow
  • negative selection
  • remaining cells become mature T cells and enter the bloodstream where they await activation by innate immune cells
293
Q

negative selection

A

removal of T cells not able to distinguish between self and non self antigens

294
Q

Bone Marrow

A
  • primary lymphoid organ
  • site of B cell maturation
  • maturation involves removal of self-reactive cells
  • enter bloodstream and migrate to lymph nodes and spleen to await introduction to the antigen
295
Q

Spleen

A
  • secondary lymphoid organ
  • filters blood and traps blood borne particles by phagocytes and B cells
  • present antigens to T cells, activating specifc immune response
296
Q

Lymph Nodes

A
  • secondary lymphoid organ
  • capture pahgocytosed antigens and present them to T cells
  • outer region is rich in B cells that can bind antigen directly from blood
297
Q

Follicles

A

inner region where T cells await interaction B cells

298
Q

Microbe-associated molecular patterns

A
  • alert host about the presence of microbe
299
Q

Toll-like receptors

A
  • pattern recognition receptor
  • transmembrane proteins that detect microbe associated molecular patterns
  • stimulate immune response
300
Q

Antigen presenting cells

A

macrophages and dendritic cells

301
Q

Exocytosis

A
  • process used by neutrophils to expel microbial fragments after they have been digested
  • leads directly to antigen presentation
302
Q

Inflammation

A
  • innate response
  • release of chemical signals that trigger vasodilation
  • defense reaction to issue injury
303
Q

Selectins

A
  • cell adhesion molecules on activated endothelial cells that line blood vessels nearby
  • cause neutrophils to roll along endothelium where they encounter pro-inflammatory signals
304
Q

integrins

A

adhesion receptors on neytophils activated by selectins

305
Q

Chemotaxis

A

chemotactic factors at infection site

306
Q

Cardinal signs

A
  1. redness
  2. warmth
  3. pain
  4. swelling
  5. altered function
307
Q

kallikrein

A

tissue injury leads to activation of this

308
Q

bradykinin

A

cleavage of kallikrein releases this
- swelling

309
Q

fibrin clot

A

restrict infectious agents to bloodstream

310
Q

Chronic inflammation

A
  • causes permanent tissue damage
  • granuloma
311
Q

granuloma

A

mass of cells that form when phagocytic cells can’t destroy pathogen and instead attempt to wall off the site

312
Q

name two physical barriers to infections. How are they different?

A
  • skin: dead cells packed together
  • Mucosal membranes: live cells that produce mucous moved by cilia
313
Q

Name one antimicrobial product produced by these cells

A
  • lysozyme, lactoferrin
314
Q

what are the 5 types of leukpcytes

A
  • neutrophils
  • macrophages
  • basophils
  • lymphocytes
  • eosinophils
315
Q

Name 3 types of phagocytic cells, which are APCs

A
  • neutrophils
  • macrophages (APC)
  • dendritic cells (APC)
316
Q

what is the importance of antigen presentation

A

link to the adaptive immune response while killing pathogens

317
Q

Name one mechanism that “amps-up” the immune repsonse

A
  • pro-inflammatory cytokines, interferons, pattern recognition receptors, antigen presentation, fever
318
Q

innate activation can lead to:

A
  • inflammation
  • survival
  • apoptosis
  • immune regulation
  • proliferation of immune cells
319
Q

Cytokines comes in multiple forms:

A
  • pro-inflammatory drive cell mediated immunity
  • anti-inflammatory drives humoral immunity
320
Q

Specificity

A
  • any particular response acts against one specific target
321
Q

inducibility

A

cells activate only in response to their specific pathogen

322
Q

clonality

A

One induced, they replicate exact clones of themselves

323
Q

Discrimination

A

as a rule, does not act against healthy host cells

324
Q

Memory

A

long living cells remain to respond more quickly when that pathogen is seen again

325
Q

Adaptive immune response rely on

A

lymphocytes

326
Q

Humoral response

327
Q

Cell-mediated response

328
Q

Adaptive immunity anatomy

A
  • lymphocytes grow in bone marrow
  • lymph is intracellular fluid and waste along with APCs
  • drains to lymph nodes where APCs and lymphocytes interact
329
Q

lymphocytes act via

A

receptors on their surfaces

330
Q

NK cells

A
  • innate immunity
  • non-specific receptors
  • all cells have Nk cell ligands
  • all cells have MHC class I
331
Q

Normal Nk cell

A

tells the NK cell “stop”

332
Q

Abnormal or missin NK cell

A

tells the cell “kill”

333
Q

Antigens founded

A

surface of extracellular pathogens, or expressed on the surface of infected cells for intracellular pathogens

334
Q

adaptive immune responses are against

A

antigens not the pathogen as a whole

335
Q

Adaptive immunity: antigens

A
  • “non-self” molecular shapes
  • immune cells can recognize and attack
336
Q

B cell receptor (BCR)

A
  • an immunoglobulin protein (IgD)
337
Q

B cells and antibodies

A
  • multiple of the same BCRs on the surface of each B cell
  • Different B cells have different variable regions, recognize different antigens
  • if bound to a B cell it is a BCR, if it is free floating it is an antibody
338
Q

B cell response

A
  1. BCR finds its match during an infection
  2. Activated by T cell help
  3. Clonally replicate
  4. some will live for 50+ years, able to produce B cells at the next sign of the SAME pathogen
339
Q

B cells and antibodies order

A
  1. binding to antigen
  2. chemical signal
  3. becomes plasma cell
  4. releases antibodies
340
Q

IgD

A
  • found in: B cells surface
  • role: B cell receptor
341
Q

IgM

A
  • found: blood
  • role: fixing complement, first antibody response
342
Q

IgG

A
  • found: blood
  • Role: fix complement, neutralization, opsonization
343
Q

IgA

A
  • found: mucous, tears, saliva, and breast milk
  • role: protect mucous membranes
344
Q

IgE

A
  • found: blood
  • role: allergies
345
Q

T cell receptor (TCR)

A
  • NOT an immunoglobulin
  • multiple copies of the same receptor per cell
  • one antigen is recognized by each cell using the variable region
346
Q

Major Histocompatibility complex (MHC)

A
  • TCR recognize antigens ONLY when presented by this
  • antibodies can float through the blood on their own
347
Q

MHC class I

A
  • expressed on all cell types
  • presenting antigens
  • viral proteins
  • mutated proteins
  • interacts with: CD8 + T cell (cytotoxic T cells)
348
Q

MHC class II

A
  • found ONLY on antigen presenting cells
  • presents antigens from phagocytosis
  • interacts with CD4 + T cell (Helper T cells)
349
Q

CD8+: Cytotoxic T cells

A
  • driver of the cell-mediated adaptive immune response
  • interacts w/ MHC class I to identify sick cells and kill them
  • inducing apoptosis (cell death) using perforin and granzyme
  • effective against cancer and viruses
350
Q

CD4+: T helper cells

A
  • drive towards a humoral approach or cellular response
  • activate B cells and T cells
  • cannot activate without T cell help
351
Q

Protection against re-exposure

A
  • long live plasma cells in bone marrow
  • effector T cells
352
Q

3 major lymphocytes

A

Innate: NK cells
Adaptive: T cells and b cells

353
Q

what receptors are on their surface

A
  • innate: inhibitory and stimulatory receptors
  • adaptive: T cells: CD4, CD8 and TCR. B cells: B cell recptor
354
Q

What do these receptors interact with? Cell type? Receptor Type?

A
  • Innate: NK - inhibitory and stimulatory receptors - MHC class I
  • Adaptive: T cells - CD4-TCR - MHC class II on APCs. CD8- TCR- MHC class I. B cells - B cell receptor - antigen/pathogen directly
355
Q

How does this kill pathogens

A
  • T cells: recognize abnormal autoantigens perforins/ granzymes trigger apoptosis
  • B cells: antibodies bind to promote phagocytosis and compliment, or neutralize directly
356
Q

How do we name the response/

A
  • T cells: cell mediated
  • B cells: Humoral
357
Q

The isotypes that naturally protect a breastfed baby in the first 6 months of life are

A

IgA and IgG

MicroBio (7 decks)

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