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MICB 3301 > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

Metabolism [Definition] (10.1)

A
  • All chemical reactions in a cell

- Requires the flow of energy (capacity to do work) and the participation of enzymes

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2
Q

Catabolism [Definition] (10.1)

A

Breakdown of complex molecules into smaller ones with release of energy for anabolism

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3
Q

Anabolism [Definition] (10.1)

A
  • Reactions that build cells

- Synthesis of complex molecules from simpler ones with the input of energy

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4
Q

What does ATP stand for? (10.2)

A

Adenosine Triphosphate

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5
Q

What does the amount of Gibbs Free Energy (delta G) determine in a reaction? (10.2)

A
  • It determines how much energy is available to do work such as:
    • Rotate a flagellum
    • Build a cell wall
    • Store information in DNA
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6
Q

What does Gibbs Free Energy measure? (10.2)

A

The change in free energy that can predict the direction of a reaction

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7
Q

What do solutes (such as sugar / salt) do to the availability of water? (7.1)

A
  • Solutes decrease the availability of water to microbes
  • Availability of water affects growth of all cells
  • Expressed as: a (sub w)
    • Higher solute = Lower a (sub w)
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8
Q

Hypotonic (7.3)

A
  • Low extracellular solute concentration
  • Water flowing into the cell
    • Ex: Freshwater lakes & streams
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9
Q

Isotonic (7.3)

A

-Same concentration of solute both in & out of the cell

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10
Q

Hypertonic (7.3)

A
  • High extracellular solute concentration
  • Water flowing out of the cell
  • Low a (sub w)
    • Ex: Dead Sea, Great Salt Lake, Peanut butter
  • Osmophiles live in these conditions
    • Microbes living in these conditions have compatible solutes in an effort to increase the materials inside the cell
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11
Q

Halobacterium [archaea] (7.3)

A
  • A halophile
  • Cause of pink coloration to Pink Lake in Australia
  • –Yes, this is an archaea even though it has ‘bacterium’ in its name
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12
Q

Staphylococcus [bacteria] (7.3)

A
  • A halophille
  • Found on human skin
  • Isolated using Mannitol Salt Agar
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13
Q

Compatible Solutes (7.3)

A

Help halophiles to survive under high salt concentrations

–Also help other osmophiles live in their highly concentrated environments

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14
Q

What are the two types of extremophiles that can withstand strong pHs? (7.3)

A
  • Alkaliphiles
  • –Withstand high pH (basic conditions)
  • Acidophiles
  • –Withstand low pH (acidic conditions)
  • –Ex: E. coli can withstand pH of 2 - 10 — very wide range, though not typically thought of as an extremophile
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15
Q

What is a Biofilm? [overview] (7.4)

A
  • Microbial community
  • Attached to a surface
  • Covered with a matrix of polysaccharide, DNA, & protein
  • –“Protective Matrix”
  • The cells + The Protective Matrix = Biofilm
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16
Q

Four Stages of Biofilm Formation (7.4)

A

1) Attachment
2) Colonization
3) Maturation
4) Dispersal

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17
Q

Attachment - Biofilm Formation Stage (7.4)

A
  • First stage

- Use of pili & adherence proteins

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18
Q

Colonization - Biofilm Formation Stage (7.4)

A
  • Second stage
  • Quorum sensing
  • –Cell-cell signaling
  • –Density dependent
  • Activates gene expression
  • –Genes that make the Protective Matrix are turned on
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19
Q

Maturation - Biofilm Formation Stage (7.4)

A
  • Third stage
  • Forms a “mushroom” with:
  • –Channels for nutrients
  • –Oxygen gradients
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20
Q

Dispersal - Biofilm Formation Stage (7.4)

A
  • Fourth / Final stage
  • Reactivation of motility
  • Allows the bacteria to spread out again
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21
Q

Dental plaque (7.4)

A
  • A biofilm

- Bacterial film on tooth surface (over 300 microbial species)

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22
Q

Caries (7.4)

A
  • A biofilm
  • Tooth decay
  • Bacterial fermentation –> Acidic products –> Damage to enamel
  • –Streptococcus mutans - fermentation
  • –Poryphromonas - fermentation
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23
Q

Periodontal disease (7.4)

A
  • A biofilm

- Inflammation & tissue destruction

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24
Q

How is ATP created in aerobic & anaerobic respiration? (10.3)

A

ATP is created via Oxidative Phosphorylation

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25
Q

How is ATP created in fermentation? (10.3)

A

ATP is created via Substrate-Level Phosphorylation

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26
Q

How is ATP created in photosynthesis? (10.3)

A

ATP is created via Photophosphorylation

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27
Q

Exergonic reaction (10.2)

A
  • Favors products
  • – [A+B] ——-> [C+D]
  • K(eq) > 1
  • Delta G Prime
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28
Q

Endergonic reaction (10.2)

A
  • Favors reactants
  • – {A+B] 1
  • Energy required
  • -Fig. 10.2
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29
Q

Oxidation - Reduction Rxns [general] (10.3)

A
  • Electrons move from donor to acceptor
  • Utilize carriers
  • Redox rxns can result in energy release, which can be used to form ATP
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30
Q

O.I.L.R.I.G. (10.3)

A 
Oxidation
Is
Loss
Reduction
Is
Gain
  • -Oxidation: Removal of e-
  • –Substance that is oxidized in the donor
  • -Reduction: Addition of e-
  • –Substance that is reduced is the acceptor
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31
Q

In the following reaction, what is oxidized? Reduced? What enzyme is required to catalyze the reaction? (10.3)

[Malate + NAD+] —–> [Oxaloacetate + NADH + H+]

A

Oxidized: Malate
—Oxidized to oxaloacetate

Reduced: NAD+
—Reduced to NADH

Enzyme: Malate Dehydrogenase

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32
Q

Rhodoferax metabolins [bacteria] (10.3)

A
  • Psychrophilic, obligate anaerobe that oxidizes acetate w/ the reduction of iron
  • –Habitat: Cold, no oxygen
  • –Donor:Acetate
  • –Acceptor: Iron
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33
Q

Enzymes (10.6)

A
  • Proteins (usually) that catalyze reactions
  • –Ribozymes: catalytic RNAs
  • Act on substrates & convert to products
  • Require activation energy to bring reacting molecules together
  • Increase the rate of reaction by lowering the activation energy
  • Often named for the reactions that they catalyze
  • –Ex: Phophotase, Kinase, Cellulase
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34
Q

How do Enzymes Lower Activation Energy? (10.6)

A
  • Increase local concentrations of substrates

- Orient substrates properly for reactions to proceed

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35
Q

Reduction Potential [E(0)] (10.3)

A
  • Equillibirum constant for redox rxns
  • Measure the tendency of the donor to lose electrons
  • More negative E(0) is a better donor
  • More positive E(0) is a better acceptor
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36
Q

What does a redox reaction accomplish? (10.3)

A

It pairs molecules with a negative E(0) to molecules with a positive E(0)

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37
Q

Electron Tower (10.3)

A
  • Reference fig. 10.6
  • Negative delta G’ - Better e- donors
  • Positive delta G’ - Better e- acceptors
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38
Q

How do microbes transfer energy [4 steps]? (10.4)

A
  • Microbes transfer energy by moving electrons from:
  • –Reduced food molecules (glucose) –>
  • –Diffusable carriers in the cytoplasm –>
  • –Membrane-bound carriers –>
  • –O2, Metals, or oxidized forms of N & S

Overall: From food to O2, Metals, or oxidized N & S

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39
Q

What are the two types of electron carriers? (10.4)

A
  • Freely diffusable
  • –Ex: NAD+ & NADP+
  • Membrane-bound
  • –Ex: Flavoproteins, cytochromes, quinones
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40
Q

What does NAD stand for? (10.4)

A

Nicotinamide Adenine Dinucleotide

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41
Q

What does NADP+ stand for? (10.4)

A

Nicotinamide Adenine Dinucleotide Phosphate

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42
Q

What do the reduced forms of NAD & NADP look like? What do they do for the cell? (10.4)

A
  • Reduced forms:
  • –NAD: NADH
  • –NADP: NADPH
  • These reduced forms are the “reducing power” of the cell
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43
Q

Quinones (10.4)

A
  • A membrane-bound carrier
  • Made of organic compounds
  • Ex: Coenzyme Q
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44
Q

Cytochromes (10.4)

A
  • A membrane-bound carrier
  • Made of proteins
  • Use iron to transfer electrons
  • –Iron is part of a heme group
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45
Q

What are the two types of metabolic groups in the carbon cycle? (11.1)

A
  • Heterotrophs

- Autotrophs

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46
Q

Heterotrophs (11.1)

A
  • Use reduced, preformed organic compounds as their source of carbon
  • Convert huge amounts of C –> CO2
  • Ex: Animals, many kinds of microbes
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47
Q

Autotrophs (11.1)

A
  • Use CO2 as their source of carbon
  • Synthesize organic compounds that are used by heterotrophs
  • Also called Primary Producers
  • Ex: Plants, many kinds of microbes
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48
Q

Phototrophs (11.1)

A

-Use light as a source of energy

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49
Q

Chemotrophs (11.1)

A
  • Oxidize chemical compounds as source of energy

- Often the same chemicals that are used for the carbon source

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50
Q

Lithotrophs (11.1)

A
  • Use inorganic molecules as their source of electron donors
  • Use respiration to accept electrons
  • Table 11.1 & 11.2
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51
Q

Organotrophs [basic] (11.1)

A
  • Use organic molecules as their source of electron donors
  • Use fermentation to accept electrons
  • Table 11.1 & 11.2
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52
Q

What would a photolithoautotroph use for a source of energy? Electrons? Carbon? (11.1)

A
  • Energy : Light (photo)
  • Electrons: Inorganic compounds (litho)
  • Carbon: CO2 (auto)
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53
Q

What kinds of organisms are lithotrophs? (11.1)

A
  • Microbes (prokaryotes) exclusively

- –Eukaryotes are either photoautotrophs or heterotrophs

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54
Q

What are the three basic needs that fulfill all sources of energy, carbon, and electrons? (11.1)

A

1) ATP as energy currency
2) Reducing power to supply electrons for chemical reactions
3) Precursor metabolites for biosynthesis

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55
Q

Organotrophs [complex] (11.1)

A
  • Many different energy sources are funneled into common degradive pathways
  • Most pathways generate glucose or intermediates of the pathways used in glucose metabolism
  • Substrate Level Phosphorylation (high energy)
  • Oxidative phosphorylation
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56
Q

What are the two functions of organic energy sources? (11.1)

A

1) Oxidized to release energy
2) Provide building blocks for anabolism
- Amphibolic pathways
- –Catabolic & anabolic
- –Ex: Glycolysis

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57
Q

Aerobic Respiration (11.2)

A
  • Process that can completely catabolize an organic energy source to CO2 using:
    i) Glycolytic pathways (glycolysis)
    ii) Tricarboxylic Acid cycle (TCA cycle / citric acid cycle)
    iii) Electron transport chain with oxygen as final electron acceptor
  • Produces ATP (mostly indirectly, via electron transport)
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58
Q

What are the three different paths in the breakdown of glucose to pyruvate? (11.4)

A

i) Embden-Meyerhof (glycolysis)
ii) Pentose phosphate
iii) Entner-Dourdoroff

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59
Q

Glycolysis / Embden-Meyerhof [general] (11.4)

A
  • Most common form of glucose breakdown
  • Occurs in the cytoplasm
  • Functions in the presence or absence of CO2
  • Ten reactions in two stages
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60
Q

Glycolosis [in-depth] (11.4)

A
  • 6C Stage: Glucose is phosphorylated twice
  • –Requires ATP
  • –Generates fructose 1,6 biphosphate
  • 3C Stage: Fructose 1,6 biphosphate split into two glyceraldehyde 3-P, then converted to pyruvate
  • –Key Steps in 3C Stage:
  • —–i) Oxidations –> NADH
  • —–ii) Substrate-Level Phosphorylation –> ATP
  • Big Picture: Glucose –> Pyruvate
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61
Q

What is the net yield of glycolysis? (11.4)

A

2 ATP, 2 NADH, 2 pyruvate

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62
Q

In glycolysis’ 3C stage, how are NADH & ATP generated? (11.4)

A
  • G3P is oxidized and phosphorylated
  • –Generates high-energy phosphate bond
  • –Uses G3P hydrogenase to do this
  • NAD+ is reduced to NADH
  • Phosphorylation of ADP by high energy metabolic substrate
  • –Generates ATP
  • –3PG Kinase (phosphoryglycerase)
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63
Q

Pentose phosphate pathway (11.4)

A
  • Occurs in both prokaryotes & eukaryotes
  • Starts by converting Glucose-6-P to Ribulose-S-Phosphate (pentase)
  • Many sugars for biosynthesis
  • –Transketolases & transaldolases
  • Yields 6 NADPH (the reducing power of biosynthesis)
  • Net yield of 1 ATP (indirectly)
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64
Q

Entner-Doudoroff pathway (11.4)

A
  • Occurs in a few prokaryotes, does NOT occur in eukaryotes
  • Combines the reactions of glycolysis & pentose phosphate
  • Net yield: 1 ATP, 1 NADH, 1 NAHPD
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65
Q

Tricarboxylic Acid Cycle (TCA) / Citric Acid Cycle / Krebs Cycle (11.5)

A
  • Pyruvate is completely oxidized to CO2
  • Eukaryotes - Occurs in mitochondria
  • Prokaryotes - Occurs in cytoplasm
  • Generates:
  • –CO2
  • –Numerous NADH & FADH(2) (another type of diffusable electron carrier)
  • –Precursors for biosynthesis
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66
Q

Describe the steps of the TCA / Citric Acid / Krebs Cycle [5 steps] (11.5)

A
  • Fig 11.8
    i) Pyruvate is oxidized to CO2 & Acetyl CoA
  • –Acetyl CoA - high-energy molecule (thioester bond)
    ii) Acetyl CoA condensed with oxaloacetate
    iii) Oxidation & decarboxylation forming NADH & CO2
    iv) Succinyl CoA –> Succinate
  • –Generates high-energy guanosine triphosphate (GTP) via substrate-level phosphorylation
    v) More oxidations form NADH & FADH(2)
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67
Q

How many ATP molecules are synthesized directly from the oxidation of glucose? (11.6)

A
  • Four

- Most ATP in cells is made when NADH & FADH are oxidized in the electron transport chain

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68
Q

Explain how the electron transport chain creates ATP (11.6)

A
  • Electrons flow from the NADH & FADH2 –> Terminal acceptor
  • Flow from carriers with more negative electron potential (Eo) to more positive Eo
  • –Energy is released by doing this
  • Used to make ATP by oxidative phosphorylation
  • —3 ATP per NADH using O2 as the acceptor
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69
Q

Where are electron transport chains located in the cell? (11.6)

A
  • Eukaryotes: In the mitochondrial membrane
  • Prokaryotes: In the plasma membrane
  • Ex: Paracoccus denitrificans
  • –Aerobic conditions
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70
Q

Oxidative phosphorylation (11.6)

A
  • Chemiosmotic Hypothesis
  • –Energy released during electron transport use to establish proton gradient & charge difference across membrane
  • —–Proton motive force (PMF)
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71
Q

Explain how the proton motive force (PMF) drives ATP synthesis (11.6)

A
  • Electron flow causes protons to move outward across membrane, ATP made when they come back in
  • ATP synthase (F1Fo ATPase)
  • –Enzyme
  • –Uses proton movement to catalyze ATP synthesis
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72
Q

Bacterial ATP synthase structure (11.6)

A
  • Fig. 11.16
  • Fo
  • –Proton channel
  • –The part in the plasma membrane
  • –Ring of C subunits rotates
  • F1
  • –The part in the cytoplasm
  • –Gamma shaft rotates
  • –Conformational changes in sphere of alpha & beta subunits
  • –ATP synthesis
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73
Q

Shewanella [bacteria] (11.6)

A
  • Aquatic, gram-negative bacterium
  • Capable of extracellular electron transport
  • –Transfers electrons to extracellular metals
  • Facultative anaerobe
  • –Prefers oxygen, but can live without it
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74
Q

Microbial Fuel Cell (11.6)

A
  • Anoxic (low O2) chamber
  • –Anode
  • Oxic (high O2) chamber
  • –Cathode
  • Harnesses microbes’ extracellular electron transfer to create electricity by connecting the two chambers
  • ex: Using Shewanella
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75
Q

Organic electron donor [3 kinds] (11.6)

A

i) Fermentation
- –Endogenous organic electron acceptor
- –Ex: Pyruvate
ii) Aerobic respiration
- –O2 as acceptor
iii) Anaerobic respiration
- –NO3-, SO4(2-), CO2, fumarate as electron acceptor

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76
Q

Inorganic electron donor (11.6)

A
  • Chemolithortophy

- –O2, SO4(2-), NO3- as electron acceptor

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77
Q

Anaerobic respiration (11.7)

A
  • Table 11.3
  • —Don’t need to know all of these, he said he will point out which we need to know
  • Produces less ATP than aerobic respiration
  • Ex: Paracoccus
  • Ex: Geobacter
  • Use of anaerobic chamber to study these microbes
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78
Q

Dissimilatory Nitrate Reduction (11.7)

A
  • Also known as nitrification
  • ex: Paracoccus denitrificans
  • Uses nitrate (NO3-) as terminal electron acceptor
  • Reduced to nitrogen gas (N2)
  • Major loss of nitrogen in soil
  • –This is why farmers till the land– in an effort to kill these anaerobic bacteria by exposing them to air, because they take nitrogen out of the soil
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79
Q

Fermentation (11.8)

A
  • Completion of catabolism without the electron transport system & a terminal electron acceptor
  • Occurs in the cytoplasm
  • Hydrogens from NADH transferred onto pyruvate
  • Generates:
  • –Fermentation products
  • —–Ex: Lactic acid, ethanol
  • –NAD+ (oxidized form of NAD)
  • ATP by substrate level phosphorylation
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80
Q

Sulfolobus [archaea] (11.10)

A
  • Thermoacidophile
  • –Lives in sulfur hot springs
  • Oxidizes H2S –> H2SO4
  • Chemolithotroph
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81
Q

Chemolithotrophs (11.10)

A
  • Acquire electrons from the oxidation of inorganic sources such as H2, NO2, or Fe(2+)
  • –Unlike most organisms which acquire electrons from the catabolism of an organic molecule such as glucose
  • The electrons are transferred to terminal acceptors (usually O2) by electron transport chains
  • Tables 11.5 & 11.6
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82
Q

Acidithiobacillus ferroxidans [bacteria] (11.10)

A
  • An iron-oxidizing bacteria
  • Oxidizes ferrous (Fe(2+)) –> ferric (Fe(3+))
  • Uses O2 as electron acceptor
  • Forms insoluble ferric hydroxide
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83
Q

Iron-oxidizing bacteria (11.10)

A
  • Ex: Acidithiobacillus ferroxidans
  • Very low reduction potential - Small amount of energy created
  • –Look at the electron tower - Fe –> O is very small
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84
Q

Nitrifying bacteria (11.10)

A
  • Obligate aerobes
  • Nitrification: ammonia oxidized to nitrate
  • Requires 2 genera to do this
  • –i) Nitrosomonas - Reduces ammonia –> nitrite
  • –ii) Nitrobacter - Reduces nitrite –> nitrate
  • Used to reduce ammonia in wastewater
  • Often followed by denitrification
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85
Q

Phototrophs & Photosynthesis (11.11)

A
  • Two parts
  • – i) Light energy trapped & converted to chemical light (light reactions)
  • – ii) Chemical used to reduce CO2 & synthesize cell material (dark reactions)
  • Many phototrophs are also autotrophs
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86
Q

Oxygenic photosynthesis (11.11)

A
  • Provides all of the O2 for the Earth by oxidixing H2O –> O2
  • A lot comes from microbes in the ocean
  • Eukaryotic:
  • –Higher plants
  • –Green, brown, & red algae
  • –Unicellular algae
  • —–Ex: Euglenoids, dinoflagelates, diatoms
  • Prokaryotic:
  • –Cyanobacteria (gram negative)
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87
Q

Anoxygenic photosynhesis (11.11)

A
  • Photosynthesis that does not oxidize water & therefore does not provide oxygen
  • Prokaryotic only
  • –Green sulfur bacteria
  • –Purple sulfur bacteria
  • –Green nonsulfur bacteria
  • –Purple nonsulfur bacteria
  • –Prochloron (bacteria)
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88
Q

Light reactions (11.11)

A
  • Chlorophylls (Oxygenic)
  • –Major light-absorbing pigments – found in eukaryotic organisms & cyanobacteria
  • Bacteriochlorophylls (Anoxygenic)
  • –Major light-absorbing pigments – found in purple & green bacteria
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89
Q

Prochlorococcus [bacteria] (11.11)

A
  • Habitat: Tropical oceans
  • > 100,000 cells / 1 mL of seawater
  • Smallest known photosynthetic organism (1 um)
  • Oxygenic photosnthesis
  • Uses chlorophyll
  • Small genome: ~ 2000
  • Thylakoids in tree-ring like formation
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90
Q

Accessory Pigments (11.11)

A
  • Transfer light energy to chlorophylls
  • Absorb different wavelengths than chlorophyll
  • Quench toxic forms of oxygen (photoprotection, antioxidants)
  • Ex: Carotenoids (lycopene, beta-carotene), Phycobiliproteins
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91
Q

Photosystems (11.11)

A
  • A light-harvesting arrays composed of chlorophylls & accessory pigments
  • Two types:
  • –Photosystem I (PSI)
  • –Photosystem II (PSII)
  • Embedded into the thylakoid
  • Occur in cyanobacteria & plants
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92
Q

Thylakoid (11.11)

A

Membranes that contain photosystems

93
Q

What basic thing does biosynthesis require? (12.1)

A
  • Requires energy & raw material
  • These materials come from intermediates of central metabolic pathways
  • Precursor metabolites examples: pyruvate, fructose-6-P, oxaloacetate
94
Q

Cyclic photophosphorylation (11.11)

A
  • Occurs in Photosystem Stage I (PSI)
  • Has a reaction center of P*(700) - this is the wavelength of light that it absorbs at
  • Makes ATP
  • H2O is electron source
  • Generates Proton Motive Force (Fig. 11.32)
  • Fig 11.31
95
Q

Non-cyclic photophosphorylation (11.11)

A
  • Occurs in Photosystem Stage II (PSII)
  • Makes ATP & NADHP - dark reactions
  • H2O is electron source
  • Generates Proton Motive Force (Fig 11.32)
  • Fig 11.31
96
Q

Describe light reactions in green & purple bacteria (11.11)

A
  • Only 1 photosystem
  • Can only make ATP (not NADPH)
  • –Uses reverse electron transport to create NADPH
  • Uses bacteriochlorophyll (Bchl)
  • Anoxygenic
  • Uses H2S or an organic donor to replace electrons lost
  • Fig. 11.34
97
Q

Photosynthesis in Archaea (11.11)

A
  • Some archaea do perform photosynthesis, however, they do not contain chlorophylls or bacteriochlorophyll
  • Use Rhodopsin
  • –A protein
  • –Mostly in archaea, but some bacteria have this
98
Q

Rhodopsin (11.11)

A
  • Light-driven proton pump
  • Contains seven trans-membrane helices
  • Pigment protein
  • Retinal - the pigment in rhodopsin
  • –Absorbs light
  • –Induces conformational changes in rhodopsin
  • –Pumps proton out
  • —–Generates proton movement gradient
99
Q

Calvin Cycle (12.3)

A
  • Anabolic pathway for fixing CO2 into carbohydrate
  • Dark reactions of photosynthesis
  • Energy demanding
  • Plants: Occurs in chloroplasts
  • Bacteria: Occurs in cytoplasm
  • Crucial to life, provides organic matter for heterotrophs
100
Q

What are the 3 key steps in the Calvin Cycle? (12.3)

A
  • Fig. 12.4
    i) Carboxylation phase
    ii) Reduction phase
    iii) Regeneration phase
101
Q

Carboxylation stage in Calvin Cycle (12.3)

A
  • Use of rubisco (very important)
  • Often occurs in carboxysomes
  • –Proteinaceous shell containing large concentrations of rubisco
102
Q

Reduction phase in Calvin Cycle (12.3)

A
  • Reverse of two key reactions in glycolysis

- Requires NADPH

103
Q

Regeneration phase in Calvin Cycle (12.3)

A
  • Numerous carbohydrates produced

- Requires 18 ATP to make glucose

104
Q

Gluconeogenesis (11.2)

A
  • Functional reversal of glycolysis
  • Glucose synthesis
  • Occurs in animals, plants, fungi, bacteria
  • –Humans use this to maintain blood glucose levels
  • Requires ATP & GTP
  • 6 enzymes also used in glycolysis, but 4 unique to gluconeogenesis
105
Q

What are the three processes of genetic information flow (central dogma)? (13.1)

A

i) DNA Replication
ii) Transcription
iii) Translation

106
Q

Griffith’s Transformation [experiment] (13.2)

A
  • Proved that DNA is the genetic material
  • Used Streptococcus pneumoniae on mice
  • Fig 13.1
  • Found that the capsulated smooth strain killed mice, non-capsuled rough strain did not kill mice, killed smooth strain did not kill mice
  • Found that when killed smooth strain and living rough strain were put together, it killed the mice
  • Translation: When a microbe takes up free DNA from the environment and incorporates it into its own genome
  • –The rough Streptococcus took up the genes for the capsule from the dead smooth strain
107
Q

Gene (13.2)

A
  • Functional unit of genetic information
  • Deoxyribonucleic acid (DNA)
  • Genes: (italicized) pilA, lacA
  • Proteins: PilA, LacA (not italicized)
108
Q

Genome (13.2)

A
  • All the genetic material in a cell or virus

- Bacterial genomes consist of one (usually) or more DNA chromosomes

109
Q

Genotype (13.2)

A

-Specific set of genes carried in the genome

110
Q

Phenotype (13.2)

A

-Set of observable characteristics (ex: motile bacteria, shape, etc)

111
Q

Promoter (13.3)

A
  • Place on DNA where the RNA polymerase binds to begin transcription
  • Found upstream of the DNA fragment that is going to be transcribed
112
Q

Transcription start site (13.3)

A

-Called +1 when in monocistronic

113
Q

Operator (13.3)

A

-Where repressor proteins bind to block transcription

114
Q

Operon (13.3)

A

-Cluster of genes regulated by one promoter (ex: Lac operon)

115
Q

DNA Structure (13.3)

A
  • Polymer of nucleotides
  • –Each nucleotide is three parts – sugar, nitrogenous base, & phosphate group: deoxynucleotide
  • Double helix, 2 complementary strands
  • –Each helix: Deoxynucleotides connected by phosphodiester bonds
  • Sequence of one strand determines the other
  • –Adenine (A) pairs with Thymine (T) - 2 hydrogen bonds
  • –Guanine (G) pairs with Cytosine (C) - 3 hydrogen bonds
  • ——Purines: G & A
  • —–Pyrimidines: C & T
116
Q

Name two bacteria that perform fermentation in the human mouth (7.4)

A
  • Streptococcus mutans

- Poryphromonas gingivalis

117
Q

How is DNA organized in prokaryotes? (13.3)

A
  • Double helical
  • Closed, circular, supercoiled molecule
  • Bacteria pack their DNA into loops, collectively called the nucleoid
  • Archaea have circular chromosome that contain histones
118
Q

How is DNA organized in eukaryotes? (13.3)

A
  • Double helical
  • Linear
  • Wrapped around histone proteins, collectively called a nucleosome
  • Genes in the human genome are interrupted by introns
119
Q

What does DNA being ‘semiconservative’ mean? (13.3)

A
  • The two strands separate in order to replicate
  • Each of the two separated strands serves as a template for synthesis for a new strand
  • Ends up with two parents strands each paired with a new daughter strand
120
Q

In eukaryotes, is replication unidirectional or bidirectional? Is there one origin of replication or multiple? (13.3)

A
  • Bidirectional synthesis

- Multiple origins of replication (ori)

121
Q

In prokaryotes, is replication unidirectional or bidirectional? Is there one origin of replication or multiple? (13.3)

A
  • Bidirectional synthesis

- One origin of replication (ori)

122
Q

Which three things does DNA polymerase need in order to function? (13.3)

A

i) Template
ii) Deoxynucleotide triphosphates (dNTP)
iii) Primer (usually RNA) with a 3’ OH group

123
Q

What is the major replication enzyme in bacteria? (13.3)

A

DNA polymerase III

124
Q

In what direction does synthesis occur? (13.3)

A

ALWAYS in the 5’ -> 3’ direction

125
Q

DNA gyrase (13.3)

A
  • Type II Topoisomerase
  • Unwinds the DNA (releases tension from overcoiling)
  • Cuts one DNA, passes through gap
  • Seals the gap
  • A target for quinoline antibiotics
126
Q

What do quinoline antibiotics target? (13.3)

A
  • Topoisomerase

- If the DNA becomes too overcoiled, it can’t continue synthesis, so this effectively kills the infection

127
Q

DnaB Helicase (13.3)

A

-Breaks the hydrogen bonds between the base pairs so that translation can occur

128
Q

DNA Primase (13.3)

A

-Primes the DNA for replication using an RNA primer

129
Q

What does SSB stand for? (13.3)

A

Single-stranded Binding Proteins

130
Q

Single Stranded Binding Proteins (13.3)

A
  • A coating on the lagging strand of DNA

- Keeps the DNA from rejoining together before replication is done

131
Q

Okazaki Fragments (13.3)

A
  • Occur on the lagging strand (which is discontinuous)
  • The sections of DNA that are replicated on the lagging strand
  • In the 5’ -> 3’ direction still
132
Q

DNA Polymerase I (13.3)

A

-Removes the RNA primers after replication has been started, replaces the RNA with DNA

133
Q

Ligase (13.3)

A

-Seals the gaps together between sections of replicated DNA (seals together okazaki fragments)

134
Q

What does a DNA sequence of a gene correspond to? (13.4)

A

-It corresponds to the amino acid sequence of the protein encoded

135
Q

What two processes are required to get DNA –> protein? (13.4)

A

i) Transcription

ii) Translation

136
Q

What does the antibiotic Rifampin target? (13.4)

A
  • RNA polymerase

- Targets this in order to prevent transcription

137
Q

What dictates where transcription should begin and end in bacteria (not the promoters–what controls the promoters)? (13.4)

A
  • A combination of core and sigma factors

- Sigma factors: Proteins that direct the core promoters

138
Q

Terminator (13.4)

A

-The sequence that signals RNA polymerase to stop translating

139
Q

Start codon (13.4)

A
  • In RNA

- Signals the start of translation

140
Q

Describe Rho-dependent termination (13.4)

A
  • A DNA sequence that tells the Rho protein that it is time to bind
  • Protein Rho binds to RNA
  • This causes the RNA polymerase to pause
  • The Rho protein moves towards polymerase quickly, and it boots the polymerase off the strand
  • Ends translation
141
Q

Describe rho-independent termination (13.4)

A
  • A DNA sequence that encodes an RNA stem-loop structure

- Causes RNA polymerase to release

142
Q

Two-component signal transduction systems (13.4)

A
  • Bacteria use these to control gene transcription in response to their environment
  • Slide 13, Lecture 11
143
Q

How is mRNA modified in eukarya? (13.4)

A
  • Capping: Methylguanosine added to the 5’ end of RNA

- Polyadenylation - Adenine nucleotides added to the 3’ end – Poly-A Tail

144
Q

Five features of transcription in Eukarya (13.4)

A
  • Occurs in the nucleus
  • Uses 3 RNA polymerases
  • Only contains transcription factors (no sigma factors)
  • TATA Box - Promoter element
  • Uses RNA splicing to remove introns
145
Q

What does translation require to synthesize protein? (13.7)

A

-It requires ribosomes & energy in the form of ATP & GTP

146
Q

What does GTP stand for?

A

Guanosine triphosphate

147
Q

What are the two subunits in a bacterial ribosome? (13.7)

A

i) 30S
- –21 proteins + 16S rRNA
ii) 50S
- –34 proteins + 23S and 5S rRNA

148
Q

Translation definition (13.7)

A

The synthesis of polypeptide directed by mRNA sequence

149
Q

What two rRNAs are used in translation? (13.7)

A
  • 23S rRNA

- 16S rRNA

150
Q

23S rRNA (13.7)

A
  • Peptidyltransferase

- Ribozyme

151
Q

16S rRNA (13.7)

A
  • Aligns mRNA with the ribosome

- Has sequence complementary to the Shine-Dalgarno sequence of the mRNA

152
Q

Ribosomes (13.7)

A

-Read the mRNA sequence as a code

153
Q

Codons (13.7)

A
  • Triplets (3 nucleotides)
  • 64 difference codons
  • 61 codons encode protein
  • –“Sense codon”
  • 3 codons do not encode a protein
  • –“Nonsense codon”
  • –Stop codons
  • The code is degenerate – multiple codons can encode the same amino acid
154
Q

Name the three stop codons (13.7)

A

UAG, UGA, UAA

155
Q

Name the start codon (13.7)

A

AUG - codes for Methionine (Met)

156
Q

What function does the tRNA serve? (13.6)

A
  • It converts the language of RNA into that of proteins
  • Collects amino acids and then gives them to the mRNA to assemble
  • Clover-leaf shape
157
Q

What does the 3’ end of tRNA do? (13.6)

A
  • Synthetase (an enzyme) attaches an amino acid to this end

- ATP is required to do this

158
Q

What does the anticodon of tRNA do? (13.6)

A
  • It is complementary to a codon in mRNA

- Tells the synthetase which amino acid it should attach to the 3’ end

159
Q

How does translation begin (Initiation) (13.7)

A

-Formylmethionine (f-Met) on a tRNA binds to the start codon in mRNA at the P-site

160
Q

What does the Shine-Dalgarno sequence do? (13.7)

A

It aligns the mRNA with the 16S rRNA of the ribosome

161
Q

A-Site (13.7)

A

-Aminoacyl / Acceptor Site

162
Q

P-Site (13.7)

A

-Peptide Site

163
Q

E-Site (13.7)

A

-Exit Site

164
Q

Elongation [translation phase] (13.7)

A
  • The tRNA with the proper amino acid attaches to the A-Site
  • –GTP required to do this
  • A peptide bond joins this new amino acid to the f-Met
  • Ribosome moves 1 codon along the mRNA
  • The empty tRNA (used to have f-Met) moves from P to E and exits the ribosome
165
Q

Termination [translation phase] (13.7)

A
  • Ribosome comes along a stop codon
  • –There are no corresponding tRNAs for stop codons
  • Release factors (RF) cleave & release the polypeptide
166
Q

Translation & Transcription in Prokaryotes - Summary (13.7)

A
  • Translation and transcription can (and often do) take place simultaneously in the cytoplasm in prokaryotes
  • Fig. 13.30
167
Q

How is genetic variation created? (16.1, 16.4)

A
  • Mutations
  • –Gives rise to new alleles & new phenotypes
  • Vertical gene transfer
  • Horizontal gene transfer
168
Q

Vertical gene transfer (16.4)

A
  • Sexual reproduction
  • Occurs in Eukarya only
  • New combinations of genes when gametes from parents fuse
169
Q

Horizontal gene transfer (16.4)

A
  • Occurs in Bacteria & Archaea
  • Transfer from one independent organism to another
  • 3 mechanisms: Conjugation, Transformation, & Transduction
170
Q

Conjugation overview (16.6)

A
  • DNA transfer by direct cell-to-cell contact
  • Requires pili & plasmids
  • Major mode of spreading antibiotic resistance genes among a bacterial population
171
Q

Plasmids (16.6)

A
  • Double-stranded, circular DNA
  • Extrachromosomal
  • Carry genes that confer an advantage
  • Can be transferred by conjugation
  • Are replicons
  • Can be episomes
172
Q

Replicons (16.6)

A

A gene having its own origin of replication

173
Q

Episome (16.6)

A

Plasmids that can exist with or without integrating into the chromosome

174
Q

What does F-factor stand for? (16.6)

A
  • Fertilization factor

- Fig. 16.16

175
Q

Name the Four Steps in F(+) x F(-) Conjugative Mating (16.6)

A

1) Pilus connects the cells
2) F-factor begins replication & transfer
3) F-factor is replicated & transferred
- –Rolling circle replication
4) Now both cells are F(+)
- –Both contain the F-factor

176
Q

In F(+) x F(-) Conjugative Mating, what does each F stand for? (16.6)

A

F(+) : Bacterial cell which contains the gene (F-factor) which is going to be transferred
F(-) : Bacterial cell which is going to receive the gene from the F(+)

177
Q

Rolling Circle Replication (16.6)

A
  • How plasmids replicate

- Allows both cells at the end of the F(+) x F(-) mating to be F(+) instead of just transfer from one to the other

178
Q

Hfr Cell (16.6)

A
  • Fig 16.22)
  • Can transfer the integrated F-factor AND part of the original bacterial chromosomal F-cell
  • Leads to a high frequency of recombination
  • –May accidentally give a bit of its regular chromosome when transferring its F-factor
179
Q

Agrobacterium tumefariens [bacteria] (16.6)

A

-Causes crown gall disease in plants
Has a tumor-inducing (Ti) plasmid
-Piece of the Ti is transferred by conjugation into the plant cell
—Then that piece integrates into the plant genome

180
Q

Transduction [definition] (16.8)

A

-The transfer of bacterial genes via phages

181
Q

Phages (16.8)

A
  • Cause of transduction gene transfer
  • Abundant & diverse – Over 10 billion per liter of seawater
  • Impact the composition & behavior of microbial communities
182
Q

What are the Two Major Types of Phages? (16.8)

A

i) Virulent
- –Lytic cycles (cause the host cell to lyse)
ii) Temporate
- –Lysogenic cycles (host cell remains intact)

183
Q

Lytic Cycle (16.8)

A
  • Fig. 16.27
  • Phage attaches to host cell & injects its DNA into the cytoplasm
  • Phage DNA undergoes replication & synthesizes new phages
  • –Host genome becomes degraded during this process
  • Host cell lyses to release the new phages
184
Q

Lysogenic Cycle (16.8)

A
  • Fig. 16.27
  • Phage attaches to host cell & injects its DNA into the cytoplasm
  • Phage DNA integrates into the host chromosome
  • –Becomes a prophage
  • —–Prophage: Phage genome that is integrated into the bacterial chromosome
  • Prophage DNA replicates alongside the bacterial cell’s replication
  • Exposure to stress (such as UV light) can trigger excision from the host chromosome
  • –General idea: GTFO before the host cell dies
185
Q

Generalized Transduction (16.8)

A
  • Occurs during the LYTIC cycle
  • Any random part of the bacterial genome could be transferred
  • During viral assembly, pieces of degraded host DNA can be mistakenly packed into the phage
  • –The phage then goes on to put this DNA into a new bacterial cell
186
Q

Specialized Transduction (16.8)

A
  • Occurs during the LYSOGENIC cycle
  • Specific part of the genome is transferred
  • If the prophage incorrectly excises as it leaves the cell, it takes part of the bacterial genome with it
187
Q

CRISPR-Cas System overview

A
  • The prokaryotic “immune system”
  • CRISPR is a cluster of genes, Cas is a protein
  • Bacteria & archaea have RNA-based defense programs to destroy invading DNA from phage infection & sometimes conjugation
188
Q

What does CRISPR stand for?

A

Clustered Regularly Interspaced Short Palindromic Repeats

189
Q

Describe the CRISPR-Cas System

A
  • When a phage attacks, bacteria incorporate sequences of the viral DNA into their own genetic material, placing it between repeats
  • Next time the bacteria encounter the phage, they use the DNA in the clusters to make RNAs that recognize the matching viral sequences
  • The RNA guides the Cas proteins to viral DNA, where the Cas protein cuts the invading DNA
190
Q

Spacer segments

A
  • Part of the CRISPR-Cas system

- Bits of phage DNA in the bacteria’s genome from a previous infection

191
Q

What does the Cas protein do?

A
  • Processes the RNA

- Cuts the DNA of invading phages

192
Q

Transformation [definition] (16.7)

A

-Uptake of free DNA from the enivronment

193
Q

Transformation [overview] (16.7)

A
  • Discovered by Fred Griffith (did the experiments with the pneumonia in mice)
  • Only a few genera of bacteria can do this naturally
194
Q

Name two Gram + Genera of Bacteria that are Naturally Competent (16.7)

A

i) Streptococcus

ii) Bacillus

195
Q

Name two Gram - Genera of Bacteria that are Naturally Competent (16.7)

A

i) Haemophilus

ii) Neisseria

196
Q

Competent Cell (16.7)

A
  • A cell which can undergo transformation naturally

- –Can naturally take up free DNA from the environment

197
Q

Artificial Transformation (16.7)

A
  • A way to make genera which are not naturally competent undergo transformation
  • –Ex: E. coli
  • A critical step in cloning
198
Q

What are the two techniques of Artificial Transformation? (16.7)

A

i) Calcium Chloride - Makes cell more permeable
ii) Electroporation - Pulses high-voltage, temporary holes through the cell wall & cell membrane to allow DNA through

199
Q

Bacterial RecA Protein (16.7)

A
  • Integrates DNA by homologous recombination
  • Makes a stable transformation
  • Fig. 16.34
200
Q

Membrane-Bound Complexes (16.7)

A
  • Bring DNA into the cell
  • DNA is changed during this process
  • –Fig. 16.26
  • –Proteins labeled “com” mean “competence”
  • –Nucleases
201
Q

Nucleases in Transformation (16.7)

A
  • Convert double-stranded DNA into single-stranded DNA as it enters the cell during transformation
  • Does this because single-stranded DNA is much easier to incorporate into their genome, and also because single-stranded is easier to break down for nutrients if the cell decides to do that instead
202
Q

Mobile DNA (16.7)

A

Segments of DNA that can move from one site to another within other DNA molecules
-Made up of transposable elements
Moves via the process of transposition

203
Q

Transposable Elements (16.7)

A
  • Fig. 16.13
  • Two components: Transposons & Insertion Sequences
  • –Insert & turn genes on or off
  • IR - Inverted Repeats
  • –Help the transposons move
  • Transposase Enzyme
  • –Cuts & Pastes
204
Q

Mutations [definition] (16.1)

A

Stable, heritable changes in nucleotide sequence relative to the wild-type
—May or may not affect the phenotype

205
Q

Wild-Type Strains (16.1)

A

-Possess the typical or representative characteristics of a species, whereas mutant strains contain mutations

206
Q

Forward Mutation (16.1)

A

-A mutation from a wild-type to a mutant type

207
Q

Reversion Mutation (16.1)

A
  • A mutation reversing the initial mutation done to the wild type
  • A mutation from mutant type to wild-type
208
Q

Morphological mutation (16.1)

A

-Change colonial or cellular morphology

209
Q

Lethal mutation (16.1)

A

Kill the cell

210
Q

Conditional mutation (16.1)

A

Expressed only under certain conditions

—Ex: High temperature

211
Q

Tomich et al 2004

A

-Showed a bacterial cell with pili vs. a pili mutant which contained no pili

212
Q

Hirota et al (1968)

A
  • Showed a rod-shaped E. coli (30 degrees C) vs. a mutant filamentous E. coli (42 degrees C)
  • Found the existance of ftsZ
213
Q

Spontaneous mutation (16.1)

A
  • Absence of added agents
  • Errors in DNA replication
    i) Transitions
    ii) Translations
214
Q

Transitional Mutation (16.1)

A
  • Type of spontaneous mutation
  • Changes a purine –> purine OR Pyrimidine –> pyrimidine
  • Ex: A–>G
215
Q

Translational Mutation (16.1)

A
  • Type of spontaneous mutation
  • Changes a purine –> pyrimidine or vice versa
  • Ex: A–>T OR C–>A
216
Q

Rarity of DNA Replication Errors (16.1)

A
  • DNA polymerase works at a rate of 1000 base pairs / second
  • Only makes a mistake 1 / billion base pairs
  • –Has a proofreading activity
217
Q

Induced Mutation (16.1)

A
  • Occurs after mutagen exposure

- –Chemical or physical agents

218
Q

How does UV Light cause a Mutation? (16.1)

A
  • Generates thymine dimers
  • Fig. 16.5
  • Weak covalent bond between two adjacent thymines
  • Causes the DNA polymerase to not realize that there are two thymines
219
Q

Base Analogs (16.1)

A
  • A type of induced mutation
  • Resemble bases & cause mispairing
  • Ex: 5-bromouracil
  • –It is a T analog, but it base-pairs with G
220
Q

Intercalating Agents (16.1)

A
  • A type of induced mutation

- Ex: Ethidium bromide

221
Q

Missense Mutation (16.1)

A
  • Single base substitution
  • Changes codon for one amino acid for a codon into another
  • May not affect the expression of the nucleotide (because the genetic code is redundant)
222
Q

Nonsense Mutation (16.1)

A

-Converts a sense codon into a stop codon

223
Q

Frameshift Mutation (16.1)

A

-Insertion or deletion of one or two base pairs in the coding region of a gene

224
Q

Auxotrophs (16.2)

A
  • Have mutations in biosynthetic pathways
  • Can’t make the product of that pathway
  • Require that product to be in the media
  • Ex: Lysine auxotroph - lys-
  • –Bacterial cell that cannot make the amino acid lysine
225
Q

Replica Plating (16.2)

A
  • Fig. 16.6
  • Use a piece of sterile velvet to stamp a grown plate and then press that onto a changed media to determine if any colonies have a mutation that doesn’t allow them to grow on this new media (usually a chemical component is taken out of the altered media)
226
Q

Light Repair (16.3)

A
  • Also called Photoreactivation
  • Light-activated photolyase (enzyme)
  • Binds to and cuts the bond holding together thymine dimers
  • Fig. 16.5
227
Q

Dark Repair (16.3)

A
  • Also called Nucleotide Excision Repair
  • Fig. 16.9
  • UvrABC endonuclease removes a section of damaged nucleotides (generally a thymine dimer)
  • DNA polymerase I fills in the gap
  • Ligase joins the segment back to the rest of the DNA
228
Q

Ames Test (16.2)

A
  • Method of identifying mutagenic substances
  • Uses bacteria as guinea pigs instead of using actual guinea pigs
  • Uses Salmonella mutant that cannot grow on media lacking histadine b/c it lacks the hisG gene
  • If, when grown on a plate with the suspected mutagen, a reversion mutation occurs to allow the Salmonella to grow on a plate without histadine, then the substance is a mutagen
  • In essence, if a substance can induce a reversion mutation, then it is a mutagen

MICB 3301 (14 decks)

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