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MT 2 Flashcards

1
Q

What are macronutrients?

A

These are nutrients that the microbe requires in large amounts

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2
Q

What are micronutrients?

A

These are nutrients that the microbe requirs in smaller amounts

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3
Q

How much of a cell is H2O?

A

75%

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4
Q

How much of the cell is dry weight?

A

96%

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5
Q

How much of the cell are trace elements?

A

3.7%

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6
Q

How much of the dry weight is DNA and RNA?

A

96%

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7
Q

What are heterotrophs?

A

These are organisms that need to consume organic molecules to extract their source of carbon

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8
Q

What are autotrophs?

A

These are organisms that use CO2 as a carbon source and synthesize themselves

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9
Q

What do microbes need P for?

A

DNA
Phospholipids

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10
Q

What do microbes need Mg for?

A

Stabalize the ribosome

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11
Q

What do microbes need Ca/Na for?

A

Anti-porters

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12
Q

What are growth factors?

A

They differ from metals these are organic micronutirents that are necessary for growth such as vitamins

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13
Q

What is defined media?

A

Media where the exact composition is known

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14
Q

What is complex media?

A

Media where the exact breakdown is not known

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15
Q

What is differential media?

A

This is when the media contains pigments that are impacted by the metabolic reaction during growth

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16
Q

What is a pure culture?

A

A culture of only 1 type of microorganism

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17
Q

What is microscopy counting?

A

This is when the total counts of the microbes can be determined visually there is a grid that that divides the sample into a large square (25 of them) each one consists of 16 small squares

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18
Q

In microscopy what is the staining for?

A

To differentiate dead and living cells

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19
Q

What are the disadvantages?

A
  • Motile cells die
  • Debris can cloud the counting
  • Not effective
  • Prone to error
  • Small cells are hard to see
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20
Q

What is a viable cell?

A

This is a cell that is alive and grows

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21
Q

Why is culture media used to distinguish living and dead cells?

A

Some viable cells grow on lab culture which can help notice the living or dead cells compared to a microscope

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22
Q

How is a viable count performed?

A

When there colonies spread and counted on the plate

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23
Q

What are the 2 ways that plate counts can be performed?

A
  1. Spread plate
  2. Pour plate
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24
Q

What is the MAJOR viable cell assumption?

A

That each colony arose from a single cell

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25
Q

What is the spread plate method?

A

When less than <0.1mL sample of the diluted culture is spread over an agar surface

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26
Q

What is the pour plate method?

A

Add the sample to an empty sterile plate then pour the agar over top

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27
Q

How do you choose the plate for determining the viable count?

A
  • Too many colonies can lead to error in the counting since some can fuse
  • Too few colonies can lead to results that are not statistically significant
  • Pick a plate that has between 30-300 colonies
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28
Q

Why do we use CFU and not cell number?

A

CFU helps us account for clumps containing more than 1 viable cell

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29
Q

What has to be done before the viable plate count?

A

A serial dilution 1:9 with 1 part culture and 9 parts solvent

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30
Q

What are the advantages of viable plate counts?

A
  • Can tell us about pathogen growth by selectivity
  • Effective and efficient
  • Highly sensitive
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31
Q

What is the disadvantage of viable plate count VS microscopy?

A

Microscopy lets you count a large number of cells at once and the results of the viable plate count are less reliable

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32
Q

What is the great plate anomaly?

A

There is large variation among plate counts

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33
Q

Why is the plate count lower than microscopic counts?

A

This is because of selectivity - the media that is used can inhibit certain cells from growing as a result it is an underestimate of the cells actually growing

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34
Q

Why is the recovery of cells near 100% for sewage bacteria?

A

The physiology is known so the media used can be specific and not prevent growth

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35
Q

What is turbidity?

A

When there is a liquid culture and there are a lot of cells present - although cells are small they are large enough to refract or scatter light that passes through the suspension and make the solution appear cloudy

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36
Q

How is turbidity measured?

A

Using a spectrophotometer which is a diffraction grating or prism and it measures the amount of refracted light

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37
Q

Why are turbidity measurements advantageous?

A

They are quick and you can count the cells without severely destroying or disrupting the bacteria

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38
Q

What are the cell types that lead to turbidity?

A

Some cells are planktonic but some can produce biofilms

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39
Q

What is growth the result of?

A

Cell division

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40
Q

What is binary fission?

A

This is a cell division process where a single cell divides by forming a partition called a septum equal amounts of genetic material is divided into the cells as a result the 2 daugter cells are identical

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41
Q

What is the generation time?

A

The time it takes for the cell to double

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42
Q

What is a batch culture?

A

This is a sample that exists in a finite amount of nutrient media as a result it is in a closed system and growth can’t occur forever

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43
Q

What growth curve do batch cultures exhibit?

A

Microbial growth curve

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44
Q

What is the lag phase?

A

This is a phase where the cells are slowly growing if that because they are exposed to new media for growth and not only can some of these cells be in a dormant state it can take time to produce enzymes

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45
Q

What is the relationship between media and lag phase length?

A

If the media is very different the phase will be longer the more similar the shorter it will be

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46
Q

What is the exponential phase?

A

It is the growth phase where the cells double at regular intervals

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47
Q

What is the stationary phase?

A

There is no net increase or decrease in the population size because the nutrients are being used to the maximum so the amount dying and growing are equal

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48
Q

Why does the stationary phase occur?

A
  1. Nutrient depletion
  2. Waste accumulation
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49
Q

What is the decline phase?

A

The population is decreasing due to cell death

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50
Q

What is cryptic growth?

A

The few bacteria that canablize the nutrients and dying cells to grow

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51
Q

What is the specific growth rate?

A

This is the rate at which the population grows at any instant

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52
Q

What is the different between specific growth rate and generation time?

A

Specific growth rate has the units (h-1)

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53
Q

What is the method of developing a continuous culture?

A

A chemostat

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54
Q

What is a chemostat?

A

A chemostat is a continuous culture it is an open system where known volumes of new sterile media is added but at the same time equal volumes of spent media is being washed out at the same rate

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55
Q

What is spent media?

A

Old media that contains waste and cells

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56
Q

What is the dilution rate?

A

The rate at which the supply of the media is defined

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57
Q

What is the flow rate?

A

The volume per unit time

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58
Q

What does the dilution rate control?

A

The specific growth rate

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59
Q

How does the dilution rate control the specific growth rate?

A

As new media is put in the cells use up all of the nutrients so they grow however the cells are also being washed out so eventually at the maximum growth rate the amount of nutrients exceeds maximum growth and the cells can’t keep up because they are all washed out

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60
Q

What is the steady state?

A

This is the equilibirium phase where the cell grows at the same rate they are removed by the outflow from the system k = D

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61
Q

What happens at the steady state?

A

The cells compete for limiting nutrients

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62
Q

What is the washout effect?

A

Where at too high of a dilution rate the organism is washed out

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63
Q

Does the dilution rate effect the growth yield (biomass)?

A

No

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64
Q

What is the growth yield?

A

These are the number of cells or biomass

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65
Q

How does the concentration effect the growth yield?

A

When the nutrients being added is of a higher nutrient concentration this increases the growth yield but does not change the specific growth rate

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66
Q

Why is the specific growth rate not impacted by the change in nutrient concentration?

A

The cells use up all of the nutrients therefore it will not change the rate at which the cells are growing the only thing that will change that is the dilution rate which is the rate at which new media is added

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67
Q

What is enrichment culture?

A

This is culture that is selective for some bacteria but counterselective for others

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68
Q

What is the next step from positive enrichment?

A

Having the microorganism on a pure culture

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69
Q

What is the agar dilution tube method?

A

Purifying bacter through repeated dilutions of cell suspended in agar

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70
Q

What is the roll tube method?

A

A serial dilution process where tubes of agar are used and on the inner surface it is then streaked and anaerobic microbes are extracted

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71
Q

What is the most-probable-number (MPN) technique?

A

Serial dilutions are used to estimate viable cell numbers

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72
Q

What were the first genomes to be sequenced?

A

The genomes of small viruses

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73
Q

What can gene sequencing tell us?

A
  • It can communicate how prokaryotes adapt to extreme conditions and make specific enzymes/proteins
  • Horizontal gene transfer
  • Determining medical mysteries
  • Determining which phyla the microbes belong to
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74
Q

What is sequencing?

A

The order of subunits that make macromolecules - for DNA the order and alignment of the nucleotides that make up DNA

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75
Q

What step follows sequencing and assembly?

A

Gene annotation

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76
Q

What is gene annotation?

A

This is the conversion of raw sequence data into lists of genes and other functional sequences present in the genome and identifying genes or functional regions that are usually done with bioinformatics

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77
Q

What is bioinfomatics?

A

Using computer analysis to store and analyze sequences and structures of the nucleic acids and proteins

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78
Q

Which step as the “bottleneck” for the genome sequencing process?

A

Gene annotation - genes are being sequenced faster than they are being analyzed

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79
Q

What would you need for Sanger sequencing?

A
  • Fluorescently labelled ddNTPs for each nitrogenous base (A, T, C, G)
  • dNTPs
  • Template DNA
  • PCR
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80
Q

What are the steps for Sanger sequencing?

A
  1. PCR amplify the SS template DNA using vectors
  2. Add a mixture of ddNTPs + dNTPs to make a new DNA strand
  3. Use capillary ectrophoresis of fragments of fluorescent labels
  4. Automated sequencer reads outputs
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81
Q

Why do ddNTPs truncate the DNA?

A

It lack a 3’-OH and has 3’-H instead so elongation can’t occur and nothing can be added to the end

82
Q

What is pyrosequencing?

A

It is a second generation sequencing technique that uses ATP catabolism and luciferase enzymes

83
Q

How does pyrosequencing take place?

A
  1. When a new dNTP is added a PPi is released from the DNA
  2. Sulfurylase converts AMP + PPi -> ATP
  3. Luciferase consumes the ATP and emits light
  4. Light flash is detected by the sensor
  5. Apyrase cleaves the unused dNTP
84
Q

What are some limitations of Sanger sequencing?

A
  • Not time efficient
  • Only 800bp/reaction can be sequenced
  • Limited to primers that bind to known sequences
85
Q

What is the process of assembly?

A
  1. The sequence reads are organized based on overlap
  2. The overlap forms contig sequences
  3. When all of the contigs are organized it forms a scaffold
86
Q

What is a sequence read?

A

A segment of DNA that has a known sequence

87
Q

What is a contig?

A

A set of sequence reads that are organized in order based on overlapping overhangs

88
Q

What is a scaffold?

A

The ordered set of contigs

89
Q

What are ORFs?

A

These are open reading frames which determine the start and end of a gene

90
Q

What does the computer determine for an ORF to be counted in a genome?

A
  1. Start codon
  2. Stop codon
  3. Ribosome binding site
  4. Distance (in codons) between the start and stop codons
91
Q

How can we determine if an ORF is functional?

A

If the ORF DNA sequence is present in the sequence of other organisms and it is conserved because proteins with similar functions share sequences and features

92
Q

Can 100% of the ORFs be detected?

A

No, currently only 70% are detected while the other 30% encode hypothetical proteins or it is because there are non-coding RNA ex., tRNA and rRNA which don’t have start codons just many stop codons

93
Q

What is a hypothetical protein?

A

A protein where the function is unknown because the amino acid sequence is unique and does not have any homologs with similar sequences to determine its function

94
Q

What is comparative genomics?

A

Comparing the genome between species or organisms

95
Q

Is there a correlation between genome size and ORF?

A

Yes, for bacteria and archaea not eukaryotes which have a large genome that is mostly consisting of introns

96
Q

How many genes are necessary for the survival of free living bacteria?

A

~1300

97
Q

Who do the smallest cellular genome belong to?

A

Parasites or endosymbionts

98
Q

What are endosymbionts?

A

These are cells that host other cells the host provides protection for the symbiont and the symbiont provides nutrients and resources that the host can’t make on its own

99
Q

What happens as the genome gets smaller?

A

The percentage of genes that encode for translational processes increases

100
Q

What happens as the genome gets larger?

A

The percentage of genes that encode for transcriptional regulation and signal transduction increases

101
Q

What is metagenomics?

A

This is a pool of DNA from the environmental sample of a microbial community with organisms that have not been isolated or identified

102
Q

Why is metagenomics used?

A

There are environments that are species rich and abundant so it is difficult to isolate those organisms and sequence their genome

103
Q

What did studies from natural habitats find?

A

That genes were mostly recovered from viruses

104
Q

What did studies from ocean environements find?

A

Most DNA is not present in the living cells but rather 50-60% is present in the sediment due to dead organisms

105
Q

What is a transcriptome?

A

This is the total RNA collection of an organism

106
Q

What is a microarray or gene chip?

A

This is a solid surface where oligonucleotides are fixed to the surface then fluorescently labelled DNA is flooded over the chip and hybridization levels are detected

107
Q

What are oligonucleotides?

A

Known sequences of DNA and it is also known as probes

108
Q

Can a microarray occur with RNA?

A

Yes
1. PCR amplify the RNA
2. Reverse transcribe to cDNA
3. Hybridize to the probes on the chip

109
Q

Where are the largest carbon reservoirs?

A

Rock, sediment, and the earth’s crust

110
Q

What is humus?

A

A layer of soil that is nutrient rick from dead organisms and decomposition

111
Q

Which reaction takes CO2 from the atmosphere?

A

Photosynthesis

112
Q

\Which reaction produces CO2 to the atmosphere?

A

Respiration

113
Q

What is the ratio that needs to be maintained in order for organic matter to accumulate?

A

Photosynthesis > Respiration

114
Q

What is the single most important contributor of CO2 to the atmosphere?

A

Decomposition of dead matter

115
Q

Where can phototrophic organisms survive?

A

Where there is light

116
Q

What are the 2 groups of phototrophs?

A
  1. Plants
  2. Microbes
117
Q

Where do plants inhabit?

A

Terrestrial environments

118
Q

Where do microbes inhabit?

A

Aquatic environments

119
Q

What happens when CO2 is reduced with H2?

A

CH4 is made

120
Q

What happens when acetone is split?

A

CO2 and CH4 is made

121
Q

What do high levels of carbon stimulate?

A

N2 fixation

122
Q

What do low levels of carbon inhibit?

A

Denitrification

123
Q

What do high levels of NO3- stimulate?

A

Carbon fixation
Nitrification
Denitrification

124
Q

What do high levels of NO3- inhibit?

A

N2 fixation

125
Q

What is nitrification?

A

NH4+ -> NO3-

126
Q

What is denitrification?

A

NO2- -> N2

127
Q

What is N2 fixation?

A

N2 + 8H -> 2NH3 +H2

128
Q

What is ammonification?

A

NOn -> NH4+

129
Q

What is anommax?

A

NH4+ + NO2- -> N2 + 2H2O

130
Q

What is the harm of denitrification?

A

In agriculture fertilizers contain NO3- which the plants need to uptake so NO3- is lost

131
Q

What is the benefit of denitrification?

A

NO3- is converted to a volatile state N2 so less algal bloom water treatment plants

132
Q

What are the greenhouse gases that are made in the N cycle?

A

N2O, NO

133
Q

What form of iron is the most prevalent?

A

Ferric = Fe3+
Ferrous = Fe2+

134
Q

What is iron used for?

A

Fe3+ final e- acceptor in anaerobic respiration

135
Q

What is a rhizobia?

A

A microbe that can freely grow in soil or infect legumes and establish a symbiotic relationship

136
Q

What is endosymbiosis?

A

Where 2 organisms form a relationship of dependency since they are unable to form nutrients

137
Q

What do you need to have N2 fixation in root nodules?

A

Rhizobia

138
Q

Why is low O2 maintained?

A

High O2 inhibits nitrogenase

139
Q

What is nitrogenase?

A

This is the key N2 fixing enzyme in the bacteroid that fixes N2

140
Q

How is low O2 maintained?

A

Leghemoglobin - has an Fe group that binds to O2

141
Q

What do the NodABC genes in the rhizobia do?

A

It encodes for Nod factors

142
Q

What is the role of a Nod factor?

A
  1. Triggers cell division
  2. Root hairs are curled
  3. Nodule formation and specificity
143
Q

What are the bacteria that are hosted by root nodules that have lipochitin oligosaccharides that are bound by substituents>

A

N2 fixing bacteroides

144
Q

How does nodule formation occur?

A

When the Nod factor binds to the cell surface receptor NRF1 and NRF2

145
Q

What is NodABC?

A

A universal gene that encodes for the backbone of the Nod factor

146
Q

What is the NodD gene?

A

Controls transcription and modifies the Nod backbone encoded by NodABC

147
Q

What inhibits Nod factor synthesis?

A

Flavenoid - biovar violate

148
Q

What inducess Nod factor synthesis?

A

Flavenoid

149
Q

What is the biochemical process of N2 fixing in root nodules?

A
  1. CAC intermediates transferred across the symbiosome
  2. Oxidized to pyruvate
  3. e- Pass through ETC to O2 and generates a PMF
  4. ATP is made
  5. ATP + e- (pyruvate) +N2 -> NH3
  6. NH3 is brought out of the bacteroid to make Glu and Asn
150
Q

What is a virus?

A

This is an organism that can’t exist outside the host cells

151
Q

What is a virion?

A

This is a virus that is on the extracellular side of the cell

152
Q

What is the form of the virus when it is in the cell?

A

Replicating genome

153
Q

What is a capsid?

A

It is a protein protective layer that the virus has

154
Q

What makes up the capsid?

A

Capsomeres

155
Q

What is a nucleocapsid?

A

When the capsid contains the nucleic acid

156
Q

What is the envelope?

A

This is a protective phospholipid coat around the capsid

157
Q

Where do the spike proteins bind?

A

To the envelope and then attach to the host cell

158
Q

What are large viruses called?

A

Pandoravirus

159
Q

What are small viruses called?

A

Poliovirus

160
Q

What are the 3 shapes of head-tail phages?

A
  1. Icosahedral
  2. Non-symmetrical
  3. Helical tail
161
Q

What are the stages of a virus undergoing the lytic pathway?

A
  1. Attachment
  2. Penetration
  3. Synthesis
  4. Assembly
  5. Release
162
Q

What is the 1 step growth curve?

A

The process of making virions where the number of virion does not increase until the burst

163
Q

Why is there an initial decline in viruses?

A

The viruses are binding to host cells and can bind to fewer cells

164
Q

What happens during the eclipse phase?

A

The viral genome and proteins are made and replicated

165
Q

What happens during the maturation phase?

A

Packaging of genomes in capsids

166
Q

What do the eclipse+maturation phase make?

A

Latent phase

167
Q

What happens at the end of maturation?

A

The cells burst with new virion

168
Q

How does attachment happen?

A

When the phage binds to projections from the bacteria such as the LPS of E.coli for T4

169
Q

How does penetration occur?

A
  1. Tail fibers are used to travel to the cell
  2. The tail fibers retract so the tail pins can bind to the outer membrane
  3. The lysozyme makes a hole in the peptidoglycan
  4. The tail tube penetrates through
  5. Genetic material is pushed into the host cytosol
170
Q

What do early proteins make?

A

Enzymes and proteins for replication or proteins that modify the host material

171
Q

What do late and middle proteins make?

A

Proteins that prepare for release

172
Q

What pushes the DNA into the heads?

A

ATP

173
Q

What is a virulent virus ie., T4?

A

A virus that lysis the cell

174
Q

What is a temperate virus?

A

Develops a longterm relationship with the virus

175
Q

What is a prophage?

A

The integrating viral DNA

176
Q

What is a lysogen?

A

A host cell with the viral DNA integrated

177
Q

What are the differences between phages and animal infecting viruses?

A
  1. The entire virion enters not just the nucleic acid
  2. Virion go to the nucleus to replicate (often)
  3. Eukaryotic cells act as viroplasms
178
Q

What is the difference between animal and plant infecting viruses?

A
  1. The virion are naked
  2. There is a broader range of host cells
  3. Virion only enter when the plant cell is injured ie., cuts or stepped on
179
Q

What is the similarity between animal and plant infecting viruses?

A

Both contain RNA genomes

180
Q

What does the Cro gene do?

A

Cro inhibits C11 (which induces C1 activity) so the C1 is inactive and the cell will undergo the lytic pathway due to Cro accumulation

181
Q

What does the C1 gene do?

A

C1 inhibts Cro so in the accumulation of C1 the cell will undergo the lysogen pathway

182
Q

What is lamda?

A

This is a phage that infects E.coli and has dsDNA like T4 but can undergo the lysogen pathway

183
Q

What are the steps to the lysogen path?

A
  1. Lambda DNA linearizes
  2. There are “cohesive ends” at the ends of the base sequence
  3. Lambda DNA enters the host cell and base pairs to form Cos sites and circularizes
  4. Endonuclease makes staggered cut sites in the DNA
  5. Ligase seals the nicks
  6. Rolling circle replication
184
Q

What is an anti-sigma factor?

A

This is what the T4 makes to stop the host from producing its material and transition to producing the viral material

185
Q

What is a concatamer?

A

Long combined DNA units

186
Q

Which type of bacteria is most abundant in the GI?

A

Gram (-)

187
Q

Which type of bacteria is most abundant on skin?

A

Gram (+)

188
Q

Which type of bacteria are bacteriodetes?

A

Gram (-)

189
Q

Which type of bacteria are firmicutes?

A

Gram (+)

190
Q

What is the difference to the baby from a vaginal birth VS a c-section?

A

The microbial community is different

191
Q

What are germ free mice?

A

Sterile mice

192
Q

What are methanogens?

A

These are components of lean mice that consume H2 and convert the fermentable substrates to volatile fatty acids (VFAs)

193
Q

What is the benefit of VAFs?

A

The fatty acids are absorbed

194
Q

What happens to methanogens in obese mice?

A

They lack methanogens so the substrates are not converted to VFAs

195
Q

What is the firmicutes to bacteriodetes ratio in obese mice?

A

More firmicutes

196
Q

What is the firmicutes to bacteriodetes ratio in normal mice?

A

More bacteriodetes growth is supported by the VFAs

197
Q

What is the form of treatment for patients with C.defficile?

A

Transplant of fecal matter

198
Q

What are probiotics?

A

Foods that integrate live bacteria

199
Q

What are prebiotics?

A

Foods that support microbial growth

200
Q

What are synbiotics?

A

Mix of probiotics and prebiotics

343 (6 decks)

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