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BIO 2EE3 > Exam (after Midterm 1 Content) > Flashcards

Exam (after Midterm 1 Content) Flashcards

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1
Q

What was the purpose of the Griffith Experiment and how was it performed

A

Evidence that DNA may be the hereditary material
When killed smooth and live rough streptococcus pneumoniae were separately added to separate mice, they both lived
Live smooth killed the mouse
When killed smooth and live rough we’re added together, the mouse died
Rough cells converted to smooth

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2
Q

Avery, MacLeod, and McCarty experiment: steps and purpose

A

Purpose: is DNA, RNA, or protein the causative agent of transformation
Heat killed smooth strain was treated with enzymes that killed proteins, DNA or RNA, and then were incubated with living rough cells
Rough cells do not grow on agar
All plates showed growth except one treated with DNase
DNA is the transforming principle

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3
Q

Packaging of DNA in the 3 domains

A

Bacteria: singular circular chromosome, supercooled
Archaea: singular circular chromosome, histones
Eukarya: multiple linear chromosomes, histones

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4
Q

Replication initiation in E. coli

A

DnaA molecules interact with the oriC bp repeats forming a complex, DNA is unwound
DnaC delivers the DnaB helicase to the replication complex
Single stranded binding proteins present

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5
Q

Initiation of DNA replication in eukaryotes

A

Multiple origins of replication on each chromosome
Origin replication complex (orc) binds Automatically replicating sequence (ARS)
Proteins such as Cdt1, Cdc6 and MCM are recruited
DNA is unwound and SSB proteins keep strands apart

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6
Q

Replication elongation in bacteria

A

DNA polymerase III adds nucleotides to RNA primers that are synthesized by RNA primase
Continuous and discontinuous strands (leading and lagging)
Clamp keeps DNA polymerase III bound to DNA
RNA primers removed and replaced with DNA by DNA polymerase I which has 5’ to 3’ exonuclease activity
Sealed by DNA ligase

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7
Q

Clamp processivity factor

A

Found in all 3 domains

Beta clamp in E. coli

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8
Q

Circular Replication termination

A

Tus proteins interact with DnaB to open DNA then they bind ter sites stopping elongation
Topoisomerase is recruiter
Chromosomes disentangled

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9
Q

Linear replication termination

A

RNA primer removed, produces 5’ end that cannot be extended by DNAP
telomerase binds and extends the 3’ end using an RNA template

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10
Q

Meselson and Stahl

A

Add N15 labelled cells to N14 medium and grow for 4 gen
Results consistent with semi conservative replication
Generation 2 had one N15 and one N14 strand

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11
Q

Approximate length of mRNA

A

500-10,000 nt

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12
Q

Typical gene size of bacteria

A

1 kb

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13
Q

mRNA can be _______________, meaning it encodes several proteins

A

Polycistronic

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14
Q

Do bacterial genes contain introns

A

No

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15
Q

Length of tRNA

A

75-100 nt

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16
Q

tRNA orientation

A

3’ to 5’

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17
Q

rRNA size

A

1500 to 1900 nt for small subunit

2900 to 4700 nt for large subunit

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18
Q

Eukaryotic ribosome subunit size

A

Small 40S
Large 60S
Total 80S

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19
Q

Bacteria ribosome subunit size

A

Small 30S
Large 50S
Total 70S

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20
Q

Small subunit rRNA in eukaryotes

A

18S

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21
Q

Small subunit rRNA in prokaryotes

A

16S

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22
Q

Which has more rRNA? Pro or eukaryotes

A

Eukaryotes

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23
Q

More proteins or rRNA in the ribosome?

A

Proteins

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24
Q

————- factors bind bacterial promoters to allow RNAP to recognize them

A

Sigma

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25
Q

Positions of consensus regions in E. coli

A

-10 and -35

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26
Q

What is the main sigma factor in E. coli

A

RpoD

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27
Q

Transcription initiation elements in eukaryotes bound by transcription factors

A

Octamer box
CAAT box
GC box
TATA box (-20)

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28
Q

Different sigma factors in bacteria can_______________________

A

Direct RNAP to different sets of genes that are co-regulated

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29
Q

How many RNA polymerase in bacteria

A

1

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30
Q

How many RNA polymerase in eukaryotes

A

3

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31
Q

This protein interacts with the TATA box

A

TATA Binding protein (TBP)

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32
Q

What is TFIIB

A

A transcription factor in eukaryotes which binds the promoter

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33
Q

Transcription initiation in archaea is similar to _______ in regard to transcription factors and similar to ______ in regard to RNAP

A

Eukaryotes , bacteria

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34
Q

Transcription termination in bacteria can be done by the _____ protein or through ________

A

Rho

Rho-independent termination

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35
Q

Rho independent termination involves a _______ rich in _________ followed by a ____ rich sequence

A

A hairpin structure
GC
Uracil

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36
Q

What is the function of the uracil rich sequence in Rho independent termination

A

Has less H bonds so is easier to separate

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37
Q

3 pots transcriptional modifications in eukaryotes

A

5’ 7-methyl guanosine cap
3’ polyA tail
Intron splicing

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38
Q

Which enzyme adds amino acids to tRNA

A

aminoacyl tRNA synthetase

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39
Q

Which nucleotide is responsible for the wobble effect

A

3rd in codon

1st in anticodon

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40
Q

Which amino acid charges tRNA that initiates translation of AUG in bacteria

A

N-formyl methionine

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41
Q

Amino acids are added to the __ end of the tRNA

A

3’

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42
Q

The shine delgarno sequence is

A

A sequence complementary to the 16S sequence in bacteria

Interacts with 16S in ribosome to initiate translation

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43
Q

In eukaryotes mRNA is bound by ___________ and one binds the ________

A

Several polypeptides

5’ cap

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44
Q

Eukaryal mRNA is _______

A

Monocistronic

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45
Q

Charged tRNAs enter the _____ site

A

A

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46
Q

Termination of translation

A

Release factors when stop codon is reached

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47
Q

_______ help proteins fold

A

Chaperones

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48
Q

Protein modifications in eukaryotes include

A

Phosphorylation
Acetylation
Methylation
Glycosylation

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49
Q

______________ direct proteins to appropriate locations

A

Signal peptides

Short AA sequences at N terminus

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50
Q

How many genes in human cells that encode proteins

A

Approx 22,000

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51
Q

When does regulation of gene expression occur

A

During transcription
Translation
Post translation

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52
Q

Composition of lactose

A

Galactose and glucose

Linked by beta 1,4

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53
Q

Function of beta galactosidase

A

Cleaves beta 1,4 linkage in lactose

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54
Q

Substrate for the detection of beta galactosidase

A

ONPG

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55
Q

Lactose permease function

A

Transports lactose into cell across cell membrane

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56
Q

When e.coli are grown with glucose and lactose, which is consumed first

A

Glucose

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57
Q

Lac Operon not expressed until

A

All glucose is used up

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58
Q

LacI function

A

Codes for lacI repressor which binds the operator inhibiting transcription

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59
Q

CAP site function

A

Activator binding site

DNA site bound by activator

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60
Q

Promoter function in lac operon

A

Bound by RNAP to direct initiation of transcription

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61
Q

LacO function

A

Operator

Bound by repressor

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62
Q

Effector function lac Operon

A

Binds activator or repressor proteins to modify gene activity

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63
Q

Inducer function

A

Increases transcription levels by enabling activator or disabling repressor

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64
Q

Corepressor

A

Decreases transcription by binding repressor

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65
Q

LacZ codes for

A

Beta galactosidase

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66
Q

LacY codes for

A

Lactose permease

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67
Q

When is lacI transcribed

A

Always

At a low basal level

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68
Q

What recognizes the allosteric site on the laci repressor

A

Allolactose

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69
Q

The trp operon encodes for

A

Proteins in the tryptophan synthesis pathway

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70
Q

When trp is not present

A

It cannot bind the trp repressor, so it cannot bind the operator
Transcription continues

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71
Q

When trp is present

A

It binds the repressor so it can bind the operon

No transcription

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72
Q

When glucose levels are high and cAMP levels are low

A

cAMP cannot bind the CRP activator

RNAP has a low affinity for the promoter and will not bind

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73
Q

When glucose levels are low and cAMP levels are high

A

cAMP bind CRP

The CRP-cAMP complex binds the activator binding site increasing RNAP affinity for the promoter

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74
Q

Sigma 70 (RpoD) function

A

Housekeeping

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75
Q

Sigma 32 (RpoH) function

A

Heat shock

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76
Q

Sigma 54 (RpoN) function

A

Nitrogen starvation

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77
Q

Sigma-38 (RpoS) function

A

Stress

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78
Q

Purpose of SOS response in bacteria

A

Allows cells to recognize and respond to serious DNA damage

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79
Q

SOS response experiment with E. coli

A

Bacteria exposed to UV light and infected with damaged phages repaired these phage but they had high rates of mutation (more phage, more mutations)
Bacteria that were not exposed to UV and that were infected with damaged phages could not repair them as efficiently and lower mutation rates (few phage, few mutations)

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80
Q

lexA function

A

DNA binding transcriptional repressor of the SOS genes

Binds the operator and shuts of transcription

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81
Q

recA function

A

Recombination and regulation of the SOS response, binds ssDNA
Becomes a protease which cleaves lexA so the genes can be expressed

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82
Q

SOS regulon no DNA damage

A

LexA keeps SOS regulon genes repressed

RecA is inactive

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83
Q

SOS regulon DNA damage

A

RecA cleaves the LexA repressor

SOS genes expressed

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84
Q

Quorum sensing definition

A

Chemical signalling system that controls gene expression

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85
Q

What is the function of autoinducers

A

Cells release them into the environment and as the population density increases in an area the concentration of autoinducer does too
Detecting changes in autoinducer levels causes regulation of gene expression

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86
Q

The lux quorum sensing system is found in this bacteria

A

Vibrio fischeri

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87
Q

Where do Vibrio fischeri live in

A

Hawaiian bobtail squid

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88
Q

When do Vibrio fischeri emit light and what enzyme do they use

A

When in the light organ of the squid

Luciferase

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89
Q

What is the autoinducer made by Vibrio fischeri

A

AHL

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90
Q

This activator interacts with AHL when it reaches a high concentration

A

LuxR

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91
Q

The AHL LuxR complex binds the _________ for activation

A

Lux box

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92
Q

At high AHL concentration

A

AHL and LuxR interact and transcription is activated transcribing luxA and luxB which are needed for luciferase production

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93
Q

At low AHL levels

A

AHL and LuxR do not interact
Lux box is not bound for activation of transcription
Light and luciferase is not produced

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94
Q

Mechanisms controlled by quorum sensing

A

Motility
Conjugation
Biofilm formation
Pathogenesis

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95
Q

Components of the two component regulatory system

A

A sensor kinase and a response regulator

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96
Q

Sensor kinase function

A

Often a histidine protein kinase (HPK)
Located in plasma membrane
Detect environmental stimulus

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97
Q

Response regulator function

A

Inside the cytoplasm

Regulate transcription

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98
Q

Two component regulatory system in Agrobacterium tumefaciens

A

Genes expressed under similar conditions to plant wound
virA is an HPK protein which interacts with sugars and phenolic compounds at low pH
virG is an activator RR protein for other vir genes

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99
Q

Regulatory RNAs

A

Small non coding RNA that control gene expression at transcriptional or translational levels

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100
Q

General attenuation mechanism

A

If the ribosome quickly follows RNAP, a terminator hairpin will form in the leader sequence and RNAP detaches
Stalling out of the ribosome on the leader sequence allows transcription to continue

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101
Q

Can attenuation occur in eukaryotes? Why or why not?

A

No, because transcription and translation occur separately

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102
Q

High levels of tryptophan: attenuation

A

Terminator loop forms (regions 3 and 4) and stops transcription, tryptophan not made
Ribosome stops at stop codon

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103
Q

Low levels of tryptophan: attenuation

A

Terminator loops does not form and transcription continues
Tryptophan made
Ribosome stops at trp codons
Region 2 anneals to 3

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104
Q

Where in bacterial mRNA are riboswitches found

A

The 5’ UTR

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105
Q

Riboswitch function

A

Acts as a binding site for ligands which influence downstream structure regulating transcription and or translation
Transcriptional: terminator loop
Translational: ribosome binding site

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106
Q

Intrinsic factors that effect food spoilage

A 
Water activity 
Osmolarity
Nutrient content 
pH
Antimicrobial constituents
Biological structures
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107
Q

Extrinsic factors that effect food spoilage

A

Temperature
Humidity
Gases

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108
Q

Adding solutes to water ———- it’s water activity

A

Decreases

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109
Q

Bacterial pathogens cannot grow at a water activity _______ and yeasts and moulds ________

A

<0.86

<0.65

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110
Q

Reducing water activity by:

A 
Drying 
Adding solutes (sugar or salt)
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111
Q

Most microorganisms require a water activity greater than

A

0.99

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112
Q

Canning process

A

Heating food to 100 degrees for extended period under pressure

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113
Q

Pasteurization process

A

Heating liquids to 63 degrees Celsius for minimum 30 min

Kills 99% of organisms

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114
Q

Pickling process

A

Using acid (vinegar)

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115
Q

Modified atmosphere packaging

A

Vacuum seal

Change atmosphere to inhibit microbial respiration (oxygen depletion)

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116
Q

Chemical preservatives

A

Lower pH

Interfere with cellular respiration

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117
Q

Irradiation for food preservation

A

Ionizing radiation causes oxidative damage and toxic free radical production
UV radiation causes thymine dimers

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118
Q

Hurdle technology

A

Apply multiple constraints to more effectively preserve food

Ex temp, ph, aw, etc.

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119
Q

Clostridium botulinum

A

Gram positive
Obligate anaerobe
Produces botulism neurotoxin (most potent neurotoxin known)
Associated with improperly canned food

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120
Q

How to control botulism

A

Pickling, pH less than 4.6
Salt curing, aw less than 0.96
High oxygen
Temp less than 4.4 deg

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121
Q

What was the bacteria responsible for the Romaine lettuce infection outbreak?

A

E.coli O157:H7

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122
Q

What toxin was responsible for the Romain lettuce infection and what is its function

A

Shiga toxin

Inhibits protein synthesis in target cells

123
Q

How did E.coli O157:H7 acquire the shiga toxin gene

A

Horizontal gene transfer from a prophage

124
Q

Which bacteria was responsible for the listeria outbreak of 2008

A

Listeria monocytogenes

Gram positive firmicute

125
Q

Why can listeria monocytogenes evade control in human foodstuffs

A

Can grow at temperatures as low as 0 deg C
Can move within eukaryotic cells by polymerization of actin
Facultative anaerobe (can grow with or without oxygen)

126
Q

Which bacteria is one of the most common causes of food poisoning

A

Camplyobacter jejuni
Gram negative bacteria
Spiral shaped

127
Q

Which bacteria grows best in aerobic environments but can also grow anaerobically, and causes food poisoning

A

Staphylococcus aureus

128
Q

Lactic acid bacteria characteristics

A

Gram positive
Ferment glucose to lactic acid
Grow anaerobically but can grow with oxygen
Lack catalase (have alternative enzymes)

129
Q

Lactic acid bacteria must grow in:

A

Environment where sugars are present

Complex media that fulfills nutrition requirements

130
Q

Some LAB cause disease, most notably members of the genus ________

A

Streptococcus

131
Q

Why are LAB so important for food fermentation

A

Taste and texture

Inhibit food spoilage by producing lactic acid and growth inhibiting substances

132
Q

Preparation of yogurt involves:

A

Pasteurization, adding starter cultures, and fermentation

133
Q

What is the purpose of starter culture in food

A

Helps control fermentation

Produces acid lowering pH and preventing spoilage

134
Q

_________ is used in koji fermentation to produce products like soy sauce

A

Mold

Koji is the starter culture for various molds

135
Q

Kombucha starter culture

A

SCOBY

Starter culture of yeast and bacteria

136
Q

How to make mash for beer

A

Barley malt added to warm water, enzymes activated, and starch is broken down by amylase to maltose creating wort

137
Q

Boiling step of beer making

A

Boiling kills unwanted microbes

Hops are added to add flavour and act as an antibacterial

138
Q

Beer fermentation

A

Wort is cooled and yeast is added

Maltose is converted to ethanol and co2 which carbonates beer

139
Q

How is vinegar produced

A

Acetic acid bacteria metabolize ethanol to acetic acid

Ethanol sprayed on wood chips with a biofilm of bacteria

140
Q

Which bacteria are used to make vinegar

A

Gluconobacter and acetobacter

141
Q

Foodborne intoxication

A

Microbial toxins in food, symptoms appear quickly

142
Q

Foodborne infection

A

Contaminating microbes in food, delay in symptoms (after growth)

143
Q

Goals for treating wastewater sewage

A

Remove total organic carbon
Remove harmful organisms
Reduce inorganic compounds
Reduce persistent organic pollutants

144
Q

Wastewater treatment steps

A

Pre treatment: remove large objects
Primary treatment: remove sediments and grease
Secondary treatment: uses activated sludge (aerobic), microbes to break down organic compounds
Tertiary treatment: filtration of nitrogen and phosphates
Disinfection: chlorination, UV, ozonation

145
Q

Drinking water purification steps

A 
Screening
Flocculation
Sedimentation 
Sludge treatment 
Filtration 
Disinfection 
Storage
146
Q

The casein milk protein family contains ________ and _________ at pH 4.6

A

Phosphorous

Precipitates

147
Q

The serum whey proteins do not contain ________ and _________ at pH 4.6

A

Phosphorous

Does not Precipitate

148
Q

Which protein family provide a good source of calcium for milk consumers

A

Casein

149
Q

Carbon cycle in plants, algae and photosynthetic bacteria

A

CO2 to C6H12O6

150
Q

Carbon cycles in eukaryotes, bacteria and archaea

A

C6H12O6 to CO2

Decomposition

151
Q

Carbon cycle in methanogens

A

C6H12O6 to CH4

152
Q

Carbon cycle in methanotrophs

A

CH4 to C6H12O6

153
Q

The carbon cycle summary

A

Incorporation of carbon from the atmosphere into biomass and release of carbon into the atmosphere through decomposition of biomass
Photosynthesis and respiration

154
Q

Methanogenesis

A

Metabolism of organic matter or CO2 to methane under anaerobic conditions

155
Q

Methanogens rely on ______ to produce __________ for methanogenesis

A

Other organisms

Simple organic substrates

156
Q

Methanogens form __________ with other organisms

A

Syntrophic relationships

157
Q

What sources produce methane

A 
Termites 
Wetlands 
Landfills 
Rice cultivation 
Domestic animals
Fossil fuels 
Oceans
158
Q

Type I methanotrophs utilize the ____________ pathway

A

RuMP

159
Q

Type II methanotrophs utilize the _________ pathway

A

Serine

160
Q

Are methanotrophs aerobic or anaerobic

A

Can be both

161
Q

Which pathway do aerobic methanotrophs use

A

Either the RuMP or serine

162
Q

Which enzyme do aerobic methanotrophs use to oxidize methane

A

Methane monooxygenase MMO

163
Q

What process converts biologically inaccessible N2 to accessible NH3

A

Nitrogen fixation

164
Q

Nitrogen fixation is generally under ____ conditions but can be under _____

A

Aerobic

Anaerobic

165
Q

Ammonia is used to:

A

Make amino acids or by lithotrophs as energy

166
Q

Denitrification

A

Removes nitrate and converts it to nitrogen gas

167
Q

As nitrogen is converted from nitrate to ammonia, it’s oxidation state:

A

Decreases

168
Q

Which enzyme reduces N2 to ammonia

A

Nitrogenase

Very sensitive to oxygen

169
Q

Nitrification

A

Oxidation of NH3 to nitrite to nitrate

170
Q

Nitrifying bacteria are:

A

Chemolithoautotrophs

171
Q

Ammonia oxidizers harvest energy from oxidation of ammonia using

A

AMO and hydroxylamine oxidoreductase

172
Q

Nitrifiers _______ from the oxidation of nitrite to nitrate using ______

A 
Harvest electrons 
Nitrite reductase (NOR)
173
Q

Which process accounts for 50% of loss of nitrogen from marine environments

A

Denitrification

174
Q

Bacteria and archaea use ___ and ____ as terminal electron acceptors in anoxygenic environments

A

Nitrogen and sulfur compounds

175
Q

Chemical fertilization through the _____________ has nearly doubled flux of reactive nitrogen into the environment

A

Haber-Bosch

176
Q

Ecosystem

A

Interactions and exchange of materials between organisms and their environment

177
Q

Success of microbes in a niche depends on

A

Their ability to obtain nutrients and produce biomass

178
Q

Formation of a biofilm

A

Adhesion by a primary colonizer
Cells divide
Microcolony produces EPS
Introduction of secondary colonizers

179
Q

EPS/slime function in a biofilm

A

Protects biofilm

Forms water filled channels for transport of nutrients and wastes

180
Q

What percentage of microbes can be cultured in a laboratory

A

0.1%

181
Q

Enrichment cultures

A

Promote growth if desired microbes over undesired cells

182
Q

Winogradsky column

A

lake sediment in a cylinder
Carbon and sulfur added
Placed in sunlight
Creates layers of different microorganisms

183
Q

Direct sequencing

A

Extract DNA from environmental sample
PCR using universal primers for rRNA and sequencing
Compare to known databases

184
Q

Fluorescent in situ hybridization

A

Labeled oligonucleotide probes bind specific RNA or DNA in a mixed population of cells
Visualized under microscope

185
Q

Metagenome library

A

DNA from an environmental sample used to construct a genome library

186
Q

Primary producers

A

Capture light through photosynthesis

Inorganic carbon to organic carbon

187
Q

Consumers

A

Heterotrophs that ingest organic carbon molecules

188
Q

How much of the marine biomass is made up of microbes

A

Over 98%

189
Q

These microbes are often present in marine environments

A

Oligotrophs

Low levels of nutrients including N,P, Fe

190
Q

Nutrient influx effects

A

Farmland runoff adds N and P to the water
Phytoplankton proliferate
Heterotrophic microbes feed on phytoplankton and consume too much oxygen
Heterotrophs die due to low oxygen levels

191
Q

Coastal dead zones

A

Hypoxic

N and P stimulate growth of algae and Cyanobacteria and upon their death heterotrophic organisms use all of the oxygen

192
Q

How to enrich for nitrogen fixing bacteria

A

Medium without nitrogen containing organic material

Can use nitrogen gas from air to convert to usable molecules

193
Q

Photosynthetic microbes in the ocean produce how much of the atmospheres oxygen

A

1/3

194
Q

Surface photic zone

A

Penetrated by light
Populated by photosynthetic phytoplankton And Cyanobacteria
Non photosynthetic zooplankton
Pelagibacter (SAR11) present in very high quantities

195
Q

Pelagibacter

A

Small genome, energetically efficient

Highly specified for the environment, little junk DNA

196
Q

Dark mid water zone

A

Fed by organic matter produced in upper surface water

197
Q

Deep sea zone

A

Barophiles and pliezophiles which withstand high pressure

198
Q

Dilution to extinction method

A

Inoculate very dilute sea water into autoclaved sea water followed by incubation
25-30% of cells were SAR11 proteobacteria

199
Q

Proteorhodopsin

A

Light driven proton pump
Genes that encode for it are present in SAR11
Many sequences found in aquatic sample similar to proteorhodopsin

200
Q

What nutrients are often limiting in the ocean

A

Fe and P

201
Q

How do soils form

A

Microbial decomposition of plant and animal matter combines with abiotic minerals and nutrients excreted from plant roots

202
Q

Rhizosphere

A

Area around the plant root

Supports growth of microbes

203
Q

Can life exist in the absence of photosynthesis driven primary production?

A

Yes

Nutrients can be carried from primary producers to areas where sunlight cannot reach

204
Q

Microbes in harsh, deep surface environments depend on ___________ for production of organic compounds

A

Chemolithoautotrophy

205
Q

454 sequencing

A

DNA or RNA sheared into small fragments
Adapter sequences ligated to the fragments which each anneal to one bead
Fragments amplified by PCR and each bead is placed in the well of a slide containing DNA sequencing reagents
Each of the 4 dNTPs is added sequentially to the wells sequencing the fragments through fluorescence
Based on pyrosequencing

206
Q

Illumine sequencing

A

4 Fluorescently labelled nucleotides and terminator added one cycle at a time to a slide
Terminator and previous base removed after each cycle

207
Q

Nanopore sequencing

A

Guides ssDNA through protein pore that reads bases as they exit
Reads longer sequences than illumina

208
Q

PacBio sequencing

A

High accuracy and longer sequences

Can explore epigenetics

209
Q

Horizontal gene transfer

A

Movement of DNA between organisms rather than from parent to offspring
Can be found by comparing GC content of organisms

210
Q

Proteomics

A

Separate proteins on a gel
Split proteins into smaller peptides and determine molecular weight using mass spec
BLAST to sequence

211
Q

Symbiont definition

A

An organism that has entered a long-standing and intimate relationship with an organism of another species

212
Q

Syntrophy

A

Provision of nutrients from a microbes that the organism is unable to synthesis themselves

213
Q

In syntrophic relationships, both partners depend on each other for:

A

Energetic reasons

Perform a fermentation process neither could run on their own

214
Q

Ectosymbionts

A

Live on the surface of their host

215
Q

Endosymbionts

A

Live within the body or cells of a host

216
Q

_______ and __________ live on the human skin and play a role in immunity

A

Firmicutes and actinobacteria

217
Q

What is the most enriched part of the human body with anaerobic bacteria

A

The intestinal tract

218
Q

What is the order of microbes in the small intestine (10^?)

A

10^10

219
Q

How do herbivorous vertebrates break down cellulose from food

A

Depend on their symbiotic microbes for most of their caloric intake
Don’t posses enzymes to break down cellulose

220
Q

Humans are __________ fermenters, where the primary site of fermentation is in the _______

A

Colonic

large intestine

221
Q

Cecal fermenters: definition and examples

A

Enlarged cecum that acts as primary fermentation site for breakdown of plant tissue
Rabbits, mice, herbivorous birds

222
Q

Rumen fermenters: definition and examples

A

Evolved a specialized organ (the rumen) as the primary site of microbial fermentation
Deer, cattle, sheep

223
Q

Primary endosymbionts of insects show evidence of:

A

Co-speciation

224
Q

Primary endosymbionts of invertebrates are found exclusively in:

A

Specialized host cells called bacteriocytes which are transmitted from mother to offspring
Can be required for survival or fertility

225
Q

Secondary endosymbionts live:

A

Can live outside of the host and aren’t restricted to specialized cells
Not always present or maternally transmitted

226
Q

Example of primary and secondary symbionts of invertebrates

A

Primary: Buchneria with sap-feeding aphids
Secondary: Wolbachia can colonize many insect species, can reduce dengue virus spread in mosquitos

227
Q

What is lichen composed of and what is the role of each component

A

Fungi (mycobiont) and and a photosynthetic microbe (photobiont, which can be Cyanobacteria or algae) in a symbiotic relationship
Photobiont performs photosynthesis and supplies C and N
The mycobiont provides inorganic nutrients and a protected environment

228
Q

~85% of plant families participate in symbiosis with:

A

Mycorrhizal fungi which colonize roots
Roots provide fixed carbon, and fungus aids in nutrient acquisition from soil by penetrating the plant cell wall with its hyphae

229
Q

What is the only way nitrogen can enter the biosphere

A

Nitrogen fixation by bacteria or archaea

230
Q

What is the nitrogen fixing bacteria that forms a symbiotic relationship with legumes

A

Rhizobium
Legume forms a root nodule for the bacteria and they fix and provide nitrogen to the plant
Legume provides fixed carbon

231
Q

What protects the oxygen sensitive nitrogenase in rhizobium

A

The root nodule and leghemoglobin of the legume plant which tightly binds oxygen

232
Q

How do rhizobia infect the legume

A

Attach to the root hair, formation of a Shepards crook and an infection thread

233
Q

Infectious disease definition

A

Disease caused by a microbe that can be transmitted from host to host

234
Q

Zoonotic disease definition

A

Infectious disease in animals that can cause diseases when transmitted to humans
Ex. Rabies

235
Q

Pathogen definition

A

Microbes that can cause disease

236
Q

Primary pathogen

A

Produce disease readily in healthy hosts

237
Q

Opportunistic pathogens

A

Only cause disease when displaced to an unusual site or when host has weakened immune system

238
Q

Exotoxin

A

Secreted proteins that negatively affect the host cells

239
Q

Endotoxins

A

Part of the microbial structure itself

240
Q

Do viruses produce toxins?

A

Typically no, replication typically induces cell death via immune responses to viral spread

241
Q

What is the purpose of mucus in the inner surfaces of the body

A

Sticky layer that traps microbes, which is then swept out by cilia

242
Q

Innate immune response

A

All multicellular eukaryotes
Immediate and nonspecific immune response
Inflammatory response recognizes PAMPs which are detected by TLRs

243
Q

TLR 1 and 2

A

Recognize lipoteichoic acids

244
Q

TLR 2 and 6

A

Recognize lipopeptides

245
Q

TLR 4

A

Recognize LPS

246
Q

TLR 5

A

Recognize Flagellin

247
Q

TLR 10

A

Ligand unknown

248
Q

Adaptive immune response

A

In vertebrates
A specific immune response
B cells and T cells coordinate to recognize and remember specific antigens

249
Q

Three steps for a microbe to cause disease

A

Gain access to host tissues
Overcome host defences
Obtain nutrients from host

250
Q

Virulence factors purpose

A

Help the pathogen gain access to the host tissues, evade host defences, and access limiting nutrients

251
Q

What is fibronectin

A

A large glycoprotein found in plasma and in extracellular matrix
Prime target for pathogen binding

252
Q

How does gonorrhoea attach and invade host cells

A

Uses fimbriae to attach
Endocytosis and exocytosis
Replication and spread of infection

253
Q

Fimbriae

A

Specialized pili used for attachment
Binds to receptor on host cell
Can be altered to evade immunity

254
Q

Special adherence proteins

A

E.coli can engineer attachment with virulence factors Tir and Intimin protein
Tir is made by bacteria and excreted through the type III secretion system
Intimin produced by bacteria and interacts with Tir to act as a landing pad for bacterial cell

255
Q

What microbe causes gastric ulcers

A

Helicobacter pylori

256
Q

Effect of LPS on mammals

A

An endotoxin
Toxic to mammals, released upon bacterial death triggering inflammation
Can lead to septic shock or death

257
Q

What can act as an endotoxin in gram positive bacteria

A

Lipoteichoic acids

258
Q

Components of LPS

A

Lipid A: toxic activity
Core polysaccharide
O-antigen

259
Q

AB toxin structure

A

A subunit has toxic enzymatic activity

B subunit binds the cell receptor

260
Q

Diphtheria, pertussis, and cholera toxins work by ______

A

ADP ribosylation of target molecules (EF2 and Cyclase)

261
Q

Function of shiga toxins

A

Cleaves rRNA preventing ribosome synthesis

262
Q

Function of botulism and tetanus toxins

A

Inactivate motor neuron proteins involved in activation of halting of muscle contraction
Results in paralysis

263
Q

Cytolysins

A

Toxins that act on the plasma membrane to encourage cell lysis to provide nutrients for pathogens

264
Q

Hemolysins

A

Cytolysins that target and lyse red blood cells to get iron from host

265
Q

alpha toxin and listerolysin are:

A

Pore forming cytolysins

Cause apoptosis and membrane disruption

266
Q

Lecithinases are:

A

Membrane degrading cytolysins

267
Q

How does an egg yolk plate work

A

The egg yolk contains lipids that when degraded produce a precipitate

268
Q

Superantigen function

A

Act on helper T cells, over activating them and causing a systemic inflammatory response which does not efficiently target the pathogen

269
Q

The type III secretion system is similar to _______

A

Flagella

270
Q

Type IV secretion system is similar to ________________

A

Bacterial conjugation machinery

Spans inner and outer membrane and injects effectors into host

271
Q

_______ systems are associated with pathogenesis

A

Type III and IV secretion

272
Q

Capsules as virulence factors

A

Extracellular polysaccharide matrix used to evade the host immune response and hide from receptors on immune cells
Can also play a role in attachment

273
Q

Siderophores

A

Iron binding molecules that compete with host iron binding proteins

274
Q

Mechanisms to obtain iron from host cells for pathogens

A

Siderophores
Bacterial transport proteins
Lower pH
Hemolysin

275
Q

How do bacteria become pathogens

A

Horizontal gene transfer

Uptake of DNA from the environment, conjugation, transformation

276
Q

Pathogenicity islands

A

Can encode various virulence factors
Usually have low GC content
Flanked by repeat units and enzymes for movement
Often adjacent to tRNA genes

277
Q

Lysogenic phages can _____________ by transduction and incorporation into genome

A

Transfer pathogenicity genes to bacteria

278
Q

What is the natural role of restriction enzymes in bacteria

A

To protect against viruses

Will cleave unmethylated phage DNA while methylated bacterial DNA is protected

279
Q

CRISPR cas function

A

CRISPR locus is transcribed forming crRNA
Cas genes expressed to form cas proteins
CRISPR cas complex surveys cells for complementary phage DNA targeting the DNA for destruction

280
Q

What are the 2 main uses of microbes in the pharmaceutical industry

A

Produce secondary metabolites with therapeutic properties

Hosts for production of human proteins

281
Q

What was the best selling pharmaceutical in history

A

Atorvastatin

282
Q

Antibiotics interfere with

A 
Peptidoglycan synthesis 
Membrane integrity 
DNA synthesis 
Transcription 
Folic acid synthesis 
Ribosome function
283
Q

Basic principle of industrial fermentation

A

Convert low cost biomass to high value products that are used in medicine and proteins

284
Q

Primary metabolite

A

Product of metabolic process associated with growth

Ex. Fermentation byproducts such as alcohol

285
Q

Secondary metabolites

A

Non-growth associated metabolic product, often in stationary phase
Ex. Antibiotics

286
Q

Systems used for industrial fermentation

A

Fed-batch reactors

Chemostat

287
Q

How can molecular biology tools be used to improve microbial strains

A

Random mutagenesis by chemical/radiation exposure followed by screening for mutations
The best antibiotic producers are kept
Drawbacks: possibility of negative mutations, screening can be difficult

288
Q

Conditions for penicillin production

A

Aerobic
Various carbon sources
Sterile
Extracted with acetate

289
Q

Original penicillin strain used __________ yielded 1mg/L, and now ___________ yields 50g/L

A

Penicillium notatum

Penicillium chrysogenum

290
Q

How are bacteria used to express desired proteins for pharmaceuticals

A

An expression plasmid for the production of the a tagged fusion protein is transformed into the bacteria to be expressed, the cells are lysed and the lysate is purified

291
Q

Arnold’s discovery of directed enzyme evolution

A

Start with an enzyme with similar properties to the desired ones
Introduce random mutations into the genes and insert them into bacteria to express mutant enzymes
New enzymes are tested and most effective are selected
New mutations introduced and cycle is repeated

292
Q

Why are microbial enzymes favoured over chemical synthesis

A

They produce stereospecific reactions

293
Q

Biotechnology definition

A

Use of biological processes or organisms for the production of goods or services

294
Q

Which bacteria allows for the engineering of transgenic plants

A

Agrobacterium tumefaciens

295
Q

What process causes crown galls to form

A

The pTi plasmid contains T-DNA that is transferred into the plant cell through the action of the vir gene products
The DNA is inserted into the plant genome and expression leads to production of phytohormones and opines that result in plant cell proliferation
The bacteria then reside in the tumour and use the opines as nutrients

296
Q

What triggers the sensor in the bacterial cell membrane to transcribe vir genes for the dna transfer

A

Phenolic compounds produces from wounded plants

297
Q

How can plant genomes be modified using the Ti plasmid

A

Exchange genes in the Ti plasmid with transgene of interest

298
Q

How does the glyphosate herbicide work

A

Inhibits EPSP synthase, which is important for amino acid synthesis

299
Q

How is Bacillus thuringiensis used to engineer traits into plants

A

The bacteria produce Bt toxins that are harmful to insects from cry genes
Plants engineered to express Bt toxin to be resistant to insects

300
Q

What is the refuge strategy used for resistance management of Bt crops

A

Resistant and vulnerable populations of insects will mate and produce offspring that are less resistant than if both parents were resistant
Grown non Bt crops next to Bt crops so there are populations of resistant and non resistant that can mate

301
Q

Biofortification

A

Engineering increased nutrient levels in crop plants

Ex. Golden rice

302
Q

How is the synthetic Mycoplasma mycoides genome synthesized

A

Small 1kb fragments that overlap are synthesized and then assembled into larger and larger units to produce a synthetic genome

303
Q

How is the synthetic M. mycoides genome characterized

A

Rare restriction enzyme cut sites are added to the genome, then electrophoresis is preformed with the synthetic and the original plasmid

304
Q

Applications of yeast 1.0

A

Over express single genes
Complex gene modifications
a DNA assembly host
Capture of large DNA fragments

BIO 2EE3 (2 decks)

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