Learning outcomes Flashcards
1
Q
What is an operon? What are the advantages of a cell for organizing genes as operons?
A
a cluster of genes that are transcribed as a single messenger RNA.
advantages =allows many genes to be turned on or off due to specific signals.
I.e. lac operon which allows enzymes for the metabolism of lactose to only be produced when glucose is not present and lactose is.
2
Q
What is a repressor protein?
A
A regulatory protein that binds to specific sites on DNA and blocks transcription; involved in negative control.
3
Q
What is a helix-turn-helix motif?
A
The shape of a protein so it can bind to DNA
two segments of the polypeptide chain that have an a-helix secondary structure connected by a short sequence forming the “turn.”
4
Q
Explain how the different portions of the helix turn helix structure help bind to proteins
A
First helix = recognition helix, which interacts specifically with DNA.
Second helix = stabilizing helix stabilizes the first helix by interacting with it by way of hydrophobic interactions.
Turn linking the two helices = consists of three amino acid residues, the first of which is typically a glycine.
5
Q
When do cells break down lactose
A
In the absence of glucose
6
Q
Which operon is used to break down lactose in many prokaryotes
A
Lac operon
7
Q
List the key players in the lac operon
A
Repressor protein, An inducer (allolactose), RNA polymerase, CAP binding Site, cAMP-CAP complex,
8
Q
When does the repressor fall off of the lac operon?
A
In the presence of allolactose which binds to it and reshapes resulting in it falling off
9
Q
Why is allolactose present to bind to the repressor protein in the lac operon
A
Occasionally the repressor protein falls of the lac operon at the same time that DNA polymerase is present resulting in about 3 copies of the lacZ enzyme in the cell at all times. when lactose is present these proteins break it down to create the allolactose
10
Q
What is the inducer in the lac operon
A
allolactose
11
Q
Once the repressor is off the operon why doesn’t it turn on immediately
A
Because you still need the cAMP-CAP matrix bound to the CAP binding site.
This reshapes the DNA making it so DNA polymerase can bind
12
Q
When is cAMP present in the cell?
A
When glucose is present any cAMP present in the cell is shipped out to be used elsewhere. Once there is no glucose is used up the ATP is broken down into cAMP is used in the cell …. = can bind to CAP
13
Q
What is catabolite repression used for in regards to the lac operon?
A
It is used to ensure that only the most efficient fuel (glucose ) is used, once glucose is depleted then other fuels can be used.
14
Q
How does the CAP binding site interact with the lac operon?
A
When the cAMP-CAP complex binds to the CAP binding site is straightens out the DNA which allows RNA polymerase to bind
15
Q
What are two examples of global control mechanisms
A
- Catabolite repression - Changing the binding site to control when RNA polymerase binds
- Alternative Sigma Factors - Change the shape of RNA polymerase to control when it binds /where it binds to
16
Q
What is the normal sigma factor for E. coli
A
Sigma ^70
17
Q
What does the superscript mean in sigma proteins?
A
indecates the mass of the protein in kilodaltons (1 dalton = molecular weight of hydrogen)
18
Q
Why does the size of the sigma protein matter?
A
because this is what controls where sigma (part of RNA polymerase) binds to the DNA. the shape of it is kind of like a bean so it attaches normally in two spots (on 35 base pairs upstream of the promoter site and the other 10) but if the bean is changed the size that gap will change size too.
19
Q
Why aren’t alternate sigma factors constantly used by the cell
A
They are either destroyed very quickly or in some other way deactivated until needed
20
Q
Can you explain alternate sigma factors using an example
A
- Heat shock response is controlled by Sigma 32 (called RpoH)
- sigma 32 is usually inactive because it is bound to DnaK
- When the cell experiences high temperatures, DnaK is denatured and lets go of sigma 32
- Then sigma 32 binds to RNA polymerase and tells it where to transcribe to make heat shock proteins.
21
Q
Name the two components of a two-component system
A
- Sensor Kinase
2. Response protein
22
Q
In a two-component system where is sensor kinase and where is the response regulator?
A
kinase = cytoplasmic membrane
Response regulator = cytoplasm
23
Q
What are ompF porin proteins and when are they used
A
-Large pores used for osmotic regulation when the conditions are cold a low nutrients
24
Q
What are ompC porin proteins and when are they used
A
-small pores under high temp high nutrient conditions
25
Define signal transaction
the external signal is transmitted from a surface protein to the interior of the cell.
26
Is histadine kinase hydrophobic or hydrophobic
Two hydrophobic ends and a hydrophilic middle
-This allows it to have a sensor outside of the cell and then components in the cell to interact with
27
Where does the phosphate come from in a 2 component system
The histadine kinase autophosphoralates its self
28
Explain the basics of a two component system when its a promoter protein
- environmental signal interacts with histidine kinase
- kinase autophosphorilates
- kinase passes phosephate to protein
- protein binds to DNA upstream of promoter site (think cap binding site)
29
In osmotic regulation what happens when there is high osmotic pressure?
-low nutrients
-little phosphorylation of EbvZ
-few OmpR-P
-OmpR-P only binds to the high afinity site
===Only OmpF is made
30
In osmotic regulation what happens when there is low osmotic pressure
- high ammounts of nutrients
- Lots of EnvZ-P is made
- lots of OmpR-P
- Binds to low and high affinity binding sites
- micF (backwards ompF) is made
- micF binds to ompF turn it off
- ompC is turned on
31
What is feedback inhibition
- Controls enyzmatic activity
- biosynthetic pathways are temporarily shut off because of excess products
-From what i understand its when something produces too much of something further production is stopped do to the high conc of product
32
in chemotaxis what is a run? (flagella)
- Flagella moving counterclockwise
- Runs
- Coherant motion
33
In chemotaxis what is happening in a tumble (flagella)
- Clockwise motion
- Bundle is a messs
- timbles randomly
34
How many types of MCP's are there?
4
35
What are the proteins involved in chemotaxis
- MCP
- CheW
- CheW
- CheY
- CheB
- CheR
- CheZ
36
Which protein in chemotaxis is the sensor kinase
CheA
37
What does CheW do
ITs a coupling protein that changes the pattern of autophoshorylation of by CheA
38
What is the response regulator in chemotaxis
CheY and CheB
39
What does CheY do?
- Response regulator
- Bumps into Flagella motor
- when phosphorylated it changed the direction of the flagella motor clockwise (tumble)
40
What does CheB do
- Response Regulator
| - Demethylates MCP's to help reset the system once CheB is Phosphorylated
41
What does CheR do?
- Methylates MCP
| - -Controls Adaptation to signal (idk)
42
What does CheZ do
- Dephosphorylates CheY-P
| - Promotes Runs
43
Whats going on when cell is running
- MCP changes Conformation
- CheW helps attach CheA to the MCP
- When attached CheA autophosphorylates less
- Less phosphorylation of CheY
- Flagella moving clockwise
- Longer runs
- CheR decreases MCP's responce (sensitivity to stimulant) by adding methyl groups
44
How does CheB reset the system
- CheR keeps adding CH3's until its saturated
- This builds up the ammount of CheA
- CheB is methylated and removes CH3's from MCP
45
What happens if a repellant binds to the MCP
-Increased formation of CheA-P
-Increased tumbling
(when the concentration of the repellant decrease the runs become longer)
46
Explain quorum sensing on a protein level
- Autoinducer signaling molecule that crosses membranes and responds to osmotic pressure.
- When is builds up in a cell it activates transcription of of quorum specific genes
47
What is quorum sensing used for
- Toxin production
- Biofilms
- Bioluminescence
48
What are the three possible general habitats
- Lithosphere
- Atmosphere
- Hydrosphere
49
Define Autochthonous
An organism that is indigenous to a habitat
50
Define Allochthonous
Organisms that are transient (usually lived somewhere else and then were transported there)
51
Lake zone: Littoral zone
Light penetrates to the bottom
| Submergerd/ emergent plants
52
Lake zone Limnetic Zone
-Open water from surface to lowest level where photosynthesis is occuring
53
Lake: Benthos
- Bottom
| - Lots of nutrients due to gravity
54
Define Oligotrophic
A low nutrient lake, usually deep, LArger hypolimnion
55
Define Eutrophic
A lake with high nutrients, Usually shallow and warmer
56
Define and Give an Example of predation
- Short interation
- Predator engulfs prey
- Often stops when prey numbers decrease to 10^10 cfu.ml
EX: filter feeding
57
Define and give an example of mutualism
- Both benefit
- Obligatory relationship
- Both organisms must be in close proximity
- Married people
EX: Nodules (legumes and rhizobium)
58
Define and give and example of neutralism
-Lack of interaction
-Requires low population densities (spatially separated)
-No overlapping functions
EX: to allochthonous organisms in an env that doesnt support growth (ice matrix)
59
Define and give an example of antagonism
- Produce substances toxic to other population
| - May allow uncontested colonization (produce lactic acids or antibiotics)
60
What is the difference between mutualism and synergism
Synergism = Both benefit but its not obligatory (swingers)
Mutualism = Both benefit, Is obligatory (MArried), Very specific,
61
What is the main difference between predation and parasitism
-parasitism = long period of contact, uses hosts nutrients,
Predation = Short contact, engulfs other organism
62
What are the general steps of biofilm formation
1. Attachment
2. Colonization
3. Development
4. Dispersal
63
Explain the attachment stage of biofilm formation
- Stage 1
- Random collision of cells with a surface
- Attached by structures such as Flagella, pili or proteins (lectins)
64
Explain the colonization stage in biofilm formation
- Attachment leads to colonization
- Signal of biofilm specific genes
- encoding proteins that produce intercellular molecules and extracellular polysaccarides that initiate matrix formation
65
Explain the Development stage of biofilm formation
- Further growth
| - further excretion of polysaccharides
66
Explain the dispersal stage of biofilm formation
- Environmental conditions cause them to disperse
| - Cells regain mobility (grow back flagells) and get the heck outa there
67
How is Quorum sensing involved with biofilm formation
-Biofilm formation genes are not expressed until sufficient amounts of the autoinducer are present
68
What happens in biofilms when the autoinducer AHL is present in high enough quantities
The accumulation of AHL triggers genes for extracellular polysaccharide and c-di-GMP synthesis
- Biofilm specific genes are regulated by c-di-GMP and eventually triggers the switch from planktonic to biofilm growth (loss of flagella)
- Extracellular polysaccharides also are the scaffold for the biofilm community
69
What triggers the loss of flagella in biofilms
c-dipGMP which regulates the biofilm specific genes including loss of flagella
70
How to microbial populations interact within a living biofilm
Quorum sensing determined by population density
71
What are some benifits of biofilms
- available nutrients
- film protects cell from predation/antimicrobial agents
- colonization can form optimum environment (temp, pH, ect)
72
What are some of the genetic changes that occur in a biofilm
- Loss of flagella
| - Reduced activity of flagella motor
73
Define the rhizosphere
the region immediately
| adjacent to plant roots
74
What are the advantages of microbes living in the rhizosphere
- Tend to have high nutrients
- Water uptake
- release of organic matter
75
Describe the role of rhizosphere bacteria to plant health
- More nitrogen available to plants
- Increased stabilization of soil
- Synthesis of vitamins/amino acids ect
- stimulate plant growth
- antagonism of plant pathogens
76
What are mycorrhiza and what do they do?
Mutualistic relationship between plant roots and fungi
- improves nutrient absorption
- fungi decompose freshly fallen material at high rates and hyphae move it to host plant
77
Is mycorrhiza a specific or non specific relationship
Very specific
78
How does nitrogen fixation work?
- Nitrogenase complex is responsible for catalysis
- Nitroganase is extremely oxygen sensitive
- Very energy Expensive (12 ATP)
79
Describe the symbiotic relationship between plants and microbes in nitrogen fixation (Legume/rhizobium)
Plants get:
-Fixed nitrogen
Rhizobium get:
- space
- Energy requirements
- Low o2 env (10000x more o2 bound to leghemoglobin)
80
How does rhizobium find the correct legume plant
- Rhizobium are a small part of the soil community
- Plant releases flavonoid compounds
- Chemotaxis moves bacteria towards flavenoids (very specific)
81
How does rhizobium bind to the plant
-binds to root hairs
-plant proteins (lectins) that bind carbohydrates and calcium
-dependant on the bacterial proteins (rhicadehesins) to plant
-Develops cellulose fibrils between cells and plant
(VERY SPECIFIC)
82
What happens once rhizobium is bound to root
-In the presence of flavonoids the NodD protein in rhizobium will turn on a large number of genes used in nodulation
83
What is NodD
A transcriptional activator protein in rhizobium
84
Why do legume root nodules curl when rhizobium is bound
The tryptophan excreted by the plant is converted to indole acetic acid by bacteria (plant hormone)
85
How does Rhizobium get into the cells of legumes
polygalacturonase is made and partially degrades plant cell wall and allows rhizobia to contact plant plasma membrane
86
What is an infection thread
The bacterium induces formation by the plant of a
cellulosic tube which
spreads down the root hair. Root cells adjacent to the root hairs subsequently become infected by rhizobia, and plant cells divide
87
What is normal flora and how does it act to protect a plant or animal
- Organisms that live in/on a healthy body
| - helps prevent infection by pathogens by taking up available nutrients and binding sites
88
What are endosymbionts
are intracellular bacteria and are typically localized
| at specialized organs within the insect.
89
Advantages of endosymbionts in animals
1. Constant supply substrate
2. Wastes are removed
3. Animal mulches substrate - better growth
4. Consistent environment
90
How do chemoautotrohs support vent communities
Bacteria gain protection, transport of CO2/H2S/O2
| -Animals gain organic molecules needed for energy production
91
Explain microbe farming in the context of animal-microbe interactions
- ant supplies leaf tissues
- inoculates leaves (disperses culture)
- Shields farm from contamination
- ants get food
92
Define rumen
Rumen is a specialized organ that houses protozoa and bacteria that digest the animal’s food
93
How does ruman function as a microbial endosymbiont activity
Cellulose is broken down by bacteria which are then eaten by protozoa which is then broken down by the ruminant
Allows the animal to subsist on low protein foods like grass
94
How does chemotaxis and quorum sensing relate to light production in animal symbiotic
-squids release mucus from their pores which is an attractant to photobacterium which use chemotaxis to move towards the squid and then determine that there are in a large enough group they activate their luminescent genes
95
Explain what a reservoir is in the context of nutrient cycles
chemical form of an element and its turnover depends on cycle rate and size of reservoir.
96
Why are smaller reservoirs more vulnerable to disruption
Smaller volume means they get more circulated quickly, therefore changes applied to the system are easily put into operation, making them more vulnerable
97
describe strict anaerobes
No o2, anoxic conditions can result from degradation of organic matter in habitats that are not eqilibrated with atmospheric o2
98
Explain Facultative anaerobes
can function anaerobically but are more efficient from aerobic resiration
99
Explain faculative aerobe
more successful anaerobically but can survice aerobically
100
explain microaerophilic
prefers low O2 atmosphere
101
Describe two examples of ways microbes may protect and provide energy
Rhizobium/legumes use leghemoglobin (binds to oxygen)
Free living cells e.g. Azotobacter use “super charged” respiration
102
How are carbon hydrogen and oxygen cycling related
All cycle in respiration and photosynthesis
103
Clearly distinguish between assimilatory and dissimilatory reactions?
Assimilatory = convert highly oxidized forms into forms that can be made a part of proteins or other cellular structures.
Dissimilatory =convert highly oxidized forms to those that are highly reduced to produce energy for the cell.
104
Define extremeophile
Any organism that is able to grow outside the growth parameters of most organisms
105
Describe some biochemical alterations that contribute to extreme thermophilic adaptations
- Increased chain length of membrane fatty acids
- more growth factors may be needed
- greater number of G-C base pairs
106
What are phychrophiles
cold loving microbes
107
Describe the biochemical alterations that contribute to the survival of psychrophiles.
- Less packed membranes which mean more fluidity
| - slime layers
108
Describe methods that a cell may use to adapt to heavy metal contaminated sites.
Pumping the metal ions out of the cell or enzymatic detoxification. Sequestering may also be used.
109
define halophile
organisms that must grow in the presence of salt.
110
what is a compatible solute
any small molecule compatible with growth and metabolism when present in high intracellular concentrations
Uses: Most cells can withstand temporary exposure to hypertonic conditions by synthesizing or taking up compatible solutes.
111
Industrial uses of dunaliella
i. Glycerol ii. B-carotene iii. protein
112
Issues with cell harvesting on an industrial scale
- -growth of other undesired species
- centrifugation too expensive on industrial scale
- flocculation with positively charged polymers -> make toxic so can’t use as animal feed
- filtration clogs up quickly
113
What are stress proteins?
- in every prokaryote and eukaryote
| - protect cells and proteins from damage
114
What is the microbiological cell cycle (log phase) and how does it impact industrial uses of microbes
-All enzymes/ribosomes need to be present in order for growth to occur
- cell repairs occur in this stage
- appropriate operons are turned on or off
115
What is the microbiological cell cycle (exponential) and how does it impact industrial uses of microbes
- rapid division
- used in industrial fermentors
- requires optimization to stay here as long as possible
116
What is the microbiological cell cycle (stationary) and how does it impact industrial uses of microbes
- cell growth = cell death
- increase in toxic products
- decrease in nutrients
- cells start shutting down non essential pathways
- some industrial processes and bioremediation need to optimize this stage (antibiotic production)
117
What is the microbiological cell cycle (death phase) and how does it impact industrial uses of microbes
-cellular lysis
118
Describe the process of scale-up and the parameters involved.
- Lab flask (first indicates interest)
- 5-10 L fermenters (test variations of media, temp, pH, aeration)
pilot plant 30-3000L (more modification, without full commitment)
Commercial fermentor 2o,000-500,000L (viable product or service )
119
Describe heat as a method to control microbial growth
- Death occurs exponentially over time
| - pasteurization, autoclave, freezing/refrigeration
120
Explain pasteurization
passing foods through a heat exchanger to heat rapidly to 71 degrees for 15 seconds and then rapidly cool
121
Explain autoclave as a microbial growth control
121 degrees celcius all cells die
122
explain freezing as microbial growth control
slows growth down
123
explain radiation as a microbial growth control
- kills cells by DNA damage
- good for exposed surfaces
- bacteria are more then 20x as resistant to radiation then humans
- used for vaccines drugs and spices
124
Explain filter sterilization as a microbial growth control
-very fine filters (0.25um) to capture contaminants from heat sensitive liquids or gases
125
explain anti microbial agents as a microbial growth control
agents that inhibit or kill microorganisms
126
Explain chemotherapeutic agents as a microbial growth control
-antimicrobial agents that are selectively toxic
127
Explain disinfectants as a microbial growth control
Chemicals that kill microorganisms and are used on inanimate objects that are not practical to heat
128
Explain antiseptics as a microbial growth control
chemials that kill microbes (or inhibit their growth) and can be used on living tissue
129
Explain food preservatives as a microbial growth control
low molecular weight acids or salts that inhibit growth
130
What are the pros or single cell proteins as a food source for humans
- contains high ammounts of protein
- -affordable
- can be grown with molasses or cellulosic waste
131
What are the cons to single cell proteins as a food source for humans
- high nucleic acid content =excessive uric acid = kidney stones and gout
- some polymers are toxic
- food is cultural
132
What are the pros of using biofuels
- methanol and ethanol obtained from fermentation of agro waste
- ethanol can be mxed with gasoline and added to current engines
133
What are the cons of biofuels
-production requires large supply of fermentable substrate (conflicts with food production)
134
what are anaerobic digesters for producing methane
-digest things (algea, waste, landfills) anaerobically by methanogenesis
then you can tap produced methane but its tricky because you have to separate it from all the other gases produced
135
Define bioremediation
the use of microorganisms to clean up pollutants
136
define reductive halogenation
removes halogens from haloalkyl propellants and solvants and substitutes then with something like hydrogen
