Microbiology semester 2 Flashcards
(670 cards)
1
Q
When the temperature is at its minimum what process happens to the bacterial cell membrane?
A
Gelling of the membrane.
2
Q
What temperature does a psychrophile survive at?
A
4 degrees. (Can not survive more than 20).
3
Q
What temperature does a mesophile survive at?
A
39 degrees.
4
Q
What temperature does a thermophile survive at?
A
70 degrees.
5
Q
What temperature does a extreme thermophile survive at?
A
106 degrees.
6
Q
E.coli is a psychrophile. True or false?
A
False. It is a mesophile.
7
Q
Psychrophile’s can survive at very low temperatures. This is partly because they have __________ membrane fludity.
A
Increased.
8
Q
There is a higher content of what in the membrane of a psychrophile?
A
Unsaturated, polyunsatured and methyl branched fatty acids.
9
Q
The membranes of psychrophiles have shorter acyl chain length. True or false?
A
True. This allows for increased membrane fluidity.
10
Q
Psychrophiles produce antifreeze proteins. How do these help the bacteria survive at low temperatures?
A
They bind to small ice crystals inhibiting their growth by covering the water accessible surfaces of the ice.
11
Q
Apart from antifreeze proteins, what other two substances do psychrophiles produce to help them survive in low temperatures?
A
- Cryoprotectants.
2. Cold adapted enzymes.
12
Q
How do cold adapted enzymes differ from enzymes not adapted for cold temperatures?
A
There are more alpha helices and less interdomain interactions. This makes the enzyme more flexible.
13
Q
Thermophiles use what to stabilize their DNA?
A
DNA binding proteins.
14
Q
Themophiles have supercoils in their DNA. What produces these?
A
Reverse DNA gyrases.
15
Q
What base pair is more commonly found in thermophiles?
A
GC.
16
Q
The membrane of a thermophile is not linked by ester bonds. What type of bond does it use instead?
A
Ether bonds.
17
Q
What interactions happen more commonly in the proteins of thermophiles?
A
Ionic and hydrophobic.
18
Q
What is the concentration of H+ in the cell of a neurtophile?
A
10^-7.
19
Q
What ion is pumped out of the respiratory chain, drives substrate symport, ATP synthesis and motility in alkaliphiles?
A
Na+.
20
Q
What ion is pumped out of the respiratory chain, drives substrate symport, ATP synthesis and motility in acidophiles?
A
H+.
21
Q
In response to osmotic stress water movement is regulated in bacteria. What is produced to help with this?
A
Compatible solutes.
22
Q
What releases compatible solutes?
A
Mechano-sensitive channels.
23
Q
What stabilizes the s-layer glycoprotein in some bacteria to help in varied osmotic pressure?
A
Na+.
24
Q
What are the three toxic oxygen forms?
A
- Superoxide.
- Hydrogen peroxide.
- Hydroxyl radical.
25
How does superoxide form?
O2 + e- --> O2-
26
What enzymes detoxify hydrogen peroxide in water?
Catalase and peroxidase.
27
What enzymes detoxify superoxide in hydrogen peroxide and then in water?
Superoxide dismutase and catalase.
superoxide reductase and catalase.
28
What enzymes do obligate aerobes use to detoxify ROS?
Catalase and SOD.
29
What enzymes do facultative aerobes use to detoxify ROS?
Catalase and SOD.
30
What enzymes do aerotolerant anaerobes use?
SOD.
31
What is a Petroff-Hausser used for?
To count cells.
32
What does flow cytometry allow you to do?
Distinguish between live and dead cells.
33
Serial dilutions are used in what method of cell counting?
Viable counting.
34
Optical density is an example of how you can indirectly look at bacterial growth. What are three limitations of this method?
1. High cell density needed.
2. Can not distinguish between live and dead cells.
3. The OD value given depends on the shape of the organism.
35
What type or organism can you not use a spectrometer on?
Moulds and fillamentous bacteria.
36
Are dry weight and looking a metabolic activity of a bacterial cell direct or indirect methods in determine the bacterial growth?
Indirect.
37
What are the four stages on the bacterial growth curve?
Lag, log, stationary, death.
38
What is the definition of the thermal death point?
The minimal temperature in which all organism are killed in 10 minutes in a particular liquid.
39
What is the thermal death time?
The minimum time needed to kill all organisms in a particular liquid at a given temperature.
40
What conditions are needed in the .moist heat' method of bacterial control?
15 minutes at 121 degrees.
If the culture consists of spores you need to place the culture under pressure.
41
What conditions are needed for the 'dry heat' method of bacterial control?
Direct flaming or incineration over 150 degrees for 2 hours.
42
What conditions are needed for the pasteurization method of bacterial control?
Below 100 degrees.
HTST is at 72 for 15 seconds.
UHT is at 140 for 2 seconds.
43
Filtration can be used to sterilize gases and what type of liquids?
Liquids that are sensitive to the heat methods.
44
What does a bacteriostatic chemical to do bacterial growth?
It stops the growth.
45
What does a bactericidal chemical to do bacterial growth?
It stops growth AND kills the bacteria.
46
What does a bacteriolytic chemical to do bacterial growth?
It causes the cells to lyse. You can hence not measure this interaction with a spectrometer as it will not have an OD value.
47
What do sterilants do?
They completely eradicate all forms of bacteria including spores. Used on objects.
48
What is ethylene oxide gas an example of?
A sterilant.
49
What do disinfectants do?
They kill microorganisms but not necessarily spores. Used on objects.
50
What is 60-85% alcohol an example of?
A disinfectant.
51
What do antiseptics and germicides do?
Inhibit growth or kill microorganisms on living tissues.
52
Do you need a pure culture for the disk diffusion technique, testing antibiotic resistance?
Yes.
53
What is the definition of the 'minimum inhibitory concentration' (MIC)?
The lowest concentration of a drug inhibiting the visible growth of a test organism after overnight incubation.
54
What is the definition of the ' minimum bacterial concentration' (MBC)?
Lowest concentration of drug killing 99.9% of a test organism after overnight incubation.
55
What are TCP, chlrohexidine and Triclosan examples off?
Phenolytic compounds.
56
What can phenolytic compounds be used as at low concentrations?
A local anesthetic.
57
What do phenolytic compounds do to the cell at high concentrations?
They disrupt the cytoplasmic membrane and denature proteins.
60-85% alcohols also do this to the cell.
58
What are QUATS?
Quaternary ammonium compounds, an example of cationic detergents.
59
What do QUATS do?
Interact with phospolipids of the cytoplasmic membrane.
60
What sort of chemical used for antimicrobial control is an alkylating agent?
Aldehydes.
61
Formatin solution and formaldehyde gas do what to a cell?
They modify proteins and DNA causing cell death.
62
What are the two types of halogen releasing agents?
1. Chlorine releasing agents.
| 2. Iodine releasing agents.
63
What do chlorine releasing agents do to the cell?
They form chlorinated bases in DNA and oxidise proteins.
64
What type of halogen reducing agent causes stains?
Iodine reducing agents.
65
When was the Black Plague?
1328-1350.
66
What percentage of Europe's population was killed by the black plague?
30-50%
67
When was the Flu pandemic?
1918.
68
What percentage of the worlds population was killed in the 1918 flu pandemic?
3-5%.
69
What did Rudolph Emmerich & Oscar Loew discover?
That Pyocynase had antibacterial properties. However their effectiveness was sporadic and it is toxic.
70
What did Gerhard Domagk discover?
Protosil red.
71
There are 10 main classes of antibiotics all inhibiting processes in the cell. What are these processes ?
1. Cell wall synthesis.
2. Fatty acid metabolism.
3. Cytoplasmic membrane structure and function.
4. Lipid biosynthesis.
5. Protein synthesis (tRNA).
6. Protein synthesis (30s inhibitors).
7. Protein synthesis (50s inhibitors).
8. DNA directed RNA polymerase.
9. RNA elongation.
10. DNA gyrases.
72
According to WHO, how many people die of health care associated infections each year in Europe?
4.5 million.
73
According to WHO, how many people die of health care associated infections each year in the USA?
1.7 million.
74
It costs the US an estimated £4 billion a year to treat health care associated infections. How much do they cost Europe a year in direct costs?
£6 billion.
75
B-lactams and Glycopeptides belong to which class of antibodies?
Cell wall inhibitors.
76
Aminoglycosides, cyclines, MLS and oxazolidinones all belong to which class of antibodies?
Protein synthesis inhibitors.
77
Quinolones belong to which class of antibodies?
DNA metabolism inhibitors.
78
What must a good antibiotic do?
Must inhibit and essential process.
79
What is the definition of pharmacokinetics?
The branch of pharmacology concerned with the movement of drugs within the body.
80
What is the definition of pharmacodynamics?
The branch of pharmacology concerned with the effects of drugs and the metabolism of their action.
81
What does B lactam inhibit?
Peptidoglycan polymerisation.
82
What mediates peptidoglycan polymerisation?
D.D- transpeptidases. These are also known as penicillin binding proteins.
83
B lactams bind to penicillin binding proteins, inactivating the enzymes irreversibly. This happens because penicillin is a structural analogous of what?
D-ala-D-ala-C residues in the peptide stem.
84
Resistance has caused a ______ in the Penicillin Binding Proteins affinity for beta lactams.
Reduction.
85
Can gram positive or gram negative bacteria secrete antibodies?
Gram negative.
86
Because of resistance developing there has been modifications in the ________ targeted by B lactams.
Synthetic pathway.
87
What enzyme can inactive B lactams?
B lactamases.
88
How do B lactamases work?
1. Nucleophilic attack by catalytic serine.
2. Covalent complex formed from penicillin and B lactamases.
3. Hydrolysis of penicillin.
89
What do autotrophs fix into organic molecules?
CO2.
90
What organic molecules are generally produced from auxotrophs?
Sugars, especially sucrose.
91
What type of organism obtains energy from chemical reactions?
Phototrophs.
92
What organisms maintain energy from oxidation and reduction reactions?
Chemotrophs.
93
What type of organism uses organic molecules as a source of electrons?
Lithotrophs.
94
What is the definition of phototrophy?
The harness of photo excited electrons to power cell growth.
95
How many light driven pumps does Bacteriarhodopsin have?
1.
96
What sort of organisms contain proteorhodopsin?
Marine proteobacteria.
97
What sort of bacteria contain Bacteriarhodopsin?
Halophillic bacteria.
98
______ alpha helices span the BR membrane in alternating directions. These surround a molecule of _______ which is linked to a ________ residue.
1. 7
2. Retinal
3. Lysine.
99
When a photon is absorbed by retinal it's conformation changes. How?
Cis to trans.
100
What type of synthase does BR have?
F1F0.
101
BR only provides a mechanism for what?
ATP synthase. Another method for metabolism is also needed.
102
What bacterium contains ER?
Halobacterium salinarium.
103
BR forms trimers which pack into ________ arrays.
Hexagonal.
104
What colour membrane does Haliobacterium salinarium have?
Purple.
105
What metabolic process does Haliobacterium salinarium use?
Photoheterotrophy.
106
What happens to water because of photoexcitation?
Photolysis.
107
What photosystem is water split at?
2.
108
What type of chlorophyll splits the water?
P680.
109
Cyanobacteria have a different set of ________.
Accessory pigments.
110
What type of chlorophyll is in PS1?
P700z
111
Can both photosystems absorb light?
Yes.
112
What is shape does the pathway of hydrogen ions make?
Z.
113
What reduction potential does photosystem 2 have?
+820mv.
114
How many photosystems are used in anoxygenic photosynthesis?
1.
115
What type of system uses bacteriochlorophyll?
Anoxygenic photosynthesis.
116
What end of the spectrum does bacteriochlorophyll absorb?
Red.
117
Can bacteriochlorophyll allow photolysis?
No. There is not enough energy at the red end of the visible light spectrum to split water.
118
Why can organisms with bacteriochlorophyll exploit deep bodies of water?
Because red lights wavelength is long enough to penetrate down.
119
What photosystem does green sulphur bacteria use?
1.
120
What are chlorobia?
Green sulphur bacteria.
121
What type of light do green sulphur bacteria use?
Far red.
122
Where are electrons transferred to in anoxygenic photosynthesis which just uses photosystem 1?
NAD+.
123
What is the redox potential at PS1?
-400mv. It is not far down enough to split water but it can split H2S.
124
Is cyclic phosphorylation in lived in anoxygenic photosynthesis at photosystem 1 or 2?
2.
125
What type of bacteria use photosystem 2 in anoxygenic photosynthesis?
Alphaproteobacteria.
126
What are alphaproteobacteria also known as?
Purple non sulphur bacteria.
127
What light to purple non sulphur bacteria use?
Infra red.
128
Where do purple non sulphur bacteria separate the electrons from?
Bacteriochlorophyll.
129
Where do green sulphur bacteria get their electrons from?
H2S or an organic electron donor such as succinate or reduced iron.
130
Cyclic phosphorylation can make ATP and NADPH. True or False?
False. It can not make NADHP or NADH. To do this it has to use reverse electron transport.
131
What is the definition of lithotrophy?
Acquisition of energy by oxidation of inorganic electron donors.
132
What can reduced inorganic electron donors be oxidised by?
Fe2+, NH4+, H2S.
133
What does the terminal electron acceptors have to be when reduced inorganic compounds are acting as electron donors in lithotrophy?
A strong oxidant, such as oxygen and NO3-.
134
Why is a strong oxidant required as an electron acceptor in lithotrophy?
Most inorganic substrates are relatively poor electron donors.
135
What is the following process also known as?
Ammonium- Hydroxylalamine- Nitrous acid (Nitrite)- Nitric acid (Nitrate)
Nitrogen oxidation.
136
What is the following process also known as?
Hydrogen sulphide- Elemental sulphur- Thiosulphate- Sulphuric acid
Sulphur and metal oxidation.
137
What can microbial sulphur oxidation cause?
Severe environmental acidification and eroding of structures.
138
Microbes that carry out sulpur/ metal oxidation are adapted to a low pH. True or false?
False. Although they are adapted to the low pH of sulphuric acid they are not adapted to the low pH caused by any other acid.
139
What organism can oxidise ferrous sulphide?
Ferroplasma.
140
Lithotrophy is similar to anerobic respiration. True or false?
True.
141
What is the process called that uses hydrogen as an electron donor?
Hydrogentrophy.
142
What is used as the electron donor in dehalorespiration?
Hydrogen.
143
What is dehalorespiration an example of?
A a process which allows bioremediation.
144
Tetrachloroethane is a common environmental pollutant used in what?
Dry cleaning.
It is still used to removed deposits from engines.
145
Where does tetrachloroethane end up in the environment?
Aquifers and water sources. This includes the South Downs in the UK. The same issue happens in the US and India.
146
What can tetrachloroethane be reduced to?
Ethane.
147
The reduction of tetrachloroethane into ethane can have negative effects if tetrachloroethane is only partially reduced- forming what?
Vinyl chloride, a toxic compound.
148
Will one organism do each step in the reduction/ oxidation process?
No- it will normally do the step that gives it the most energy. This is normally one or two steps.
149
As each successive TCA is used up it's reduced form appears; the next best electron acceptor is used generally by what?
By a different microbe species.
150
Where are the quinol electrons transferred to in aerobic respiration?
A terminal oxidoreductase eg Cyt.
151
What drives the proton motor force?
A change in pH. Not a single proton.
152
Besides ATP synthesis what three things does the proton motor force drive?
Rotation of flagella, uptake of nutrients and efflux of toxic drugs.
153
What is the definition of biosynthesis/ anabolism?
The building of complex biomolecules. This requires the central elements and metal ions.
154
What three things can produce energy for anabolism?
1. coupling of ATP hydrolysis.
2. NADPH oxidation.
3. Ion flown down a transmembrane concentration gradient.
155
Is NADPH a reducing or oxidising agent?
Reducing agent.
156
What 4 categories of organisms perform CO2 fixation?
1. Oxygenic phototrophic.
2. Chloroplasts.
3. Facultative anaerobic purple bacteria.
4. Lithotrophic bacteria.
157
What is methanogenesis?
Reduction of carbon dioxide and other single carbon compounds to methane.
158
What class of organisms are methanogens?
Archaea.
159
What process do methanogens do?
Methanogenesis.
160
What is the simplest form methanogenesis?
Hydrogen reduction in carbon dioxide.
161
Why is methane as problem in landfill sites?
It is very flammable.
162
What organisms can utilise methane?
Methanotrophs.
163
What is this an example off?
CO2 + 4H2 --> CH4 + 2H20
Methanogenesis.
164
How many ATPs are used in the reverse TCA cycle?
4-5.
165
Is the reverse TCA cycle described as oxidative or reductive?
Reductive.
166
What is Biosynthasis/anabolism?
The building of complex molecules. This requires the essential elements and some metal ions.
167
Where can the energy for anabolism come from?
1. Coupling of ATP hydrolysis.
2. NADPH oxidation.
3. Ion flow down a transmembrane concentration gradient.
168
What molecule is fixated in the reductive pentose phosphate cycle?
CO2.
169
What categories of organisms perfrom the reductive pentose phosphate cycle?
1. Oxygenic phototrophic bacteria.
2. Chloroplasts of algae and plants.
3. Facultative anaerobic purple bacteria.
4. Lithotrophic bacteria.
170
What are methanogenesis and lithotrophy both similar too?
Anaerobic respiration.
171
What is anaerobic respiration?
The use of a compound that isn't oxygen as the final electron acceptor.
172
What organisms use NO3-, NO2- and fumerate as the final electron acceptor?
Archae and bacteria.
173
What type of respiration do E.coli use?
Facultative.
174
What are the two best final electron acceptors to use in anaerobic respiration?
Hydrogen and NADH.
175
Hydrogen and NADH are the best final electron acceptors to use in anaerobic respiration. What other three electron acceptors can be used?
Formate, lactate and succinate.
176
Does rubisco have a low or high affinity to CO2?
Low.
177
What is photorespiration?
The process in which oxygen competes with carbon dioxide by binding to rubisco. This leads to the production of 2-phosphoglycolate instead of 3-phospoglycolate.
178
If you could improve the affinity of carbon dioxide to rubisco what else could you improve?
Crop yield. Unfortunately the affinity cant be improved as it would involve changing the structure of the enzyme which is essential for its structure.
179
What does CCM stand for?
Carbon concentrating mechanism.
180
What does the CCM covert carbon dioxide to through the use of carbonic anhydrase and why?
HCO3-. It does this as HCO3- can be retained in the cell, unlike CO2 which can diffuse out of the cell membranes.
181
What special structure is Rubsico found in in many organisms?
A carboxysome. Carbonic anhydrase acts within this structure.
182
What happens in the carboxysome?
Carbonic anhydrase converts HCO3- back to CO2.
183
Are all the reactions in the TCA cycle reversible?
No, but most of them are.
184
What can happen as a result of the TCA cycle being reversible?
A small amount of CO2 can be produced and fixated to regenerate TCA cycle intermediates.
185
What organisms can reverse the whole TCA cycle?
Some archae and some bacteria.
186
What three enzymes can be reversed in the TCA cycle?
1. ATP citrate lysase.
2. Fumerate reductase.
3. Oxoglutarate: FD oxidoreductase.
187
What performs reduction in the reverse TCA cycle?
NADPH or NADH.
188
What is reduced in the reverse TCA cycle?
Ferredoxin.
189
The reverse TCA cycle may predate the TCA cycle. True or False?
True.
190
Nitrogen fixation only happens in bacteria and archae. True or false?
False. It may happen at a low level in fungi.
191
What have aquatic cyanobacteria developed to allow them to fixate nitrogen?
Heterocysts (filaments).
192
What can attach to bacteria to further reduce oxygen levels?
Sugars.
193
What is turned of to allow nitrogen fixation to occur?
Photosynthesis. This allows anaerobic conditions to be maintained.
194
What enzyme catalyses nitrogen fixation?
Nitrogenase.
195
How many ATPs are consumed per N2 fixed in nitrogen fixation?
Around 28.
196
The harber bosch process fixates nitrogen to produce what?
Nitrogen fertiliser.
197
How many reduction cycles through nitrogenase occur in nitrogen fixation?
4.
198
What is the first reduction cycle to occur through nitrogenase in nitrogen fixation?
Fe protein gains 2 electrons from an electron transport protein (eg ferredoxin.) The electrons are then transferred to a FeMo centre.
199
What is the second reduction cycle to occur through nitrogenase in nitrogen fixation?
The FeMo centre binds 2H+ which is then reduced into H2 gas.
200
What is the third reduction cycle to occur through nitrogenase in nitrogen fixation?
N2 binds to the active site displacing the H2 gas.
201
What is the fourth reduction cycle to occur through nitrogenase in nitrogen fixation?
Successive pairs of H+ and e- reduce nitrogen to ammonium.
202
Do the number of complexes in nitrogenase vary between organisms?
Yes. However the complex is only thought to have evolved once.
203
What is the definition of the immune system?
An integrated system of cells and molecules that defend against disease by reacting against a parasite.
204
Herceptin is an antibody used in the treatment of what?
Cancer.
205
Invertebrates and vertebrates both use negative surveillance in their immune response. What does this mean?
All cells are labelled with proteins. Any unlabelled cells will be destroyed by phagocytes.
206
What is the downside of using negative surveillance in the immune response?
It is relatively easy for pathogens to learn how to mimic.
207
What protein is used in the vertebrate negative surveillance system to overcome the problem of mimicry?
Major histocompatibility proteins. These are very polymorphic which makes them hard to mimic.
208
What can positive surveillance do that negative surveillance can not do?
It can specifically identify foreign cells and destroy them.
209
What are the major two branches of the immune system?
Innate and Adaptive.
210
Which of the following statements is false?
1. You are born with the innate immune system.
2. There is an enhanced second response.
3. It can responded within minutes/hours.
Statement two. There is no enhanced second response with the innate immune system.
211
Which of these following statements is false?
1. You are born with no adaptive immune system, instead it develops throughout your life.
2. It is a highly specific response which improves after the first encounter.
3. It is a slower response than the innate immune system. It takes days/weeks instead of months and hours.
Statement one is false. You are born with some adaptive immunity although most does develop throughout your life.
212
Phagocytes, NK cells, and B/T lymphocytes are all examples of what?
Leucocytes / White blood cells.
213
Phagocytes, NK cells and B/T lymphoyctes are all examples of white blood cells. Which one of the above is part of the adaptive immune response?
B/T lymphocytes.
214
Lysosome, complement, interferons and antibodies are all exmaples of what?
Soluble factors.
215
Lysosomes, complement, interferon's and antibodies are all soluble factors. Which one is also part of the adaptive immune response?
Antibodies.
216
What is something 'non self' usually described as?
An antigen.
217
After initial contact with an antigen the innate response is triggered. Is the adaptive response also triggered?
Yes, but it is weak.
218
When there is a secondary contact with an antigen is the innate response still triggered?
No. The adaptive response is triggered.
219
Are external barriers classified as innate or adaptive methods of response?
Innate.
220
Tears and sweat contain lysosomes. What do these do to the bacteria?
Break down their cell wall.
221
The pH of the stomach allows a large amount of microorganisms to be killed. What is this pH?
2.5.
222
What are commensals?
Friendly bacteria which produce chemicals to influence the immune system.
223
Where do leucocytes originate from?
The bone marrow.
224
What did Elie Metchnikoff discover in 1883?
Phagocytes.
225
What is the comment phagocyte in the blood?
Neutrophils.
226
What do neutrophils contain?
A strange shape nucleus and granules compromised of specialised lysosomes.
227
When will neutrophils not be short lived?
If they find an infection.
228
What do lysosomes in the granules of neutrophils release?
Enzymes and H2O2.
229
What colour tinge do the granules in neutrophils have?
Green.
230
Mononuclear phagocytes can be found in and outside of the blood. When in the blood they are called monocytes. What are they called when they are found in tissues?
Macrophages.
231
How long can monocytes/macrophages live for?
Months and years.
232
Do mononuclear phagocytes (monocytes/macrophages) or neutrophils help initiate an adaptive response?
Mononuclear phagocytes as these are more complex.
233
What two types of infections are phagocytes good at fighting?
Bacterial and fungal.
234
Are neutrophils, monocytes and macrophages all examples of phagocytes?
Yes. They are also all leucocytes and are part of the innate immune response.
235
Natural killer cells are a type of leucocyte. What do they do?
Kill virally infected host cells non specifically.
236
What may Natural Killer cells be able to kill?
Cancer cells.
237
What are PRR's?
Pathogen recognition receptor. These are found on the surface of phagocytes. Eg Toll- Like receptor 4 recognises lipopolysaccharides.
238
When will a natural killer cell kill a cell?
When it does not recognise a self protein (eg. MHCI).
239
How quickly are soluble factors produced in response to an infection?
Very quickly.
240
What is the compliment system mad up of?
Approximately 20 proteins in the blood which are only activated when there is an infection. They can cause cell lysis and phagocytosis.
241
What are defensins?
Small positively charged proteins that can disrupt bacterial membranes. They are produced by neutrophils. Defensins are an example of a soluble factor
242
What are interferons?
Interferons are produced by virally infected cells. They protect unaffected cells and activate macrophages and natural killer cells. They can interfere with viral replication.
243
What causes swelling?
The shrinkage of cells lining the capillaries allowing tissue to leave the blood and enter the tissues. Phagocytes then migrate into tissues.
244
What is inflammation induced by?
The production of cytokines. These cytokines are produced by macrophages already resident in the tissue. The cytokines send signals to other cells resulting in a larger response.
245
What can histamine cause?
Inflammation.
246
What type of response is a temperature rise after infection?
An acute phase response.
247
To stimulate an acute phage response what do macrophages produce apart from produce cytokines?
Interleukin 1 (IL-1).
248
What three things does Interleulkin 1 (produced by macrophages) do?
1. Raises temperature.
2. Stimulates phagocytosis.
3. Reduces the level of iron in the blood.
249
Although Interleukin 1 is produced locally, where does it act upon in the body?
The hypothalamus in the brain.
250
One of the things Interleukin 1 does as part of the acute phase response is to reduce the levels of iron within the blood. Why is this helpful?
As bacteria are very reliant on iron for growth.
251
The adaptive immune system can cause a ______ response.
Specific.
252
What are the receptors for B lymphocytes?
Antibodies.
253
What are the receptors for T lymphocytes?
T cell receptors.
254
What type of organism causes sleeping sickness?
Parasites.
255
What happens inside the peripheral lymphoid tissue?
Antigen dependant differentiation.
256
Is the response from B cells known as humoral or cell mediated?
Humoral.
257
Is the response from T cells known as humoral or cell mediated?
Cell mediated.
258
How do B cells respond to antigens?
They secrete antibodies with bind to foreign material targeting it for destruction.
259
How do T cells respond to antigens?
They can kill the infected cells directly or make proteins called cytokines which instruct other cells to behave.
260
T cells can produce cytokines when coming across an antibody which instruct other cells on how to behave. What are these other cells?
B cells, natural killer cells and macrophages.
261
Can natural killer cells or T cells kill infected cells more directly?
T cells.
262
Extracellular bacterial and 2andry viral antigens are all targeted by what type of lymphocyte?
B.
263
Viral, intracellular bacterial and intracellular parasitic antigens are all targeted by what type of lymphocyte?
T.
264
What happens to lymphocytes that recognise 'self' cells?
They are deleted early in development.
265
What does the clonal selection hypothesis say happens when a B lymphocyte recognises the correct antigen?
It divides and differentiates.
266
What are the two things that can compromise a vaccine ?
1. Subunits (eq toxoids)
| 2. Attenuated strains.
267
Can T cells only recognise an antigen when it is bound to a host cell?
Yes.
268
What happens in the primary lymphoid tissue in regards to lymphocytes?
The lymphocytes reach maturity.
269
What happens in the secondary lymphoid tissue in regards to lymphocytes?
The mature lymphocytes can be stimulated by antigens.
270
What are the two types of T cells?
T helper and T cytotoxic cells.
271
What are antibodies widely used in outside the human body?
Research and medicine.
272
Antigens are detected by B lymphocytes. There are they turned into what to ultimately produce a soluble antibody?
Plasma cells.
273
What type of molecule is an immunoglobulin?
A soluble glycoprotein.
274
Where were immunoglobulins discovered?
Serum.
275
What does the Fc region of antibody/ immunoglobulin allow?
Antigen elimination. The region is constant allowing it to act with elements of the innate immune system.
276
What is the total size of an immunoglobulin?
150kd. Each light arm is 25kd and each heavy arm is 50kd.
277
What does the Fab region on an immunoglobulin stand for?
Fragment antigen binding.
278
What does the Fc region on an immunoglobulin stand for?
Fragment crystallisable.
279
Who discovered that there were 4 polypeptide chains and 12 domains in an antibody?
Rodney Porter.
280
What amino acid is present in the hinge region of an antibody?
Proline.
281
When Rodney Porter treated the antibody with papain 2 fragments where produced. One of these was bound to the antibody and the other was crystallised in a solution. There was a 2:1 ratio. What enzyme was used to cleave the other side of the hinge?
Pepsin.
282
Are the variable and constant regions of an antibody encode for by the same exon?
No.
283
How do the imunoglobin classes differ?
In amino acid sequence in the heavy chain.
284
What are the two types of light chain?
Kappa and Lambda.
285
In one molecule will there only be one type of light chain?
Yes.
286
What are the 5 classes of antibodies?
G,M,A,D,E (discovered in that order).
287
What can happen in regards to exons to give antigens more specificity?
Multiple variable region exons can recombine and mutate during B cell differentiation.
288
What is the main class of antibody found in tissue and serum?
G.
289
What class of antibody can cross the placenta?
G.
290
What is the IgG antibody important for?
Secondary/memory responses.
291
What is the first type of antibody made in primary responses?
M.
292
What class of antibody forms a pentamer (polymer)?
M.
293
What type of antibody forms a dimer/ polymer in secretions?
A.
294
What class of antibody is found in saliva, tears, breast milk and mucus?
A.
295
What class of antibody has a long hinge?
D.
296
What percentage of antibodies are D class?
1%.
297
What class of antibody has extra domains?
E.
298
What class of antibody is present at very low levels?
E.
299
What class of antibody is involved in allergies?
E.
300
IgM is the first antibody type to be made in primary responses. Is it made at higher levels in secondary responses?
No.
301
What is the main way that antibodies can protect against infection?
Specific binding/ multivalency of FAB.
302
What can IgG and IgA do to help protect against infection?
They can neutralise toxins.
303
What antibody class can immobilise motile microbes due to the fact that it is a pentomer and can bind up to 10 antigens?
M.
304
What are IgA and IgM both very good at forming?
Complexes.
305
What class of antibody protects mucosal surfaces?
A.
306
What type of antibodies form an active complement?
G and M, but especially M.
307
Phagocytes have FC receptors for which classes of antibodies?
G and A.
308
Mast cells have FC receptors for which class of antibodies?
E.
309
Natural killer cells have Fc receptors for which class of antibodies?
G.
310
Is compliment the immune defence against bacteria, fungi or viruses?
Bacteria. It is not known if it is the immune defence against viruses.
311
What enzyme is first activated when compliment is stimulated?
Proenzyme 1.
312
What does proenzyme 1 activate in the compliment cascade?
Enzyme 1. This activates proenzyme 2 which in turn activates enzyme 2 and so on.
313
What pathway is activated specifically by antigen/antibody complexes?
Classical pathway.
314
What pathway is activated by certain bacteria?
MB-Lectin or Alternative pathway.
315
What does the 3rd component of the pathway have?
Protease activity. It is also the most abundant. Other components have protease activity too just not as much.
316
What is the definition of complement?
A series of proteins in serum normally inactive but can be activated in different ways.
317
What are the three main activities of complement?
1. Activation
2. Opsonisation
3. Cell lysis.
318
What does activation involve?
Phagocyte recruitment and the induction of inflammation.
319
C5a and C3a are chemoattractants. What stage of complementation are they involved in?
Activation.
320
What stage of complement is being described here?
Chemoattractants, such as C5a and C3a influence cell movement. Phagocytes have receptors for C5a and C3a so will move to areas which have a higher C5a/ C3a concentration. This is known as phagocyte recruitment. Anaphylatoxins are produced in an extreme allergic reaction. This causes widespread inflammation. Mast receptors will then release histamine.
Activation.
321
What can anaphylatoxins also be known as?
Compliment proteins.
322
What stage of complementation is being described here?
C3B binds to the bacterial cell surface making it more attractive to phagocytes. This is because phagocytes have receptors for C3b. This allows the phagocytes to bind better to the bacterial cell.
Opsonisation.
323
What stage of complement is being described here?
The whole complement is involved in this step (C1 - C9). There is formation of a membrane attack complex. C9 polymerises this which forms a hollow cyndrical structure which can insert into the bacterial membrane causing pores and lysis. This process also allows the disruption of envelopes in some viruses.
Cell lysis.
324
What does the classical pathway require?
Ab/Ab2. It also needs two antibodies bound next to each other on a bacterial cell surface.
325
What is the structure of C1 in the classical pathway?
Tulip branch structure of 6 globular heads and a collagen stalk.
326
How many Fc regions must C1 interact with?
2.
327
When C1's tulip branch structure interacts with the Fc region of two antibodies what happens to allow the C1 to act as a protease?
A steric change.
328
When C1 acts as a protease what does this activate?
The rest of the compliment.
329
Does the collage stalk in C1 have any flexibility when it comes to binding antigens?
Yes, some.
330
Why it is easier for IgM to find two antigens?
It is a pentemer.
331
Some classes of antibodies can act as opsonins. What is an opsonins?
An antibody or other substance which binds to foreign microorganisms or cells making them more susceptible to phagocytosis.
332
What classes of antibodies can act as opsonins?
G and A.
333
What do sudapods encapsulate bacteria in once Fc receptors have bound to the phagocyte?
A phagosome.
334
What happens to phagosomes?
They get destroyed by lysosomes.
335
Do lysosomes tends to be basic or acidic?
Basic. They contain toxic oxygen derivatives. These are produced by increase rates of respiration.
336
What do lysosomes contain other than toxic oxygen derivatives?
Ion binding proteins and enzymes which can break down bacterial cell walls.
337
Do natural killer cells have Fc receptors?
Yes.
338
What do Fc receptors bound to natural killer cells mediate?
Antibody dependent cell-mediated cytotoxicity
| ADCC
339
Fc receptors bind to ____ on natural killer cells?
IgG.
340
What are natural killer cells similar to in structure?
C9.
341
What do natural killer cells secrete?
Perforin.
342
What process is described here?
A hollow cylinder penetrates membrane into the infected host cells. Granules in the cytoplasm are then secreted in the channel. These granules can contain enzymes. The target then undergoes apoptosis. This is better than cell lysis as enzymes are not released that could cause tissue damage.
The killing process of natural killer cells.
343
What cell involved in the immune response has some activity against tumours?
Natural killer cells.
344
Where are mast cells found in the body?
Under mucosal surfaces in tissues.
345
What do mast cells contain?
Large specialised secretory granules.
346
What type of cell mediates a defence against large parasites?
Mast cells.
347
What receptors are found on mast cells?
IgE. Receptors for IgE bind to Fc receptors on the mast cells.
348
The first time a mast cell becomes in contact with an antigen there is no response. What happens the second time it comes into contact with an antigen to produce a response?
The antigen becomes an allogen due to cross linking in the Fc receptors causing them to release granules from the mast cells in 5-10 minutes. This process is called degranulation.
349
What does histamine do to smooth muscle?
It causes it to contract.
350
In most parts of the world the response of mast cells is not needed. What is it needed more often in poorer parts of the world?
Parasite infections such as tapeworm are more common.
351
What type of antisera is also classed as conventional antisera?
Polyclonal antisera.
352
What can polyclonal antibodies recognise multiple of?
Epitopes (the part of an antigen molecule to which an antibody attaches itself.)
353
Antibodies can lack specificity so are difficult to standardize. True or false?
True.
354
Closely related antibodies can have the same shape meaning they may not only recognise the protein you want them to in an experiment. True or false?
True.
355
How do you isolate monoclonal antibodies with single specificity?
B cells are taken from an animal immunised with antigen A. These are fused with a tumour cell line. The hybrid cell can only make the A antibody and divide indefinitely.
(The tumour cell line can not make antibodies.)
356
Is there variation in antibody composition within the same animal?
Yes.
357
What are 'magic bullets'?
Humanized antibodies that can be used in therapy.
358
Antibodies can label molecules in complex mixtures, stereotype pathogens and characterise cell surface proteins. True or false?
True.
359
What are T cells most important in the defence of?
Intracellular pathogens.
360
Do T cells have a memory component?
Yes.
361
What receptor is found on a T helper cell?
CD4 +ve.
362
What does the CD4 protein on the surface help in the production of?
Antibodies. (Produced by the B cells)
363
What can T helper cells help devilment of?
T cytotoxic cells.
364
What cells can T helper cells activate?
Macrophages and natural killer cells.
365
What receptor is found on the surface on T cytotoxic cells?
CD8 +ve.
366
What is the TCR?
The T lymphocyte receptor.
367
What is the structure of the TCR similar too?
The FAB arm of the antibody.
368
What four regions are found in the TCR?
V alpha, V beta, C alpha, C beta.
369
What can B cells recognise?
Soluble proteins and free native antigens.
370
What can T cells determine?
If own cells are infected.
371
What chromosome contains the Major histocompatibility protein gene?
6.
372
What two things do major histocompatibility proteins play a major role in?
1. Initiating a T cell response
| 2. Graff rejections.
373
What is the MHC?
The major histocompatibility gene complex.
374
What are MHCI and MCHII examples of?
Major histocompatibility gene proteins.
375
Where is the major histocompatibility gene protein MHCI expressed?
All nucleated cells.
376
What do the MCHI display the antigen to?
T cytotoxic cells with the CD28 +ve receptor.
377
Where is the major histocompatibility gene protein MCHII expressed?
Dendritic cells, macrophages and B cells.
378
What do MCHII cells display the antigen to?
T helper cells with the CDC24 +ve receptor.
379
What do Macrophages, dendtric cells and B cells have to allow the interaction with multiple T helper cells?
Finger like projections.
380
How do T cytotoxic cells recognise in viral infected cells?
By the peptide bound to MHCI.
381
What breaks down viral proteins in the cytosol?
Proteosomes.
382
What happens to the viral peptides once they have been broken down by proteasomes?
The peptides are taken to the ER. This allows the peptide to interact with MHCI which takes it to the cell surface, displaying it to T cytotoxic cells.
383
T cytotoxic cells use perforins to induce what in an infected cell?
Apoptosis. No toxic enzymes are produced and the dead cell can be taken up by macrophages.
384
How many infectedcells can one T cytotoxic cell kill?
100's. It is a very efficient process.
385
What are sometimes described as 'hormones of the immune system'?
Cytokines.
386
Cytokines do not have autocrine or paracrine activity. True or false?
False. In rare occasions they can. IL1 acting with the hypothalamus to raise temperature is an example of endocrine activity.
387
When a macrophage takes up a bacterium is it then infected itself?
No.
388
In MHCII what are the peptides bound to to take them to the cell surface?
Endosomes. These then activate B helper cells.
389
How large a cytokines?
5-20kd meaning they are fairly small.
390
Are cytokines usually are produce and act locally?
Yes.
391
Why are cytotoxins usually produced and made to act locally?
They are extremely toxic and can cause inflammation.
392
What are the four main groups of cytokines?
1. Interleukins.
2. Interferons.
3. Chemokines.
4. Colony stimulating factors.
393
Interleukins are a type of cytokine. How many types of interleukins is it thought that there is?
38.
394
What cells usually produce interleukins?
T cells.
395
Interferons are a type of cytokine. When are they produced?
When there is a viral infection. INF alpha and beta are made in this case.
396
Interferons are a type of cytokine. What interferon is involved in cell activation?
INF gamma.
397
Chemokines are a type of cytokine. What do they cause?
Cell movementand chemotaxis. IL8 is involved in chyemotaxis.
398
What type of cytokine causes a neutrophil to move out of the blood?
Chemokines- these can cause cell movement.
399
Colony stimulating factors are a type of cytokine. What do they cause?
Leukocyte production. An example of a colony stimulating factor is GM-CSF which can also stimulate T helper cells.
400
Different types of cytokine can produce different types of T _____ cells.
Helper. More specifically TH1 and TH2.
401
What is the role of TH1?
It can produce Inter leukins-2 gamma intefron which interacts with macrophages and TNFB which is a tumour necrosis factor. It can also cause inflammation.
402
What is the role of TH2?
They direct antibodies to make IgE antibodies. These can fight parasitic infections and allergy.
403
What can TH2 produce?
Interleukins (IL) 4-5-6-10-13.
404
Will a person who suffers from allergies have more TH1 or TH2? Does this differ from a normal person?
They will have more TH2 than TH1 however a normal person will have more TH1.
405
When a cytokine buds to its receptor what can it cause?
Cell activation and changes in gene expression.
406
What type of receptors are chemokine receptors?
G protein coupled receptors. Many are also dimeric and enzyme coupled.`
407
Where are all haemopoietic cells derived from?
Pluripotent stem cells.
408
What are the two main linages derived from pluripotent stem cells?
Myloid cells and lymphoid cells.
409
What two cells come from the myloid linage?
Plasma cells and natural killer cells.
410
Platelets, granulocytes, macrophages, mast cells and dendritic cells all come from which linage?
Lymhoid.
411
What other cell found in the blood can act as an inflammatory mediator?
Platlets.
412
Where in the body is there high amounts of lymphnode tissue and why?
By the respiratory, digestive and gasteotract. There is more here as these areas are more prone to infection.
413
Lymphocytes and lymph return to the blood via the _______ duct.
Thoracic.
414
Naïve lymphocytes enter the lymph nodes from the _____.
Blood.
415
Antigens from sites of infection reach _____ _____ via lymphatics.
Lymph nodes.
416
What cells in the immune system take up foreign material enter the immune system and travel to the nearest lymph?
Dendritic cells and macrophages.
417
Why can dendritic cells and macrophages present the antigens to nieve T cells found in the lymph?
Because they have high amounts of MCHII.
418
When nieve T cells are presented with antigens from MCHII contains dendritic cells/ macrophages will they stay in the lymph to divide and differentiate?
Yes.
419
Once the T cells have matured they leave the lymph via the efferent lymphatic vessel Where do they go?
The infected tissue. Compliment and innate methods are also activated in these tissues.
420
What do the nieve T cells help to divide when they are presented with an antigen in the lymph?
B cells which then form plasma cells to make antibodies.
421
Did adaptive and innate immunity coevolve?
Yes.
422
Do adaptive responses augment or initiate innate responses?
Augment. Innate responses initiate adaptive responses.
423
How many copies of RNA enters the cell in aids?
2.
424
Do reteroviruses use reverse transcriptase?
Yes.
425
When was AIDS or the HIV virus recognised first?
Aids. It was recognised in 1981 in California. HIV was identified in 1983 in France.
426
What does the HIV virion use to stick to the host?
gp120 (glycoprotein).
427
What part of the HIV virus enters the cytoplasm?
The nucleocapsid.
428
When is the HIV viruses reverse transcriptase activated?
Once the nucleocapsid has entered the cytoplasm. The newly synthesised ds DNA can then enter the nucleus.
429
Are the viral particles of HIV lytic as soon as they are made?
No. They are permissive when there are only a few particles.
430
Are CD4+ve or CD8+ve cells susceptible to HIV infection?
CD4+ve (T helper cells).
431
Once the CD4+ cell is infected with HIV what initially happens?
The infection is initially cleared. However the pool of infected cells gradually increases.
432
What does activation of T cells infected with HIV also cause?
Virus activation.
433
What can macrophages and dendritic cells also become infected with HIV?
They have low levels of CD4+ve on their surface.
434
Why does the patient eventually die from HIV?
Their CD4+ cells become too depleted.
435
Once HIV has infected macrophages and dendritic cells what can it do?
Infect the whole body via the lymph. It can also spread to T cells as these can interact with dendritic cells.
436
What explains why HIV can get into the brain?
The fact that monocytes can become infected as these can cross the blood brain barrier.
437
Is CD4+ expression sufficient for HIV infection?
No.
438
What is needed in addition to CD4+ expression to allow the HIV virus to fuse with the host?
A co receptor which functions as a chemokine receptor. This was discovered in 1996.
439
For a HIV virus to infect a cell the cell must express CD4+ receptors and a chemokine receptor, which acts as a co receptor. What cells in the immune system express this co receptor?
T cells, macrophages and dendritic cells.
440
Some people are not susceptible to HIV due to mutations in their chemokine receptors. True or false?
True. This is common in Nordic countries.
441
What do younger/ healthier people produce more off to help complete with the HIV virus, prolonging how long it takes for AIDS to develop ?
Chemokines. These compete with the chemokine receptors.
442
What initially clears high levels of the HIV virus from the blood?
Mainly cytotoxic T cells.
443
How long can it take for antibodies of the HIV virus to be detected?
3-6 months.
444
What is seroconversion?
When a specific antibody becomes detectable in the blood, and the corresponding antigen becomes undetectable
445
What type of cell is particularly important in the immune response towards HIV?
T cytotoxic cells.
446
The HIV virus mutates to avoid CD4+ cells. True or false?
False. They mutate to avoid CD8+ cells (T cytotoxic cells.)
447
Depletion in what type of cell causes AIDS?
T helper cell depletion.
448
Where are cells infected by HIV found?
In lymphoid tissue.
449
What three phases occur after infection from HIV and the before development of Aids?
1. 'Flu like disease' (sometimes, sometimes no disease)
2. Asymptomatic phase
3. Symptomatic phase.
450
Seroconversion happens between the asymptomatic and the symptomatic phase. True or false?
False. It happens between stage 1 and 2. These are the 'flu like symptom phase' and the asymptomatic phase.
451
In what two ways can the infected T helper cells be killed?
1. Cell lysis directly from the virus.
| 2. Other immune mechanisms eg by natural killer cells.
452
Infected T cells are often found in the lymph. Why can these not be detected?
They are in the latent phase.
453
Can Aids cause cancer?
Yes. in rare cases.
454
When a T cell gets infected with HIV and AIDS develop, what can they activate in other cells?
Other latent viruses.
455
A person with AIDS will not loose their T memory cells. True or false?
False. T memory cells are lost when someone develops AIDS.
456
Can AIDS cause dementia?
Yes.
457
What type of infection are AIDS patients most susceptible to?
Opportunistic.
458
Where did HIV1 originate?
Central Africa.
459
Where did HIV2 originate?
West Africa.
460
Is HIV1 or HIV2 older?
HIV2. HIV1 is only 50-100 years old.
461
Where was HIV1 originally found?
Chimps.
462
HIV1 was originally found in chimps. Did the virus cause damage to these chimps?
No.
463
Where was HIV2 originally found?
Sooty mangabees.
464
What type of HIV has infected humans for longer?
HIV2.
465
What type of HIV is more likely to cause AIDS?
HIV1.
466
What is the main cause of AIDS?
Unprotected sex. This accounts for around 70% of cases.
467
What percentage of AIDS patients caught the HIV virus via blood transmission?
28%.
468
The HIV virus can only spread from mother to child via breast feeding. True or false?
False. It can also pass directly to the foetus during pregnancy.
469
Why will blood testing not always detect HIV?
As sometimes the test will be taken before the antibodies are expressed.
470
Due to error in reverse transcriptase flu mutates 60% faster than HIV. True or false?
False. HIV mutates 60% faster than flu due to error in reverse transcriptase.
471
Why has it been difficult to develop a HIV vaccine (4 reasons)?
1. There are different clades of the virus
2. Mutation rates are high.
3. May not protect against humoral immunity.
4. T cytoxic cells need to be induced.
472
What does azidothymidine treat?
Aids.
473
How does azidothymidine work?
It acts as a nucleotide and blocks reverse transcriptase.
474
What are four problems with the azidothymidine drug?
1. Toxicity (as virus takes over own cells).
2. Viral latency.
3. Mutation rate of virus.
4. Cost.
475
What does combination therapy involve?
At least three drugs with different viral targets.
476
Combination therapy often includes the drug azidothymidine which blocks reverse transcriptase. What 3 types of inhibitors are also often found in combination therapy?
1. Other reverse trascriptase inhibitors.
2. HIV protease inhibitors.
3. Fusion inhibitors.
477
Has combination therapy been successful?
Yes. In the west.
478
What would passive immunisation against HIV involve?
Using human monoclonal antibodies in the vaccine.
479
What would gene editing to treat HIV involve?
A bone marrow transplant from someone who could not express the needed chemokine receptor.
480
What does the 'kick and kill' method to treat HIV involve?
Reactivating latent virus cells with combined immunotherapy so they can be killed by the patients own T cells.
481
What are the three reasons why eukaryotic genomes are much harder to sequence than bacteria/ archaea genomes?
1. They are much larger.
2. They contain uncoded DNA.
3. There are often duplicated copies of genes.
482
What process do eukaryotic cells go through in order to loose structures?
Reductive evolution.
483
What are the 3 main groups of eukaryote?
1. Opisthokonta
2. Viridaplantea
3. Protists.
484
Opisthokonta are a main eukaryotic group. What do they contain?
Fungi and animals.
485
What main eukaryotic group contains primary algae and green plants?
Viridaplantea.
486
The protists are a main eukaryotic group. What do they contain?
Algae that have undergone secondary symbiotic events.
487
There is the greatest diversity of size and shape in eukaryotes than in the other domains of life. What is the less diversity in?
Metabolism.
488
What does the name 'Opisthokonta', the group of eukaryotes dedicated to fungi and animals, refer to?
The backwards pointing flagellum found in the sperm of animals and zoospores of fungi.
489
The word 'opishokonta' refers to backwards pointing flagellum contained by the group members. Do all fungi have this flagellum?
No, due to reductive evolution. Some fungi are now non motile but at some point they would have had them.
490
What is thought to be the missing link between multicellular eukaryotes and multicellular fungi?
Choanoflagellates ( a type of eukaryote) are very similar to chanocytes found in sponges.
Nb. choanoflagellates can be grouped to form sponges.
491
Modern genetic analysis has caused some fungi to be regrouped as what?
Protists.
This includes slime and water moulds.
492
Microsporidians used to be classified as protists however they have now been moved into the Opistokonta group. Why is this?
They contained a highly conserved peptide sequence only found in animals and plants.
493
Where did primary endosymbiotic algae come from eukaryotes that had already developed a mitrochondria or eukaryotes that had already developed chloroplasts?
Eukaroytes that had already developed a mitochondria.
494
What do primary endosymbiotic algae use cyanobacteria for?
Feedstocks.
495
What rare event would have taken place to allow a symbiotic relationship to form between primary endosymbiotic algae and cyanobacteria. What was formed as a result of this event?
The cyanobacteria cell wall would not have been digested properly -this would have caused a chloroplast to form.
496
What indicates the development of a symbiotic relationship between primary endosymbiotic algae and cyanobacteria?
The double membrane surrounding the chloroplast.
| One of these membranes would have come from the cyanobacteria and one would have come from the food vacuole.
497
What event happened to cryptophyte algae?
A second endosymbionant.
498
Cryptophyte algae have two nucli due to a second endosymbiotic event. What did they engulf in this second event?
An algal cell.
499
Due to a second endosymbiotic event in cryptophyte algae they have two nuclei however the one taken up via the algal cell is inactive. What is this inactive nuclei called?
A nucleomorph.
500
What are Chlorophyta also known as?
Green algae.
501
What are Chlorphyta very similar to?
Plants.
502
What is Chlamydomonas reinhardtii classes as?
A green algae.
503
Is C. reinhardtii, an example of a chlorophyta, uniceulluar or multicellular?
Unicelluar.
504
C. reinhardtii has 2 ____ flagella at the ______ (front) end of the cell. They move by using a _____ ______ swimming actin.
Equal, anterior, breast stroke.
505
The cell ultrastructure of the Chlamydomonas is typical
| of algal cells. What are the cell walls made of?
Cellulose and glycoproteins.
506
What is most of a typical algae cell made up of?
One large chloroplast.
507
Is cytoplasm at the end closest to the flagella in an algae cell?
Yes.
508
A pyenoid is fully surrounded by the chloroplast at one end of the algae cell. What is this for?
The pyenoid concentrates CO2 for fixation.
509
The pyenoid in an algae cell is directly surrounded by a starch body. What is the purpose of this starch body?
Energy storage.
510
Although the genetics of most algae are not well understood, they are for Chlamydomonas. reinhardtii (a type of chlorophyta). Do they have a haploid cycle for asexual and sexual reproduction or is only the asexual cycle haploid?
Both cycles are haploid. They will sexually reproduce if two mating types meet.
511
What other algae which has no cell wall looks like C. reinhardtii?
Dunaliella.
512
Dunaliella and C.reinhardtii are both unicellular algae. Which one is also halotolerant?
Dunaliella.
513
Recently there has been a number of newly discovered picoeukaryotes which are only 0.5um to 3m in size. What are they classed as?
Chlorophyta (green algae).
514
What is Ostereococcs tauri an example off?
A picoeukaryote, which is also a type of green algae.
515
What are Rhodophyta also known as?
Red algae.
516
Rhodophyta are unicellular algae. True or false?
False. They can be unicellular or filamentous/ multicellular. Green algae however are all unicellular.
517
Where are Rhodophyta often found?
They are often found in association with seeweed.
518
Why are Rhodophyta often found in association with seedweed?
They provide important compounds that can be used as gelling agents. These include agar and agarose.
519
What is the name of the pigment that cause Rhodophyta to be red?
Phycoerythrin.
520
The pigment phycoerythin causes Rhodophyta to be red. Where is this pigment also found?
In cyanobacteria, however it is not similar in them.
521
Are red or green algae often used as foodstuff?
Red algae (Rhodophyta) are often used as foodstuff. This includes Nori in Japan and Laverbread in Wales.
522
Are red or green algae associated with higher plants?
Red.
523
The protists contain a mixture of groups which used to be divided into what?
Algae and protozoa.
524
What two traits separate secondary endosymbiotic algae with primary endosymbiotic algae?
1. They have at least two membranes around their chlorophyll.
2. They use a mixture of mixotrophy and heterotrophy.
525
What can primary endosymbiotic algae catabolise?
Simple substrates such as acetate, glycerol and glucose.
526
What type of organism is very widespread but not yet categorised?
Hapophytes.
527
What major group is responsible for at least 20% of the Earths photosynthesis?
Diatoms.
528
What larger eukaryotic group do the Diatoms fall into?
Protists.
529
Diatoms have overlapping frustules. What are these?
Very tough silica cell walls. These cell walls produce diatomaceous Earth.
530
What happens in asexual reproduction in Diatoms which must be reserved by sexual reproduction?
A reduction in size.
531
What are the two major forms of Diatoms?
Centric and Pennate.
532
What is the difference between Centric Diatoms and Pennate diatoms?
Centric diatoms have radical symmetry and Pennerate diatoms have radical symmetry.
533
Seeweeds are what type of algae?
Brown/ Phaeophyceae.
534
How long can Phaeophycee algae be?
70km. They can also form kelp forests.
535
Apart from from foodstuffs, why else would you harvest brown/ phaeophycee algae?
They provide a source of iodine.
536
Brown algae posses vacuoles of oily liquid for energy storage. What is the liquid called?
Leucosin.
537
What is an example of an Haptophyte?
Coccolithophores such as Emilania huxleyi.
538
What do Coccolithopores, an example of an haptophyte, produce to protect them from predators?
An exoskeleton of coccoliths made of calcium carbonate.
539
What can Coccolithopores absorb lots of
CO2.
540
What can E. huxleyi form which go on for thousands of km?
Ocean blooms. The cause of these blooms is currently unknown and it is difficult to recreate them in a lab. If more is found out, especially in regards to the side effects, they could be used to help combat climate change.
541
What are dinoflagellates an example off?
Secondary endosymbiotic algae.
542
Dinoflagellates are an example of secondary endosymbitoic algae, however they are grouped with the aveolates. Why is this?
They have alveoli.
543
Why do Dinoflagellates move with a swimming motion?
Because their flagella are very different in length. these are known as transverse and longitude.
544
Several species of what organism are toxic, producing red tides in coastal waters?
Dinoflagelattes.
One example of a toxic form is Gonyaulax.
545
How are Alveolates grouped together?
Based on flattened vacuoles (alveoli) beneath their membrane.
546
Paramecium is an example of a Cilitate. What group is this included in?
Alveolates.
547
Paramecium is an example of a Ciltate with is classed as an Alveolate. It has two nuclei. What can this generate?
The diploid micronucleus can generate a macronucleus which has many copies of DNA for gene expression.
548
Paramecium contains two nuclei. Does the micronucleus, macronucleus, or both take part in conjuction?
Only the micronucleus.
549
What where Apicomplexans formally known as?
Sporozoa.
550
What are Apicomplexans?
A parasite. This includes P. falciparum.
551
What unique organelle do Ampicomplexans contain which was originally derived from the endosymbiotic chloroplast?
The apicoplast. It has no photosynthetic activity remaining but it is still essential.
552
What do Ampicomplexans have to allow them to enter the host cell?
An apical complex.
553
What do Amoebas use to move?
Pseudopodia.
554
Amoebas use Pseudopodia to move. How does this work?
They flow via a gel-sol transition based on actin polymerisation.
555
Amoebas are harmful and other cause dysentery. True or false?
False. Most amoebas are harmless. Only Entamoeba histolytica causes dysentery.
556
Slime moulds are amoebas that aggregate in their thousands into a complex fruiting body. What does this resemble?
A fungal fruiting body.
557
What acts the aggregation molecule in slime mould formation?
cAMP.
558
What is Dictyostelium an example off?
A cellular slime mould (this means that the individual cells remain cellular.)
559
In a cellular slime mould individual cells remain cellular. What is he other type of slime mould where the cells become a giant multinucleate structure?
Plasmodial.
560
What is Euglenozoa (eg Euglena) an example of?
A Secondary endosymbiotic algae.
561
What can happen to Euglenozoa?
It can loose its flagella completely and grow heterotrophically.
562
What are some Euglena ?
Acid tolerant. They can grow in the acid tar lagoon in North West England which has an average ph of 2.6.
563
What caused acid tar lagoons.
62,000 tons of liquid oil refinery waste was poured into an exacutaved clay pit which was 9m deep.
564
Is the acid lagoon in north west England the only one of its kind?
No, they are a world wide problem.
565
Euglenoza include Egulena, an organism that can survive in acid tar lagoons. What other major organism is part of the Euglenoza class?
A group of obligate parasites called trypanosomes.
566
Trypanosomes are a parasite and are part of the Eugulenozoa group. What illness can they cause?
Sleeping sickness.
567
What mainly are the class of organism Metamonda?
Parasites.
568
Metamonda (such as Giardia lamblia) have lost what through degenerative evolution?
Mitochondria.
569
Apicomplexans contain a apicoplast derived from a chloroplast. Are they photosynthetic?
No.
570
What is Dictyostelium an example off?
A cellular slime mould.
571
Does the Euglenozoa group contain PEA or SEA?
SEA.
572
Metamonda have undergone degenerative evolution and have lost their chloroplasts. What other organelle do they not have?
Golgi bodies.
573
Microbes recycle _______ material in _______ and ________ ecosystems. This provides resources for ________ _________.
Organic, aquatic, terrestrial, higher organisms.
574
What is an ecosystem?
A population of species (often called a community of species) plus their habitat or environment.
575
What is a nieche?
A subset of conditions enabling an organism to grow and reproduce.
576
What two things make lakes a good ecosystem to study?
1. They are self contained
| 2. They have many nieches.
577
Van Niel described two main principles of ecology. What where these?
1. Every molecule existing in nature can be used as a carbon and energy source for a microbe somewhere on Earth.
2. Microbes are found in every environment on Earth.
578
Does the total volume of anerobic microbial community exceed that of the oxygenated biosphere?
Yes.
579
How far below the Earths surface have microbes been found?
3km.
580
What process is performed by primary producers?
Assimilation.
581
What is dissimilation?
Breakdown of organic nutrients to inorganic materials eg CO2 and NO2-.
582
What three things can be used to calculate biomass?
1. Cell number
2. Wet weight
3. Dry weight
583
What do microbial food webs consist off?
Primary produces, grazers, predators, secondary predators.
584
What is parasitism?
A microbe benefits at the expensive of another microbe in a very specific manner?
585
What is amensatism?
A microbe benefits at the expense of another in a non specific manner.
586
What is commensalism?
A microbe benefits, but has no discernible impact on another species.
587
What is mutualism?
Both species benefit and may not grow independently.
588
All microbes can be cultured. True or false?
False. Some need very specific nutrients, physical conditions and the presence of other microbes.
589
Not all microbes can be cultured. What two methods are available to overcome this problem?
1. DNA sequencing.
| 2. Environmental samples.
590
Some microorganisms survive better on agar. True or false?
True.
591
What environment has the largest diversity of organisms by far?
The soil.
592
What environment has the lowest amount of diversity and why?
The air, this is because it lacks nutrients.
593
What is the name given when all genomes in a particular community are represented?
A metagenome.
594
What are the 6 steps involved in producing a metagenome?
1. Ecosystem is sampled.
2. Filter/ concentrate the sample.
3. Break open the cells without breaking the DNA.
4. Clone DNA with PCR.
5. Read DNA sequence.
6. Build scaffolds and sample genomes.
595
Why are 16s RNA genes used in forming a metagenome in prokaryotes and 18s RNA genes used in forming a metagenome in eukaryotes?
As they are highly conserved.
596
What is the term 'operational taxonomic units' used instead of species during the formation of a metagenome?
Because it is unknown if each band is a species.
597
How can you estimate community diversity?
By plotting operational taxonomic units (OTUs) identified against the number of species. This levels of in water and air samples but not soil.
598
If there is more than _____ difference and less than ______ similarity between bands they are then classed as a different species.
3%, 90%.
599
What environment, other than air has a small species diversity?
Extreme environments. The acid tar lagoon only has 50-60 species present in it.
600
Through technological advancements producing a metagenome is now relatively cheap. True or false?
False.
601
Is forming a metagenome or culturing organisms more important?
Culturing an organism.
602
What can be used to find microbes of interest in a culture?
Changed physical conditions such as pH or carbon source.
603
What can microorganisms provide through reducing organic minerals?
Resources for higher organisms.
604
What is an ecosystem?
A population or species and their habitat/environment.
605
What is a nieche?
A subset of conditions enabling an organism to grow and reproduce.
606
Why are lakes mainly nieches?
They are self contained.
607
What can microbes do to provide resources for higher organisms?
Reduce organic material.
608
What is an ecosystem?
A population of species plus their habitat.
609
What is a nieche?
A subset of conditions enabling an organuism to grow and reproduce.
610
Why are lakes good nieches?
they are self contained.
611
Who formulated the two key points of microbiology?
Van Neil.
612
What two points did Van Neil come up with?
1. Every molecules in nature can be sued as a carbon and energy source by some form of microbe somewhere on Earth.
2. Microbes are found in every environment on Earth.
613
What exceeds the total volume of oxygenated biosphere?
The total volume of anerobic biosphere.
614
How far below the surface have microbes been found?
5km.
615
No microbes can grow more than 5km below the surface. true or false?
False. it is not known as further depths have not been sampled.
616
What type of producer allows for assimilation?
Primary.
617
What is dissimilation?
The breakdown of organic nutrients to inorganic minerals such as carbon dioxide and NO2-.
618
What is the definition of biomass?
Bodies of living organism. Cell number, wet mass and dry mass can be used.
619
Each environemnt can support a certain amount of biomass. true or false?
True.
620
Do foodw ebs exist in the microbial world?
Yes.
621
What is the definiton of parasitisum?
When a microbe benefits at the expensive of another microbe in a very specific manner.
622
What is the definition of amensalism?
When a microbe benefits at the expensive of another microbe in a non specific manner.
623
What is the definition of commensalism?
When a microbe benefits of another but has no impact on the other organism.
624
What is the definition of mutualism?
Both species benefit and may not grow independently.
625
How much of the Earths surface do oceans cover?
2/3.
626
What are the primary produces in ocean ecosystems?
Microbes. On land these are plants.
627
What is the iopen ocean water column also called?
The pelagic zone.
628
What is the neuston?
Where the water meeets the air.
629
How thick is the neuston?
10 micrometres.
630
How far down does the euphotic zone reach?
200m metres although is is variabke depending on organims above and poluttion.
631
What can the euphotic zone recieve?
Light.
632
What lives in the aphoitic zone?
Hetereotrophs and lithotrophs.
633
What is special about the photic zone?
it can not receive light.
634
what is the oicean floor also be known as?
The benthos.
635
The benthos is in the deep ocean. True or false?
False. it is just the ocean floor so can also be shallow.
636
The opean ocean can be described as oligotrophic. What does this mean?
It is low in nutirents.
637
What can cause more growth on coastal shelf?
Sewage columns.
638
What are microplankton?
20-200um large cilliated protists and algae.
639
What are nanoplankton?
2-20um in size, smaller algae and flagellated protists. Also includes fillamentous bacteria.
640
WHat are picoplankton?
0.3-2um in size. Bacterial phototrophs, hetereotrophs and lithotrophs. All prokaryotes.
641
What can microrganisms use to float?
Gas vesicles and flagella.
642
Why does the coastal shelf have the highest concerntration of microorganims
As it has the highest concentration of nutrients.
643
Why is the light penetration lower on the coastal shelf than in the open ocean?
There is a higher concentration of microorganisms.
644
What has the shallow photeic zone have less off?
Diversity in microorganisms.
645
What can not normally be cultured in labs with standerd techniques?
Marine microorganims.
646
The metagenome allows all marine microorganisms to be cultured. True or false?
False. It still can miss some.
647
How can a measure of expressed genes from an ecosystem be given?
A megatranscriptosome of mRNAs can be transcribed into cDNA and then amplified/ sequenced.
648
What genes were rarely in the metagenome?
Highly expressed genes.
649
What did 40% if expressed genes in the metagenome not have?
A match to genomic DNA.
650
What was the most transcribed in the metagenome?
Lowest abundant DNA. This showed that many organism were missed in the metagenome.
651
Who went on the Socrecer II Expedition?
Craig Venter.
652
When did Craig Venter go on the Sorcerer II Expedition?
2003-2004.
653
Where did Craig Venter sail on his expedition?
Down the east coast of the US, though the Panama Canal, along the coast of South America and then to the Galápagos Islands.
654
How often did Craig Venter take a sample?
Every 200 miles.
655
What depths were mainly sampled on the Sorcerer II expedition?
1-5m. Some coastal samples would have been 10-100m and some deep samples would have been up to 4500m.
656
How many samples were taken another by Craig Venter?
44.
657
Craig Venter made the samples fair by using the same sample size. True or false?
False. 20-0.1um pore sizes were used.
658
What temperature were the samples stored at on the Sorcerer II expedition?
-20 degrees.
659
How long did Craig Venters expedition take?
2 years.
660
Where did most of the sequence data come from after the Sorcerer II expedition?
The smallest size organisms. These were mainly archaea and bacteria.
661
What technique was used to sequence the samples taken on the Sorcerer II expedition?
Shotgun sequencing.
662
How much of the sequenced DNA found on the Sorcerer II expedition matched known samples?
30%.
663
What was one of the most abundant strains identified from the Sorcerer II expedition?
Pelagibacter.
664
What do Pelagibacter use?
Proteorhodopsin.
665
What is Synechoccocus also a type off?
Cyanobacteria. These along with Prochloroccus were highly abundant.
666
What is a special feature of Prochlorococcus?
They are extremely small even compared to prokaryotes. They are the smallest known oxygenic phototroph. 0.5-0.7um.[
667
What are Prochlorococcus?
A dominant photoautotroph in ocean surface waters. One of the most dominant organisms on earth.
668
What organisms contains unique divinyl chlorophyll and no phycobilisomes?
Prochlorococcus.
669
It is difficult to isolate Prochlorococcus. True or false?
False. They are easily isolated and grown.
670
How large is the genome of Prochlorococcus?
2000 genes so it is small.
