Questions for Archaea

longchengzu

Questions for Archaea
1.        List the differences between Bacterial and Archaeal Cell Membrane and Cell Walls.
The differences between bacterial & archaeal cell membrane and cell walls :
  
        bacteria        archaea
Cell membrane        无聚异戊二烯甘油醚类脂而是磷脂(ester linkage of lipid), 脂肪酸        含聚异戊二烯甘油醚类脂(ether linkage of lipid)
Cell wall        有胞壁酸,D-amino acids        无胞壁酸(muramic acid), D-amino acids only have L-amino acids
Archaea lack fatty acids , instead have hydrocarbon moieties bonded to glycerol by ether( instead of ester) linkages.
Glycerol diethers and diglycerol tetraethers are the major classes of lipids presented.
Do not contain muramic acid and D-amino acids
A pseudopeptidoglycan is found in some archaea, it consists of  2 amino sugars: N-acetylglucosamine , N-acetyltalosaminuronic acid.

2.        What archaea have you learned so far?
Extremely Halophilic Archaeal(极端嗜盐的古细菌)
-Halobacteriales(盐杆菌目)
  -Halobacteriaceae(盐杆菌科) -Halobaterium盐杆菌属
                             -Haloferacx盐小盒菌属
                             -Haloarcula盐丰产菌属
                             -Halococcus盐球菌属
                             -Natronobacterium嗜盐硷杆菌属
                             -Natronococcus嗜盐硷球菌属
Methane-producing archaeal(产甲烷的古细菌):
-Methanobacteriales (甲烷杆菌目)
  -Mehanobacteriaceae(甲烷杆菌科)-Methanobacterium甲烷杆菌属
                                 -Methanobrevibacter甲烷短杆菌属
  -Methanothermaceae(甲烷嗜热菌科)-Methanothermus甲烷嗜热菌属                     
-Methanococcales(甲烷球菌目)
  -Methanococcaceae(甲烷球菌科)-Methanococcus甲烷球菌属
-Methanomicrobiales(甲烷微菌目)
  -Methanomicrobiaceae(甲烷微菌科)-Methanomicrobium甲烷微菌属
                                    -Methanospirillum甲烷螺菌属
                                    -Methanogenium产甲烷菌属
-Methanosarcinaciae甲烷八叠球菌科-Methanosarcina甲烷八叠球菌属
                                   -Methanolobus甲烷叶菌属
                                   -Methanothrix甲烷发菌属
                                   -Methanococcoides甲烷类球菌属
Hyperthermophilic (极端嗜热的古细菌):
-Thermococcales-Thermococcaceae-Thermococcus, Pyrococcus
-Thermoproteales-Thermoproteaceae-Thermoproteus,Thermofilum
                 -Desulfurococcaceae-Desulfurococcus
-Sulfobales-Sulfolobaceae-Sulfolobus, Acidianus
Thermoplasma(热原体属)
3.        Where to isolate halophilic Archaea?
   高盐浓度的自然界，如盐湖，硷湖和盐场，也常见于晒制的粗盐和用晒盐腌制的蛋白质品(咸鱼和皮革) 。
4.        What are the physiological features of halophiles?
The physiological features of halophiles are:
细胞杆状或球状，并出现许多退化类型，从圆盘形到三角形都有。不运动或靠丛生极端鞭毛运动。革兰氏染色阴性和阳性(2%乙酸固定后) 。好氧或兼性厌氧。需要很高浓度的盐，生长至少需要1.5mol/L(约为9%) NaCl, 但大多数菌种在 3.5-4.0mol/L NaCl生长最好。由于细胞内含有C50类胡萝卜素(菌红素) ，使其菌种落具有各种红色色调，并使得该菌在自然环境中群体生长时现红颜色。视黄醛类色素在这类细菌中可能是普遍存在的，它们能使离子运动并穿过细胞膜。含菌视紫素者，可用菌视紫素为质子pump，被光能所驱动所产生的质子梯度合成ATP。最适的生长温度是35-50°С。化能有机营养，利用氨基酸或碳水化合物作为碳源。在细胞内，通过积累高浓度的KCl来实现其渗透调节。

5.        What are the three major classes of methane-producing archaea?
The three major classes of methane-producing archaea:
Methanobacteriales (甲烷杆菌目)
The first: CO2-type substrate consumers, the second type: reduction of methyl group of methyl-containing compounds to methane, the third type: grow on alcohol rather than methanol for making methane.
Methanococcales (甲烷球菌目)
Methanomicrobiales (甲烷微菌目)

6.        List several species of methane-producing archaea you have learned.
Methanobacterium formicicum甲酸甲烷杆菌,
Methanobrevibacter ruminantium反刍甲烷短杆菌，
Methanothermus fervilus沸腾甲烷嗜热菌,
Methanococcus vanniellii万尼氏甲烷球菌,
Methanomicrobium mobile运动甲烷微菌,
Methanospirillum hungatei洪氏甲烷螺菌,
Methanogenium cariaci卡利亚奇产甲烷菌,
Methanosarcina barkeri巴氏甲烷八叠球菌,
Methanolobus tindarius丁氏甲烷叶菌,
Methanothrix soehngenii 索氏甲烷发菌,
Methanococcoides methylutens甲基甲烷类球菌

7.        List several unique methanogenetic coenzymes we have learned.
     辅酶M(Coenzyme M)，辅酶F420(Coenzyme F420 ) ，辅酶F430(Coenzyme F430) ，亚甲基喋呤(mehanofuran), methanopterin, HS-HTP.

8.        Describe the general properties of hyperthermophilic archaea you have learned.
The general properties of hyperthermophilic archaea r:
    细胞杆状，丝状或球状。大多数严格厌氧。专性嗜热，最适生长温度为70-105°С。嗜酸性和嗜中性。自养或异养。大多数种代谢硫。

9.        Describe at least four hyperthermophilic archaea you have known.
Thermococcus celer
Pyrococcus furiosus
Thermoproteus tenax
Thermofilum pendens依赖热丝菌-
细胞呈细杆状，长度变化大。常在细胞两端形成球状突起物，有时还形成膨大的部分，空细胞可变成螺旋状。革兰氏染色阴性，厌氧，专性化能无机营养，无机营养，嗜热嗜酸。通过硫的呼吸作用多肽。最适生长温度为85-90°С，最适pH值约为5。
Desulfurococcus mucusus粘质脱硫球状菌-
细胞呈球状，细胞壁柔韧，革兰氏染色阴性。通过硫的呼吸作用或发酵，可利用蛋白质，多肽或碳水化合物。温度97°С和pH2.2-6.5。
Sulfolobus acidocaldarius嗜酸热硫化叶菌-
细胞呈球状，形状高度不规则，形成独特的裂片，通常单个细胞存在。细胞可紧紧地粘附在硫结晶体上，细胞壁由以六边形排列的蛋白质亚单位组成。好氧，可氧化硫，硫化物或连四硫酸盐形成硫酸，并固定CO2作为碳源，进行无机营养生长。也能氧化复杂的有机物质，糖或氨基酸，进行有机营养生长。有些菌株在有氧条件下能氧化Fe2+成Fe3+。嗜热嗜酸，能在50-87°С和pH1-6 的条件下生长。
Acidianus infernus下层酸菌-
细胞呈球状，形状高度不规则，几乎只以单个细胞存在。细胞壁由以六边形排列的蛋白质亚单位组成。兼性厌氧。在好氧条件下，通过元素硫的氧化作用，或者在厌氧条件下，通过元素硫和H2的还原作用，进行无机营养生长。嗜热嗜酸，能在65-95°С和pH1-6的条件下生长。耐盐，最适生长的NaCl浓度为0.2%左右，最高浓度为4%。
10.        There are two bacteria that exhibits hyperthermophilic tendencies. Describe them a bit.
Aquifex产液菌属- 专性化能无机营养的超嗜热细菌，在微好氧条件下氧化氢或还原态硫化物。最适温度约为85°С，而且能在95°С生长。
Thermotoga栖热袍菌属- 严格厌氧的能发酵的细菌，生长在55-90°С，最适温度约为80°С。该菌产生独特的脂类，内含极其长链的脂肪酸，但其细胞壁含有肽聚糖这一细菌的标记分子。
11. What is Thermoplasma?
      Thermoplasma(热原体属) ：
1)        无真正细胞壁，仅由1个三层膜所包围，越5-10nm厚
2)        细胞有多种形状
3)        细胞膜有二甘油四醚侧链的40 C 类异戊二烯的醚酯
4)        Gram-negative
5)        兼性厌氧，专性嗜热嗜酸(55-59゜C，PH 1-2 )
6)        化能有机营养
7)        基因组很小，GC含量约46%，被高度硷性的DNA结合蛋白包围构成似真核细胞核小体的球状颗粒。其硷性的DNA结合蛋白与Histone 的A.A Sequence 同源性高。
12. What seems to be the maximal temperature for life to exist? 140-150゜C
13. Why it is said that archaea may be the earliest life on earth?
      Reason:
      The early geochemical conditions in earth r
      High temperature, high salt , low pH, strict anoxic condition.
Most of the archaea can live in the high temperature (e.g. thermopasma) else high salt (e.g. halophiles) else low pH(e.g. acidianus) and normally r anoxic microorganism.
Questions for Eukarya
1.        List the Eukaryotic Microorganism you have learned.
Eukaryotic microorganism r :
Algae（藻类）: phototrophic eukaryotic miroorganisms
Fungi (真菌类) : nonphotosynthetic eukaryotic microorganisms that             contain rigid cell walls.
Slime molds (粘液菌): nonphototrophic eukaryotic microorganisms that lack cell walls and that aggregate to form fruiting structures (cellular slime molds) or mass of protoplasm (acellular slime molds)
protozoa(原生动物) : unicellular eukaryotic microorganisms that lack cell walls.

2.        Describe the differences between various eukaryotic microorganisms.
The differences between various eukaryotic microorganisms r like below:

        藻类 algae        真菌类 fungi        粘液菌 slime molds        原生动物 protozoa
光合作用               Y                N               N              N
细胞         单细胞或群体        多细胞(除了酵母外)           多/单细胞           单细胞
细胞壁        有（除蜂窝藻外）             有               N              N
运动能力               N                N        某个世代(‘变形虫’世代)有              Y
叶绿体               Y                N               N              N
子实体               N                Y               Y              N
菌丝体               N                Y                            N              N

3.        Why do algea have various colors?
　　因含有各种不同类型的色素但主要为叶绿体，但当所含的其它色素如胡萝卜素较多时则显红色, 或其它颜色。
4.        How to classify algae?
有：　１）叶绿体。２）碳内聚合物３）细胞壁的结构４）形态的不同。
5. List six major algae and describe their characteristics you have learned?
Algae group                                 characteristics
        Morphology        Pigments        Carbon reserve materials        Cell wall
Chlorophyta(Green algae)        Unicellular to leafy        Chlorophylls a, b        Starch, sucrose        Cellulose
Euglenophyta(Euglenids)        Unicellular,flagellated        Chlorophylls a, b        Paramylon                  _____
Chrysophyta(Golden-brown algae, diatoms)        Unicellular        Chlorophylls a, c, e        Lipids        Many have 2 over-lapping components made of silica
Phaeophyta(Brown algae)        Filamentous to leafy, occasionally massive and plantlike        Chlorophylls a,c, xanthophylls        Laminarin,mannitol        Cellulose
Pyrrophyta (Dinoflagellates)        Unicellular flagellated        Chlorophylls a, c         Starch        Cellulose
Rhodophyta(Red algae)        Unicellular, filamentous to leafy        Chlorophylls a, d, phycocyanin, phycoerythrin        Floridean starch, fluoridoside        Cellulose
6. What are the differences and similarities between fungal cell wall and bacterial cell wall?
The differences and similarities between fungal cell wall and bacterial cell wall just like below:
        Fungal cell wall        Bacterial cell wall
differences        含80-90% 多糖 & 多聚磷酸盐        含  肽 聚糖
        多含几丁质，有些含纤维素        不含几丁质和纤维素
similarities        都含有脂类，蛋白，无机离子

7. List the types of fungi you have learned.
Neurospora,  Saccharomyces,  Morchella,  Amanita,  Agaricus,  
Rhizopus,  Allomyces,  Penicillium,  Aspergillus， Mucor,
8. How to classify fungi?
Classification of fungi based on:
Morphological properties (形态特征)
Sexual life cycles(性世代)that the fungi exhibit considerable diversity
9. What groups do Saccharomyces, Aspergillus, Mucor, Agaricus belong to?
     Ascomycetes (子囊菌) - Saccharomyces
     Basidiomycetes (担子菌) - Agaricus
     Zygomycetes (接合菌) - Mucor
     Oomycetes (卵菌) - Allomyces
     Deuteromycetes (半知菌) - Aspergillus   
10. Give an example of how cellular slime molds go through their various life cycles.
Dictyostelium discoideum, a cellular slime mold life cycles r like below:  
Aggregation of amoebas:
无组织性，聚合成像变形虫一样，可运动。
Migration of the slug formed from aggregated amoebas:
由amoebas成链状排列，形状有规则，可移动。
Culmination and formation of the fruiting body
Mature fruiting body
11. How do protozoa distinguish themself from algae, yeast, fungi, and slime molds
　protozoa distinguish from algae by their lack of chlorophyll (一般没有叶绿体); distinguish from yeast and other fungi by their mobility and lack of cell wall(是可运动的，无细胞壁); distinguished from slime molds by their lack of fruiting body formation(无子实体).
12. List five groups of protozoa we have learned.
     MASTIGOPHORA（鞭毛纲）, SARCODINA（肉足纲）, CILIOPHORA（纤毛纲）, SPOROZOA（孢子纲）, EUGLENOIDS（眼虫纲）
13. Which protozoa causes the African Sleeping Sickness?
　　Trypanosoma Gambiense
14. What is the unique properties of Paramecium?
　　有２个细胞核：小核具有繁殖的功能，大核具有在细胞的不同阶段转录不同ｍＲＮＡ　的功能。
15. Give an example of one protozoa that causes health problem.
疟原虫（Malaria Parasites）
Chapter 10 Industrial Microbiology 1
1.        What major industrial products have been produced by microbial fermentation processes?
They are
Microbial cells (微生物细胞)-yeast cultivated for food baking, mushrooms cultivated for food(酵母培养在食物的烘培及蘑菇的培养)
Enzymes - eg: glucose isomerase , lipases, proteases, rennin(高血压蛋白原酶), amylases(淀粉酶)  
Pharmaceutical agent- eg. Antibiotic , steroids, alkaloids.
Food additives- eg. Amino acid, vitamins
Chemical – special chemicals: aspartic acid , phenylalanine.
          - commondity chemicals: ethanol, acetic acid, lactic acid, glycerol.
2.        What steps are required for the development of an industrial microbial fermentation process?
Strain selection(链的选取)-> laboratory process development(实验室中改进步骤)-> pilot scale up(小型工业化)-> industrial scale up (工业化)-> downstream process development -> product packaging technique(包装工艺)-> other commercial consideration
3.        How to obtain a strain for our fermentation process development?
We can obtain a strain for fermentation process development from
Purchase from culture collections
Screening of nature circumstances
Genetic engineering
Mutations
Cell biology techniques
(*?)4. How to carry out a lab scale fermentation process?
     We have 4 type lab scale fermentation process:
Batch process, fed-batch process, continuous process, semi-continuous process.
Choose the RIGHT strain -> OPTIMIZE the strain GROWTH AND PRODUCT FORMATION CONDITIONS-> SUBSTRATE OPTIMIZATION-> KINETIC STUDY FOR BEST PRODUCT YIELDS.
5.        (!?)Why do we need to use shake flasks for lab scale process development? What can we obtain from shake flask experiment?
Because we have to make sure that the strain is suitable or not for scale up. We have to find several conditions and improve the product and strain. To SAVE the cost , if we DO NOT SUCCESS we can change the CULTIVATION conditions , strain , environment factor by waste little cost. We can obtain the CONDITIONS to PRODUCE the product SUCH AS the suitable strain , environment factorS ( tempERATURE, pressuRe, OD etc).
6.        What is scale up? Why do we need a pilot experiment before we move to industrial scale production?
Scale up: the transfer of a process from small-scale laboratory equipment to large-scale commercial equipment.
Because the cost is least then commercial scale but the conditions ARE more closely RESEMBLY the commercial scale. we can USE the instrumentation and computer control, further more if we fail we can change the conditions, find out the problem and solve it more easy and faster than commercial scale.
7.        (*?)How many fermentation processes do you know? describe them!
Batch process, fed-batch process, continuous process, semi-continuous process (You should describe them in more details).
8.        What paramenters must be monitored during fermentation?
The concentration of  the product, substrate, enzymes else microorganism, environment factor such as OD, pressure , temperature,agitation rate for fermentation etc.
Substrate consumption, product formation, cell dried weight.
9.        (*?)Schematically describe a fermentor.
Fermentor is the vessel in which the industrial process is carried out. It is VARIABLE in size and r depend on the process and how it WILL BE USED. It must have pH controller, impeller, motor, sterile seal, sparger, cooling jacket, culture broth, harvest OUTLETS, cooling water out and in.
10.        (*?)What is the most critical problem during process scale up in microbial fermentation?
The most CRITICAL problem is surface-volume ratioS decrease IN BIG VESSELS and DECREASE OXYGEN gas transfer EFFICIENCY.
11. How to maintain a constant dissolved oxygen concentration during the fermenation process?
We can contain it with
Increase stirring rate, increase air pressure, use pure oxygen, increase air inlet.

12. How to make high-fructose corn syrup?
Need 3 steps and 3 enzymes. The enzymes r :
alfa-amylase->brings about the initial attack on the starch polysaccharide , shortening The chain , and reducing the viscosiy of the polymer. (thinning reaction)
qlucoamylase->produces glucose monomers form the shortened polysaccharides, NAMELY OLOGOSACCHARIDE.(saccharification)
glucose isomerase->glucose convert to fructose.(isomerization)
13. How many ways can you use to immobilize enzymes or cells?
We can immobilize enzymes or cells in 3 ways :
1)        cross-linkage (polymerization) of enzyme molecules.
Usually done by chemical reaction with a bifunctional cross-linking agent . involve the amino groups of the wnyme prothein (WHAT IT THIS) with cross-linking agent like glutaraldehyde.
2)        Binding of the enzyme to a carrier.
Through adsorption, ionic bonding, or covalent binding .
3)        Enzyme inclusion
Involve incorporation of the enzyme into semi-permeable membrane.
Enzymes can be enclosed inside microcapsules, gels, semi-permeable polymer membranes, or fibrous polymers.
14. Do you know how vinegar, citric acid, yeast are made?
     Vinegar(醋): the product from the conversion of ethyl alcohol to acetic acid by acetic acid bacteria.
Materials: wine or alcoholic apple juice(cider), mixture of pure alcohol in water(distilled vinegar).acetic acid bacteria.
Key requirement: (cause acetic bacteria is           high oxygen demand during growth). Ensure sufficient oxygen.
Three type process :
Open-vat (Orleans method):wine is placed in shallow vats with considerable exposure to the air, acetic acid bacteria develop as a slimy layer on the top of the liquid. Not very efficient ! only the substrate in the surface is product to vinegar.
Trickle method: trickly the alcoholic liquid over beechwood twings or wood shavstream of air enters at the bottom and passes upward. Is operated in a continuous fashion.
Bubble method: alcohol liquid is added at a rate just sufficient to balance removal of vinegar. The product must undergo more filtering t remove the bacteria.
Citric acid: primary metabolic product formed in the tricarboxylic acid cycle.
Key requirement: medium must be low in iron.
Material: carbohydrate sources(starch, glucose sucrose , several kind of sugar).fungus.
Two type product process:
Surface processes: culture medium is solid or liquid, solid substrates. Take 5-8 days.
Submerged processes: apply 3 factor-(a)quality of the material used to construct the fermentor.(b)mycelium structure.(c)oxygen supply.
Yeast: key requirement: can’t added the material once time cause
The yeast will convert some sugar to alcohol.
Material: molasses, phosphoric acid, ammonium sulfate.
Process- pure stock culture->several intermediate stages (flask culture, seed culture, intermediate fermentor)r needed to build up the inoculum to a size sufficient to inoculate the final stage(production fermentor)-> recovered from the broth by centrifugation-> washed by dilution with water and recentrifuged until they r light in color-> package.
15. Describe how the following alcoholic beverages are made: wine, dry  wine, sweet wine, fortified wine, sparkling wine, whiskey, brandy,
rum, vodka?
There r only last part is different from wine , dry wine , sweet wine , fortified wine, sparkling wine, whiskey , brandy, rum , vodka have been made. They are all fermated by yeast just different in the alcohol concentration , the sugar left in the product and the last  fermentation occur. Dry wine r wine in which the sugars of the juice r practically all fermented, sweet wines r still some sugar left or additional sugar is added after the fermentation; whiskey , brandy, rum, vodka : the distilled alcohol is added after fermentation; Fortified wine is one to which brandy or some other alcoholic spirit is added after the fermentation; sparkling wine is one in which considerable CO2 is present, arising from a final fermentation by the yeast directly in the bottle(secondary fermentation). (PEASE REFER TO THE TEXTBOOK FOR MORE DETAILS)
The main process to make the wine r like below:
1)        harvesting of grapes
2)        crushed the grapes-> must
3)        adding SO2 to kill the wild yeast
4)        press
5)        fermentation
6)        filtration
16. How mushroom is grown?
    Cultivated in mushroom farms. The organism is grown in secial beds( prepared by mixing soil with a material very rich in organic matter), in buildings where temperature and humidity r carefully controlled. If light is not necessary, THEY can BE grown in basements of homes, in caves. Beds r inoculated with mushroom spawn(pure culture of the mushroom fungus that grown in large bottle ).  the mycelium grows and spreads through the substrate in bed-> adding to the sruface of the bed a layer of soil(casing soil) -> when flushing occurs is collected immediately-> package and kept cool.

What are the strengths and weaknesses of a technological process.
strength & weatnessesof technological process:
  strengths                                                  
1.reliance on renewable feedstocks
2.versatility with different feedstocks
3.food,feed &drug application
4.fine chemicals to bulk chemical applications
5.low temperature
6.operation in aqueous media
7.several reactions achieved in a single fermentation step
8.high level of automation
9.stereoLs pecificity
10.complex molecules converted & or produced
11.'Benign' effluents producted weaknesses:
1.feedstocks are oxidized & unsuitable for many application
2.feedstock costs fluctuate
3.sterilization is a major cost
4.product often in dilute aqueous solutions
5.product recovery costly
6.equipment costs high
7.reactions slow leading to poor volumetric productivity
8.complicated reaction conditions
9.mainly batch operation
10.high cell(catalyse) regeneration costs
11.high BOD wastes.

How to develop a fermentation process for antibiotic production?
isolation or collection of cultureses->
screening of cultures to detect those with antimicrobial activity->
development of methods for submerged-culture production->
development of methods for isolation & purification of antibiotic->
determination of antibiotic properties->
(physical: adsorption & absorption
chemical: reactions, solubility in solvents ,stability to acids,
           alkalis, heat etc.)
evaluation of antibiotic->
pharmacological tests->
antimictrobial activity->
comparison with existing antibiotic->
development of pilot plant production methods->
submission of licence for clinical trials->
testing of purified antibiotic->
development of plant scale production methods->
obtaining a product licence for clinical use->
other miscellaneous considerations:
development of methods to control production of antibiotic
development of new applications
development of marketing & distribution system
financing of business

What will you do if you are assigned as a chief engineer to develop a fermentation-based project?
先考虑以下问题：
1)市场需求
2)目前关于这方面的资料&所要开发的产品的情况。
3)赞助经费来源&夺得资助费的可能性
4)如何取得好的菌种(find the new strain)
5)产品的用途，优缺点，是否会引起环境污染etc
6)所须的原料来源
7)收率
进行以下步骤：
(一)实验阶段(laboratory process development)
1)选取适合的育苗：通过各种各样的试验手段选取，改良(增强物理化学稳定性，降低毒等)，筛选适合的育苗
2)提纯所须的育苗或基因片段
3)在实验室进行试验以夺得相关的条件，如环境条件(T ，P，PH ，OD.... )，需要改进的地方
4)重复3)以夺得相关的，所须的资料
5)复制所须的育苗或基因片段
6)pilot scale up
(二)寻找投资者
(三)扩大生产(industrial scale up, downstream process development)
(四)经各方面的检测&手续处理
(五)出售: includes product packaging techniques
Questions list for Bacteria I
1. Draw the phylogenetic tree of the major lineages of Bacteria based on 16S ribosomal RNA
Sequence comparisons.
2. How many groups of purple bacteria you have learned?
3. Describe the differences between purple bacteria, green bacteria an cyanobacteria?
4. Why do purple bacteria, green bacteria and cyanobacteria have various colours?
5. Describe the difference between nonsulfur purple bacteria and sulfur purple bacteria.
6. List four purple sulfur and nonsulfur bacteria you know, respectively.
7. Describe the difference between green nonsulfur bacteria and green sulfur bacteria.
8. List three green sulfur and green nonsulfur bacteria you know, respectively.
9. What are the uniqueness in heliobacteria?
10. How are cyanobacteria grouped?
11. What is heterocyst in cyanobacteria?
12. What is prochlorophyte?
13. List three nitrosifying and nitrifying bacteria, respectively.
14. Give two species of sulfur and iron oxidizing bacteria and tell what they can do.
15. Describe the unique properties hydrogen-oxidizing bacteria have.
16. How to classify methanotrophs and methylotrophs?
Questions list for Bacteria II
1 List three sulfate- and sulfur-reducing bacteria you have learned, respectively.
2 Describe two homoacetogenic bacteria you have learned and what are their physiological properties?
3 What are prosthecate bacteria? Are flagellates prosthecae? Why?
4 List two spirilla you have learned, give their Chinese names too.
5. Bdellovibrio is a group of interesting bacteria, what are their unique properties?
6. Give two names of the important spirochetes, describe the importance to study them.
7. Why is gliding myxobacteria interesting?
8. What is sheathed bacteria?
9 Tell as much as you know about Pseudomonads.
10 List at least three major genera of free-living, aerobic and nitrogen-fixing bacteria.
11 How can acetic acid bacteria be used for practical purposes?
12 Why is Zymmomonas interesting?
13. What are the major genera of vibrio and related genera? Why do some fishes emit light?
Questions list for Bacteria IIB
1 List as many as possible the enteric bacteria you have known. What diseases they may cause?
2 What Neisseria species causes sexual disease?
3 Compare the differences and similarity among Rickettsia, Chlamydia and Viruses
4 What are the major groups of Gram-positive bacteria?
5 List two gram-positive Cocci you have learned.
6 What is the uniqueness of Deinococcus radiodurans?
7 List at least three lactic acid bacteria you have learned, both in English and Chinese.
8 What group of bacteria are gram-positive, endospore-forming bacteria?
9 Which bacteria can be used as bioinsecticides?
10 Differences between protoplasts and Mycoplasma?
11 What are the major groups of the High GC Gram-Positive Bacteria: “Actinomycetes”?
12 List two major groups of corynebacterium.
13 Where was propionibacterium fast discovered?
14 What is the bacteria that causes tuberculosis?
15 What is streptomycete so interesting?
Cell biology
•Gram Staining procedure?
•Components of prokaryotic cells?
•Morphology of prokaryotes?
•Components of eukaryotic cells?
•Structure of cytoplasmic membrane?
•How cytoplasmic membranes are stabilized?
•Differences between archeal and prokaryotic membranes?
•Functions of cytoplasmic membrane?
•Actions of carrier proteins?
•Differences in cell walls between Gram-positive and Gram-negative bacteria?
•Why is the bacterial cell wall rigid layer called peptidoglycan?
•What are the chemical reasons for the rigidity that is conferred on the cell wall by the peptidoglycan structure?
•List several functions for the outer wall layer in Gram-negative bacteria?
•What is the bacterial periplasm?
•What types of Bacteria have a periplasm and of what significant is the periplasmic space?
•Why sucrose is able to stabilize bacterial cells from lysis by lysozyme?
•Describe the structure and function of a bacterial flagellum.
•What is the energy source for the flagellum?
•What types of cytoplasmic inclusions are formed by prokaryotes?

Questions to Translation(molecular _genetics)
Describe the translation process.
What are the differences between prokaryotic and eukaryotic ribosomes?
What are involved in initiation o protein synthesis?
What are polysomes and its function?
What is the function of molecular chaperones?
Start codon and stop codons?
Universal codons?
Open Reading Frame (ORF)?
Bioinformatics?

Questions for microbial ecology
1.        What is Microbial Ecology and What do microbial ecologists study?
2.        What is a microevironment?
3.        Describe biofilms and their functions and significance in practical applications.
4.        What are the factors affecting microbial ecology?
5.        List methods commonly used to study microbial ecology.
6.        What is the Winogradsky column and the bacteria enrichment technique?
7.        What is the Winogradsky column used for? Schematically draw it.
8.        How to carry out isolation of anaerobic bacteria in pure culture?
9.        How to do Identification and Quantificationof environmental microorganisms using Nucleic Acid Probes, Fluorescent Antibodies, and Viable Counts?
10.        How to do the Measurements of Microbial Activity in Nature using radioisotope technique and microelectrodes?
11.        What Stable Isotopes are used in Microbial Biogeochemistry? How to decide the biogenic or abiogenic of a material?
12.        What are aquatic habitats and primary producers? How do they distribute in nature?
13.        What is Biochemical Oxygen Demand (BOD)?
14.        How are microbial activities looked like in various layers of soil?
15.        What are the conditions under deep sea? What microorganisms inhabit in deep sea?
16.        What makes microorganisms under deep sea so unique compared with normal microbes?
17.        Why can tube worms live under deep sea where little organic nutrients are available?
18.        List microorganisms you have known that tend to live in hydrothermal vents?
19.        Schematically describe carbon and oxygen cycles.
20.        What microorganisms are involved in C and O cycles?
21.        How is methane produced from complex organic materials via microbial activities?
22.        What are primary and secondary fermenters in methane production?
23.        List two syntrophic microorganisms and describe a bit.
24.        How ruminants digest cellulose and starch?
25.        Schematically describe nitrogen and sulfur cycles and microorganisms involved.
26.        What bacteria is best understood in Bacterial iron reduction and oxidation.
27.        Describe the microbial leaching process for recovering copper from CuS.
28.        Why some microorganisms are resistant to mercury?
29.        Microorganisms are sometime used for cleaning of environmental pollutions, such as petroleum and pesticides?
30.        What is lichen and mycorrhiza?
31.        How is Ti-plasmid transfer T-DNA from Agrobacterium to plant genome?
32.        Why is Root nodule bacteria and symbiosis so important for legumes?

Viruses Questions
What are viruses? How to classify viruses?
How are viruses different from bacteria?
Describe viral structures.
What are two common symmetry structures?
What are the most common enzymes brought with by viruses themselves ? How to grow viruses?
How to quantify viruses?
What is the virus life circle?
How host cell protect themselves from virus attacks?
How do minus, plus or ss-, ds DNA viruses replicate?
What are the major bacteriophages? Describe Phage 174 and its genome.
Describe RNA Bacteriophage MS2 and its genome.
What is rolling circle replication?
Questions for Microbial Genetics
•        Describe as much as you know about plasmids.
•        What is the difference between a plasmid and an episome?
•        What are Hfr strain? F+ or F-, or F’ strain?
•        Draw the F plasmid and describe functions of various DNA regions.
•        Why is it said that conjugative plasmid contributes to evolution?
•        How many types of plasmids and their functions you have learned?
•        Schematically describe R100 plasmid and its functions.
•        How do R plasmids inactivate antibiotics?
•        What is an engineered plasmid?
•        What points do F plasmid provide to its host?
•        How to detect genetic recombination. Please cite one example.
•        How is bacterial genome mapped? What are the three types of transposable elements?
•        Explain transposon mutagenesis and its possible application.
•        Give an example to explain conversible DNA and phase variation.
•        What techniques are used to map bacterial DNA genome?
Introduction
•What is Microbiology?
•What are Microorganisms?
•What are Prokaryotes?
•What are Eukaryotic Microorganisms?
•Structural differences between P & E cells and virus?
•What can microbiology do?
•Five common characteristics of microorganisms?
•opulations, communities and ecosystems?
•Brief history of microbiology?
•How are microorganisms cultivated?
•Cellular evolution?P
Microbial Evolution and Systematics
bWhy is Ribosomal RNAs used as Evolutionary Chronometers
bWhy is 16S rRNA employed to study phylogenetics rather than the smaller 5S rRNR and the large 23S rRNA in Prokaryotics?
bHow to sequence 16S rRNA from inside the cells?
bHow to identify a prokaryotic or eukaryotic organism based on 16S or 18S rRNA?
bHow to build Phylogenetic Trees from DNA Sequences?
bWhy it is said the archaea closer to eukarya than bacteria is?
bWhat is signature sequence and how can it be used?
Metabolism, Biosynthesis and Nutrition
•Macro- and micronutrients? Defined medium and complex medium?
•What are growth factors?
•What environmental factors affect growth of microorganisms?
•How to prepare a medium for cultivation microorganisms?
•How to obtain a pure culture? How to calculate cell growth?
•How cells divide themselves? How to do viable count?
•What is the microbial cell growth cycle?
•How to maintain exponential growth?
•How to name microorganisms that grow best at a temperature?
•How do you you name microorganisms having various O2 tolerance?
•What enzymes are involved in detoxifying toxic active oxygen?
•What are the physical- and chemical ways to halt microbial growth?
•On what sites do antibiotics act on cells?
•How to preserve food?