Microbiology 2

Front 1

What forms of activated glucose are used for synthesis of prokaryotic polysaccharides.

Back 1

Adenosine diphosphoglucose is a precurser for glycogen and uradine diphosphoglucose is a precurser for some glucose derivitives needed for biosythesis of N-acetylglucosamine and N-acetylmuramuc acid.

Front 2

Glutamine synthase covelant modification mechanism.

Back 2

Glutamine synthase has 12 binding points to AMP, as each is bound, the enzymes is slightly more inhibited, and more bind as more glutamine is made. This process is energetically expensive (requires ATP), but is important for nitrogen fixation. When NH3 assimilation requires no ATP, AMP blocks the glutamine sythetase completely and no ATP is needed.

Front 3

How do we sterelise media

Back 3

Sterilization of the media is first done using an autoclave at 121 degrees Celsius, this kills the endspores of the microbes in the media. Aseptic techniques is then applied later to prevent contamination of the media.

Front 4

Balanced growth continuous cultures.

Back 4

the levels of bacteria, bacterial products, media components and waste products are constant.

Front 5

Washout chemostat cultures

Back 5

Washout occurs at very fast flow rates when the cells can not divide fast enough to keep pace with the flow in the system and so instead get washed out of the culture vessel. The bacterial cell conc. Will decrease quite dramatically and the substrate concentration will increase dramatically due to not being consumed.

Front 6

4 phases cell growth.

Back 6

Lag phase- little increase in cells, the cells adjust to media.

Exponential stage- all cells begin to actively divide - balanced growth. All the cells have the same composition and metabolic ability.

Stationary phase- all substrate in media is used up. Rate of growth in cells slows down and then stops.

Decline phase- cell death occurs due to cell lysis causing decrease in total num of cells.

Front 7

4 steps in binary fission

Back 7

DNA replication, elongation, septum formation, separation.

Front 8

Great plate count anomaly

Back 8

The observation that most microbes seen in the microscope cannot currently be grown under laboratory conditions.

Front 9

Cryptic growth

Back 9

Small increases in cell number due to growth on nutrients releaased following death of other cells in the culture.

Front 10

What happens in stationary phase of bacterial growth

Back 10

Eventually the population growth experienced in the lag phase begins to declines as the available nutrients becomes depleted and waste products start to accumulate. Bacterial cell growth reaches a plate or stationary phase when the num of dividing cells equals the num of dying cells. This results in no overall. Pop growth.

Front 11

Bacterial numbers and bacterial mass

Back 11

Bacterial nums. Are mesured by being counted as live viable cells by playing onto growth media or as total numbers (live and dead) by counting bacteria as particles (microscopy). Bacterial mass: determined by measuring turbidity of culture in liquid medium using a spectrometer or by using protein conc. and comparing with know. Protein conc. using a standard.

Front 12

2 mechanisms employed by psychrophiles

Back 12

-By having enzymes that operate at low temps by having (fewer hydrophobic amino acids and greater affinity to water) and also fewer hydrogen and ionic bonds within tertiary structures-more flexible.

-Flexible cytoplasmic membranes with more unstaurated short chain fatty acids in lipids.

Front 13

2 factors that determine minimum growth temp of psychrophylic mircobes.

Back 13

Need enzymes that operate at low temps tend to be unstable at slightly high temps. Minimum growth is at or below 0. More flexible cell membranes suit cold conditions

Front 14

Thermophiles and hyperthermophiles

Back 14

Thermophiles- temp optimumabove 45degress. Found in decomposing piles and surface soils.

Hyperthermophiles- temp optimum above 80degrees. Have restricted geothermal habitats- need high temps

Front 15

4 reasons why H2O is a good solvent

Back 15

-It's is a good liquid solvent- particles are at a good medium density.

-Remains a liquid over wide range of temps 0-100degrees

-high heat capacity and high heat of evaporation

Has high surface tension

Front 16

Intracellular pH of alkaliphiles and and acidophiles

Back 16

Always near neutral no matter the external pH tollerance. This is because DNA is acid-liable and RNA is alkaline-liable.

Front 17

Explain why many extreme halophiles use KCL instead of NACl as there compatible solute.

Back 17

Because they cannot get a low water availability of the cell using NaCl so they have to use a different solute to get a low intracellular water content to the environment to stay at a positive tuber pressure.

Front 18

List two toxic oxygen species (both name and chemical formula) and enzymes that detoxify them.

Back 18

H2O2(hydrogen peroxide) Enzyme that removes hydrogen peroxide is catalase.

02- (superoxide anion) superoxide dimutase will convert will convert it to H2O2 which can then be removed by catalase.

Front 19

What is pasteurisation and it's benefits

Back 19

Process of heat processing a liquid or a food to kill pathogenic bacteria to make it safe to eat or drink. It is effective as it results in a 5log (99.99%) reduction in microorganisms and has a very minor effect on the nutritional content of the food/liquid being pasteurized.

Front 20

List three types of radiation that can be used for microbial growth control and their mode of action

Back 20

Ionising radiation- eg microwaves and infared which has thermal effects.

Ultraviolet-damages DNA and reduced viability used for decontamination of surfaces.

-Ionising radiation (x-ray, gamma Ray's) create enough energy to make electrons and hydrocyl and hydrogen radical s that are designed to cause rapid damage to macromolecules within cells.

Front 21

Three broad categories growth control

Three broad categories growth control

Three broad categories growth control

Back 21

Cide-cidal: kills. Irreversibly inhibit cellular processes. Will rapidly decrease viable cell count and not effect the total cell count. Static- inhibits growth(intereferes with protein synthesis. Viable cells and total cell count don't change. Lytic- destabilizes cells(disrupts cell structure)this causes cell lysis which means a decrease in total cell count and viable cells.

Front 22

Chemical atimucribal agent effective against all bacteria and it's mode of action.

Back 22

Sterilant- will kill all bacteria and endospores

Front 23

Household antimicrobial agents

Back 23

Sterilants- kill all bacteria and endospores. Used to kill microbes when heat treatment isn't possible and used to control known contaminants in an environment.

Disinfectant- kill vegetatitve cells but not endospores, suitable for routine infection control.

Sanitizers- reduce viable cell count and therefore reduce chance of infection.

Antiseptics-sanitizers and disinfectants at lower concentrations used for application to living tissues-hands. Topical application

Front 24

Role of regulatory system bacteria

Back 24

Improve fitness or organsim and ability to produce max num of cells resources allow.

-control the amount of enzymes/proteins produced in the cell at level of transcription/translation.

-control activity of proteins/enzymes via post translational regulatory processes.

Front 25

Function of global control systems and function of catabolite repression

Back 25

Global control systems regulate the expression of many diff gene's simultaneously. Catabolite repression is an example of a global control system which ensures the best carbon source is used first. The lac operon would transcribe genes that lead to the metabolism of lactose. If there is no lactose present, and glucose is still present then the repressor will stay bound. Lactose must be present when there is no glucose, inorder to prevent lactose repressor from being bound.

Front 26

Two components regulatory systems are important in controlling cellular metabolism. 2 proteins involved, their location and function.

Back 26

Sensor kinase protein-found in cytoplasmic membrane and is responsible for detecting environmental stimuli.

Response regulator protein- DNA binding protein that regulates transcription, found in cytoplasm

Front 27

What is quorum sensing and how does it work for. We

Back 27

Mechanism by which bacteria and some archaea communicate with other cells to access their population density. Works by: all species of bacteria produce a specific autoinducer signalling molecule. These diffuse across the cell envelope. Once the autoinducer reaches high enough conc. The response will be initiated. Once at high enough concentrations it binds to an activator protein or sensor kinase and triggers transcription of genes that signal the beginning of the response.

Front 28

Stringent repsonse nutrient and environmental stress and what regulatory molecules trigger this response. And an example.

Back 28

Shuts down the synthesis of macromolecules causing the cell to become dormant the cell also activates stress survival pathways. The stringent response is triggered by two proteins guanosine tetraphosphate ppGpp and guanosine pentaphosphate pppGpp which accumulate in the cell during a stressful event, stopping macromolecule production. An example of this is an E. coli that survive in animal intestines. They are in perfect high nutrient environments in the intestines in the body but once they are excreted out of the body and into the environment they experienced low nutrients and must exhibit a stringent response in order to survive

Front 29

Describe the function and importance of the (pho) phosphate regulon.

Back 29

Important for cells due to a cells high demand for phosphate (P) for things like DNA, RNA, membrane synthesis, energy generation and cell signalling. The phosphate regulon works using a two component regulatory system which regulates extracellular enzymes, Pi transporters and storage enzymes which together help accumulate phosphate for the cell. The phosohate regulon can also repress many genes and control some aspects of pathogenesis.

Front 30

Which system is involved in the general stress response, and what stress is this responding to?

Back 30

RpoS regulon, responds to harsh conditions stress situations such as extreme pH and oxidative stress. controlled by the RpoS sigma factor which controls many genes that allow the cell to adapt to survive stressful conditions.

Front 31

What is the key protein involved in regulating chromasome regulation in E coli.

Back 31

DnaA-ATP

Front 32

Which two processes facilitate the rapid replication of the bacterial genome.

Back 32

bidirectional replication. By having multiple replication forks allowing replication to occur much faster

Front 33

Which system ensures the equal distribution of chromosomes during cell division in most bacteria

Back 33

Par(partitioning) system

Front 34

What role do the following proteins play in cell division.

Back 34

FtsA- ATP hydrolyzing enzyme, which provides energy for divisome assembly.

FtsK-assists in chromosome replication

Ftsl- involved in peptidoglycan synthesis.

FtsZ-forms a ring of proteins around the centre of the cell and is the point with septum formation occurs so the cell can divide.

ZipA-anchors the FtsZ ring to the cytoplasmic membrane.

Front 35

What is the role of the min proteins during cell division.

Back 35

Min proteins assist FtsZ in locating the midpoint of the cell so that it can initiate growth and division.

Front 36

Which molecule facilitates the transport of new glycan units across the cytoplasmic membrane and how does it achieve this.

Back 36

Bactoprenol transport new glycan units across the cytoplasmic membrane. It does this by making the glycan units hydrophobic so they can cross the membrane.

Front 37

What is transpeptidation and how do we inhibit and stop the synthesis of new cell walls and what provides the energy for transpeptidation

Back 37

Transpeptidation is the formation of the cross Links between muramic acid residues in adjacent glycan chains. This transpeptidation step can be inhibited by antibiotic penicillin which causes the cell to lyse, stopping synthesis of the cell wall. Removal of the d-alanine is what supplies the energy for the this reaction to take place.

Front 38

With which structures are the oldest identifiable bacterial fossils associated, and what organisms are most likely to be part of those structures.

Back 38

Stromatolites were the fossilised microbial mats which contained filamentous prokaryotes. It was anoxygenic Phototrophic filamentous bacteria which formed ancients stromatolites.

Front 39

Why is it unlikely that life arose on the surface of the planet, and why is the subsurface hypothesis more plausible.

Back 39

it is unlikely that life of rose on the Earth's surface due to the dramatic conditions at the time such as temperature fluctuations, mixing from meteor impacts, dust clouds and storms. The subsurface hypothesis is more plausible due to the conditions being more stable in the hydrothermal springs at the ocean floor such as a steady and abundant supply of energy and the likely first sources of organic compounds (eg.fatty acids), that could have reacted with sulfides.

Front 40

What is the RNA world theory and why is it plausible?

Back 40

The RNA world hypothesis is the idea that the first replicating systems were rna-based. It is plausible as RNA is good at binding free molecules and has catalytic activity. Evidence of this hypothesis is shown in the ribosome. The mechanisms of translation are catalyzed by RNA. This suggests that the use of RNA by early life forms to carry out chemical reactions precedes the use of proteins.

Front 41

What was the great oxidation event in why is it significant for life on earth

Back 41

The great oxidation event was the biologically induced appearance of molecular oxygen in the Earth's atmosphere. This caused a mass extinction but was also the key event that allowed for the evolution of multicellular eukaryotes.

Front 42

What are the two hypothesises for the endosymbiotic origin of eukaryotes and what data supports one there in the most.

Back 42

The first one is that Eukaryotes began as a nucleus bearing lineage that later acquired mitochondria and chloroplasts by endosymbiosis.

the second hypothesis is the hydrogen hypothesis which explains that the eukaryotic cell arose from the intercellular association between hydrogen producing bacteria (symbiont) which gave rise to mitochondria and a hydrogen consuming archael host.

The most data supported hypothesis is the hydrogen hypothesis as it is shown that eukaryotes have similar lipids and energy metabolism methods to bacteria and also eukaryotes have transcription and translational machinery most similar to archaea.

Front 43

A classic experiment involving a phototrophic organism demonstrates how rapidly microbial evolution can occur within a population of cells. What attributes of the metabolism of this model organism were important for the study and what did the experiment show.

Back 43

An experiment involving an organism named rhodobacter, which has two different metabolisms, if light is present it will grow phototrophicly and if light is not present it will go chemotrophicly. In the experiment, mutants that appeared that had no pigments were lost in light. In the dark, it was shown that non-pigmented mutants increased their abundance and out competed the pigmented organisms.

Front 44

What are the three genes which are most widely used in phylogenetic information.

Back 44

Small subunit 16s rRNA gene, recA, gyrB .

Front 45

Why rRNA molecules useful for phylogenetic analysis.

Back 45

They are functionally constant across all microbes, have an essential/central biological function, are sufficiently conserved/slow-changing (so good for looking at large scale evolutionary changes), and are of sufficient length.

Front 46

Why are some regions of the 16s rRNA molecule more sequence variable than others.

Back 46

Some regions are highly conserved because their precise sequence is essential to the function of the RNA and so many mutations here would likely result in the death of the organism, not passing on the mutation. mutations can be neutral persist how weather in the lesser send you areas so here is where the sequence is more variable.

Front 47

Bacterial taxonomy has traditionally relied on phenotypic analysis as the basis for classification, what are the key phenotypic characteristics of taxonomic value.

Back 47

Nutrition, environmental conditions, antibiotic sensitivity, pigmentation, shape, fertility, cell inclusion, surface layers, key enzymes and gram stain.

Front 48

What is polyphasic taxonomy

Back 48

The combination of phenotypic analysis and genotypic analysis to identify and classify microbial species.

The combination of phenotypic analysis and genotypic analysis to identify and classify microbial species.

Front 49

Why is evolutionary change in genes much more constrained in thermophiles than mesophiles.

Back 49

Thermophiles are generally closer to the root of the phylogenetic tree, and their existing genes code for already thermally resistant proteins, however any changes are likely to lead to denaturation. Therefore mutations are more likely to be harmful rather than neutral, and so don't persist.

Front 50

What is ribotyping.

Back 50

Identifying microbes from the analysis of DNA fragments generated from restriction enzyme digestion of single subunit rRNA genes (gel electrophoresis). Its specific and rapid and has a clinical applications but is being overtaken by sequencing in lab settings.

Front 51

Why and when is DNA:DNA hybridization usedful.

Back 51

It is a useful compliment to single subunit are RNA sequencing. It measures that percent of hybridization between the same sequence of DNA from two different types of bacteria. The more hybridization, the more closely related the species are. 25 to 70% indicates the species are of the same genus, 70 to 100% indicates they are the same species. This makes it is good for differentiating between closely related species.

Front 52

What is glucogenesis

Back 52

formation of glucose from phosphoenolpyruvate and CO2. Used when the cell isn't growing on a hexose but still needs glucose for biosynthesis.