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Flashcards in Bacteria basics Deck (73)
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1
Q

What are bacteria?

A

Very small and morphologically simple organisms lacking a nuclear membrane, multicellularity or complexity.

A group of organisms which are capable of degrading almost anything and living almost anywhere.

Capable of exponential growth and have sophisticated methods of growth regulation.

Contain most of the evolutionary diversity on Earth, and store half of the world’s carbon.

2
Q

What do bacteria possess?

A

Cytoplasmic membrane
Cell wall
Flagellum
Magnetosome

3
Q

What is Brownian motion?

A

Constant movement due to collisions with water molecules meaning that they hardly coast if they stop powering their movement, due to the relative viscosity of water.

4
Q

Consequences of their shape?

A

Only soluble material can enter the cell, and only by diffusion.

Maintain small structures in order to limit internal gradients, so the whole of a small cell therefore has the same chemical makeup.

Small cell can actually exceed demand due to high SA:Vol ratio.

5
Q

Link between mitochondria and bacteria?

A

Complex infolding on mitochondria to increase surface area for ATP production are seen in bacterial membranes as mitochondria originated from bacteria.

6
Q

What is binary fission?

A

The cells elongate and then form a partition (septum) which eventually separates the cells into two daughter cells.
The septum is a result of the inward growth of the cytoplasmic membrane and cell wall from opposite directions until the daughter cells are pinched off.

7
Q

Why are some bacteria classified as extremophiles?

A

Can live almost anywhere on Earth.
Min temp: -137 degrees Celcius
Can use iron as a food source when living in a stream bed.

8
Q

Consequences of no nuclear membrane?

A

Ribosomes can attach to mRNA as it is being synthesised so simultaneous transcription and translation can occur.

9
Q

Some key genetic features

A
No sexual reproduction. 
All mutations are immediately effective as they are haploid. 
Circular nucleoid. 
Supercoiled DNA. 
Sexually isolated (species issue).
10
Q

Conjugation?

A

A pilus forms between the two organisms, transferring DNA in one direction. Source of variation in addition to mutations occurring.

The donor bacterium carries a DNA sequence called the fertility factor, or F-factor. The F-factor allows the donor to produce a thin, tubelike structure called a pilus, which the donor uses to contact the recipient. The pilus then draws the two bacteria together, at which time the donor bacterium transfers genetic material to the recipient bacterium. Typically, the genetic material is in the form of a plasmid, or a small, circular piece of DNA.

11
Q

Main features of flagellum?

A

Energy efficient.
All of bacteria’s external features spontaneously assemble as there is no cytosis.
Helical twist to act as a propeller.
Cells cans sense chemotaxis and move away/towards a stimulus.

12
Q

Functions of the cell membrane?

A

Solute transport and respiratory electron transport.

13
Q

Two types of cell wall?

A

Gram positive and gram negative.

14
Q

What are the main features of gram positive cell walls?

A

Very strong and determines cell shape.
Outside of the phospholipid bilayer is a thick sac of murein chains/sheets called peptidoglycan.

Show a big evolutionary divide.

15
Q

What are the main features of gram negative cell walls?

A

Peptidoglycan is sandwiched between bilayer and the outer membrane.
The space between the membranes is called the periplasmic space.

16
Q

How to test the difference between Gram positive and negative?

A

Gram positive will stain purple due to presence of more Peptidoglycan.

17
Q

What is peptidoglycan?

A

Forms cell backbone layer for strength. Able to let sugars, amino acids and ions into the cell as needed.

18
Q

What phenetic characters can be used for bacterial classification?

A

Morphological characters: gram stain & motility.

Biolog: different carbon source in each well and see which bacteria can use each substance.

19
Q

Phenetic species concept?

A

A group of organisms that look similar to each other and distinct from other groups.
A form of artificial classification.

20
Q

Biological species concept?

A

A reproductively isolated group, whose genes do not combine with those of outsiders, but are able to combine continually by sexual reproduction within the group.
A form of natural classification.

21
Q

How is strain denoted?

A

An additional name is added to binomial name. Often related to pathogenicity as this can majorly affect humans.
Might relate to one single important gene product.

22
Q

What is transformation?

A

Genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane.

For example, dsDNA from environment can bind to the outside of the cell. Endonuclease digests ds to ss. The ssDNA associates with competence proteins so cell wall is altered to let DNA pass through more easily. The other strand gets replaced by donor DNA.

23
Q

What is transduction?

A

Process by which foreign DNA is introduced into a cell by a virus or viral vector.

24
Q

Consequences of horizontal gene transfer?

A

If very common and promiscuous – all bacteria would share a common gene pool and all belong to same species
If very uncommon and confined to intra-species exchange – very little gene pool mixing and the taxonomic unit could be individual clone
If common but confined to intra-species exchange – reproductive isolation and mixing of species gene pools would give equivalent of Biological Species Concept

25
Q

What is ribosome sequence analysis?

A

Universal mechanism of protein translation so is a good molecule for comparison.

The ribosome is a mixture of ribosomal RNA and protein. Various parts of the structure is responsible for different functions.

Failure of ribosomal function is lethal so very strong purifying selection.

Ribosomal DNA can be assumed to be monophyletic as doesn’t undergo HGT - too large.

rRNA is a universal chronometer suitable for all organisms, a chronometer suitable for very long and very short evolutionary times, suitable for phylogeny of bacteria.

26
Q

Why is it hard to describe bacteria?

A

Many bacteria cannot be cultured as the niche conditions cannot be reproduced. This is why bacteria were commonly described using phonetic characters.

Now use rRNA.

27
Q

How to tell if a bacteria exists in a certain area?

A

Make a complementary strand, with radioactivity/fluorescence and can easily stain a kingdom.

28
Q

Ecological species concept?

A

A species is a set of organisms adapted to a particular set of resources, called a niche, in the environment.

29
Q

Where does most of the biodiversity come from?

A

The enormous metabolic flexibility, as all the prokaryotes are small and look simple

30
Q

What does unity of biochemistry mean?

A

The metabolic flexibility derives mainly from diversity in fuelling reactions rather than from biosynthesis.

Biosynthetic pathways are similar in all organisms and building blocks start from the same point.

31
Q

What do most biological reactions involve?

A

A change in oxidation state (transfer of electrons to an internal carrier).

32
Q

What does an energy yielding reaction involve?

A

Releasing bond energy which is captured in ATP or GTP.

33
Q

In which pathways are the 12 essential precursors synthesised?

A

Glycolysis
Krebs Cycle
Pentose phosphate shunt

34
Q

External requirements for growing life?

A
Carbon for biosynthesis 
Electron acceptors 
Mineral nutrients for biosynthesis 
Energy 
Electron donors 
Water
35
Q

Yield of ATP during glucose metabolism?

A

In E.Coli, 38 mol of ATP per 72g glucose.

36
Q

How is most ATP generated?

A

By oxidising NADH2, via a membrane electron transfer chain. Energy is generated via a proton motive force generated by pumping protons across the membrane.

37
Q

Phototrophs?

A

Phototrophs synthesise all their building blocks from the precursor metabolites.

38
Q

Autotrophs?

A

Autotrophs rely on other life forms to form some building blocks.

39
Q

Alternative sources of energy?

A

Light: Cyclic photophosphorylation in purple bacteria. Transfers energy to bacteriochlorophyll, molecules, different pigments absorb different parts of the light spectrum

Chemoautotrophy: Prokaryotic only. The synthesis of an organism’s energy by the oxidation of electron-donating molecules in the environment. Synthesise all necessary organic compounds from carbon dioxide.

40
Q

Alternative sources of electron acceptors?

A

Anaerobic respiration:
Many externally sourced electron donors: sulphate and nitrate. Energy yield is lower than with oxygen. Methanogenesis is a form of anaerobic respiration which produces methane.

Lithotrophy:
Photosynthesis using water.

41
Q

Alternative sources of carbon?

A

Carbon dioxide.

Chemoautotrophs are organisms that synthesise all necessary organic compounds from carbon dioxide. Use inorganic energy sources, and are extremophiles that live in hostile environments. Tend to be the primary producers.

42
Q

Alternative sources of nitrogen?

A

Nitrogen fixation.

Nitrogenase converts atmospheric Nitrogen into Ammonium. A widespread ability amongst bacteria and archaea suggesting likely lateral gene transfer.

43
Q

Which biochemistries are unique to bacteria?

A

Chemoautotrophy
Anaerobic respiration
Anaerobic photosynthesis
Nitrogen fixation

44
Q

What is chemotrophy?

A

Any of various forms of nutrition in microorganisms in which energy is derived from the oxidation of simple organic or inorganic chemical compounds without the involvement of light.

45
Q

Why are bacteria so useful in biotech?

A
  1. Fast growth on cheap substrates
  2. Growth and composition are very predictable
  3. Enormous evolutionary depth
  4. Exotic biochemistries and physiologies
  5. Rapid evolution into new niches
  6. Tolerant of extreme conditions of temp, pH
  7. Relatively easy to genetically modify
46
Q

Steps of using bacteria in biotech?

A
  1. Define the product
  2. Identify known microbes with desired activity
  3. Develop enrichment parameters and screening assays
  4. Define source of organisms – culture collections, environmental sample
  5. Define enrichment for target microorganisms – batch enrichment culture
  6. Isolation of targets and screening of targets for activity
  7. Product development/optimisation
  8. Scale up & Production
47
Q

Gallium example?

A

280 000 kg per year is the current demand. Used in the electronics industry.

Source: bauxite mining waste.

Bayer liquor waste is high ph and toxic.

Conventional extraction is expensive and polluting. Acid leaching.

Biotech extraction allows for recovery of 60% of Gallium. Isolated by three types of alkalophilic bacteria.

48
Q

An example in agriculture?

A

Use of nitrogen fixing bacterial inoculants. Trials show that routine inoculation with Rhizobium is cost effective.

49
Q

De-odorising treatments for sewage plants?

A

Use hydrogen sulphide-degrading bacteria to form a biological scrubber unit which has total annual savings of $30, 000 per year instead of the chemical scrubbing
By converting 25-40% of chemical scrubbers worldwide would represent $1-3 billion and net savings of $0.25-2 billion per year

50
Q

Where can heat stable proteins be found? And what can they be used for?

A

Foun in hydrothermal vents, where there is a temperature range of 70-106 degrees. Can be used for washing powders.

51
Q

Where is heat stable DNA polymerase isolated from and what is it used for?

A

Thermus aquaticus, originally isolated from Yellowstone Park is the basis of an industry with a $5 billion annual turnover (2015).

Heat stable DNA polymerase (Taq polymerase) allows artificial amplification of DNA via PCR

52
Q

How to increase the yield?

A

Stronger promoter.
Duplicate the genes.
Convert to an extracellular protein by changing the lead sequence.

53
Q

Do prokaryotes have exons?

A

No. They have very small intergenic regions compared to eukaryotes.

54
Q

Describe bacterial genomes?

A

Mostly single, circular chromosomes.

Episomal elements include plasmids and phages which are mostly circular.

55
Q

Gene content of genome?

A

As the genome size increases, as does the repertoire of genes encoded and metabolic capacity.

Genomes are highly compact. As the size increases as do the number of genes. Follows a linear relationship.

56
Q

Mobile DNA in prokaryotes?

A

Conjugative plasmids promote sexual conjugation between different cells, which allows for mobilisation of the chromosome/plasmid.

Transposons are sequences of DNA that move from one location in the genome to another.

Insertion sequences are DNA sequences repeated at various sites on the bacterial chromosome.

57
Q

Meaning of pangenome?

A

All the genes available to a particular bacterium. Entire gene set of all strains of a species. Includes genes present in all strains, and genes present only in some strains of a species.

58
Q

What genes are included in the core genome?

A

DNA replication
Ribosomes
Cell envelope
Key metabolic pathways

59
Q

What genes are included in the accessory genome?

A

Alternative metabolic pathways

Transport systems

60
Q

What is “Muller’s ratchet”?

A

Small asexual populations are vulnerable to the accumulation of deleterious mutations which can lead to reductive evolution.
As soon as one individual begins to carry at least one deleterious mutation, no genomes with fewer mutations can be expected to be found in future generations – genetic load
Eventually the genetic load becomes so great that the population goes extinct
Relies on genetic drift

61
Q

What are pathogens?

A
  • viruses including bacteriophages
  • bacteria (not archaea)
  • single celled eukaryotes (fungi and protists)
  • multicellular eukraryotes (helminthes)
  • host derived infections (incl certain infectious cancers)
62
Q

What can infection be?

A

Pathological (disease)
Commensal (benefit and neutral effects)
Symbionts (both benefit)

63
Q

Lifecycle of a lytic bacteriophage?

A

Bacteriophage infect their bacterial host.
Replicate at the expense of their host.
Phage particles are released back into the environment by bacterial lysis.
The phage life cycle is complete when they infect another bacterium.

64
Q

Example of a STD?

A

Chlamydia.
Resides permanently in the host population without an environmental reservoir. Affects 4.2% of women and 2.7% of men.
Relatively small genome.
Evidence from genome sequencing for high rates of recombination among strains - must be a consequence of mixed infections.
Doesn’t necessarily have symptoms so easily spread.

Exists in two cellular types:
Elementary bodies infect host cells but are non-growing and have a rigid cell wall.
Reticulate body has a fragile cell wall due to its growing form. This is non infectious.

Elementary infect cells then turn to reticulate which then convert to elementary to infect more cells.

The Chlamydia trachomatis chromosome (STD type) lacks a gene encoding the protein FtsZ which is a key protein involved in septum formation during binary fission.

65
Q

What is horizontal transmission?

A

Passing of infectious agents amongst different individuals, could be through coughing, sex, etc.

66
Q

What is vertical transmission?

A

Passing of infections from parent to offspring. Could be inter-cellular or via milk/during birth.

67
Q

What is host immunity?

A

When a host becomes immune to further infections and so gets removed from the transmission system. The duration of protection can vary up to lifetime immunity.

68
Q

Example of a childhood disease?

A

Measles.
Passes from one host to another via a respiratory route in humans.
Single infection provides lifelong immunity.
Virus and its disease becomes extinct in small island populations.

69
Q

What is an acute infection?

A

Occurs over a short period of time during which they pass onto another host, making them vulnerable to immunity or excess host death.

Establishing a chronic infection can avoid this by remaining inactive in the host before becoming reactivated (e.g. chicken pox which has latency in nerve cells before a reactivation results in replication in the skin producing infectious lesions).

70
Q

What is a species leap?

A

Pathogens that have evolved in one host species occasionally infect another host species. The recipient species - dead end hosts won’t be capable of passing on transmission (e.g. Rabies – spread among hosts by biting, virus spreads through nervous system and can cause changes in behaviour when reaches brain). If transmission among new species becomes established then a new infectious cycle emerges – the concern when new pathogens invade human populations.

71
Q

What is a multi host transmission system

A

Pathogens take advantage of one species in order to infect another.

Costly to the pathogen as they have to survive in a variety of different environments & evade a variety of immune responses

72
Q

Example of a multi host transmission system

A

Schistosomiasis

Humans are infected by contact with contaminated water, by penetration of the skin. Reside in the veins.
Eggs are made and move to intestine, released into environment
Eggs hatch and infect snails
Release cercariae which then infect humans

73
Q

Define chemoheterotroph?

A

Unable to fix carbon to form their own organic compounds. Can utilise inorganic energy sources such as sulphur, or utilise organic energy sources such as carbohydrates, lipids and proteins.