Class notes

Introduction to Microbiology

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Course
MICR271 (MICR271)

Institution
Queen’s University (QU )

Complete set of notes from Microbiology course including: -Microbial Evolution & Diversity -Impact of microbial structure on survival -Microbial metabolism and environmental influences -Replication, transcription, and regulation of gene expression -Interactions between microbes and the enviro...

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Uploaded on July 1, 2024
Number of pages 47
Written in 2018/2019
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Module 1- Microbial Evolution & Diversity
September 6, 2018 1:06 PM

Evolution and the role of microbes (Section 1)

> Connections between prokaryotes and eukaryotes

>3 Domains of life:
Prokaryotes;
• Bacteria
• Archaea

All organisms with nucleated cells
• Eukaryota

-All supported by endosymbiont theory
*endosymbiont theory; eukaryotes evolved more complex structures and metabolic processes by building upon prokaryotic attributes ..eukaryotes evolved from prokaryotes
>Mitochondria and chloroplast evolved from free-living bacteria via symbiosis within a eukaryotic host cell. Two key differences between mitochondria and chloroplast; these organell
contain their own DNA and a distinct translation system.
>α-proteobacteria = ancestor of mitochondria
>2 theories of mitochondrial symbiosis
1. Archezoan scenario; primitive mitochondrial eukaryote cell phagocytosed an α-proteobacterium which led to the evolution of the mitochondrion
2. Symbiogenesis scenario; single endosymbiotic event involving uptake of an α-proteobacterium by an archaeal cell led to the generation of mitochondria and led to the evolution of t
nucleus and compartmentalization of the eukaryotic cell (complexity of the eukaryotic cell came after the mitochondrial symbiosis)
>main difference: mitochondrion led to formation of eukaryotic cell, or formation of eukaryotic cell led to formation of mitochondrion
-Functional differences (ex; affects mechanisms of energy generation) and structural differences (affects steps in transcription/translation)

>Links between microbes and eukaryotes
-Microbe; microscopic living organism (prokaryotic or eukaryotic)
>simple multicellular organism
>eukaryote= complex multicellular organism (ex, animals, plants)

Categorizing organisms - phylogeny (Section 1B)

Phylogeny; the evolution of a genetically related group of organisms as distinguished from the development of the individual organisms

Q: What would account for the overlap between the different domains of life ?
-Archaea viewed as an intermediate between bacteria and eukaryota domains (shares characteristics of each, while bacteria and eukaryota have more evident differences). Archaea and
eukaryota diverges more recently than bacteria and eukaryota which could account for the similarities between the 2 domains as well as the similarities between bacteria and archaea (clo
to each other on the tree)

Micr 271 Page 1

,^Tree of life created based on comparisons of rRNA sequences

^Phylogenomic trees of life (based on genomes of organisms)
>assumes the higher the level of genetic similarity between 2 organisms, the more related they are evolutionarily.
-Lack of single cell root in current web of life supports that early life forms probably evolved from a population of primitive cells that differed in their genes. Links within web symbolize the
large amount of horizontal gene transfer (movement of genetic material between organisms other than by vertical transmission ex; transition of DNA from parent to child) of single/multip
genes that occur between unicellular organisms

Where did viruses come from? (Section 1C)

-Viruses are obligate intracellular parasites (cannot reproduce outside host cell; relies on intracellular resources/machinery)
-Virion ; viruses not inside a host
>consists of 2-3 parts:
-genetic material (DNA/RNA)
-capsid ("protein coat)
-envelope (layer of lipids surrounding protein coat)
-Three theories on the origin of viruses;
▪ Virus-first theory: viruses are ancestral to cells
>viruses evolved from macromolecules of nucleic acids and protein before cells appeared
>self-replicating units of RNA may have gained the ability to infect cells. RNA molecules (ribozymes) have enzymatic properties (can catalyze chemical reactions). The virus-like partic
then evolved into the RNA and DNA viral lineages by continuing to evolve within evolving hosts
▪ Escape theory: cells came before viruses; viruses derived from bits of cellular RNA/DNA fragments that leaked or 'escaped' fr om cells. These fragments become independent entities
and can interact with other cells when they acquire a protein
>viruses are derived from mobile genetic elements that may have resembled a specialized type of RNA called a retrotransposon ;a vesicle could have formed during cell fission,
engulfing a self replicating RNA with a coat-encoding RNA segment. Particle would continue to evolve through interactions with additional early cell types.
▪ Reduction theory: cells came before viruses ; viruses come from small primal cells that lost cellular elements over the cours e of evolution but maintained genetic material and certai
elements needed for replication
>viruses come from proto-cells that infected other cells and became dependent upon the host cell. As cellular elements were lost to evolution they mai ntained genetic material and
replication resources. The 'reduced' cells evolved into viruses while the more complex cells evolved into cells with a nucleu s
-Viral replication strategies
>uses their hosts machinery for transcription/translation of viral genes and proteins and replicate the viral genome
>can integrate their genetic information into host genome which can lead to the ability for the exchange of genetic material ; viral genome integration (animals) or lysogeny (bacterial
viruses)
-Viruses interact with all domains of life
>2 principal categories of life forms:

Micr 271 Page 2

, >2 principal categories of life forms:
-Viral; informational (genetic) parasites
-Cellular; genetically self-sustained organisms
>viruses can carry genetic information between different kinds of organisms and between domains = method in which genetic information can be transferred between unrelated specie
leading to increased genetic diversity in the web of life

The generation and impact of microbial diversity (Section 2)

Microbial diversity
-microbes most diverse, abundant cellular life forms on Earth
-extremophiles; organisms that live in harsh environments (areas of high temp, limited nutrient sources)
-not directly involved in infectious disease, but may contribute to the genetic info that confers successful infection strategies to pathogens

Q: How might the size of a microbe affect its fitness?

Classification of microbes

Hierarchy of recognized bacterial taxa: Kingdom, Phylum, Class, Order, Family, Genus, Species
Hierarchy of recognized viral taxa: Order, Family, Sub-family, Genus, Species

Selective Pressures result in microbial diversity
-microbes compete for nutrients, ability to transition into a less competitive environment promotes evolutionary adaptation to these environments
-Selective pressure; any phenomena that alters behaviour and fitness of a living organism in its environment
-in a environment where conditions and membership of bacterial populations shift, accumulation of adaptive mutations may result if new conditions stabilize and competition between
species is intense
-Thermophiles; microbes (hyperthermophilic bacteria, archaea) that have adapted through selective pressure capable of surviving in hot spring where there is high temp, extremely acidic
alkaline waters, etc.

Diversity of the human microbiome
-Human microbiome dominated by 4 phyla
1. Actinobacteria
2. Bacteroidetes
>most predominant bacteria in gut
3. Firmicutes
>Streptococci bacteria predominant in the mouth
4. Proteobacteria
-Bacteria in human microbiome can be grouped in 2 main types:
1. Pathogenic
>pathogens or opportunistic pathogens; take advantage of an opportunity not usually available to infect another organism (ex, weakened immune system)
>able to cause infection
2. Commensal bacteria
>non-pathogenic
>commensal; characterized by a biological relationship in which one species benefits and the other is neither benefited nor harmed
>symbiotic relationship with host
>large composition in human microbiome
-bacteria in microbiome have potential to express much greater number of different genes

Genetic diversity in bacteria
-to gain genetic diversity and pass it on to future generations, change must occur within their genome by:
1. Mutations
>can occur spontaneously (errors in DNA replication or repair) or induced by external agents (chemical mutagens in environment)
>can be deletions, replacements, inversions or insertions of a few or many base pairs
>most harmful, few may confer a selective advantage
2. Gene transfer and genetic recombination
>can occur through transformation, transduction, conjugation or transposition
>genetic info can be transferred via plasmids
>horizontal gene transfer = major mechanism for transfer of genetic info between unrelated organisms
-HGT can introduce new genes that may undergo recombination into the bacterial chromosome
HGT can occur through 3/4 gene transfer methods used in bacteria;

Transformation: uptake of naked genetic material from the surrounding
environment

Conjugation: direct transfer of genetic material from one bacteria to the
other (bacterial mating)

Micr 271 Page 3

, Conjugation: direct transfer of genetic material from one bacteria to the
other (bacterial mating)

Transduction: bacterial DNA moved from one bacteria to another by a virus,
often a bacteriophage

Transposition:
>"jumping" of genes from one chromosomal location to another within an organism
>allows translocation of a discrete DNA sequence (transposon) from one site to another within organism
>causes rearrangements of DNA and can result in a decrease/increase in gene expression depending on new arrangement; if transposon has inserted into the coding region of a gen
likely that gene will no longer be made. If inserted to a promoter region of gene, may increase the gene expression.

Q: Is transposition a mechanism that promotes HGT?
-Transposition not a method of HGT since HGT is the transfer of genetic material BETWEEN unicellular organisms and transposition occurs WITHIN an organism where a piece of DNA
transfers to a new site on a chromosome

Impact of HGT on human health-accumulation of virulence determinants
>commensal organisms can collect genes through HGT that enhance survival or their ability to invade the human host
Ex, in the gastrointestinal tract, iron (Fe) isn't readily available. Inflammation causes host cell lysis, making it more available. If microbes acquired a mechanism to take up Fe, it would
pose as a growth advantage during times of intestinal inflammation

-acquisition of virulence factors that enhance inflammation and cause tissue damage can increase the bacterium's ability to invade deeper into the tissues

Maintenance of genetic diversity
-maintenance of genetic diversity in the form of mutations or acquired genes makes sense if diversity is necessary for survival (the range of gene products are necessary to compete in a
population)
-if selective pressure is taken away, cost to maintaining unused genetic material (especially in the form of extrachromosomal DNA ; plasmids which require energy and resources to replica
may select against maintenance
-Fitness cost; reduced growth and persistence of bacteria in the host and environment or increased clearance from the infected host and reduced transmission between hosts
-initial fitness cost of mutations/acquired genes can be partly or fully restored by more compensatory mutations which correct for a loss of fitness due to earlier mutations

Relationship of genetic diversity to resistance (Section 2B)
-Antibiotic resistance genes occur naturally in microbes found in environment, but increased presence in the environment due to extensive antibiotic use by humans increase the spread o
resistance genes to broader range of organisms = multi-antibiotic resistant strains

Microbial diversity and the spread of antibiotic resistance
-antibiotic; any substance produced by a microorganism that is antagonistic to the growth of other microorganisms when highly diluted
-"postantibiotic era" references the widespread resistance to antibiotics in common use post-WWII

Origin of antibiotic resistance genes
-microbes produce compounds, some of which are antibiotics, to act as weapons, communicate with other microbes, and potentially to contribute to processes to protect their niche.
-antibiotic-synthesizing bacteria need to be able to protect themselves thus carry genes that allow resistance against the compounds they synthesize (Antibiotic resistome)
-some bacteria carry genes coding for enzymes capable of catabolizing antibiotics, therefore gaining energy from them and making them resistant
-widespread presence of antibiotics in environment selected for the evolution of highly specific resistance elements even though there isn't that much production of antibiotics (naturally)
-antibiotic production and resistance mechanisms can be spread between organism via HGT

Mechanisms of resistance of bacteria to antibiotics
-Multiple processes in which bacteria can develop resistance to antibiotics;
>Target protection; expression of a molecule impairing antibiotic recognition and activity
>Target substitution; alteration of amino acid sequences in target sites in bacteria

>Prevention of intracellular antibiotic accumulation; increased expression of bacterial efflux (flowing out) mechanisms which result in increased ability of bacteria to remove antibiotic fr
cell

>Antibiotic detoxification; increased ability of bacteria to alter or degrade antibiotic, therefore reducing antibiotic effects

Micr 271 Page 4

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