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Chapters 19 & 27 - Coggle Diagram
Chapters 19 & 27
Concept 27.6
- Mutualistic bacteria
- Human intestines are home to about 50-1k species of bacteria
- Intestinal bacteria cells collectively outnumber all human cells in the body by a factor of 10
- Pathogenic bacteria
- all pathogenic prokaryotes are bacteria, bacteria cause about half of all human diseases
- Some bacterial diseases are transmitted by other species
- ex: Lyme disease which can cause arthritis, heart disease etc. is carried by ticks
- Pathogenic prokaryotes cause disease by releasing exotoxins and endotoxins
- Exotoxins are proteins secreted by bacteria that can cause disease even if the bacteria are no longer present
- ex: cholera is a diarrheal disease caused by an exotoxin secreted by a vibrio cholerae
- Endotoxins are lipopolysaccharide components of the outer membrane of gram - bacteria
- they are released only when bacteria die and their cell walls break down
- ex: endotoxins released by species in the genus Salmonella cause food poisoning
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- Since the intro of antibiotics in 1940s, resistance to antibiotics has evolved rapidly in many bacteria
- Discovery of new antibiotics has not kept pace w the rate at which bacteria have evolved resistance
- For every antibiotic now in use atleast one species of bacteria has developed a resistance to it
- Rapid reproduction enables bacterial cells carrying resistance genes to quickly produce large numbers of resistant offspring
- Resistance genes spread rapidly within and among bacterial species by horizontal gene transfer
- High lethal, drug resistant strains of tuberculosis bacteriam have arisen since 2006
- by 2017 more than 100 countries had confirmed cases of the resistant strain
- few treatment options are available, and they are more toxic than treatments for standard strains
- A new class of antibiotics called malacidins was recently discovered through metagenomic analysis of soil bacteria
- Malacidins are effective against multi-drug-resistant gram + pathogens
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- Virus like particles capable of targeting and killing particular species of multidrug resistant bacteria were developed in 2018
- Humans reap many benefits from bacteria including many food productions: cheese, yogurt, beer, wine, pepperoni, fermented cabbage & soy sauce
- Experiments using prokaryotes have led to important advances in DNA technology
- E. coli is used in gene coding
- DNA polymerase from Pyrococcus furiosis is used in the PCR technique
- CRISPR-Cas9 system: which helps prokaryotes defend against viral attack has been developed as a gene altering tool
- this system has been used to study HIV the virus that causes AIDS
- Bacteria can be used to produce natural plastics
- Engineering bacteria to produce ethanol from agricultural waste, switchgrass and corn can help reduce dependence on petroleum
- Prokaryotes can also be used in bioremediations, the use of organisms to remove pollutants from soil, air or water
-ex: bacteria that metabolize oil can be used to increase the breakdown of oil following a spill
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Concept 19.2
- Viruses replicate only in host cells
- Viruses are obligate intracellular parasites which means they can replicate only within a host cell
- Each virus has a host range, a limited number of host species that it can infect
- Some viruses have broad host ranges while others are able to infect only one species
ex: measles virus only infects humans
- General features of viral replicative cycles
- the viral genome enters the host cell in a variety of ways
- Once a viral genome has entered a cell the cell begins to manufacture viral proteins
- the virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP and other molecules
- Viral nucleic acid molecules and capsomeres spontaneously self assemble into new viruses
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- Replicative cycles of phages
- phages are the best understood of all viruses
- Phages have two alternative reproductive mechanisms: lytic cycle and the lysogenic cycle
- The lytic cycle is a phage replicative cycle and culminates in the death of the host cell
- the lytic cycle produces new phages and lyses (breaks open) the host's cell wall, releasing the progeny viruses
- a phage that reproduces only by the lytic cycle is called a virulent phage
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- The Lysogenic Cycle replicates the phage genome without destroying the host
- the viral DNA molecule is incorporated into the host cell's chromosome
- Phages that use both the lytic & lysogenic cycles are called temperate phages
- a temperate phages called lambda is widely used in biological research
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- the integrated viral DNA is known as a prophage
- every time the host divides, it copies the phage DNA and passes the copies to daughter cells
- an environment signal can trigger the virus genome to exit the bacterial chromosome and switch to the lytic mode
- Some prophages are expressed during lysogeny, and some cause the host bacteria to secrete toxins that are harmful to humans
- Bacteria have their own defenses against phages
- Natural selection favors bacterial mutants w surface proteins that cannot be recognized as receptors by a particular type of phage
- foreign DNA can be identified as such & cut up by cellular enzymes called restriction enzymes
- the bacterium's own DNA is protected from the restriction enzymes by being methylated
- both bacteria and archaea can protect themselves from a viral infection w the CRISPR-Cas system
- it's based on sequences called clustered regularly interspaced short palindromic repeats (CRISPRs)
- Each spacer sequence between the repeats corresponds to DNA from a phage that had infected the cell
- Particular nuclease proteins interact w the CRISPR region; these are called CRISPR associated Cas proteins
When a phage infects a bacterial cell that has the CRISPR-Cas system, the phage DNA is integrated between two repeat sequences
- if the cell survives the infection, it can block any attempt of the same type of phage to reinfect it
- the attempt of the phage to infet the cell triggers transcription of the CRISPR region
- the resulting RNA's are cut into pieces and bound by Cas proteins
- the Cas proteins use the phage-related RNA to target the invading phage DNA
- the phage DNA is cut and destroyed
- Natural selection favors phage mutants that can bind to altered cell surface receptors or that are resistant to enzymes
- the relationship between phage and bacteria is in constant evolutionary flux
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- Replicative Cycles of Animal Viruses
- there are two key variables used to classify viruses that infect animals:
- RNA or DNA genome, either single-stranded or double-stranded
- the presence or absence of a membranous envelope
- whereas few bacteriophages have an envelope or an RNA genome, many viruses have both
- Viral envelopes
- many viruses that infect animals have a membranous envelope
- Viral glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell
- the viral envelope is usually derived from the host cell's plasma membrane as the viral capsids exit
- other viral membranes form from the host's nuclear envelope and are then replaced by an envelope made from Golgi apparatus membrane
ex: herpesvirus
- Evolution of Viruses
- Viruses do not fit our definition of living organisms
- since viruses can replicate only within cells, they probably evolved as bits of cellular nucleic acids
- Candidates for the source of viral genomes include plasmids and transposons
- Plasmid, transposons and viruses are all mobile genetic elements
- the largest virus identified about 20 years ago is the size of a small bacterium
- its genome encodes proteins involved in translatioin, DNA repair, protein folding and polysaccharide synthesis
- there is controversy about whether this virus evolved before or after cells
-in the past decade several even larger viruses have been identified; how these evolved is an unresolved question
Concept 19.3
- viruses and prions are formidable pathogens in animals & plants
- diseases caused by viral infections affect humans, agricultural crops and livestock worldwide
- smaller less complex entities called prions also cause disease and animals
- Viral diseases in animals
- viruses may damage or kill cells by causing the release of hydrolytic enzymes from lysosomes
- some viruses cause infected cells to produce toxins that lead to disease symptoms
- other have molecular components such as envelope proteins that are toxic
- A vaccine is a harmless derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen
- Vaccines can prevent certain viral illnesses, such as smallpox, rubella, mumps and others
- viral infections cannot be treated by antibiotics
- Antiviral drugs can help to treat, not cure, viral infections by inhibiting synthesis of viral DNA and by interfering w viral assembly
- Emerging viruses are those that suddenly become apparent
- HIV, the AIDS virus is a classic example
- the ebola virus is one of several emerging viruses that cause hermorrhagic fever, an often fatal illness
- in 2014 a widespread outbreak (epidemic) of Ebola virus occurred
- In 2017, 2018, and 2019, smaller outbreaks occurred in the democratic republic of the congo
- other examples: chikungunya virus and Zika virus (2015)
- Flu epidemics are caused by type A influenza viruses; these infect a variety of animals & humans
- Strains of influenza A are given standardized names based on the viral surface proteins hemagglutinin (HA) and neuraminidase (NA)
- As of 2017 18 types of HA and 11 types of neuraminidase have been identified
- The H5N1 strain is quite deadly because it is very different from influenza strains circulating among people for a long time
- it is thus difficult for people to mount an effective immune response to this strain
- However it has not caused an epidemic because it is not transmitted from person to person
- A deadly strain of H1N1 originally called the swine flu, was not actually transmitted to humans from pigs
- Instead the story was more complex, H1N1 was a unique combination of swine, avian and human influenza genes
- An epidemic of H1N1 occurred in2009 reaching 207 countries infecting over 600,000 people and killing almost 8000
- A global epidemic like this is called a pandemic
- Influenza viruses have 9 RNA segments in their genome, leading to many new genetic combinations and also have a high rate of mutation
- Normal seasonal flu viruses are not considered emerging viruses because variants of these viruses have been circulating among humans for a long time
- However, these viruses still undergo mutation and reassortment
- Variations thought to be most likely to occur each year are selected to generate vaccines
- Changs in host behavior or the environment can increase the spread of viruses responsible for emerging diseases
- New roads into a remote area may increase spread of viral diseases
- The use of insecticides and mosquitos nets may help prevent the spread
- It is possible that global climate change may allow mosquitoes that carry viruses to expand their range
- One cause of rapidly emerging viral disease in humans is mutation of existing viruses into new ones that can spread more easily
- a second cause is the spread of a viral disease from a small, isolated human population
- a third cause is the spread of existing viruses from other animals
- it's estimated that about 3/4 of new human diseases originate in this way
- 2000 viral diseases of plants are known and cause spots on leaves and fruits, stunted growth and damaged flowers or roots
- Most known plant viruses have an RNA genome
- Many have a helical capsid, while others have an icosahedral capsid
- Plant viruses spread disease by two major routes
- horizontal transmission entering through damaged cell walls
- veritcal transmission inheriting the virus from a parent
- Prions are infectious proteins that appear to cause degenerative brain diseases in animals
- Scrapie in sheep, mad cow disease and Creutzfeldt-Jakob disease in humans are all caused by prions
- Prions are incorrectly folded proteins can be transmitted in food act slowly and are virtually indestructible
- Prions are somehow able to convert a normal form of a protein into the misfolded version
- Then several aggregate into a complex that can convert more proteins to prions which join the chain
- Prions might also be involved in diseases such as alzheimers and Parkinson's disease
- There are many outstanding questions about these small infectious agents
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Concept 27.2
- 3 factors contribute to high levels of genetic diversity observed in prokaryote populations
- rapid reproduction
- mutation
- genetic recombination
- Cells produced by binary fission are generally identical but differences can arise through mutation
- Mutation rates typically low but accumulate rapidly w short generation times and large populations
- Rapid production of genetic diversity in prokaryote populations enables rapid adaptation by natural selection
- prokaryotes are highly evolved
- Genetic recombination, the combining of DNA from two sources contributes to prokaryote diversity
- DNA from different individuals can be combined by transformation, transduction, or conjugation
- Movement of genes between individual prokaryotes of different species is called horizontal gene transfer
- In transformation, prokaryotic calls incorporate foreign DNA taken up from their surroundings
- ex: a nonpathogenic cell could take up a piece of DNA carrying allele for pathogenicity & replace its own allele w the foreign allele
- resulting recombinant cell would be pathogenic
- In transduction, phages (from "bacteriophages" viruses that infect bacteria) carry prokaryotic genes from one host cell to another
- Transduction is generally an unintended result of the phage replicative cycle
- Conjugation is the process in which DNA is transferred between two prokaryotic cells
- In bacteria, the DNA transfer is always one way; One cell donates the DNA & the other receives it
- In E.coli conjugation occurs by the following steps:
- A pilus of the donor cell attaches to the recipient
- the pilus retracts pulling the two cells together
- DNA is transferred through a temporary structure called the "mating bridge"
- A piece of DNA called the F(fertility) is req for the production of pili
- The F factor can exist either as a plasmid or a segment of DNA w /in the bacterial chromosome
- Cells containing the F plasmid (F+ cells) function as DNA donors
- Cells lacking the F factor (F- cells) are recipients
- An F+ cell can convert and F- cell to an F+ cell if it transfers an entire F plasmid to the F- cell
- If only part of the F plasmid DNA is transferred, the recipient cell will be recombinant
- Cells that have the F factor in their chromosome (Hfr cell: high frequency recombination) function as donors during conjugation
- Homologous segments of the chromosomal DNA from the Hfr cell recombines w that of the F-cell
- recombinant recipient cell becomes a new genetic variant on which evolution can act
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- Antibiotics kill most bacteria but not those w R plasmids, plasmids that carry resistance genes
- Some R plasmids carry genes for resistance to multiple antibiotics
- R plasmids also have genes that encode the pili used to transfer DNA between the cells, enabling the rapid spread of resistance
Concept 19.1
A virus is an infectious particle consisting of genes packaged in a protein coat. They are structually simpler than prokaryotic cells.
- viruses can cause a wide variety of diseases but cannot reproduce or carry out metabolism outside of a host cell.
- Viruses lead a "borrowed life"
- Discovery of viruses: Tobacco mosaic disease
- In 1800s researchers blamed a small bacteria, late work suggested that the infectious agent did not share features w bacteria (like growing on nutrient media)
- In 1935 Stanley confirmed his latter hypothesis by crystalizing the infectious particle, now known as tobacco mosaic virus (TMV)
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- Structure Viruses
- Viruses are not cells
- a virus is a very small infectious particle consisting of nucleic acid enclosed in a protein coat & in some cases a mebranous envelope
- the simple structure of viruses make them a useful biological system
- Some viruses have accessory structures that help them infect hosts
- Viral envelopes (derived from membranes of host cells) surround the capsids of influenza viruses and many other viruses found in animals
- Viral envelopes contain a combination of viral host cell molecules
- Bactriophage also called phages are viruses that infect bacteria
- they have an elongated capsid head that encloses their DNA
- a protein tail piece attaches the phage to the host and injects the phage DNA inside
- Viral Genomes
- double stranded or single stranded DNA
- double stranded or single stranded DNA
- Viruses are classified as DNA viruses or RNA viruses
- the genome is either a single linear or circular molecule of the nucleic acid
- viruses have between 3 & 2000 genes in their genome
- Capsids & Envelopes
- Capsid: the protein shell that encloses the viral genome. They are built from protein subunits called capsomeres.
- A capsid can have a variety of structures; associated viruses may be referred to as helical or icosahedral viruses
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Concept 27.1
- Prokaryotes were the first organisms to inhabit Earth
- Most are unicellular, but some species form colonies
- Most prokaryotic cells are 0.5-5um, much smaller than the 10-100um of many eukaryotic cells
- They have a variety of shapes including spheres (cocci), rods (bacilli) and spirals
- Cell surface structures, cell wall maintains shape,protects the cell and prevents it from bursting in a hypotonic environment
- Most prokaryotes lose water and experience plasmolysis in hypertonic environments
- Salt is used as a preservative because water loss slows reproduction of food-spoiling prokaryotes
- Eukaryote cell walls are made of cellulose or chitin
- Most bacterial cell walls instead contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides
- Archael walls contain a variety of polysaccharides & proteins but lack peptidoglycan
- Scientists use Gram Stain to classify bacteria by cell wall composition
- Gram-positive bacteria have simpler walls w a large amount of peptidoglycan
- Gram-Negative bacteria have less peptidoglycan & are more complex w an outer membrane that contain lippolysaccharides
- Gram-Negative bacteria tend to be more resistant to antibiotics than gram positive bacteria
- Many antibiotics target peptidoglycan and damage gram + bacterial cell walls
-Humans cells lack peptidoglycan and are unaffected by antibiotics
- Many prokaryotes have a sticky layer of polysaccharide or protein surrounding the cell wall
- It is called a capsule if it's dense and well-defined, or a slime later if it's not well organized
- Both types enable adherence to the substrate or other individuals, prevent dehydration and protect the cell from the host's immune system
- Some bacteria form metabolically inactive endospres when water or nutrients are lacking
- The cell copies its chromosome and surrounds it with a multilayered structure
- Endospores can withstand extreme conditions & remain viable for centuries
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- Some prokaryotes have hairlike appendages called fimbriae that allow them to stick to their substrate or other individuals in a colony
- Pili (or sex pili) are longer than frimbriae and function to pull cells together enabling the exchange of DNA
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- Internal Organization
- Prokaryotic cells lack complex compartmentallization
- Some prokaryotes have specialized membranes that perform metabolic functions
- These are usually infoldings of the cell membrane
- Prokaryotes have less DNA and produce fewer proteins than the eukaryotes
- Prokaryotes have one circular chromosome; eukaryotes have two circular chromosome multiple linear chromosomes
- Prokaryotes lack a nucleus; the chromosomes is in the nucleoid a region w no membrane
- Prokaryotes may also have smaller rings of independently replicating DNA called plasmids
- There are minor differences in DNA replication, transcription and translation between eukaryotes & prokaryotes
- These differences allow antibiotics to kill or inhibit bacterial cell growth without harming human cells
- Reproduction
- Prokaryotes reproduce quickly by binary fission and can divide every 1-3 hours under optimal conditions
- There are 3 key features of prokaryote biology
- small
- reproduce by binary fission
- short generation times
Concept 27.3
- Prokaryotes can be categorized by how they obtain energy and carbon
- phototrophs obatain energy from light
- Chemotrophs obtain energy from chemicals
- Autotrophs req CO2 or related compunds as a carbon source
- Heterotrophs requites an organic nutrient to make other organic compounds
- Energy & carbon sources are combined to give four major modes of nutrition
- Photoautotroph
- Chemoautotroph
- Photoheterotroph
- Chemoheterotroph
- Prokaryotic metabolism varies w respect to O2
- Obligate aerobes req O2 for cellular respiration
- Obligate anaerobes are poisoned by O2 and live by fermentation or use substances other than O2 for anaerobic respiration
- Facultative anaerobes can use O2 if it is present or carry out fermentation or anaerobic respiration if not
- Nitrogen is essential for the production of amino acids and nucleic acids in all organisms
- Prokaryotes metabolize nitrogen in many forms
- ex: some prokaryotes convert atmospheric N2 to ammonia (NH3) in a process called nitrogen fixation
- Prokaryote cells may cooperate to use resources unavailable to individual cells
- ex: anabaena, cells are specialized for nitrogen fixation or photosynthesis
- Nitrogen fixation is isolated in cells called heterocysts that prevent oxygen penetration
- Photosynthetic cells exchange carbs for the fixed nitrogen produced by the heterocysts
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- Cells of one or more prokaryote species cooperate to form surface-coating colonies called biofilms
- Cells near the edge release signaling molecules to recruit new cells
- Channels in the biofilm allow nutrients to reach cells in the interior and wastes to be expelled
- Biofilms are common in nature but can cause many problems for humans including
- corrosion of industrial structures and products
- contamination of medical devices
- tooth decay
- chronic, antibiotic resistant infections
Concept 27.4
- Prokaryotes date back to 3.5 billion years ago
- They now inhabit every environment known to support life
- Advances in genomics are just beginning to reveal the extent of prokaryotic diversity
- genetic analysis conducted in the 1970s led to the division of prokaryotes into Bacteria and Archaea
- In the past the polymerase chain reaction was used to analyze individual prokaryote genes
- metagenomic is used to obtain entire prokaryotic genomes from environmental samples
- Horizontal gene transfer has played a key roll in the evolution of prokaryotes
- Significant portion of the genomes of prokaryotes are mosaics of genes imported from other species
- Bacteria include the vast majority of prokaryotic species familiar to most people
- every major mode of nutrition and metabolism is represented among bacteria
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- Proteobacteria
- Gram - bacteria include photoautotrophs, chemoautotrophs and heterotrophs
- Heterotrophic proteobacteria include several pathogens
- Neisseria gonorrhoeae causes gonorrhea
- Vibrio cholerae causes cholera
- Helicobacter pylori causes stomach ulcers
- Chlamydia: All species parasitize animal cells and have gram negative walls lacking peptidoglycan
- Spirochetes: these bacteria are helical gram negative heterotrophs that sprial through the environment by the rotating internal filaments
- Many are free-living but others are pathogens
- Cyanobacteria: gram neg photoautotrophs, plant like chloroplasts likely evolved from cyanobacteria by the process of endosymbiosis
- Solitary and filamentous cyanobacteria are abundant components of fresh water and marine phytoplankton
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Concept 27.5
- If prokaryotes were to disappear, the prospects for any other life surviving on Earth would be dim
- Prokaryotes play a major role in the recycling of chemical elements between the living and non-living components of the enviroment
- Prokaryotes can convert some molecules to forms that are taken up by other organisms
- Autotrophic prokaryotes use CO2 to produce sugars and O2 that are consumed by other organisms
- Prokaryotes can immobilize or decrease the availability of nutrients by using them w/in their own cells
- Symbiosis: an ecological relationship in which two species live in close contact: a larger host w a smaller symbiont
- prokaryotes often form symbiotic relationships w a larger organism
- Mutualism: both symbiotic organisms benefit
- Commensalism: one organims benefits while neither harming nor helping the other
- Parasitism: an organisms called a parasite harms but does not kill the host
- Parasites that cause disease are called pathogens
- The existence of some ecosystems depends on prokaryotes
- ex: ecological communities of hydrothermal vents depend on the chemoautotrophic bacteria for energy