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Intro To Biology > 4.5 Viruses and Prokaryotes > Flashcards

4.5 Viruses and Prokaryotes Flashcards

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1
Q

Viruses

A

Obligate intracellular parasites that must have access to host’s cells to function

Only able to infect cells containing the correct receptors

non-cellular and lack the ability to metabolize and grow

Unknown whether they respond to external stimuli

Genetic code is heritable allowing for adaptation and evolution but completely dependent on their host for reproduction

Diverse group that infects all domains of living organisms

Adapt to their changing environments and evolve through natural selection

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2
Q

Virion

A

an individual viral particle

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3
Q

Origin of viruses

A

A single virus has been found in the fossil record from 30,000 year old permafrost in Siberia

Remnants of ancient viral genes are found in “junk” DNA of living species

Researchers generally agree that viruses don’t share a single common ancestor

Three hypotheses of virus evolution: regressive, progressive, and virus-first

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4
Q

Regressive hypothesis

A

AKA de-evolution hypothesis

Viruses were once free-living cells or intro cellular parasites that decreased complexity and eventually lost ability to reproduce on their own

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5
Q

Progressive hypothesis

A

AKA escapist hypothesis

Viruses arose from RNA or DNA, or from self-replicating mobile genetic material like transposons, that acquired the ability to leave their native host cell for another

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6
Q

virus-first hypothesis

A

Viruses existed as the first self-replicating entities, predating cells

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7
Q

Baltimore classification system

A

Developed in early 1970s by Nobel prize-winning virologist David Baltimore

Grouped based on how they produce the positive-strand mRNA from the genome needed to produce required proteins

Groups include dsDNA, ssDNA, dsRNA, (+)ssRNA, (-)ssRNA, ssRNA-RT, dRNA-RT

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8
Q

Retroviruses

A

Virus that contains reverse transcriptase that converts their RNA to DNA which can then be incorporated into the host genome

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9
Q

Group I virus

A

dsDNA: mRNA is transcribed from the dsDNA genome

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10
Q

Group II virus

A

ssDNA: ssDNA genome is converted to dsDNA before transcription

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11
Q

Group III virus

A

dsRNA: mRNA transcribed from the dsRNA genome

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12
Q

Group IV virus

A

(+)ssRNA or positive sense single straaquirednded RNA: genome acts as mRNA or several rounds of transcription produce mRNA

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13
Q

Group V virus

A

(-)ssRNA or negative sense single stranded RNA: genome transcribed to +mRNA to be used as mRNA

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14
Q

Group VI virus

A

ssRNA-RT: ssRNA converted to dsDNA by RT and then incorporated into host genome for transcription

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15
Q

Group VII virus

A

dsDNA-RT: dsDNA converted to ssRNA intermediate that acts as mRNA, ssRNA converted to dsDNA by RT for replication

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16
Q

Capsid

A

Shell made of protein subunits called capsomeres that package the contents of a virus

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17
Q

Envelope

A

Outer shell of some viruses, composed of phospholipids and associated proteins

Contain matrix proteins that increase stability of outer membrane, but don’t make them invulnerable to changes in temperature, pH, and certain chemicals

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18
Q

Helical capsids

A

Long cylinders

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19
Q

Icosahedral capsids

A

Multifaceted three-dimensional spheres formed from 20 equilateral triangles

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20
Q

Enveloped viruses

A

Can have an icosahedral or helical capsid

Possess a plasma membrane derived from their host surrounding the capsid

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21
Q

Complex viruses

A

Can have icosahedral and helical shapes with an outer cell wall or have the two shapes put together to form a head and tail

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22
Q

Bacteriophages

A

AKA phage

Viruses that infect bacteria

Many have an icosahedron head and helical tail

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23
Q

Viral glycoproteins

A

On the outer layer of many viruses

Attach to viral receptors on host cell, initiating key events early during the infection process

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24
Q

Permissive cell

A

Host cell that allows virus to attach and also use the cell to replicate

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25
Q

Effects of viral infection on cell

A

Viral replication cycle after the biochemistry, structure, and function of host cell frequently causing damage

May go through apoptosis to minimize amount of virions produced

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26
Q

Lytic cycle

A
  1. Attachment: capsid protein or envelope glycoprotein of virion binds to receptor on membrane of host cell
  2. Penetration: genetic material enters through endocytosis, fusion, or injection
    - If capsid enters host cell an uncoding process occurs in which the capsid is degraded
    - Low pH can promote uncoding
  3. Replication of viral genetic material and capsids
    - Exact mechanism varies from group to group
  4. Assembly: packaging viral genome into new capsids
    - Enveloped viruses obtain an outer membrane from host as well
    - Can be passive and occur spontaneously or active (requiring enzymes)
  5. Release: method depends on virus and can occur through lysis or exocytosis
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27
Q

Latency

A

A lag between when the virus infects the host, and when it replicates and affects the host

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28
Q

Lysogenic cycle

A

Viral DNA becomes integrated with host genome

Only seen in bacteriophages

  1. Phage attaches to the cell surface of bacterium
  2. Viral DNA enters the bacterial cell
  3. Virus DNA integrates into bacterial DNA
  4. Integrated prophase replicates when bacterial DNA replicates
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29
Q

Prophage

A

Bacteriophage genome that has been incorporated into a bacterial genome

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30
Q

Lysogen

A

Bacterial host whose DNA has integrated bacteriophage DNA

May cause lysogenic conversion

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31
Q

Induction

A

Shifting from lysogenic to lytic cycle

Can be triggered by environmental factors

Phage DNA removed from host DNA and enters lytic cycle

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32
Q

Lysogenic conversion

A

Bacteria infected by phage that exhibit new phenotype

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33
Q

Prion

A

Proteinaceous infectious particles that contain no genetic code

Extremely hardy and don’t break down in the intestinal tract

Disease caused by irregular variant of a normal protein produced by the host

Cause the brain to form lesions and spread by eating nervous tissue of an infected individual

Replicate by entering a cell binding to the normal version of the protein, and converting it into the infectious variant, forming a new prion, making replication exponential

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34
Q

Bovine cattle encephalopathy

A

“mad cow” disease

Spongiform encephalopathy caused by a prion

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35
Q

Creutzfeldt-Jakob disease

A

Humans can develop it by eating beef infected with BSE

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36
Q

Viroids

A

Small, circular ssRNA particles that aren’t housed in a capsid nor produce proteins

Sole function is to reproduce RNA sequence using host cellular machinery

Viroid diseases infecting agricultural crops cause losses costing millions of dollars every year

37
Q

Hepatitis D

A

Has viroid properties since it can only replicate in the presence of the hepatitis B virus

38
Q

Microbial mats

A

Consist mostly of bacteria, although archaea are sometimes present

The individual prokaryotes in a microbial mat carry out different metabolic functions

Can be found in damp areas

39
Q

Analysis of 16S ribosomal DNA

A

Has provided insight into some evolutionary relationships between different groups of bacteria

40
Q

Woese’s 11 groups of bacteria

A
  • gram-positive
  • chlamydiae, green nonsulfur, – actinobacteria
  • planctomycetes
  • spirochaetes
  • fusobacteria
  • Cyanobacteria
  • thermophilic sulfate reducers
  • acidobacteria
  • proteobacteria
41
Q

Bacterial taxonomy

A

Bergey’s Manual of systematic bacteriology

ICBM and LPSN taxonomy

Does not fit into traditional Linnaean taxon comic system, but when used authorities recognize over 1000 phyla

42
Q

Archaea clades

A

korarchaeota, euryarchaeota, crenarchaeota, nanoarchaeota

43
Q

Korarchaeota

A

Primitive archaeans only found in hot springs and deep sea vents

44
Q

Euryarchaeota

A

Includes methanogens and halobacteria

45
Q

Crenarchaeota

A

Includes many thermopiles and sulfur-dependent extremophiles

46
Q

Nanoarchaeota

A

Obligate symbionts of a crenarchaean

47
Q

Diplobacilli

A

(diplococci) pairs of cells

48
Q

Streptobacilli

A

(streptococci) chains of cells

49
Q

Staphylococci

A

Clusters of cells

50
Q

Archaean plasma membrane

A

Phospholipid composed of phytanyl sidechains instead of fatty acids seen in bacteria

Sometimes monolayer instead of bilayer

51
Q

Gelatinous capsule

A

Additional layer surrounding the cell wall that serves as camouflage from a host’s immune system and to aid in attachment to surfaces

52
Q

Nucleoid region

A

Condensed genetic material of a prokaryote

53
Q

Invaginations

A

(or infoldings) in the plasma membrane of a prokaryotic cell that function in photosynthesis or respiration

54
Q

Peptidoglycan

A

A polymer consisting of polysaccharide chains cross linked with peptides

55
Q

Penicillin

A

Antibiotic that inhibits peptidoglycan cross-linking

Effective defense against gram-positive bacteria

56
Q

Binary fission

A

Primary form of reproduction by prokaryotes

Results in formation of two identical daughter cells

DNA replicated, cell enlarges and produces material for a new cell wall, septum forms through equatorial region of the cell, cell pinches inward to form two separate cells

No recombination or exchange of genetic material

57
Q

Transformation

A

Fragments of DNA are taken in from environment and incorporated into genome

DNA fragments released to environment by ruptured or dead cells

58
Q

Transduction

A

During a bacteriophage’s switch from lysogenic stage to lytic cycle, imprecise excision of viral DNA from host genome may cause one or more bacterial genes to be packaged into the capsid

Genetic material is then transferred from one cell to another when infected by the same virus

59
Q

Conjugation (bacteria)

A

Duplication and transfer of a plasmid from a donor cell to a recipient cell

A donor cell extends a long, hollow pilus to a recipient cell forming a conjugation bridge

Donor cell replicates a plasmid by threading one of the DNA strands through the conjugation bridge while the recipient cell adds the complementary strand to form its own copy of the plasmid

Plasmid can later be reintegrated with bacterial genome at the nucleoid region

60
Q

Nitrogen fixation

A

Nitrogen in air is converted to ammonia and nitrates

Atmospheric nitrogen gas cannot be used by most living things

Ammonia can be used to build amino acids

Nitrates in the soil can be used by plants

61
Q

Symbiotic roles of prokaryotes

A
  • mutualism
  • commensalism
  • parasitism
62
Q

Mutualism

A

Prokaryotes live in GI tract of many animals

In humans they help produce certain vitamins such as b-12 and vitamin k and digest some proteins and carbohydrates

In many animals that eat grass and woody plants, such as cattle and termites, bacteria that live in the gut digest cellulose for them, allowing them to receive nutrients

63
Q

Commensalism

A

Symbiosis in which one species benefits and the other is unharmed

Bacteria inhabiting skin consume and metabolize their host’s sweat but cause no harm

64
Q

Parasitism of prokaryotes

A

Pathogenic prokaryotes are considered parasites

Harm host by infecting them

65
Q

Uses of genetically engineered bacteria

A

Production of pharmaceutical agents, antibiotic, enzymes, vitamins

66
Q

Use of bacillus thuringiensis

A

Used in biological control to produce natural toxins that target pest insects such as mosquitoes, black flies, and agricultural pests.

67
Q

Bioremediation

A

Bacteria are used to degrade or remove pollutants from the air, water, and soil

68
Q

Pathogens

A

Infectious microorganisms responsible for causing illness

69
Q

Robert Koch

A

German physician and early supporter of the germ theory of disease

70
Q

Koch’s postulates

A

Link specific microorganism to a disease

  1. The microorganism can be found in high abundance in symptomatic individuals. The microorganism isn’t present in healthy individuals.
  2. The microorganism can be isolated from a symptomatic individual and grown in a laboratory culture.
  3. Inoculating a healthy individual with the cultured microorganism produces the disease
  4. The microorganism in the inoculated, diseased individual can be retrieved and identified as the same microorganism from the original diseased host

Have been significant revised within the field of modern microbiology:

Seemingly heathy individuals can be asymptomatic carriers

Pathogens little viruses and prions can’t be cultured

Complex disease associations can’t be linked by a simple set of methodological principles

71
Q

Horizontal transmission

A

Spread of an infection from one person to another usually due to contact with bodily fluids

72
Q

Outbreak

A

Disease occurs suddenly and in high numbers within an area

73
Q

Epidemic

A

Disease outbreak spreads to a greater number of people over a larger area

74
Q

Pandemic

A

Declared if original outbreak rapidly spreads to multiple countries, continents, or entire globe

75
Q

Oncogenic viruses

A

Have the capacity to cause cancer

HPV → cervical cancer

Long-term hepatitis B → liver cancer

76
Q

Vaccine mechanism

A

Expose healthy individuals to small amounts of inactivated viruses specific proteins or subunits of a virus, or live, attenuated viruses

Help develop immunity by imitating infection so immune system can produce T cells and antibodies to fight that infectious agent

77
Q

Attenuated virus

A

Weakened virus

78
Q

Influenza

A

Causes fever, sore throats runny nose, coughing, and exhaustion

Symptoms begin two days after exposure and can continue for 1-2 weeks

Individuals are contagious about 2-7 days after infection

Typically caused by influenza A virus which occurs naturally in wild birds and several other animal species

Influenza A subtyped based on glycoproteins on surface of viral envelope

79
Q

HIV-1

A

Enveloped (+)ssRNA retrovirus

Primarily attacks CD4+ helper T-cells, macrophages, and other immune cells

Causes AIDS leading to the eventual failure of the immune system

Arose through zoonosis when it crossed the species barrier from chimpanzees to humans in West Africa during the early 1900s

80
Q

Ebola

A

Virus causes fever , sore throat, muscle pain, headaches, rash, and hemorrhage, both internal and external bleeding

Transmitted through contact with bodily fluids

Symptoms develop within a few days or weeks of infection

Mortality of about 50% but can be as high as 90%

Death occurs about onset of symptoms

Enveloped (-)ssRNA viruses with a long filamentous shape

Infects monocytes, macrophages, liver cells, fibroblasts, and endothelial cells

Replication of virus triggers inflammatory response and can lead to sepsis

81
Q

COVID-19

A

SARS-CoV-2 or severe acute respiratory syndrome coronavirus 2 is an enveloped (+)ssRNA virus in the coronavirus family

Infects cells in the respiratory tract by exploiting their ACE2 (angiotensin-converting enzyme) cell surface receptors to gain entry

Bats have been identified as an animal reservoir though scientist are still evaluating the possibility of an intermediate mammalian host in the zoonotic jump to humans

Symptoms include fever, dry cough, shortness of breath, and fatigue

82
Q

Hypothetical archaean pathogens

A

Of prokaryotes, only bacteria are known to cause disease, though it is speculated that the high similarity between archaean and eukaryotic proteins could mean that symptoms of hypothetical archaean pathogens might present similar to autoimmune disease

83
Q

Biofilms

A

Thin films of bacteria that stick to surfaces

84
Q

Tuberculosis (structure and treatment)

A

Caused by Mycobacterium tuberculosis

Weakly gram-positive aerobic bacillus with an outer membrane

Difficult to treat due to outer structure and existence of drug-resistant strains

Invade air sacs in the lungs and consumed by alveolar macrophages, where they reproduce

Other immune cells that aid the macrophages form inflammatory granulomas

In granulomas, can evade destruction by cytotoxic T lymphocytes or entering dormant state

These granolas, characterized by necrosis in their centers, are called tubercles

85
Q

Tuberculosis (stats, symptoms)

A

1% infection rate per year

Estimated that about 1/3 of world’s population is infected, though mostly dormant

Most cases in Africa and South East Asia

90% of cases produce latent, asymptomatic disease

Symptoms include fever, weight loss, and fatigue

Symptoms of pulmonary TB include chest pain productive cough, and in up to 20% of cases extra-pulmonary spread of disease

86
Q

Tuberculosis disease process

A
  1. Mycobacteria enter the air sacs in the lungs
  2. Mycobacteria are consumed by alveolar macrophages
  3. Immune cells surround the infected macrophages
  4. The immune response forms a granuloma
  5. Mycobacteria reproduce within the granuloma and are released
  6. Mycobacteria disperse to continue the infection cycle
87
Q

Foodborne illness

A

Symptoms include nausea, vomiting, diarrhea, cramps, and fever

Severe complications or death can occur it bacteria enters blood stream

Common culprits include viruses such as norovirus and hepatitis A and bacteria such as salmonella, escherichia coli, campylobacter, and listeria

Can be avoided by washing hands, practicing safe food handling, storing refrigerated foods below 40°F keeping raw foods separated from other foods, cooking meats to their recommended temperatures, and avoiding raw or unpasteurized dairy products

88
Q

MRSA

A

Methicillin-resistant Staphylococcus aureus

Gram-positive non-spore forming coccus that grows in clusters or chains

Staphylococcus aureus typically found on the skin and upper respiratory tract but causes disease if able to enter other tissues

Symptoms include red pustular bumps, fever, or deeper abscesses that reach into the soft tissue under the skin

Life-threatening if untreated and can cause necrotizing fasciitis or toxic shock syndrome

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