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Microbiology > Lecture Exam #2 > Flashcards

Lecture Exam #2 Flashcards

1
Q

Define taxonomy

A

The science of biological classification

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2
Q

List and define the 3 parts of taxonomy

A

1) Classification: based upon a selected scheme
2) Nomenclature: Assignment into taxa using rules
3) Identification: Determining where each organism fits

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3
Q

What are the 4 main reasons for classifying organisms?

A

1) Establish relationships, and to differentiate
2) We have only scratched the surface
3) Serves as valuable reference
4) Opens line of communication

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4
Q

How did Carl von Linne classify organisms?

A

-Used mainly anatomical characteristics
-Used 2 kingdoms and latinized names

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5
Q

How did Carl von Nageli classify organisms?

A

Bacteria and fungi into plant kingdom

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6
Q

What did Ernst Haeckel do for taxonomy?

A

He proposed Kingdom Protista

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7
Q

Edouard Chatton proposed the term ‘________’

A

prokaryote

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8
Q

Who founded the 5 kingdom system of taxonomy?

A

Robert H. Witaker

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9
Q

Who proposed the idea of 3 domains? What were they based on, and in what other three ways did they differ?

A

1) Carl Woese
2) Based on rRNA sequences
3) Also differ in membrane lipid structure, tRNA, and antibiotic sensitivity

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10
Q

Define phylogeny

A

The evolutionary development of a species

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11
Q

Name the 3 phylogenetic groups and define them

A

1) Monophyletic: organisms that arose from a single common ancestor
2) Paraphyletic: A common ancestor, but doesn’t include all descendents
3) Polyphyletic: Multiple origins and do not share a common ancestor

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12
Q

The binomial system consists of what 2 things?

A

Genus + species

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13
Q

True or false: the binomial system always italicizes genus and species

A

True

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14
Q

Define a strain. What does a strain descend from?

A

-Defined as a population of organisms that are distinguishable from others of the same species
-Descended from a single organism or pure culture

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15
Q

List the 3 ways strains can vary, and define them

A

1) Biovars: biochemical and physiological properties
2) Morphovars: morphological properties
3) Serovars: antigenic properties

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16
Q

Describe a type strain

A

-One of the first strains studied, it is the most characterized strain
-Most species have multiple type strains, depends on how much the species has been studied
-The strain that is the most typical for the species as a whole

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17
Q

What are the 3 broad ways to classify bacteria? Which is the most accurate?

A

1) Phenotypic classification
2) Analytic classification
3) Genotypic classification
-Genomic is most accurate

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18
Q

Define morphology

A

The form and structure of an organism or group of identical organisms

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19
Q

Differentiate between microscopic and macroscopic classification

A

1) Microscopic classification: shape, pattern of groups, staining
2) Macroscopic classification: colony morphology, pigment production

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20
Q

Differentiate between biotyping and serotyping

A

1) Biotyping: Biochemical markers
2) Serotyping: Detection of specific antigens

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21
Q

Define antibiogram patterns and phage typing

A

1) Antibiogram patterns: Susceptibility to various antibiotics
2) Phage typing: Susceptibility to viruses that infect bacteria; bacteriophages

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22
Q

Name 7 types of phenotypic classification

A

1) Morphology
2) Microscopic classification
3) Macroscopic classification
4) Biotyping
5) Serotyping
6) Antibiogram patterns
7) Phage typing

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23
Q

What type of classification requires expensive instrumentation (e.g. mass spectrometry) and is labor intensive?

A

Analytic classification

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24
Q

Give 4 examples of analytic classification

A

1) Cell envelope fatty-acid analysis
2) Whole cell lipid analysis
3) Whole cell protein analysis
4) Multilocus enzyme electrophoresis

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25
Q

Give 6 examples of genotypic classification

A

1) Guanine plus cytosine ratio
2) DNA hybridization
3) Nucleic acid sequence analysis
4) Plasmid analysis
5) Ribotyping
6) Chromosomal DNA fragment analysis

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26
Q

Name 4 classical characteristics used to identify organisms

A

Morphological, physiological/metabolic, biochemical, and ecological

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27
Q

What are the 2 main types of classical characteristics that can be used to classify organisms?

A

1) Physiological/ metabolic
2) Ecological

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28
Q

Name 4 physiological/ metabolic characteristics that can be used to classify organisms

A

1) Motility
2) Luminescence
3) Photosynthetic pigments
4) Energy sources

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29
Q

Name 5 ecological characteristics that can be used to classify organisms

A

1) Life cycle patterns
2) Symbiotic relationships
3) Ability to cause disease 4) Habitat preference
5) Growth requirements

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30
Q

What are the two main categories of characteristics that can be used to identify organisms?

A

1) Classical characteristics
2) Molecular characteristics

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31
Q

Name 5 molecular characteristics

A

1) Nucleic acid base composition
2) Nucleic acid hybridization
3) Nucleic acid sequencing
4) Genomic fingerprinting
5) Amino acid sequencing

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32
Q

Describe nucleic acid base composition

A

Usually measures G&C content, which usually only varies by ~10% in a genus

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33
Q

Describe nucleic acid hybridization

A

-Complete hybridization can occur if the organisms are identical
-Partial hybridization can occur if they’re related
-No hybridization if they’re not related

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34
Q

Describe nucleic acid sequencing and when it is best used

A

-Utilizes small subunit rRNAs (SSU rRNAs)
-Best measure for relatedness

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35
Q

Describe small subunit rRNAs (SSU rRNAs)

A

-The molecules of choice for phylogenetics
-Have the same role in all organisms
-Part of complex ribosome structure (intolerant of mutations)
-Very well conserved (change very slowly over time)

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36
Q

What are the molecules of choice for phylogenetics? Why?

A

SSU rRNAs, because they have the same role in all organisms and they’re very well conserved

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37
Q

What does genomic fingerprinting consist of?

A

-PCR: polymerase chain reaction
-Amplifies a region of the DNA, can be used to identify causative agents

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38
Q

Describe amino acid sequencing; what does it reflect and what can it be differentiated based on?

A

-Directly reflects mRNA sequences
-Can be differentiated based on charge, immunogenicity, and fragmentation

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39
Q

Define the root

A

The last universal common ancestor (LUCA) of the 3 domains

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40
Q

How do we know the eukarya and archaea have common ancestry at some point?

A

They share key proteins

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41
Q

What 3 considerations should be made for microbial genetic diversity?

A

1) The world environment(s)
2) The extraterrestrial
3) Microbial mechanisms
-Mutations and gene transfer

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42
Q

What is the root?

A

The last universal common ancestor (LUCA)

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43
Q

What does LUCA stand for and what does it mean?

A

1) Last universal common ancestor
2) Last common ancestry of the 3 domains (bacteria, archaea, and eukarya)

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44
Q

How do we know that Eukarya and Archaea had common ancestry at some point?

A

Eukarya and Archaea share key proteins

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45
Q

What 3 things should be considered when looking into microbial genetic diversity?

A

1) The world environment(s)
2) The extraterrestrial
3) Microbial mechanisms (mutations and gene transfer)

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46
Q

Name 2 microbial mechanisms

A

1) Mutations
2) Gene transfer

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47
Q

What is another word for anagenesis? What does it mean?

A

1) Genetic drift
2) Defined as small, random genetic changes that occur over generations

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48
Q

What 3 things contribute to anagenesis?

A

1) Extremely fast microbial growth
2) Type of mutation
3) Selection pressure (adaptive mutation)
-ex: pH, oxygen, temp, etc

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49
Q

Give 3 examples of selective pressures

A

pH, oxygen, temp

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50
Q

Name 4 mechanisms of genetic variation

A

1) Gene mutation 2) Gene duplication
3) Gene loss
4) Recombination

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51
Q

Name 2 models for evolutionary mechanisms of diversity and briefly describe them

A

1)Metapopulation model: Small changes (gradual)
2) Stable ecotype model: Rapid bursts of speciation

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52
Q

Describe the metapopulation model of evolutionary mechanisms of diversity

A

1) There are small changes in the environment along with small changes in the DNA of the organisms.
2) Patches (niches) of microbes can either expand:
a) Clonally
b) Heterogeneously
3) Migrate when nutrients wane
4) All local populations have a chance of extinction

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53
Q

Describe the stable ecotype model of evolutionary mechanisms of genetic diversity

A

1) Members of microbial population undergo genetic changes
2) So they outcompete the rest, which means that the winners advance and losers go extinct.
3) Results in rapid bursts of speciation.

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54
Q

Define ecotype

A

A population of microbes that’s genetically similar but ecologically distinct

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55
Q

Define a core genome (most conserved). Any variation in this genome is based on what?

A

The set of genes found in all members of a species; any variation in this genome is mutation-based.

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56
Q

Define pan-genome and name its 3 parts

A

1) The complete gene repertoire of taxon (all strains)
2) Core + ‘housekeeping’ + dispensable genes

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57
Q

Describe the 3 parts that make up the pan-genome of a species

A

1) Core: needed genes
2) ‘Housekeeping” genes: genes needed for normal growth and metabolism
3) Dispensable genes: extra genes you don’t need (genes for flagella, virulence factor genes, etc)

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58
Q

How is the pan-genome acquired?

A

By horizontal gene transfer (HGT)

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59
Q

1) What does horizontal gene transfer require?
2) What is the rate of transfer like in HGT?
3) What is HGT associated with?

A

1) Horizontal gene transfer requires a heterogeneous population
2) The rate of transfer is extremely variable
3) Associated with rapid adaptation to new environments

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60
Q

List and describe the 3 methods of horizontal gene transfer (HGT)

A

1) Conjugation: Physical connection between bacteria mediates transfer
2) Transformation: Uptake of naked DNA from the environment
3) Transduction: Viral transfer of DNA into bacteria

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61
Q

What 3 things is horizontal gene transfer important for?

A

1) Evolution
2) Adaptation
3) Pathogenicity

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62
Q

List 3 mechanisms of horizontal gene transfer (HGT)

A

Gene acquisition, plasmid acquisition, phage infection

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63
Q

Describe the importance of Bergey’s Manual of Systematic Bacteriology

A

1) Contains descriptions of all known bacterial and archaeal species
2) An extremely valuable reference for microbiologists

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64
Q

Describe the central dogma of bacterial genetics

A

1) From existing DNA to make new DNA (DNA replication)
2) From DNA to make new RNA (transcription)
3) From RNA to make new proteins (translation)

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65
Q

List and describe the 3 forms of DNA. Where are they typically found?

A

1) B form: the one typically seen
2) A form: a slightly tighter coil, found in dehydrated specimens
3) Z form: an even tighter coil, left-handed helix; unknown role in cells, but has been found in many animals (mammals, protozoans, plants) and may provide torsional strain relief (supercoiling)

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66
Q

What do complementary and antiparallel describe in terms of DNA?

A

1) Complementary: base pairing rules (A&T and C&G)
2) Antiparallel: backbones run in opposite directions

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67
Q

Describe DNA replication in microbes

A

1) Semiconservative replication
2) The two strands of the parental double helix unwind, and each specifies a new daughter strand by base-pairing rules.
3) “The daughter cells are born pregnant”; i.e. new DNA is already being formed in daughter cells as soon as they’re replicated.

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68
Q

Initiation of DNA synthesis predates what?

A

Any initiation of cell division

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69
Q

Name 3 features of DNA replication in bacteria

A

1) OriC: origin of replication
2) Replisome: where proteins and nutrients go to aid in replication
3) Ter: site where replication ends

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70
Q

Describe replication of the E. Coli chromosome

A

It’s bidirectional

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71
Q

Describe 3 ways a bacterial chromosome can be compacted

A

1) Can be circular
2) Negatively supercoiled, 3) Negatively supercoiled and mediated by DNA binding proteins (histone-like proteins).

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72
Q

DNA binding proteins are what kind of proteins?

A

Histone-like proteins

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73
Q

Describe why DNA may be negatively supercoiled and mediated by DNA binding proteins (histone-like proteins).

A

The nucleoid is supercoiled and compacted, and the scaffolding from the DNA binding proteins keeps it compact, but also allows regions of the chromosome to be accessible.

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74
Q

More organization of the chromosome allows for what?

A

Faster gene expression

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75
Q

Describe the bacterial chromosome, replication speed, error rate, and okazaki fragment length

A

1) Chromosome: circular, some linear
2) Replication speed: 1,000bp/s
3) Error rate: 10^-8
4) Okazaki fragment length: 1,500nt

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76
Q

Describe bacterial transcription and translation

A

Transcription: Polycistronic & no post transcriptional modification
-Ribosomes can jump around and translate several proteins at once
Translation: 50S, 30S ribosomes / Protein splicing

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77
Q

Define polycistronic transcription

A

Ribosomes can jump around and translate several proteins at once

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78
Q

Describe the eukaryotic chromosome, replication speed, error rate, and okazaki fragment length

A

1) Chromosome: Linear
2) Replication speed: 100bp/s
3) Error rate: 10^-10
4) Okazaki fragment length: 100nt

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79
Q

Describe eukaryotic transcription and translation

A

1) Transcription: Monocistronic mRNA & post-transcriptional modification
2) Translation: 60S, 40S ribosomes / Protein splicing

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80
Q

Describe the reading frame of transcription and translation

A

1) There’s a coding strand (5’-3’) and template strand (3’-5’) used during transcription; mRNA strand ends up looking the same as the coding strand but with U instead of T.
2) Then translation occurs via ribosomes to produce a polypeptide from the mRNA

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81
Q

What are the 3 stop codons?

A

UAA, UAG, and UGA

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82
Q

Describe the importance of redundancy in genetic code

A

The redundancy of the genetic code allows for mistakes to be made, since a single nucleotide mutation may still be able to produce the same amino acid as the original

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83
Q

Name 3 types of mutations and describe what they result in

A

1) Missense mutation: The changing of an entire nucleotide (i.e. T&A) and you are now coding for a different amino acid
-The least detrimental to a cell
2) Nonsense mutation: Results in a premature stop codon
3) Frameshift mutation: A nucleotide is lost and affects all downstream amino acids; usually a very different protein

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84
Q

What is the least detrimental mutation to a cell?

A

A missense mutation

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85
Q

What are the 3 possible outcomes of genetic mutations?

A

1) No effect (no change in phenotype)
2) Change in phenotype
3) Fatality

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86
Q

What are the two types of mutations?

A

1) Transition: purine > purine or pyrimidine > pyrimidine (staying the same type of nucleotide)
2) Transversion: purine <> pyrimidine (switching type of nucleotide)

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87
Q

What is the most common type of mutations?

A

Point mutations

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88
Q

What are the two main categories of mutations?

A

Point mutations and frameshift mutations

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89
Q

Define a transversion mutation and list its 3 possible outcomes

A

1) Transversion: purine <> pyrimidine (switching type of nucleotide)
2) a) None
b) Nonsense: truncated protein
c) Missense: different amino acid; altered protein

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90
Q

What are the two types of transversion mutations? What do each of these result in?

A

1) Nonsense: truncated protein
2) Missense: different amino acid; altered protein

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91
Q

List and define the 2 types of frameshift mutations

A

1) Deletion: deletion of 1 or more nucleotides
2) Insertion: the addition of 1 or more extra nucleotides

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92
Q

List 2 things that can cause mutations and give an example of each

A

1) Chemical mutation
-Ex: N-methyl-N-nitro-N-nitroguanidine can alter guanine into O^8 methylguanine
2) Environmental mutation
-Ex: The alteration of thymine with UV light into a thymine dimer

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93
Q

We must have ways to differentiate wild-type vs mutant; name and define what this process is called

A

Screening: detection system for a mutant phenotype

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94
Q

Name 4 kinds of mutations

A

1) Morphological mutations
2) Lethal mutations
3) Conditional mutations
4) Biochemical mutations

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95
Q

Give 2 examples of biochemical mutations and define them

A

1) Auxotroph: must obtain nutrient from the environment because it has lost the ability to synthesize it
2) Resistance mutant: resistance to a pathogen, chemical, antibiotic

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96
Q

Name 4 ways to screen for mutants

A

1) Replica plating
2) Mutant libraries
3) Phage-sensitivity
4) Plasmid selection

97
Q

Describe the replica plating process for screening for mutants

A

Involves creating two replica plates (one with complete medium and one with an incomplete media) and looking for a species that grows on the complete media but not on the incomplete media

98
Q

What does the Ames test do? Where has it previously been successful?

A

1) The Ames test is an inexpensive method using bacteria as test subjects to determine the potential carcinogenicity of a substance. (i.e. identifies mutagens)
2) Has been successful in identifying only half of animal carcinogens.

99
Q

Describe the Ames test

A

1) A culture of auxotrophs is plated onto two petri dishes; one with a minimal media with a small amount of histidine, and another with minimal media with a test mutagen and small amount of histidine.
2) Then the first dish may lead to a few spontaneous revertants (some eventually learn how to survive without histidine), and the second dish can lead to many revertants induced by the mutagen (if the mutagen is a mutagen, this dish should have more revertants/ survivors).

100
Q

Define genes, phenotype, and genotype

A

1) Genes: The basic unit of inheritance
2) Phenotype: features that are expressed (ex: blue eyes, metabolic trait, etc)
3) Genotype: the gene sequence that exists in an organism

101
Q

Describe cis acting elements and name 3 of them

A

1) Elements that are intrinsic to the DNA itself
2) Promoter, operator, and terminator

102
Q

Define promoter, operator, and terminator. Also, what do these 3 things have in common?

A

1) Promotor: areas where RNA polymerase binds and transcription starts
2) Operator: area where effectors bind to limit or allow transcription
3) Terminator: region of DNA that tells RNA polymerase to stop transcribing
4) They are all cis acting elements

103
Q

What’s the differences between cis and trans acting elements?

A

Cis acting elements are a part of the genetic code, trans acting elements are not a part of the DNA

104
Q

Name 3 things that help with gene organization

A

Operons, regulons, and trans acting elements

105
Q

Define operons and regulons

A

1) Operons: multi-gene organizations; often several genes in tandem, all controlled by the same promoter
2) Regulons: functional groups consisting of several operons; same promoter precedes [same condition (internal or external) activates transcription of multiple operons at the same time]

106
Q

Define constitutive expression and inducible operons

A

1) Constitutive expression: always expressed at high levels
2) Inducible operons: (+) or (-) control

107
Q

Name 4 types of trans acting elements

A

Repressors, activators, corepressors, inducers

108
Q

Describe what allows bacteria to build large structures quickly

A

Bacteria has many transcription factors and proteins because they’re organized in operons, which allows them to make large structures very quickly

109
Q

Name 2 genetic elements

A

1) Chromosome
2) Plasmid

110
Q

Describe what plasmids consist of

A

Always has an origin of replication, typically has an antibiotic resistance marker, an enzymatic marker gene, and RE cut sites

111
Q

What are RE cut sites made by?

A

Made by restriction enzymes that cut DNA.

112
Q

Describe plasmids:
1) Describe their size, and do they replicate independently?
2) Describe their shape and number of base pairs, 3) Are plasmids essential to growth?

A

1) Small genetic elements that replicate independently of the bacterial chromosome
2) Most are circular, double-stranded DNA molecules. Size ranges from 1,500 to 400,000 base pairs
3) Plasmid genetic information may not be essential for growth

113
Q

What does plasmid genetic information often provide?

A

Selective advantages (such as antibiotic resistance, toxins, virulence determinants, etc)

114
Q

Name 3 selective advantages

A

Antibiotic resistance, toxins, virulence determinants

115
Q

Define horizontal gene transfer

A

The mechanism by which bacteria exchange/ acquire DNA

116
Q

What 3 methods of transfer can be used in horizontal gene transfer? Describe them.

A

1) Conjugation: Physical connection between bacteria mediates transfer
2) Transformation: Uptake of naked DNA from environment
3) Transduction: Viral transfer of DNA into bacteria

117
Q

What 3 things is horizontal gene transfer important for?

A

Evolution, adaptation and pathogenicity

118
Q

Describe the process of horizontal gene transfer; what does donor DNA go through and result in, and what two things can happen to the result?

A

1) Donor DNA can go through conjugation, transformation, or transduction to result in a partly diploid recipient cell with the DNA.
2) Then the donor DNA can either be integrated into the chromosome or the donor dna can self replicate (plasmid)

119
Q

Define conjugation

A

Transfer of DNA, often in the form of a plasmid, by direct cell-to-cell contact

120
Q

What does the donor cell in conjugation contain, and what does it use to transfer genetic material?

A

1) The donor cell contains a plasmid
2) It uses a sex (F) pilus to transfer DNA or a plasmid

121
Q

Who discovered conjugation and what did he use? Describe his experiment

A

1) Conjugation was discovered by Bernard Davis using a U-tube
2) One half of a U-tube had strain A, the other had strain B, and they were separated with a fine filter. The filter was too small for entire bacteria to pass through or to physically touch the other side, but media could flow through. He discovered that if you didn’t allow physical contact, the two strains would not mix, but that if you allow contact, the two strains would mix (i.e. the transfer of genetic information, some of the auxotrophs received genes to allow them to make something they couldn’t)

122
Q

What did Bernard Davis find?

A

That physical contact is necessary for the transfer of genes

123
Q

What 3 things do conjugative plasmids require?

A

1) Have to have the pilin protein (to make the sex pilus)
2) Have to have a type IV secretion system
3) Have to have a coupling protein

124
Q

What allows for plasmids to be integrated into a chromosome?

A

IS elements, which contain inverted repeats

125
Q

What 2 things are involved in F factor mediated conjugation?

A

Involves a donor and recipient; the donor has the F-plasmid that encodes for the pilus (which allows for conjugation). F+ donor, F- recipient.

126
Q

Describe the process of F factor mediated conjugation

A

1) Donor can sense when it’s near an F- recipient, so it constructs a pilus which makes physical contact with the F- cell. Sex pilus then shortens to bring the cells close together.
2) Then a type IV secretion system is constructed (makes the needle accessible for the transfer of something), which now joins the two cells
3) The coupling factor initiates contact with the plasmid and couples it with the type IV secretion system to begin feeding it through
4) The relaxosome makes a cut at the origin of transfer and begins to separate one DNA strand. 5) The intact strand is replicated by the rolling-circle mechanism; creates a single strand of DNA to be fed through the type IV secretion system to the other cell.
6) Accessory proteins of the relaxosome are released.
7) The DNA/ relaxase complex is recognized by the coupling factor and transferred to the secretion system
8) The secretion system pumps the DNA/ relaxase complex into the recipient cell
9) As the DNA enters, the F-factor DNA is replicated to become double-stranded. The new cell now has the ability to make a pilus.

127
Q

What is rolling circle replication found in? List its 5 steps.

A

-F factor mediated conjugation
1) DNA is ‘nicked’
2) 3’ end elongated; 5’ end is displaced
3) 5’ end complemented with Okazaki fragments
4) DNA replication
5) Circularization

128
Q

What makes physical contact with the recipient cell in F factor mediated conjugation?

A

The sex pilus physical contact with the F- cell. It then shortens to bring the cells close together.

129
Q

What joins the two cells together in F factor mediated conjugation?

A

A type IV secretion system

130
Q

F factor mediated conjugation: What initiates contact with the plasmid, and what does it couple the plasmid with?

A

1) The coupling factor initiates contact with the plasmid
2) It couples the plasmid with the type IV secretion system to begin feeding it through

131
Q

F factor mediated conjugation: What makes a cut at the origin of transfer?

A

The relaxosome makes a cut at the origin of transfer and begins to separate one DNA strand.

132
Q

F factor mediated conjugation: Which strand of DNA is replicated? What is it replicated by?

A

The intact strand is replicated by the rolling-circle mechanism.

133
Q

1) What does HFR stand for?
2) Define HFR conjugation

A

1) Stands for high frequency conjugation
2) When the donor cell integrates the F plasmid into its chromosome.

134
Q

Describe HFR conjugation

A

1) HFR cell initiates conjugation by constructing a sex pilus
2) HFR cells transfers its unique genes and the plasmid integrated in its chromosome into a F- cell
3) Longer conjugation leads to more transfer
4) Recombination between donor DNA and recipient DNA occurs

135
Q

1) During HFR conjugation, what determines the amount of material transferred?
2) Does the F- recipient cell typically remain F-?

A

1) Longer conjugation leads to more HFR cell genes being transferred to the F- cell; 100 minutes at most. 2) It’s rare that the entire F factor is transferred, so some is left behind; this is why the recipient typically remains F-.

136
Q

Describe conjugation in gram positive bacteria (3 steps)

A

1) The recipient cell has the ability to produce a pheromone that attracts and primes a donor cell
2) Donor cell’s plasmid interacts with the pheromone and transmits aggregation substance (AS) which migrates to the cell surface
3) AS then binds to a binding substance (BS) on the recipient cell(s), forming a clump of cells within which genetic exchange occur.

137
Q

Define transformation and list its two types

A

1) The uptake of naked DNA from the environment
2) Can be either transformation of DNA fragments or transformation of a plasmid

138
Q

Transformation with DNA fragments can result in two different outcomes; what are they?

A

1) Integration by nonreciprocal recombination
2) Degradation of DNA

139
Q

Define competence

A

The ability of a cell to take in DNA

140
Q

Describe transformation in gram positive bacteria (4 steps)

A

1) A competent cell binds a double-stranded DNA fragment
2) DNA is cleaved into smaller fragments (5-15kb)
3) One strand is hydrolyzed at the surface, the other strand is imported
4) Homologous recombination leads to a transformed cell

141
Q

Describe the difference in gram positive and gram negative cells regarding their DNA uptake machinery

A

Gram negative cells have more machinery (particularly a PiiQ) due to having an outer membrane.

142
Q

True or false: Only certain strains and species are transformable

A

True

143
Q

1) What did Fredrick Griffith’s Streptococcus experiment demonstrate?
2) Describe the experiment

A

1) He demonstrated that DNA from a dead cell can be taken up by a live cell.
2) This was proven by using an R-strain that had a capsule and an S-strain that did not. He found that the R-strain is innocuous, but that the S-strain kills mice. He then heat-killed the S-strain and found that the dead cells did not kill the mouse. He then mixed dead S-strain bacteria and live R-strain bacteria and found that this combination killed the mice; he concluded that the live R-strain was transformed to the S-strain by taking up their DNA.

144
Q

1) What did Avery, MacLeod, and McCarty’s experiment confirm?
2) What was the experiment?

A

1) That it was the DNA from the heat-killed bacteria that caused pathogenicity. 2) They used different combinations of R cells and S cells (one type R cells only, one type R cells and type S DNA extract, etc)
Found that it was indeed the genes being transferred from the S cells to the R cells that caused pathogenicity

145
Q

What are the two main types of transformation?

A

Natural and artificial

146
Q

1) Define natural transformation
2) Define artificial transformation

A

1) Natural transformation: These bacteria have the necessary machinery and will readily acquire and maintain exogenous DNA
2) Artificial transformation: By molecular methods, we make bacteria capable of taking up DNA (genetic engineering). This can be through either chemically-induced competence (heat-shock) or electroporation (electrical shock)

147
Q

What two things can be done to initiate artifical transformation?

A

Chemically-induced competence (heat-shock) or electroporation (electrical shock)

148
Q

Describe artificial transformation (5 steps)

A

1) Vector, such as a plasmid, is isolated
2) DNA containing gene of interest from a different species is cleaved by an enzyme into fragments
3) Desired gene is selected and inserted into the plasmid
4) Plasmid is taken up by a cell, such as a bacterium
5) Cells with the gene of interest are cloned with either one of two goals in mind:
a) Create and harvest copies of the gene OR
b) Create and harvest protein products of a gene

149
Q

Define transduction and list its two outcomes

A

1) The viral delivery of DNA (bacteriophages); a type of horizontal gene transfer
2) Results in:
a) Lytic infection: Replication into large numbers and causing the cell to lyse
b) Lysogenic state: Integration into the host genome without killing the host

150
Q

Define lytic infection and lysogenic state. What are they the two potential outcomes of?

A

1) Lytic infection: Replicate into large numbers and cause the cell to lyse
2) Lysogenic state: Integrate into the host genome without killing the host
3) These are the two potential outcomes of transduction

151
Q

1) Prophages are a part of what cycle?
2) Define prophages

A

1) The lysogenic cycle (of transduction)
2) Defined as a phage or viral DNA that is integrated into the host’s chromosome and has the ability to leave it.

152
Q

When do cells switch from the lysogenic cycle to the lytic cycle?

A

Cells can switch from the lysogenic cycle into the lytic cycle by factors that cause the phage DNA to no longer be integrated with the chromosome (ex: UV light, antibiotic treatment)

153
Q

2) Define generalized transduction.
2) Typically only what type of DNA is transferred?

A

1) The transfer of DNA from one bacteria cell to another via a bacteriophage (which transfers DNA from one host to another). 2) Typically only bacterial DNA is transferred.

154
Q

List the steps of generalized transduction (5 steps)

A

1) Phage infects a bacterial cell, which then hydrolyzes the host DNA into pieces, and phage DNA and proteins are made.
2) The phages assemble and occasionally carry a piece of the host cell chromosome.
3) The transducing phage then injects its DNA into a new recipient cell.
4) The transduced DNA is recombined into the chromosome of the recipient cell.
5) The recombinant bacterium has a genotype that is different from the recipient bacterial cell.

155
Q

Describe the steps of specialized transduction (3 steps)

A

1) Begins with a prophage that’s induced (UV light, stress, etc) and the phage is de-integrated from the chromosome.
2) Replication of the defective virus DNA with incorporated host genes occurs, which causes the assembly and release of transducing phage particles, which leads to infection of the next cell.
3) After the next cell is infected, one of two things happen:
a) Crossover to integrate bacterial genes, which leads to a bacterial chromosome containing only donor DNA.
b) Integration as a prophage leads to a bacterial chromosome that contains both virus and donor DNA.

156
Q

What are the two potential outcomes of specialized transduction?

A

A) Crossover to integrate bacterial genes occurs, which leads to a bacterial chromosome containing only donor DNA.
b) Integration as a prophage leads to a bacterial chromosome that contains both virus and donor DNA.

157
Q

What can de-integration include?

A

Sometimes the rare event of de-integration can include some bacterial genes (up to 5 or 10%)

158
Q

1) Define transposition
2) What thing does transposition require?

A

1) When DNA ‘jumps’ from one location to another
2) Transposons

159
Q

1) Define transposons
2) What can complex transposons do?
3) What do replicative transposons contain?

A

1) Mobile genetic elements that can transfer DNA within a cell, contain transposase
2) Complex transposons can carry genes providing resistance to antibiotics or virulence genes grouped together in a pathogenicity island.
3) Replicative transposons contain a resolvase gene

160
Q

How does transposition occur? (2 steps)

A

1) Transposase cuts DNA
2) Ligation of transposon into target site

161
Q

Name 4 effects of transposon insertions

A

1) Causes mutations, DNA rearrangements
2) Block transcription and translation
3) Can activate genes
4) Move between plasmids, spreading antibiotic resistance cassettes

162
Q

Describe Agrobacterium:
1) Gram positive or negative? Do they have any appendages?
2) Where are they found?
3) What are they the causative agent of?
4) What’s unusual about them?
5) How are they useful?

A

1) Gram negative bacilli with flagella
2) Found in the rhizosphere (root area)
3) Causative agent of crown gall disease and Morgellons disease (maybe, researchers moving away from bacteria as cause of Morgellons)
4) Unusual chromosomal organization
5) A good research tool for tumor induction and transfection

163
Q

Describe the virulence of agrobacterium; how do they infect plant cells and what gives them a selective advantage?

A

1) Has its own chromosome and a Ti (tumor-inducing) plasmid that contains virulence genes, which is what infects the plant cell and incorporates into its chromosome. This causes the plant to release excess growth hormones which cause tumorogenesis.
2) During tumorogenesis the plant secretes opines, which the bacteria then feed off (other bacteria don’t eat these) and gives them a selective advantage.

164
Q

How do agrobacterium find plants to infect?

A

Secretion of acetosyringone from wounded plant tissue act as a powerful chemoattractant for Agrobacterium.

165
Q

Describe agrobacterium as a tool for plant genetics

A

Discs of leaves can be removed and incubated with agrobacteria whose plasmid has been altered to confer positive genes, and the agrobacteria can transfer these positive genes to the leaves and create a new (and better) plant genotype.

166
Q

Describe Charles Chamberland’s contributions towards microbiology

A

1) Charles Chamberland (1851-1908) worked with Louis Pasteur, he developed Chamberland’s Porcelain Bacterial Filter which filtered out most microbes (bacteria, some viruses).
2) Marketed it as a water filter.

167
Q

List the properties of viruses (6)

A

1) Viruses are filterable agents; small size allows them to pass through filters designed to retain bacteria
2) Viruses are obligate intracellular parasites
3) Viruses cannot make energy or proteins independently of a host cell
4) Viral genomes may be RNA or DNA but not both
5) Viruses have a naked capsid or an envelope morphology
6) Viral components are assembled and do not replicate by division

168
Q

In order to be a successful pathogen, what 5 things must be true about the virus?

A

1) Viruses are not living
2) Viruses must be infectious to endure in nature
3) Viruses must be able to use host cell process to produce their components
4) Viruses must encode any required processes not provided by the host cell
5) Viral components must self-assemble

169
Q

1) How big are viruses?
2) Are viruses diverse?
3) What does a complete virus particle or virion consist of?

A

1) Viruses range in size from about 10 to 400 nm in diameter (big range)
2) Very diverse
3) A complete virus particle or virion consists of one or more molecules of DNA or RNA enclosed in a coat of protein. The virion is the entire viral particle

170
Q

Name 3 structures that can be found in viruses

A

1) Nucleocapsid core
2) Capsid
3) Envelope (some viruses)

171
Q

Define in terms of viruses:
1) Nucleocapsid core
2) Capsid

A

1) Viral nucleic acid (DNA or RNA) that is held within a protein coat called a capsid
2) The protein coat that surrounds the viral nucleic acid genome

172
Q

Define in terms of viruses:
1) Enveloped virus
2) Naked virus

A

1) Enveloped: The viral nucleocapsid is surrounded by an additional layer that can be very complex containing carbohydrates, lipids, and additional protein.
2) Naked virus: Viruses lacking an envelope

173
Q

The three types of viral capsid architecture are based upon what?

A

The symmetry of the capsid/ nucleocapsid

174
Q

Name and describe the three types of viral capsid architecture

A

1) Icosahedral: usually naked viruses, a few are enveloped
2) Helical: can be naked or enveloped
3) Complex: A complex structure that is neither of the above

175
Q

What are the 3 functions of the capsid?

A

1) Packages the genome/provides structural support
2) Protects the genome from nucleases (in serum) and adverse environmental conditions
3) Participates in attachment and entry of host cells

176
Q

1) Icosahedral capsids are made up of what?
2) What is the smallest repeating structural unit visible by electron microscopy that makes up the icosahedral nucleocapsid?

A

1) The capsids are constructed from ring or knob-shaped units called capsomers
2) A capsomer

177
Q

1) In terms of viruses, what are capsomers made up on?
2) What are capsomers made of?

A

1) Capsomers are made up on one or more viral structure (or capsid) proteins
2) Each capsomer is usually made of five or six protomers

178
Q

1) What groups of viruses have envelopes?
2) What do virus envelopes usually arise from?
3) What usually codes for viral envelope proteins?

A

1) Many animal viruses, some plant viruses, and at least one bacterial virus have an envelope.
2) Virus envelopes usually arise from host cell nuclear or plasma membranes;
their lipids and carbohydrates are normal host constituents
3) Viral envelope proteins are coded for by virus genes

179
Q

1) What are projected proteins in viruses and what are they called?
2) What do many projected proteins act as? What do the rest do?

A

1) Viral envelope proteins may project from the envelope surface
Projected proteins are called spikes. 2) Many act as VAPs: Viral Attachment Proteins. Some are enzymes (e.g. neuraminidase, polymerases).

180
Q

1) Name the 2 proteins found on the surface of the influenza virion
2) How many pieces of RNA or DNA does it have?
3) What species can be infected by influenza, and what changes about influenza when it changes species?

A

1) Hemagglutinin (HA) spike and neuraminidase spike
2) Very few genes; only 8 pieces of RNA that encode for all the proteins it needs.
3) Goes through pigs, birds, and humans.
Temperature changes and amino acid changes occur as the virus makes its way through different species.

181
Q

1) What can the viral factors of influenza do?
2) What are the host factors (vulnerability factors) for influenza infection?

A

1) Has viral factors (based on its genotype) that can block interferons from helping the immune system, aid in replication, and HA spike determines receptor binding.
2) Host factors: Underlying health issues, elderly age, etc.

182
Q

List the component, properties, and consequences (5) of the naked capsid viral structure

A

1) Component: Protein
2) Properties: Is environmentally stable to temperature, acid, proteases, detergents, and drying; is released from cells by lysis
3) Consequences:
1) Can be spread easily
2) Can dry out and still retain infectivity
3) Can survive the adverse conditions of the gut
4) Can be resistant to detergents and poor sewage treatment
5) Antibody many be sufficient for immunoprotection

183
Q

List the components (3), properties, and consequences (5) of the enveloped capsid viral structure

A

1) Components:
a) Membrane
b) Lipids
c) Proteins and glycoproteins
2) Properties: Is environmentally labile and is disrupted by acid, detergents, drying, and heat; modifies cell membrane during replication and is released by budding and cell lysis.
3) Consequences:
a) Must stay wet
b) Cannot survive the gastrointestinal tract
c) Spreads in large droplets, secretions, organ transplants and blood transfusions
d) Does not need to kill the cell to spread
e) May need antibody and cell-mediated immune response for protection and control

184
Q

Are naked or enveloped viruses more resistant to drying out?

A

Naked viruses

185
Q

1) What two types of genome can viruses contain?
2) What are the two types of DNA or RNA genome a virus can have?

A

1) Viruses can contain a DNA or RNA genome
2) The DNA or RNA genome can be single (ss) or double stranded (ds)

186
Q

1) How does the Baltimore classification system classify viruses? (what is it based on?)
2) What two things are true of all viruses?

A

1) Sorts viruses based on their genome
2) a) Eventually need to get to mRNA to create proteins.
b) Have the ability to replicate their genome

187
Q

List the 5 generalized steps of the viral life cycle

A

1) Adsorption: Host cell recognition and attachment of virus
2) Entry: of viral nucleocapsid or nucleic acid
3) Synthesis: of viral proteins and nucleic acids (eclipse phase)
4) Self-assembly: of virions
5) Release: of progeny virions

188
Q

Each cell can produce _______ particles (viruses) but only ______ of those are infectious due to the high mutation rate because of self-assembly.

A

100,000; 1-10%

189
Q

Describe the ‘attachment’ phase of the viral life cycle:
1) What is it mediated by?
2) What is usually its cell surface receptor?
3) What is it the determinant of?
4) What has the ability to block this interaction?
5) What do cell surface receptors normally do when not attached to a virus?

A

1) Mediated by viral envelope/capsid protein (called a viral attachment protein or VAP) that binds to a target cell receptor molecule.
2) Cell surface receptor is usually a specific cell surface glycoprotein or a carbohydrate moiety attached to a lipid.
3) Determinant of cell/tissue tropism (which cells it can infect).
4) Interaction can be blocked by a neutralizing antibody; the attachment step is major target for the immune system.
5) Cell surface viral receptors have important functions in normal host cellular metabolism.

190
Q

Give an example of attachment using influenza

A

Influenza’s hemaglutinin attachment protein recognizes target vertebrate cells and initiates fusion between host and viral membranes, determines how well it can infect.

191
Q

Describe the ‘entry’ phase of the viral ‘life’ cycle in enveloped viruses:
1) What two ways can they use to enter the host cell?
2) What mediates their fusion?
3) When is the viral envelope removed?
4) What is the fusion process dependent on?

A

1) Enveloped viruses can enter by fusion of viral envelope with a cellular membrane or by endocytosis
2) Fusion is mediated by a viral “fusion” protein
3) Viral envelope is removed when fusion occurs and the viral nucleocapsid is ‘ejected’ into the host cell’s cytoplasm
4) Fusion process is pH dependent; cell surface at neutral pH vs fusion occurs in an endosome at an acidic pH

192
Q

Describe the ‘entry’ phase of the viral ‘life’ cycle in naked viruses:
1) How do they enter the host cell?
2) What is released after entry? What is extruded?

A

1) Naked viruses enter by receptor mediated endocytosis
2) After entry, the viral nucleocapsid is released into host cell cytoplasm and uncoated, or the viral genome is extruded into host cell cytoplasm through the endosome or plasma membrane (viropexis)

193
Q

Describe the ‘uncoating’ phase of the viral ‘life’ cycle:
1) What is stripped away from the viral nucleic acid?
2) Where does the viral genome travel after it’s uncoated?

A

1) Nucleocapsid proteins are partially or completely stripped away from the viral nucleic acid
2) Uncoated viral genome travels to site of genome replication

194
Q

1) Where do DNA viruses usually replicate?
2) Where do RNA viruses usually replicate?

A

1) DNA viruses usually replicate in the nucleus of a host cell
2) RNA viruses usually replicate in the cytoplasm of a host cell

195
Q

1) Define the ‘replication’ phase of the viral ‘life’ cycle
2) What 3 things occur during this phase?

A

1) Defined as the production of viral components
2)
a.Genome replication
b. Production of viral mRNAs
c. Production of viral proteins

196
Q

What two things are produced during the ‘replication’ phase of the viral ‘life’ cycle?

A

1) Viral mRNAs
2) Viral proteins

197
Q

1) Define the ‘assembly’ phase of the viral ‘life’ cycle
2) Where are DNA viruses usually assembled?
3) Where are RNA viruses usually assembled?
4) What directs the genome to new capsids?
5) How do the viral proteins assemble?

A

1) The assembly and maturation of new virions
2) DNA viruses are usually assembled in the host cell nucleus
3) RNA viruses are usually assembled in the host cell cytoplasm
4) The viral genome contains “packaging signals” that direct it to new capsids
5) The viral proteins “spontaneously” assemble at the correct site in the cell (along with the nucleic acid genome)

198
Q

1) Define the ‘release’ phase of the viral ‘life’ cycle
2) How are enveloped viruses released? When do they pick up their membrane?
3) How are non-enveloped viruses usually released?

A

1) The release of new virions
2) Enveloped viruses are released by budding through the appropriate cell membrane
Viruses pick up their membrane during the process of budding
3) Non-enveloped viruses are usually released by lysis of the host cell

199
Q

1) Where are DNA viruses replicated? Where are they assembled?
2) Where are RNA viruses replicated? Where are they assembled?

A

1) DNA viruses are usually both replicated and assembled in the host nucleus
2) RNA viruses are usually both replicated and assembled in the host cytoplasm

200
Q

Describe replication in the Herpes Simplex Virus Type I

A

Rolling circle replication creates a byproduct called concentric DNA, which is where multiple copies of that DNA are readily available in the nucleus

201
Q

There are 3 possible outcomes of a viral infection of a cell (viral pathogenesis); what are they?

A

1) Abortive infection: Failed infection; virus was unsuccessful.
2) Lytic infection: Ends in cell death
3) Persistent infecation: Infection without cell death (persistent infection)

202
Q

There are 3 possible outcomes of a viral infection of a cell (viral pathogenesis); what are they?

A

1) Abortive infection: Failed infection; virus was unsuccessful.
2) Lytic infection: Ends in cell death
3) Persistent infection: Infection without cell death

203
Q

What are the 3 types of persistent infections? Describe them

A

1) Senescence: Viruses are produced and the cell stops dividing but is still alive. A type of persistent infection.
2) Latent: Virus production may stop and start, has no effect on the cell. A type of persistent infection.
3) Transforming (of a host cell; the integration of viral DNA in the cell): DNA viruses are not produced, RNA viruses are produced. Causes immortalization (cancer). A type of persistent infection.

204
Q

What type of viral infection results in a cell becoming cancerous?

A

Transforming infections (a type of persistent infection)

205
Q

Define cytocidal infection and cytopathic effects

A

1) Cytocidal infection: an infection that results in cell death
2) Cytopathic effects: microscopic or macroscopic degenerative changes or abnormalities in host cells and tissues

206
Q

List the 8 possible mechanisms for host cell damage (by viral pathogens)

A

1) Inhibition of host DNA, RNA, and protein synthesis
2) Damage of cell endosomes; results in release of hydrolytic enzymes
3) Alteration of plasma membranes by insertion of viral proteins; infected cells are attacked by host immune system
4) High concentrentration of viral proteins can have direct toxic effect on cells and organisms
5) Formation of large intracellular structures called inclusion bodies (often composed of subunits of viral proteins or host cell components) which disrupt cell structure
6) Chromosomal disruptions
7) Host cell is not destroyed, but is transformed into a malignant cell
8) Cell fusion: expression of viral envelope/ fusion proteins on the surface of an infected cell. Can cause it to fuse with nearby, uninfected cells. Fused cells usually die and are called syncytia or multinucleated giant cells.

207
Q

What are the 8 steps of the viral disease process (viral pathogenesis)?

A

1) Transmission
2) Entry into host
3) Primary viral replication
4) Viral local/ systemic spread
5) Secondary viral replication/ cell tropism
6) Cell damage/ disease production
7) Shedding of virus
8) Host death/ recovery

208
Q

What are the 3 primary modes of transmission of viruses?

A

1) Direct transmission (horizontal and vertical transmission)
2) Animal to human transmission
3) Transmission by arthropod vector

209
Q

Define horizontal and vertical transmission of viruses

A

1) Horizontal transmission: from person to person
2) Vertical transmission: from mother to child (perinatal and natal)

210
Q

What are the most common ways viruses are transmitted?

A

Inhalation and inoculation of virus into mucosa on contaminated hands/ objects are the most common ways viruses are transmitted

211
Q

1) Where do viruses enter their host cell?
2) What are the two main barriers for entry of viruses?

A

1) Portal of entry
2) Mechanical/ physical barriers and adaptive barriers (the immune response)

212
Q

Differentiate between:
1) Primary replication
2) Primary replication + secondary infection

A

1)The production of disease at a virus’s portal of entry (short incubation times)
2) Cells at the portal are infected, virions are produced, and systemically spread to a second site. Requires longer incubation times.

213
Q

What mechanisms of spread can be used by viruses in secondary infection? (3)

A

1) Bloodstream (viremia)
2) Lymphatics
3) Neuronal spread: uses neurons as conduits.

214
Q

What are the 3 types of tissue tropism?

A

Specific tissue, cell tropism, specific cell type

215
Q

What two barriers in the human body are highly effective in keeping viruses out?

A

1) Blood-brain barrier
2) Placental barrier

216
Q

Define direct and indirect tissue damage

A

1) Direct tissue damage: damage that occurs by replicating in, and killing or transforming host cells
2) Indirect tissue damage: the immune response to viral infection causes cell/ tissue damage (symptoms)

217
Q

1) Where are viruses typically shed?
2) When are those infected with a virus most contagious?

A

1) Usually the virus is shed from the same body surfaces at which it enters
2) During active shedding

218
Q

What influences whether or not a host lives or dies from a viral infection?

A

Just like with bacteria, all of the following play a role:
1) Strains
2) Type of virus
3) Host genetics and immune system

219
Q

Differentiate between apparent and inapparent viral infections. Which is more common?

A

1) Inapparent infections: subclinical or asymptomatic infection
a) Virus replicates in the host, but no clinical symptoms develop
Most common type of infection
2) Apparent infection: symptomatic infections; can either be acute or persistent

220
Q

1) What are the two types of apparent viral infection?
2) What are the two types of persistent viral infection?

A

1) Acute and persistent
2) Chronic and latent

221
Q

Differentiate between acute and persistent viral infections

A

1) Acute infections:
Overall rapid onset and last for a short period of time (days to weeks; ex: influenza)
2. Persistent infections: Lasting many years; can be chronic or latent

222
Q

Differentiate between chronic and latent viral infections. Give examples of each.

A

1) Chronic virus infections; virus is almost always detectable, but clinical symptoms may be either mild or absent for long periods
a) Examples: Hepatitis B virus and HIV
2) Latent virus infections; virus stops reproducing and remains dormant for a period before activating again.
During latency there are no symptoms (viruses are hidden or less potent)
a) Examples: Herpes simplex virus, Varicella-zoster virus, Epstein-Barr virus

223
Q

What causes latency in viral infections? (4 steps)

A

1) Viral genome was incorporated into the chromosome (provirus or phage).
2) Virus becomes less antigenic (less susceptible to immune attack). 3) The virus hides in an area that can’t be reached by the immune system (ex: nervous system). 4) Then the virus mutates to the less virulent form, which slows production.

224
Q

List the 8 different ways viruses evade host antiviral immune defenses

A

1) Overwhelming the host quickly
2) Production of large quantities of virus and/or viral antigens
3) Shedding of virus from site of primary infection
4) Infection of cells of the immune system
5) Production of “Anti-Immune” Substances (Molecular Bombs)
6) By replication in immune privileged sites (ex: eye or CNS)
7) Establishment of latent infection.
8) By undergoing antigenic variation (alteration of viral antigens); the emergence of new variants.

225
Q

Overwhelming the host quickly is characteristic of what viruses?

A

Characteristic of acutely lethal viruses (e.g. Ebola)

226
Q

1) Why does producing large quantities of the virus or viral antigens work against the host immune system?
2) Why does shedding the virus from the primary site of infection work against the host immune system?

A

1) The immune system can’t keep up
2) The immune response has not developed

227
Q

What are the 4 types of anti-immune substances (molecular bombs) that can be made by viruses?

A
  1. Virokines: virally encoded cytokine analogues
  2. Viroreceptors: virally encoded cytokine receptor analogues
  3. Inhibitors of MHC class I antigen presentation
  4. Inhibitors of the Interferon response
228
Q

Differentiate between virokenes and viroreceptors

A
  1. Virokines: virally encoded cytokine analogues
  2. Viroreceptors: virally encoded cytokine receptor analogues
229
Q

What are the two types of viral antigenic variaiton? Describe them.

A

1) Antigenic drift: accumulation of point mutation in viral gene(s) changes their antigenicity.
2) Antigenic shift: exchange of genome segments between two different serotypes of virus infecting the same cells results in production of viral progeny which contain genes/antigens from both parental virus strains. Can result in the emergence of new pathogens.

230
Q

Differentiate between antigenic drift and antigenic shift

A

1) Antigenic drift: accumulation of point mutation in viral gene(s) changes their antigenicity.
2) Antigenic shift: exchange of genome segments between two different serotypes of virus infecting the same cells results in production of viral progeny which contain genes/antigens from both parental virus strains. Can result in the emergence of new pathogens.

231
Q

What mediates the innate immune response to viral infection?

A

Interferons

232
Q

Describe how DAIs (double-stranded RNA-activated inhibitor) work (3 steps)

A

1) A part of our innate immune system that’s normally inactive, until it sees a virus with double-stranded RNA.
2 )Then DAI phosphorylates and becomes active, and recruits initiation factor II and activates it.
3) Then it deactivates initiation factor II by phosphorylating it, which slows down synthesis of viral proteins and gives the cell more time to kill the virus (or kill itself).

233
Q

How do viruses combat DAIs of the innate immune system?

A

Some viruses have extra genetic material called ‘small RNAs’ that they bring with them in their capsules; these small RNAs have the ability to bind to and lock DAI in an inactive state (so it can’t phosphorylate to activate)

234
Q

List the 3 primary bacterial evasion strategies and how viruses respond to them

A

1) Receptor issues: The bacteria changes the receptor to prevent the virus from binding. The virus in turn learns how to bind to the new receptor.
2) Running interference: Bacteria put tons of sugars on their surface, preventing the virus from reaching the host cell surface. Viruses then begin to carry enzymes that break down sugars.
3) New coat: The bacteria modify their sugars and create variations in them so the viruses can no longer interact with the sugar coat.

235
Q

How do you cultivate viruses?

A

1) Create a lawn of bacteria on a plate
2) Add virus to the bacterial lawn
3) The virus begins to form plaques and lyse bacterial cells

236
Q

1) Define viroids.
2) How do viroids replicate?
3) What do viroids infect?
4) What are the two families of viroids?

A

1) Viroids are unencapsulated nucleic acids that consist of only RNA
2) Despite their small size and limited genetic info, they replicate autonomously (rolling circle replication)
3) Cause diseases in higher plants
4) One replicates in nucleus, other in chloroplasts

237
Q

1) How do viroids move?
2) How old are viroids?
3) How do viroids act as pathogens?

A

1) Move intracellularly, accessing neighboring cells through plasmodesmata
2) They’re ‘molecular fossils’ and predate the current world of DNA and protein (supports RNA World Hypothesis).
3) They don’t encode proteins, they act through a method called RNA silencing (binds and stops things from happening in host cell)

238
Q

1) Define prions
2) What are the two forms prions exist in?
3) What happens if the two prion types interact?
4) How do prions act as pathogens?

A

1) Proteinaceous infectious particles that cause neurodegenerative disease
2) Abnormally folded form and normal cellular form
3) Interaction between the two prion types usually causes the normal form to turn into the abnormal form.
4) Crosslinking of normal protein > triggers apoptosis > neuron loss

Microbiology (42 decks)

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