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Microbiology > Lecture Quiz #3 > Flashcards

Lecture Quiz #3 Flashcards

Lectures 5,6, and part of 7

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; what things do they each include?

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

1) Morphological
2) Physiological/metabolic
3) Biochemical
4) 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 identification tools

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.

54
Q

Define ecotype

A

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

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.

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

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)

58
Q

How is the pan-genome acquired?

A

By horizontal gene transfer (HGT)

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

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

61
Q

What 3 things is horizontal gene transfer important for?

A

1) Evolution
2) Adaptation
3) Pathogenicity

62
Q

List 3 things that can result from horizontal gene transfer (HGT)

A

Gene acquisition, plasmid acquisition, phage infection

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

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)

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)

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

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.

68
Q

Initiation of DNA synthesis predates what?

A

Any initiation of cell division

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

70
Q

Describe replication of the E. Coli chromosome

A

It’s bidirectional

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).

72
Q

DNA binding proteins are what kind of proteins?

A

Histone-like proteins

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.

74
Q

More organization of the chromosome allows for what?

A

Faster gene expression

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

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

77
Q

Define polycistronic transcription

A

Ribosomes can jump around and translate several proteins at once

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

79
Q

Describe eukaryotic transcription and translation

A

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

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

81
Q

What are the 3 stop codons?

A

UAA, UAG, and UGA

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

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

84
Q

What is the least detrimental mutation to a cell?

A

A missense mutation

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

86
Q

What are the two types of point mutations?

A

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

87
Q

What is the most common type of mutations?

A

Point mutations

88
Q

What are the two main categories of mutations?

A

Point mutations and frameshift mutations

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

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

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

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

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

94
Q

Name 4 kinds of mutations

A

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

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

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.

Microbiology (42 decks)

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