Lecture Quiz #3 Flashcards
Lectures 5,6, and part of 7
Define taxonomy
The science of biological classification
List and define the 3 parts of taxonomy
1) Classification: based upon a selected scheme
2) Nomenclature: Assignment into taxa using rules
3) Identification: Determining where each organism fits
What are the 4 main reasons for classifying organisms?
1) Establish relationships, and to differentiate
2) We have only scratched the surface
3) Serves as valuable reference
4) Opens line of communication
How did Carl von Linne classify organisms?
-Used mainly anatomical characteristics
-Used 2 kingdoms and latinized names
How did Carl von Nageli classify organisms?
Bacteria and fungi into plant kingdom
What did Ernst Haeckel do for taxonomy?
He proposed Kingdom Protista
Edouard Chatton proposed the term ‘________’
prokaryote
Who founded the 5 kingdom system of taxonomy?
Robert H. Witaker
Who proposed the idea of 3 domains? What were they based on, and in what other three ways did they differ?
1) Carl Woese
2) Based on rRNA sequences
3) Also differ in membrane lipid structure, tRNA, and antibiotic sensitivity
Define phylogeny
The evolutionary development of a species
Name the 3 phylogenetic groups and define them
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
The binomial system consists of what 2 things?
Genus + species
True or false: the binomial system always italicizes genus and species
True
Define a strain. What does a strain descend from?
-Defined as a population of organisms that are distinguishable from others of the same species
-Descended from a single organism or pure culture
List the 3 ways strains can vary, and define them
1) Biovars: biochemical and physiological properties
2) Morphovars: morphological properties
3) Serovars: antigenic properties
Describe a type strain
-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
What are the 3 broad ways to classify bacteria? Which is the most accurate?
1) Phenotypic classification
2) Analytic classification
3) Genotypic classification
-Genomic is most accurate
Define morphology
The form and structure of an organism or group of identical organisms
Differentiate between microscopic and macroscopic classification; what things do they each include?
1) Microscopic classification: shape, pattern of groups, staining
2) Macroscopic classification: colony morphology, pigment production
Differentiate between biotyping and serotyping
1) Biotyping: Biochemical markers
2) Serotyping: Detection of specific antigens
Define antibiogram patterns and phage typing
1) Antibiogram patterns: Susceptibility to various antibiotics
2) Phage typing: Susceptibility to viruses that infect bacteria; bacteriophages
Name 7 types of phenotypic classification
1) Morphology
2) Microscopic classification
3) Macroscopic classification
4) Biotyping
5) Serotyping
6) Antibiogram patterns
7) Phage typing
What type of classification requires expensive instrumentation (e.g. mass spectrometry) and is labor intensive?
Analytic classification
Give 4 examples of analytic classification
1) Cell envelope fatty-acid analysis
2) Whole cell lipid analysis
3) Whole cell protein analysis
4) Multilocus enzyme electrophoresis
Give 6 examples of genotypic classification
1) Guanine plus cytosine ratio
2) DNA hybridization
3) Nucleic acid sequence analysis
4) Plasmid analysis
5) Ribotyping
6) Chromosomal DNA fragment analysis
Name 4 classical characteristics used to identify organisms
1) Morphological
2) Physiological/metabolic
3) Biochemical
4) Ecological
What are the 2 main types of classical characteristics that can be used to classify organisms?
1) Physiological/ metabolic
2) Ecological
Name 4 physiological/ metabolic characteristics that can be used to classify organisms
1) Motility
2) Luminescence
3) Photosynthetic pigments
4) Energy sources
Name 5 ecological characteristics that can be used to classify organisms
1) Life cycle patterns
2) Symbiotic relationships
3) Ability to cause disease
4) Habitat preference
5) Growth requirements
What are the two main categories of characteristics that can be used to identify organisms?
1) Classical characteristics
2) Molecular characteristics
Name 5 molecular identification tools
1) Nucleic acid base composition
2) Nucleic acid hybridization
3) Nucleic acid sequencing
4) Genomic fingerprinting
5) Amino acid sequencing
Describe nucleic acid base composition
Usually measures G&C content, which usually only varies by ~10% in a genus
Describe nucleic acid hybridization
-Complete hybridization can occur if the organisms are identical
-Partial hybridization can occur if they’re related
-No hybridization if they’re not related
Describe nucleic acid sequencing and when it is best used
-Utilizes small subunit rRNAs (SSU rRNAs)
-Best measure for relatedness
Describe small subunit rRNAs (SSU rRNAs)
-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)
What are the molecules of choice for phylogenetics? Why?
SSU rRNAs, because they have the same role in all organisms and they’re very well conserved
What does genomic fingerprinting consist of?
-PCR: polymerase chain reaction
-Amplifies a region of the DNA, can be used to identify causative agents
Describe amino acid sequencing; what does it reflect and what can it be differentiated based on?
-Directly reflects mRNA sequences
-Can be differentiated based on charge, immunogenicity, and fragmentation
Define the root
The last universal common ancestor (LUCA) of the 3 domains
How do we know the eukarya and archaea have common ancestry at some point?
They share key proteins
What 3 considerations should be made for microbial genetic diversity?
1) The world environment(s)
2) The extraterrestrial
3) Microbial mechanisms
-Mutations and gene transfer
What is the root?
The last universal common ancestor (LUCA)
What does LUCA stand for and what does it mean?
1) Last universal common ancestor
2) Last common ancestry of the 3 domains (bacteria, archaea, and eukarya)
How do we know that Eukarya and Archaea had common ancestry at some point?
Eukarya and Archaea share key proteins
What 3 things should be considered when looking into microbial genetic diversity?
1) The world environment(s)
2) The extraterrestrial
3) Microbial mechanisms (mutations and gene transfer)
Name 2 microbial mechanisms
1) Mutations
2) Gene transfer
What is another word for anagenesis? What does it mean?
1) Genetic drift
2) Defined as small, random genetic changes that occur over generations
What 3 things contribute to anagenesis?
1) Extremely fast microbial growth
2) Type of mutation
3) Selection pressure (adaptive mutation)
-ex: pH, oxygen, temp, etc
Give 3 examples of selective pressures
pH, oxygen, temp
Name 4 mechanisms of genetic variation
1) Gene mutation
2) Gene duplication
3) Gene loss
4) Recombination
Name 2 models for evolutionary mechanisms of diversity and briefly describe them
1)Metapopulation model: Small changes (gradual)
2) Stable ecotype model: Rapid bursts of speciation
Describe the metapopulation model of evolutionary mechanisms of diversity
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
Describe the stable ecotype model of evolutionary mechanisms of genetic diversity
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.
Define ecotype
A population of microbes that’s genetically similar but ecologically distinct
Define a core genome (most conserved). Any variation in this genome is based on what?
The set of genes found in all members of a species; any variation in this genome is mutation-based.
Define pan-genome and name its 3 parts
1) The complete gene repertoire of taxon (all strains)
2) Core + ‘housekeeping’ + dispensable genes
Describe the 3 parts that make up the pan-genome of a species
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)
How is the pan-genome acquired?
By horizontal gene transfer (HGT)
1) What does horizontal gene transfer require?
2) What is the rate of transfer like in HGT?
3) What is HGT associated with?
1) Horizontal gene transfer requires a heterogeneous population
2) The rate of transfer is extremely variable
3) Associated with rapid adaptation to new environments
List and describe the 3 methods of horizontal gene transfer (HGT)
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
What 3 things is horizontal gene transfer important for?
1) Evolution
2) Adaptation
3) Pathogenicity
List 3 things that can result from horizontal gene transfer (HGT)
Gene acquisition, plasmid acquisition, phage infection
Describe the importance of Bergey’s Manual of Systematic Bacteriology
1) Contains descriptions of all known bacterial and archaeal species
2) An extremely valuable reference for microbiologists
Describe the central dogma of bacterial genetics
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)
List and describe the 3 forms of DNA. Where are they typically found?
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)
What do complementary and antiparallel describe in terms of DNA?
1) Complementary: base pairing rules (A&T and C&G)
2) Antiparallel: backbones run in opposite directions
Describe DNA replication in microbes
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.
Initiation of DNA synthesis predates what?
Any initiation of cell division
Name 3 features of DNA replication in bacteria
1) OriC: origin of replication
2) Replisome: where proteins and nutrients go to aid in replication
3) Ter: site where replication ends
Describe replication of the E. Coli chromosome
It’s bidirectional
Describe 3 ways a bacterial chromosome can be compacted
1) Can be circular
2) Negatively supercoiled, 3) Negatively supercoiled and mediated by DNA binding proteins (histone-like proteins).
DNA binding proteins are what kind of proteins?
Histone-like proteins
Describe why DNA may be negatively supercoiled and mediated by DNA binding proteins (histone-like proteins).
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.
More organization of the chromosome allows for what?
Faster gene expression
Describe the bacterial chromosome, replication speed, error rate, and okazaki fragment length
1) Chromosome: circular, some linear
2) Replication speed: 1,000bp/s
3) Error rate: 10^-8
4) Okazaki fragment length: 1,500nt
Describe bacterial transcription and translation
Transcription: Polycistronic & no post transcriptional modification
-Ribosomes can jump around and translate several proteins at once
Translation: 50S, 30S ribosomes / Protein splicing
Define polycistronic transcription
Ribosomes can jump around and translate several proteins at once
Describe the eukaryotic chromosome, replication speed, error rate, and okazaki fragment length
1) Chromosome: Linear
2) Replication speed: 100bp/s
3) Error rate: 10^-10
4) Okazaki fragment length: 100nt
Describe eukaryotic transcription and translation
1) Transcription: Monocistronic mRNA & post-transcriptional modification
2) Translation: 60S, 40S ribosomes / Protein splicing
Describe the reading frame of transcription and translation
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
What are the 3 stop codons?
UAA, UAG, and UGA
Describe the importance of redundancy in genetic code
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
Name 3 types of mutations and describe what they result in
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
What is the least detrimental mutation to a cell?
A missense mutation
What are the 3 possible outcomes of genetic mutations?
1) No effect (no change in phenotype)
2) Change in phenotype
3) Fatality
What are the two types of point mutations?
1) Transition: purine > purine or pyrimidine > pyrimidine (staying the same type of nucleotide)
2) Transversion: purine <> pyrimidine (switching type of nucleotide)
What is the most common type of mutations?
Point mutations
What are the two main categories of mutations?
Point mutations and frameshift mutations
Define a transversion mutation and list its 3 possible outcomes
1) Transversion: purine <> pyrimidine (switching type of nucleotide)
2) a) None
b) Nonsense: truncated protein
c) Missense: different amino acid; altered protein
What are the two types of transversion mutations? What do each of these result in?
1) Nonsense: truncated protein
2) Missense: different amino acid; altered protein
List and define the 2 types of frameshift mutations
1) Deletion: deletion of 1 or more nucleotides
2) Insertion: the addition of 1 or more extra nucleotides
List 2 things that can cause mutations and give an example of each
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
We must have ways to differentiate wild-type vs mutant; name and define what this process is called
Screening: detection system for a mutant phenotype
Name 4 kinds of mutations
1) Morphological mutations
2) Lethal mutations
3) Conditional mutations
4) Biochemical mutations
Give 2 examples of biochemical mutations and define them
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
Name 4 ways to screen for mutants
1) Replica plating
2) Mutant libraries
3) Phage-sensitivity
4) Plasmid selection
Describe the replica plating process for screening for mutants
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
What does the Ames test do? Where has it previously been successful?
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.
Describe the Ames test
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).
Define genes, phenotype, and genotype
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
Describe cis acting elements and name 3 of them
1) Elements that are intrinsic to the DNA itself
2) Promoter, operator, and terminator
Define promoter, operator, and terminator. Also, what do these 3 things have in common?
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
What’s the differences between cis and trans acting elements?
Cis acting elements are a part of the genetic code, trans acting elements are not a part of the DNA
Name 3 things that help with gene organization
Operons, regulons, and trans acting elements
Define operons and regulons
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]
Define constitutive expression and inducible operons
1) Constitutive expression: always expressed at high levels
2) Inducible operons: (+) or (-) control
Name 4 types of trans acting elements
Repressors, activators, corepressors, inducers
Describe what allows bacteria to build large structures quickly
Bacteria has many transcription factors and proteins because they’re organized in operons, which allows them to make large structures very quickly
Name 2 genetic elements
1) Chromosome
2) Plasmid
Describe what plasmids consist of
Always has an origin of replication, typically has an antibiotic resistance marker, an enzymatic marker gene, and RE cut sites
What are RE cut sites made by?
Made by restriction enzymes that cut DNA.
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?
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
What does plasmid genetic information often provide?
Selective advantages (such as antibiotic resistance, toxins, virulence determinants, etc)
Name 3 selective advantages
Antibiotic resistance, toxins, virulence determinants
Define horizontal gene transfer
The mechanism by which bacteria exchange/ acquire DNA
What 3 methods of transfer can be used in horizontal gene transfer? Describe them.
1) Conjugation: Physical connection between bacteria mediates transfer
2) Transformation: Uptake of naked DNA from environment
3) Transduction: Viral transfer of DNA into bacteria
What 3 things is horizontal gene transfer important for?
Evolution, adaptation and pathogenicity
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?
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)
Define conjugation
Transfer of DNA, often in the form of a plasmid, by direct cell-to-cell contact
What does the donor cell in conjugation contain, and what does it use to transfer genetic material?
1) The donor cell contains a plasmid
2) It uses a sex (F) pilus to transfer DNA or a plasmid
Who discovered conjugation and what did he use? Describe his experiment
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)
What did Bernard Davis find?
That physical contact is necessary for the transfer of genes
What 3 things do conjugative plasmids require?
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
What allows for plasmids to be integrated into a chromosome?
IS elements, which contain inverted repeats
What 2 things are involved in F factor mediated conjugation?
Involves a donor and recipient; the donor has the F-plasmid that encodes for the pilus (which allows for conjugation). F+ donor, F- recipient.
Describe the process of F factor mediated conjugation
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.
What is rolling circle replication found in? List its 5 steps.
-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
What makes physical contact with the recipient cell in F factor mediated conjugation?
The sex pilus physical contact with the F- cell. It then shortens to bring the cells close together.
What joins the two cells together in F factor mediated conjugation?
A type IV secretion system
F factor mediated conjugation: What initiates contact with the plasmid, and what does it couple the plasmid with?
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
F factor mediated conjugation: What makes a cut at the origin of transfer?
The relaxosome makes a cut at the origin of transfer and begins to separate one DNA strand.
F factor mediated conjugation: Which strand of DNA is replicated? What is it replicated by?
The intact strand is replicated by the rolling-circle mechanism.
