Chapter 26 and 27 Flashcards
What is phylogeny
Phylogeny is the evolutionary history of a species or group of related species .
show evolutionary relationships
What is systematics
Systematics is the scientific discipline focused on classifying organisms and determining their evolutionary relationships.
What is taxonomy
Taxonomy is the scientific discipline concerned with naming and classifying the diverse forms of life .
2 part binomial scientific name scheme
First word is the genus to which species belong to followed by the epithet .
Binomial italicized and genus name capitalized
Taxon
Taxonomic unit at any level of the hierarchy
There is genetic diversity within a taxon
What is a phylogenetic tree and what is it used for ?
A phylogenetic tree a branching diagram to represent a hypothesis about the evolutionary history of a group of organisms
- shows patterns of descent
- shows common ancestors
- shows evolutionary relationships
- shows info about similar characteristics in closely related species.
What is the pholygenic tree vocab
• Each branch point represents the divergence of two species
• Sister Taxa are groups that share a common immediate ancestor
• Rooted tree- branch to represent the last common ancestor of all taxa in a tree
• Basal taxon- diverges early in the history of a group and originates from the common ancestor of the group
• Polytomy a branch from which more than two groups emerge
What are homologies
Homologies are phenotypic and genetic similarities due to shared ancestry
Difference between homology and analogy
Homology is similarity due to ancestry but analogy is similarity due to convergent evolution aka homoplasies
Example of homologies bat wing and bird wing have forelimbs from a common ancestor.
should consider the explanation that
reflects the most likely sequence of evolutionary events, given rules
about how DNA changes over time
Example of analogs have functional wings developed differently not in a common ancestor between a bat and a bird.
What are molecular homologies
Computers and mathematics are used to compare DNA sequences.
What are clasidistics and clades?
Clade is a group of species that includes an ancestral species and all it’s descendants
clades can be nested to other clades.
Claudistics is a method of grouping organisms to a common descent.
identified using shared derived characters.
What are the clade types ?
•
Clade types
Monophyletic group- has an ancestor species and ALL its descendants- most valid
• Paraphyletic group- has an ancestral species and SOME of the descendants
Polyphyletic group- Group includes distantly related species but does not include their most recent common ancestor
give an example of the clade types
monophyletic group is a clade saying we know that common ancestor and what derived from all the descendants. meaning you have ancestors and descentants
paraphyletic group is when a common ancestor known and knows groups a,b,c,d,e but hasn’t studied for g descendants. there is a hole in knowlege.
polyphletic group - A group composed of a collection of organisms in which the most recent common ancestor of all the included
organisms is not included.
group includes distantly related species but dies not include their recent most common
ancestor so there is two or more different
ancestors.
what is an example of shared ancesteral chaarcter and shared derived character ?
example of shared ancestor character is all mammals have a backbone and the backbone pre dates mammals branching from all other veterbrates.
example of shared derived characteristics is all mammals have hair but the hair is not found in the ancestors and is unique to mammalian clade.
hair on mammals when compared to other veterbrates .
what is the difference and similarities between maximum parisomy and maximum likelihood.
maximum parisomy assumes the fewest evolutionary events and appearance of shared derived characters is most likely. first investigate the simplest explanation that is consistent with the facts.
maximm likelihood should consider the explanation that
reflects the most likely sequence of evolutionary events, given rules
about how DNA changes over time
both help scientists narrow the options when it comes to making a phylogenetic tree.
difference between shared ancesteral and shared derived character ?
shared ancesteral character is shared by members of a clade orginated in an ancestor that is not a member of the clade.
shared derived character is an evolutionary novelty unique to a particular clade.
difference between ingroup and outgroup?
ingroup is the group of species being studied and shares common traits/ characteristics.
Outgroup is the group that completely unlike all the other organisms . ( outside of a group of taxi being studied) excluded
analogous morphology versus homologous morphology ?
analogous morphology structures that have similar functions but with dissimilar evolutionary changes.
homologous morphology is a structure found in two or more different species but derived from a common ancesteral structure.
differences due to heterochrony an evolutionary change in the rate or timing or development of events.
molecular homology vs molecular homoplasies ?
molecular homology is when the sequence of genes or DNA is similiar if descended from a common ancestor.
Sequence nucleotides and align comparable genes/DNA regions
Humans and chimpanzees share a similarity in the sequence of amino acids in haemoglobin
molecular homoplasies is a nucleotide or base sequence within two different organisms that may align due to concidental matches but not common ancestor.
the difference between gene duplications and gene families
gene duplications increase the number of genes in the genome.
repeated duplications in gene families.
groups of related genes within an organism’s genome, and two types of homologous genes
duplications can be used to share ancestry.
paralogs similiar genes in one species and orthologs similar genes in two species.
what is a biological community ?
A biological community is a group of populations living close enough to interact.
all organisms living in asia.
interspecific communities vs intraspecific communities ?
Interspecific interactions define the relationship between individuals of species in a community
Competition
Predation
Symbiosis
intraspecific interactions is between members of a species.
what is interspecific competition and give an example of it.
occurs when indivisuals of different species compete for a resource that affects their growth and survival.
competitive exclusion is populations with 2 same species compete for the same resources and one species eventually is eliminated .
what are the types of competiton
ecological niche is the sum of species use of the abiotic and biotic resources in their environment.
The species’ fundamental niche is the niche potentially occupied by that species
The realized niche is the portion of its fundamental niche actually occupied by the species.
Resource partitioning is the division of environmental resources by coexisting species such that a niche of each species differs significant factors from the niches of all coexisting species.
what is character displacement
character displacement is the tendancy or charcteristics to be more divergent in sympatic populations of two species than allopatric.
what is predation
prediation is when a predator eat and kills their prey.
predator ambushes, claws, and pursues
preys adaptations behaivoral defenses, alarm calls, morphological and physiological adaptions.
what are the types of coloration ?
cryptic coloration is camoflauge blending in.
aposematic coloration is bright warning coloration of animals with effective chemical defenses.
what are the types of mimicry.
batesian mimicry a harmless species mimics a harmful one.
mullerian mimicry two unplatable species mimic each other. you avoid all wasps because you know one type of wasps sting.
what is symbiosis
an elogical relationship between organisms of 2 different species that live together in direct and intimate contact.
paratism a parasite derives nourishment from the host.
mutualism both species benefits
Obligate mutualism: At least one species has lost the ability to survive without the partner
Facultative mutualism: Both species can survive independently
Commensalism (+/0): Interaction benefits one species but neither helps nor harms the partner species
What is species diversity
Species diversity is the number and relative abundance of species in a biological community.
Composed of species richness which is the number of species present in a biological community .
Composed of relative abundance the proportional abundance of different species in a community .
Example vast majority of your species is made up of species A is 80%.
What is the difference between tropic structure ( food chain) and food web
Food chains is the pathway along which food energy is transferred.
Food web is the interconnected feeding relationships found in an ecosystem .
Trophic structures is the entirety of how you have feeding relationships amongst different organisms.
Keystone species
Species that exert strong control on a community structure by the nature of its ecological roles or niches .
Holds a community together
Not the most abundant
Types of Motility
Taxis - directed movement which is the Ability to move away or towards a stimulus.
Chemotaxis- Specifically the movement towards or away from a chemical substance.
away from toxins is negative chemotaxis, ( high level )
towards nutrients, oxygen positive chemotaxis.
Dominant species
Dominant species are species that are most abundant or that collectively have the highest biomass and exert powerful control over occurrence and distribution of species.
Classification of prokaryotes bs eukaryotes
3 domain classification
Bacteria
Archaea
Eukarya
There are differences between bacteria and archea at the DNA molecular level and differences in the way that they build cellular structure.
Analogous structure of the cell wall has similar functions but different in the way it was built together ( building blocks) in bacteria and archea.
Cell wall in prokaryotes
Maintains shape and protection
Prevents cell from bursting in hypotonic environments ( water entering the cell ).
In hypertonic environment prokaryotes lose water shrink away from cell wall inhibit reproduction .
Cell wall in bacteria vs archaea
In bacteria it contains peptidoglycan a polymer composed of modified sugars cross linked by short polypeptides.
- encloses entire bacterium
- anchors molecules that extend from cell surface.
In archaea contains polysaccharides and proteins.
Similar outcomes but fundamental building blocks are different.
analogus structures coming from different lineages.
What is the purpose of gram staining?
To be able to determine the composition of the cell wall.
Gram positive
Delivery of other antibiotics into the cell.
Virulent strains emerge that are resistant to one or more antibiotics.
Sensitive to antibiotics that inhibit peptidoglycan cross linking cell wall no longer functional.
Gram negative
Outer membrane impedes entry of antibiotics.
Outer membrane helps protect it from host immune defenses.
Lip-polysaccharides in cell wall are toxic cause fever or shock.
fimibriae versus pilli
fimbriae is like an appendage that helps a prokaryotic cell adhere to substrate (surface) or other prokaryotic cells.
pilli are appendages that pull 2 cells together to dna transfer during conjugation. (lasso effect)
prokaryotes internal organization
lack organelles ( complex compartmenzilation)
can perform metabolic functions
invaganitation and infolding of plasma membrane
motility (flagella)
may be scattered over entire celluar surface or concentrated at both ends .
ATP driven pumps in the motor transport protons out of cell diffusion of protons into cell turned curved hook filament rotates to propel cell.
beacterial and archeal flagella similar in size and mechanism made up of different proteins analogous structures.
capsule and slime layer
a capsule is a dense and well defined layer of polysaccharide or protein
slime layer fufills the same role which is adherence and preventing dehydration but the way it’s constructed is different.
cell wall sticky layer functions
adhere to the substrate or other individuals in the colony
prevent dehydration
stay protected from host immune diseases .
genome
located in a nucleoid a nonmembrane bounded region in the cell where DNA is concentrated .
have plasmids smaller rings of independantly replicating DNA usually carries few genes
f plasmid ( fertility)
r plasmiid ( resistance)
reproduction is limited by
exhaustion of nutrient supply
consumed by other organisms
compettition from other microorganisms
accumulation of metabolic wastes ( toxic )
rapid production is key to variation.
types of genetic diversity
genetic recombination creates additional diversity by combining DNA from 2 individual cells ( within the same species)
horizontal gene transfer refers to the transfer of genes across species through mechanisms such as transposable elements plasmid exchange, plasmid exchange, viral activity, and perhaps fusion of organisms .
types of genetic recombination
transfer is a change in genotype or phenotype due to assimilation of external DNA by a cell.
transduction is a process in which phages (viruses) carry bacterial DNA from one bacterial cell to another
conjugation prokaryotes) is the direct transfer of DNA between two cells that are temporarily joined
Bacteria: Movement in one direction from donor to recipient (not a bi-directional process)
E. coli:
Pilus from donor cell attaches to recipient
Pilus retracts, pulling two cells together
“Mating bridge” formed between two cells; DNA transfers from donor to recipient
compare and contrast conjugation, transformation, and transduction.
Conjugation is similar to transduction in that DNA is moved directly from one bacterial cell to another.
In transformation, a bacterium takes up a piece of DNA floating in its environment. In transduction, DNA is accidentally moved from one bacterium to another by a virus. In conjugation,is where genetic matieral is transferred between prokaryotic cells.
there are a few similarities between transformation and transduction: -Both are involved in horizontal gene transfer from one bacterium to another.
conjugation
Ability to act as donor cell during conjugation results from presence of DNA called the F factor (f for fertility)
conjugation f plasmid
mating bridge forms between f plus (donors) and f minus ( recipents)
One strand of F+ cell plasmid DNA
breaks at arrowhead.
Broken strand peels off and enters F− cell.
Donor and ecipient cells synthesize
complementary DNA strands.
Recipient cell is now a recombinant
F+ cell for each.
f minus recipent —- gets a new f plus donor
f donor gets a f donor.
conjugation f factor in chromosome hfr
An Hfr cell forms a
mating bridge with an F− cell.
A single strand of the F factor
breaks and begins to move
through the bridge.
Crossing over can result in exchange of homologous genes.
Enzymes degrade and
DNA not incorporated.
Recipient cell is now a recombinant F− cell.
hfr donor —–> hfr donor
f- recipent goes to a f - recipent cuz it lacks infertility.
What is a virus
•A virus is an infectious particle incapable of replicating outside of a cell
what are unique types of archaea
Extreme halophiles live in highly saline environments
Extreme thermophiles live in very hot environments
Methanogens are archaea that release methane as a byproduct
what are prokaryotes metabolic diversity ?
Phototrophs: Organisms that obtain energy from light
Chemotrophs: Organisms that obtain energy from chemicals
Autotrophs: Organisms that need only CO2 in some form as a carbon source
Heterotrophs: Organisms that require at least one organic nutrient, such as glucose, to make other organic compounds
R plasmid antibiotic resistance
- R plasmids carry antibiotic resistance genes
– The ability to survive treatment with antibiotics
Mutation in a chromosomal gene can confer resistance altered protein may no longer transport an antibiotic into the cell
Resistance genes carried on R plasmids enzymes that specifically destroy/hinder effectiveness of certain antibiotics
Natural selection: Cells without resistance die in presence of antibiotic; cells with R plasmid persist
Many R plasmids contain genes which allow DNA transfer by conjugation
oxygen in metabolism
– Obligate aerobes
* Need oxygen for cellular respiration
– Obligate anaerobes
* Are poisoned by oxygen
* Use fermentation or anaerobic respiration to make ATP
– Facultative anaerobes
* Can survive with
* or without oxygen
vObligate aerobes absolutely require oxygen for cellular respiration and cannot grow without it
Obligate anaerobes cannot tolerate oxygen (toxic) and must live in a niche deficient in O2
Fermentation: A catabolic process that makes a limited amount of ATP from glucose (or other organic molecules) without an electron transport chain, producing a characteristic end product such as ethyl alcohol or lactic acid
Anaerobic respiration: Utilizes an electronic transport chain but uses substances other than O2 (nitrate ions or sulfate ions) as electron acceptors
Facultative anaerobes use O2 if it is present, but can also utilize fermentation or anaerobic respiration in an anaerobic environment
types of symbiotic relationships
Mutualism
– Benefits both host and symbiont
* Commensalism
– One organism benefits
– The other organism is not affected in a significant way
* Parasitism
– One organism benefits- the parasite
* Parasites that cause disease are known as pathogens
– One organism is harmed- the host
domains of bacteria
Every major mode of nutrition and metabolism represented
Major groups:
Proteobacteria: Gram Negative
Alpha (Ancestor organism from this group = hypothetical origin of mitochondria)
Beta important in nitrogen fixation and strains causes diseases.
Gamma bacteria that cause salmonella.
Delta can produce spores that can survive droughts.
Epsilon contain many pathogens
Chlamydias: Gram “Negative” (no peptidoglycan); parasites
Spirochetes: Gram Negative; internal, flagellum-like filaments
Cyanobacteria: Gram Negative, photoautotrophs (Ancestor organism from this group = hypothetical origin of chloroplasts)
Gram-positive bacteria: Extremely diverse; include false-positive Mycoplasma
what is the structure of a virus ?
Nucleic acid genome can be either DNA or RNA
DNA virus
RNA virus
Either single-stranded or double-stranded molecule
linear or circular.
structure of viruses capsid
capsid is the protein shell that encloses a viral genome
Rod-shaped
Polyhedral
Complex assembly
Composed of protein subunits called capsomeres
Each capsid contains limited number of kinds of proteins
Large number of capsomeres assembled to create capsid
capsid protein coat that covers viruses .
structure of viruses - capsid shapes
helical virus is a rigid rod shaped capsoid and encases coiled rna genome ( example tobacco mosaic virus)
adenovirus has glycoprotein spike located at each vertex and encloses dna genome .
t even bacteriophages have a complex capsid structure
Elongated icosahedral head encloses DNA
Protein tail apparatus used to attach to bacterial host cell
viruses that infect bacteria.
information about viral envelopes
viral envelopes are derived from the protein cell and also contain viral particles.
envelope can surrond capsules of a viral particle.
what is a host range and define a host range.
host range of a virus is the limited number of species whose cells can be infected by a particular virus
Recognition systems: Virus has specific interaction between viral surface proteins and specific receptor molecules on the host cell
Wide range: Infect multiple species
West Nile virus: mosquitos, birds, horses, humans
Narrow range: Infect single species
Measles: humans only
Specific cell type within multicellular eukaryote
HIV: CD4+ T cells
Specific interaction between host cell and virus the result of evolution
Viruses have been found that infect every form of life
structure of viral envelope
The viral envelope is derived from the host cell membrane and cloaks the capsid
Host phospholipids and membrane proteins
Viral proteins and glycoproteins
May also help package viral enzyme molecules
example of viral envelope influenza virus
the steps of replication ?
Specific attachment
- Penetration
Tail apparatus injection (T-even phages)
Endocytosis
Fusion of viral envelope with host plasma membrane
3.Synthesis
Viral genome
Capsid proteins
4.Spontaneous assembly
- Release of new particles
lyctic cycle
A phage replicative cycle that culminates in death of the host cell is called a lytic cycle
A phage that replicates using only a lytic cycle is called a virulent phage
lysogenic cycle
A lysogenic cycle allows replication of the phage genome without destroying (lysing) the host – but retains the ability to generate active phages via a lytic cycle
A phage capable of replicating within a bacterium using both modes (lytic and lysogenic) is called a temperate phage
Integrated viral DNA is called a prophage
Prophage genes replicated along with host genome
Prior to entering lytic cycle, prophage excised from bacterial chromosome, yields two separate circular DNA molecules
plant viruses
vexternal source
Virus must penetrate plant’s outer protective layer of cells
Associated with tissue damage by wind, injury, herbivores (insects also carriers)
Vertical transmission refers to infection inherited from a parent
Asexual propagation (cuttings)
Sexual reproduction (infected seeds)
Infection can spread through plant via plasmodesmata, the cytoplasmic connections that penetrate the walls between adjacent plant cells
animal viruses
Animal viruses classified into 6 classes based on genome:
dsDNA double strnded
ssDNA single stranded
dsRNA
ssRNA (serves as mRNA)
ssRNA (serves as template for mRNA synthesis)
ssRNA (serves as template for DNA synthesis)
retrovirus replication
Class VI RNA animal viruses are called retroviruses
Replicate by transcribing RNA into DNA and insert the DNA into a cellular chromosome
Utilize an enzyme called reverse transcriptase which transcribes an RNA template into DNA, creating the RNA DNA (retro) information flow
Reverse transcriptase is packaged into the viral particle along with the viral genome
Human Immunodeficiency Virus (HIV)
Contains two identical molecules of ssRNA and two molecules of reverse transcriptase
Viral infection causes Acquired Immunodeficiency Syndrome (AIDS)
compare and contratst the lyctic and lasogenic cycle.
The lytic cycle involves the reproduction of viruses using a host cell to manufacture more viruses; the viruses then burst out of the cell. The lysogenic cycle involves the incorporation of the viral genome into the host cell genome, infecting it from within.
Both lytic cycle and lysogenic cycle are mechanisms of viral reproduction. Both lytic cycle and lysogenic cycle only occur inside a host cell. Both lytic cycle and lysogenic cycle may produce thousands of original copies of the original virus.
