Biology evolution
Cell theory postulates
All living things are composed of cells, the cell is the smallest unit of life, and cells only arise from pre-existing cells
Nutrition
A function of life. Feeding by either synthesis or organic molecules (e.g photosynthesis) or the absorption of organic matter
metabolism
A function of life. The web of all the enzyme-catalyzed reactions in a cell or organism
growth
A function of life. An irreverseible increase in size and volume
response (sensitivity)
a function of life. Perceiving and responding to changes in the environment
Homeostasis
A function of life. Keeping conditions inside the organism within tolerable limits (ex. pH and water)
reproduction
A function of life. Producing offspring either sexually or asexually
excretion
A function of life. The removal of metabolic waste
Paramecium (uni-cellular organism) functions of life
Metabolism: Most metabolic pathways happen in the cytoplasm, Nutrition: food vacuoles contain organisms the paramecium has consumed + they are broken down in cytoplasm, Growth: after assimilating consumed biomass it will get larger until it divides, Reproduction: nucleus can divide to allow for mitosis, Response: wave action of the cilia moves the paramecium in response to environmental changes, Homeostasis: contractile vacuole, Excretion: plasma membrane controls entry and exit of substances
Exceptions to the cell theory
Some exceptions include striated muscle, giant algae, and aseptate fungal hyphae - due to the fact that they are very large and multinucleated.
Miller and Urey experiments
Demonstrated that simple organic molecules like amino acids can be produced in abiotic conditions. They reproduced the environment thought to exist on early earth (methane, ammonia, hydrogen, simulated water cycle warm temperature, uv radiation exposure, electric sparks for lighting). They noticed after a week organic compunds had formed inside the primordial soup model
conflicts with the miller-urey experiment
carbon compounds were possibly introduced from comets and meteorites stiking earth. Some scientists also believe the simulated environment was ddifferent from early earth's atmosphere (thought it came from volcano gases, no methane or ammonia). Miller-urey used a reducing environment but some think early earth had a non-reducing environment. A necessity of life is also the ability to polymerize, which the amino acids in the primordial soup did not do.
formation of vesicles
A type of fatty acid (phospholipid) that was present during early earth had hydrophilic and hydrophobic properties. In water they organized themselves into double layer bubbles (vesicles). These vesicles are refered to as liposomes and were likely the first protocells.
Formation of polymers that can self-replicate
DNA cannot replicate without ezymes however RNA can store info and self-replicate and catalyze the formation of copies of itself with ribozymes. RNA is in ribosomes and helps with peptide bond formation. They can assemble spontaneously
LUCA evidence
A universal genetic code in DNA is shared by all cells, over 300 genes/DNA sections are common to all cells, both RNA and DNA share the same building blocks in all cells, common molecular processes within cells, similar transport mechanisms for cellular materials within through cells. Hypothesized other forms of life existed but were out competed by LUCA
Dating techniques
fossil records are the sum of all discovered and undiscovered fossils and their relative placement in rock. The layer of rock in whjich a fossil is found can be dated to deduce the age of the fossil (relative dating). Fossils within the layers are called index fossils. Sometimes geological processes can disturb these layers and provide inaccurate fossil ages
Absolute dating
Radioactve dating involves comparing the ratio of radioactive isotopes in the fossil to that found in the atmosphere today.
Half life
Radioisotopes decay at a constant rate to form a more stable daughter isotope, the time taken for half of the original radioisotope to decay is known as the half-life. Different radioisotopes have different half lives and can be used to date fossils by looking at how many years it would take to get to the half life
Development of the nucleus
as a prokaryote grows it develops folds in its membrane to maintain an efficient SA:vol. The infoldings are pinches off which forms an internal membrane. THe nucleoid region is enclosed in it and becomes the nucleus
development of mitochondria and chloroplast
An aerobic protobacterium enters a larger anaerobic prokaryote and survives digestion. The protobacterium provides ATP to its host, enabling it to out-compete other anaerobic prokaryotes. As the host cell grows and divides the aerobic proteobacterium does to, other generations will contain it, it assimilated and becomes a mitochondrion.
Evidence of endosymbiotic theory
Mitchondria and chloroplasts: have their own DNA, have ribosomes similar to prokaryotes, a double membrane, and inner membrane, has similar proteins to prokaryotes. They are roughly the same size as bacteria. They transcribe their DNA and use the mRNA to synthesize their own proteins. They have RNA present that resembles RNA in prokaryotic ribosomes. THey can only be produced by the division of a pre-existing one
Criticisms of endosymbiotic theory
Mitochondria and chloroplasts cannot survive on their own outside of the cell. THe ability to engulf another cell and have it survive does not guaruntee that the host cell will pass the genetic information to make the new organelle to its offspring
speciation
the process by which a population of one species diverges to become two distinct species while inhabiting the same geographic region. Various barriers isolate the gene pool of one population from another and each population will start to diverge from each other.
Allopetric speciation
More common than sympatric. Populations become geographically separated by a long, sslow process like the movement of a glacier. In their separate areas, the two populations independently evolve and accumulate different gene mutations in response to different selective pressures. The two populations evolve to the point of not being able interbreed and are two separate species.
sympatric speciation
rarer than allopatric. Occurs without geographical separation. They can be separated by differences such as reproductive isolation, temporal isolation, and behavioural isolation
reproductive isolation
species from the same population may not interbreed any longer. The members of the isolated population will evolve so that they can no longer mate with the original population
temporal isolation
some members of the population mate and reproduce at a different time or different seasion than the rest of the population. E.g eastern spotted skunk mates in late winter, western spotted skunk mates in late summer
Behavioural isolation
some members of the population have different courtship behaviours like mating songs, dances, etc. E.g eastern vs western meadowlark, they don't mate because of the differences in their songs
biodiversity
the number and relative abundance of species found in an area
Ecological niches
The role of a species in an ecosystem (characteristic shared by members of same species). This can include the abiotic environmental conditions a species can tolerate, te biotic interactions a species has with other species, the activity pattern of a species (e.g nocturnal), and how the species obtains energy and nutrients
Adaptive radiation
Many species rapidly evolve from a common ancestor to occupy a range of vacant ecological niches. E.g mass extinctions, any remaining species will evolve to fill the niches without competition. Isolated islands also allow for pioneeringg species to fill niche vacancies
radiation of mammals after dinosaur extinction
After the extinction of dinosaurs, mammals evolved and adapted to the newly available niches with few competitors for resources. This led to a suden expansion of species diversity, including the first fully aquatic mammals, flying mammals, rodents, and primates
adaptive radiation in galapagos finches
one species of finch migrates to the galapagos from the mainland of central or south america. This one migrant species would give rise to multiple species that exploit different niches. On various islands, species have adapted for different diets like seeds, insects, flowers, etc.
Hybrids
The offspring resulting from the sexual reproduction between two closely related, but separate species. E.g a horse has 64 chromosomes, and a donkey 62, so mules typically have 63. The mismatched chromosomes prevent homologous chromosomes from pairing during meiosis, preventing the production of functional gametes.
Barriers to hybridization
many species have evolved barriers to prevent the development of hybrid offspring, ensuring that energy is not wasted producing sterile hybrids and preventing the mixing of alleles between species.
Prezygotic barriers
prevent fertilization of egg and sperm between two separate species. Includes habitat isolation, temporal isolation, behavioural isolation, mechanical isolation, and gametic isolation.
Post zygotic barriers
occur after the fertilization that prevent the zygote from developing into a viable, fertile adult. Includes reduced hybrid viability, reduced hybrid fertility, and hyrbid breakdown.
Mechanical isolation
If individuals of two different species attempt to mate, differences in the anatomy of the reproductive organs may prevent successful breeding. E.g Damselfly males of different species have different shaped reproductive organs, so if they try to mate with the female of another, their body parts don't fit together.
Gametic isolation
If individuals of two different species attempt to mate, the proteins on the surface of the gametes will not be complementary (fetilization requires fusion of proteins on sperm with receptor proteins on egg). E.g purple sea urchin and red sea urchin.
Reduced hybrid viability
if fertilization occurs, then postzygotic mechanisms may occur that prevent the offspring from surviving. E.g hybrids of salamanders cannot camouflage well or mimic well, so they are vulnerable to predators and less likely to survive to adulthood
Reduced hybrid fertility
if the hybrid is able to survive, there may still be mechanisms that prevent the hybrid from successfully reproducing. E.g zebroids are sterile, cultivated bananas are seedless and sterile so they must be propagated vegetatively
Hybrid breakdown
If a first generation hybrid is able to survive and reproduce with another hybrid or the parent species, the offspring of the hybrid may be feeble or sterile
Gradualism
the theory that speciation is a slow change through a series of intermediate forms. Gaps in the fossil record caused controversy for this theory.
Abrupt speciation
If long periods of relative stability is punctuated by periods of rapid evolution, speciation is said to occur abruptly without a long sequence of intermediate forms, Can be caused by a sudden change in the structure or number of chromosomes
Polyploidy
In polyploidy, multiple sets of chromosomes have formed (unlike typical diploid). Mostly restricted to plant cells and associated with low fertility as mispairing during meiosis is a likely risk. Triploid = 3x, tetraploid = 4x. Polyploid organisms tend to be larger because of larger nucleuses that have to accomdate more genetic material. Polyploidy results from an error in meiosis where all the chromosomes move into one cell instead of separating.
Autoploidy
In some cases, a polyploid individual will have two or more complete sets of chromosomes from its own species.
formation of polyploids
If there is an error in meiosis that results in all the chromosomes moving to one cell instead of seperating, a diploid gamete may be produced instead of the typical haploid gamee. It will then fuse with a haploid gamete from the same species to create a triploid zygote, or with another diploid gamete to create a tetraploid zygote.
Allopolyploids
polyploids with multiple chromosome sets derived from two different species. Gametes from two species, at least one of which has had an error in meiosis, combine to form allopolyplod offspring
speciation due to polyploidy
Polyploid individuals would immediately be unable to reproduce with the ancestral species. However, they could either self-pollinate or reproduce with other plants with gametes having the same diploid number. A form of sympatric speciation as the different number of chromosomes from the parent species prevents them from breeding with members of the parent species.
Biological species concept
The predominant way to define many species. A species is a group of actually or potentially interbreeding populations which are reproductively isolated from other such groups.
conflicts with biological species concept
The biological species concept does not work well with organisms that reproduce asexually, form populations or related but genetically isolated clones, and acquire genes from other groups without reproduction. E.g dandelions only reproduce asexually by mitosis. Offspring is identical to the parents (clones)
Asexual reproduction
Occurs when a single parent passes on its full set of genes to offspring, resultingin genetically identical offspring. Asexually reproducing organisms are classified into species based on appearance or biochemical similarities.
Apomixis
Some species of plants produce flowers but do not require fertilization of gametes to produce seeds. The seedlings that germinate are genetically identical clones of the parent plant. A huge number of genetically unique clones can form via apomixis, resulting in populations of related, but genetically isolated clones. Because they don't interbreed, they are all considered different species. The biological species concept doesn't work here because there would be countless species of "dandelions" or other plants that use apomixis.
Horizontal gene transfer
Genes from one bacterial species might be transferred without sexual reproduction to another bacterial species. It is how bacterial resistance can move from one bacteria to another, so species don't really stay separate from one another. The populations are not genetically isolated and cannot be defined according to the biological species concept.
Dchotomous Key
a tool used to identify a species based on observable traits. Each step of the key gives two distinct choices that will lead users to the correct identification.
Developing a dichotomous key
Select a species, pick a characteristic that could divide the selected organisms into two groups (easily observed), two choices should be a yes or no option. Pick another characteristic that divides the organisms in those groups into an additional two groups. Continue down the branching key until only one organism remains on each branch. Number each organism. Create the written key by following the numbers put beside each branch point.
identification of species from environental DNA
DNA barcodes are short sections of DNA from one gene distinctive enough to identify a species. Scientists can identify species from small samples with the DNA barcode. Barcodes are established and stores in databased by DNA extaction and sequencing.
the gene pool
The collection of all the genes and the various alleles of those genes within a population. It is the sum of all genes (alleles) in a population at a given time. It is of the same species and reproductively isolated from other species. A gene pool can change over time through evolution.
Gene flow
Any movement of individuals and the genetic material they carry, from one population to another. In this case, the different populations share a single gene pool.
Gene flow on evolution
Gene flow can introduce new alleles to a population, increasing the genetic variation of that population. By moving genetic material around, gene flow can make distant populations genetically similar to one another, reducing the chance of speciation. The less gene flow between two populationsm the more likely that two populations will evolve into two species
Allele frequency
the prevalence of a specific allele out of all alleles for a gene in a gene pool. The frequency can be espressed as a percentage, decimal, or fraction. The frequency of the alleles of a gene must equal to 1.
Allele frequencies of geographically isolated populations
A common allele in one population may be much rarer in another due to different environmental factors and selection pressures. The frequencies may be different from each other due to genetic drift, the founder effect, natural selection, and new mutations
Genetic drift
when a population is altered due to random events, such as natural disasters. The surviving individuals are a sample of the original population and their allele frequencies may be very different than other populations.
Founder effect
a type of genetic drift (chance event) that occurs when a small group of migrants establish in a new area. The new population will have different allele frequencies than the original population
Stabilizing selection
Occurs where environmental conditions are largely unchanging. Does not lead to evolution, but maintains a fevorable characteristic and the alleles responsible for it. Useless or harmful variants and abnormalities are eliminated.
Directional selection
A type of natural selection that favours one extrmee phenotype over the mean or other extreme. Usually seen in environments that have changed over time like climate, weather, or food availability.
Disruptive selection
Individuals from the center of a phenotype are removed because natural selection favours both ends of the phenotypic variation. Over time, the two extreme variations will become more common and the intermediate states will be less common or lost. It is likely the gene pool will split into two as a result.
Hardy-Weinberg equilibrium
Used to predict the frequency of alleles from genotype frequencies, or to predict phenotypic frequencies and allele frequences from recessive phenotypes. Concluded that allele frequencies in a gene pool will remain stable generation to generation unless evolution is occuring. Allele frequency is calculated by dividing the number of times a specific allele is observed in a population by the total number of all alleles for that gene in the population
Hardy-weinberg equation (two alleles)
For a gene with two alleles, p is the frequency of the dominant allele (A) in the population, and q is the frequency of the recessive allele (a) in the population. p + q must = 1.
hardy-weinberg equation (three genotypes)
p^2 is the frequency of the homozygous dominant genotype (AA) in the population, 2pq is the frequency of the heterozygous genotype (Aa), q^2 is the frequency of the homozygous recessive genotype (aa). p^2 + 2pq + q^2 = 1.
Hardy-weinberg conditions for equilibrium
In order for a population to be in Hardy-weinberg equilibrium: the population is large to minimize the impact of changes due to chance (genetic drift), there is random mating between organisms, natural selection does not favour one phenotype over another, there are no new mutations, and no gene flow. If the population is not in hardy-weinberg equilibrium, it is evolving.
non-random mating
When mating is not fully random in a population, allele frequencies will change. It cna occur when: mates are chosen based on genetic traits like sexual selextion, mating more often with close neighbors than distant members of the population, and when organisms choose mates that are most like themselves.
Artificial selection
When humans deliberately breed crop plants and domesticated animals with particular phenotypic traits. First, there is the overproduction of offspring for opportunity for variation, variation in haritable traits, a selection pressure that affects survival and reproduction of individuals of a population, differential survival and reproduction of individuals in response to the selection pressure, and a change in the frequency of the hertiable trait in the population over time.
Hierarchical classification
a classification system suing seven taxonomic categories, or taxa. These categories are based on shared physical characteristics. Beginning with kingdom, each successive level of classification becomes more specific (Kingdom, phylum, class, order, family, genus, species). Organisms within the same order have more in common with one another than organisms in the same class, and so on.
Taxonomy
classification of organisms using hierachical taxa. Classifies species into groups with shared traits belonging to more comprehensive groups. Benefits are communication between scientists, predictions of characteristics for species in taxonomic groups, and info about how a species evolved from a common ancestor.
difficulties classifying organisms
Traits based on morphology and the physical characteristics to distinguish one species from another are often arbitrary and subjective. A system based on hierarchy has strict ranking regulations, if one organism is moved out of a group it compromises all other ones in the same group. The more organisms are discovered, the more often the hierarchy doesn't work, hybridization complicates the system.
Advantages of classification corresponding to evolution
instead of only looking at morphology, scientists classify by looking at molecular differences in protein sequences and DNA, this study is called phylogeny. Advantages are that it is not subjective, every organism that has evolved from a common ancestor is included in the same taxonomic group and reflects the gene flow, and features can be predicted as they are shared with members of their clade.
clades
cladistics is a system of classification for goruping taxa based on the characteristics that have evolved most recently. The diagram illustrating this is a caldogram. If members of a group did not all evolve from a comon ancestor, they are polyphyletic. If they came from a shared common ancestor, they are monophyletic. A clade is a group that includes an ancestor and all of its descendants.
Analyzing cladograms
More closely related taca are connected by shallowed nodes (near tip of tree), the root is the base of the cladogram and is the hypothetical common ancestor. Deeper nodes are older than shallower nodes. Typically, a time scale will be included beside the tree to indicate the timing of branching events.
Gradual accumulation of sequence differences
There is evidence that mutationsin DNA or amino acid sequences occur at a roughly constant and regular rate so they can be used as a molecular clock. THe number of differences in sequence can be used to deduce how long ago species split from a common ancestor.
Base sequences of genes for constructing cladograms
The amino acid sequence of cytochrome x has been analyzed as an important evolutionary conservative protein. Comparison of cytochrome c sequences from different species has been used to order the divergence of species in relative time.
Classification of all organisms into 3 domains
All living organisms used to be grouped into two overarching categories based on cell types (prokaryotes + eukaryotes). Base sequences of RNA have revealed that prokaryotes are much more diverse. As a result prokaryotes are now divided into bacteria and archea, resulting in a three domain system of eukarya, archea and bacteria.
Why are viruses not living
They are not made out of cells, they cannot keep themselves in a stable state, they do not grow, they cannot replicate themselves, and they cannot perform independent metabolism.
Structural features common to viruses
SIze: between 20-30 nm, they must be smaller than their hosts so that they can enter them. Fixed size: they do not grow, a virus is assembled inside a host cell with a fixed number of components. Capsid: a protein coat encloses their genetic material (can be multiple or one protein). Genetic material: a nucleic acid like RNA or DNA. No cytoplasm + few enzymes: viruses use the metabolism of their host cells and most of their enzymes.
Diversity of structure in viruses
Viruses have relatively few shared features, suggesting they have multiple evolutionary origins. They vary in shape and size, and the length and shape of their DNA/RNA. Capsids can be helical or icosahedral, and a few viruses have a complex architechture.
Virus evelope
Viruses can be non-enveloped or enveloped. Non-eveloped viruses affect plants or bacteria and do not become enclosed in a membrane, cell lysis is their mode of exit, and they are more resistant to factors like pH, heat, etc. Enveloped viruses affect animals, they become covered with a membrane when breaking free from the host cell, they don't always cause cell lysis, and they are more sensitive to pH, heat, etc.
Viral genomes
highly variable in the number and type of genes, however they all have the same mission to hijack cellular machinery to force the cell to make more virus nucleic acid and assemble new virus molecules.
Lyctic cycle - phage attachment to host cell
In order to enter the host cell, the phage must attach itself to a receptor protein within the cell's membrane. Initial contact often happens through random collisions. Not all bacteria-phage combinations have compatible receptors so it is selective.
Lyctic cycle - phage DNA entry
Injection of the phage's genetic material into the host cell is coordinated by the phage tail. The tails can vary widely but many have a tube for delivering genetic material, surrounded by a sheath of contractle proteins. The tail contracts like a coiled spring and on release drives the genetic material into the cell.
Lyctic cycle - DNA replication
exact copies of the phage DNA are produced using rolling-circle replication, where one strand is nicked and replication enzymes are used to extend the free 3' end. As a complementary strand is synthesized around the circular DNA, the 5' end is peeled off, leading to a displaced strand that grows in length. The ends of the linear phage DNA join to form a circle.
Lyctic cycle - protein synthesis
The phage DNA is used to synthesize viral proteins using the host cell's machinery. The host RNA polymerase is used to transcribe the phage DNA to phage RNA, and the host's ribosomes are used to translate that RNA into proteins.
lyctic cycle - assembly
one all the component parts have been synthesized they are assembled into new phage viruses. Capsid proteins assemble to form empty heads where condensed phage DNA is packed. The tail parts assemble independently of the head and the last step in synthesis is joining them together.
Lytic cycle - lysis
enzymes produced by the phae weaken the cell wall and the cells lyse, releasing on average 100-200 phage progeny into the environment.
lytic cycle - spread
the new virus particles are now able to infect other cells. When actively infecting they are called "virulent"
Lysogenic cycle
The phage infects the cell, and the phage DNA becomes incorporated into the host genome. The cell divides and prophage DNA is passed on to daughter cells. Under stressful conditions, the prophage DNA is excised from the chromosome and enters the lytic cycle.
Virus first hypothesis
proposes viruses existed in a precellular world as self-replicating units. THis hypothesis is not supported by current evidence as all viruses require a cell to replicate and survive. Viruses also use the same genetic code as cells.
progressive hypothesis
states that viruses are built up in a series of steps by taking and modifying cell components. Supported currently
regressive hypothesis
asserts that viruses developed from cells in a series of steps by loss of cell compontents. Supported by current evidence
Rapid evolution in viruses
Viruses evolve rapidly because they have a high generation rate, a high mutation rate which allows for variation, and natural selection imposed by pressures from the host cells causes the viruses to evolve.
Generation time
the average time between two consecutive generations in the lineages of a population. A species with a shorter generation time will have undergone more rounds of selection, and vice versa. Each virion produces many offspring viruses, causing competition between virions for access to the next host cell and more evolution.