Bio notes.pdf

7 properties of life - Made up of cells: which form highly ordered structures with internal order, specific arrangements and functions - Energy processing: carry out metabolism - The maintenance of cells requires ENERGY - Every living organism must obtain FUEL...

7 properties of life - Made up of cells: which form highly ordered structures with internal order, specific arrangements and functions - Energy processing: carry out metabolism - The maintenance of cells requires ENERGY - Every living organism must obtain FUEL - Energy stored in light (used in photosynthesis) or food (chemical energy) is transformed to a source of energy that the cell can use (ATP: Adenosine triphosphate) (cellular respiration) to power metabolism: all the chemical reactions in our bodies - Regulation: our metabolism must be regulated to maintain a constant internal environment - Homeostasis: ability of an organism to maintain a relatively stable internal environment; organisms maintain homeostasis by adjusting physiological processes (ex: temperature regulation) - Growth (increase in size and in number of cells, can be determinant or indeterminate) and development (changes that take place) - Response to stimuli of the environment: organisms respond to physical and/or chemical changes to their external or internal environment - Reproduction: organisms come from previously existing organisms - Asexual: organisms reproduce offspring that are exact copies of themselves (often mistakes during the duplication process, leading to genetic diversity) - Sexual: involves fusion of 2 cells, offspring produced by sexual reproduction vary genetically from their siblings and their parents - Evolve and adapt: the ability to change in response to the environment (from generation-to-generation species change: sometimes a little, sometimes a lot) Cells: life’s basic and fundamental unit of structure and function, the latter of which is the basis for the actions of organisms; smallest unit of organization that can perform all activities required for life; made up of many different kinds of molecules - ALL cells: have a membrane that separates the interior of the cell from its external environment, DNA, cytoplasm (internal mass), organelles called ribosomes and can harness materials and energy from the environment - Prokaryotes: - DNA NOT separate from cytoplasm because NO nucleus, contained in nucleoid - LACKS membrane bound organelles - Mostly unicellular - ~1/10 the size of eukaryotes - Eukaryotes: - DNA in a membrane enclosed nucleus - Membrane enclosed organelles - Unicellular AND multicellular - DNA: deoxyribonucleic acid: the blueprint for an organism - Life processes require the expression and transmission of genetic information - DNA ensures faithful inheritance of genetic information from generation to generation - In nucleus contained by chromosomes - Molecule made up of two long chains (strands) arranged in a double helix, which is made up of four kinds of chemical building blocks called nucleotides, abbreviated A, T, C, and G - Specific sequences of these four nucleotides encode the information in genes, in most cases providing the blueprint for making a protein: major players in building and maintaining the cell and carrying out its activities - Gene expression: the manufacture of a cellular product directed by the information in a gene which performs a function: protein production controlled by protein-encoding genes using a related molecule called ribonucleic acid (RNA) (some can manufacture proteins or regulate the functioning of protein-coding genes) as an intermediary: the sequence of nucleotides along a gene is transcribed into RNA, then translated into a linked series of protein building blocks called amino acids. Once completed, the amino acid chain forms a specific protein with a unique shape and function. - In carrying out gene expression, all forms of life employ essentially the same genetic code: a particular sequence of nucleotides says the same thing in one organism as it does in another. Differences among organisms reflect differences among their nucleotide sequences rather than among their genetic codes. This universality of the genetic code is a strong piece of evidence that all life is related. Comparing the sequences in several species for a gene that codes for a particular protein can provide valuable information both about the protein and about the relationship of the species to each other. - Organized into GENES: units of inheritance - A segment of DNA that encodes the information necessary to build all of the molecules synthesized within a cell, which in turn establish that cell’s identity and function. You began as a single cell stocked with DNA inherited from your parents. The replication of that DNA during each round of cell division transmitted copies of the DNA to what eventually became the trillions of cells of our body. As the cells grew and divided, the genetic information encoded by the DNA directed our development. - A GENOME is a complete set of DNA Levels of biological organization Reductionism: zooming in through the levels of the biological hierarchy at ever-finer resolution and reducing complex systems to simpler components that are more manageable to study Systems biology: exploration of a biological system by analyzing the interactions among its parts to explore emergent properties Correlation between structure and function: analyzing a biological structure gives us clues about what it does and how it works while knowing the function of something provides insight into its structure and organization - Biosphere: consists of all life on Earth and all the places where life exists; all of Earth’s ecosystems together - Ecosystems: the community of organisms (biotic) present in a particular area AND all the nonliving (abiotic) components of the environment with which life interacts - Biotic factors: all the living organisms present in an ecosystem - Ex: plants, insects, fungi, etc. - Abiotic factors: all the nonliving components - Ex: temperature, pH, humidity, salinity, sunlight, etc. - Communities: DIFFERENT populations living together, interacting with each other and dependant upon each other in a particular ecosystem - Populations: group of the SAME KIND of organisms, living in one area - Organisms: individual living things, vary in size and complexity (blue whale vs. bacteria: billions of cells organized into tissues, organs and organ systems vs. single cell) - Organ systems: group of organs that cooperate to perform specific functions - Organs: body part made up of multiple tissues (having a distinct arrangement and contributes particular properties to organ function) and has specific functions in the body - Tissues: aggregations of cells that work together to perform a specific function - Cells - Organelles: functional components present in cells - Molecules/macromolecules: chemical structure made up of 2 or more atoms Biological classification From the same ancestor: - Domain eukarya - Kingdom animalia - obtain food by eating and digesting other organisms - Kingdom plantae - produce their own sugars and other food molecules by photosynthesis - Kingdom fungi - absorb dissolved nutrients from their surroundings - Kingdom protista - Domain and kingdom archaea - Domain and kingdom bacteria - Phylum - Class - Order - Family - Genus - Species Ecosystem dynamics Life requires the transfer and transformation of energy and matter: 2 major processes: - The cycling of nutrients - Ex:  - The one-way flow of energy - All the activities of life require organisms to perform work, and work requires a source of ENERGY. - The input of energy, primarily from the sun, and the exchange of energy between an organism and its environment with transformation of energy from one form to another make life possible. 3 types of organisms: - Producers: produce their own food from simple raw materials - ex: plants, algae - Consumers: depend on producers for food: obtain energy by breaking down food originally produced by producers and feed on other organisms or their remains - ex: animals - Decomposers: break down (recycles) waste products, organic debris, and the bodies of dead organisms and obtain energy from them - ex: bacteria, fungi When a plant’s leaves absorb sunlight, molecules within the leaves convert the energy of sunlight to the chemical energy of food, such as sugars, in the process of photosynthesis. The chemical energy in the food molecules is then passed along by producers to consumers. When an organism uses chemical energy to perform work, such as muscle cells moving, it is converted to kinetic energy, some of that energy is converted to thermal energy, which is lost to the surroundings as heat. As a result, energy flows through an ecosystem in one direction, usually entering as light and exiting as heat. In contrast, chemicals are recycled within an ecosystem. Chemicals that a plant absorbs from the air or soil may be incorporated into the plant’s body, and then passed to an animal that eats the plant. Eventually, these chemicals will be returned to the environment by decomposers. The chemicals are then available to be taken up by plants again, thereby completing the cycle. Metabolic diversity: different metabolic strategies that organisms use that have enabled them to adapt and use all available energy and organic and inorganic matter sources - Sources of energy: - PHOTOtrophs: Radiant energy from the SUN (light energy) - CHEMOtrophs: Energy from CHEMICAL bonds (can be organic compounds (carbohydrates, hydrocarbons, etc.) or inorganic substrates (H2S, NH4, etc.)) - Sources of carbon (essential): - AUTOtrophs: INORGANIC CO2 (i.e. from the AIR) - HETEROtrophs: ORGANIC COMPOUNDS such as sugars, fats, amino-acids and proteins - Combining energy and carbon: - Photoautotrophs: energy from sun, carbon from atmospheric CO2 - Most plants, some prokaryotes and some protists - Photoheterotrophs: energy from sun, carbon in organic form = organic carbon (i.e. other living or things) - Prokaryotes only - Chemoautotrophs: energy from chemical bonds (organic or inorganic compounds), carbon from atmospheric CO2 - Prokaryotes only - Chemoheterotrophs: energy from chemical bonds (organic or inorganic compounds), carbon in organic form = organic carbon (i.e. other living or things) - All animals and fungi, many protists and prokaryotes Evolution: descent with modification - Aristotle: Scala Naturae - Old testament: each specie individually designed by God and therefore is perfect - Carolus Linnaeus: organismal adaptations is evidence that the Creator had designed each species for a specific purpose: adopted nested classification system and developed binomial naming format - Fossils: the remains or traces of organisms from the past - The fossils in a particular stratum provide a glimpse of some of the organisms that populated Earth at the time that layer formed. - Paleontology: study of fossils - Georges Cuvier: each boundary between strata represented a sudden catastrophic event - James Hutton and Charles Lyell: slow, continuous geologic processes operating today as in the past: Earth is very old - Jean-Baptiste de Lamarck: species evolve through use of and disuse of body parts and inheritance of acquired characteristics Charles Darwin: on the origin of species - 3 broad observations: - The unity of life - The diversity of life - The match between organisms and their environment The organisms living on Earth today are the modified descendants of common ancestors. Accounts for life’s unity and diversity: species share certain traits (evident on all levels of biological hierarchy: ex: similar skeletons, universal genetic language of DNA, features of cell structure) (unity) simply because they have descended from a common ancestor but have differences (diversity) because certain heritable changes occurred after the two species diverged from their common ancestor - The history of life is like a tree with branches representing life’s diversity. Natural selection is the MECHANISM for this evolutionary change; it leads to evolutionary adaptation, an accumulation of inherited characteristics of organisms that enhance their survival and reproduction in specific environments. - How it works: - Overproduction of offspring than what the environment can support - Up to a certain point, population stays stable - Struggle and competition for existence: resources (water, food, space, light) are limited - Only a fraction survives - Variation in population due to genetic diversity - For natural selection to work, variations that are selected for must be heritable - Unequal ability of individuals to survive and reproduce: - Individuals whose inherited traits give them a high probability of surviving and reproducing are likely to leave more offspring than other individuals, passing on their genes: survival of the fittest - leads to gradual change in a population, with favorable traits accumulating over generations - Darwinian fitness: relative ability of an individual to survive and reproduce in its environment - Depends on reproductive success - More surviving offspring an individual produces, higher its fitness will be - Adaptation: trait that increases fitness relative to individual without that trait Natural selection acts on individuals. Populations evolve, individuals do not. It is called natural selection because the natural environment “selects” for the propagation of certain traits among naturally occurring variant traits in the population. The product of natural selection is the increasing adaptation of organisms to their environment. Artificial selection: humans have modified other species by selecting and breeding individuals with desired traits Proofs of natural selection: - Homologous structures: anatomical resemblances that represent variations on a structural theme that was present in a common ancestor, but structures serve different functions - Ex: - All vertebrate embryos have structures called pharyngeal pouches in their throat at some stage in their development. These embryonic structures develop into very different, but still homologous, adult structures, such as the gills of fish and parts of the ear for humans. - All life forms use essentially the same genetic code (DNA): humans & bacteria share genes! - Vestigial structures: seemingly useless organs or structures that no longer performs the function for which it evolved; indicate that the organism evolved from ancestors in which the organ was functional - DIVERGENT EVOLUTION: process whereby groups from the same common ancestor evolve and accumulate differences, resulting in the formation of new species. - Analogous structures: similar but NOT derived from the same ancestor: demonstrate that organisms with separate ancestors may ADAPT in similar ways to similar environmental demands - Ex: Shark and dolphin fins - CONVERGENT EVOLUTION: independent evolution of similar structures in distantly related organisms - Fossil records in which we can observe succession of forms: consistent with other inferences about the major branches of descent in the tree of life - Can document important transitions: for example, the transition from land to sea in the ancestors of cetaceans (mammals adapted to aquatic life) - Considerable evidence suggests that prokaryotes are the ancestors of all life and should precede all eukaryotes in the fossil record. In fact, the oldest known fossils are prokaryotes. - Biogeography: species tend to be more closely related to other species from the same area than to other species that live in different areas: suggests that a common ancestor adapts to various habitats - Earth’s continents were formerly united in a single large continent called Pangaea, but have since separated by continental drift: an understanding of continent movement and modern distribution of species allows us to predict when and where different groups evolved: resulting in populations becoming isolated in different environments and having evolved differently. - Ex: marsupials from Australia developing in isolation - Compromise/bad design Microevolution: change in allele frequencies in a population over generations, does not result in a new species but changes the genetic makeup of a species; allow for phenotypic and genotypic differences and directly influences the traits and characteristics of a species, caused by the following factors: - Natural selection - Genetic drift - Gene flow - Mutation Gene: section of DNA that codes for a specific protein which is then responsible for the expression of a characteristic or trait. - Allele: a different version of a gene, leads to variations in their traits - A diploid individual may be either homozygous (HH, hh) or heterozygous (Hh) - Gene pool: consists of the total diversity of genes and alleles in a population or species; each individual only has a small fraction of the alleles present in the population’s gene pool - Locus: location of a gene - Homologous chromosomes: similar but not identical (not the same sequence), they code for the same traits, one homologue inherited from each parent - Genotype: the combination of alleles - Phenotype: appearance as a result of the genotype, can be affected by environmental differences like diet and exercise Gene variation is essential for evolution: - Can be measured as gene variability or nucleotide variability (A, T, C and G) - Nucleotide variability is measured by comparing DNA sequences of pairs of individuals: nucleotide variability rarely results in phenotypic variation Sources of genetic variation: - New genes and alleles can arise by mutation or gene duplication - A mutation is a random change in nucleotide sequence of DNA - A point mutation is a change in one base in a gene - Can be a good thing, harmful, cause diseases or simply a neutral variation (differences in DNA sequence that do not confer a selective advantage or disadvantage) - Only mutation is cells that produce gametes can be passed to offspring - Can be silent and manifest in later generations (masked by dominant allele) - Sexual reproduction can result in genetic variation by recombining existing alleles (a lot of potential for evolution and diversity) Only genetically determined variation can have evolutionary consequences; without genetic variation, evolution cannot occur. Genetic equilibrium: a population whose allele frequency does not change from one generation to the next are at equilibrium, i.e not evolving with respect to the locus being studied. - Frequencies of alleles do not change from generation to generation unless influenced by outside factors. If allele frequency changes over generations: evolution is occurring. Hardy-Weinberg equation: describes the genetic makeup we expect for a population that is not evolving at a particular locus. - Conditions for Hardy-Weinberg equilibrium - No mutations - Random mating - No natural selection - Extremely large population size - No gene flow Describes the constant frequency of alleles in such a gene pool - p: dominant allele - q: recessive allele - Frequency of all alleles in a population will add up to 1: p + q = 1 Can be used to calculate the frequency of genotype - p2 + 2pq + q2 = 1, where p2 and q2 represent the frequencies of the homozygous genotypes and 2pq represents frequency of the heterozygous genotype If the population is at equilibrium, these frequencies will stay constant. If the observed genetic makeup of the population differs from HardyWeinberg expectations, it can be concluded that the population may be evolving. Deviations from Hardy-Weinberg: - Natural selection: differential success in reproduction results in certain alleles being passed to the next generation in greater proportions - Directional selection: favors individuals at one extreme of the phenotypic range - Disruptive selection: favors individuals at both extremes of the phenotypic range - Stabilizing selection: favors intermediate variants and acts against extreme phenotypes - Genetic drift: chance and random events determine which alleles are passed onto the next generation; describes how allele frequencies can fluctuate unpredictably from one generation to the next: tends to reduce genetic variation within a population, which can prevent a population from adapting to change in environment, can cause harmful alleles to become fixed and has the most impact in small populations - Bottleneck effect: the numbers of individuals in a population are drastically reduced by events like natural disasters, leaving behind a small, random assortment of survivors: allele frequencies in this group may be very different from those of the population prior to the event: some alleles may be overrepresented and others underrepresented or even eliminated among the survivors. - Founder effect: a few individuals become isolated from a larger population and establish a new population, bringing with them only a small fraction of the genetic variability in the original population: allele frequency of newly found population differs from those of the parent population.  - Gene flow: movement of alleles among populations, results from the movement of fertile individuals: migration of breeding individuals between populations cause a movement of alleles - May cause a population to lose alleles (losing genetic variability), and other populations to gain some (increasing genetic variability). - Mixing of individuals between populations tends to reduce differences between populations over time. - Can counter genetic drift and natural selection. Non random mating: sexual selection: selection for mating success - Can result in sexual dimorphism: marked differences between the sexes in secondary sexual characteristics - INTRAsexual selection: direct competition among individuals of one sex for mates of the opposite sex: can have specialized adaptations for fighting - INTERsexual selection: Occurs when individuals of one sex (usually females) are choosy (favoured characteristics) in selecting their mates from individuals of the other sex (aka mate choice) Natural selection does not remove all unfavorable alleles: balancing selection - Frequency dependent selection: fitness of a phenotype depends on how common it is in the population - Heterozygote advantage: individuals who are heterozygous at a particular locus have greater fitness than do both kinds of homozygotes Natural selection cannot fashion perfect organisms, but operates on a “better than” basis: - It can only act on existing variations of phenotypes - It is limited by historical constraint - Adaptation are often compromises - Chance, natural selection, and the environment interact