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AP Biology BIGIDEA project

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McKenzie Beers

on 19 December 2012

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Transcript of AP Biology BIGIDEA project

Big Idea ONE Relation Big Idea Two Big Idea Three Big Idea Four Limited resources drive decent with modification or change in genetic composition because organisms with more favorable traits (adaptations) have greater fitness and thus reproduce more successfully. This is called natural selection, which is one way in which evolution can occur. Living systems require free energy and matter to maintain order, grow and reproduce. Organisms employ various strategies to capture, use and store free energy and other vital resources. Energy deficiencies are not only detrimental to individual organisms; they also can cause disruptions at the population and ecosystem levels. Big Idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes.
Genetic material is the key to life, for it is what keeps us alive and allows us to reproduce and pass down our genes to future generations via DNA. DNA is a double stranded structure that provides for an efficient way for the transmission of heritable information, by using each strand as a template, existing information can be stored and duplicated with the help of DNA polymerase. However the process of replication is not perfect. Random changes in nucleotide sequences can cause mutation. To prevent this , cells have multiple mechanisms that respond to and correct these errors. Our cells must communicate with one another and take action on what is at hand to keep us alive. All biological systems are composed of parts that interact with each other. These interactions result in characteristics not found in the individual parts alone. All biological systems from the molecular level to the ecosystem level exhibit properties of diversity. Biological systems with greater complexity and diversity often exhibit an increased capacity to respond to changes in the environment. At the molecular level, the subcomponents of a biological polymer determine the properties of that polymer. At the cellular level, organelles interact with each other as part of a coordinated system that keeps the cell alive, growing and reproducing. Evolution and the unity of life (big idea one) is connected to all four big ideas. Because all changes in life affect the process of evolution in ways like survival of the fittest and the creation of new stronger offspring, all three other big ideas have a hand in affecting the evolutionary process differently. Big idea two is when biological systems utilize free energy and molecular building to grow, to reproduce, and to maintain homeostasis. This relates to big idea one in the fact that the prevention of pathogens and diseases that stem from pathogens can kill off the naturally healthy and stable species preventing them from creating offspring, so big idea two is about the ability to maintain a healthy lifestyle, including a defense system to protect yourself from outside affects. As a process of evolution, the strong are supposed to survive and if something were to get in the way of that then evolution will not prevail. Instead the body learns to accumulate defense mechanisms to carry the strong on to procreate. Big idea three is when living systems store, retrieve, transmit, respond to information essential to life processes. This idea is all about genetics and DNA. DNA affects the evolutionary process by the elimination of weak or incapable cells in the life systems that will not sustain the life of the host. This eliminates the weak and keeps the strong alive. (Survival of the fittest). This furthers the evolution of the strongest offspring and is estimated that it makes the world's overall immunity to diseases, and modern medicine what it is today. Because of this, genetics also plays a part because all of the strongest survivals will then carry on to produce strong offspring and therefore the cycle continues. Big idea four is the concept that biological systems interact, and these systems and their interactions possess complex properties. This concept produces genetic differences. Meaning there is diversity in the life around us. When this occurs it refers back to big idea three and forms the survival of the fittest species. The combination of two different species that are dying out could be the solution to both species' strongest qualities to survive on. These interactions further the survival techniques of different species. It also creates an option for some of the "weaker" characteristics that could be detrimental to a species to be "cured" or be rid of. Like if you're sick and you take medicine, you are then eliminating the weak link in your body in order to survive. Big Idea Project

McKenzie Beers
Lily Lau
Rusty Cole The End Autotrophic cells capture free energy through photosynthesis and chemosynthesis. Photosynthesis traps free energy present in sunlight that, in turn, is used to produce carbohydrates from carbon dioxide. Chemosynthesis captures energy present in inorganic chemicals. Cellular respiration and fermentation harvest free energy from sugars to produce free energy carriers, including ATP. The free energy available in sugars drives metabolic pathways in cells. Photosynthesis and respiration are interdependent processes. Membranes allow cells to create and maintain internal environments that differ from
external environments. The structure of cell membranes results in selective permeability; the movement of molecules across them via osmosis, diffusion and active transport maintains dynamic homeostasis. In eukaryotes, internal membranes partition the cell into specialized regions that allow cell processes to operate with optimal efficiency. Each compartment or membrane-bound organelle enables localization of chemical reactions. Organisms also have feedback mechanisms that maintain dynamic homeostasis by allowing them to respond to changes in their internal and external environments. Negative feedback loops maintain optimal internal environments, and positive feedback mechanisms amplify responses. Changes in a biological system’s environment, particularly the availability of resources, influence responses and activities, and organisms use various means to obtain nutrients and get rid of wastes. Homeostatic mechanisms across phyla reflect both continuity due to common ancestry and change due to evolution and natural selection; in plants and animals, defense mechanisms against disruptions of dynamic homeostasis have evolved. Additionally, the timing and coordination of developmental,
physiological and behavioral events are regulated, increasing fitness of individuals and
long-term survival of populations. Living systems require energy to maintain order, grow and reproduce. Organisms use various energy-related strategies to survive; strategies include different metabolic rates, physiological changes, and variations in reproductive and offspring-raising strategies. Not only can energy deficiencies be detrimental to individual organisms, but changes in free energy availability also can affect population size and cause disruptions at the ecosystem level. Several means to capture, use and store free energy have evolved in organisms. Cells can capture free energy through photosynthesis and chemosynthesis. Autotrophs capture free energy from the environment, including energy present in sunlight and chemical sources, whereas heterotrophs harvest free energy from carbon compounds produced by other organisms. Cellular respiration and fermentation use free energy available from sugars to phosphorylate ADP, producing the most common energy carrier, ATP. The free energy available in sugars can be used to drive metabolic pathways vital to cell processes. The processes of photosynthesis and cellular respiration are interdependent in their reactants and products.

Heritable information provides for continuity of life.
The storage and transfer of genetic material, DNA and RNA, is crucial for life to continue and evolve. Replication of genetic material, reproduction, occurs at the cellular and organismal level. There are important structural and chemical differences between DNA and RNA that result in different modes of replication.Both have three components; sugar, phosphate and a nitrogenous base, which form nucleotide units that are connected by covalent bonds to form a
linear molecule with 3' and 5' ends, with the nitrogenous bases perpendicular to the sugar-phosphate backbone. In order for information stored in DNA to direct cellular processes, the information needs to be transcribed , DNA to RNA, and in many cases, translated, RNA to protein. The results of both these processes determine cell activities such as growth, metabolism, and phenotypes. In eukaryotic organisms, genetic information is placed into chromosomes, which carry essential heritable information that must be passed down to daughter cells. The process of Mitosis ensures that each daughter cell receives an identical set of chromosomes which carries the heritable information. Prokaryotes, viruses and eukaryotes contain plasmids, which are small extra-chromosomal, double-stranded circular DNA molecules. This process is different in diploid organisms, fertilization must occur, in which the recombination of heritable information from both parents through the fusion of their gametes.Meiosis reduces the number of chromosomes from diploid to haploid by following a single replication with two divisions. There is a random assortment of maternal and paternal chromosomes which causes the offspring to all be genetically unique with respect to individual alleles and allele combinations. Meiosis/Fertilization provides for a spectrum of possible phenotypes, traits, which natural selection acts, allowing for evolution to take place. Interactions between external stimuli and gene expression result in specialization and divergence of cells, organs and tissues. As environmental conditions change, community structure changes both physically and biologically. Interactions, including competition and cooperation, play important roles in the activities of biological systems. Interactions between molecules affect their structure and function. Competition between cells may occur under conditions of resource limitation. Cooperation between cells can improve efficiency and convert sharing of resources gain be a universal gain for the cells as a whole. Variations in components within biological systems provide a greater flexibility to respond to changes in its environment. Variation in molecular units provides cells with a wider range of potential functions. Species with genetic variation and the resultant phenotypes can respond and adapt to changing environmental conditions. Interactions within biological systems lead to complex properties. All biological systems, from cells to ecosystems, are composed of parts that interact with each other. When this happens, the resulting interactions enable characteristics not found in the individual parts alone. The properties of a polymer are determined by its subcomponents and their interactions. Other polymers important to life include carbohydrates, lipids and proteins. Organelles interact with each other and their environment as part of a coordinated system that allows cells to live, grow and reproduce. In development, interactions between regulated gene expression and external stimuli, such as temperature or nutrient levels or signal molecules, result in specialization of cells, organs and tissues. Cells, organs and tissues may change due to changes in gene expression triggered by internal cues, including regulatory proteins and growth factors, which result in the structural and functional divergence of cells. Organisms exhibit complex properties due to interactions of their constituent parts, and interactions and coordination between organs and organ systems provide essential biological activities for the organism as a whole. Interactions between populations within communities also lead to complex properties. As environmental conditions change in time and space, the structure of the community changes both physically and biologically. Communities are comprised of different populations of organisms that interact with each other in either negative or positive ways DNA Replication
Step 1: The Helicase enzyme "unzips" the parent strand by breaking the hydrogen bonds holding the base pairs. This area is called the replication fork.
Step 2: The enzyme DNA polymerase binds to one strand of the DNA and begins moving along it in the 3' to 5' direction, using it as a template for assembling a leading strand of nucleotides and reforming a double helix. Another enzyme of DNA polymerase binds to other strand, lagging strand, must synthesize discontinuous segments (called Okazaki fragments). Another enzyme, DNA ligase I then stitches these together into the lagging strand.
Step 3: As a result, two DNA ,identical to each other and identical to the original ,have been produced. Each strand of the "parent" DNA will then serve as a template strand for the next complementary DNA. This process is semi conservative (one-half of each new molecule of DNA is old, one-half new. )Watson and Crick had suggested that this was the way the DNA would turn out to be replicated. Proof of the model came from the experiments of Meselson and Stahl. Transcription
The process that involves the transcribing of genetic material from DNA to RNA, specifically mRNA.
DNA is a double stranded structure made up of four nucleotide bases, adenine (A), guanine (G), cytosine (C) and thymine (T).Purines ,G and A, have a double ring structure. Pyrimidines ; C, T and U, have a single ring structure. Purines must bind with pyrimidines to form the double helix structure, A pairs with T, and C pairs with G. Nucleotide bases are the genetic code that is carried on and passed down from generation to generation: They are the instructions for Protein synthesis. RNA is single stranded and it also has nucleotide bases, however the base thymine (T) is replaced with Uracil (U).

Step 1: DNA is transcribed by the enzyme RNA polymerase. RNA polymerase attaches to the DNA at a specific area called the promoter region.
Step 2: Elongggationnnnnn!- Proteins called transcription factors "unwind" the DNA strand and allow RNA polymerase to transcribe only a single strand of DNA into a single stranded RNA polymer called messenger RNA (mRNA).
Step 3: Termination-RNA polymerase moves along the DNA until it reaches a terminator sequence. At that point, RNA polymerase releases the mRNA polymer and detaches from the DNA.
In a eukaryotic cell, the mRNA transcript goes through a series of enzyme regulated modifications.
Such as:
Addition of a poly-A tail- At the 3' end, a poly(A) tail of 150 or more adenine nucleotides is added. The tail plays a role in the stability of the mRNA.
Addition of a GTP cap -At the 5' end, a cap, containing a modified GTP (guanosine triphosphate) enzyme is added . This occurs at the beginning of transcription. The 5' cap is used as a recognition signal for ribosomes to bind to the mRNA during protein synthesis.
Excision of introns - RNA Splicing- Is the process of removing introns, leaving an excess amount of exons which will then allow the mRNA to exit the nucleus and begin translation. Protein Synthesis
One of the most important processes that DNA does is protein synthesis. Proteins are extremely important for any living organism. Without them, we would not be able to do anything!
Step 1: The first step in protein synthesis is transcription. Protein Synthesis
Step 2: Translation- With these modifications taken place, the mRNA is now ready to exit the nucleus and enter the cytoplasm and find a ribosome. The mRNA interacts with rRNA on the large subunit of the ribosome to intiate translation at the start codon, such as AUG. Codons are sequences of nucleotides that are read in triplets. Each codon codes for a specific amnio acid which are the building blocks of proteins. The tRNA binds to the ribosome at the smaller subunit and contains anticodons that have to match up with the correct codon from the mRNA. The amino acid is transferred into a growing peptide chain out from the ribosome.
Step 3: Termination-The mRNA is moved along the tRNA until a stop codon is reached and the growing peptide chain is released. The first step in Mitosis is Prophase, during this phase the chromatin in the nucleus begins to condense and is now visible under the microscope.The Nucleus disappears and the centrioles begin to move towards opposite ends of the cell The cell goes through many complex stages throughout its life in order to preform its duties. In between each cell stage is a checkpoint that signals the cell to move on to the next stage. The checkpoints are controlled by the enzymes cyclins and cyclin-dependent- kinases (CDKs).
The first stage a cell goes through is interphase.
During interphase, the cell is growing and maturing and replicating its genetic material in order to prepare for future stages (Mitosis). There are three phases in interphase:
G1 Phase- The cell is growing in preparation for DNA synthesis. G stands for GAP, Gap 1.
S Phase- s stands for synthesis, during this phase the DNA is being synthesized and replicated
G2 Phase-Prior to the start of prophase, the cell is increasing again and is also synthesizing proteins. Gap 2 Mitosis
Mitosis follows interphase, after the genetic material (DNA) is replicated. It is a continuous asexual reproduction. ProMetaphase-The nuclear membrane dissolves, proteins attach to the centromeres creating the kinetochores. Microtubules attach at the kinetochores and the chromosomes begin moving. Metaphase- Chromosomes are aligned in the middle of the cell, by means of spindle fibers, on the imaginary metaphase plate. Anaphase-The paired chromosomes begin to separate at the kinetochores and move towards opposite sides of the cell. Telophase-The Chromatids arrive at opposite sides of cell, and new membranes form around the daughter nuclei. The chromosomes are no longer visible under a microscope. Cytokinesis- The cells are cleaved at either the cleavage furrow in an animal cell, or the cell plate in a plant cell. The end of Mitosis results in two identical daughter cells. Meiosis
Meiosis is a sexual method of reproduction. Each parent gives a half of his or her genes to the offspring. This allows for diversity in the gene pool unlike mitosis where the "daughter Cell" is an exact copy of the parent. Somatic cells have two sets of chromosomes; one set from each parent.The two chromosomes in each pair are referred to as being homologous chromosomes. The Separation of the homologous chromosomes ensures that each gamete receives a haploid (1n) set of chromosomes composed of both the maternal and paternal chromosomes. During Meiosis the sperm of the male is injected into the female where it travels until it finds an egg. Once the sperm meets the egg, the egg becomes fertilized and a zygote begins to form. Baby forms in mom and boom you have a child who will eventually repeat this process with his or her special someone. In Meiosis, there is much genetic variation. Thanks to Mendel's laws of segregation and independent assortment in that chromosomes randomly pair up and are segregated from the others. Some genes that are located next to each other on the same chromosome tend to move as a whole, linked genes. Genes can be predicted from data of the parents genotypes and phenotypes, Punnett square.
Monohybrid - A genetic cross made to examine the distribution of one specific set of alleles in the resulting offspring
Example: tall peas x short peas or TT x tt

Dihybrid - Hybridization using two traits with two alleles each.
Example: tall peas with round seeds x short peas with wrinkled seeds or TTRR x ttrr Divergent evolution occurs when organisms with a common ancestor evolve separately and over time become dissimilar. This results in homologous structures and explains how evolution drives diversity. An example of a homologous structure are underlying skeletons of arms, forelegs, flippers, and wings of various organisms. Convergent evolution occurs when organisms originating from dissimilar ancestors evolve to share similar traits. Similar environments can give rise to analogous traits. One example of this is the marsupial sugar glider and the flying squirrel. Although similar traits are shared, the two species are not closely related. There are 3 types of natural selection. Directional natural selection shifts the average degree of a phenotype to become either more or less extreme. Disruptive natural selection occurs when a species is better suited when a phenotype is in either extremes. This is an example of evolution causing diversity. Stabilizing natural selection occurs when it is disadvantageous to possess an extreme degree of a particular phenotype. In these instances, evolution is promoting unity within a population. Genetic drift can cause significant fluctuations in allele frequency in a population, especially those that are small. Genetic drift occurs by chance, unlike natural selection which favors more advantageous adaptations. The bottleneck effect occurs by random chance. A catastrophe may wipe out members of a population and can decrease the allele frequency significantly. As a result, inbreeding increases which can lead to the "fixation" of an allele. Fixed alleles can make an inherited disorder permanent within a population and as a result is an example of unity caused by evolution, The founder effect is a subcategory of the bottleneck effect because it is specific to small populations that have been isolated and begin to form its own population. The allele frequency of the founders population may be completely disproportional from its original population, thus explaining diversity due to evolution. Within the populations, however, lower variation in alleles and inbreeding can result in a very homogeneous population and thus results in the unity of a population. Gene flow occurs when alleles from one population are shared between another population. Speciation occurs when a population diverges and develops into a daughter species. Gene flow and speciation work against each other. Gene flow repairs differentiating allele frequencies populations by recombining the gene pool. If the two populations do not come in contact again or are differentiating at too quick of a rate, then allele frequencies may be manipulated enough to cause speciation which is diversity by evolution at its core. DNA Mutations
DNA makes essential proteins that help keep us alive, it is passed down to our offspring so they can survive. So its a pretty big deal when mutations happen in DNA. Mutations can happen from errors in DNA replication and external factors such as radiation. These mutations cause genetic variation in the gene pool, again all leading back to big idea 1 (Evolution).
Substitution- in this mutation, the bases are switched ( A switches with G): and know all the sudden you have a different codon that codes for a specific amino acid. Horrid diseases such as sickle cell anemia can happen from substitution.
Insetion- mutation in which extra sets of base pairs are added.
Deletion-Base pairs are deleted Viruses play a huge role in evolution. Viruses find host cells and inject their viral genetic material into the host cell causing their DNA to combine. This leads to huge genetic variations. Viruses are able to replicate at very rapid speeds because they lack the checkpoints in their life cycle that slow down each step. In the lytic cycle, the virus injects its DNA into the host cell and takes over the cell and replicates itself and destroys the cell in search of another cell. In the lysogenic cycle, the virial DNA is inject and combined with the host cells dna on the chromosome. The host cell replicates the viral dna along with its own and the viral DNA is slowly being spread from cell to cell waiting for event to trigger it to go into a lytic cycle. Cell communication is extremely important, it allows cells to receive vital information and respond to it. Receptors on the outside of the cell retrieve the information which is usually a protein or a signaling molecule. Examples of such processes are tyrosine kinases and G- Coupled proteins. In both of these cases a signaling molecule binds to a receptor, and with the help of energy ATP or GDP, a protein is phosphorylated which causes enzymes to bind with the protein, opening up transduction pathways triggering cell responses. Second messengers such as calcium and IP3 are essential for the phosphorylation of these proteins. An example of cell communication at its finest: virus infects a host cell, the cell puts out a receptor signaling the cytotic T-cells to neutralize the host cell, to prevent further spreading of the virus. The Nervous System
Allows for the brain to communicate with all parts of the body and order them what to do. Signals are sent to target cells which in turn respond. The signal is sent through neurons, which are cells located everywhere in your body that send nerve impulses to either another neurons or a target cell. The neuron contains dendrites which receive the impulse and send it throught the cell body, down the axon, where it will then have to jump the synapse to either reach another neuron or a target cell. The axon contains a myelin sheath the insulates the impulse and increases its speed. In order for the nerve impulse or action potential to take place. Many proteins and minerals are need. Such as sodium, calcium, chloride, and potasium. In the axon, the charge is negative to to the excess chloride(Cl negative), on the outside the charge is positive due to an excess of sodium(Na positive) and potasium(K positive). In order for impulse to be triggered, polarization must occur. Sodium enters the cell switching the charge in the inside to positive, and potasium, after the sodium enters, exits the causing the outside to be more negative. This reaction diffuses across the neuron until it reaches the synapse. This where calcium enters and activates neurotransmitters to guide the sodium across the synapse into another neuron or target cell. Reproductive barriers can explain the unity in life. If two populations cannot reproduce, then the allele frequencies between the population will remain within the population. Prezygotic barriers include habitat, temporal, behavioral, mechanical, and gametic isolation. Any one of these barriers will prevent the fertilization of an egg. If fertilization is successful, however, there are still a number of postzygotic barriers that will prevent speciation. Many hybrids endure reduced viability and fertility. Hybrids are often both weak and sterile. Phylogenetic tree and cladagrams assist in depicting the similarities and differences among species overtime. Branching off depicts the diversity and speciation while branches that are closely connected represent the unity of life.
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