Chapter 19 and 20

II. Connections
1. Sympatric Speciation is a speciation model that occurs within the home range of an already existing species, or in other words without the presence of a physical barrier. This is caused by polyploidy, in which individuals inherit three or more sets of chromosomes of their species due to the failure of mircotubules to attach to chromosome kinetechores during mitosis or meiosis. With the extra chromosomes, the offspring are unable to mate with their parent species but can reproduce asexually or with another polyploid individual, resulting in the creation another species of organisms.

2. Endosymbiosis is a theory for the origin of organelles such as the mitochondria and chloroplasts that claims that heterotroph cells consumed autotroph cells due to their ability to engage in aerobic respiration, but since they nefused to digest them, the consumed cells remained and lived out their lives in the host cell. Each cell in this interaction is benefited, classifying it as a symbiotic relationship. The reason for heterotrophs preying on aerobic prokaryote cells was due to the alteration of atmospheric gases by the emergence of photosynthesis, for they introduced free oxygen, therefore allowing eukaryotic cells to evolve from prokaryotes.

3. Adaptive radiation is a type of speciation that is characterized by a burst of divergences from a single lineage that results in a entirely new species. This occurs either when a lineage uptakes a vacant adaptive zone (set of  niches) or competes with other resident species well enough to force them adopt another niche. This latter incident refers to character displacement, which is a phenomenon in where a species will adopt a new niche if its original one conflicted with that of another species, relating to Gause's principle in that no two species can share the same niche.

4. Proto-cells comprise the transitional forms between simple organic compounds and the first living cells. They are self- replicating membrane-bound sacs that have systems of enzymes and other agents of metabolism. It is believed that their ability to self-replicate arose with the spontaneous assembly of RNA subunits due to an increase in temperature, and the formation of an enclosed membrane due to the moistening of protein chains.

III. Essentials
1. Prezygotic Mechanisms
    -Mechanical Isolation: A species's body parts are not physically compatible to another species for the purpose of mating, or pollinating

    -Temporal Isolation:When specific timing for reproduction differs between populations, those populations cannot interbreed

    -Behavioral Isolation: Since certain species of organisms include courtship displays in their reproductive process, species that are not pre-wired to perform or recognize a particular courtship display will not be able to interbreed with a similarly related species that is pre-wired to do such.

    -Gamete Morality: Gametes of different species are incompatible, so no fertilization occurs

Postzygotic Mechanisms
    - Hybrid Inviability: Hybrid embryos die early or the new individuals die before they can reproduce

    - Hybrid Sterilty: Hybrid individuals are unable to produce functional gametes


2. The gradual model of speciation, known as "gradualism", holds that speciation occurs as a result of slight morphological changes of individuals throughout a relatively long span of time. On the contrary the punctuated model of speciation, or “punctuated equilibrium”, claims that most morphological changes occur in a smaller, more brief geologic period, due to factors such as directional selection, genetic drift, the founder effect, and bottlenecks, for such accelerate the rate of speciation.

3. In the attempt the prove the hypothesis formed by chemical processes, Stanley Miller placed water, methane, hydrogen, and ammonia in a reaction chamber. Then he disrupted the mixture by circulating it and zapping it with sparks, to simulate lightning strikes. Amino acids and other small organic compounds were present in the chemical mixture a week later, therefore affirming the hypothesis.

4. A critical example that supports the endosymbiosis theory is the chance discovery of Jeon Kwang in 1966, in where his culture of amoebas was infected by rod-shaped bacteria cells, which caused some cells to die, while the the others, which were smaller, just grew more slowly. After 5 years of maintaining the infected culture, the infected amoebas were producing additional bacteria cells while thriving. When exposed to antibiotics, only the bacteria and non-infected cells perished, not the amoebas. Evidence then showed that infected cells became unable to manufacture a specific enzyme, so instead they depended on their invader bacterium to synthesize it, therefore exemplifying a endosymbiotic relationship.

5. The cladogram is on the cards we turn in for the chapters…

Chapters 17 and 18

II Connections
1. During Prophase I of meiosis, the two duplicated homologous chromosome pairs are temporarily attached to one another at the chaism. While connected, the two homologous chromosomes can exchange genetic material at their junction points, which is called crossing over. Thus, due to this event, variation in genes are produced for the eventual offspring, influencing the whole population's allele frequency, or relative abundance of alleles of a specific gene among individuals of a population. Specifically, moving a population from a specific allele frequency state called genetic equilibrium, due to the new diversity in alleles brought on by events such as crossing over.

2. Analogous structures are different responses of different body parts to similar challenges, such as the common challenge of flight faced by bats, birds, and flies that had a part in  influencing their development of various wing structures. In terms of natural selection, the selective progression of traits favorable to a certain environment due to competition, both analogous structures and natural selection occur as a result of the nature of the environment.

3. A Gene pool is a complete set of unique alleles in a given population, for the individuals of a population inherit the same number and kind of genes from their parents. if a population of organisms were to experience a bottleneck or drastic reduction in population size due to various environmental pressures, the gene pool of that population will be relatively less diverse than before. Since a reduction in population size occurs, there are only few individuals left to reproduce and pass on their own genes, and renew the population size, which is why diversity of the gene pool is less.

4. Balanced polymorphism is the persistence of two or more alleles at relatively high frequencies within a population. This allele frequency is maintained in certain populations under certain conditions, for if the predators of a specific population develop a search image, variation in exterior aspects of the prey would more favorable for survival under this circumstance. Therefore, balanced polymorphism is sustained because of the benefits of being heterozygous or phenotypically varied.

III. Essentials
1. -Natural populations, by nature are able to increase in size over time, due to their inherent reproductive capacity
    - Population size is checked from consistently growing due to the exhaustibilty of limited resources
    - Conclusion: Eventually, competition will arise between individuals since there are
    - Individuals  share a common gene pool with respects to its population
    - Genetic Variation within a population begins with alleles, or slightly different forms of genes that result from mutations
    - Conclusion: Certain traits prove more able to secure survival than counterpart traits of different alleles, and so the alleles that encode for the more fit traits will become more frequent in the population of that environment over time.
    - Conclusion: Natural Selection is the result of the trait variation of a population, due to certain environmental factors, that in all could produce evolution of that population.

2. 1.Chemical, molecular evolution that resulted in the origin of life 4,600 million years ago
    2. Accumulation of oxygen in the atmosphere that produced eukaryotic cells
    3. Breakup of Gondwana and Pangea that created environmental differences and initiated mass extinction
    4. Recurrent Ice Ages that caused mass extinctions
    5. Major Crustal movements that created various biomes and therefore diversity of life

3. "Individuals don't evolve, populations do", is the accurate view of evolution, for natural selection and other types of evolution result from changes in the DNA of an individual, so no organism can evolve itself because no individual can alter their own DNA. Rather organisms evolve as a result of the changes of a parent's DNA, and if these changes do not hinder the survivability of the resultant offspring than that new allele could be passed on, thereby evolving the population(micro evolution)

4. Phenotypic variation is generated by a number of factors, such as genetic mutations in where the base sequence of DNA is alter slightly, not to change survivability or reproduction. A second source would be crossing over during prophase I of meiosis because it creates numerous unique gene combinations in the produced gamete. Also, independent assortment of homologous chromosomes during meiosis I, mixes orientation of maternal and paternal chromosomes and also helps create genetically varied gametes. Furthermore, fertilization of two gametes from two different individuals, combines alleles of two random gametes, explaining why phenotypic expression of traits also vary between siblings. Lastly, chromosome mutations, or alterations in the structure of chromosomes, results in the loss, duplication, or repositioning of genes.

5. p²(AA) + 2pq(Aa) + q²(aa) = 1.0

p and q are the frequencies of the dominant and recessive alleles (A, a), respectively.  

Conditions: 1. No mutation exists
                  2.The population is infinitely large
                  3..The population is isolated from ll other populations of the species
                  4. Mating is random
                  5. All individuals survive and produce the same number of offspring

CH. 15, 16, 21

Connections
1. Viruses multiply via a process called the Lysogenic Pathway. In this process, viruses cut into the chromosomal DNA of a host cell and integrate its viral genes with that of the host. If that cell were a prokaryote, once it divided through binary fission, when cell wall material is deposited at the middle section of the cell to sever the cytoplasm, the replicated DNA, which also contained the viral DNA, manifest themselves in the creation of new infectious viruses.

2. The plasmid is the bacterial unit of DNA that contains genes that enable the transfer of genetic material between two cells. This process, which is called conjugation, causes a recipient cell to integrate foreign genetic material with its own genetic material, and, as a result, replicate the foreign DNA. The incorporating of external and internal genetic material will result in the recipient bacteria cell expressing new or alternated traits, in all called Bacterial Transformation.

3. A plasmid is the circle of DNA that is self-replicating and present in bacteria cells. When this genetic material becomes corrupted when the incorporation of DNA of an infective virus occurs, its self-replicating nature will benefit the virus because it only helps its proliferation. If this was a RNA retrovirus, the organism infected could express deadly diseases such as AIDS, for HIV is a retrovirus that destroys certain white blood cells, and, as a result, the immune system as a whole.

4. The prokaryotic organism E. Coli,, which resides in the large intestines of various mammals, feeds off the nutrients consumed by the host organism, If it infects the digestive system of a human baby ,for example, glucose is not as readily provided as lactose sugar from milk. In order to digest this hydrolysis composed disaccharide, E. Coli utilizes operator to regulate the production of the enzymes that breack down lactose. Operators serve as binding sites for repressor proteins that disable the transcription of the gene coding for lactose enzymes.

5. Okazaki fragments are disconnected DNA segments complimentary to the 5'->3' DNA parent strand that result from the discontinuous replication process of DNA polymerase on the lagging strand. Similarly restriction enzymes create fragmented DNA strands by cutting specific sequences on strands so that the genetic material of another organism can be incorporated by occupying the gaps. Both the Okazaki segments and the segments of restriction enzymes rely on the protein Ligase to consolidate the nicks and little openings resulting from fragmentation.

III. Essentials
1. The first stage of gene regulation is before transcription, for in the nucleus, before a DNA molecule is transcribed it can become attached to acetyl groups that loosen the grip of histones for an activating function, or inhibitory methyl groups which block an allele's expression on a trait. The second stage is after transcription in which an mRNA needs to exit the nucleus, for before traveling to the ribosomes certain proteins termed Y-boxed proteins can be binded to the transcript to completely stop its translation, in other words leaving it inactivated.

The third stage of regulation takes place during translation, for due to the fact that the longer a transcript lasts in the cytoplasm the more times it can be translated, enzymes digest and remove transcripts at certain times. The last stage is after translation because various factors can inhibit or activate a new protein, as seen by Y-box proteins that are only activated when a phosphate group is bonded to them by enzymes.


2. *This will be included in the notecards that get turned in later*

3. Prior to gel electrophoresis, a single-stranded DNA template is placed in a mixture containing the necessary enzymes, nucleotides, etc. to produce new strands of DNA. The numerous new copies of DNA fragments that have been produced are then separated from each other through the gel electrophoresis process, in which fragments pass through a semisolid gel slab in response to an electric field. Because each fragment's end is fluorescent-tagged, as they move through the gel and become subject to a laser, a computer can subsequently record what specific color the fragments express, and since the colors correspond to specific nucleotides a DNA sequence can thus be concluded (DNA fingerprint).

4. The primary difference between eukaryotic and prokaryotic genomes is the DNA of eukaryotes is linear whereas in prokaryotes it is circular (plasmids). In addition, the method in which prokaryote cells divide is very different when compared to mitosis. Known as prokaryotic fission, this process begins with the replication of DNA. Following duplication, the genetic materials attach to the cell's plasma membrane. Using newly produced lipids and proteins, the cell adds the molecules to the membrane to separate the attached strands, thereby stretching the length of the cell and the DNA attached to its walls. The cell finally undergoes  cytokinesis by depositing cell membrane material in the midsection of the now elongated cell, soon resulting in a new membrane being formed.

5. The lytic pathway is a variation cycle of how viruses multiply from cells. In the lytic cycle, viruses inject their genetic material in a host cell so that new viral particles can be synthesized within the cell. These infectious agents are released from the host after it goes through the process lysis, when the cell dies. This pathway is different from the lysogenic cycle in that it is relatively quicker since the lysogenic cycle is essentially an extension of the lytic pathway. Instead of just killing the cell, the lytic cycle focuses on incorporating the viral DNA with the genetic material of the host cell, so that when that cell divides, the foreign DNA will successfully spread, resulting in proliferation of the viruses.

Ch. 13 and 14

II. Connections
1. 5', or five prime end refers to the fifth carbon of the deoxyribose sugar of DNA, which is bonded to a phosphate molecule. This is a covalent bond  due to the electronegativities of the two molecules being relatively equal and therefore resulting in shared electrons. However, if one molecule's electronegativity is substantially greater than that of another, then the bond would not be covalent but ionic.

2. mRNA is read by ribosomal subunits via a method in which the nitrogen bases are read by translating them into amino acids three bases at a time, one group of three bases being termed a 'codon'. The codon containing the nitrogen bases Adenine, Uracil, and Guanine is known as the start codon and it signals the ribosomes to begin translating the mRNA three at a time as soon as it is read, which is why the start codon is found at the beginning of transcipts. Once the 'start codon' is read and the mRNA is translated into proteins, each codon that is read corresponds to a specific amino acid, and ultimately each transcript results in a unique expression of the specific codons collectively. No codon is dominant in determining the outcome of the protein which is relevant to genetic incomplete dominance because codons are expressed as a mixture of different amino acids.

3. Semiconservative refers to one of the theoretical methods that DNA is replicated in every cell, stating that two copies of DNA are ultimately produced, each one containing one original strand and one newly synthesized strand. This replication would be hampered in females if that one specific DNA strand was an x-chromosome destined to be inactivated and remain a Barr Body, for such restricts one of a female’s x-chromosomes from extending out of its condensed chromatin form and therefore disables the replication of that DNA in every cell.

4.  The enzyme RNA polymerase is a protein that catalyzes ribonucleotides in a new RNA strand by utilizing one strand of DNA as a template. The RNA molecule that is created during this process leaves the nucleus to be translated into proteins by ribosomes, whose subunits are also synthesized in the nucleolus in the nucleus.

5. DNA polymerase is an enzyme that is a protein that replicates DNA by catalyzing free nucleotides to each new strand of deoxyribonucleases on to a original strand belonging to the parent DNA. These deoxribose sugars are bonded to the nucelotides by glycosidic linkages..

6. The process of DNA replication begins with the helicase enzyme which unzips the two strands of DNA by breaking the hydrogen bonds between the DNA’s nitrogen base pairs. As a whole this process of replication is similar to s-phase of the cell cycle which results in the doubling of the amount of a cell's chromesomes, as a karyotype, which is a digital image of chromosomes, of a cell in the following G2 stage of the cell cycle would relate to the DNA replication.


III. Essentials

1. Because the two strands of DNA molecule are antiparallel, the enzyme DNA helicase can only assemble new nucleotide strands in the 5'-3' direction. Despite this, assembly is discontinuous where nucleotides of a 3'-5' strand are only joined to exposed -OH functional groups that are themselves connected to the 3' carbon of a growing strand.  Despite the choppy DNA strand, the enzyme ligase initiates the integration of all short stretches of strand.

2. -RNA is composed of only strand of nucleotides, while DNA consists of two.

 -RNA nucleotides contain the sugar ribose whereas DNA's have the sugar deoxyribose.

- one of DNA’s nitrogen bases is labeled thymine, while RNA's version of the same base is called uracil.

3. -mRNA (messenger RNA) is the class of RNA that contains the recipe for the construction of proteins. They are the outcome of the transcription process of protein synthesis centered in the nucleus.

    -tRNA (transfer RNA) is the type of RNA that serves as a transport of amino acids to ribosomes for the production of proteins. They arrange themselves in alignments which the mRNA specifies.

   - rRNA (ribosomal RNA) is the of RNA molecules that becomes a vital part of ribosomes, because they provide for the decoding of mRNA and assist tRNA in translation.


4. A.Transcription- In the process of transcription, the enzyme RNA polymerase reads a template strand of DNA and synthesizes a new complimentary strand, after recognizing the start signal of a promoter or specific base sequence.

B. RNA Splicing- Before mRNA molecule leaves the nucleus to be translated by ribosomes, it must be modified or spliced by which introns or base sequences that don't code for proteins are 'snipped' and exons or protein-coding base sequences are retained.

C. Translation- When a ribosome initiates the translation phase, it reads a mRNA strand three base sequences at a time. Each series of three bases, or codon, corresponds to a specific amino acid which are delivered by tRNA, who in addition carry the anticodon base pairs that are complementary to those of the mRNA. The creation of the protein, or polypeptide from the ribosome is called elongation.

Chapter 11 and 12: Inheritance VISIBLE VERSION! yay

II. Connections

a. The locus of a gene is the specific area of a gene, which is read and copied by proteins in order for the ribosomes to produce new proteins. The shape and structure of these proteins, while influenced by interactions between amino acids and interactions between ‘r’ groups, is determined by disulfide bridges, which are covalent bonds between two cysteine amino acids.

b.  Nondisjunction is the failure of sister chromatids or homologous chromosomes to move apart and separate during meiosis or mitosis.  This can happen due to the centromeres and centrioles, which are arranged in a nine-triplet pattern, leaving the chromosomes stuck together and not moved into each cell that is a product of the process.

c. Autosomes essentially are all chromosomes except the sex chromosomes X and Y, which differ in males and females. This difference in gender is accompanied by the effects of steroids because some steroids, such as estrogen and testosterone, also differentiate between males and females in terms of molecule concentration.

d. Polygenic refers to traits that are determined by a specific number of genes, which allow for diversity within populations. An example of such would be the glycocalyx because, in eukaryotic cells, depending on the genes, they take a specific shape that allows the cell to which it is attached to interact with specific cells and have a unique identity.

III. Essentials

a.  Mendel’s  Law of Segregation states that, during metaphase I of meiosis, homologous pairs of chromosomes are separated, resulting in the gametes of the organism only containing one version of each chromosome. Ultimately, the offspring created by the fertilization of two gametes will contain two versions of each gene, resulting in an increased diversity within the population. Mendel’s Law of Independent Assortment states that in metaphase I of meiosis, when homologous chromosomes temporarily attach to each other at the chaism and form a tetrad, which chromosome faces which "pole" of the meiotic cell is completely random. In other words the maternal version of chromosome # 5 can be facing the right pole while the maternal version of chromosome #6 can be facing the left side of the cell. This, just like the Law of Segregation, creates variety and diversity within a population.

Chapter 10 Notes

II. Connections

1.  Homologous chromosomes are nonidentical sex chromosomes that have the same length, shape, and assortment of genes that line up with each other during meiosis.  Duplicated chromosomes are DNA strands that are replicated and stay attached at the centromere.

2.  Kinetochore is a mass of protein and DNA in the centromere to which microtubules of the spindle attach.  These microtubules which pull apart the connected chromatids are directed by microtubule organizing centers which dictate how microtubules will be organized and oriented in a given type of cell.

3.  Somatic cells are also known as body cells which,, after mitosis, result in the creation of 2 diploid cells with two sets of chromosomes each.  In reproductive sex cells, however, meiosis results in 4 haploid cells or gametes that contain only one set of chromosomes.

4. Nucleosomes are repeating subunits of chromatin occurring at intervals along a strand of DNA that are coiled around histones.  Dehydration reactions are dangerous to these nucleosomes as they can disrupt, uncoil, and destroy the DNA structure.

III. Essentials

a.       Prophase I

Chromosomes become visible and pair with their homologue. Microtubules begin to form, nuclear envelope starts to breakup

b.      Metaphase I

Mics. Connect to both chromosomes and homologous pairs. Chromosomes align midway between the poles

c.       Anaphase I

Mics. Shorten and move towards spindle pole, pulling chromosomes apart.

d.      Telophase I

One of each type of chromosome has arrived at spindle poles, cytoplasm divides, forming two haploid cells

e.       Prophase II

New bipolar spindle forms in each haploid cell, centrioles move to opp. Sides of cell, chromatids become tethered.

f.       Metaphase II

Chromosomes line up at poles. Same process as Metaphase I.

g.      Anaphase II

Sister chromatids break apart, mics. Move chromosomes toward spindle poles.

h.      Telophase II

4 nuclei form as new nuclear envelope encloses each cluster of chromosomes. Daughter cells are haploid.

10.4 Outline

I. How meiosis introduces variation in Traits

A. Crossing over in Prophase

            1. sister chromatids become stuck at certain point of chromosome

            2. when Dna strands break, segments break off and fuse with opp chromatid. This is called gene swapping, creating vast variety in genes.

B. Metaphase I Alignments

            1. random tethering of duplicated chromosomes to microtubules

                        a. more variation!

            2. either chromosome partner can endu up at either spindle pole

            3.  This means that there are 8,388,608 possible combinations of maternal and paternal chromosomes in human sperm and egg cells.

Differences between Mitosis and Meiosis

            Meiosis                                                            Mitosis

-          Purpose: reproduction                                     Purpose: growth and repair

-          Occurs only in reproductive cells                    occurs in all somatic cells

-          Results in 4 haploid gametes                          results in 2 Diploid cells

-          Results in genetically variable cells                 results in genetically identical cells

-          2 rounds of division                                        1 round of division

-          Results in cells w/ 23 chromosomes                results in cells w/ 46 chromosomes    

Chapter 45 and 47

II. Connections

a.       Both biotic potential and carrying capacity refer to the limits of a certain population within its own ecosystem. Biotic potential is the maximum rate of increase per individual for any population growing under ideal conditions, while carrying capacity is the maximum number of individuals in a species or population that a  given environment can sustain indefinitely.

b.      A trophic level is all organisms the same number of transfer steps away from the energy input into an ecosystem. Biological magnification relates to trophic levels because it is a process in which a substance that degrades slowly or not at all becomes ever more concentrated in tissues of organisms at higher trophic levels of a food web.

c.       Both autotrophs and detritovores play crucial roles in the flow of matter through the biosphere (including water, carbon and nitrogen).  Autotrophs  are the primary producers of energy in the energy pyramid , while detitivores decompose some organisms and are responsible for returning water , carbon, and nitrogen back into the soil which then returns to the atmosphere.

d.      Mitochondria  are the organelles in which the second and third stages of aerobic resp. take place.  With an increase of human population, as well as other factors such as cars and industrial factories, green house gases can be created by the increase of carbon in the atmosphere, resulting in global warming.

III. Essentials

a.       I. Density-dependent limiting factors

A.     Populations cannot keep growing due to lack of resources

a.       Essential source in short supply is a limiting factor on pop. Growth

b.      Often more than 1 factor that limits growth

II. carrying capacity and logistic growth

A.     Populations require more resources as they grow

a.       Carrying capacity is max # of individuals in a pop.  That can sustain in environment

b.      Once limit is passed, pop. Will go down until balance

B.     Logistic growth

a.       Shows what affects carrying capacity has on growth

b.      Density dependent controls help reduce the odds for individual survival

III. Density independent limiting factors

A.     Cause less births andmore deaths regardless of pop. Density

a.       Ex. Monarch butterflies in central mexico threatened by deforestation and freezes

b.  Type I curves reflect high survorship until fairly late in life, then high mortality rates, such as in elephants. Type II curves reflect a fairly constant death rate at all ages, which is seen in snowy egret populations. Type III curves signify a death rate  that is highest early in life, exemplified in sea star larvae populations.

c.    1. An age structure diagram depicting negative growth would have bars representing reproductive and post reproductive ages much larger than  pre-reproductive ages. 2. An age structure diagram depicting no growth would show all bars representing all ages generally at the same size.  3.  An age structure diagram depicting rapid growth would have the pre-reproductive year bars substantially larger than the reproductive years, which would be greatly larger than post-reproductive years.  4. An age structure diagram depicting slow growth would, like a rapid growth diagram, have the younger ages bigger than older ages, just not as drastic.

d. I. Inputs into ecosystems

            A. Nitrogen mainly enters via nitrogen fixation

            a. moves up trophic levels

            b. ammonification transfers ammonium into soil

            c. nitrification helps the ammonium become nitrogen

            B. Loss of nitrogen via denitrification

            a. other factors of loss include runoff and leaching

    II. disruptions by human activities

A.     Deforestation and grassland conversion

a.       Erosion

B.     Rotation of crops

a.       Helps counter nitrogen losses

C.     Fertilizers

a.       Pollutes bodies of water with nitrogen waste

b.      Does promote algal blooms

(for diagram see pg. 860)

Nitrifying bacteria are located on the cycle when nitrification occurs, denitrifying bacteria are located where denitrification occurs on the cycle, ammonifying bacteria are located where ammonification occurs, and nitrogen-fixing bacteria are located where nitrogen-fixing occurs.