# IB Biology/Study Guide
## Biotechnology
### Block 1B

PCR
PCR, or Polymerase Chain Reaction, was developed by Kari Mullis for the purpose of amplifying DNA obtained from crime scenes. In short, it's replication GONE CRAZY. In just a few hours, DNA can be replicated millions of times. In the procedure, DNA Polymerase uses nucleotides and primers to replicate a small sequence of DNA so that it is visible when comparing DNA obtained from a crime scene with samples. There are four steps to the process:
1. Denaturation – breaks Hydrogren bonds, splits them with heat
2. Anneal – adds primers, cools DNA
3. Extension – DNA Polymerase adds nucleotides to the DNA sequence
4. Repeat – in three hours, one can obtain three million copies of the DNA.
The DNA polymerase of Thermus aquaticus, a bacterium that lives in hot springs, is often used during PCR because the enzyme is able to survive the extremely hot temperatures needed to break hydrogen bonds in the DNA. One can replicate specific sequences of the DNA by utilizing specific primers in the replication process.
Gel Electrophoresis
Gel electrophoresis is a method of separating the strands of DNA based on their charge and size. Based on charge, DNA molecules have a negative charge. When placed on a magnetic field, the DNA strands move toward the positive pole. In addition, they can be separated based on size. Larger DNA molecules move much slower than small ones, so different sized DNA strands stop at different points along the magnetic field. Through this technique, the DNA leaves a distinctive pattern, and it can be compared to other samples to match DNA.
Restriction Enzymes
Restrictions enzymes, or molecular scissors, are used to cut DNA molecules in specific places. Bacteria produce restriction enzymes for the purpose of seeking out and destroying bacteriophage DNA. Researchers use these restriction enzymes to cut DNA at specific points, called palindromes, into manageable segments. Later this DNA can be inserted into a vector molecule, which will take the plasmids (DNA segments) into the cell. Once inside the nucleus of the cell, this plasmid DNA is replicated and distributed to any daughter cells. Restriction enzymes cut the DNA in a staggered pattern, producing sticky ends to which other DNA molecules which have been cut with the same restriction enzyme can bind.
Recombinant DNA
When DNA is spliced into a vector, the newly-formed product is known as recombinant DNA. Genetic engineering enables individuals to change viruses so that they can more easily introduce DNA into cells of more complex organisms, creating more complex and advanced recombinant DNA.
Human Genome Project
The human genome project aims to find the location of all of these genes on the human chromosomes and the base sequence of all of the DNA that makes them up. The project is an international cooperative one, with laboratories in many countries involved. The sequencing of the entire human genome will make it easier to study how genes control human development. It will allow easier identification of genetic diseases and the production of new drugs bases on DNA base sequences of genes or the structure of proteins coded for by these genes. It is estimated that the project could contain anywhere from 30,000 to 40,000 different individual genes.
Cloning
Cloning produces an organism with and identical genotype as to its host/donor. A clone is a group of genetically identical organisms or a group genetically identical cells derived from a single parent. Two types of cloning exist: cloning by embryo splitting, an earlier procedure, and cloning by nuclear transfer, used to clone the sheep Dolly. To clone the sheep Dolly, udder cells were taken from a donor sheep and unfertilized egg cells were taken from another sheep. The nucleus was removed from each egg, which were then fused with the donor cells using electricity. The fused cells developed into embryos, which were then implanted into a surrogate mother. The mother gave birth to a sheep genetically identical to that of the donor cell organism. Cloning by embryo splitting is an earlier method with differences in the method by which a clone is achieved. First, the actual egg cell of an animal is removed to be fertilized in a petri dish. In the dish, the zona pellucida is a chemical coating that promotes cell division. After the first division, this zona pellucida is removed by an enzyme and the two cells separate to become two individual cells. Within the petri dish, an artificial zona pellucida is added to the individual eggs and they continue development separately. This method is often used in cloning favorable livestock. Livestock are often selected for cloning based on favorable commercial qualities, including wool, meat, or milk productivity.
Use of Reverse Transcriptase in Biotechnology
In the biological world, reverse transcriptase is an enzyme used mostly by viruses to convert single-stranded RNA molecules into double-stranded DNA molecules. In terms of biotechnology, reverse transcriptase is utilized in reverse transcription PCR. In this way, by converting RNA to DNA before beginning the process of PCR, RNA can be examined in the same way that DNA can be through the process.
Bio Tech Ethics
There are many controversial issues concerning biotechnology. Cons- 1. New chemicals can kill agriculture
Pros- 1. With Biotech, we can feed the rapidly growing world population better

### Block 3B

PCR: Polymerase Chain Reaction: The polymerase chain reaction is used to amplify DNA in a small amount of time. There are four basic steps that outline this amplification. Denaturation: heat(extreme) is used to break hydrogen bonds and separate the strands of DNA; Anneal: Primers are then added to the separated strands during this step; Extension: Thermus aquaticus provides the enzyme DNA polymerase; Repeat: The process is then repeated multiple times. Each hour yields approximately one million copies. (five hours = about five million copies)
Restriction Enzymes
Restriction enzymes are DNA scissors. They cut both strands at specific bases in order to remove needed genes and open bacterial plasmids. By cutting at certain bases, they can create sticky ends, helpful in the creation of recombinant plasmids (i.e. insulin).
Gel Electrophoresis:
Gel electrophoresis is used to separate DNA according to size and charge. Due to the phosphate groups that make up DNA, DNA has a negative charge. Therefore, DNA will migrate towards the positively charged pole. In addition, large molecules will move slower than the smaller molecules.
Reverse Transcriptase
Reverse Transcriptase is used to create DNA from RNA. It is found in retroviruses. Biotechnology uses this to create DNA without the garbage introns from RNA.
The Human Genome Project The Human Genome Project was started by United States scientists in 1990. Although originally planned to last for fifteen years because of the extensive amount of work that was planned to be done, it only took until 2003. The Human Genome Project successfully determined the sequences of over three billion base pairs in DNA and identified all of the genes in DNA. The ultimate goal of the Human Genome Project was to map out human DNA so that it would be easier to cure diseases and sickness.
Cloning
Dolly is the name of a sheep that was cloned by nuclear transfer. Another way of cloning is embryo-splitting.
Recombinant DNA After a specific section of DNA is spliced off, it can be inserted into an organism via a vector. A vector is a means of transporting this DNA fragment, such as a gene gun or bacteriophage (which we steal to inject the recombinant DNA). This allows us to insert new genes into organisms, forming the basis for genetic engineering.

### Block 4B

Restriction enzymes are “molecular scissors” used to cut DNA molecules in specific places. Restriction enzymes cut DNA in a staggered manner, which produces pieces with identical, complementary, single-stranded “sticky ends”. These “sticky ends” can pair up with single-stranded ends of other DNA molecules that have been cut with the same restriction enzyme.
PCR is also known as the Polymerase Chain Reaction. It was created/discovered in 1983 by Kary Mullis. The main purpose of PCR is to make many many many copies of DNA (1 to over 3 million in 3 hours!!). The first step is Denaturation which breaks the Hydrogen bonds and separates the strands of DNA using heat. Then there is Anneal, which adds DNA Primers using DNA Poymerase. The final step is Extension where DNA Polymerase adds nucleotides(dNTPs).
Gel Electrophoresis is an example of DNA profiling that is used to separate strands of DNA based on charge and size. Smaller molecules move much faster than the larger molecules. When DNA has a negative charge, because of the phosphate groups, it will migrate towards a pole with a positive charge.
Recombinant DNA is formed when DNA is spliced into a vector, it is the DNA that has been created artificially. Engineered viruses are used to introduce DNA into the cells of more complex organisms.
The Human Genome Project was a project launched officially in 1990 at a cost of 3 billion US dollars with a coalition of countries such as the U.S., U.K., Germany, France, Japan, and China. The purpose of this project was to identify all of the 20000-25000 genes in the human DNA, determine sequences, store the information in the database, improve tools for analysis, among other goals. The sequence of the last chromosome was published in 2006; although, the genome itself was finished in 2000. With the completion of the project, scientists are closer to their goal of isolating genes that could cause certain diseases/ disorders.
Gene therapy is used to treat genetic diseases by altering the genotype. In theory, it would be possible to eliminate genetic diseases in the future by changing the base sequence of the allele that causes the disease. For example, if the disease-causing allele is recessive, one could insert the dominating allele that would prevent the disease into the cells that have been infected. Although this procedure could be done at several different stages during the human life cycle, the best cells to use are stem cells. They can divide repeatedly to replace lost body cells.
Gene mutation is any change to the base sequence of a gene. Although there are several types of gene mutations, the smallest possible change that can occur (when one base is replaced by another) is called a base substitution. One of the most notable examples of a gene mutation is non-disjunction in chromosome 21 (trisomy-21), otherwise known as Down syndrome.
Cloning Cloning is a process by which a genetically identical copy is made of something. The most famous example to date is Dolly the Sheep. Dolly was the product of somatic cell nuclear transfer where 1) the nucleus from a somatic cell is placed inside an egg cell, which has had its nucleus removed 2)An electrical shock initiates the egg that contains the somatic cell's nucleus to begin dividing 3)It will eventually form a blastocyst, which has almost identical DNA to the original organism.
Scientists have said that it is possible to clone humans, but the process is considered controversial. On the positive side cloning of embryos would allow scientist to screen for genetic diseases earlier. Then infertile couples would have a better chance if their embryos were cloned. On the negative side those groups who were genetically identical might suffer psychological problems. Also, if differentiated cells could cause a high risk of fetal abnormalities and a high rate of miscarriages. Then differentiated cells have already begun ageing and it might cause the humans clones to grow old quickly.
Reverse transcriptase is the molecule which allows a single strand of RNA to be made into a double strand of DNA.

## Cellular Biology
### Block 1B

Viruses/Reverse Transcriptase
Viruses are non-cellular infections agents that must have a host cell to replicate. They are also considered non-living; however, this is debated, as the current definition for life may be contestable. Viruses are self-propagating, and they undergo some of the same biological processes that other classifed living organisms do. Viruses also contain nucleic acid (either DNA or RNA) which is surrounded by a protein coat, or capsid. An argument against viruses being considered living organisms is that they rely on other cells to perform metabolic activities, with no independence. The most widely accepted theory for the origin of viruses is that they are bits of nucleic acid that have escaped from cells. Phages are viruses that invade bacteria.
Reverse transcriptase, also known as RNA-dependent DNA polymerase, is a DNA polymerase enzyme that transcribes single-stranded RNA into double-stranded DNA. Normal transcription involves the synthesis of RNA from DNA, hence reverse transcription is the reverse of this.
Prokaryotic/Eukaryotic Cells
Eukaryotic cells feature membrane-bound organelles, compared to prokaryotic cells which do not. Prokaryotic cells feature both a cell wall and a cell membrane, while eukaryotic cells feature only the membrane. Prokaryotic cells are also typically smaller than eukaryotic cells and likely evolved first. Prokaryotic cells feature circular DNA which is naked, while eukaryotic cells contain linear DNA contained within a nucleus. Lastly, prokaryotic cells feature 70s ribosomes, in contrast to 80s ribosomes found in eukaryotic cells.
Plant/Animal Cells
Plant cells feature chloroplasts and mitochondria, while animals cells only contain mitochondria. Plant cells are surrounded by a cell wall made of cellulose, whereas animal cells only have the cell membrane. Plant cells contain one large vacuole to store water, while animal cells have many smaller vacuoles for the storage of other substances. Lastly, animal cells have cilia and flagella to promote movement, while plant cells are stationary.
Cellular Organelles: Functions, Structure
Nucleus - Contains DNA, regulates cell processes
Nucleolus - Creates ribosomes
Chloroplast - Site of photosynthesis
Mitochondria - Make energy
Endoplasmic Reticulum (rough or smooth) - Pathway for transport of materials throughout cell
Ribosomes - Synthesize proteins
Lysosome - Digests food, recycles organic material, suicice sac, contains digestive enzymes
Golgi Apparatus - Packaging center for proteins
Vacuole - Storage, disposal of waste
Vesicles - Transfers proteins through cytosol
Plasma Membrane - Selectively permeable membrane that allows the passage of materials in and out of the cell
Cell Wall - Maintains shape, water intake, and protection for the cell
Cilia/Flagella - Provide movement
Microtubule - Structure
Centrioles - Assist in cell division
Plasma Membrane/Structure
Plasma membrances for cells are made of a phospholipid bilayer. Each phospholipid is made up of two fatty acid chains linked to a glycerol molecule.
Cell Cycle
INTERPHASE
GROWTH 1 (or G0) - 11 hours long (longest phase), rapid growth of organelles
SYNTHESIS - 7 hours, DNA replication
GROWTH 2 - 13 hours (I'm not sure why G1 is the longest phase, but that's what my diagram says), growth continues, final preparation for mitosis, spindles form
MITOSIS - 1 hour (shortest phase), Prophase, Metaphase, Anaphase, Telophase
Cytokinesis then leads back to >>>>>>>> INTERPHASE
Cells
Cells are the building blocks of all living things

### Block 3B

Prokaryotic/Eukaryotic Cells
Prokaryotic cells and eukaryotic cells have many differences, such as the following: Prokaryotic cells have circular DNA/Eukaryotic cells have linear DNA Prokaryotic cells have 70 Svedburg Ribosomes/Eukaryotic cells have 80 Svedburg Ribosomes Eukaryotic cells have membrane-bound organelles, while prokaryotic cells do not.
Animal and Plant Cells
Plant Cells • Surrounded by both Plasma membrane and rigid cell wall • Contain mitochondria and chloroplasts • Rigidly held in place by cellulose wall • Has one single large vacuole that holds mostly water and offers structural support. Animal Cells • Surrounded by plasma membrane only • Retains the ability to move (cilia/flagella) • Has many small vacuoles sporadically sprinkled throughout the cytoplasm
Cellular organelles: • Nucleus: Used to control protein synthesis and hold DNA. "The brain." •Nucleolus: Used to make ribosomes • Chloroplast:The site of photosynthesis in plants • Mitochondria: Site of cellular respiration, which is the catabolic process that generates ATP by extracting energy from other sugars, fats, and other fuels with the aid of oxygen)"The Powerhouse" • Rough Endoplasmic Reticulm: Holds the ribosomes which create proteins for export • Smooth Endoplasmic Reticulum: The site for the synthesis of lipids and detoxification • Ribosomes: Manufacture Proteins • Lysosomes: They digest unwanted material and waste in the cell • Golgi Apparatus: The packaging center that receives and transports vesicles • Vacuole: Stores material and for plants it provides structure • Vesicles: Membrane bound transportation sacs • Plasma Membrane: Selective and permeable barrier that controls the movement of materials into and out of the cell
Endosymbiosis
Endosymbiosis is a theory that attempts to explain how cell organelles developed to form eukaryotes.Lynn Margulis is credited as the founder of this theory. Endosymbiosis states that early prokaryote cells engulfed other prokaryote cells, which formed a mutual symbiosis in which the outer cell provided protection, while the inner cells produced energy. This explains how mitochondria and chloroplasts developed as separate cells which later evolved into their present organelles. There are several "proofs" claimed for endosymbiosis. Chloroplasts and mitochondria have several characteristics of early prokaryotes
* Circular DNA
* 70S Ribosomes
* Undergo Mitosis on their own
* Separate membranes

### Block 4B

Organisms can either be unicellular or multicellular. It is the unicellular organisms, however, that are needed to carry out life functions. The cells in multicellular organisms are unique in that they can they are able to perform specialized functions by expressing certain genes, but not others.
Robert Hooke first discovered cells. Anecdote to help remember said fact: While looking at the small entities, their compartmentalized appearance reminded him of tiny, connected rooms (also known as "cells" during this time). Hence he decided to name the entities "cells".
Viruses need a host cell to replicate in. Retroviruses use reverse transcriptase to insert the virus DNA into the host DNA, making the virus unrecognizable from the host. One of the most notable retroviruses of today is HIV.
Plant cells have a cell wall, chloroplast and a plasma membrane but do not have centrioles. Plant cells also contain a central vacoule, for water storage.
Animal cells do not have a cell wall, chloroplast or plasma membrane but have centrioles. Animal cells also can have movement organelles, such as flagella.
Cell Size
A cell's rate of metabolism is equal to the ratio mass:volume. Likewise, the rate of material exchange is equal to a cell's surface area. It's vital that a cell has a high surface area to volume ratio. It can only do this by remaining small, because it's surface area increases much more slowly than its volume. If a cell becomes to large, it will lose its ability to maintain levels of homeostasis. Microvilli can help to increase a cell's surface area without changing its size. The type of microscope used to view a cell can significantly change the viewers image of the cell. A light microscope is used to view living organisms, uses color images, has a large field of view, has a low resolution with a magnification of 1000x, and is relatively inexpensive, and portable, as well. An electron microscope, on the other hand is used to view dead organisms, uses monochrome images, has a small field of view, has a high resolution with a magnification of 250,000x, is rather expensive, and cannot be moved.
Components of the Prokaryotic Cell
Cell Wall-Provides protection & support; made of peptidoglycan.
Plasma Membrane-Allows for the regulation of intra/extra material in the cells.
Mesosome-Located in the infolding of the plasma membrane. DNA replication occurs here.
Cytoplasm-Intercellular fluid that suspends organelles.
Ribosomes-Involved with protein manufacturing.
Nucleoid region-"Naked" DNA is located here.
Components of Eukaryotic cells
Cytoplasm-watery material that contains materials involved in cell metabolism
Endoplasmic Reticulum (ER)- pathway for the transportation of materials throughout the cell; associated with synthesis and storage
Nucleus-control center for cell metabolism and reproduction
Ribosome-site of protein synthesis
Lysosomes- digestion of food within the cells
Mitochondria- "powerhouse" of the cell; site of cellular respiration. It has two membranes (inner, outer). All eukaryotic cells have mitochondria.
Golgi bodies- packages and secrets products of the cell
Centrioles- cell division in animals
Vacuoles- Fluid filled organelles sheltered by the membrane, holds stored food and waste
Nucleolus- site of the production of ribosomes
Nuclear membrane- controls movement in and out of nucleus
Cell wall- gives shape and provide production in plants
Cilia- hairlike structure that helps the cell move. Composed in a 9x2 arrangement of microtubules.
Flagellum- long, hairlike tail used for movement. Composed in a 9x2 arrangement of microtubules.
Chloroplast- site of photosynthesis
Cell plate- new cell wall that begins to form during cytokinesis
Chlorophyll-traps light and used to reproduce in plants
microtubles-microscopic cylinders that give cell shape. They are larger than the thin microfilaments
microtubules-transport chromosomes during cell division, as well as organelles and vesicles throughout the cell.
chloroplast-site of photosynthesis. It contains the pigment chlorophyll. The chloroplast has three membranes (inner, outer, thylakoid). Plants, algae, and some other protists carryout photosynthesis with the chloroplast.
There are numerous enzymes that are actually imbedded in membranes. The following membranes are a part of the endomembrane system: ER, nucleus, Golgo complex, lysosome, vacuoles, and plasma membrane. Eukaryotic cells have a cytoskeleton that provides shape and allows for locomotion.
Prokaryotic cells: circular DNA, mesosome, lack membrane bound organelles, 70S ribosomes, smaller
Eukaryotic cells: linear DNA, no mesosome, contain membrane-bound organelles, 80S ribosomes, larger
Cell Cycle I: Interphase- longest phase G: Growth (transcription and translation occur) S: synthesis of DNA (replication occurs)

## Cell Division
### Block 1B

Mitosis: Purpose? Stages?
Purpose - growth and repair; allows for direct replication of a cell
Stages - Interphase, Prophase, Metaphase, Anaphase, Telophase1
Meiosis: Purpose? Stages?
Purpose - reproduction; allows for the formation of haploid gamete cells
-Germ cells of Eukaryotes produce gametes
-2 Divisions ending in 4 cells that are different from each other and parents
Stages
INTERPHASE
-chromosomes replicated in the S-phase
PROPHASE I
-nucleus and nuclear membrane break down
-centrioles move towards opposite poles
-tetrads formed
METAPHASE I
-homologous pair line up along equator
ANAPHASE I
-homologues separate and move to opposite poles
TELOPHASE I
-chromosomes at opposite poles
-new cell membranes form through cytokeneisis
PROPHASE II
METAPHASE II
ANAPHASE II
TELOPHASE II
When homologous chromosomes meet at the equator to form a tetrad, crossing over can sometimes occur among sister chromatids. In crossing over, the genes switch chromosomes at the chiasma and travel with their new chromosomes through the remained of the process of meiosis. The term tetrad refers to the structure formed when these two homologous chromosomes come together. Independent Assortment refers to the quality that chromosomes will sort into different cells during meiosis independent of one another. Both crossing over and independent assortment increase genetic variation in reproduction of a species, allowing for evolution. Species which reproduce by mitosis have less genetic variation, which can only be achieved through mutations.
MICROTUBULES
Microtubules are one of the components of the cytoskeleton. Microtubules serve as structural components within cells and are involved in many cellular processes including mitosis, cytokinesis, and vesicular transport.
CENTRIOLES
A centriole in biology is a barrel shaped microtubule structure found in most animal cells and algae though not often in plants. It constitutes the compound structure known to cell biologists as the centrosome. Centrioles are very important in the cell division process. They organize the pericentriolar material (PCM) which plays a role in organizing the mitotic spindle, which in turn helps the cells to divide. The mitotic spindle functions in the chromosomes. During cell division the centrioles are duplicated, so that there will be a pair for each daughter cell.

### Block 3B

Mitosis The purpose of mitosis is to make two identical cells by chromosome duplication. Stages are the following: -Interphase -Prophase -Prometaphase -Metaphase -Anaphase -Telophase -Cytokinesis
Meiosis: The purpose is to create four haploid germ cells (such as sperm/eggs). This process ensures genetic variation in offspring. The daughter cells are genetically different from the parent cell, unlike in mitosis. Meiosis can be broken down into roughly nine steps: Prophase I-Metaphase I- Anaphase I - Telophase I- Prophase II - Metaphase II - Anaphase II- Telophase II- Cytokinesis
Microtubules Microtubules are hollow filament structures in eukaryotic cells that help chromosomes move to opposite sides of the cell (especially in anaphase of mitosis). They also aid in the structure and support of a cell.
Variation There are several ways that Meiosis produces variation in organisms.
* Crossing Over - When a tetrad forms, the tips of the homologous chromosomes can switch, allowing for random variation during Prophase I.
* Mutations - Random freak genetic accidents can mutate genes.
** Insertion - DNA put in
** Deletion - DNA taken out
** Inversion - DNA reversed
** Translocation - DNA cut out somewhere and stuck back in somewhere else
* Independent Assortment - Chromosomes line up independently during meiosis, creating a near infinite amount of combinations.

### Block 4B

Mitosis Mitosis is asexual reproduction. It creates two new, identical nuclei. Stages:
Cell Cycle
The cell cycle begins in the first gap phase, also known as the G1 phase. This phase of growth is the longest phase of the cell cycle. Near the end of this phase, the enzymes that allow the cycle to move into its second phase become increasingly active. Some cells do not divide, and are stuck in this phase of the cell cycle, which, in that case, would be G0. The next phase, the S phase, DNA is synthesized, along with some chromosomal proteins. This is also the stage in which the complex process of chromosome replication takes place. Upon the completion of the S phase, the cell enters it's second gap phase, the G2 phase. As the cell prepares for division, more proteins are synthesized. This phase is relatively short compared to the previous two phases. The final stage of the cell cycle, mitosis, occurs next. Although it is the shortest phase of the cell cycle, this is the part in which the most action takes place. Near the conclusion of mitosis, the cytoplasm divides to form two cells in a process called cytokinesis. Cytokinesis overlaps into the G1 phase, which starts the cycle over again.
Mitosis is the process in which a cell duplicates its chromosomes to generate two, identical cells. It is associated with growth and asexual reproduction. Stages: Interphase (uncondensed chromosomes), Prophase (chromosomes condense), Metaphase (chromosomes line up at the metaphase plate), Anaphase (chromatids separate), Telophase (2 new identical cells).
Crossing over allows for genetic variation in gametes. It occurs on non-sister chromatids. The chiasma is the site of crossing over.
Tetrads form only during Meiosis and consists of 2 homologous chromosomes.
Chromosome= DNA+Protein
Variation occurs during meiosis because of two things. The first being because of crossing over. Crossing over provides a new arrangement of genetic information, which then increases the chance for variation. The other method that variation occurs is because of the law of independent assortment. In the law of independent assortment alleles of different loci are randomly distributed into gametes.

## Genetics
### Block 1B

GENETIC TERMS
- Homozygous: Having two identical alleles of a gene
- Locus: The particular position on homologous chromosomes of a gene
- Co-dominant Alleles: Pairs of alleles that both affect the phenotype when present in a heterozygote.
- Test Cross: Testing a suspected heterozygote by crossing it with a known homozygous recessive.
- Carrier: An individual that has a recessive allele of a gene that does not have an effect on their phenotype.
- Phenotype: The observable physical of biochemical characteristics of an organism, determined by both genetic make up.
- Heterozygous: Having two different alleles of a gene.
- Dominant Allele: An allele that has the same effect on the phenotype whether it is present in the homozygous or heterozygous state.
- Recessive Allele: An allele that only has an effort on the phenotype when present in the homozygous state.
- Genotype: The combination of alleles located on homologous chromosomes that determines a specific characteristic or trait.
Linked Genes are located on the same chromosome and are inherited together. They do not assort independently. Linked genes will only form recombinants if crossing over has occurred
Genetic Recombination: production of offspring with different traits than the parents
Recombination Frequency: (# recombinants)/(total # offspring) x 100%
Mutation- a change, different from the parents', that occurs on a chromosome that marks for a specific trait

### Block 3B

Genetic terminology: “Allele”- one of two expressions of a gene that occupies a single locus on a chromosome.
“Dominant” – a gene that, once inherited, results in the occurrence of a specific phenotype (ex. Having the dominant gene for a widow’s peak means you have a widow’s peak on your forehead)
“Recessive”- a gene that results in the absence of the stated phenotype (ex. Being recessive for the widow’s peak means you DO NOT have one),
“Homozygous”- describes a gene with two identical alleles, either dominant of recessive (ex. HH or hh)
“Heterozygous”-describes a gene containing one dominant allele and one recessive allele (ex. Hh)
“Polyploid”- refers to the possession of more than one set of chromosomes. [Polyploid organisms, especially plants, are larger than normal and have larger cells. Affected animals are often abnormal in appearance and usually infertile.]
Polygenic Inheritance
Polygenic inheritance refers to traits that are determined by more than one gene. For instance, skin color, hair color, or eye color. There isn't just black or blonde hair, but varying shades of each due to polygenic inheritance.
Sex-linked Traits A sex-linked trait is due to a gene found only on the X chromosome, otherwise known as the sex chromosome. One example is colorblindness, which males are more likely to get because they have one X chromosome and one Y chromosome. If the allele for colorblindness is on the X chromosome, it will be expressed regardless of whether it is on the Y chromosome or not. For the colorblindness trait to be expressed in females, who have two X chromosomes, the allele for the trait must be present in both X chromosomes. Karyotype A karyotype is a picture of an individual's chromosomes. Karyotypes are used to identify certain genetic disorders. For example, if the karyotype reveals trisomy on chromosome 21 then the person has Down syndrome.
Linkage Group: Genes in a particular chromosome that tend to be inherited together. A one to one ration should be obtained if the genes are linked. They will from recombinants solely in the event that crossing over has occurred. In order to calculate the frequency one can use the formula: % Recombinants/total offspring x 100%= recombination (in percent, centimorgans, or map units)

### Block 4B

Genotype – alleles on a homologous chromosome that show the characteristics of the trait that the homologous chromosome codes for
Phenotype – The observable physical characteristics determined by genes
Locus – The position of a gene on a chromosome
Homozygous – two identical alleles of a gene [gene with two identical alleles, either dominant of recessive (ex. HH or hh)]
Heterozygous- two different alleles of a gene [one dominant allele and one recessive allele (ex. Hh0]
Dominant Allele- an allele that is dominant in regards to the phenotype whether it is part of a homozygous or heterozygous combination
Recessive Allele- An allele that does not show if a dominant allele is present, but shows when an organism has a trait that is homozygous recessive
Test Cross-Testing for a heterozygote by crossing it with a known homozygous recessive organism
Genetic Recombination-offspring that has different genotypes from its parents
Carrier- An organism that has a recessive allele of a gene that does not effect it, but that it may pass down to its offspring
Co-dominant Alleles-Pairs of alleles that equally affect the phenotype even though they are heterozygote
Linked genes -genes that are located on the same chromosome.
Karyotype - the chromosome composition of an individual and a photomicrograph showing the composition (generally numbered in order of size)
P Generation: Parent generation F1 Generation: The offspring of the parent generation F2 Generation: The offspring of the F1 generation
Multiple alleles-three or more alleles of a single locus. ex. blood types
The phenotypic ratio of a monohybrid cross is 3:1. The phenotypic ratio for a dihybrid cross is 9:3:3:1.
Sometimes when traits are crossed people end up getting traits that are known as hybrid vigor. This is when superiority arises from the heterozygote as oppose to homozygous genotypes. Some examples of hybrid vigors are mules, and Sickle cell when it is a heterozygote because the people can not get malaria, but they can still carry oxygen.
Polygenetic inheritance is when multiple independent pairs of genes have similar and additive effects on the same trait - Coded for by more than one gene - Appear in a normal distribution curve Examples: Skin, eye, hair colors
Mutation – a change on the chromosome or in the gene that gives the offspring different DNA/ traits from the parents.
Polyploid organisms have more than two copies of each chromosome.
Polygenetic inheritance is when multiple independent pairs of genes have similar and additive effects on the same trait - Coded for by more than one gene - Appear in a normal distribution curve Examples: Skin, eye, hair colors
Diploid: having the full set of chromosomes (2n or 46 chromosomes) Haploid: gametes (egg and sperm) only half the number of chromosomes (n)
Mathematics and Genetics
Probability – The fraction, percentage, or ratio that is used to describe the chance of an event occurring. In genetics, probabilities predict phenotypes and genotypes that come from genetic crosses.
Product Rule – The probability that two or more independent events will occur together is found using the product of the individual probabilities of each event. If the probability of a cross between a tall pea plant and a short pea plant producing a short pea plant is 25%, what is the probability of three short plants being produced in a row? The answer can be found using the product rule: 0.25×0.25x0.25=0.015625 or 1/64. So there is a 1 in 64 chance that three short plants will be produced in a row.
Hardy–Weinberg principle – Named after English mathematician Godfrey Hardy and German physician William Weinberg, this principle shows the expected frequencies of different genotypes in a population. Though this rule represents an ideal population in which there is random mating, no mutation, a large population size, no migration (emigration of immigration) and no natural selection, it helps us understand that in large populations, the process of inheritance does not cause changes in allele frequencies alone. There are two equations used in Hardy-Weinberg: p$^2$ + 2pq + q$^2$ = 1 and p + q = 1, where p$^2$ is the dominant genotype frequency (AA), 2pq is the heterozygous genotype frequency (Aa) and q$^2$ is the recessive genotype frequency (aa). Therefore, p represents the dominant allele (A) while q represents the recessive allele (a).

## DNA
### Block 1B

Structure DNA's structure is quite complicated. STRUCTURE
The structure of DNA is illustrate by handed double helix, with about 10 nucleotide pairs per helical turn. Each spiral strand, composed of a sugar phosphate backbone and attached bases, is connected to a complementary strand by hydrogen bonding (non- covalent) between paired bases, adenine (A) with thymine (T) and guanine (G) with cytosine (C).
Adenine and thymine are connected by two hydrogen bonds (non-covalent) while guanine and cytosine are connected by three.
This structure was first described by James Watson and Francis Crick in 1953.
Transcription
-Occurs in the nucleus
-Occurs in a 5'-3' direction
-RNA Polymerase recognizes the start point at the promoter region. Ribonucleoside triphosphate supply the energy for transcription and become RNA nucleotides by losing a phosphate. Transcription ends at the terminator region. RNA undergoes splicing to remove introns before it leaves the nucleus. Before splicing mRNA = hn RNA. After splicing mRNA = mature m RNA
Translation
-Occurs in the cytoplasm/ribosomes
-Occurs in a 5' - 3' direction
-tRNA activating enzyme binds a specific amino acid to tRNA using ATP energy. At the 3' end of every tRNA are the three nitrogenous bases: CCA. Translation consists of initiation, elongation, and termination. The start codon is always AUG.
DNA = Deoxyribonucleuic Acid DNA is the blueprint for who we are and for who we have become

### Block 3B

DNA is shaped as a double helix. One strand of DNA contains a sugar and phosphate backbone and a base. The subunits of DNA are Nucleotides. The bases are adenine, guanine, cytosine, and thymine. Adenine and guanine are purines. Thymine and cytosine are pyrimidines. Adenine pairs with Thymine and Guanine pairs with Cytosine. Most of DNA is repetitive sequences that don't code for anything, only a small portion is coding. The nucleotides are held together by phosphodiester bonds which links the sugar and the phosphate. DNA strands also run anti-parallel. Basically, this means that on any give strand, one end of the phosphate is attached to a 5' carbon and the other to a 3' carbon. When two DNA strands join the 5' carbon attaches itself to the 3' carbon end.
Structure
Chromosome Composition Chromosomes are made up of DNA and protein. The DNA is coiled around the proteins (histones) and then folded over itself. Histones make up a nucleosome, which is a complete coil of DNA around the histone core (eight histones) held together by one histone stabilizing protein.
DNA Replication DNA replication is semi-conservative. This means that each new DNA molecule has half of the original. In order to begin replication, DNA is unwound (unzipped) by DNA helicase. Helix-destabilizing proteins keep the helix in the unzipped position until the complimentary bases are added. DNA Polymerase III catalyzes the linking together of nucleotide subunits in a 5' to 3' direction as always. The energy and nucleotides are provided by Deoxynucleoside Triphosphate. When replication is about to begin, RNA primase lays down RNA primers which are replaced by DNA by DNA Polymerase I before replication is complete. Replication is initiated at many points and is discontinuous in one strand and continuous in the other. The lagging strand moves away from the replication fork and is synthesized in fragments because DNA polymerase cannot move too far from the replication fork and the leading strand goes toward it. The fragments on the lagging strand are known as Okazaki fragments and the fragments are joined together by DNA ligase.
quiz yourself! can you label every number in the picture below?
Polysomes and Nucleosomes A polysome is a bunch of ribosomes bounded together by mRNA. A nucleosome is made up of eight histones with DNA wrapped around it and a stabilizing histone on top. Nucleosomes package DNA into chromosomes.
Transcription: In a general sense, transcription is the process of copying the specific needed recipe from the huge cookbook, slimming off all the excess and sending out to be made. *happens within the nucleolous and cytoplasm *always occurs in 5’-3’ direction How its done: 1.RNA polymerase finds the specific base-coded unit called the “promoter” it's a start sign written in A’s T’s G’s and C’s. 2. The RNA polymerase then lays down the needed coinciding base units on the anti-sense strand. 3.this strand of RNA is known now as hnRNA, it still has introns. 4.In the open are of the nuclear membrane, the strand is “spliced” all of the intron garbage is removed, and it is now called mature DNA. 3 bases of said strand is called one codon, or one amino acid.
Translation:
Translation is the actual cooking of the recipe. It is the process of ribosomes reading the specific amino acids and sending the instructions out into the cell. This whole awesome process goes down in the cytoplasm.
* The start codon, AUG meets • between the two parts of the ribosome : The large and small sub units. The anit codon (UAC) connects with the codon at the Peptide station on the large s.u. • The enzyme peptydil transferase then moves this connected unit from the P to the A area, thus sending the chain down the line. • This process continues until all the little jellyfish are made.

### Block 4B

The structure of DNA, its double helix shape, was discovered by Watson and Crick. DNA is a nucleic acid (polymer) made from nucleotides (the monomers of nucleic acids). Each nucleotide is made made of a phosphate, a sugar, and a base. The base is bonded to the sugar which is bonded to phosphates. The sugars and phoshpates bond together (phosphodiester bond) in an alternating pattern the forms the backbone of DNA. The nucleotides of DNA contain 4 bases, the purines encompassing Adenine and Guanine and the pyrimidines which include Cytocene and Thymine. These nucleotides combine to form a strand of DNA. DNA is a double stranded molecule. The strands are linked by hydrogen bonds between the bases. Adenine bonds with Thymine and is held by two hydrogen bonds, and Cytocene bonds with Guanine and is held together by three hydrogen bonds. It is this difference in bond number and thus strength that accounts for the helicle shape. Due to the phosphates in the DNA strand a DNA molecule of DNA has a slightly negative charge.
Chromosome composition includes DNA (genes) and a protein.
* DNA Synthesis begins at specific based sequences termed the ORIGINS OF REPLICATION (there are many)...The replication fork occurs at both ends so DNA replication proceeds in both directions.
DNA Replication
There are three types of replication:
1. Semi-conservative replication - The new DNA molecules have half the genetic material as the original.
2. Conservative replication - The new molecules have all the genetic material of original.
3. Dispersive replication - Each molecule contains a mixture of genetic material in various regions on each strand.
Replication of DNA begins at certain sites on the DNA molecule known as origins of replication. The Y-shaped structure at which both DNA strands are replicated simultaneously is known as the replication fork. There is a lagging strand, which is always leaving the replication fork, as well as a leading strand, which continuously moves toward the fork. The lagging strand, however, is synthesized in an irregular fashion since the DNA polymerase, which catalyzes the linking of DNA subunits, cannot be too far from the replication fork. As a result, small Okazaki Fragments are created & synthesized.
Replication occurs in the nucleus, always in a 5’ to 3’ direction.
1)Helicase unwinds and unzips DNA.
2)Primase then lays down a primer.
3)DNA Polymerase I replaces RNA primers with DNA
4)DNA Polymerase III adds the nucleotides
5)Ligase joins together the Okazaki fragments, which form because the DNA Polymerase III cannot move too far away from the replication fork. Okazaki fragments are present on the lagging strand, where replication is discontinuous. Replication on the leading strand is continuous.
A nucleosome is made up of DNA that is wrapped around eight histone proteins, where one of the histones stabilizes the structure.
DNA Transcription occurs in a 5'-3' direction in the nucleus. First the promotor reginon allows RNA polymerase to recognize the start point. Then Ribonucleoside Triphosphate supplies the energy that is used in transcription and will then become RNA nucleotides by losing a phosphat. Transcription is done when it reaches the terminator region. In order for it to leave the nucleus it must be spliced(the removal of the non coding introns) transforming it from hnRNA to mature RNA.

## Photosynthesis/Respiration
### Block 1B

Photosynthesis occurs in the chloroplast, which is found in plant cells. The light-dependent reactions occur in the thylakoid membrane, located in the chloroplast. Photons, which are packages of light from the sun, first go to photosystem II. The photo activation of photosystem II occurs due to the light activating it. The accessory pigments found in the photosystem absorb the light and give the energy to chlorophyll, which is another pigment that is also absorbing light. The chlorophyll then gets excited with the energy it received and loses two electrons. Chlorophyll wants to regain the two electrons it lost, so a water molecule splits into two hydrogen and one oxygen using a process called photolysis, where light is used to split a water molecule. The chlorophyll then takes the two hydrogen in order to become more stable and replace the two electrons lost. Meanwhile, the two electrons lost go to the Primary Electron Acceptor, and then travel down the Electron Transport Chain. The electrons go through the Electron Transport chain in one direction, thus creating energy. The energy made is used to undergo photophosphorylation where ADP combines with Phosphate to make ATP. The ATP is then needed to help take the hydrogen out of the stroma and undergo chemiosmosis where ATP synthetase is a protein channel that allows the hydrogen to move through and out of the thylakoid membrane. The process creates more ATP. Back to the electron traveling through the Electron Transport Chain, the electrons then go to Photosystem I, which is photo activated. In Photosystem I, there are accessory pigments absorbing energy and giving it to chlorophyll that then loses two electrons. The chlorophyll does not need replace the two electrons by using hydrogen from photolysis because more electrons are coming from the Electron Transport Chain. The two electrons go to the Primary electron Acceptor and then go to Ferrodoxin. Ferrodoxin, a protein, transfers the electrons to NADP that then undergoes reduction because it uses the electrons to combine with a Hydrogen and become NADPH. With light-dependent reactions, there is also cyclic and non-cyclic photophosphorylation. Non-cyclic photophosphorylation is the normal light-dependent process that produces ATP and NADPH; however, cyclic phosphorylation is different and not normal. Cyclic photophosphorylation is a process where electrons go through the Primary Electron Acceptor, down the Electron Transport Chain, and into Photosystem I. The accessory pigments in Photosystem I absorb the energy and give it to chlorophyll. The chlorophyll then has energy and gets excited so that it loses two electrons. The two electrons then go to the Primary Electron Acceptor, and the process repeats itself. Cyclic photophosphorylation cannot go on continuously and produces only NADPH. Light-independent reactions take place after light-dependent reactions. Light-independent reactions occur in the stroma. RuBP carboxylase helps in combining carbon dioxide and RuBP in a process called carbon fixation. The process produces a 6 carbon intermediate. The 6 carbon intermediate then becomes two 3 GP carbon compounds. ATP and NADPH created from the light-dependent reaction are used to change the arrangement of atoms so that GP undergoes reduction and creates two 3 TP. The ATP and NADPH oxidize and become ADP and NADP, which can be used again in light-dependent reactions. Five of the six carbons in TP are used to recreate RuBP and the other carbon helps in producing a carbohydrate.
One may increase the rate of photosynthesis by increasing the temperature, sunlight, or CO$_2$ in the atmosphere
One may decrease the rate of photosynthesis by increasing the amount of wind on the plant.
CAM/C4
C4 and CAM plants both have an enzyme called PEP (phosphoenolpyruvate). This enzyme can fix CO2 at very low concentrations.
C4 patway:
CO2 + PEP (3C) yields oxaloacetate (4c) Oxaloacetate is converted into malate (using NADPH) Malate enters itno the bundle sheath cells and is decarboxylated into Pyruvate. Pyruvate (3c) is converted into PEP (using ATP) The CO2 goes into the Calcin Cycle (light independent cycle) just as it does in the normal c3 pathway.
CAM pathway
CAM plants only open their stomata at night. They join co2 with PEP forming oxaloacetate and convert this into malate in the same method that c4 plants use. However, they store the malate in a vacuole until daytime and decarboxylate in to gain the co2 needed for the Calvin Cycle.
CHEMIOSMOSIS
Chemiosmosis is the diffusion of ions across a membrane. More specifically, it relates to the generation of ATP by the movement of hydrogen ions across a membrane. An Ion gradient has potential energy and can be used to power chemical reactions when the ions pass through a channel. Hydrogen ions (protons) will diffuse from an area of high proton concentration to an area of lower proton concentration.
ATP synthase is the enzyme that makes ATP by chemiosmosis. It allows protons to pass through the membrane using the kinetic energy to phosphorylate ADP making ATP. The generation of ATP by chemiosmosis occurs in chloroplasts and mitochondria as well as in some bacteria.

### Block 3B

Xerophyte and Hydrophytes have several differences that enable them to survive in their given environment. Xerophytes (arid plant): Thick cuticle to retain water, Deep, branching roots, Few stomata for gas and water exchange, Greatly reduced leaves (they can have spines, be rolled, or hairy); Hydrophytes (aquatic plant), Thin/no cuticle, Shallow, short roots, Many stomata, Large and finely divided leaves.
Cytochromes are used to transport the electrons down the electron transport chain.
Oxidation is loss, reduction is gain. A neat way to remember this is: OIL RIG.
Glycolysis, The Krebs Cycle, and the Electron Transport Chain are the main three steps in Cellular Respiration, which mainly takes place in the mitochondria.
Photophosphoylation
A really long complicated word that really just means making energy with light. Noncyclic vs Cyclic Photophosphorylation Noncyclic
* What normally occurs during photosynthesis.
* Produces a normal amount of ATP
* Can occur forever (theoretically)
* Produces NADPH
Cyclic
* Unnaturally occurs when there is not enough H20
* Produces abnormally high ATP
* Cannot go on forever
* Produces no NADPH
PII and PI
-An excited pigment loses two electrons when it is struck by a photon of sunlight -Chlorophyl breaks open a water molecule to get the two missing electron, thus turning the water molecule into floating hydrogens and oxygens (called Photolysis) -The first 2 electrons bounce down the ETC, fueled by ATP.
-The 2 electrons bounce off the ETC and into the next chlorophyll just as its pigment loses them to the photon again. -These 2 electrons in turn aid ferrodoxin in turning NADP and H into NADPH

### Block 4B

Chemiosmosis is the movement of hydrogen ions through the thylakoid membrane (where the photosystems I &II are located).
Xerophytes:thick epidermis, sunken stomatas, dry habitats
Hydrophytes: stomata on surface, often floating or submerged, moist habitats
Light Energy
Light emission is an important part of photosynthesis. Visible light is a small part of the electromagnetic spectrum. Light travels in waves. A wavelength is the distance from one wave peak to the next one. Light is also made up of packets of energy called photons. A photon's energy is inversely proportional to its wavelength.
When a molecule absorbs on of these photons, one of its electrons become energized, shifting the electron from a lower-energy orbital to one of higher energy that is farther from the nucleus. The electron then either returns to its ground state or leaves the atom to be accepted by and electron acceptor molecule (the latter occurs in photosynthesis).
Chlorophyll
A leaf is made up of a green pigment called chlorophyll, which is also the main pigment of photosynthesis. It absorbs light mostly in the blue and red areas of the visible light spectrum, since most green light that hits the leaves is reflected, giving plant leaves a green appearance. There is more than one type of chlorophyll. Chlorophyll a initiates the light-dependent reactions of photosynthesis. Chlorophyll b is an accessory pigment that absorbs and reflects light in a way that gives it a yellow-green appearance, while chlorophyll a has a more bright-green appearance. The spectrum of light that can provide energy for photosynthesis can be broadened with another accessory pigment called a cartenoid, which can be yellow or orange. Chlorophyll can be excited by light directly by photons or indirectly by energy it receives from these accessory pigments. The absorption of light is often monitored by graph. A pigment's absorption spectrum is a graph of its absorption of light of different wavelengths. The action spectrum shows the effectiveness of certain wavelengths of light. It can be obtained by measuring the rate of photosynthesis at each wavelength for leaf cells or tissues that have been exposed to light of one wavelength (monochromatic).
Photosynthesis takes place in the chloroplast, while respiration takes place in mitochondria. Plants and algae carry out photosynthesis. Respiration occurs in all eukaryotes.
Key Idea to Remember: Oxidation is loss and Reduction is Gain (OIL RIG)
Cellular respiration has three metabolic stages. The first is Glycolysis cycle, is the splitting of sugar and occurs in the cytosol, the fluid between membranes. This process is anaerobic and is at substrate level phosphorylation. It begins with 6C Glucose and becomes 2 (3C) Pyruvate while gaining 2 ATP and 2 NADH, thus is it demonstrating oxidation. The gaining of 2 NADH is the reduction of a co-enzyme. The second stage is the Krebs Cycle occurs in the mitochondria. This stage begins with pyruvate (3C) and decarboxylates (loses CO2) to become 2C Acetyl CoA. Then 4C is added to form 6C intermediatie which decarboxylates into 5C which decarboxylates into 4C which begins the cycle again. There is a link reaction between the 4C oxaloacetate and the 3C pyruvate. This process is also oxidation as it gains NADH, 2 ATP and FADH2. One turn of the Krebs/Citric Cycle yields 2CO2, 3NADH, FADH2, and ATP. The third and final stage is the Electron Transport Chain which occurs in the inner mitochondria membrane and yields 32 ATP. It transports 2 hydrogens and 2 electrons from FADH2 or NADH to molecular oxygen forming water, which eventually makes ATP. Oxygen is the final electron acceptor in the ETC.
The rate of photosynthesis increase as the amount of light increase, until it reaches a certain point then it will stay constant not increasing or decreasing. It will also increase as the rate of Co2 concentration increases, but photosynthesis does not occur at very low Co2 concentrations and will eventually level out at very high concentrations. As the temperature increases the rate of photosynthesis will continue to increase until it reaches its optimum rate, then the rate of photosynthesis will rapidly decline. ALL PLANTS need water and oxygen to survive

## Chemistry
### Block 1B

Water is an important part of the chemistry of all living things as well. Some of the main characteristics of water are as follows:
ELEMENTS
Elements are substances that cannot be broken down into simpler substances. The three most frequently occurring elements found in living systems are carbon = C, oxygen = O$_2$ and hydrogen = H$_2$. Other important elements include nitrogen = N$_2$, phosphorus = P, iron = Fe, calcium = Ca, potassium =K, and magnesium = Mg.

### Block 3B

The three most common elements are carbon, oxygen, and hydrogen. Hydrogen is the most abundant element on earth and carbon is found in all life. Examples of Organic Molecules: Lipids (they have twice the energy of Carbs.)-Monomer=Glycerol/Fatty Acids, Bond= Ester, Uses= cushioning/insulation/energy storage/structure, Examples=Fats/Oils/Waxes Carbohydrates' 'MonomerGlucose or monosaccharide Uses break down of protein, storage of energy, energy Examples: Amylose, sucrose, ribose, glucose..any protein with -ose instead of -ase. Carbohydrates have -ose' Proteins contain carbon, oxygen, hydrogen, sulfur, and other organic elements. Their monomer is amino acid which is written as OHHNRCHCOHH, where R represents a functional group, specific to that protein. Uses include storage, protection, muscles. Are bonded by peptide bonds which form through a linkage of carbon and nitrogen with a byproduct of water.
Redox reactions
Oxidation: When a molecule LOSES an electron. Reduction: When a molecule GAINS an election.
OIL RIG: Oxidation is Loss, reduction is Gain.

### Block 4B

The three most common elements in organic chemistry are Carbon, Hydrogen, and Oxygen.
Other Important Elements
Nitrogen-Used in DNA, proteins, and enzymes.
Calcium-Helps build strong bones, & used in sending nerve impulses.
Phosphorus-Used for ATP.
Iron-Transports oxygen.
Sodium-Keeps a balance of H$_2$0. Also used for nerve impulses and muscle contractions.
ORGANIC MOLECULES
* Carbohydrates
* Proteins
* Lipids
* Nuclei Acids...phosphodiester bonds
Fatty Acid: CH3-CH2-C=O (also branching off from the C on right is an OH by a single bond)
Polar bonds are the result of covalently bonded atoms that have unequal electronegativity. Non-polar bonds are the result of covalently bonded atoms that have equal electronegativity. Water is a polar molecule- one end of the molecule has a partial positive charge and the other end has a partial negative charge.
More Bonding
Covalent bonds: Electrons are shared between atoms so that each atom has a filled valance shell.
Electronegativity measures the attraction of an atom to shared electrons in a bond.
Ionic bonds: Form as a result of the attraction between a cation and an anion.
Hydrogen bonds: Bonds between a partially-charged negative atom and an atom in a hydrogen bond with either oxygen or nitrogen. Can form between two molecules or two parts of one molecule.
Organic molecules: Carbohydrates are used for energy and stored energy. There chemical makeup has a 1:2:1 ratio of carbon to hydrogen. Monomers include glucose and monosaccharides. Proteins are connected by peptide bonds. They are used for structural movements, like muscles. They are also used for transport (hemoglobin), storage, protection, and regulation. Protein’s monomers are amino acids, of which there are twenty. Lipids are insoluble in water. Monomers include glycerol and fatty acids. Ester linkages bond lipids. Lipids are used for insulation, energy storage, cushioning, and have structural purposes (cell membranes). Examples include fats, oils, waxes, carotenoids, phospholipids, and steroids. Nucleic acids store information. RNA is used for transmission. DNA is responsible for expression of genetic information. Nucleic acids are linked by phosphodiester bonds. Nucleic acid monomers are nucleotides, which are composed of a sugar, a phosphate, and a base.

## Evolution
### Block 1B

Lynn Margulis proposed the theory of Endosymbiosis, which provides a possible explanation for the formation of eukaryotic cells. It is believed that mitochondria and chloroplast, which are located in eukaryotic cells today, were once on their own like prokaryotic cells. There is evidence that the two organelles were prokaryotic because mitochondria and chloroplast contain circular DNA just like prokaryotic cells. Also, mitochondria and chloroplast have 70s ribosomes that is similar to the 70s ribosomes of prokaryotic cells. The theory provides the explanation that the prokaryotic cells took in the mitochondria and chloroplast and a symbiotic relationship formed. The prokaryotic cell provided shelter and protection, and the chloroplast made food and the mitochondria broke down the food in order to make energy that the cell could use. Thus, the creation of eukaryotic cells occurred.
MILLER AND UREY
They conducted an experiment which would change the approach of scientific investigation into the origin of life. Miller took molecules which were believed to represent the major components of the early Earth's atmosphere and put them into a closed system. The gases they used were methane (CH4), ammonia (NH3), hydrogen (H2), and water (H2O). Next, he ran a continuous electric current through the system, to simulate lightning storms believed to be common on the early earth. Two percent of the carbon had formed some of the amino acids which are used to make proteins. Perhaps most importantly, Miller's experiment showed that organic compounds such as amino acids, which are essential to cellular life, could be made easily under the conditions that scientists believed to be present on the early earth. This enormous finding inspired a multitude of further experiments.
Human Evolution
-Features that define humans as primates:
digits with nails
eyes in front of the head
five grasping digits with opposable thumb
long, slender limbs that rotate freely at the hips and shoulders
acute hearing
relatively large brain
long life-spans
-Evidence for bipedalism:
curvature of spine provides better weight distribution
foramen magnum is centered in the base of the skull
increase in the length of legs in comparison to the arms
shorter, broader pelvis for attachment to leg muscles
alignment of the big toe with the rest of the toes
-Genus Australopithecus: the immediate ancestors of the genus Homo
Darwin-Wallace Theory of Natural Selection
Evolution is based on four observations about the natural world:
1. Overproduction: each species produces more offspring than will survive
2. Variation: individuals in a population exhibit variation
3. Limits on population growth: environmental factors limit growth, causing a struggle for existence
4. Differential reproductive success: those with the most favorable characteristics are more likely to survive and reproduce
Modern Examples of Evolution
-In response to the widespread use of the Warfarin pesticide, some species of rat have become immune/resistant
-Penicillin resistant strains of bacteria due to the widespread use of the antibiotic
-Some mosquitoes resistant to DDT
-Evolution of Peppered Moth due to predation and changes in environment
Other Theories of How we got here
* Panspermia- The theory that a life form came from another planet, traveling on a comet or asteroid and landed on earth, leading to the evolution to humans

### Block 3B

Miller and Urey’s experiments: What you need to know: •Miller and Urey conduced experiments to test if life could have formed in the primordial soup •They used"
W-ater H-ydrogen A-mmonia M-ethane
•They boiled the water and used electric shocks to simulate the various stages of heating and cooling and lightning that were likely present on early earth’s surface •They produced organic molecules form this experiment, but no life. However, such a find sent a wave through the science community
Exogenesis (sick word), but more commonly known as panspermia, originates as far back as the Greek philosopher Anaxagoras (sweet name). The actual theory of panspermia speculates that life came to earth from another planet, perhaps being carried by a meteorite that crashed here. This theory solves the time gap that we currently have in our evolution chart, but it only moves the problem to another planet, so it really doesn't solve anything.
The Darwin-Wallace Theory of Evolution has four key points. The first is that individuals in a population exhibit variation. Next is overproduction, the reproductive abilities of a species causes an increase (geometric) over time. Then, there are limits on population growth caused by things such as; food, water, light, growing space, and other resources. Lastly, the individuals that have the most favorable traits and adaptations are more likely to survive and reproduce (differential reproductive success).
Natural Selection
Natural Selection is the principle that nature tends to favor organisms with certain traits. These organisms therefore have a greater chance of survival in that environment than other organisms without the trait. This gives the organisms with the trait a significant advantage in the environment. Because it has a greater chance of survival, and organism with the trait is less likely to die young and has a greater chance of reproducing early and often to spread its genes. It then can pass on this beneficial trait, allowing the trait to proliferate throughout the species. In this way, natural selection favors organisms with certain traits, giving them a greater chance to survive and pass on these traits so that more of the population can survive using this favorable trait.

### Block 4B

Modern examples of evolution include: peppered moth, DDT resistance in some mosquitoes, penicillin resistant strains of bacteria as a result of the widespread use of the antibiotic and a warfarin strains of rat in response to the widespread use of the pesticide.
Evolution is the change in a populations overall traits and usually refers to the genes passed on from generation to generation. Evolution is used to map out the growth of a population as well as the mutations that affect/ change it. Natural selection is one way of causing a population to evolve and natural selection means that heritable traits that are more helpful to survival are the ones most likely to be passed on from generation to generation
Evolution as a theory was first developed by Darwin and Wallace. Before that, there was the Lamarckian theory which stated that traits acquired during a lifetime would be passed on to the next generation.
Some reasons why it is believed that Humans evolved from Primates: -5 Digit Hands...Pentadactyl -Grasping Ability -Erectness -Stereoscopic Vision
Recombination and assortment allow for variation (and mutations) in a population.
Miller and Urey simulated the conditions on pre-biotic Earth in order to test for chemical evolution. They sealed Water, Hydrogen, Ammonia, and Methane in a flask (WHAM) in order to model the conditions. Electrodes were used to simulate lightning.
Humans have evolved from mammal-like reptiles that existed over 200 million years ago. Early humans were classified under the genus Australopithecus. The species include: afaransis, africanus, and robustus. Next came the genus Homo. Species include: habilis, erectus, neanderthalensis and sapiens. Current humans are classified as Homo sapien sapiens.
Okay Panspermia basically rules because it says life may have come from another planet. If you watch Star Trek there was an episode discussing this. It also linked several species such as Andorians, Klingons, Vulcans, Romulans, and most importantly humans to a common ancestor from another planet.
Other then Panspermia and evolution, another theory that is used to explain evolution is creationism. This describes how God created the Earth and everything that surrounds it. Another theory that describes evolution is the theory of intelligent design. This talks about some higher being created everything on Earth and is guiding them through their existence.
Endosymbiosis is the theory proposed by Lynn Margulis which suggests that eukaryotic cells evolved from prokaryotic cells.
Okay basically endosymbiosis states that a prokaryotic cell consumed other prokaryotic cells, in this case mitochondria and chloroplasts. They grew to have a symbiotic relationship and eventually went on live together in peace. The reason this is believed to be true is because mitochondria and chloroplasts have their own DNA.
Darwinism
Adaptation: An evolutionary modification that increases the likelihood of survival and successful reproduction.
Natural Selection: Organisms that are better adapted have a greater chance of being able to survive and bring forth the next generation.
Charles Darwin - Darwin believed that the Earth was very old and its form had transformed over a period of time. Artificial selection supposedly could allow breeders to choose traits that they liked. Darwin used this process to explain a similar process that occurs in nature.
Alfred Wallace – Sent Darwin a published paper of his ideas, which were quite similar to those of Darwin himself. Thus, the Darwin-Wallace Theory of Evolution was born, this theory held that four key aspects of life lead to evolution: population variation, overproduction, limits on population growth, and differential reproductive success.
Thomas Malthus - Wrote An Essay on the Principle of Population as It Affects the Future Improvement of Society. In it, he stated that growth in a population is not always desirable. Populations can increase exponentially, while the population's food supply can only increase arithmetically. Because of this problem between food supply and population, famine, disease and war can occur, halting population growth.
Evidence for Evolution: - Geological Distribution of living organisms - Fossilization- radioactive dating - Biochemical evidence: the universality of DNA and protein structures - Embryo evidence because all embryos look alike in the early stage of development - Pentadactyl limb

## Classification/Ecology
### Block 1B

Classification is pretty much the single greatest thing since sliced bread. Maybe even before sliced bread. It allows organisms to be grouped together based on their similar characteristics. There are a lot of organisms, so this is important. This variety of organisms (and their ecosystems!) is known as biological diversity. The study of said diversity is systematics. Classifying and naming organisms is known as taxonomy. We use a binomial nomenclature when referring to organisms. The binomial nomenclature was designed by Carolus Linnaeus and consists of an organisms genus and species. Both words have Latin roots.
In case you were wondering, the system of classification is as follows: kingdom phylum class order family genus species
A species is: A potentially interbreeding population. Remember, the offspring must also be able to reproduce. A population is a group of the same species. A community is a group of populations, cohabitating. This habitat is known as the ecosystem. A group of ecosystems makes up a biome (think temperate forest, or tundra!) The entire world, and/or all the biomes and life and everything, makes up the biosphere.
PLANTS
There are four major groups of plants:
Bryophytes
- Non vascular
- Dominant Gametophyte generation
- Seedless plants
- Small, require moist environment, reproduce by spores
- mosses, liverworst
Filicinophytes
- Vascular
- Dominant Sporophyte generation
- Seedless plants
- Reproduced by Spores
- Ferns, Horsetails
Coniferophytes
- Vascular
- Dominant Sporophyte Generation
- Seed plants (naked seeds)
- reproduce by seeds
- Conifers, Cycads, Ginkgoes
Angiospermophytes
- Vascular
- Dominant sporophyte gen
- Seed plants (seeds encased in fruit)
- Reproduce by seeds
- Flowering plants, monocots, dicots

### Block 3B

Classification System
A classification system is something that helps scientists to organize animals, plants, and other life into categories so that we can see similarities and differences.
Our modern classification system consists of:
* Kingdom
* Phylum
* Class
* Order
* Family
* Genus
* Species
Binomial Nomenclature
This is the specific system of naming in which scientists derive names of organisms with respect to their Genus and Species. For instance, humans are classified as Home (Genus) Sapiens (Species). This allows for a continuity and common ground for naming organisms throughout science, facilitating research and building a foundation for further study into biology.
Plants can be categorised into several different groups: 1. Bryophtyes- Non-vascular seedless plants that are small and require moist environments. Such examples are mosses and liverworts and their dominant generation is the gameophyte. 2. Tracheophtyes which are broken down further into --> a.) Filicinophtyes- Vascular seedless plants that reproduce by spores. The dominant generation id the sporophtye and examples are ferns and horsetails. b.) Coniferophtyes- Vascular seed plants (naked seeds) that also reproduce by spores. Examples are conifer and ginkgo tree and the dominant generation is the sporophtye. c.)Angiospermophtyes- Vascular seed plants (encased in fruit) that reproduce by spores. The dominant generation is also sporophtye and examples are monocots and dicots.
Plants
Bryophytes -nonvascular -Dominant Gametophyte generation -seedless -small -thrives in moist environments -reproduce by spores -E.x.: mosses (hornwarts etc)
Filicernophytes -vascular -Dominant Spor. generation -seedless -reproduce by spores
Coniferophytes
-vascular -Dom. Spor. Gen. -seeds (but naked seeds) -E.x. COnfers (ginkoes, Cyands...)
Angiosperophytes -vascular -Dom. Spor. Gen. -have seeds, in fruit -reproduce by seeds -e.x. Flowering plants (daffodils, roses, monocots, dicots)

### Block 4B

Classification is how scientists group different organisms and their species. They can be determined through different methods.
This is how a regular classification system works:
Kingdom=> Phylum=> Class=> Order=> Family=> Genus=> Species
A way to remember this is Kings Play Cards On Fat Green Stools
FOR HUMANS: Animalia, Chordata, Mammalia, Primate, Homindae, Home, Sapien, Cro-Magnon/ Sapien
Species-a particular kind of organism; members possess similar anatomic characteristics and have the ability to interbreed and produce fertile offspring.
There are four main groups of plants. Filicinophytes, Coniferophytes, and Angiospermophytes are grouped together under a larger set called Tracheophytes. Bryophytes and Filicinophytes reproduce by spores, while Coniferophytes and Angiospermophytes reproduce by seeds. The seeds in Angiospermophytes are encased in fruit, while Coniferophytes have naked seeds. Examples: Bryophytes- moss, liverworts, hornworts; Filicinophytes- ferns, club mosses, horsetails; Coniferophytes- conifers, cycads, ginkgoes; Angiospermophytes- flowering plants, monocots, dicots.
Plants and the Cell
Plants show Alteration of Generation in which they spend some of their lives in a haploid stage, and another part in a diploid stage. In the gametophye generation, the haploid stage leads to gametes through mitosis, while meiosis is used in the sporophyte generation, where the diploid state leads to haploid spores. Gametophytes produce a small gametangia called antheridia (the female version is called archegonia). The zygote forms when an egg and sperm cell unite. The first stage in the sporophyte generation, the newly-formed diploid zygote, divides by mitosis and becomes a young, multicellular sporophyte plant. Once it matures, it gains special cells that divide using meiosis to form haploid cells known as spores. These spores divide by mitosis, producing a multicellular gametophyte, thus restarting the cycle.
Seed Germination- 1. Imbibition- Seed absorbs water 2. Embryo releases Gibberellic Acid (GA) 3. GA triggers the alueron layer to release amylase 4. Amylase digests amylose into maltose 5. Maltose is used by embryo to grow
Every seed needs water and oxygen to grow. Other things that might be necessary include: Light, digestion by mammals or birds, bacterial digestion, and/or fire.
There are many different parts of a seed. The first one that people meet is the testa (seed coat), then there is the aleurone layer. Because the embryo has to go through these two layers that is why germination takes so long. Then in the seed is the cotyledon and the embryo. The embryo is made of the embryonic shoot and the embryonic root.
Binomial nomenclature is the formal system of naming species. It involves names for the genus, then the species. The name for the genus is always capitalized, but the species name is lower case. Both names are italicised however. For example: Passer domesticus
Biological Organization: Organism, Population, Community, Ecosystem, Biome, Biosphere