3.B.2 

      In gene regulation, the regulatory genes control to transcription of genes. Operons will be the main area of gene regulation in DNA. Repressors will bind to the operator region to prevent transcription. Promoters will begin transcription with the use of inducers all the way to the terminator. Activators will begin transcription in the enhancer region. The trip operon codes for a tryptophan, a amino acid. When there is too much tryptophan in the cell, the operon will become a repressible operon The Lac operon allows RNA polymerase by becoming a inducible operon. Eukaryotes use transcription factors to regulate genes.

      Gene regulation is involved in a number of cells with signal transmission. Cytokine signal for when cyclin must be produced during the cell cycle. In Seed germination, gibberellin signals seedling. Morphogens assist in appoint stem cells into different cell types. The P53 gene can cause disruptions in cell division if mutated or damaged. 

3.A

3.A DNA, RNA and Genetics 

3.A.1

1. James Watson and Francis Crick used Muric Wilkins and Rosalind Franklin's crystallography data and X-Ray diffraction to create the first DNA model. 
2. The Avery, McLeod, and McCarthy experiments were based off of Fredrick Griffiths discovery of a transforming factor in bacteria. What these scientist did was that they provided further evidence by disproving that RNA and protein was not the transforming factor 
3. The Hershey and Chase Experiments used phage which injected DNA into a cell. In the first part of the experiment they put the phage with radioactive amino acids, but the DNA was remained the same. When the phage injected the DNA, the phage that were produced were not radioactive. In the second part of the experiment, the DNA was radioactive and what they found was the DNA, not protein is what carries genetic information.
4. Genetic information is stored and carried through DNA and in some cases RNA.
5.  Noneukaryotic organisms have circular chromosomes while eukaryotic organism have multiple linear chromosomes 
6. A plasmid is a small extra chromosomal double stranded circular DNA molecule.
7. DNA Replication, 

1.  

• Replication: Initiation See above, binds to the promoter region and helps with the transcription factors 
• The transcription factors bind to a region within the promoter called the TATA box 
• RNA polymerase binds to the promoter, forming an initiation complex.

• A regulator protein can sometimes bind just upstream from the promoter in the regulator region, activating the initiation complex.
• Activators proteins bind the the enchanter region 
• Transcription begins 

• Elongation: 
• The RNA polymerase continues to move down the DNA while it continues to untwist the helix and exposes the DNA bases to pair with RNA nucleotides 
• RNA polymerase reads DNA in 3>5 while mRNA is assembled in the 5>3 direction 

f

Termination: the mRNA transcript is released when polymerase reaches the termination site. 

Translation: Occurs in the Ribosome, RNA synthesis of a polypeptide (protein)

• The first site enters the ribosome at the P site to initiate translation 
• Another tRNA brings the next amino acid into the A site of the ribosome.
• A peptide bond forms between the two amino acids. the tRNA then removes the A site to P site and ribosome moves over one codon.

Translation: Elongation

• Amino Acids are added one by one to the preceding amino acid chain
• The amino acid is transferred to the growing peptide chain
• The process continues along until the mRNA until a stop codon is reached

1. Retroviruses is a special case and has an alternate flow of information, instead viral genome RNA into DNA. 
2. DNA and RNA both contain three components sugar, phosphate and nitrogenous base. Differences between the two is that DNA contain deoxyribose while RNA contains ribose, RNA also contains uracil in lieu of thymine in DNA. DNA is also double stranded while RNA is single stranded.
3. In Prokaryotes, Since they do not contain a nucleus, the whole process of translation occurs inside of the cell instantaneously.
4. mRNA when it leaves the nucleus, it is tagged by proteins that directed towards the cytoplasm and into the cytoplasms.
5. There are many ways that DNA can be manipulated for human usage including electrophoresis, plasmid based transformation, restriction enzyme analysis and polymerase chain reaction In electrophoresis, electric currents separate DNA fragment that have been cut by restriction enzyme. Restriction enzymes cut DNA at specific nucleotide sequences called restriction sites. Different sizes will move at different speeds through the gel, the smaller fragments will go farther hill the larger ones will stay by the DNA start period. Then DNA fragments can be compared using markers, DNA fragments of known sizes. Plasmid based Transformation is when a cell is altered using foreign DNA.  Cell can be altered to be made into antibiotics and other commercial uses.  Restriction enzyme analysis of DNA is using DNA electrophoresis to identify patterns. Polymerase Chain Reaction (PCR) is a technique to amplify quantities of DNA. PCR uses a thermocycler which can make billions of copies of DNA.
6. Genetically modified foods (GMOs) were commercially began selling in 1994. GM food have been engineered for faster growth, resistance to pathogens, production of extra nutrients and other purposes Transgenic animals are animals that have foreign DNA incorporated into their genome. Mice are used to express human diseases for medical research, products such as insulin and possibly human.  Cloned animals is when scientists use nuclear transplantation and put the nucleus of an unfertilized egg cell and replace it with a nucleus of a differentiated cell.  Pharmaceuticals are used to Recombinant DNA technology to modify E.coli bacteria to produce human insulin and Factor X

3.A.2

1. The first step of Interphase which has period of growth, synthesis of DNA and preparation of mitosis (G1,S,G2 and M) G1 is when the cell grows and functions normally, S is DNA replication and G2 is when the cell continues to grow for mitosis.
2. The checkpoints in the cell cycle are G1, G2, and M. G1 decides whether the cell divides, deals devision or enter a resting stage (G0). The G2 checkpoint determines if the DNA has been replicated and decides if the cell is ready for mitosis. The M checkpoint determines if the chromosomes are alined correctly at metaphase. 
3. The purpose of the Mitosis Promoting Factor (MPF) is a to allow the cell to go to different levels of mitosis once enough MPF has  accumulated in the body. 
4. The platelet derived growth factor (PDGF) is a protein in the cell cycle that binds to a PDGF receptor and activates it. The PDGF is a receptor tyrosine kinase.
5. Cancer occurs in a cell from disruptions in the cell cycle control.
6. Cyclin during interphase accumulates during the cell and cyclin will bind to CaK to form the MPF, when there is enough MPF, G2 ends and mitosis begins. The MPF will then degrade the cyclin and the process repeats
7. The relationship between mitosis and interphase is that a cell is usually in interphase for 95% of its life growing and preparing for mitosis which is where the actual cell division occurs and accumulates 5% of cell life.
8. The key points of mitosis is  prophase, metaphase, anaphase, tele-phase and cytokenesis . In prophase, the nucleus breaks down into chromosomes centriols and other materials. Metaphase is when the chromosomes begin to line up in the middle of the cell. Anaphase is when the centriols and spindle fibers on the opposite side of the cell split apart the cell. Telephase is when the two cells begin to form. And finally cytokenesis is when there are two cells.
9. Meiosis consists of Meiosis, PMAT one, Meiosis 2 and PMAT 2. Everything in the cell occurs just like it would in mitosis EXCEPT in prophase 1, the homologous chromosomes cross over with each other and exchange a piece of their chromosome. Once the end of Meiosis 1 has occurred you have 2 haploid cells (1n). And the PMAT 2 creates 4 (1n) cells.
10. Meiosis creates genetic variation because during meiosis chromatids exchange genetic material via crossing over and creates a cell that is different from the two diploid cells.

3.A.3 

1.  The addition rule however involves the punette square and you add up the amount of genotypes each variation can produce.
2. The law of segregation states that allele pairs separate or segregate during gamete formation
3. The law of Independent assortment states that allele pairs separate independently during the gamete formation 
4. These laws both result in genetic variation because if the two allele pairs separate and then separate independently, then the gamete formed has alleles from both parents and create a new variation of genes.
5. A example of a genetic disorder is Huntington disease. This  is the result of the autosomal dominant disorder that causes degeneration of the nervous system.
6. A example of a chromosomal disorder is Down syndrome. Down syndrome is the result of the Trisomy 21 chromosome having nondisjunction.
7.  Nondisjunction is  when the chromosomes do not separate correctly during meiosis and result in genetic and chromosomal disorders.
8. There are ethical, social and medical issues surround human genetic disorders because people may not believe in knowing what your genetic disorders are. Socially, people may discriminate you due to you have something wrong with your genetics. And the medical issues surrounding human disorders is that it is very expensive and time consuming to help these people who have these genetic disorders.

3.A.4

1. Mendels law do not apply to all traits because these genes (patterns of inheritance) do not follow mendel's laws
2. Sex linked traits are traits that are on sex chromosomes and they can effect males more because Y chromosomes carry little genetic information and males only have on X gene.
3. Nonnuclear inheritance are traits that are not found in the nucleus. Plants have Chloroplast and animals have mitochondria and these traits are determined by cpDNA and mtDNA 

2.D.4

Essential knowledge 2.D.1: All biological systems from cells and organisms to

populations, communities and ecosystems are affected by complex biotic and abiotic interactions involving exchange of matter and free energy.

1.Provide examples of how biotic and abiotic factors affect organism behavior,

community interactions, and ecosystem structure. Utilize the following examples

in your responses:

○ Water availability

If there is not enough water in a environment (abiotic), then the organisms living there will die.

○ Sunlight

Plants (biotic) that receive little to no sunlight (abiotic) will die because they cannot undergo photosynthesis. 

○ Symbiosis (mutualism, commensalism, parasitism)

Symbiosis; Clown fish are protected by the anemone.

Mutualism: Bees pollinating a plant, both benefit

Commensalism: Barnacles living on a whale, one is benefiting but neither hurts the other.

Parasitism: Tapeworms living inside of a human, the parasite ( tapeworm) is receiving nourishment from the host.

○ Predator–prey relationships

A mongoose eating a snake is a example of a predator-prey relationship.

○ Water and nutrient availability, temperature, salinity, pH

If there is low resources and water (abiotic), then organisms in a environment will die

○ Availability of nesting materials and sites

If birds want to nest on a cliff (biotic), the geography (abiotic) may not be large enough to support all of the birds.

○ Food chains and food webs

If wolves were moved from a ecosystem, then the populations of the surrounding organisms like beavers, foxes, and trees would decrease or increase dramatically

○ Species diversity

In a diverse ecosystem, if you remove a species from a environment, then populations of other species will be greatly effected.

○ Population density

If there are is a large amount of fish in a small lake, then the fish will have to compete with the other fish for the limited resources.

○ Algal blooms

In the St. Johns river, the water is warm and the sunlight is abundant and causes alga to boom and massive fish die off during the night because there is not enough of water of oxygen

Essential knowledge 2.D.2: Homeostatic mechanisms reflect both common

ancestry and divergence due to adaptation in different environments.

1.     How do homeostatic mechanisms relate to evolution?

Homeostatic mechanisms relate to evolution because they reflect a common ancestry in all organisms

2. How is the concept of common ancestry supposed by continuity in homeostatic

mechanisms.

The concept of common ancestry is supported by continuity in homeostatic mechanisms because every organism has a response but they have different responses to different environmental conditions

2.     How do changes in environmental conditions affect this continuity.

Changes in a environmental condition affects continuity by how a organism responds to that condition

4. Explain how the following mechanisms are used for obtaining nutrients and eliminating wastes.

 

Flatworm excretory system

Stomata

○ Gas exchange in aquatic and terrestrial plants

Both aquatic and terrestrial plants both use gas exchange by diffusion however both of them have a different way of acquiring water. In terrestrial plants get water through openings called stomata, while aquatic plants exchange gas through direct diffusion in surrounding water.

○ Digestive mechanisms in animals such as food vacuoles, gastrovascular cavities, one-way digestive systems

Protists take food in through phagocytosis and store the food in a food vacuole. In a gastro vascular system, there is one opening that take nutrients and gases from the environment. A one-way digestive system there is one opening for food and another opening for waste.

○ Respiratory systems of aquatic and terrestrial animals

Lungs

In aquatic animals, gills are used to filter water and for the animal to get oxygen. In land animals, oxygen enters the body through tubes in insets, vertebrates have internal lungs and mammals and amphibians use positive pressure breathing to force air down the trachea.

○ Nitrogenous waste production and elimination in aquatic and terrestrial animals

All organisms produce and eliminate waste in aquatic and terrestrial animals.

5. Explain how homeostatic control systems in species of microbes, plants an animals support common ancestry. Use the following to help illustrate your explanation:

○ Excretory systems in flatworms, earthworms and vertebrates

Flat worms regulate the excretory system by protonephridia. They are branching canals that allow waste out of their body. Earth worms go through metanephridia to release toxic urea. Vertebrates use kidneys to release waste.  Shows that all organisms release waste

○ Osmoregulation in bacteria, fish and protists

Osmoregulation shows that all organisms go through this process.

○ Osmoregulation in aquatic and terrestrial plants

Both plants and animals have openings to balance gas

○ Circulatory systems in fish, amphibians and mammals

All organisms need to transport nutrients through blood to all their cells

○ Thermoregulation in aquatic and terrestrial animals (countercurrent exchange)

All organisms need a flow to keep homeostasis in their body

Essential knowledge 2.D.3: Biological systems are affected by disruptions to their dynamic homeostasis.

1. How do disruptions at the molecular and cellular levels affect the health of the organism? Use the following to explain your answer:

○ Physiological responses to toxic substances

Organisms that are expose to toxins in food, water, or in the air can be affected by causing cancer in organisms and can threaten wildlife.

○ Dehydration

If a organism undergoes dehydration, the organism can experience darker urine, respiration increase, delirium and then death.

○ Immunological responses to pathogens, toxins and allergens

If a organism is not able to fight off an infection, such as a person having HIV, then any pathogen can invade the body and the body will not respond to the pathogen.

2. Provide examples of how disruptions to ecosystems can affect the dynamics of the  ecosystem. Utilize the following examples in your responses:

● Invasive and/or eruptive species

An invasive species can cause other species in the environment to start to compete with aggressive species for resources

● Human impact

Farmland can reduce biological activity

● Hurricanes, floods, earthquakes, volcanoes, fires

Natural disasters can disrupt a ecosystem by killing trees, organisms, and reducing resources in a ecosystem

● Water limitation

Limited water will cause organisms to compete with each other and can cause death to those that aren’t fit enough.

● Salination

If a soil does not have a proper amount of nutrients, then plants will grow slowly or will not be able to live in that environment

Essential knowledge 2.D.4: Plants and animals have a variety of chemical

defenses against infections that affect dynamic homeostasis.

1.     Explain how plants, invertebrates and vertebrates have multiple, nonspecific (innate) immune responses. Include how they work and structures/chemicals involved.

Invertebrates use their exoskeleton and the digestive system to fight off pathogens. Hemocytes are found in hemolymh of insects. They engulf pathogens through phagocytosis. Plants use PRRs that detect microorganism associated molecular patterns (MAMPs). Once the PRRs have detected MAMPS they will begin systemic acquired resistance and destroy infect and adjacent cells. Vertebrates have multiple types of non-specific responses such as skin, mucus and lysozymes. These responses stop pathogens from entering the body and lysozymes.

2. Describe mammalian specific immune responses.

• Describe the two types of specific responses in the Mammalian

immune system

• In the cell-mediated response, what is the role of cytotoxic T cells?

• In the humoral response, what is the role of B cells?

In cell mediated response cytoxic T cells attach to a pathogen and turn into a killer T cell, which will kill the pathogen. In the humoral response, B cells create antibodies to shut down a pathogen so a macrophage could digest it.

3. Explain how antigens and antibodies work together.

• What is an antibody?

• How does a second exposure to an antigen differ from the primary exposure?

An antibody is Y shaped protein that identifies and neutralizes pathogens.  If a person was exposed to the antigen a second time, Memory cells would know what the specific antigen is an will be able to clone B and T cells much faster than in a primary exposure

2.C.2

Feedback mechanisms

2.C.1 – Organisms use feedback mechanisms to maintain their internal environments and respond to external environmental changes.

·      Discuss how negative feedback works. Discuss the following two examples – Thermoregulation in animals and plant responses to water limitations.

Negative feedback is a mechanism that maintains dynamic homeostasis by returning a changed condition set to its target set point. ­­­­­­An example of negative feedback is thermoregulation in animals. The central thermo receptors in your body respond to a change in your body temperature by either releasing sweat to reduces heat in your body, or shiver and your skin will get goose bumps to contain heat and produce heat to bring your body temp to its set point. Another example in plants is its responses to water limitation. If a plant has a low supply of H20 in in its system it can create a acid that will close the stomata so little water is lost.

·      Discuss how positive feedback works. Discuss the following three examples – lactation in mammals, onset of labor in childbirth, and ripening of fruit.

Positive feedback is a mechanism that amplifies  responses. Three examples of positive feedbacks are lactation in mammals, onset of labor in childbirth, and ripening of fruit. In lactation, sucking stimulates cause nerves to tell the hypothalamus to create Oxytocin which in term creates milk. In childbirth, the head of the baby is presses against the cervix and causes nerve impulses to stimulate a pituitary glad to secrete oxytocin and causes the uterine to contact to push the baby out towards the cervix. When fruit is ripe. A chemical called ethylene is produced by the fruit, which acts as a chain reaction towards other fruit and makes them produce ethylene

·      Discuss how an alteration in the mechanism of feedback can result in dire consequences by using the following three examples: diabetes mellitus in response to decreased insulin, dehydration in response to decreased antidiuretic hormone and Grave’s disease.

Diabetes mellitus is a example of an alteration in a feedback mechanism because in type 1 diabetes, the pancreas is unable to create insulin and results in high blood sugar if not monitored due to a autoimmune disease to insulin. Type 2 diabetes is a alteration in a feedback caused by an unhealthy diet and also results in cells not producing insulin because the cell producing insulin stop production. Some people are unable to produce the hormone, antidiuretic and one of the side effects is grave disease. Grave disease is the result of no antidiuretic hormone and causes a persons eyes to hyperthyroid.

2.C.2 – Organisms respond to changes in their external environments.

·      Discuss how organism respond to changes in their environment by using the following examples:

o   Photoperiodism and phototropism

Photoperiodism is a physical response in plants that results in flowering. The photoperiod of the plant, which is the length of night and day so the plant knows what time of year it is. Is regulated by a phytochrome. A phytochrome is ultimately that makes a plant flower. 

o   Hibernation and migration in animals

Hibernation and migration are both results of a change in conditions. Hibernation is a state of inactivity endotherms go through to slow down metabolic rate and to survive cold and harsh winters. Animals that do not hibernate go on migration, which is a long distance movement of individuals on a seasonal basis.

o   Taxis and kinesis in animals

A taxi is a automatic movement towards or away from a stimulus. A animal will move closer or away from a stimulus . Kinesis is a simple nondirection change in activity or turning rate in response to a stimulus. This cause animal to run in a frenzy in response to something in its environment.

o   Chemotaxis in bacteria, sexual reproduction in fungi

Chemotaxis is a process in bacteria where they can detect food or poison and will move away or to the stimulus. For fungi to reproduce, pheromones are released as a social response to members of the same species to produces gametes.

o   Nocturnal and diurnal activity: circadian rhythms

Circadian rhythm is the biological clock that both plants and animals activity. Bats are nocturnal because they are inactive during the day and their circadian rhythm allows them to wake up for the night. In humans, the average person is designed to sleep during the night and be active during the day, people also can feel tired right after they wake up and they are in the middle of their circadian rhythm.

o   Shivering and sweating in humans

Your body respond to a change in your body temperature by either releasing sweat to reduces heat in your body, or shiver and your skin will get goose bumps to contain heat and produce heat to bring your body temp to its set point