Notes and Study Guides

Vaccine Views:

Video #1:

The purpose of this video is primarily to explain the differences between the Sabin (live) and Salk (killed) versions of the Polio vaccinations and how they represent the benefits of vaccinations as a whole. To really emphasize the advantages of vaccinations like these, the producer presents significantly more advantages compared to disadvantages. The disadvantages are still included to make it seem like the video is unbiased, but the author uses the imbalance to make the advantages appear to outway the disadvantages. Also, when discussing the risk factor of the vaccines the producer reiterated several times that the risk was extremely low, thereby dimming down the risk at all. Finally, the producer also tries to explain that the vaccines are beneficial by beginning the video talking about them positively, using an enthusiastic tone and discussing how they are a medical miracle.

Video #2:

1. What diseases do vaccines prevent?
• Vaccines prevent many dangerous diseases such as polio, whooping cough, and chicken pox.
2. What is herd immunity? 
• Herd immunity occurs when a large amount of individuals in a population are immune to a contagious disease, preventing a spread of the disease.
3. What does it mean to be immunocompromised? 
• To be immunocompromised means that an individual’s immune system is not working properly, keeping it from fighting pathogens and infectious diseases.
4. What kind of people would be considered immunocompromised? 
• Babies could be considered immunocompromised, as they have not been able to build up their innate immune system yet. Patients undergoing radiation or chemotherapy might also be immunocompromised, as their immune system is working overdrive to fight the chemicals. Older people and pregnant woman also do not have as strong immune systems, classifying them sometimes as immunocompromised.
5. How does herd immunity help people who are immunocompromised? 
• If someone who was immunocompromised received a contagious disease, they would be unlikely to beat the virus. Herd immunity could prevent them from ever receiving the disease.
6. What does it mean to “exempt vaccines”?
• To exempt vaccines is to not take vaccines that are required by law.
7. What two ways can parents “exempt vaccines”?
• If a child has a medical reason that may cause the vaccine to work incorrectly or pose a threat to their health, parents may get an exemption from their doctor. For a nonmedical reason or religious reason, parents need to take an online module and get a certificate for their exemption.

The purpose of this video was to show what we have been saved from with the invention of vaccines. The infectious diseases that we are spared from dealing with are life-threatening, and the video explains that we are incredibly fortunate to have vaccines to prevent them. One use of rhetoric involved the tone, as it was somber with soft yet intense music. This helped portray the gravity of the diseases to help prove their point. Video footage was used as well, with children being shown since it draws more compassion and sadness out of the viewers. No one wants to see a child suffering of a deadly disease. Finally, the grave faces of the medical students watching created an even more intense, and mournful environment. This sad environment made viewers empathize for the people who had to go throw chicken pox or the whooping cough, and feel grateful that them and the people they know do not have to, thanks to vaccines.

Video #3:

(only watched first 16 minutes)

1. What is the theory behind vaccines?
• To introduce the body to something that causes diseases, in order to prime it for when the virus comes.
2. What is the stigma around a person who questions vaccines?
• Someone who questions vaccines is automatically seem as anti-vaccine, although it might not always be black and white. Specifically those who questions vaccines are seen as crazy and illogical. 
3. What is “informed consent”?
• When a doctor tells patients beforehand all the potential advantages and disadvantages to a procedure.
4. Do doctors give “informed consent” to patients on vaccines?
• Most doctors do not, as they have not done the proper research nor have to time to explain everything.Plus, it is not legally required for informed consent to be provided.
5. Who controls vaccine laws?
• Vaccine laws are state laws.
6. What is California’s vaccine law? (Not mentioned in video, please Google it.)
• Children who do not receive the required vaccines are not allowed to go to school.
7. How much knowledge do doctors receive about vaccines in medical school?
• Vaccines disadvantages are not discussed very much in medical school, but only really what they are supposed to do. Nothing about what is within the vaccines and what they can potentially do is taught.

The producer of this video uses rhetoric by stating right away that they are not biased for vaccines or against them, but rather want to look at what is safest for our population. This makes them seem like “good guys” who are not going to press their opinion (though they likely are), but rather state the facts. Strangely enough, this makes viewers more susceptible to believing their perspectives. To solidify their arguments, the producer brought in reliable sources in the form of doctors and members of large organizations. Their accounts compliment each others, and what the video is trying to get across. Also, like in the previous video, and intense sort of music is used in the background that creates a tone screaming evidence and investigation.

Summary Questions:

1. What is the “vaccine war”? 
• The vaccine war involves the debate whether or not vaccines should be taken to fight infectious diseases, and the issues that come with it regarding informed consent and exemptions.
2. How has media shaped the “vaccine war”?
• As with all debatable issues, media allows individuals to share their opinions on the problem and sometimes press their opinions onto others using forms of rhetoric. 
3. How has researching vaccine ingredients, learning about the immune system, and watching three videos with separate agendas helped you?
• I agree with what was said in the last video about how most people are not pro-vaccines nor anti-vaccines. I personally think that vaccines spare us a lot of harm against life-threatening diseases, and I support it in that sense. However, I think informed consent is necessary, as also discussed in the last video, and I believe people should be given options most of the time. Furthermore, there needs to be more information about it available to the public, as finding what was inside the vaccines should not have been as difficult as it was for us.

____________________________________

Immune System Sketchnote: 

The below sketchnote focuses on the aquired immune system, consisting of T-cells and B-cells which work together to target specific pathogens.

_________________________________________________

Role of Phagocytes in Innate or Nonspecific Immunity:

youtu.be/O1N2rENXq_Y

• The whole point of the immune system is to keep bad things out of the body and to kill them if they come in such as:
• Pathogens: dangerous proteins, viruses, bacteria, parasites, and fungi
• Two lines of defense in the body
• Nonspecific/Innate immunity means that the defenses respond to any pathogens, not a specific virus or only a particular bacteria
• Inn
• First line of defense (keeping things out) - nonspecific/innate immunity
• Skin
• Mucus membranes
• Acidic environments like stomach acid
• Digestive tract is really like the outside of you
• Second line of defense (inside the body) - nonspecific/innate immunity
• Inflammatory response - blood, pus flowing to the site where the pathogen is
• Phagocytes
• Phagocytes
•  = a class of cells that can eat pathogens
• Nonspecific
• Bonds with foreign molecules, which triggers a reciptor, causing the phagocyte to wrap around the pathogen and consume it
• After it is fully engulfed, the phagocyte surrounding the pathogen is called the phagosome
• Lysozymes within the phagosome merge with the pathogen once completely engulfed, and break it up (digesting it)
• Phagocyte takes some of the broken down proteins (peptide chain) and attatch them to some other proteins which is called a major histocompatibility complex
• Bonds the major histocompatibility complex combined with the peptide chain to its surface to present it to others that attack specific pathogens, so they know to watch out for them, essentially
• Phagocytes are therefore also called antigen presenting cells
• Antigen
• A protein or a peptide chain that will trigger or that can be dealt with within the immune system
• Different types of phagocytes:
• Neutrophils (most common phagocytes): fast and numerous
• Macrophages: the most versitile (do the heavy lifting)
• Dendritic cells: the best activators of the specific immune system

SEE LAB "OUR BODIES' DEFENSES" UNDER LABS

_________________________________________________

In an activity called "viral tag", viruses tried to
infect the cells by taggin them.

What is a Virus?

• Pretty much all life has some kind of virus designed specifically to infect it
• Viruses = super tiny even in comparison to bacteria
• Not living, but a complex collection of organic matter that can self-replicate
• Consist of a shell made of protein
• Either RNA or DNA are located inside the shell
• Have enzymes for replication and manipulation of their genetic materials
• A virus's genome is a single or double strand of genetic information which allows it to replicate itself
• Viruses need to use cells as a host to replicate
• Virus uses outer protein coat covered in small molecular receptors to join itself to the membrane of a cell, then it forces the cell to admit the virus inside or accept the genetic material
• Virus integrates itself into the DNA the cell is replicating, forcing the cell to create viral protein cells and making copies of the virus
• The new viruses eventually burst from the cell and carry on to replicate themselves using other host cells
• Theory that viruses millions of years ago helped form the first cell nucleus

Illustration of a virus, on a very microscopic level.

http://bit.ly/2miQsCC

_________________________________________

Vaccine Introductions:

Polio:

• 9 ingredients
• 6 are benign, 3 are toxic

MMR 2:

• Treats measles, mumps and rubella
• 13 ingredients
• All 13 = benign (toxic in high quantities)

HIB (Haemophilus influenzae type B)

• Treats influenza
• 12 ingredients
• 4 = benign

Hepatitis B:

• One version has 5 ingredients, another version has 9
• Most of the ingredients are benign and familiar (salt, sugar)
• Most ingredients are toxic in high quantities

Hepatitis A:

• 16 ingredients
• Only 3 are non-toxic

Varicella/Chickenpox/Varivax"

• 15 ingredients
• 2 = benign

HPV:

• Stands for human papillomavirus vaccine
• Protects against cancer and genital warts
• Sexually transmitted disease
• 10 ingredients

Overall:

• Many ingredients lack information about them 
• The chemicals going into the body are unknown
• Sodium chloride (salt) and sugar = in many of the vaccines
• All of the ingredients are bad in large quantities for the body
• Most have more toxic ingredients than benign ingredients

Questions:

• How many people experience undesired effects from these vaccines?
• How much toxicitiy can the human body handle?
• How are we measuring toxicity?
• Why is there such limmitted research on many ingredients?
• Who monitors the amount of intake and the vaccine requirements?

________________________________________________

___________________________________________

3/31/17

An Inconvenient Truth Questions:

An Inconvenient Truth is a film that has Al Gore explaining the importance of spreading the message of global warming, and its disastrous effects on the environment.

_________________________________________________

3/29/17

Ecology Vocabulary #3:

Word:	Meaning/Part of Speech/Examples:
1. fauna	Noun The animal life in an area Ex: The fauna of Sonoma County includes birds, deer, etc.
2.  flora	Noun Plant life in an area Ex: The flora of Sonoma County includes redwood trees, vineyards, etc.
3. food web	Noun Many food chains put together to show how energy flows through the ecosystem Ex: An aquatic food web might show predators such as sharks towards the top, with smaller fish near the bottom
4. food chain	Noun The order in which animals feed on plants and other animals (shows how energy flows from producer-consumer-decomposer) Ex: Humans are at the top of the food chain, whereas grass is at the bottom with many other plants
5. population	Noun All the members of one species that live in one area Ex: The population of birds in Sonoma County
6. predator	Noun An animal that hunts, kills, and eats other animals Ex: Tigers, lions, sharks
7. prey	Noun An animal that is hunted, killed and eaten by a predator Ex: Mice, bunnies
8. producer	Noun An organism that can make its own food Ex: Plants
9. primary consumers	Noun Animals that eat primary producers - herbivores - plant-eaters Ex: Cows (eat grass)
10. secondary consumers	Noun Animals that eat primary consumers - they can be carnivores and omnivores Ex: Humans can be secondary consumers
11. tertiary consumers	Noun A carnivore at the top of the food chain that feeds on other carnivores or only on secondary consumers Ex: Shark, lions

_____________________________________________

3/28/17

Ecology Vocabulary #2:

Word:	Meaning/Part of Speech/Examples:
1. decomposers	Noun An organism, such as bacteria or fungus, that breaks down dead matter and returns nutrients to the soil Ex: Earthworms
2.  estuary	Noun A body of water where freshwater and saltwater ecosystems merge together Ex: Where a river merges with an ocean
3. habitat	Noun The place and surroundings where an organism normally lives Ex: The habitat of aquatic organisms is the ocean
4. herbivores	Noun An organism that eats only plants Ex: Deer and cows
5. host	Noun A living organism on which a parasite lives Ex: Dogs can often be hosts to fleas
6. limiting factor	Noun Something in an environment that keeps the population of an organism from increasing as much as it could Ex: Water scarcity, human activities, disease
7. niche	Noun The habitat that supplies everything needed for a species or an organism to survive Ex: A small pond might contain all the food an animal needs
8. omnivores	Noun A consumer that eats both plants and meats Ex: Rats, bears and humans
9. parasite	Noun An organism that lives in or outside the body of an organism (the host) Ex:  Mosquitos, fleas, mistletoe, and ticks.

_________________________________________________________________________________

Fossil Fuels:

• Fossil fuels = a group of energy sources that were formed from ancient plants and organisms hundreds of millions of years ago (Carboniferous era)
• During this times the land was very swamp-like, so when plants and animals died they fell to the bottom of the bodies of water, where they were kept "safe"
• Over millions of years these organisms started decomposing under layers of sand, clay and other minerals
• Main fossil fuels = oil, coal and natural gas
• The type of organic matter, temperature, time, and pressure conditions all led to the variety in fossil fuels
• Coal was formed from plants and trees that harden from heat and pressure 
• Oil was formed from small organisms such as zoo plankton and algae, which required more pressure and heat since they were more complex matter
• Natural gas was formed by the same processes, but with even more pressure and heat
• Fossil fuels have a high energy density, which makes them desirable
• Fossil fuels are the world's dominate energy source, with nuclear, biomass, and renewables making up a very small portion
• Some uses = transportation, electricity, and common products such as cosmetics and medicines
• Powered industrialization
• Have caused geopolitical issues because of their scarcity and value
• Nonrenewable form of energy
• The largest emmitter of carbon dioxide, a greenhouse gas which causes climate change

______________________________________________

More Water Cycle Notes:

• During evaporation water vapor rises because the sun has heated the surface of the body of water
• As the water droplets rise the temperature drops considerably, causing it to condense into tiny air particles
• When it is cold these form small ice crystals, which then join to form clouds
• When the droplets become heavy enough they fall down as precipitation
• The precipitation could return back to a water source, or it might fall into a cold region and fall as snow
• If it falls on a mountain it generally falls as snow because it is much colder there, and once it warms up it would cause snow melt run-off
• When it is not cold enough for snow then the water obviously falls as rain and then peculates into the soil
• There is actually a lot more water below the ground than there is in rivers and lakes
• This water forms in underground aquifers which exist between the soil and rocks underground
• When the ground is very saturated it cannot soak up more water, therefore creating creaks, rivers, etc.  
• The ground beneath lakes and big bodies of water either is very saturated, which prevents all the water for soaking through, or has rocky bottoms preventing perculation
• Plants take up groundwater with their roots, and then when they are consumed their water enters the cycle
• Transpiration is the process where plants absorb water through the roots and then give off water vapor through pores in their leaves
• Sublimation is when water goes from the solid form of ice straight to the gas form - water vapor
• This occurs when the weather is very cold and dry
• Cells in our bodies are 70% water

__________________________________________________

The Water Cycle: 

3/8/17

Water could be described as the most essential antibiotic factor on Earth. It can be found in a variety of different forms and different places, and as the world has progressed technologically there has been new ways to derive this water. Fresh water is pivotal to the survival of humans, and the availability of it is limited.

Fig. 1. Image credit: Biogeochemical cycles: Figure 1 by OpenStax College, Concepts of Biology, CC BY 4.0

Figure 1 [above] shows just how limited fresh water is on Earth. Only a small fraction of Earth's water is fresh water, and therefore drinkable, as illustrated by the pie chart. Of that small fraction there is an even smaller portion that is deemed accessible by humans. The majority of fresh water is frozen within glaciers, where it remains in such a form often for millennia. Figure 2 further explains how long water remains in a certain form.

Fig. 2. Image credit: "Biogeochemical cycles: Figure 3" by OpenStax College, Biology, CC BY 4.0.

Figure 2 [above] lists exactly how long water remains in a particular place (residence time) before continuing to cycle and relocated itself. Water within the atmosphere and on the surface are constantly running through the water cycle, whereas water below the surface and within glaciers rarely relocate. 

Fig. 3. Image credit: The water cycle by NOAA National Weather Service Jetstream, CC BY 2.0.

The final figure [above], Figure 3, illustrates the water cycle with each of its steps. Those to be highlighted are the evaporation of the surface water, condensation as it develops into clouds, and precipitation as the water falls once again to the Earth. In addition, smaller processes occur such as when the water soaks into the ground and fills in cracks between soil and rocks. Each seemingly minor process is pivotal to the water cycle and therefore humans and all of nature.

_________________________________________________

3/6/17

Ecology Vocabulary #1:

Word:	Meaning/Part of Speech/Examples:
1. Ecology	Noun The study of how living things interact with one another and their environment
2.  Ecosystem	Noun All the living and nonliving things in an area and their interactions
3. Abiotic Factor	Noun The part of the ecosystem that is not alive and has never been alive Ex: The Sun, the weather, etc.
4. Biotic Factor	Noun The part of an ecosystem that is alive Ex: Animals, bugs, plants
5. Adaptation	Noun A characteristic that helps an organism to survive in its environment An alteration in the structure or function of an organism that allows it to have an advantage, or to survive better Ex: The adaptation of cacti being able to store water allows it to survive and multiple in dry climates
6. Biome	Noun A plant and animal community that covers a large part of the Earth Ex: Forests, Grassland, Savannah, Aquatic, etc.
7. Detritivore	Noun An organism that feeds on dead and decomposing organic matter Ex: Earthworm, fungus, bacteria
8. Community	Noun A group of organisms living together in a certain area Ex: Class community, community of monkeys living together
9. Consumers	Noun An organism that survives by eating producers or other consumers in its ecosystem
10. Carnivore	Noun An organism that eats only other consumers Meat eaters Ex: Lion
11. Deforestation	Verb The cutting down and clearing of forest land  Usually leads to increased soil erosion in the area E

__________________________________________________

3/1/17

DNA Diagram:

For clarification and understanding purposes, I mapped out important details relating to protein coding. It might look a little crazy, but it sometimes helps me to write out what I know, and to go from there.

Just to help you make sense of this, the diagram really is not focused on DNA replication (since there are many notes below), but on the processes that follow. At the top of the diagram there is a strand of DNA, with part of it highlighted. Regions that code for specific proteins (or for tRNA or rRNA) and called genes. We get our genes from our parents, one from our mother and one from our father. These variants in DNA are called "alleles". For example, somewhere in a chromosome is a gene that might code for eye color. Chromosomes come in sets, and in the same exact region of the chromosome's counterpart there would be another gene coding for the same thing. As mutations occur, it is possible for slight alterations to be made and passed on in the genes, therefore creating alleles in the pair of genes.

Anyway, the top left corner shows a hypothetical "zoom-in" of the DNA strand in the latter-like shape. Technically the latter would have to be twisted around itself to be the true shape of DNA, but for simplicity purposes I drew it unwound. Under "replication" there is a brief review of what happens in DNA replication. Helicase breaks the weak hydrogen bonds of the DNA, but eventually DNA polymerase lays down new nucleotides, creating two new strands of DNA. 

Then comes the transcription process, where a section of DNA is replicated as mRNA. The coding is the same (i.e. Cytosine matches with Guanine, etc.), except instead of adding a Thymine beside an Adenine, a different base called Uracil is added. Thus, in RNA the four bases are A, C, G, and T.  

Unlike DNA, mRNA can move outside of the nucleus where it will go to a ribosome. Once there amino acids are created from the code in the mRNA. Three bases in the mRNA make up a codon, and each codon codes for an amino acid. There are 64 different codons and 20 different amino acids, meaning that some codons code for the same amino acids. The amino acids are matched with the codons by tRNA. As mentioned earlier, genes can also code for tRNA, so that is where that comes from. In addition, rRNA can be coded by genes as well, and this makes up the structure of the ribosomes.

You can see in the top right corner that a sequence of amino acids makes up a protein. Therefore, we now have the gist of protein-coding.

________________________________________________________________

2/24/17

DNA Splitting and Replication

• DNA helicase is the enzyme that breaks open the DNA (breaks open the hydrogen bonds)
• As helicase breaks the DNA in half, the process is called unzipping
• The nitrogenous bases that have been split apart from their counterpart are called "open bases"
• DNA polymerase is the enzyme that "lays down" new matching nucleotide to the split DNA
• One side of the DNA flows from 3 prime to 5 prime, and the other flows from 5 prime to 3 prime
• New nucleotides can only be added from the 3 prime side
• The "leading strand" is the strand that can continuously add new nucleotides, as it flows from 3 prime to 5 prime
• The "lagging strand" is discontinuous in its laying out of new nucleotides, as the polymerase enzyme must place the new base pairs in sections
• "Okazaki fragments" are the new, short sections formed by the lagging strand
• Video about DNA Splitting and Replication

1/25/17

DNA

• Cell > nucleus > chromosome > DNA
• Real name = Deoxyribonucleic acid
• DNA is wound up super tightly into chromosomes
• Anything that is living, has DNA
• Viruses sometimes have DNA, and sometimes have RNA which is another nucleic acid
• DNA is a molecule and is made of nucleotides
• There are 4 different types of macromolecules that make up the human body, one being Nucleic Acids
• DNA is a "double helix" meaning it takes on a ladder type format that spins on itself
• 5-carbon sugar phosphate (strong covalent bond) = the vertical lines within the ladder
• Nitrogen bases make up the rungs of the ladder: Cytosine (Pyrimidine-  1) - Guanine (Purine - 2), Adenine (Purine) - Thymine (Pyrimidine) CGG AAT
• In order for DNA to replicate itself, it needs to break apart
• There are Hydrogen Bonds between the pairs, which is relatively weak so the DNA can still split apart
• DNA has three main functions:
• Gene coding - heredity transferred from parent to offspring
• Codes for proteins (amino acids) - proteins have many functions and are coded from DNA
• DNA replication - growing new hair, skin, etc.
• The sequence of nitrogen bases act as information storage in the form of codes to build proteins
• The molecules of the DNA are long to store more information - very dense and effective way to store information
• The base pairing means that complementary strands of information can be replicated
• The double helix gives the molecule stability
• Hydrogen bonds allow for easy unzipping for copying and reading information
• Over 99% of our DNA sequence is the same as other humans'
• DNA replicates itself during "Replication"
• One half of the DNA can be used to replicated the other, because the base pairs are always the same
• A gene is a portion of DNA used to code for a certain type of protein, used to express a certain trait
• Backbone of DNA strands is made of alternating deoxirobose sugars and phosphates

12/14/16

The Brain

• The human brain is the fattest organ in the body and is made of 60% fat
• While awake, the brain generates enough energy to power a light bulb
• Excess stress alters brain cells, brain structure, and brain function
• Insulin in the brain promotes memory
• Nervous system is the system that the organ the brain is in
• Nervous tissue is within the brain
• organ systems > organs > tissue > cells > organelles > molecules > atoms
• Neuron = a cell found within the nervous system
• Neurons are surrounded by a cell membrane
• Have a nucleus that contains genes
• Contain cytoplasm, mitochondria, and other organelles
• Carry out basic cellular processes such as protein synthesis and energy production
• Neurons have specialized cell parts called dendrites and axons
• Neurons communicate with each other through an electrochemical process
• Contain some specialized structures - synapses and neurotransmitters
• Anatomy of a neuron - dentrites, cell body (nucleus), axon, myeln, and presynaptic terminal
• Function of a neuron
• Cell body contains all the neuron's organelles - where cellular respiration occurs (another names is soma)
• Dentrites bring information to the cell body - receive the information. Each cell has multiple dentries which are rough.
•  Axon takes information away from the cell. Each cell only has one which is smooth and usually has myelin
• Myelin = a mixture of proteins and fat insulating the axon and increasing the speed at which impulses are conducted.
• The information that the neurons are sending is actually electrical impulses that trigger the release of neurotransmitters

Brain Anatomy Quizlet Link

_____________________________________________________________

12/15/16

Brain Key Terminology

1. Brainstem - The brain stem controls the flow of messages between the brain and the rest of the body, and it also controls basic body functions such as breathing, swallowing, heart rate, blood pressure, consciousness, and whether one is awake or sleepy.
2. Cerebellum - Connects brain to spinal cord and regulates muscular activities. It is associated with higher thought function such as actions and thought.
3. Right brain - The the right side of the brain is in charge of the left side of the body and preforms tasks like logic
4. Left brain - The left side of the brain, deals with logic, analysis, math, lyrics, language, think in words, sequencing, linear, facts, and computation.
5. Frontal lobe - The frontal lobe is located at the front of the brain and is associated with reasoning, motor skills, higher level cognition, and expressive language.
6. Parietal lobe - The parietal lobe is located in the middle section of the brain and is associated with processing tactile sensory information such as pressure, touch, and pain.
7. Temporal lobe - The temporal lobe is located on the bottom section of the brain. This lobe is also the location of the primary auditory cortex, which is important for interpreting sounds and the language we hear. (hearing, smell, fear)
8. Occipital lobe - The occipital lobe is located at the back portion of the brain and is associated with interpreting visual stimuli and information. (sight, vision, memory of things seen)
9. Hypothalamus - uses the nuclei inside of it to do a number of functions such as connecting the nervous system to the endocrine system. (maintain homeostasis)
10. Pituitary gland - Produces critical hormones, which are chemical substances that control various bodily functions - hormone control center.
11. Pineal gland - found in vertebrates that is the source of melatonin, a hormone derived from tryptophanthat plays a central role in the regulation of circadian rhythm (the roughly 24-hour cycle of biological activities associated with natural periods of light and darkness).
12. The thalamus - relays sensory impulses from receptors in various parts of the body to the cerebral cortex
13. Pons- connects the medulla oblongata to the thalamus.
14. Medulla - Helps transfer messages to the spinal cord and the thalamus, which is in the brain, from the body. Helps regulate breathing, heart and blood vessel function, digestion, sneezing, and swallowing

Works Cited: "Pituitary Gland." Pituitary Gland Function, Location & Definition. Body Maps. N.p., n.d. Web. 02 Dec. 2016. "Medulla oblongata." Pituitary Gland Function, Location & Definition. Body Maps. N.p., n.d. Web. 02 Dec. 2016. "The Definition of Left-brained." Dictionary.com. Web. 02 Dec. 2016. "Hypothalamus." Hypothalamus Function, Definition & Location | Body Maps. Healthline, Feb.-Mar. 2015. Web. 02 Dec. 2016. . "Learn the Basic Structures of Brain Anatomy." Verywell. N.p., n.d. Web. 02 Dec. 2016. "Left Brain Vs Right Brain." UCMAS. N.p., n.d. Web. 02 Dec. 2016. Robertson, Sally. "What Does the Thalamus Do?" News-Medical.net. N.p., 21 July 2016. Web. 02 Dec. 2016. “Pineal Gland." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 02 Dec. 2016.

_____________________________________________________________

12/14/16

Neurotransmitters

• Neurotransmitters are brain chemicals that communicate information throughout our brain and body
• Tells your heart to beat, lungs to breath, etc.
• Can affect mood, sleep, concentration, weight, etc.
• Acetylcholine controls muscle contractions
• Epinephrine controls heart rate and helps body deal with stress
• Dopamine blocks pain and removes feeling (reward sensation)
• Endorphines control pain
• Serotonin regulates mood and sleep (dark chocolate increases serotonin which helps the mood)
• Substance P responds to stress
• Glutamate can cause migraines
• Norepinephrine is linked to depression, the heart beat, and blood pressure
• GABA helps one stay calm and normal 
• Too much dopamine can cause an addiction
• Neurotransmitters relay messages from different neurons, travelling through the synapse

_____________________________________________________________

12/12/16

Addiction

• People are exposed to morphine in hospitals, which is essentially pure heroine. Why are these people not becoming addicted? Addiction might not be about your chemical hooks, but an adaptation to one's environment.
• If someone is traumatized and not close with other humans (or work, animals, etc.), they might look for bonding with something else - drugs, alcohol, smartphones, etc.
• One who grows and addiction may just not have the want to be present at particular parts of life.
• Barriers are created between addicts and non-addicts, further isolating the already isolated.
• When bonds are recreated, addictions and overdoses decrease significantly.
• Face-to-face relationships are so much more valuable than friends over social media.
• The United States is actually probably the loneliest county, and we create a parody of connections over social media.
• Addiction is all in our brains - created a way to feel certain things in our brain that are not actually real
• Chemistry of addiction takes place mostly in the brain's limbic system
• Set of structures in the center of the brain that controls our emotional behavioral responses to the received information 
• The brains reward center
• Reponds to new information by releasing neurotransmitters (chemical messengers) that pass signals from one neuron to the next
• Brain produces at least 100 different kinds of neurotransmitters
• Most important neurotransmitters related to addiction are the ones key to our survival and success
• Two main types of neurotransmitters that are in balance in a normal brain
• Excitatory neurotransmitters - get targetted cells fired up
• Inhibitory neurotransmitters - keep targetted cells calm
• Dopamine - an excitatory neurotransmitter 
• Released whenever the brain believes we should take strong note of our behavior to remember it
• Levels thrive in response to pleasurable events like eating and sex
• Also released when for example, a car charges at you - it helps you react to do things important to your survival
• Addictive drugs mess with levels of dopamine and other neurotransmitters
• Keeps brain from remembering unnatural highs and motivate itself to find more of them
• Scientists not sure if dopamine exists to make you feel good, or to seek things that make you feel good.
• Makes people and rats repeat things that make dopamine levels rise
• May just create a desire, whether or not resulting in a pleasurable outcome
• After using drugs long term the amount of defense systems available to balance out the brain decrease
• Hypofunctioning reward system
• Makes artificial and natural highs harder to come by
• The reason why some people develop a tolerance towards drugs

_____________________________________________________________

12/6/16

Temperament and Erikson's Development

Today we have the interesting experience of dipping into causes of depression and how it is involved with the development of a person throughout their life. Furthermore, we saw directly the effects in a "circle", where students talked about issues they are facing, or have faced, in their own lives. 

For the circle we had half the class, about 25-30 people, arranged in a circle. A few general questions were brought up and students went in depth about what they are currently going through. To conserve the privacy of each student I cannot go much further in depth about that topic than that, but essentially the topics were correlated to the issues we are studying now.

We looked at two articles, the first being "What Causes Depression?" from Harvard Medical School. This described some potential causes of depression. Everything is related to the brain and how it works. Some key points:

• How you view the world is developed early on in life.
• As children we start to decide what we think of the world, and this image is often carried throughout one's life. Thus it is very critical to ensure children can have a steady view of the world to keep them strong emotionally later on.
• Your outlook and attitude (temperament) can make you more or less susceptible to depression. 
• The attitude and way of thinking can make you more or less susceptible to depression, meaning if you decide to undertake a positive attitude you will be less likely to grow depressed.
• Moods and attitudes are something easily altered, and something that can be possible to control. 
• Traumatic events are considered "stressful", and if not overcome early, then depression can occur.
• Huge events such as a parent's divorce or the loss of a loved one causes lots of stress in one's life. If they cannot get over this stress quickly and the stress stays with them for an extended period of time, the brain reacts with depression.
• Losses early on in life can set the stage for depression at a later point in one's life.
• If a child loses someone while young, that loss frequently stays with them and affects them for a long time.

The second article was called "Erikson's Stages of Development", and it went into depth about the importance of growth in different areas at various stages of one's life. 

• Infancy: 
• Birth - 18 months
• Should develop optimism, trust, confidence, and security if nurtured well
• If trust does not develop, insecurity, worthlessness, and general mistrust to the world can occur
• Toddler/Early Childhood Years:
• 18 months - 3 years old
• Development of self-esteem, pride and learning right from wrong
• If unable to learn certain skills, shame and low self-esteem may develop
• Children especially vulnerable in this stage
• Preschooler:
• 3 - 5 years old
• Begin to take initiative, and constantly want to know "Why?"
• Begin to feel guilt in certain situations
• School Aged Child:
• 6 - 12 years old
• "if we experience unresolved feelings of inadequacy and inferiority among our peers, we can have serious problems in terms of competence and self-esteem"
• Lots of incoming knowledge and new skill sets
• Adolescent:
• 12 - 18 years old
• Deciding who you are in life and what you want to do
• Struggle to fit-in, and devotion to different ideals set in
• Young Adult:
• 18 - 35 years old
• Seeking of relationships and companionship (families as well)
• Isolation can occur if this is not found
• Middle-Aged Adult:
• 35 - 55/65 years old
• Looking to have an impact in society and for life to not be a waste
• Seeking stability and control
• Late Adult:
• 55/65 - death
• Reflection on rest of life: did they contribute and was their life worth it?
• Either a time of contentment or of depair
• What the rest of life leads up to

Taking in all this information prior to the circle was very interesting because it makes you wonder how each of the traumatic events in peers' lives came about. For example, perhaps the reason certain students felt like they could not easily tell other's about their situations was because they gained an early-on mistrust, particularly during infancy. Many students discussed depression or anxiety stemming from a traumatic, or stressful, event that they had undergone. The circle was definitely very saddening, but it is interesting to have some insight about how the emotions of students are affected from horrible events. 

_____________________________________________________________

 Iron Chef - Notes from Presentations

Strawberries:

Group 1 -

• Hypothesis: IF you drop 20 organic and conventional strawberries in amylase, the organic will dissolve quicker.
• Conventional and organic strawberries placed in different enzymes - which would dissolve more?
• Procedures:
• Labelled different beakers and added enzymes inside
• Added strawberries to corresponding beakers
• Stored them, then measured displacement
• Variables:
• Some beakers were in different areas, so light and evaporation were a factor
• Not enough strawberries used for reliable data
• Measurements could have been off
• Mold growth increased displacement
• Results:
• The difference between organic and conventional was not prevelant in this experiment
• Amylase is weakest solvent
• Results not very reliable
• Would want a higher temperature to replicate body temperature
• No light in future experiments

Group 2 -

• Which strawberries grow mold faster? Which grow more?
• Procedures:
• Made agar 
• Swabbed the strawberries
• Kept in incubator for 2 weeks
• Put under microscope - gram stained
• Determined which fungi was on the stain
• Did not find as much fungi as they wanted, and could not identify them
• Variables:
• Incubator was turned off by another class
• Did not have one of the stain colors
• Could not identify all the fungi/bacteria
• Some contamination occurred (fingerprints, hair)
• Timing was slightly off due to every other day schedule
• Should have done OHT stain instead
• More controlled environment needed
• Other experiments within incubator at the same time
• Temperature got tampered with
• Learning was in the process, despite lack of results
• Growth seemed about the same

Pesticides:

Group 1 -

• Hypothesized that pesticides would affect animal cells more than plant cells because pesticides attack the nervous system
• Tended yeast for a time period, feeding it, etc.
• Activated yeast and gave it sugar, pesticide
• Beaker containing no pesticide remaining activated, with live yeast
• Variables:
• Ants go into the classroom (within beakers) - died 
• Tested pesticides with basil as well as yeast
• Basil without pesticides remained green and alive, whereas the others died and leaves broke off
• Pesticides do affect the plants that we eat
• All with pesticide decreased in their growth
• Hypothesis was correct
• Plants and yeast without pesticides remained alive longer
• If pesticides affect these so much, they could definitely affect us humans who consume them.

Group 2 -

• Hypothesis: If organic and inorganic samples of: ground chuck, and apples are exposed to the same pesticides, then the organic food’s cellular structure will be more damaged by the pesticides than the non organic foods, because non-organic food has been altered to resist pesticides
• Meat and apple wasn't rotted completely within its first stage of decomposition
• At the second to last day of the experiment clear signs of various fungi/bacteria growth was visible
• Previous knowledge from nutrition unit sparked idea for project
• Non-organic foods have pesticides within, and so hypothesized an immunity between
• Bacteria grew on organic chuck more
• Variables:
• Agar was put inside incubator, which was turned off
• Smelled really bad, attracting ants
• Could not check dishes every day - only every other day
• Could not have as many dishes as they wanted
• Incubator overheated at one point - melted agar down and killed some bacteria
• Order got mixed up of photos - could be wrong
• Would have liked a more controlled environment
• More quantifiable data would have been nice
• More growth on the organic than the non-organic
• Very little differences, however
• More diversity in bacteria on the organic
• Apples had more of a fungus growth (turned yellow from oxygen); chuck got more slimy

Sugars: 

Group 1 -

• Question: How different sugars affected growth of bacteria
• Hypothesis: if bacteria is exposed to the various different sugars - two weeks - bacteria with light fructose sugar would have the most bacteria growth - added chemicals stimulate bacteria growth
• Procedures:
• Made agar
• Poured agar into dishes and added to incubator
• Started process of bacterial growth
• Swabbed to add bacteria to the dishes and then added sugars
• Watched for 2 weeks and observed
• Counted colonies and determined percentage bacteria per plate
• Results:
• Honey grew the most bacteria
• Low fructose corn syrup showed less consistency than the sugar and honey
• Cane sugar had the second most bacteria growth
• No sugar added produced little bacteria
• Sugar can help bacteria grow
• Food addiction linked to how processed foods are
• More processed sugars create the least growth in bacteria
• Health effects such as cancer growth may be linked to the processing within sugars (and foods in general)
• Variables:
• Incubator turned off at one point

Group 2 -

• Hypothesis: If three girls and three boys get their glucose levels tested for one week on regular diet, then substituting in the three types of sugar, corn syrup would have greatest impact on blood sugar levels
• Procedures:
• Wavers for test subjects
• Baseline testing - eating normal diets - recorded glucose levels
• Averaged out normal blood sugar levels
• Fed all subjects normal sugar the next week, two hours before testing them again
• Then followed up with the other types of sugar
• Compared blood sugar levels
• Researched best times to test
• Variables:
• Some subjects ate things between
• Had to rely on test subjects (absences, etc)
• Some holes in data
• Would need a lot more than 6 people for very accurate results
• Activity levels could have skewed data
• Timing was off sometimes - not same amount of test days each week
• Results:
• Honey had highest increase in blood sugar levels - may be relating to high levels of carbohydrates

Drinks:

Group 1 - 

• Hypothesis: If 15 human teeth are placed in cups of different drinks...tooth in Coca Cola will have largest increase in weight...plaque buildup.
• Procedures:
• Reached out to community to get a hold of teeth
• Got human teeth from oral surgeons
• Used 20 mL of each drink - 3 cups each for each 5 drink
• Weighed teeth every day
• Later conducted separate experiment to see which drink grew more bacteria
• Variables:
• Needed to dry teeth before measuring, and occasionally it is possible for a slight amount of liquid to be left, adding weight
• Scale was not super accurate for such light weights
• Incubator was tampered with
• Liquid spilled at one point
• Results:
• Huge plaque build up for Coca Cola - turned black
• Coffee infested teeth turned brownish
• Smoothie with natural sugars had a slight amount of buildup just from being in the liquid so long
• Water had same results as smoothie
• 1/3 Americans drink soda daily
• Drinks like this contain the most added sugars of all foods in the world
• Cause cavities and weight gain

Group 2 - 

• Hypothesis: If yeast is given different liquids with varying amounts of natural and artificial sugars in bottles with balloons on top, then the bottle with the most natural sugar will inflate the balloon the most because the yeast will thrive with the natural sugars causing the yeast to release more carbon dioxide.
• Procedures:
• Measure pHs of each drink
• Added yeast and different drinks to different beakers
• Added balloons atop the beaker, allowing the yeast to react with the drinks
• Chemical reaction occurred, continuing for 4-5 hours
• Foam from yeast built up over time
• Balloons began to fill up
• Natural sugar had largest circumference
• Repeated trial for accuracy
• Honey and natural sugar rose significantly
• Variables:
• Kept running out of materials, requiring different brands to be used
• Different colored balloons could have had different flexibilities
• Results:
• The honey and natural sugar rose highest in the first two trials
• The honey did not rise for the beginning of the third trial
• The Green Goodness and Coca Cola drinks hardly rose
• pH of Coca Cola = most acidic
• Coca Cola had worst effect on the yeast
• Concluded Green Goodness = the best for humans because of the natural sugars

_____________________________________________________________

9/23/16

Cellular Respiration Notes

Video #1:

1. Glucose - how it is received
1. What cells need in order to do work
2. Autotrophs are organisms that make glucose all by themselves
1. Plants
2. Algae
3. Bacterias
3. Photoautotrophs are organisms that make their own carbohydrates using solar energy
4. Chemoautotrophs also make carbohydrates using energy from chemical bonds that they break
5. Heterotrophs - get their glucose and carbohydrates from other organisms
1. Animals
2. Fungi
3. Bacterias
6. Store glucose for future or use it to do work

2. How glucose is used
1. 70%: basic life processes
2. 20%: physical activity
3. 10%: digestion of food
3. Use of glucose to do cell work cannot be done directly; it requires a conversion
1. Glucose is converted into ATP
2. 40% efficiency; not all food you take in is turned to energy
3. Energy Conversions produce heat, and 60% of the food is lost in the conversion process
1. We extract energy from carbohydrates through a series of reactions beginning with glycolysis  
2. Glycolysis flows into mitochondria
1. The energy transformers of the cell
2. Has an outer membrane and inner membrane: outer mitochondrial membrane and inner mitochondrial membrane (cristae)
3. Inner membrane is in folds to increase surface area
4. Space inside the inner membrane is called the matrix, where citric acid cycle takes place
5. Inner membrane space = between membranes
5. Tricarboxylic Acid Cycle (TCA)
1. Pyruvate gets chemically altered into Acetyl-CoA before entering the cycle
2. As bonds are broken by carbohydrates, carbons are released which combine with oxygen to form carbon dioxide
3. Most of the high-energy bonds from what was glucose gets oxidized, thus reducing electron carriers
4. Original energy from carbohydrates goes to electron carriers
5. They then go to the proteins in the electron transport chain
6. As the electron carriers give up their electrons the electron carriers get oxidized
7. A little bit of energy is given off as electron carriers travel through proteins

Video #2:

1. Cellular Respiration = how we derive energy from the food we eat
1. Specifically from glucose, since most of what we consume ends up as glucose
2. ATP = the energy that the body has to turn glucose into
1. Adenosine Triphosphate
2. What you need to be able to work
3. Made up of Adenine, Ribose, and three Phosphate groups
1. Energy is released when one of these phosphate groups is exerted
2. An OH pairing, or water molecule, comes to replace this phosphate group
3. Hydrolysis = when water molecules are used to break down a compound
4. Through cellular respiration, one molecule of glucose can yield a bit of heat, and 38 molecules of ATP
5. Three phases during which glucose is turned to ATP
1. Glycolysis
2. The Krebs Cycle
3. The Electron Transport Chain
6. Glycolysis - the breaking down of the glucose
1. Glucose = a sugar
2. Glucose broken into Pyruvic acids
3. Glycolysis needs the investment of 2 ATPs in order to work, but generates 4 ATPs, 2 Pyruvates, and 2 NADH
4. Glycolysis can take place without oxygen, making it an anaerobic process
1. In the absence of oxygen, pyruvates gets “rerouted” to process called Fermentation
2. Fermentation frees up some of the NAD+ which creates some byproducts
3. When your muscles use up all the oxygen they have, they kick into anaerobic respiration creating lactic acid in your muscle tissues
7. Krebs Cycle (The citric acid cycle)
1. An aerobic process - requires oxygen
2. Takes place in inner membrane of the mitochondria
3. Takes product of Glycolysis - pyruvates, and reworks them to create 2 more ATP per glucose molecule and some more energy
1. First one of the pyruvates is oxidized, or combined with oxygen
2. One of the carbons inside the pyruvates bonds with an oxygen molecule and leaves the cell as CO2
3. This leaves a two-carbon compound called acetyl coenzyme A
4. Then another NAD+ picks up a hydrogen and becomes NADH
5. Enzymes bring together a phosphate with ATP to create another ATP molecule for each pyruvate
6. Enzymes help join the acetyl coA and a 4-carbon molecule
4. Humans constantly exhale the products of the Krebs Cycle
5. Each time a carbon comes off the citric acid some energy is made, but not in the ATP form
6. NAD+ and FAD are both enzymes related to B vitamins, derivatives of Niacin and Riboflavin
1. They are like batteries that pick up hydrogen and energized
7. Each glucose molecule can produce 6 NADHs and 2 FADH2s
8. The Electron Transport Chain
1. ATP and phosphates are squeezed together to form ATP
2. Final of 38 ATPs if everything goes well

_____________________________________________________________

9/29/16

Exercise Lab Notes:

• 35-45% of diet should be carbohydrates
• Smallest portion of diet should be fats
• Fat is not always bad- avocados, salmon, nuts etc. are good
• Omega 3 supplements and fats help brain development
• Breakfast gets your metabolism going
• Protein = very important for breakfast
• Carbs “don’t stick with you very long”
• Carbs are not very good for dinner, because the energy is not worked off
• Unworked off carbs turn to fat
• Caffeine stunts growth in teenagers
• When young, your metabolism works better for you
• Body does not know how to properly burn chemicals
• Chemicals from Rock Stars and such, mess with metabolism
• Bars should have equal amounts of protein to sugar, or more protein
• Bars with lots of sugar give you quick energy, but drop soon
• Quest Bars, Luna Bars, Kind Bars are good options
• What you eat is 60-70% responsible for your weight
• Whole grain bread, nut butters
• ⅔ body weight in protein
• Peace sign: big portions = carbs and protein, small = fat
• Athletes = fully body weight of protein (grams)
• Shaking during exercising is from your body not being fueled properly; body stores fat and eats away at the muscles
• Eat 5-6 times a day!
• Eat protein when sore!
• 4 different types of protein: casein protein (slow digesting - eat when going to bed and muscles are sore), whey proteins (acts quickly - when about to go workout), soy protein, plant protein
• Eggs, nuts, beans, meat, powder
• Muscle mass is not relating to weight
• Anaerobic: Last sprint of a run (lack of oxygen) ; body functioning at max
• If anaerobic for too long, your body will give out
• Aerobic: Working heart rate, something you should be able to stick with
• 220-age = anaerobic heart rate
• That number times 0.8 = working heart rate
• Staying aerobic allows you to exercise longer and burn more fat/calories
• How quickly you can return from anaerobic determines how conditioned you actually are
• Being heart healthy is key
• Exercising in the morning gets your brain and metabolism working

Resting heart rate: 60

Exercising Respiratory: 15

Exercising heart rate: 140

Resting Respiratory: 8

_____________________________________________________________

9/23/16

Organs to Elements Notes

1. Specific Organs have a specific structure and function
1. Structure is often necessary to function.
1. Ex: Small intestine’s function is absorption, hence the representation as the nylons.
2. Tissue
1. All organs are made up of tissue.
2. Each tissue also has its own structure and function.
3. Four types of tissue in the human body:
1. Connective tissue
2. Epithelial tissue
3. Muscle tissue
4. Nervous tissue
3. Cells
1. All tissues are built up of cells
2. Each cell is a single unit of life.
3. Can metabolize and reproduce.
4. Cells have their own “organs”.
4. Organelles- A cell’s organs.
1. Lysosomes (within the organelles):
1. Hold enzymes that were created by the cell
2. Purpose of lysosomes is to digest things
3. Also break down cell when it dies
2. All organelles are made of macromolecules:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids (DNA, RNA)
3. Macromolecules are made of various elements from the periodic table
5. The 6 Main Elements
1. 6 Elements that make up 95% of all organisms
1. Carbon
2. Hydrogen
3. Nitrogen
4. Oxygen
5. Phosphorus
6. Sulfur

_____________________________________________________________

Click here to view Quizlet set: Organs to Elements

Click here to view Quizlet set: Enzymes