Big+Idea+2+Exchange+of+Energy+and+Materials

Big Idea 2: Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis.

Living systems require free energy and matter to maintain order, grow and reproduce. Organisms employ various strategies to capture, use and store free energy and other vital resources. Energy deficiencies are not only detrimental to individual organisms; they also can cause disruptions at the population and ecosystem levels.

Autotrophic cells capture free energy through photosynthesis and chemosynthesis. Photosynthesis traps free energy present in sunlight that, in turn, is used to produce carbohydrates from carbon dioxide. Chemosynthesis captures energy present in inorganic chemicals. __#|Cellular__ respiration and fermentation harvest free energy from sugars to produce free energy carriers, including ATP. The free energy available in sugars drives metabolic pathways in cells. Photosynthesis and respiration are interdependent processes. Cells and organisms must exchange matter with the environment. For example, water and nutrients are used in the synthesis of new molecules; carbon moves from the environment to organisms where it is incorporated into carbohydrates, proteins, nucleic acids or fats; and oxygen is necessary for more efficient free energy use in __#|cellular__ respiration. Differences in surface-to-volume ratios affect the capacity of a biological system to obtain resources and eliminate wastes. Programmed cell death (apoptosis) plays a role in normal development and differentiation (e.g. morphogenesis).

Membranes allow cells to create and maintain internal environments that differ from external environments. The structure of cell membranes results in selective permeability; the movement of molecules across them via osmosis, diffusion and active transport maintains dynamic homeostasis. In eukaryotes, internal membranes partition the cell into specialized regions that allow cell processes to operate with optimal efficiency. Each compartment or membrane-bound organelle enables localization of chemical reactions.

Organisms also have feedback mechanisms that maintain dynamic homeostasis by allowing them to respond to changes in their internal and external environments. Negative feedback loops maintain optimal internal environments, and positive feedback mechanisms amplify responses. Changes in a biological system’s environment, particularly the availability of resources, influence responses and activities, and organisms use various means to obtain nutrients and get rid of wastes. Homeostatic mechanisms across phyla reflect both continuity due to common ancestry and change due to evolution and natural selection; in plants and animals, defense mechanisms against disruptions of dynamic homeostasis have evolved. Additionally, the timing and coordination of developmental, physiological and behavioral events are regulated, increasing fitness of individuals and long-term survival of populations.

Homeotic Genes- Submitted by Maddy Harmon E.K.-- 2.E.1.- timing and coordination of specific events are necessary for the normal developement of an organism, and these events are regulated by a variety of mechanisms. Homeotic genes control the timing and coordination or embryonic developement in vertabrates and invertabrates alike. Homeotic genes are contained in sequences of neuclotides called homeoboxes. the sequences of these homeoboxes are similar between a wide range of vertabrates and invertabrates, and although they often have different controls between species over the developement of specific body parts, their similarity across species is an indication of a common ancestor(Big Idea 1)

Homeotic gene map comparing the similarities between humans and fruit flies (once jokingly called "little people with wings" - because of how similarly thei homeotic genes regulated themapping of certain body parts


 * G __#|Protein__-Coupled Receptors** (Text book page 211) By Jake Barry
 * Appendix A Big idea #2 letter H **

A G __#|Protein__-Coupled Receptor is a plasma membrane receptor that works with the help of a G protein. Mandy different signals use the G protein-coupled receptors, such as epinephrine. These receptors vary in their bi nding sites and in the type of G protein that they use. This makes these receptors extremely diverse and widespread in their use, including being involved in embrionic development. About 60% of all medicines today work with g protein-coupled receptors.

The G protein acts inside the cytoplasm as a molecular switch that is either on of off. When GDP is bound to the protein it is inactive. The G protein and receptor usually work with an enzyme. When the signaling molecule binds to the receptor, the receptor changes shape and binds to the G protein on the cytoplasmic side. This binding activates the G protein. The active g protein then leaves the receptor and goes to the enzyme where it changes the enzymes shape. The chnged enzyme can then trigger a pathway leading to a cellular response. The G protein reactivates when it hydrolyzes its bound GTP to GDP. This quick change back to the off position allows for strict cell signaling control when the signaling molecule is no longer present.

[|Detailed blog explanation]

**Chemical Classes of Hormones** (Text Book Page 977) By Jake Barry

** Appendix A Big idea #2 letter I **

Different types of hormones contact the receptor cell in different way depending on their solubility, and have different actions accordingly. The electrochemical properties of hormones determines if they can pass through the cell membrane or remain on the outside. Polar molecules such as polypeptide hormones and many amine hormones are water soluble due to their charge. Because they are not soluble in lipids, they cannot pass through the plasma membrane. steroid hormones and other non polar and can pass through the membrane. The insoluble ones are received by specific receptors in the target cells, that go to trigger a response. This allows for specific cells to be contacted, and amplification of the message while it is being passed down. soluble hormones can go directly into all cells and go into their nucleus and affect transcription. This is good for widespread messages that affect all cells.



Appendix A: Essential knowledge 2.B.1: Cell membranes are selectively permeable due to their structure.
 * == __** Structure, Func **__ __ ** tion, & Importance of the Cell ** Membrane __ by Grace Goodfellow ==

[[image:cell_membrane.png width="720" height="296"]]

 * 1) __Structure__


 * **Davson & Danielli Model:** In 1935, Hugh Davson and [|J] ames Danielli proposed a model of the cell membrane in which the phospholipid bilayer was situated between two layers of globular proteins.
 * **Fluid Mosaic Model:** S.J. Singer and G.L. Nicolson came up with this model in 1972, replacing the earlier model of Davson and Danielli. They presented that biologicalmembranes can be considered as a two-dimensional liquid in which lipid and protein molecules diffuse more or less easily. Although the lipid bilayers that form the basis of the membranes do indeed form two-dimensional liquids by themselves, the plasma membrane also contains a large quantity of proteins, which provide more structure. Examples of such structures are protein-protein complexes and pickets and fences formed by the actin-based cytoskeleton.
 * **Phospholipid Bilayer:** Phospholipids have two ends, one of which is hydrophilic, or attracted to water, and one of which is hydrophobic, or repelled by water. Since the inside of cells is mostly water, and the area outside of cells is mostly water, these molecules arrange themselves into two layers, with the hydrophilic ends of each layer pointing outwards, and the hydrophobic ones pointing inwards. Since they are lipids, or fats, they are not broken down by water, and are solid enough not to let large molecules pass through without the help of another substance. Smaller molecules, like oxygen and carbon dioxide, can pass through easily on their own, but larger ones like sodium, magnesium, or water can't.
 * 1) __ Function __
 * One of the main purposes of the phospholipid bilayer is to provide structure to a cell through its natural arrangement of the hydrophobic and hydrophilic ends of the phospholipids, and with the stabilizing cholesterol and sterols. Its other purpose is to regulate the types of substances that can go into the cell or connect with it, which it does in several ways using proteins. Some types of protein extend from the top of the membrane so that they can be used to identify the cell or to make a place for certain substances to bind to it.

http://www.youtube.com/watch?v=moPJkCbKjBs


 * Negative Regulatory Systems (Text pages 861-862) By: Kayla Kaufmann**
 * Appendix A Big Idea #2 Letter K ... Also Essential knowledge 2.C.1: **** Organisms use feedback mechanisms to maintain their internal environments and respond to external environmental changes. **
 * Part A **


 * Organisms use feedback mechanisms to maintain their internal environments and respond to outside environmental changes.
 * Negative feedback mechanisms maintain dynamic homeostasis for a certain condition by regulating physiological processes and returning the changing condition back to its target set point.
 * In Negative feedback systems the animal responds to the stimulus by reducing the stimulus. The goal is to stay stable and get as close to the target set point as possible (not to amplify a stimulus).


 * An common and easy to remember example of negative feedback is **temperature regulation in animals**.
 * If the human body experiences a raise in temperature then negative feedback is the homeostatic method used to try to get back to the regular tagert set point. (The hypothalmus senses the temperature change)
 * One reaction of the body as a result of negative feedback is you begin to sweat. As the water molecules from your sweat evaporates off the skin, it creates evaporative cooling (the water molecules will carry some heat with them).
 * Also, vasodialation will occur, where the blood will travel towards the surface of the skin resulting in more heat loss through convection.
 * In an animal with furr, the furr may lay flat so heat can be lost through convection
 * All these methods will cause a temperature drop.
 * If the temperature drops too far, those reactions will be shut off
 * If the body becomes too cold, negative feedback also plays a roll but the body has a different reaction to raise body temperatue
 * One reaction of the body would be to get goosebumps. This causes hair to stand up but it also causes skin to get pulled in which helps conserve heat.
 * Also, instead of vasodilating, the body will vasoconstrict, which means we pull the blood towards the inside of our body in order to maintain the heat and reduce convection causing the body temperature to increase.
 * The skeletal muscles of the body will contract rapidly causing shivering which generates heat for the body
 * **All of these methods come from __negative feedback__ regulating body temperature.**


 * These two diagrams lay out this concept of negative feedback and temperature regulation.**

Also, check out this Bozeman video on Feedback (Also used as a referance) [|Negative Feedback]


 * Alteration in the Mechanisms of Feedback with Harmful Results By: Kayla Kaufmann**
 * Text Pages (861-862)**
 * Big Idea #2 Essential Knowledge 2.C.1: **
 * Organisms use feedback mechanisms to maintain their internal environments and respond to external environmental changes. **
 * Part C **


 * Alterations of the components or mistakes in a negative or positive feedback system can result in harmful consequences to an organism
 * Blood glucose levels is an example of a negative feedback machanism. This refers to the amount of glucose moving around the blood in your body
 * The glucose can be taken in by the cells so it can help carry out respiration or it could also be stored in glycogen which is found mostly in the liver. Insulin and glucagon are the two hormones that help make this happen.
 * The pancreas helps regulate the blood glucose level and it contains two types of cells; Beta cells and Alpha cells and they sense the blood glucose level
 * If there is a lot of blood glucose outside the beta cell which will trigger an increase the amount of insulin its giving off
 * So... **when the blood glucose level is high, insulin will be secreted, then moving around the body, triggering cells to take in the blood glucose and telling the liver to store it as glycogen. This results in your blood glucose level dropping**
 * When blood glucose levels drop, the body will stop producing insulin and begin producing glucagon (produced by the alpha cells). Glucagon is released. Glucose is "freed" from glycogen in the liver as a result, increasing blood glucose levels.
 * **Type I diabetes causes an alteration in the above feedback loop.**
 * Type I diabetics have beta cells that do not function properly (Reminder: beta cells secrete insulin)
 * Blood glucose levels rise and there is not insulin to secrete (what should happen in this feedback loop)
 * As a result, the cells of the body will not take in the blood glucose and results in increased blood pressure, can effect the eyes, nausea, vommiting, etc and could eventually lead to a coma or death
 * Someone with Type I diabetes must receive insulin shots throughout the day to maintain and regulate blood glucose levels or use an insulin pump



I also used the same Bozeman video to help explain this topic (Referance) [|Type I Diabetes]

Appendix A Letter G Interdependency of Photosynthesis and Cellular Respiration Brian Millham (pg 162 textbook)



The products of photosynthesis, oxygen and glucose, are used for cellular respiration which produces ATP. The products of cellular respiration, carbon dioxide and water, are then used in photosynthesis. The products of photosynthesis are the reactants for cellular respiration and the products of cellular respiration are the reactants of photosynthesis. This is a great video to watch on photosynthesis and cellular respiration []


 * Osmoregulation by saltwater and freshwater animals** by Brian Millham (pg. 955-956)

Essential Knowledge 2.D.2: Homeostatic mechanisms reflect both common ancestry and Divergence due to adaptation in different environments

Animals can maintain water balance by either being an osmoconformer or an osmoregulator. An osmoconformer is isoosmotic with its surroundings and an osmoregulator controls its internal osmolarity independent of that its environment. Most marine invertebrates are osmoconformers because their osmolarity is the same as the seawater. These marine invertebrates are actively transporting the solutes out to maintain homeostasis because they are significantly different in specific solute concentrations. Some marine invertebrates are osmoregulators along with marine vertebrates. Cod fish drink the seawater because they are constantly lose water by osmosis. Their gills and kidneys then get rid of the salts. Freshwater fish are different because their body fluids need to be hyperosmotic because they cannot live with the salt concentrations as low as freshwater. They solve this problem by drinking very little freshwater and excreting large amounts of very dilute urine. The salts lost are regained by eating.

This is a video on osmoregulation: []


 * Understanding the formation of ATP in the Mitochondrion By: Kohl Romeiser**

Appendix A; Big Idea #2; Letter F: Visual representation of cell membrane and explanation of establishment of proton gradient and formation of ATP.

Helpful Videos: [] []

__Electron Transport Chain:__ A process in which the NADH and [FADH 2 ] produced during glycolysis, B-oxidation, and other catabolic processes are oxidized thus releasing energy in the form of ATP.

__Chemiosmotic Phosphorolation:__ The mechanism by which ATP is formed in the electron transport chain.

Inside the inner membrane of the mitochondria, a proton gradient is formed through the breakdown of NADH and FADH2 which results in the creation of H- ions, which are pumped through the electron transport chain by electron carriers. Once oxygen reaches these ions, water is formed. As electrons are passed from one electron carrier to another, hydrogen ions are then transported into the intermembrane space of the mitochondria at three different points in the ETC. The transportation of H+ ions creates a greater concentration of H+ ions in the intermembrane space. This forms the proton gradient which forces the H+ ions back across the membrane through the ATP synthase protein which drives the production of ATP.


 * Importance of mechanisms in Organism development **** By: Kohl Romeiser **

Appendix A; Big Idea #2; Letter R: Justify claims with evidence to show that timing and coordination of specific events are necessary for normal development in an organism, and that these events are regulated by multiple mechanisms.

The use of transcription factors during development results in gene expression:

Homeotic Gene: “ any of a group of [|genes] that control the pattern of body formation during early embryonic development of organisms. These genes encode [|proteins] called [|transcription factors] that direct [|cells] to form various parts of the body. A homeotic protein can activate one [|gene] but repress another, producing effects that are complementary and necessary for the ordered development of an organism.”

Embryonic Induction: ( //embryology// ) “The influence of one cell group (inducer) over a neighboring cell group (induced) during embryogenesis.”

Genetic mutations can cause severe abnormal development in organisms. To prevent this, microRNAs help to regulate development and prevent cellular errors from occurring by silencing genes.

Apoptosis: Programmed cell death.

Apoptosis plays an essential role in normal development of an organism. The morphogenesis of the human fingers and toes for example, would not occur unless cells stopped reproducing so that the hand could take shape and form properly.



Appendix A: Essential knowledge 2.A.2: Organisms capture and store free energy for use in biological processes (Letters A & B)
 * **__Acquiring Energy to Fuel Life Processes__** by Grace Goodfellow

Autotrophs capture free energy from physical sources in the environment
 * Photosynthetic organisms capture free energy present in sunlight
 * The light-dependent portion of photosynthesis is carried out by two consecutive photosystems (photosystem I and photosystem II) in the thylakoid membrane of the chloroplasts
 * The photosystems are driven by the excited chlorophyll molecules
 * The chlorophyll molecule in photosystem II is excited by sunlight and the energy produced helps to break down a water molecule (H2O) into O2 (with electrons removed) and 2H+. The removed electrons are excited by the light energy.
 * When the electrons prepare to come to their rest state, they go through an oxidative phosphorylation process and produces an ATP molecule
 * As the electrons are coming to a resting state, they are excited again in photosystem I and raised to a even higher energy state. The excited electrons are then used to produce NADP+ and H+.
 * The highly energetic NADPH molecule is then fed into the Calvin Cycle to conduct carbon fixation
 * Chemosynthetic organisms capture free energy from small inorganic molecules present in their environment, and this process can occur in the absence of oxygen
 * Chemosynthesis is the conversion of one or more carbon molecules (usually carbon dioxide or methane) and nutrients into organic matter using the oxidation of inorganic molecules (gas, hydrogen gas, hydrogen sulfide) or methane as a source of energy, rather than sunlight, as in photosynthesis
 * Carbohydrates are manufactured from carbon dioxide and water using chemical nutrients as the energy source

Heterotrophs capture free energy present in carbon compounds produced by other organisms
 * Heterotrophs may metabolize carbohydrates, lipids and proteins by hydrolysis as sources of free energyFermentation produces organic molecules, including alcohol and lactic acid, and it occurs in the absence of oxygen
 * Catabolism breaks down molecules into smaller units to release energy
 * Anabolism uses energy to construct components of cells such as proteins and nucleic acids
 * Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy and will not occur by themselves, by coupling them to spontaneous reactions that release energy. As enzymes act as catalysts they allow these reactions to proceed quickly and efficiently. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or signals from other cells.
 * Fermentation produces organic molecules, including alcohol and lactic acid, and it occurs in the absence of oxygen.
 * A form of anaerobic digestion that generates the enzyme adenosine triphosphate (ATP) by the process of substrate-level phosphorylation
 * The energy for generating ATP comes from the oxidation of organic compounds, such as carbohydrates
 * Fermentation is important in anaerobic conditions when there is no oxidative phosphorylation to maintain the production of ATP

Photosynthesis... http://www.youtube.com/watch?v=gXCEbuqC4SQ __Metabolism__ (& other processes producing energy)... http://www.youtube.com/watch?v=HeiV6838Zcg


 * __**Plant hormones help coordinate growth, development, and responses to stimuli (Test Book: Page 220)**__ By Bunyad Bhatti

Appendix A: Big Idea 2 ( S): Analyze data to support the claim that responses to information and communication of information can affect natural selection.

Hormones: are chemical messengers, which coordinate different parts of a multicellular organism. they are produced by one part of the body, and transported to another.

tropism: a plant growth response, from hormones that results in the plant groeing toward or away from a stimulus.

Phototropism: is the growth of a shoot in a certain direction in response to light.

Positive Phototropism: the growth of a plant towards light.

Negative Phototropism: the growth of a plant away from the light.

the most important actions of hormones include:

1.Auxins: stimulate the elongation of cells. Synthetic auxins are often used as hebicides. It kills dicots due to its high concentrations, but the monocots are not harmed.

2.Cytokinins: play an essential role in cell division and differentiation, thus stimulating it.

3.Gibberellins: work with the auxins, in order to stimulate cell elongation.

4.Abscisic acid: slows the growth, acting against the hormones.

5.Ethylene: it is a gas, which plays a role in apoptosis.


 * __**Feedback control loops maintain the internal environment in many animals. (Test Book: Page**__ **232)** By Bunyad Bhatti

Appendix A: Big Idea 2: ( I & J) : Provided with an example of a simple positive and negative feedback loop.

The homeostatic control systems function by having a set point, sensors to detect any stimulus above or below the set point, and a physiological response that helps return to its set point.

In Negative Feedback Systems, the animals respond in a way that reduces the stimulus. For example: when a person excersizes, the body temperature rises, and the body starts to sweat, in order to cool down the body.

In positive feedback systems, a change in a variable triggers mechanisms that amplify the response, rather than reverse the change of it. For example: during childbirth, the pressure of the baby's head against the receptors near the opening of the uterus, stimulates greater uterine contractions, causing the uterine to open and heightening the contractions of it.

A link to help understand this concept is done by Mr Anderson: [| http://www.youtube.com/watch?v=CLv3SkF_Eag]

by Maeve Dalpe
 * Appendix A Big Idea 2, N

Biotic factors are living factors such as plants, animals, fungi, protist and bacteria are all biotic. Abiotic factors are nonliving factors such as habitat, temperature, light, water, nutrients, weather, etc.

Biotic and abiotic factors combine to create an ecosystem, a whole population or systems in the human body. The elements that these living and nonliving factors determine are restricted by limiting factors.

__Biofilms__ are complex groups of microorganisms (specifically bacterial cells) on a solid substrate that cooperate metabolically. They are characterized by structural heterogeneity, genetic diversity and extracellular matrix of polymeric substances. (Bacterial) Cells in a biofilm secrete signaling molecules that call upon nearby cells which sense their local density, a process called quorum sensing. The cells also produce proteins to attach to the substrate and each other, causing the biofilm to grow (pg 565 & 207). Biofilm bacteria have an increased resistance to antibiotics due to the dense extracellular matrix. As they contain regions of specialized function, organisms like myxobacteria (figure 11.3) use chemical signaling to communicate with neighboring cells about nutrient availability. When food is limited, these cells are prompted to aggregate, forming a structure called a fruiting body which produces thick-walled spores capable of surviving until the environment improves. Periodontitis and caries are infectious diseases of the oral cavity in humans that involve biofilms.

__Temperature and pH__ are abiotic factors important to enzymatic activity. The rate of an enzymatic reaction increases with increasing temperature, partly because substrates collide with active sites more when the molecules move rapidly. However, above that temperature, the speed of enzymatic reaction slows down dramatically. The thermal sensitivity of enzymes can disrupt hydrogen bonds, ionic bonds and other weak interactions that stabilize enzyme shape. This ultimately denatures the protein molecule which can be life threatening. Just as an enzyme has an optimal temperature, it also has an optimal pH level. Similarly, a pH level that is too high can denature most enzymes in the body (pg 155).

__Water availability__ directly affects cell activity. The water that you lose when you sweat comes from the cells of your body. If that water is not replaced by drinking, your cells can become dehydrated. When water is deficient, wastes build up in the fluid that surrounds the cells, preventing nutrients from getting into the cell. When toxins accumulate, they can deprive the cells of oxygen and even cause cell mutation. When water is lacking in your body, one of the first functions that is affected is detoxification. All of the detoxification functions in the body including breathing, sweating, urinating and defecating, require water. (pg 155). A change in a biotic or abiotic factor in a system can be life threatening.


 * **__Organisms use free energy to maintain organization, grow and reproduce__ by Amanda Seale (p. 862-865)**

Appendix A: Essential knowledge 2.A.1: All living systems require constant input of free energy.

Body temperature and metabolism is maintained by organisms using various tactics. For example, organisms known as endothermic are warmed by heat produced mainly by metabolism. These animals, mostly mammals and birds, are known as endotherms. Stable body temperatures can be maintained by endotherms even in the midst of large environmental temperature fluctuations. Endotherms can generate enough heat using their metabolism so that they can keep their body warmer than the surroundings even in very cold habitats. Mechanisms like shivering allow this to happen. In a hot environment, endotherms have mechanisms like sweating to help cool the body. This allows them to survive very hot environments. Ectotherms, on the other hand, gain their heat from outside sources. Ectothermic organisms, like amphibians, lizards, snakes, most fish, turtles, and most invertebrates, consume a lot less food than endotherms, because they don’t need it to sustain their metabolism. In times of limited food sources, this proves to be an advantage. They don’t adjust body temperature by thermoregulation as they cannot generate enough heat, but attain it by behavioral means. This includes basking in the sun or cooling off in water. In some plant species, they have elevated floral temperatures. This allows for the plants to sustain some degree of varying temperature. In extreme temperature changes however, it is most likely the plant will not survive. The term poikilotherm-an animal whose temperature varies with its environment- is often associated with endotherms. The term homeotherm can be is often labeled to ectotherms, which refers to animals who have a relatively constant body temperature. However, there is no fixed relationship between the source of heat and the stability of body temperature.

Mr. Andersons video on response to external environments provides an explanation of some of the behavioral mechanisms ectotherms perform to maintain homeostasis and temperature as well as some of the mechanisms utilized by endotherms. [|__http://www.youtube.com/watch?v=BUlBwe8miTQ&feature=player_embedded__]


 * **__Energy-related pathways in biological systems are sequential and may be entered at multiple points in the pathway: The Krebs Cycle__ by Amanda Seale** (pages 170-172)

Essential knowledge 2.A.1: All living systems require constant input of free energy

If molecular oxygen is present after glycolosis, the pyruvate enters a mitochondrion where the citric acid cycle enzymes complete glucose oxidation. The Kreb’s Cycle, also known as the citric acid cycle, takes place in the mitochondria, and functions to oxidize organic fuel derived from pyruvate. In prokaryotic cells, the Kreb’s cycle occurs in the cytosol.

The steps of the citric acid cycle are as follows: 1. The two-carbon acetyl group from acetyl coenzyme A is added to oxaloacetate, and produces citrate. 2. Citrate is converted to isocitrate (it’s isomer). This is accomplished by the removal of one molecule and the addition of another. 3. Isocitrate is oxidized, and reduces NAD+ to NADH. The resulting compound loses a CO2 molecule. 4. Another Co2 molecule is lost. The resulting compound is oxidized and NAD+ is reduced to NADH. The remaining molecule attaches to coenzyme A by an unstable bond. 5. Coenzyme A is replaced by a phosphate group. It is then transferred to GDP, forming GTP. 6. Two hydrogen molecules are transferred to FAD. FADH2 is formed and succinate is oxidized. 7. A water molevule is added and the bonds in the substrate are rearranged. 8. The substrate is oxidized and NAD+ is once again reduced to NADH and oxaloacetate is regenerated.
 * GTP is a molecule that has functions similar to ATP. In some cases it can be used to generate ATP.
 * The cycle starts over*

The Citric Acid Cycle is named the Kreb’s Cycle in honor of Hans Krebs, a German-British scientist who worked out the pathway in the 1930’s.

by Maeve Dalpe
 * Appendix A, Big Idea 2, O

Homeostatic mechanisms reflect both common ancestry and divergence due to adaptation in different environments. Continuity of homeostatic mechanisms reflects common ancestry such as the c irculatory systems of plants, amphibians and mammals. Striking similarities in these systems suggest the existence of a common ancestor. They are all composed of blood, veins, arteries, capillaries and a heart. The purpose of blood in all three is to carry oxygen throughout the organism. The evolution of the chambered heart suggests the gradual “fine-tuning” of homeostasis.

The differences that separate the three circulatory systems is the method which they carry out blood flow. In fish, blood is circulated by a two-chamber heart composed of a non muscular atrium and a muscular ventricle with blood flowing from the body to the atrium. The atrium pumps the blood to the ventricle where it’s moved to the gills to absorb oxygen and travel to the body’s circulatory system. Amphibian hearts are composed of three chambers - two atrium and one ventricle. Blood from the ventricle is pumped in the left and right atrium. The left, pumps blood to the lungs where it absorbs the oxygen and is returned to the left atrium. Blood from the right atrium is sent to the body. The set back from having only one ventricle is that amphibians cannot separate oxygen rich blood from blood that is low in oxygen, limiting blood circulation. In mammals, blood is circulated by a four chamber heart (two atrium and two ventricles). Blood low on oxygen enters the right atrium where the lungs replenish the blood and send it to the left ventricle. It keeps moving to the left atrium where it is pumped back into the body. This continuous cycle is the most evolved method of circulation due to its ability to maximize the amount of oxygen and nutrients in an organism’s blow flow.

By Maggie Garrahan
 * Essential Knowledge 2.A.3: Organisms must exchange matter with the environment to grow, reproduce and maintain organization.

Matter: All material in the universe that has mass and occupies space (Solid, liquid, or gas) Matter can transform from one substance to another and can never be created or destroyed. Nutrients are elements that are greatly needed by organisms. Energy flows in one direction through an ecosystem.

1. Reproduction requires free energy beyond that used for maintenance and growth. a. Changes in free energy availability can result in changes in population size.

b. Changes in free energy availability can result in disruptions to an ecosystem.

2. Organisms capture and store free energy for use in biological processes (growth).

a. Autotrophs capture free energy from physical sources in the environment.

b. Photosynthetic organisms capture free energy present in sunlight.

c. Heterotrophs capture free energy present in carbon compounds produced by other organisms.

3.Exchange of matter

a. Molecules and atoms from the environment are necessary to build new molecules.

b. Carbon moves from the environment to organisms where it is used to build carbohydrates, proteins, lipids or nucleic acids. Carbon is used in storage compounds and cell formation in all organisms.

c. Nitrogen moves from the environment to organisms where it is used in building proteins and nucleic acids. Phosphorus moves from the environment to organisms where it is used in nucleic acids and certain lipids.

Example: http://media.collegeboard.com/digitalServices/pdf/ap/10b_2727_AP_Biology_CF_WEB_110128.pdf

By Maggie Garrahan
 * Essential Knowledge 2.E.2: Timing and Coordination of physiological events are regulated by multiple mechanisms.

In plants, physiological events involve interactions between environmental stimuli and internal molecular signals.

Phototropism= plants response to the presence of light

Photoperiodism= plants response to change in length of the night, that results in flowering in long-day and short-day plants

In animals, fungi, protists, and bacteria, internal and external signals regulate a variety of physiological responses that synchronize with environmental cycles and cues.

Examples in animals:

1. Jet lag

2. Seasonal Responses (migration, hibernation)

“Biological clocks” provide temporal coordination among physiological, behavioral, and environmental events.

Data can be collected to understand how timing and coordination of physiological events involve regulation by studying how humans act when their timing is changed and by studying plants when they lose coordination.

The example of jet lag: When humans travel to countries that have a time difference, it takes awhile for humans to adjust. It is hard for them to fall asleep and they are hungry at different times. Humans are used to their own schedules where they live, and when that is changed, our bodies do not know how to react. This shows how humans regulate time and are affected when it is disrupted.

http://www.ncbi.nlm.nih.gov/pubmed/3555232

https://docs.google.com/document/d/17YOkaT8RgrTQAD2ROfAML-GprGrZSLpgdWfLijCkbj8/preview

Emily Bernardi
 * Essential Knowledge 4.B.2 Cooperative interactions within organisms promote efficiency in the use of energy and matter.

1. At the cellular level, the plasma membrane, cytoplasm and, for eukaryotes, the organelles contribute to the overall specialization and functioning of the cell.

The plasma membrane is the cell's outer membrane, which is made up to two layers of phospholipids that have embedded proteins. It separates the contents of the cell from its outside environment, and also regulates what enters and exits the cell. The cytoplasm is the substance which fills the cell. Organelles are specialized subunits within cells that have specific functions. Depending on what organelles are present in the cell determines what the cells are specialized for. These cell perform specific functions for larger organs or tissues.

2. Within multicellular organisms, specialization of organs contributes to the overall functioning of the organism.

The Human Body contains many specialized organs that work together to provide an overall homeostasis in the body.

Essential Knowledge 2.C.2: Organisms respond to changes in their external environments.
 * **__Torpor and Environmental Changes__ – Gabriela Christian (pages 871-872)**

Animals may encounter conditions that challenge their abilities to maintain homeostasis. For example, certain seasons, the time of day, or a specific temperature could all affect an individual’s ability to balance their heat, energy and materials budgets.

//Torpor:// a physiological state in which activity is low and metabolism decreases. This is an adaptation that lets animals save energy while avoiding difficult and dangerous conditions.

An example of this is hibernation. Hibernation is a long-term torpor and is an adaptation to the cold of winter and the scarceness of food. When organisms enter hibernation, their body temperatures decline so that they can save energy, making their metabolic rates much lower. This way, hibernating animals can survive through winter on limited supplies of energy stored in its fat tissues. Similarly, estivation, summer torpor, allows animals to survive lengthy periods of high temperatures and low water through a slower metabolism.

There are also much shorter torpors that can occur every day. For example, some bats feed at night and experience torpor during the day. Often birds feed during the day and go into torpor at night.

Essential Knowledge 2.D.3: Biological systems are affected by disruptions to their dynamic homeostasis. Set points for homeostasis can change under certain circumstances. Regulated changes in the internal environment of individuals are actually essential to normal body functions. For example, many animals have a lower body temperature when they are sleeping than when they are awake. Some regulated changes can be associated with specific stages in development, like radical hormonal changes during puberty. Other changes are cyclic, like the hormones in a woman’s menstrual cycle.
 * **__Alterations in Homeostasis__ – Gabriela Christian (page 862)**

Over short term intervals, homeostatic mechanisms maintain the set point, but in the longer term, homeostasis will allow regulated change, thus altering the body’s internal environment. One way that the normal range of homeostasis could change is through acclimatization. This is the process by which an animal adjusts to changes in its external environment. This should not be confused with an adaptation, because it is a temporary change during an animal’s lifetime, whereas an adaptation is a process of change in a population over many generations.

Big idea 2 part 1 letter m Circadian rhythms are physiological cycles of about 24 hours that are present in all eukaryotic organisms. They persist even in the absence of external cues and are not paced by a known environmental variable. This clock is being traced to the synthesis of a protein that regulates its own production through feedback control, and it may also be a transcription factor that inhibits transcription of the gene that encodes the transcription factor itself. In plants, the biological clock is reset at dawn by the photochrome that triggers many of a plants developmental response to light. The combination of a photochrome system and a biological clock let the plant assess the amount of daylight or darkness, thus knowing the time of year. The molecular gears of the circadian clock are internal and function in all conditions. Pulse rate, blood pressure, temperature, rate of cell division, blood cell count, alertness, urine composition, metabolic rate, sex drive, and response to medications all fluctuate in a circadian manner.
 * **__Circadian Rhythms__** by Lea Adams (page 838)

Big idea 2 part 1 letter p Acquired immunity defends against infection of body cells and fluids, and its two branches are humoral immune response and cell-mediated response in mammals. Humoral involves the activation and clonal selection of effecter B cells, which produce antibodies that circulate in the blood and lymph. The cell mediated response involves the activation and clonal selection of cytotoxic T cells, which identify and destroy infected cells. The aspects of these two responses are shown in the diagram below. (picture wont upload so here is the link) [|http://www.bing.com/images/search?q=humoral+and+cell+mediated+immune+response&FORM=AWIR#view=detail&id=5E829AB70BAA4AE1A68B43EF14156FFB1655ABBA&selectedIndex=0]
 * **Humoral and cell-mediated immune responses** by Lea Adams (page 942)

Page 990 By: Christina Dykas Appendix A Big Idea 2 Letter l
 * __**Changes in Negative or Positive Regulatory Systems Result in Consequences: Hyperthyroidism and Grave’s Disease**__

Alterations to the negative regulatory system can cause damage to the organism. They thyroid hormone regulates homeostasis and development of vertebrates and regulates bioenergetics in mammals. Above or below the set amount of this thyroid hormone causes disorders. The thyroid secreting hormone needs to be kept in check by negative feedback to not produce too much or too little of the thyroid hormone. Hyperthyroidism is when too much of the thyroid hormone is secreted and this can cause problems such as sweating, weight loss, body temperature increase, blood pressure increase, and irritability. Grave’s disease is a specific example of hyperthyroidism. In this disease, a positive regulatory system occurs because a receptor binds to the thyroid secreting hormone and causes it to continue secreting thyroid hormones without being regulated by a negative regulatory system. The thyroid hormones continue increasing and cause symptoms such as bulging eyes from fluid buildup. This shows how when a positive system (positive feedback) replaces a negative system, the organisms suffers consequences. This diagram shows the negative feedback system that the thyroid secreting hormone should be involved in and when this becomes positive, disorders can arise.

Mariah Pennington
 * Appendix A, letter g: Interdependency of the processes of photosynthesis and cellular respiration.

The Endosymbiotic Theory describes how chloroplasts and mitochondria most likely came to be. These two organelles carry out processes that are considered “opposites” because the reactants of one are the products of the other. Photosynthesis is thought to have developed first, in an ancient species of photosynthetic bacteria. The chlorophyll in the chloroplasts trap the sunlight energy. That energy is what helps convert carbon dioxide and water into oxygen and glucose. That glucose is then used by the autotroph as a “food” source for its cells (in the form of ATP molecule). The reactants required in cellular respiration are the products of photosynthesis (oxygen and glucose). The mitochondria converts those into carbon dioxide and water vapor. Cellular respiration occurs mainly in heterotrophs. (textbook pages 185-187 and 162-165).

Mariah Pennington The miracle of life is most apparent when a new baby is forming. The first example of critical timing that occurs during normal animal development is called the cortical reaction. During fertilization, the sperm cell must penetrate the egg cell. The first one to get inside triggers this reaction, which inactivates the other sperm-binding receptors (to block competitors and prevent multiple sperm from entering). The fertilization envelope then begins to form (textbook page 1023). Once the zygote’s cells start dividing and reach gastrulation, another milestone event affects the outcome of the product (a new organism). During gastrulation, the zygote invaginates and folds in on itself to become a hollow pocket from which it can develop from the inside outward. The opening, called the blastopore, will eventually become either the mouth or anus. It’s pretty important not to get those mixed up, as it could cause serious issues in the organism’s future. Two major categories to which organisms belong are either protostomes or deuterostomes, depending on whether the mouth is the first or second opening. (page 1028 in textbook).
 * Appendix A, letter r: Timing and coordination of several events are necessary for normal development in an organism.

Appendix A Big Idea 2 Letter I
 * __**Methods of Transport Across A Membrane**__ (page 132-138) By: Christina Dykas

Diffusion is the movement of molecules so that they spread out evenly into an available space.
 * · Passive transport is an example of diffusion where no energy is needed to move the molecules across a membrane. The molecules simply move from a high concentration to a low concentration.


 * · Osmosis is the diffusion of water across a membrane so that the amount of water outside the cell balances the inside amount.

Active transport is when energy is required to move molecules against the concentration gradient across a membrane. When wanting to move from a low concentration to a high concentration, transport proteins move the molecules across the membrane and expend energy.
 * · Facilitated diffusion is when molecules passively diffuse through a membrane but are assisted by a transport protein. These proteins are specific to certain molecules.

Larger molecules cannot pass through the membrane so they need to packed in vesicles to transport into or out of the cell. This occurs by the following processes:
 * · Exocytosis is when a cell secretes molecules by the fusion of vesicles with the plasma membrane.


 * · Endocytosis is when a cell takes in moleules and matter by forming vesicles from the plasma membrane.

This video explains all of the above methods of transport and is very helpful. https://www.youtube.com/watch?v=RPAZvs4hvGA


 * **__Diffusion/ osmosis__** – Kylie Dolan

Essential knowledge 2.A.3: Organisms must exchange matter with the environment to grow, reproduce and maintain organization.
 * "Membranes allow cells to create and maintain internal environments that differ from external environments. The structure of cell membranes results in selective permeability; the movement of molecules across them via osmosis, diffusion and active transport maintains dynamic homeostasis.”


 * This concept goes all the way back to sophomore year biology but conceptually confuses me every time I have to answer those "a cell is placed in a solution that is hypo/ hypertonic to it..." questions.


 * Diffusion: This is the tendency for molecules move from higher concentration areas to lower concentration areas. This type of movement does not require energy.
 * A substance in diffusion is said to move "down the concentration gradient."
 * Passive transport is diffusion across a biological membrane
 * Osmosis:Diffusion of water across a selectively permeable membrane
 * OSMOSIS ALWAYS GOES FROM HYPOTONIC TO HYPERTONIC!
 * Hypertonic: Solution with higher solute concentration
 * Hypotonic: Solution with lower solute concentration
 * Isotonic:Solution with equal solute concentration [[image:osmosis.jpg]]


 * **__Exergonic and endergonic reactions and the laws of thermodynamics__** - Kylie Dolan

Essential knowledge 2.A.1: All living systems require constant input of free energy. Essential knowledge 2.A.2: Organisms capture and store free energy for use in biological processes.

Energy is the capacity to do work The first law of thermodynamics states that energy cannot be created nor destroyed but can change from one form to another. The second law of thermodynamics states that every energy transfer increases the entropy (disorder) of the universe Exergonic reactions are reactions that produce a net release of free energy Endergonic reactions are reactions that absorb free energy from its surroundings
 * Free energy is the total amount of energy and a system that can be tapped into do work
 * ex: plants convert light energy from the sun to make chemical energy in the form of glucose
 * AB ---> A + B + Energy
 * Example (Respiration): 6O2 + C6H12O6 --> 6CO2 +6H2O + energy
 * A + B + Energy ---> AB
 * Example (photosynthesis): 6CO2 + 12H2O + light (energy) --> C6H12O6 + 6O2 + 6H20

Owen Gaffney

Letter A) calculate surface area to volume ratios for variety of cell shapes and predict based on ratios which cell procures nutrients or eliminates waste the fastest.

-The shape that has the highest S.A. to volume ratio is the best:

Sphere- S.A. is 4pieR^2 or (4)(pie)(1cm)^2= 12.6 cm^2

- Volume is 4pieR^3 /3 or (4)(pie)(1cm)^3/3= 4.2 cm^3

- about 3:1 ration S.A. to V

Cube - S.A. is 6(side)^2 or (6)(1cm)^2= 36cm^2

- Volume is (l)(w)(h) or (1cm)(1cm)(1cm)= 1cm^3

- 12:1 S.A. to Volume ration

Squamous- S.A. is s.a. of each side...say 4cm^2+4cm^2+4cm^2+4cm^2+1cm^2+1cm^2= 20cm^2

-Volume is (l)(w)(h) or (1cm)(1cm)(4cm)= 4cm^3

-ration of S.A. to Volume is 5:1

-From this data it can be concluded that simple cuboidal shaped cells have the highest rate of diffusion because they have the most surface area compared to volume of their cells. Of course, the smaller the volume of the cell, the more efficient and quicker it can pass materials over its membrane

Owen Gaffney

Letter C) Predict 1 to 2 consequences to organisms populations and ecosystems if sufficient free energy is not available.

-if a sufficient amount of free energy is not available in an ecosystem it can have serious effects. If a higher level consumer is not able to eat enough lower-level organisms to fulfill free energy requirements to maintain homeostasis at their trophic level, they will die. Because the level of free energy available in a food chain decreases by 90% each trophic level higher level consumers must consume more in order to maintain homeostasis. Say that a keystone species in an ecosystem dies out due to overpredation or disease; an organism that usually feeds on this out of higher trophic level will lose its source of free energy and die. If overpredation or disease sweep entire population at a lower trophic level whole populations of higher organisms die off as well. With two levels of free energy being virtually deleted from an ecosystem you can have serious effects on the food what as a whole. It is possible that one free energy is not available ecosystems could downsize overall into most basic forms. One higher trophic level consumers die off they leave room for lower trophic level producers and really consumers to replenish their stock into growing numbers. So it may take time over many years the ecosystem could reset itself and rebalancing on a free energy available at each trophic level until it reaches its carrying capacity at about five or six levels.

Appendix A Big Idea 2 letter J - explain how several organelles work together to provide a specific function Amanda Vespermann The endoplasmic reticulum works closely with the golgi bodies of the cell in order to package and secrete proteins. Ribosomes, found on the surface of the rough endoplasmic reticulum, are made of ribosomal RNA and carry out protein synthesis. The ribosomes bound to the rough ER are referred to as bound ribosomes, as opposed to free ribosomes. The endoplasmic reticulum is responsible for secreting the proteins produced by the ribosomes attached to it. Proteins are stored in the ER membrane before transport vesicles transport the protein from one part of the cell to another. Glycoproteins are often formed in this way, which are proteins that have carbohydrates covalently bonded to them. After the rough ER secretes the proteins with the help of the ribosomes, the transport vesicles transport the protein to the golgi apparatus. Vesicles attach to the cis face of the golgi body and move toward the trans face direction. From this point, proteins can take one of three paths. They can form and leave the golgi, getting carried to other locations or the plasma membrane for secretion out of the cell to be used in other parts of the body. They can also be transported by vesicles backward to less mature golgi cisternae and function within the golgi apparatus. Lastly, certain proteins can be transported back to the ER, where they will function. (textbook pages 102-106) Example: [] - youtube video of a high school biology teacher explaining how the ER and Golgi apparatus work together during protein synthesis.

Appendix A Big Idea 2 letter I - explain an example of a positive feedback loop Amanda Vespermann Lactation in mammals and progression of labor in childbirth are both examples of positive feedback loops in mammals. Although negative feedback loops are more common, positive feedback loops are nonetheless still important. In lactation, the action of sucking actually stimulates the body to produce more milk. The suckling by the newborn is coupled with the changes in estradiol levels after birth, therefore causing the hypothalamus to signal the anterior pituitary to secrete prolactin. Prolactin stimulates the mammary glands to produce milk. Instead of sending a signal for the mammary glands to stop production, a positive feedback loop causes more milk production. In labor, oxytocin is a hormone found in the fetus and the mother's posterior pituitary. The oxytocin stimulates the uterus to contract and stimulates the placenta to make prostaglandins. Prostaglandins stimulates more contractions of the uterus, causing a positive feedback loop back to the initial oxytocin. (textbook page 1015) Example: [] - a Bozeman video explaining the difference between positive and negative feedback loops.

Essential Knowledge 2.B.3: Eukaryotic cells maintain internal membranes that partition the cell into specialized regions. Kayla Kaufmann (Make-up Work) Pages 104-105


 * Internal membranes assist cellular processes by minimizing competing interactions and by increasing surface area where reactions can occur.
 * Membranes and membrane-bound organelles in eukaryotic cells compartmentalize intracellular metabolic processes and specific enzymatic interactions.
 * Comparmentalization is parts within the parts and allows us to specialize so we can have parts of the cell that do specific jobs and the surface area can be increased without making the cell smaller, it just contains parts inside it that are smaller.
 * The endoplasmic reticulum is a great example and one college board recommends as a an example of this concept you should understand .... (other recommended examples include the mitochondria, chloroplasts, golgi, and nuclear envelope)
 * The endoplasmic reticulum is a specialized organelle and it also helps increase surface area for the cell.
 * The rough ER has a membrane that is continuous with the nucleus and it is highly folded and there are ribosomes sitting on the outside of it (why its called "rough") A good analogy is the rough ER is like the factory of the cell and its where proteins are "manufactured" and also the mebranes used within the cell
 * The smooth ER lacks ribosomes so its "smooth". It will produce things like lipids and carbohydrates in the cell. Its other very important function is detoxification so it breaks down toxins. It serves as a transitional area for vesicles that transport ER products to various destinations