BIO 162 Midterm 2 Objectives

(7) Explain how is the electrochemical gradient used to import K+ and NO3- (channel, cotransport)*

H+ is pumped into the environment using a H+ ATPase pump, to create a gradient that is favorable for K+ to enter the cell through an ion channel However, the NO3- (anion) must come through a cotransporter with an H+ ion (symport into the cell) because H+ is going down its gradient

(6) Describe the flow of blood through the human heart and blood vessels in the proper order (name and locate each of the atria, ventricles, valves, and the aorta, pulmonary artery, and superior and inferior vena cava).*

(both) vena cava, right atrium, tricuspid valve, right ventricle, semilunar valve, pulmonary artery --> LUNGS--> pulmonary vein, left atrium, bicuspid valve, left ventricle, semilunar valve, aorta

(10) Explain why Na+ and K+ move passively across neuronal cell membranes in the directions that they do (concentration gradient, electrical gradient, electrochemical gradient).

- After Na+ is pumped out and K+ is pumped in against their concentration gradients, the leak channels allow the Na+ and K+ to passively travel back down their concentration gradients - At resting potential, the inside of the cell is more negative and the outside of the cell is more positive. This allows the positively charged Na+ to passively travel down its electrical gradient to the inside of the cell, and it allows the K+ that is attached to a negative protein to passively travel down its electrical gradient to the outside of the cell. - An electrochemical gradient is the combination of both the electrical and the chemical (concentration) gradients.

(9) Describe an experiment you could do to determine the role of auxin in establishing apical dominance (Hint: you will do this in lab).

- Cut off the terminal part of the stem above the primary node, and examine and record what the lateral buds look like so you can detect the difference - Cover the cut surface with auxin and lanolin and observe growth of lateral buds over time - Areas with lanolin will not grow and areas with auxin will

(10) Explain how the resting membrane potential of a cell is established (Na+/K+ ATPase, leak channels, equilibrium potential).

- In resting neurons, the membrane is selectively permeable to K+. As K+ leaves the cell along its concentration gradient, the inside of the membrane becomes negatively charged relative to the outside. - The Na+/ K+ -ATPase actively pumps Na+ out of the cell and K+ into the cell. This ensures that the K+ concentration is a lot greater on the inside of the plasma membrane than on the outside - The K+ leak channel allows K+ to leak across the membrane down its electrical gradient - The eventual buildup of negative charge inside the membrane begins to attract K+ and counteract the concentration gradient that had favored movement of K+ out (the electrical gradient favors movement of K+ in which is opposite the concentration gradient) at this voltage, known as the equilibrium potential, there is no longer a net movement of K+.

(6) Distinguish between open and closed circulatory systems, and name the animal groups that have each type. *

- Open circulatory systems are systems where blood, rather than being sealed tight in arteries and veins, suffuses the body and may be directly open to the environment. (insects, lobsters and crabs, and molluscs) - In a closed circulatory system, the blood stays within blood vessels. In this way, blood is kept separate from body tissues. As such, the blood tends to be pumped at a higher pressure. In organisms with a closed circulatory system, the blood does not fill body cavities. (birds, mammals, fish, reptiles, amphibians, and some invertebrates)

(10) Explain how myelination alters the speed of conduction along the length of an axon (Schwann cell, myelin, leakage, node of Ranvier, internode, regeneration, ALS and multiple sclerosis).

- Schwann cells wrap around an axon multiple times to create a thick layer of myelin sheath, which acts as a type of electrical insulation - The myelin sheath prevents ions from leaking back out across the plasma membrane of the axon. - The axon can be split up into two parts: nodes and internodes. The internodes are the myelinated portion of the axon, and the nodes are the unmyelinated portion called the nodes of ranvier. The nodes of ranvier have a dense concentration of voltage-gated Na+ and K+ channels, which allows new action potentials to be generated at these nodes. - Myelinated axons conduct action potentials anywhere between 15-150 times faster than unmyelinated axons - In non-myelinated axons, an action potential is triggered at the beginning of a nerve fiber, and it causes the next nerve fiber membrane to depolarize, which eventually generates an action potential. However, in myelinated axons, the nodes of ranvier allow the nerve impulses to jump from one node to the next, as the action potentials are regenerated at the next node of ranvier. This results in faster nerve impulses. - Multiple sclerosis occurs when the immune system targets the oligodendrocytes, therefore destroying myelin. As damage to the myelin increases, electrical signaling becomes more impaired. This affects coordination amongst neurons, causing muscles to weaken. - ALS is characterized by the loss of motor neurons. Motor neurons use their axons to send electrical signals from the CNS (brain and spinal cord) to muscle fibers. Without motor neurons being able to send electrical signals to muscles, muscles are weakened and physical function is impacted.

(10) Describe the stages and characteristics of an action potential (threshold, rising phase, positive feedback, voltage-gated channels, inactivation, depolarization, repolarization, hyperpolarization, refractory period).

- The sodium-potassium pump opens, pumping out 3 Na+ for every 2 K+ pumped into the neuron. Once there is enough of a change in voltage to reach threshold, the action potential will be started. The neuron's resting state is at -70 mV and threshold is at -55 mV. - When the action potential begins, voltage gated Na+ and K+ channels open and sodium rushes into the cell, which causes depolarization (increase in voltage on the inside of the cell) - As some depolarization gets to the beginning of the axon, it makes some voltage gated channels open, it makes the membrane depolarize which makes more channels open which makes it even more positive which makes more channels open etc. This demonstrates positive feedback. - The voltage gated sodium channels go into an inactivated state after they have been open for a while. This means that they cannot go back into the active state, they have to wait for the cell to re-polarize first before they can become inactive. if they were to close, they might just open again bc of the positive charge inside the cell - The K+ channels take a longer time to open up, so once they finally do, potassium rushes out of the cell. The Na+ channels then close, preventing more sodium from rushing in, causing repolarization - Then, in an attempt to repolarize back to the set point, an excess amount of potassium leaves which causes the cell to become hyper-polarized - This action potential is propagated along the myelinated axon which prevents leaking of ions, and helps the action potential to regenerate at every node of ranvier. - Action potentials only propagate downstream because of the refractory period. This is a period of time in which the ion channels are open, and therefore, the neuron cannot respond to any other stimulus. The refractory period is useful to prevent signals travelling in both directions down an axon at once.

(7) How does the presence of leghemoglobin influence the efficiency of N2 fixation? Which organism (plant or rhizobia) produce this protein?

- in bacteria, N2 in converted into NH4 by using H+, 16 ATPs and 8e- - nitrogenase complex is a series of enzymes that make series of reactions happen - bacteria is in the root, N2 diffuses in and is converted to NH4+ - this NH4+ is then used in amino acids (proteins and nucleic acids)

(9) How is gravity sensed in roots? How does gravity sensing lead to the root bending down (gravitropism)? (amyloplasts, starch, auxin)*

1) Amyloplasts, organelles that containing starch granules, are pulled to the bottom of root cap cells by the force of gravity. ( starch is denser than water.) 2) The position of the amyloplasts activates sensory proteins located in the plasma membrane. These sensory proteins initiate the gravitropic response to actively redistribute *In both roots and stems, auxin accumulates towards the gravity vector on the lower side. In roots, this results in the inhibition of cell expansion on the lower side and the concomitant curvature of the roots towards gravity (positive gravitropism).[2][7] In stems, the auxin also accumulates on the lower side, however in this tissue it increases cell expansion and results in the shoot curving up (negative gravitropism).

(6) Describe the four steps by which oxygen moves from the environment to cells in the body and carbon dioxide moves from cells to the environment (convection, bulk flow, diffusion).

1: bulk flow (Ventilation) of air into alveoli -respiratory system 2: diffusion (at the respiratory surface) across lung surface- O2 moves from the air or water into blood, CO2 moves from blood to air or water -respiratory system 3: bulk flow (circulation) of blood -circulatory system 4: diffusion of oxygen into cells (specifically mitochondria) where O2 moves from blood into the tissues and CO2 moves from the tissues into the blood 5: cellular respiration- the cell's use of O2 and production of CO2 Convection: bulk flow of a fluid from one place to another Bulk flow: directional mass movement of a fluid due to pressure differences Diffusion: spontaneous movement of a substance from one region to another, often with a net movement from a region of high concentration

(10) Describe how a signal is communicated from one neuron to another neuron at a synapse (synapse, vesicle, neurotransmitter, receptor, channel, IPSP, EPSP).

1) An action potential arrives at the end of the axon 2) The depolarization created by the action potential opens voltage-gated calcium channels located near the synapse, in the plasma membrane of the presynaptic neuron. The electrochemical gradient for Ca2+ results in the inflow of calcium ions through the open channels 3) In response to the increased calcium concentration inside the axon, synaptic vesicles fuse with the membrane and release neurotransmitters into the gap between the cells, the synaptic cleft. The delivery of neurotransmitters into the cleft is an example of exocytosis. 4) Neurotransmitters bind to receptors on the postsynaptic cell. Thus, each neurotransmitter functions as a ligand, a molecule that binds to a specific site on a receptor molecule. Neurotransmitter-receptor binding leads to a change in the membrane potential of the postsynaptic cell. The combined effect on membrane potential of many neurotransmitters binding may trigger an action potential in the postsynaptic cell 5) The response ends when the neurotransmitters unbind from their receptors and diffuse out of the synaptic cleft, are broken down, or are taken back up by the presynaptic cleft EPSP: changes in the membrane potential of a postsynaptic cell that make the cell more likely to produce an action potential IPSP: changes in the membrane potential of a postsynaptic cell that make the cell less likely to produce an action potential

(9) Make a diagram similar to figure 37.2 showing the signal transduction pathway for auxin that leads to cell wall loosening. Include the receptors ABP and ARF. How does the auxin pathway differ from the 'generic' signal transduction pathway in the figure? Consider showing how the cellular components differ in the absence and presence of auxin. (ER, H+ pump)

1) Auxin goes through a channel and binds to Auxin response factor (ARF), activating it. 2) ARF acts has a primer and enable RNA polymerase to express auxin responsive genes. 3) Vesicle transports Auxin binding protein (ABP) and proton pump from ER to the plasmid membrane. 4) Proton pumped out of cytoplasm and lowers the pH of wall → activates expansin and weakens hemicellulose binding

(8) Compare and contrast the causes, prevalence, and treatments of type I and type II diabetes mellitus. *

1) Cause of type 1: autoimmune disease that causes the body not to synthesize sufficient insulin. 2) Cause of type 2: insulin receptors no longer function correctly or are reduced in number. 3) Type 1 treatment: insulin injections and careful attention to diet. 4) Type 2 treatment: prescribed diets, exercise, monitoring blood glucose levels, and taking drugs that increase cell responsiveness to insulin. ****Prevalence: 90-95% of diabetes cases are type 2.

(7) Diagram the steps in which rhizobia colonize a root. (flavonoid, infection thread, cytoplasm, nodule, cell division)*

1) Flavonoid released by root hairs to attract rhizobia, rhizobia move into hairs NH3 diffuses through root hairs 2) Rhizobia proliferate inside root hair and cause an infection thread to form 3) Infection thread grows into the cortex of the root 4) Infection thread buds off, releasing rhizobia inside cortex cells 5) Nodule begins to form from rapidly dividing cortex cells

(11) List the 4 parameters of primary sensory coding and give examples of pairs of actual sensory stimuli that differ for each parameter.

1. Stimulus type (modality) - mechanoreceptors, photoreceptors, chemoreceptors, thermoreceptors, nociceptors, electroreceptors, magnetoreceptors 2. Stimulus intensity (strength) - a strong whiff of vinegar vs a mild whiff of vinegar (olfactory nerve) 3. Stimulus duration - a quick flash of light vs a long flash of light (optic nerve) 4. Stimulus location

(9) What is the relationship between blue light and phototropism (signal, receptor, response, phototropin [PHOT1])

A key breakthrough came in the early 1990s, when researchers found a membrane protein in the tips of emerging shoots that gains a phosphate group in response to blue light. Researchers hypothesized that the membrane protein becomes activated when it is phosphorylated in response to blue light, and that the activated protein then triggers the phototropic response. Subsequent work succeeded in isolating the gene that codes for the membrane protein.

(7) In addition to pumping H+ into the environment, root acidifies soil in another way. What is it? (note, This is similar to what causes the Bohr shift in the animal body.)

Ammonium nitrogen is readily converted to nitrate and hydrogen ions in the soil. If nitrate is not taken-up by plants, it can leach away from the root zone leaving behind hydrogen ions, thereby increasing soil acidity

(8) Distinguish between autotrophs and heterotrophs

Autotrophs: produce their own food, usually via photosynthesis Heterotrophs: rely on other organisms to get their food

(8) Distinguish between the roles of bile and lipase in the digestion of fats (emulsify, catalyze)

Bile emulsifies fats before they are able to then be digested by lipase. Bile: composed of bile salts; enters the small intestine and raises the pH to emulsify fats (emulsification breaks down fats into smaller fat droplets to give the fats a larger surface area) Lipase: "Lingual" lipase, secreted by the tongue begins the digestion of fats by breaking triglycerides into diglycerides and fatty acids. "Pancreatic" lipase digests fats once they are emulsified and turns the smaller droplets into monoglycerides and three fatty acids The lipase enzymes catalyze the breakdown of fats

(8) For the human digestive system, create a table describing how each major nutrient type (carbohydrate, protein, lipid) is digested and absorbed (in what part of the tract, by what enzyme(s), by what process). *

Carbohydrates: digestion starts in the mouth via amylase in saliva. Absorption occurs mainly in the small intestine, but also a little bit in the mouth Protein: digestion occurs mainly in the stomach, but also a little bit in the small intestine. Absorption occurs in the small intestine Lipid: digestion and absorption both occur in the small intestine

(12) Name one function of cartilage and three functions of bone.

Cartilage: cushions joints where bones articulate with one another Bone: structural support (shape), movement, protection

(10) Identify the functions of the major regions of the vertebrate brain (cerebrum, cerebellum, diencephalon, brain stem, frontal lobe, temporal lobe, parietal lobe, occipital lobe) *

Cerebrum: conscious thought and memory Cerebellum: coordination and quality control of voluntary movement Diencephalon: relay center; homeostatic control of body temperature, appetite Brain stem: autonomic control of the heart, lungs, and digestive system Frontal lobe: executive control of attention, personality, and emotion Temporal lobe: contains the primary auditory cortex where auditory information is processed Parietal lobe: somatic sensation (touch) and motor function (movement) Occipital lobe: contains the primary visual cortex where visual information is processed

(11) Explain how we can distinguish different chemicals through the sense of taste (taste buds, salty, sweet, sour, umami, glutamate, H+, Na+).*

Chemoreception: occurs when chemicals bind chemoreceptors initiating action potentials in sensory neurons Gustation: the sense of taste Taste buds: structure with clustered chemoreceptor cells that sense taste The 4 basic tastes: sweet, salty, sour, bitter Umami: the meaty taste of the molecule monosodium glutamate (MSG), triggered by glutamate (amino acid) Salty: due to sodium ions (NA+) dissolved in food, sodium ions flow into certain taste cells through open sodium channels and depolarize the cells' membranes Bitter: 25% of Americans don't taste PTC, genes detect bitterness for survival: toxic plants contain bitter molecules that make animals spit them out and subsequently avoid them in the future Sour: due to presence of protons (H+), protons flow directly into certain taste cells through proton channels and depolarize the membrane Sweet: a single receptor protein has binding sites for multiple types of sweet compounds

(7) The presence of clay in soil provides both nutritional challenges and advantages for plants. What are the challenges? What are the advantages? (nutrients, cations, leaching)

Clay easily stores nutrients, but it is hard for plants to access them. A H+ pump must be used by the root hairs to absorb nutrients. Leaching also occurs.

(11) Describe the structure and function of the vertebrate eye (cornea, pupil, iris, lens, retina, rods, cones, ganglion cells, optic nerve). *

Cornea: transparent sheet of connective tissue formed on the front of the sclera - Function: covers and protects light opening, bends light Lens: transparent structure - Function: focuses light onto the retina Pupil: hole in the center of the iris - Function: allows light to enter Iris: pigmented, round muscle right inside the cornea - Function: contract or expand to control the amount of light entering the eye Retina: contains a layer of photoreceptors and several layers of neurons - Function: senses light Rods: rod-shaped photoreceptors in the retina - Function: sensitive to dim light Cones: cone-shaped photoreceptors in the retina - Function: respond to different wavelengths Ganglion cells: neurons in the retina - Function: axon projects to the brain through the optic nerve Optic nerve: a bundle of axons that runs from the eye to the brain - Function: allow signals to travel to the brain

(7) Make a list of the costs and benefits to the plant of symbiosis with rhizobium.

Costs: 1. Sugars are produced to attract and feed rhizobium 2. Special structures (nodules must be built) 3. Some gene products that help rhizobium (leg hemoglobin protein) Benefit: 1. Access to nitrogen

(9) Explain the acid-growth hypothesis (auxin, H+ pump, turgor pressure, expansin). How does acid-growth relate to phototropism?

Draw-The presence of auxin causes a sequence of responses in the cell that result in an H⁺ pump exportin protons out of the cytoplasm and into the cell wall which activates expansin that "unzip" the hydrogen bonds that form between cellulose microfibrils and other polymers in the cell wall, loosening the structure. As protons are pumped out of the cell, an electrochemical gradient is established. The inside of the plasma membrane becomes much more negative than the outside, favoring the entry of potassium (K+) or other positively charged ions. As the concentration of solutes increases inside the cell, water follows via osmosis and generate turgor pressure on the cell wall to trigger an increase in cell volume.

(7) What are the characteristics of "essential" nutrients? What is the relationship between the essential nutrients, macronutrients, and micronutrients?*

Essential nutrients are things that an organism must receive in order to survive that it can not produce itself. There are two types of essential nutrients: macronutrients are nutrients that an organism needs in excess, and micronutrients are needed in small doses, although not needed in large quantities, micronutrients are vital to survival.

(7) Explain the mechanism that allows some plants to survive in very salty soil. You should be able to explain the phenotypic difference between the transformed and control plants shown in figure 36.13 (Na+, exclusion, antiporter)*

Exclusion of ions allows for the internal root environment to remain at normal salt levels by passively or actively excluding salt ions to enter the root cells Passive: the epidermal and cortex cells simply lack the requisite membrane transporters Active: energy is required to produce metallothioneis and phtochelatins, which are proteins that bind to metal ions and prevent them from acting as a poison Active: proton pumps in the tonoplast move protons in the vacuole, creating a gradient that favors the movement of protons back out of the vacuole. The anti porter carries sodium into the vacuole while protons diffuse out of the vacuole (sodium ions are transported against their gradient)

(12) Describe the structure of skeletal muscle at levels ranging from a whole muscle to the contractile filaments within sarcomeres (muscle, thin and thick filament, myofibril, sarcomere, fiber, fascicle, z-line (or z-disc), M-line).

Fascicle: bundle of muscle cells (fibers) Fiber: long, thin muscle cell Myofibril: threadlike, contractile structures in a muscle cell Sarcomere: the repeating contractile unit of a skeletal or cardiac muscle cell; the portion of a myofibril located between adjacent Z disks Thick filament: filament composed of bundles of the motor protein myosin; anchored to the center of the sarcomere (myosin) Thin filament: filament composed of two coiled chains of actin and the regulatory proteins tropomyosin and troponin; anchored to the Z disk of the sarcomere (actin) Z-line/z-disc: the structure that forms each end of a sarcomere; contains a protein that binds tightly to actin, therefore anchoring thin filaments M-line: center of the sarcomere

(8) Distinguish the major functions of the digestive system (ingestion, digestion, absorption, secretion, excretion, motility).

Ingestion: the process of bringing food into the digestive tract (also known as alimentary canal or gastrointestinal tract) Digestion: the breakdown of food Absorption: the uptake of specific ions and molecules across the epithelium of the digestive tract Secretion: is the movement of material from one point to another, e.g. secreted chemical substance from a cell or gland. Excretion: is the removal of certain substances or waste products from a cell or organism Ex: urine from kidney Motility: is the ability of an organism to move independently, using metabolic energy. The gastrointestinal tract generates motility using smooth muscle subunits linked by gap junctions.

(6) Define Fick's law, describe how it relates to the structure of respiratory surfaces (e.g., tracheae, lungs, gills), and apply its principles to exchange across other surfaces (area, distance, partial pressure gradient).

Fick's law of diffusion is denoted by K • A • (P2-P1)/D - A: surface area - D: thickness of barrier to diffusion - K: Krogh's diffusion coefficient - P2 and P1: partial pressure of the corresponding gas The law states that the rate of the diffusion of the gas depends on 5 parameters: - Solubility of the gas in the aqueous film lining the gas exchange surface - The temperature - The surface area available for diffusion - The difference in partial pressures of the gas across the gas exchange surface - The thickness of the barrier to diffusion The surface area in the numerator of the equation indicates that a higher surface area leads to more diffusion. - This is why lungs have bronchioles/alveoli to increase their surface area; this also increases the amount of air that can diffuse into the lungs - Gills have structures called lamellae that also help to increase their surface area for gas exchange The thicker the membrane is, the slower the rate of diffusion will be. We need a larger partial pressure gradient (P2-P1 value) to increase gas exchange

(12) Compare the cost of locomotion for the three major methods of locomotion (flying, swimming, running).

Flying: drag and generate enough lift to counteract gravity Swimming: drag Running: gravitational and inertial forces

(8) Predict the food habits of an animal (herbivore, omnivore, carnivore, nectarivore) based on the structure of its teeth and gastrointestinal tract. *

Herbivore: eats plants, has flatter teeth, and longer GI tract. Omnivore: eats plants and animals, has variable teeth of both, and longer GI tract. Carnivore: eats animals, has sharp teeth, and shorter GI tract.

(6) Identify the number of atria and ventricles in the hearts of each major vertebrate group, and describe the functional consequences of differences in number of chambers and circulatory pattern.

Humans- four chambers, right atrium and ventricle separated by the tricuspid valve and a left atrium and ventricle separated by the bicuspid valve Fish- single atrium and ventricle (1 circuit) Frogs- 3-chambered heart, two circulatory loops, 2 atria, 1 ventricle Turtles & lizards- 3 chambered heart crocodiles, birds, mammals= 4 chambers Mixed chambers- mixing of oxygenated and deoxygenated blood=less blood to tissue

(8) Explain the advantages of a complete digestive system vs. an incomplete digestive system (specialization, batch vs. continuous flow)

Incomplete digestive tracts have only one hole for food intake and waste excretion which leads into a simple cavity- the gastrovascular cavity where digestion occurs. This means the processes must alternate with each other. -Complete digestive tracts have two openings- a mouth and anus. -Complete digestive tract advantages: Different chemical and physical processes can be confined to different compartments within the tract. Due to a one-way flow of food and wastes, material can be ingested and digested without interruption in a prescribed sequence.

(6) Describe how the insect tracheal system delivers oxygen through the body (spiracles, tracheae, diffusion, bulk flow). *

Insects have an extensive system of air-filled tubes, called tracheae that connect to exterior openings in the exoskeleton called spiracles. According to the textbook, oxygen is delivered through both simple diffusion and Boyle's law. Volume of the tracheae increases when the muscles relax and decreases when the muscles contract. The constant pressure change within the tracheal system moves gases much faster than diffusion alone.

(10) Distinguish between synaptic communication at ionotropic and metabotropic synapses (ion channel, receptor, G-protein, G-protein coupled receptor, 2nd messenger).

Ionotropic receptors change shape when bound by a ligand (Receptor is an ion channel) G-protein coupled receptor: rhodopsin - It is activated by a photon hitting the surface rather than by a ligand Metabotropic receptors do not have channels, but rather activate a G-protein, that in turn, activates a secondary messenger, which in turn, will activate something else by bonding to an ion channel More indirect way to activate a response

(11) Describe how some aquatic organisms utilize the lateral line system to detect the presence of prey, predators, obstacles, or mates in the surrounding water (hair cell, cupula, stereocilia). *

Lateral line system: a pressure-sensitive sensory organ found in many aquatic vertebrates in which hair cells are stimulated by pressure changes in water Hair cells: allow for the perception of pressure changes in water in fishes and aquatic amphibians Cupula: gel-like domed structures containing groups of hair cells Stereocilia: microvilli reinforced by actin filaments

(7) Create a list of macronutrients and micronutrients common to plants and animals.

Macronutrients: Oxygen, Hydrogen, Carbon, Nitrogen, Phosphorus, Potassium, Calcium, Magnesium, Phosphorus Micronutrients: Chlorine, Iron, Manganese, Zinc, Boron, Copper,. Nickel Molybdenum

(9) What are the major structural components of the cell wall and how are they organized? (cellulose microfibrils, hemicellulose)

Microfibrils overlaps each other → cellulose (bounded by H-bonds from hemicellulose)

(8) Describe the structure and function of the major organs and tissues of the digestive system, and predict how the structure of these organs might be different in other organisms that eat different types of food (e.g., cows, snakes, and others). (mouth, esophagus, stomach, small intestine, large intestine, liver, pancreas) *

Mouth: mechanical and chemical digestion starts here; chewing helps to break up food into smaller particles and amylase in saliva helps to digest carbohydrates Esophagus: transports food down to your stomach Stomach: mechanical and chemical processing; digestion of proteins Small intestine: chemical processing and absorption of nutrients and water; digestion of protein, carbohydrates, and lipids Large intestine: water absorption and feces formation Liver: secretes molecules required for digestion of fats Pancreas: secretes enzymes and other materials into small intestine

(7) What is a mycorrhizal fungi and are these fungi helpful or harmful to the plants they interact with? (nutrients, mutualism)

Mycorrhizal fungi conduct sugars to receiver plants based on metabolic need. They connect to the root of various platens to relay sugars and water between them

(7) Nitrogen is described as being "very expensive" for plants to acquire; explain this statement. (N2, energy, fixation)

N2 has a triple bond which requires a lot of energy to break, so fixation is requires, which also requires a lot of energy (16 ATP, 8e- and H+ protons)

(7) What is the origin of nitrate (NO3-) in soil and how/where does nitrate become reduced? (decomposition, NADH, NADPH)

NO3- in the soil comes from the decomposition of animal manures and other organic wastes

(8) Explain how peristalsis moves chyme through the digestive tract. *

Once the food is in the stomach, the stomach churns to create a substance called chyme. The chyme is moved along the alimentary canal via peristalsis and the organs chyme to enter due to the relaxation of the sphincters

(10) Define neuroplasticity and give examples of ways in which this is involved in learning and memory, and how it could be involved in brain repair.

Neuroplasticity: the ability of the brain to change (in terms of neural pathways and synapses) continuously throughout an individual's life This is involved in brain repair because neuroplasticity allows the brain to either repair the damaged regions, or it allows the brain to rewire and reconnect different regions of the brain in order to preserve function

(10) Apply your understanding of channels and synapses to predict how a neurotoxin might affect neural function.

Neurotoxins are poisons that affect neuron function by abolishing action potentials, blocking voltage-gated channels, etc. TTX: blocks sodium voltage-gated channels, and if sodium can't enter a cell, it won't be able to become depolarized, therefore causing paralysis Ouabain: blocks the sodium-potassium pump which helps establish a membranes resting potential, and if resting potential can't be established an action potential can't rest, therefore causing sustained contraction of muscles without relaxation

(11) Explain how the sense of smell can distinguish different chemicals and transmit that information to the brain (odorant, odorant receptor, olfactory neuron, olfactory bulb). *

Olfaction: the sense of smell Odorant: an airborne molecule that conveys information about food or the environment When odorants reach the nose, they diffuse into a mucus layer on the roof of the nose. Then they activate olfactory neurons by binding to membrane-bound receptor proteins Axons from the neurons project to the olfactory bulb. Olfactory bulb: the part of the brain where olfactory signals are processed and interpreted

(6) Describe how oxygen and carbon dioxide are transported in the blood (bound vs. free gases, hemoglobin, bicarbonate, carbonic anhydrase, HCO3-/Cl- exchanger). *

Oxygen starts in the alveolus, diffuses down its gradient to the red blood cell, binds with hemoglobin (4). Hemoglobin then carries O2 to the tissues. O2 will enter the cells and fall of hemoglobin where PO2 is lower, they will also leave hemoglobin if H+ or CO2 competes with O2 for hemoglobin binding site. The binded CO2 and H+ are then carried back to the lungs. Here the PCO2 is low in the alveolus so CO2 diffuses into alveolus, O2 competes with H+ and CO2 for hemoglobin binding sites, when the H+ comes off they bind with carbonic acid which becomes CO2 and water, the CO2 diffuses out into alveolus.

(8) Draw a negative feedback loop for blood glucose regulation, identifying the roles of insulin and glucagon. *

Pancreas (sensor) --> Beta cells release insulin --> Liver (effector) --> Body cells take up glucose --> Back to set point

(6) Distinguish between partial pressure and concentration of gases in biological solutions.

Partial pressure is proportional to concentration

(8) Explain how inactive enzyme precursors are released and then activated in the gut (zymogen).

Pepsin is the enzyme in the stomach responsible for protein breakdown. The precursor compound, which came to be called pepsinogen, is converted to active pepsin by contact with the acidic environment of the stomach. Secretion of a protein-digesting enzyme in inactive form is important: It prevents digestion of proteins in the cells where the enzyme is synthesized.

(10) Describe how the brain injuries to Phineas Gage & H.M. (Henry Gustav Molaison) aided scientists' understanding of the functions of various brain regions. (lesion, amygdala, hippocampus) *

Phineas Gage: an iron rod got blasted through his skull and damaged the majority of the left part of his frontal lobe The doctors reported a change in his personality and display of emotions - Conclusion: the frontal lobe controls character and emotion Mice: 1 control group of mice that were left alone and 1 experimental group of mice with lesions on their amygdalas The mice with the lesions were no longer scared of cats; they would climb on top of the cats and continue to do so even when the cat threatened them The control mice would freeze in the presence of the cat - Conclusion: the amygdala controls fear Patient HM: Underwent an experimental brain surgery in which ⅔ of his hippocampus was resected After the surgery, he was only able to remember select childhood memories, some facts about his parents, and some historical events, but he was unable to form new memories - Conclusion: the hippocampus is crucial for formation of new memories

(9) Give examples of some events that occur "downstream" of a receptor protein. (phosphorylation, gene expression, membrane permeability, export, cascade)*

Phosphorylation cascades: triggered when change in receptor protein's shape leads to the transfer of a phosphate group from ATP to the receptor or an associated protein - Phosphorylation activates proteins involved in signal transduction cascades causing them to phosphorylate and activate a different set of proteins which in turn catalyze the phosphorylation and activation of still other proteins Second messengers: produced when receptor proteins trigger the production of intracellular signals or their release (export) from storage areas - Calcium ions stored in the vacuole, ER, or cell wall are one of several ions or molecules that function as the second messenger in plants Response to a signal binding with a receptor can include: - Changes in gene expression from alterations in transcription activators or repressors or the translation machinery that result in new RNAs or proteins in the cell

(6) Explain how tetrapods (terrestrial vertebrates) move air in and out of their lungs and contrast the positive pressure mechanisms found in amphibians and the negative pressure mechanisms found in mammals. *

Positive Pressure- best described as a push, for example in a frog. A frog will lower the floor of their throat in order to draw in air through the nostrils into the mouth. The nostrils then close and the floor of the throat is raised. This increase in pressure pushes air into the lungs. Negative Pressure- The pressure in the lungs are about 5mm Hg less than the air outside, leaving the lungs expanded and creates a negative pressure. The diaphragm contracts in order to create a more negative pressure to draw in air into the lungs. The diaphragm then relaxes to release air.

(12) Compare and contrast the three different types of vertebrate muscle.

Skeletal muscle: exceptionally long, unbranched muscle fibers - Location: attached to the skeleton - Function: move skeleton - Nucleus: multinucleate - Striated? Striated - Branching: unbranched - Sarcomeres: contains sarcomeres - Activity: voluntary, signal from somatic motor neuron is required Cardiac muscle: makes up the walls of the heart and is responsible for pumping blood throughout the body - Location: heart -Function: pump blood - Nucleus: 1 or 2 nuclei - Striated? Striated - Branching: branched, intercalated discs form direct cytoplasmic connections between cells - Sarcomeres: contains sarcomeres - Activity: involuntary, signal from motor neuron is not required Smooth muscle: cells are unbranched, tapered at each end, and often organized into thin sheets - Location: intestines, arteries, other - Function: move food, help regulate blood pressure, etc. - Nucleus: single nucleus - Striated? Unstriated - Branching: Unbranched - Sarcomeres: no sarcomeres - Activity: involuntary, signal from motor neuron is not required

(12) Compare and contrast the three fiber types of vertebrate skeletal muscle.

Slow oxidative: slow fibers - Twitch speed: slow - Amount of SR: not so much - Fatigability: resistant - Rate of ATP use: slow - # of mitochondria: lots - Fuel used: carbs or lipids - Usage pattern: frequent Fast oxidative-glycolytic: intermediate fibers - Twitch speed: fast - Amount of SR: lots - Fatigability: intermediate - Rate of ATP use: intermediate - # of mitochondria: lots - Fuel used: carbs - Usage pattern: intermediate Fast glycolytic: fast fibers - Twitch speed: faster - Amount of SR: lots+ - Fatigability: susceptible - Rate of ATP use: rapid - # of mitochondria: not much - Fuel used: carbs - Usage pattern: occasional bursts

(8) Explain how the presence of chyme in the digestive tract leads to the release of enzymes from the pancreas and bile from the liver, including the relevant hormones and the organs that release them. *

Small intestine secretes secretin in response to the presence of chyme → induces a flow of bicarbonate ions (HCO₃⁻) from the pancreas to the small intestine (neutralizes acid arriving from stomach)

(10) Distinguish among the functional components of the nervous system (afferent, efferent, somatic, autonomic, sympathetic, parasympathetic).

Somatic Nervous System: the part of the peripheral nervous system that is associated with the voluntary control of body movements via skeletal muscles - Ex: jerking your hand back after touching a hot pan, moving your legs when you go on a jog, etc Autonomic Nervous System (ANS): the part of the peripheral nervous system that is associated with involuntary actions via organs - Ex: salivation, respiratory rate, pupillary dilation, etc Sympathetic Nervous System (SNS): part of the ANS that controls the body's response during perceived threat (fight or flight) - Body speeds up, tenses up, and becomes more alert; functions not critical to survival shut down Parasympathetic Nervous System (PNS): part of the ANS that controls the body's response while at rest (rest and digest) - Restores body to state of calm Afferent neurons: sensory neurons that carry nerve impulses from sensory stimuli towards the CNS and brain Efferent neurons: motor neurons that carry neural impulses away from the CNS and towards muscles to cause movement

(6) State a hypothesis to explain why giant insects existed 300 million years ago, but could not survive today. *

The large insects from 300 million years ago increased in size to avoid oxygen poisoning, and could therefore not survive in today's environment due to the significant decrease of oxygen in the atmosphere.

(12) Steps in neuromuscular junction synaptic transmission and excitation-contraction coupling.

Step 1: Depolarization of motoneuron axon terminal Step 2: Vesicles containing acetylcholine fuse with nerve cell membrane Step 3: Acetylcholine receptors open and conduct Na+ ions Step 4: An EPSP occurs in the muscle cell Step 5: Voltage-gated Na+ channels open in the muscle cell membrane near the neuromuscular junction Step 6: Action potential is conducted along the T-tubule Step 7: Ryanodine receptors open Step 8: [Ca2+] rises in the muscle cell cytoplasm Step 9: Ca2+ binds to troponin Step 10: Tropomyosin rotates into the groove of the thin filament (out of the way of the myosin binding site) Step 11: Myosin heads go through the cross-bridge cycle and hydrolyze ATP Step 12: Ca2+ dissociates from troponin

(11) [ANSWERED THE QUESTION BY GIVING WHAT HAPPENS IN THE PROCESS OF A FLASH OF LIGHT] Give a step-by-step explanation of how a photon can lead to a change in action potential frequency in a neuron leading from the retina to the brain (photon, rhodopsin, activated, transducin, G-protein, GTP, phosphodiesterase, cGMP, ligand-gated channels, hyperpolarization, neurotransmitter, synapse, frequency coding)

Step 1: Photons pass through the cornea Step 2: Photons are refracted by the lens Step 3: Photons pass through the ganglion and bipolar cells in the retina Step 4: A photon is absorbed by a retinal molecule Step 5: Rhodopsin changes shape to its active conformation Step 6: Transducin molecules bind GTP Step 7: Transducin molecules activate phosphodiesterase Step 8: Phosphodiesterase breaks down cyclic GMP Step 9: cGMP-gated Na+ channels close Step 10: Rod is hyperpolarized

(11) Give a step-by-step narration of the process of hearing a sound, including transmission of sound from the outer ear through the middle ear to the inner ear and transduction of sound to electrical signals, and coding so that the central nervous system can interpret these signals (ear canal, tympanic membrane, ear bones, oval window, cochlea, hair cells, stereocilia, tip links, K+ channels, mechanically gated, Ca2+ channels, voltage-gated, depolarization, neurotransmitter, synapse, afferent neuron, frequency coding).

Step 1: Pressure waves pass through the air in the ear canal Step 2: Tympanic membrane vibrates Step 3: Malleus (ear bone) vibrates Step 4: Incus (ear bone) vibrates Step 5: Stapes (ear bone) vibrates Step 6: Oval window vibrates Step 7: Pressure waves travel through the fluid in the cochlea Step 8: Stereocilia in hair cells deflect (bend) Step 9: K+ channels in the hair cell membranes open Step 10: Hair cell membrane is depolarized Step 11: Voltage-gated Ca2+ channels open Step 12: Hair cells release neurotransmitter Step 13: Afferent neurons transmit action potentials through the cochlear nerve

(8) Describe how the stomach produces acid and how acid is involved in digestion (parietal cell, proton pump (H+/K+ ATPase), carbonic anhydrase, pepsin, etc.).

Stomach acid production: 1) Parietal cells combine CO2 and H2O to produce H2CO3. 2) H2CO3 splits into H+ and HCO3-. 3) H+ is pumped out of the cell into lumen, causing a gradient. 4) HCO3- leaks out of the cell, so Cl- can leak in. 5) Cl- leaks out of the cell into the lumen and combines with H+ to produce HCl. 6) Stomach produces HCL because it is needed to convert the inactive pepsinogen into the active pepsin needed for protein digestion.

(8) Give examples of how diverse mouthparts are related to the type of food eaten (e.g., insects, snakes, humans, cichlid fishes, etc.). *

Suspension feeders (sponges, tube worms): filter small organisms or bits of organic debris from water by cilia. Deposit feeders (earthworms, sea cucumbers): swallow sediments and other types of deposited material rich in organic matter. Fluid feeders: suck or lap up fluids like blood or nectar. Mass feeders (majority of animals): seize and manipulate chinks of food by using mouthparts such as jaws and teeth, beaks, or special toxin-injecting organs. Snakes: adapted complex skull, jawbones, and associated musculature that are highly flexible to allow them to ingest large prey whole. Cichlid: adapted pharyngeal jaws that allow for biting in addition to the normal use of pharyngeal jaws which is being able to move food down the throat. Cichlids pharyngeal jaws also have specialized tooth structures depending on the main type of prey is that they feed on. Ex: Crushing snails, tearing scales, eating other fish ect.

(11) Define "transduction" and "transmission" in the context of sensory information and processes.

The ability to sense a change in the environment depends on two processes: transduction and transmission. 1) Transduction: the conversion of an external stimulus to an internal signal in the form of action potentials along sensory neurons - requires a sensory receptor cell specialized for converting light, sound, touch, or some other signal into an electrical signal 2) Transmission: of the signal to the central nervous system (CNS)

(7) What is the advantage to plants of pumping protons (H+) from root cells? (H+ ATPase, cations, clay, electrochemical gradient)

The advantage is once the H+ are pumped in cation exchange can occur where the H+ ions replace the cations (nutrients) by binding to the negatively charged soil particles. This creates an electrochemical potential driving essential nutrients into the cell.

(6) Describe the structural and functional relationship between the respiratory and circulatory systems.

The circulatory system helps to circulate CO2 and O2 around the body, and the respiratory system is what brings O2 in and takes CO2 out.

(10) Identify the major regions of a typical neuron. Where is information received, integrated, and propagated to the next neuron or target tissue. Which region or regions can fire action potentials and which ones cannot? Why/why not? (cell body (soma), dendrites, axon, axon initial segment, axon terminal).

The dendrites receive signals from the axons of other neurons and convert those chemical signals to electrical signals The cell body (soma) integrates incoming electrical signals The axon conducts the electrical signals to the dendrites and cell bodies of other neurons. The axon initial segment (hillock) is the most excitable part of the axon, used to trigger an action potential. The axon terminal releases neurotransmitters that travel between the synapse to the dendrites of the next axon.

(10) Describe how an action potential regenerates as it spreads down the length of a neuron.

The reason the action potential is so easily propagated is due to the positively charged Na+ ions repelling other positively charged ions in the cell. These ions are pushed along the axon, and when they reach the next node of ranvier, the excess positive charge is enough to cause another action potential

(7) Briefly summarize the Wood Wide Web hypothesis and site evidence (from lecture or on-line) that supports the idea of the Wood Wide Web. (fungi, carbohydrates)

The wood wide web is the metabolic network for plants

(7) What do epiphytes, parasitic plants and carnivorous plants have in common? How do they differ?*

They all need nutrients, nitrogen from another source

(9) A cellular response to a chemical or environmental signal begins when the signal is "transduced." Explain what "transduction" means in this context. (receptor, plasma membrane)

Transduction: the process by which a stimulus outside a cell is converted to an intracellular signal required for a cellular response (usually involves a specific sequence of molecular events called a signal transduction pathway which may amplify the signal) Signal transduction begins with stimulation of a receptor protein in the plasma membrane

(11) Give examples of animals that can perceive aspects of the environment via sensory modalities that humans cannot perceive, such as UV radiation, electric fields, magnetic fields, etc. *

UV radiation: goldfish, butterflies Electric fields: electric eels Magnetic fields: European robins

(10) Compare and contrast voltage-gated ion channels and ligand-gated ion channels (ligand, gating, open vs. closed state).

Voltage-gated ion channels: membrane proteins that open and close in response to membrane voltage; change shape based on the charges present at the inside of the membrane - Closed state: at resting potential - Open state: when the membrane is depolarized Ligand-gated ion channels: open in response to binding by a neurotransmitter, enabling ion flow that depolarizes or hyperpolarizes the postsynaptic cell's membrane

(7) Identify the three zones of the root. In which zone does most nutrient uptake occur? How is the structure of this zone specialized for this function?* (root hairs)

Zone of maturation is where the most nutrient uptake occurs. Root hairs are specialized to create lots of surface area for more interaction with the soil. zone of cellular elongation and zone of cellular division(7( in charge of growth.