Exam 3 Study Guide - Outlined learning goals and questions asked in class. PDF

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Outlined learning goals and questions asked in class. ...

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3.1 Biological systems are comprised of sets of components that are arranged and integrated into increasing levels of complexity ● Define a biological system and emergent properties ○ Biological system: comprised of sets of components that are arranged and integrated into increasing levels of complexity ○ Emergent properties: functions that arise due to phenomena at each level of a system ○ Structure- function: at each level of biological organization we find a correlation of structure function ● Why do humans need to breathe? ○ Breathing is essential to keep us alive, because every living cell in the body needs a continual supply of oxygen. Inside each cell, oxygen combines with food molecules in a chemical reaction called oxidation, which releases energy. This energy powers every process in the human body ● What is the purpose of gas exchange? ○ Gas exchange: the transport of oxygen and carbon dioxide between an organism and its environment ○ Gas exchange is required to supply those cells with the molecules needed for metabolism

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○ Difference between respiration and breathing ○ Respiration - the biochemical process in which the cells of an organism obtain energy by combining oxygen and glucose, resulting in the release of carbon dioxide, water, and ATP ○ Breathing - the process by which air is taken into the lungs (inspiration) and how air is removed from the lungs (expiration). What adaptations do complex, multicellular organisms have to allow them to deal with gas exchange?

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The challenges: Complex multicellular organisms have three dimensional organization, so only some cells are in direct contact with the environment. Cells buried within tissues do not have direct access to nutrients or oxygen and therefore cannot grow as fast as surface cells unless there is some way to transfer resources from one part of the body to another. Interior cells do not receive signals directly from the environment, even though all cells must be able to respond to environmental signals if the organism is to grow, reproduce, and survive. ○ Adaptations: Despite limitations of tidal respiration, mammalian lungs are well adapted for breathing air. They have an enormous surface area and a short diffusion distance for gas exchange. The lungs of mammals supply oxygen quickly enough to support high metabolic rates Steps in gas exchange: 1. Ventilation by bulk flow: breathing moves air (containing oxygen) into the lungs and air (containing carbon dioxide) out of the lungs. 2. Diffusion across the respiratory surface: oxygen diffuses from the lung into the blood and carbon dioxide diffuses out of the blood into the lungs. 3. Circulation by bulk flow: oxygen and carbon dioxide are transported by the circulatory system to and from the cells. 4. Diffusion between blood and cells: oxygen diffuses from the blood into the cells and carbon dioxide diffuses out of the cells and into the blood How does ventilation work? ○ Humans and other mammals ventilate their lungs by increasing their lung volume by expanding their thoracic cavity to draw in oxygen rich air into the lungs (inhalation  ) and reducing their lung volume to exire oxygen poor air from the lungs (exhalation) ○ Inhalation works because negative pressure draws air into the lungs. ○ Exhalation works because positive pressure expels air from the lungs. Bulk flow versus diffusion ○ Diffusion:the random motion of molecules, with net movement from areas of higher concentration to areas of lower concentration ■ Given a large enough surface area, diffusion is extremely effective over short distances (between lungs and blood vessels ) ■ It is generally ineffective over distances exceeding 0.1 mm ○ Bulk flow: any means by which molecules move through organisms at rates beyond those possible by diffusion across a concentration gradient ■ Bulk flow also distributes nutrients throughout the body. In general, bulk flow is required to supply those cells with the molecules needed for metabolism ■ Bulk flow occurs in two steps to meet gas exchange needs of cells in larger animals ● Ventilation: the movement of the animals respiratory medium (water or air) past a specialized respiratory surface

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Circulation: the movement of a specialized body fluid that carries oxygen and carbon dioxide ● What provides the pressure/ force for bulk flow of blood? ○ The heart provides the force for bulk flow ● Identify components that make up the human respiratory and circulatory system ○ Heart, arteries, veins, capillaries, red blood cells, hemoglobin, alveoli, lungs, diaphragm, bronchi, bronchioles, trachea, larynx (containing vocal chords) 3.2 Emergent properties arise at each level of biological hierarchy ● Describe how the components of the chloroplast are arranged and integrated to facilitate photosynthesis ○ The structure of chloroplasts consists of two membranes: the inner and outer membranes. Within the membranes, there is the thylakoid (membrane sacs, stacks of grana), stroma (dense fluid of the chloroplast), and chlorophyll (green pigment within the thylakoid membrane). The chloroplast is a double membrane organelle that performs the function of photosynthesis of plant cells. The chloroplasts use photosynthetic chlorophyll pigment and take in sunlight, water, and CO2 to produce glucose and oxygen. The chloroplasts' membranous sacs (thylakoids), are the site of photosynthetic light reactions and involves the transfer of electrons from a photo executed state from the chlorophyll inside the thylakoid membranes to the stroma, which then produces ATP. The chloroplasts' DNA and ribosomes reproduce into smaller cells. ● Identify the emergent properties of the human respiratory system ○ Lungs work due to all of the cells in them functioning as a unit; the cells by themselves do not aid you breathing. ○ Emergent properties of lungs: ○ Emergent properties of diaphragm: ○ Emergent properties of alveoli: ○ Emergent properties of arteries and veins: ○ Emergent properties of capillaries: ○ Emergent properties of heart: ○ Emergent properties of erythrocytes: at the cellular level, there is organization ○ Emergent properties of hemoglobin: ● Path of the respiratory gases in the circulatory system ○ (1) inhaled air (2) alveolar spaces (3) pulmonary veins (4) systemic arteries (5) body tissue (6) systemic veins (7) pulmonary arteries (8) exhaled air 3.3 Structure and function are correlated at all levels of biological organization ● Explain how the structure of the components of the respiratory and circulatory system allow for specialized functions and how the components are arranged to allow for respiration ○ Lungs: (organ) ■ Function: Bulk flow of oxygen ■ Structure: Soft organ attached to diaphragm capable of expanding and contracting to draw air in

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Diaphragm: (organ) ■ Function: Expand and contract to create negative/ positive partial pressure to allow for the lungs to draw air in or expel air out ■ Structure: Large, dome shaped muscle that expands and contracts to allow for the lungs to expand during inhalation and expel during exhalation. ○ Alveoli: (tissue) ■ Function: gas exchange between the lungs and blood ■ Structure: thin walls to allow for quick diffusion between alveoli and capillaries, surfactant to allow for diffusion (diffusion cannot happen in a dry medium), many alveoli increases the surface area capable of gas exchange ○ Arteries & Veins: (organ) ■ Function: bulk flow of oxygen throughout the body ■ Structure: arteries have a muscular layer which allows them to keep their elasticity and allows for blood to pump quickly through them. Veins have valves which keeps the deoxygenated blood flowing in one direction. ○ Capillaries: (organ) ■ Function: diffusion of oxygen into adjacent tissues ■ Structure: walls in capillaries are 1 cell thick which allows for quick and efficient diffusion ○ Heart: (organ) ■ Function: provides bulk flow by pumping oxygenated blood to tissues and deoxygenated blood to the lungs to become oxygenated ■ Structure: the chambers and valves separate the oxygenated and deoxygenated blood so that there is a higher oxygen concentration in the oxygenated blood ○ Erythrocytes: (cellular) ■ Function: carry oxygen throughout the body ■ Structure: biconcave disc creates a larger surface area for many hemoglobin molecules bind to it; they are 10 micrometers in size which means they can easily fit through capillaries ○ Hemoglobin: (molecular) ■ Function: transport oxygen ■ Structure: quaternary protein structure consists of two beta subunits and two alpha subunits, each subunit has an iron heme group where oxygen binds to Explain how hemoglobin protein structure allows for cooperativity and interpret an oxygen dissociation curve to explain the importance of cooperatively in hemoglobins role in oxygen pick up and delivery ○ Cooperativity: idea that binding to one molecule of O2 makes the hemoglobin more relaxed and makes them want to bind to more O2 molecules

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This is why on an oxygen dissociation curve it is steeply up first then it drops off because more hemoglobin is being saturated Interpret data to determine how a change in pH can alter hemoglobin binding to oxygen

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Hemoglobin retains less O2 at lower pH (higher CO2 concentration) The increase of free H+ (which means a decrease in pH), causes hemoglobin to change shape and release O2 ○ Lowering the pH to 7.2 impacts the O2 binding to hemoglobin because the hemoglobin protein is denatured and its shape changes form and the shape of the binding site changes meaning either O2 won’t bind and or CO2 will take its place. ○ Lowering the pH to 7.2 decreases binding affinity which decreases O2 saturation ○ Hemoglobin changes shape when it bumps into a proton so it cannot bind to O2. When it is more acidic (more H+), there is less affinity for O2 . CO2 in red blood cells leads to H+ being produced. O2 binding by hemoglobin

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○ ○ Hemoglobin’s oxygen dissociation curve is shown by the red line. ○ Blue is just to consider a different possibility Cooperative binding and O2 saturation

○ 3.4 Organisms have mechanisms to sense and respond to signals from other organisms or changes in their environment to maintain homeostasis ● Develop a hypothesis to describe how the human respiratory and circulatory systems will respond to a change in the environment ○ Individual responses upon exposure to hypoxia: increased breathing rate (ventilation rate), increased heart rate, increased blood pressure, increase in red blood cell production, increase in hemoglobin.

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Interpret data to determine how human individuals respond to changes in altitude (or other respiratory challenge) ○ Increased red blood cell production and increased production of the hemoglobin protein allows for more oxygen binding ○ Bronchodilation and vasodilation to help expand the surface area available for gas exchange Define homeostasis ○ Organisms face constant changes in their environment and have the capacity to respond to these changes. The response is elicited by homeostasis. ○ Homeostasis: the property of a biological system in which physiological variables (conditions) are actively regulated so that they remain stable and relatively constant. ○ Stimulus: movement away from the set point ○ Effector: causes a change ○ Response: what actually changes in organism to return back to set point Describe how the breathing control centers are a homeostatic mechanism ○ The respiratory centers contain chemoreceptors that detect pH levels in the blood and send signals to the respiratory centers of the brain to adjust the ventilation rate to change acidity by increasing or decreasing the removal of carbon dioxide (since carbon dioxide is linked to higher levels of hydrogen ions in blood) Explain how in human individuals, exposure to a different altitude can lead to changes in gene expression that lead to physiological responses; explain how these physiological responses enable maintenance of homeostasis. ○ The evolutionary adaptations that allow Tibetans to function at high altitudes are very different from the acclimatization process that most of us go through when we spend time in those places. When lowlanders visit Denver, La Paz, or Lhasa, for example, their bodies begin to produce more red blood cells. These extra cells seem to help transport available oxygen around the body, and may eventually compensate for decreased oxygen levels, allowing breathing and heart rate to return to normal. The switch to producing more red blood cells that occurs when a lowlander visits Lhasa does not reflect a new mutation, but rather the body's response to a new environment. Because they don't reflect a shift in the genetic makeup of a population, such changes, which occur within the lifespan of a single individual, are not adaptations in an evolutionary sense. ○ The Tibetan highlander population, on the other hand, has, over the course of thousands of years, evolved adaptations that allow individuals to thrive in a low oxygen environment. One of these adaptations is almost exactly the opposite of a lowlander's response to high altitude: Tibetans have gene versions that cause them to produce fewer red blood cells. It turns out that extra red blood cells make blood thicker and after a certain point, this cell-laden blood can actually get so thick that it doesn't pass through capillaries efficiently to oxygenate cells. The basis for the Tibetans' adaptation is not a change in a gene that produces hemoglobin or any one of the other proteins that make up red blood cells.

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Instead, the key change seems to be in a stretch of DNA (called EPAS1), which codes for a regulatory protein. This protein senses oxygen and helps control the process of producing red blood cells. The change in EPAS1 seems to make Tibetans less likely to overproduce red blood cells at extreme altitudes and, hence, probably helps them to avoid altitude sickness and deliver oxygen more effectively to developing fetuses. Other unique traits of Tibetans (a higher breathing rate and blood vessels which expand to allow better oxygen transport) likely also contribute to their altitude aptitude. Experiment to monitor breathing rate (ventilation rate)

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1. Focusing on just the patients treated to a hypoxic environment (closed circles), describe how the ventilation rate changes “during” the treatments compared to “before” treatment During: there was an initial spike in mean ventilation rate followed by a slow, steady decline. The mean ventilation rate remained higher than baseline. 2. Focusing on just the patients treated to a hypoxic environment (closed circles), describe how the ventilation rate changes “after” the treatments. The mean ventilation rate continues to decrease until it returns to baseline. 3. Focusing on just the patients treated to a hypoxic environment (closed circles), What conclusions can you draw from this data? Be sure to indicate statistical significance in your answer. During the treatment, the body compensates by increasing the mean ventilation rate. In 5 minutes, the ventilation rate increases by 60%. As the body adjusts, the mean ventilation rate decreases and appears to level off at approximately 11L/min. 4. Why do you think that the authors also tested ventilation in a higher than normal carbon dioxide environment (open circles)? What are the main conclusions from this data? The authors tested ventilation in a higher than normal carbon dioxide environment to see how the hemoglobin would respond as it is able to bind to

both oxygen and carbon dioxide. When the hemoglobin binds to CO2, the mean ventilation rate of the patients continues to increase in the hypoxic environment. This shows an inverse relationship between oxygen and carbon dioxide. 3.5 Groups of organisms faced with similar environmental changes have adapted independently ● Differentiate short term response of individuals to changes in an environment versus adaptations observed in populations to an environment ○ Individual- acclimatization, acclimation, response: involves a change within an individual's lifetime to maintain homeostasis ■ Individual responses upon exposure to hypoxia: increased breathing rate (ventilation rate), increased heart rate, increased blood pressure, increase in red blood cell production, increase in hemoglobin. ○ Populations- adaptation: involves a genetic change that is heritable from generation to generation ■ Population response to life at high elevations: hematological response, respiratory response, other mechanisms to be discovered ● Use genetic data and phylogeny to identify populations that have undergone natural selection to adapt to a set of environmental conditions.

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Long branch length= lots of differences between Han and tibetan gene versions How did (the researchers) determine which genes mattered? Identified several genes that they believe are involved in the hypoxia response. The most striking gene was EPAS1. Relative to other genes in the genome, this gene has a really large branch length, indicating a lot of change.

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What does the EPAS1 gene do?: It is the gene that orchestrates the response to low oxygen environments. It is a transcription factor so it binds to other genes either to express them or to deactivate them. ○ Why did the EPAS1 gene stand out? The EPAS1 locus had two mutations that had a really large frequency difference between Tibetan population and the closely related Han population. The large frequency difference implies natural selection on EPAS1 gene. Describe how a mutation in a gene region can lead to changes that allow humans to better cope with less oxygen. ○ Tibetans have a mutation in the EPAS 1 gene that stops certain homeostatic hypoxia reactions (like increased RBC production and hemoglobin production) and allows for a stronger respiratory response to occur. This is because an excess of hemoglobin would clog the blood and make it harder to flow easily. Furthermore, the high concentration of NO makes the blood vessels dilate more. Altitude sickness symptoms: ○ headaches, nausea, swelling, difficulty sleeping, dizziness, shortness of breath, disorientation. Interpret data from multiple populations of humans living long term at high altitude to describe the adaptations that allow each population to cope and survive with less atmospheric oxygen.

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People who live at sea level are the control; they are the baseline for the comparison of the adaptations. At sea level, people experience 97% oxygen saturation in the air, the hemoglobin concentration is 15.3, the arterial oxygen content is 21.1 mL/ 100mL, and have no erythrocytosis. Ethiopians have a roughly equal oxygen saturation in their atmosphere, a roughly even hemoglobin concentration, an equal arterial oxygen content and no erythrocytosis. They did not adapt because their hemoglobin can hold the necessary amount of oxygen.

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Tibetans have a drastically lower oxygen saturation and a lower arterial oxygen content but roughly equal hemoglobin concentration. They have the mutated EPAS1 gene that allows for them to not require the same amount of oxygen. ○ Bolivians have a lower oxygen saturation but a higher arterial oxygen content and higher hemoglobin concentration. They have erythrocytosis. This indicates that they do not have the mutated EPAS1 gene and their bodies respond with a homeostatic response. ● Did all high altitude populations evolve similarly? ○ Adaptation to high altitude involved heritable, genetic change. ○ Convergent evolution of high altitude living: “hematological response” (increases hemoglobin and increased RBCs), “respiratory response” (increased ventilation and dilated blood vessels, no increase in hemoglobin), TBD 3.6 Integration of molecular, biochemical, genetic, ecological, and evol...