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Bio Study Guide for Midterm #2

by: Leor Clark

Bio Study Guide for Midterm #2 BIOL 1005

Leor Clark
Virginia Tech

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About this Document

These notes cover everything from lessons 6, 7, 8, and 9. All of this will be on the next exam.
General Biology
MV lipscomb
Study Guide
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This 6 page Study Guide was uploaded by Leor Clark on Sunday September 25, 2016. The Study Guide belongs to BIOL 1005 at Virginia Polytechnic Institute and State University taught by MV lipscomb in Fall 2016. Since its upload, it has received 194 views. For similar materials see General Biology in Biology at Virginia Polytechnic Institute and State University.


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Date Created: 09/25/16
Bio study guide Unit 2 1. Lecture 6: Energy and Metabolism a. Energy: the ability to do work or create change b. Every task performed by living organisms requires energy c. Bioenergetics: word used to describe concept of energy flow through living organisms d. Metabolism: all of the chemical reactions that take place inside cells e. Metabolic pathways i. A series of chemical reactions that take molecules and modify them, yielding a final product ii. Sugar is a major energy source iii. Photosynthetic plants take energy from sunlight convert CO2 into sugar + oxygen as a waste product 1. 6CO2 + 6H2O  C6H12O6 + 6O2 iv. When oxygen is consumed and energy is provided by ATP, CO2 Is released as a waste product 1. C6H12O6 + 6CO2  6H2O + 6CO2 v. Anabolic pathways: require energy to build polymers 1. Synthesis vi. Catabolic pathways: produce energy by breaking down polymers into their monomers 1. Degradation vii. Thermodynamics: the study of energy and energy transfer involving physical matter 1. System = matter relevant to energy transfer a. Open: energy can be exchanged within surroundings b. Closed: can’t exchange energy with surroundings c. Biological organisms are open systems 2. Surroundings = everything outside matter 3. Thermodynamic laws a. Total amount of energy in the universe is constant and conserved b. All energy transfers and transformations are never completely efficient i. Heat energy: energy transferred from one system to another that is not work 1. Entropy: randomness or disorder within a system viii. Kinetic energy: energy associated with an object in motion 1. Ex: a car in motion ix. Potential energy: stored energy in an object that is unmoving 1. Ex: a wrecking ball suspended in the air x. Chemical energy: the potential energy that exists in chemical bonds and is released when those bonds are broken xi. Free energy: energy that is useable/available to do work 1. Exergonic reaction: reactions that have a negative change in free energy and release free energy 2. Endergonic reaction: on-spontaneous, won’t take place on its own without the addition of free energy, absorbs energy, change in energy will be positive xii. Enzymes 1. Catalyst: substance that helps a chemical reaction to occur 2. Enzymes: molecules that catalyze biochemical reactions a. Reduce activation energy required for reaction to take place 3. Substrates: the chemical reactants that the enzymes bond to 4. Active sites: location in the enzyme where a substrate binds a. Function best in certain conditions 5. Enzyme inhibition happens when inhibitor molecules similar to the substrate bind to the active site instead and block a substrate from bonding a. Competitive inhibition: inhibitor molecule competes with substrate for binding to the active site b. Noncompetitive inhibition: inhibitor molecule bonds to enzyme but not at the active site, and still manages to block substrate from binding c. Allosteric inhibition: inhibitor enzymes bind to enzymes in a location where induces a change that reduces the affinity of the enzyme for its substrate d. Feedback inhibition: involves use of reaction product to regulate its own further production i. Produces amino acids and nucleotides 2. Lesson 7: Energy from Organic Molecules part 1 a. ATP: adenine triphosphate, provides quick bursts of energy to perform cellular work b. AMP: adenosine monophosphate, a molecule at the heart of ATP c. Hydrolysis: release of one or 2 phosphate groups from ATP, releases energy d. Glycolysis: first step in the breakdown of glucose to extract energy for cell metabolism i. Takes place in the cytoplasm ii. ATP and NADH are produced e. Fermentation: if aerobic respiration occurs, ATP will be produced using the energy of the high-energy electrons i. Processes that use an organic molecule to regenerate NAD+ from NADH ii. Lactic Acid fermentation 1. Used in animals and some bacteria 2. Happens in red blood cells, lactic acid produced in muscles must be removed by blood and brought to liver iii. Alcohol fermentation 1. Produces ethanol 2. Carboxyl group is removed, releases CO2 as a gas 3. Removes an electron from NADH, forming NAD+ and Ethanol found in alcoholic beverages 4. If CO2 is not vented from the fermentation chamber, it remains in the medium until pressure is released iv. Anaerobic cellular respiration 1. Used by certain prokaryotes 2. Many can switch between aerobic respiration and fermentation, depending on availability of oxygen 3. Some live and grow in the absence of molecular oxygen, where oxygen is a poison to them and kills them on exposure f. Lecture 8 notes: energy from molecules part 2 i. Citric Acid Cycle: takes place in the mitochondria 1. Closed loop 2. 8 steps 3. Produces two carbon molecules, one ATP molecule, and NADH and FADH (coenzymes) 4. Results in Acetyl CoA: used to deliver the acetyl group derived from pyruvate to the next pathway in glucose catabolism 5. Aerobic pathway 6. Both anabolic and catabolic ii. Oxidative Phosphorylation: takes place in specialized protein complexes located in the inner membrane of the mitochondria in eukaryotic cells and on the inner part of the cell membrane in prokaryotic cells 1. Potential energy is used to generate ATP iii. Electron transport chain: last component of aerobic respiration, only part of metabolism that uses atmospheric oxygen 1. Oxygen diffuses into plants for this purpose 2. Electrons are passed from one component to the next until water is produced 3. Sometimes stored as potential energy to create electrochemical gradient 4. NADH and FADH2 are passed through ETC iv. No oxygen = electrons can’t be removed from system entire ETC chain would back up and stop  mitochondria wouldn’t be able to produce ATP and cell would die 1. This is why we breathe v. ATP synthase: hydrogen ions diffuse through inner membrane through this integral membrane protein 1. Chemiosmosis: flow of hydrogen ions across membrane through ATP synthase 2. Generates 90% of ATP made during aerobic glucose catabolism vi. Glycogen: a short-term energy storage molecule in animals 1. When ATP is present, excess glucose is converted into glycogen for storage 2. Stored in liver and muscle 3. Will be taken out of storage if blood sugar levels drop vii. Amino acids are recycled into new proteins 1. Excess amino acids or famine amino acids will be shunted away into pathways of glucose catabolism and then converted into ammonia viii. Lipids are connected to glucose metabolism 1. Cholesterol contributes to cell membrane flexibility 2. Triglycerides are long-term energy storage in animals 3. Fatty acids are broken into two-carbon units that enter the citric acid cycle 3. Lecture 9: Photosynthesis a. Solar energy is converted into chemical energy and then used to build carb molecules b. Photosynthesis provides most of the energy required by living things on earth c. Solar dependence and food production i. Autotroph: organism that can produce its own food ii. Photo-autotrophs: plants that use sunlight and carbon from CO2 to synthesize chemical energy in the form of carbs iii. Heterotrophs: organisms that are incapable of photosynthesis and need food to produce energy, aka humans and animals d. Structure of photosynthesis e. Carbon dioxide + water  sugar + oxygen f. In plants, photosynthesis takes place in leaves i. Mesophyll: middle layer in leaf where it takes place ii. Stomata: small openings where gas exchange occurs iii. Chloroplast: where photosynthesis takes place, exists in the mesophyll iv. Thylakoids: a 3 membrane in chloroplast that contains chlorophyll: a pigment where the whole process of photosynthesis begins v. Granum: a stack of thylakoids vi. Stroma: space surrounding the stroma g. 2 parts of photosynthesis i. Light dependent reactions 1. Take place in thylakoid membrane 2. Chlorophyll absorbs sunlight and converts it into energy 3. Releases oxygen from hydrolysis of water as a byproduct 4. What is light energy? a. Sun emits electromagnetic radiation b. Humans can only see “visible light” c. Waves = the manner in which solar energy travels i. Wavelengths: the distance between 2 consecutive similar points in a series of waves d. Electromagnetic spectrum: range of all possible wavelengths of radiation i. Longer wavelength = less energy carried ii. Shorter wavelength = more energy carried 5. Absorption of light a. Pigments absorb light light enters photosynthesis process b. Red = lower wavelengths and less energy c. Certain pigments absorb certain wavelengths and reflect the color of the wavelength they cannot absorb i. Chlorophyll a: green pigment in photosynthetic organisms, absorbs blue and red, but not green, so green is reflected ii. Chlorophyll b: absorbs blue and red-orange light and carotenoids d. Absorption spectrum: specific pattern of wavelengths that a pigment absorbs identifies the pigment 6. Photosystem: grouping of pigment molecules where all light dependent reactions begin 7. Photon: absorbed by pigment molecule, one at a time, it is a packet of light energy  travels until it reaches a molecule of chlorophyll which causes electron in chlorophyll to get excited 8. energy in light-dependent reactions is stored in ATP (phosphate atom holds energy) and NADPH (hydrogen atom holds energy a. hydrogen ions are allowed to pass through ATP synthase through chemiosmosis 9. solar energy stored in energy carriers can be used to make a sugar molecule ii. Calvin cycle 1. Takes place in the stroma 2. Chemical energy is tuned into sugar molecules 3. 2 chemicals are present that initiate Calvin cycle: the enzyme RuBisCO, and the molecule ribulose bisphosphate (RuBP) 4. Three basic stages a. Carbon Fixation: RuBisCO catalyzes reaction between CO2 and RuBP b. Reduction: ATP and NADPH use stored energy to convert 3-PGA into another compound called G3P c. Regeneration: one G3P molecule leaves Calvin Cycle to give to formation of carb molecule, glucose i. Remaining G3P molecules regenerate RuBP along with ATP 5. It takes 6 turns of the Calvin cycle to fix 6 carbon atoms from CO2. These require energy input from 12 ATP molecules and 12 NADPH molecules in the regeneration step h. Photosynthesis in Prokaryotes i. Lack membrane bound organelles ii. Have infoldings of the plasma membrane for chlorophyll attachment and photosynthesis i. The Energy Cycle i. Reaction for photosynthesis is the reverse reaction for cellular respiration ii. Photosynthesis: 6CO2 +6H20  C6H12O6 + 602 iii. Cellular respiration: 6O2 + C6H12O6  6CO2 +6H2O iv. Every single atom in nature is conserved and recycled, there is no such thing as waste 1. Substances change and move, but never disappear.


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