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Bio 160 midterm study guide

by: Alex

Bio 160 midterm study guide Bio 160

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YOU READY FOR THE TEST?!?! No? It's ok! Everything you need to know is in this Study Guide! Images of the processes help explain what words can't! Topics like signals, signal transduction, enzymes,...
Biological Sciences I
Study Guide
bio160, Biology, symula, midterm, Photosynthesis, cellularrespiration, Enzymes, Signals
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This 11 page Study Guide was uploaded by Alex on Thursday October 6, 2016. The Study Guide belongs to Bio 160 at University of Mississippi taught by SYMULA, REBECCA E in Fall 2016. Since its upload, it has received 166 views. For similar materials see Biological Sciences I in Biology at University of Mississippi.

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Date Created: 10/06/16
Study Guide for Bio 160 midterm! Signals and transduction  Once a signal is sent out, a specific receptor must be present to detect it.  Signal Transduction Pathway- a sequence of molecular events and chemical reactions that lead to a cell’s response to a signal o A pathway is basically a signal---a receptor---and a response  Chemical signals are often made in one part of the body and arrive at target cells by local diffusion or by circulation in the blood or the plant vascular system. o Autocrine is when the signals diffuse to and affect the cells that make them. o Juxtacrine is when signals affect only cells adjacent to the cell producing the signal. o Paracrine is when signals diffuse to and affect nearby cells, they go further than juxtacrine signals. o Endocrine is when signals travel through the circulatory system.  Crosstalk- interactions between different signal transduction pathways  Signals can either directly or indirectly effect the cell o They effect it directly by activating a protein, and it immediately does the action (or diffusing across the membrane to a protein in the cytoplasm) o They effect it indirectly when it activates a receptor and then sets off a chain of reactions (or when they cannot diffuse across the cell and must activate a membrane receptor instead)  Ligand- a molecule that binds to a receptor site and changes the shape that initiates a response  Receptor proteins are made for specific signals. Both are shaped uniquely to fit within one another  The sensitivity of a cell to a signal is determined by the amount of receptor proteins the cell has for the signal.  Membrane receptors- proteins in the membrane that accept the signal and start a cascade of actions  Intracellular receptors- proteins floating around in the cytoplasm accept signals that transferred across the membrane o Ion channel receptors are opened by a signal. This allows ions that can’t diffuse across the membrane into the cell. Ex: K and Na o Protein kinase- a protein that, when activated by a signal, phosphorylates itself and/or other proteins. o G protein-linked receptors receive a signal and transfer their energy to a g protein. The g protein then breaks off a part of itself to deliver the energy to an effector protein. GD  Transcription is altered when an intracellular protein is activated by a signal. The protein is previously accompanied by a chaperone protein, and once the receptor is activated, the chaperone guides the receptor to the nucleus membrane before breaking off to allow the protein to go inside. membrane Chaperone protein Nucleus membrane  Second messengers are nonprotein molecules that amplify a signal’s response in a cell. Ex: cAMP  A protein kinase cascade is when a signal lets off a large series of events in the cell o At each step of the cascade event, the signal is amplified because the kinase can activate multiple proteins through the signal o Different target proteins at each step in the cascade can provide variation in the response This is just an example. You do not need to know the steps because they vary so much  cAMP is a second messenger made by the effector protein adenylyl cyclase that amplifies the signal and allows many events happen as a result of that single event  Signals also effect enzymes by turning them on and off o Allosteric Inhibition- when the signal turns off the enzyme and it is no longer able to work. It does this by changing the shape of the enzyme and active site o Allosteric Activation- when the signal turns on the enzyme by changing its shape to open an active site. o Allosteric simply means that a molecule was added to the enzyme  Animal cells communicate with each other with gap junctions, channels between adjacent cells.  Plant cells communicate through the plasmodesmata Energy and enzymes  A chemical reaction occurs when atoms have sufficient energy to combine or change their bonding partners  Reactants are the beginning “ingredients” you have before a reaction  Products are the resulting “cake” after energy is put in  Metabolism- the sum total of all the chemical reactions occurring in a biological system  Potential energy- energy that is stored in bonds that can be used to do work. Ex: a piece of bread before you eat it has potential energy. When you eat it, it is broken down by your body to absorb the energy stored in the bread  Kinetic energy- the energy of movement. Think roller coaster going down a hill  Two basic types of metabolism o Anabolic reactions is when you link simple molecules together with energy to form a more complex molecule (think legos) o Catabolic reactions is when you break down complex molecules into simpler ones (think of the bread youre digesting. A good way to remember it is to think “the cat is exploding into pieces” Dark, but it works) st  1 law of thermodynamics is that energy is neither created nor destroyed o Its like the first law of matter  2 ndlaw of thermodynamics is that when energy is converted, some of the energy produced is lost, usually due to heat o Entropy is the measure of the amount of energy lost due to heat  Total energy is called enthalpy  Usable energy is called free energy  - G means that free energy is released  Positive G means that free energy is required  S is the amount of entropy  H is the total amount of energy added to the system  As a result of energy transformations, disorder tends to increase because some energy is always lost to entropy (heat)  An exergonic reaction only requires an activation energy for the reaction to occur and energy to be RELEASED!  An endergonic reaction requires a lot of energy to be put in to create a final product o ATP hydrolysis releases energy by breaking off the third, outermost phosphate group and releasing energy. EXERGONIC o ATP building needs the investment of energy to attach a long Pi phosphate group to ADP. ENDERGONIC o Endergonic and exergonic reactions are coupled. Meaning one fuels the other o Hydrolysis means it is broken with water  Activation energy is the amount of energy needed to overcome a barrier to let an exergonic reaction take place  Transition state is the unstable position of the particle after the activation energy and before it “falls” into its reactions  In an enzyme-catalyst reaction, the reactants are called substrated.  An active site is where the substrates bind to the enzyme  The enzyme-substrate complex is the combined formation that the substrates and enzyme form before the product is released o When substrates bind to an enzyme, they change the shape of the enzyme to form them perfectly before leaving the enzyme. Then, the enzyme returns to its original shape o E+S=ES=E+P o Enzyme + substrates = enzyme-substrate complex= enzyme + product Use of enzyme in an endergonic reaction  Enzymes lower the activation energy and the rate of reaction, but not G, or the free energy released in the reaction  They do not effect equilibrium  Some enzymes require other molecules in order to function o Prosthetic groups are distinct, non-amino acid atoms or molecules that are NOT PERMANENTLY bound to their enzymes o Inorganic cofactors are ions such as copper, zinc, and iron that are PERMANENTLY bound to certain enzymes o Coenzymes are non-protein carbon-containing molecules that are required for the activation of one or more enzymes. ARE NOT PERMANENTLY BOUND YOU MUST HAVE THE NAMES, GROUPS, AND JOBS OF EACH OF THESE MEMORIZED FAD may not be asked about since there are discrepancies, but still be familiar with it. It’s easy  Enzymes are regulated by inhibitors o Irreversible inhibitors will PERMANENTLY deactivate an enzyme if attached to the active site. This is most common in toxins o Reversible inhibitors  Negative feedback is when the product of the enzyme/process is used to shut off the enzyme/process. This is important in cellular respiration and photosynthesis  Competitive inhibitor is when you add in another molecule that can also fit in the enzyme’s active site. Therefore, the substrates are competing for the slot. Hard to understand, so I’ll give an example. Caffeine is the same shape as the substrate that relaxes your cells (so they make less ATP) and makes you tired. By introducing caffeine, it binds to the active site, blocking the other substrate from coming in and binding with the enzyme. The result is that the cell keeps working at a higher speed and more energy is produced because the substrate is not telling them to relax.  Uncompetitive inhibitor attaches to the enzyme-substrate complex and prevents it from releasing its products.  Noncompetitive inhibitor (Allosteric inhibitor) is a molecule that can deactivate an enzyme by attaching to it to change its active site shape  An enzyme that requires an allosteric activator takes longer to get started, but reaches the maximum rate faster. Maximu m rate With allosteric enzyme Maximu m rate With regular enzyme  pH and temperature effect the enzyme greatly. Any change in either can change the shape of the enzyme and cause it to either be less active or damaged to the point that it can’t work at all  enzymes best work at their optimal temperature and pH Cellular respiration  cellular respiration uses O2 from the environment, and thus is aerobic.  Fermentation does not use O2 and therefore is anaerobic  Oxidation is when electrons are taken from a molecule  Reduction is when electrons are added to a molecule o These terms are comparable. Just like hypertonic and hypotonic from the last unit. You cannot have one without the other. Reduced In- Oxidized In- Comes in with Comes in without Oxidized Out- electrons Transfers its Reduced Out- electrons and Accepts the leaves without electrons and them leaves with them  In glycolysis, glucose is partially oxidized and some energy is released o Glycolysis takes place in the cytosol. o Energy-investing stage  You need to invest 2 ATP to end with two G3P  To pull apart the glucose, a kinase ads two phosphates and pulls it apart by the phosphates o Energy-harvesting stage  1 NADH, 2 ATP, and a pyruvate. (double for one molecule)  Pyruvate oxidation o Takes place when its being transferred into the mitochondrial matrix o 1 NADH and 1 CO2 comes out per pyruvate and becomes Acetyl CoA  The citric acid cycle completely oxidizes carbon o Takes place in the mitochondrial matrix o Acetyl CoA is put in the cycle o The citric acid cycle produces 3 NADH, 1 FADH2, 1 GTP, 2 CO2, and oxaloacetate is recycled back into the process  Oxidative phosphorylation (Electron transport chain) o Respiratory chain is the series of membrane-associated electron carriers.  Occurs in the inner membrane of the mitochondria and the intermembrane space  O2 is the FINAL ELECTRON ACCEPTOR. Once it accepts it, it becomes WATER  When the electrons pass through the transmembrane proteins, the protein “shoots” out a hydrogen proton out of the matrix and into the intermembrane space  This creates an acidic, positively charged side and a gradient o Chemiosmoses is when the hydrogen protons in the intermembrane space diffuse back through a channel protein called ATP synthase that bonds together a Pi and ADP  The hydrogen proton moves down its gradient, giving energy to the ATP synthase to create the phosphate bond.  Fermentation occurs when there is no oxygen available o In animals, fermentation only occurs when vigorously working out. The oxygen you breathe in isn’t enough for cellular respiration, so our body goes through fermentation to keep up with the exercise. As a result, lactic acid is produced o In fungus, like yeast, fermentation is only used. Instead of lactic acid, the product is ethanol.  Other things can enter this cycle at different times. Glycerol and some amino acids can go through glucose. Some fatty acids can also go into the citric acid cycle and some amino acids can join in the middle of the citric acid cycle. Photosynthesis  The energy of light is called a photon. This reacts as both a particle and a wave.  The wavelength of the photon is relative to the color it is portrayed.  Chlorophyll is stored in proteins called photosystems in the membrane of the thylakoid. o When a photon hits the photosystem, the electron in the chlorophyll is excited and travels all over the protein  Autotroph- an organism that makes its own food from the sun  Heterotroph- an organism that consumes other autotroph and heterotrophs  Light reactions occur on the thylakoid membrane in a chloroplast. They need sunlight as energy o This is like the electron transport chain. But it has two subcategories  Cyclic process- photons hit Photosystem 1 and excite the electrons  The electrons travel through to the other membrane protein that pumps a hydrogen proton through to the inside of the thylakoid membrane.  The hydrogen proton then travels down an ATP synthase to give energy to make ATP (just like in the electron transport chain)  Then the electron RETURNS to the photosystem 1  Noncyclic process- photons hit photosystem 2 and excite electrons  It travels through other proteins in the membrane until it gets to photosystem 1  Then, it must be reenergized by another photon and sent through to the end of the chain.  The NADP+ is the final electron receptor- plays the role of O2 in the electron transport chain. It becomes NADPH  Since the electron is transferred out to NADPH, photosystem 2 needs to replace its electrons. So, it splits water and takes the electrons from that  Hydrogen protons are pumped into the thylakoid interior as well and so move down the gradient through ATP synthase and makes ATP  light independent reactions o the calvin cycle takes place in the stroma of the chloroplast  6 CO2 are needed to start the process and then converted to G3P  The ATP and NADPH produced in the light reactions is used to fuel the calvin cycle  Don’t need to know specifics except that it produces a 3 carbon sugar  But to replenish the RuBP (a 5 carbon molecule) in the Calvin Cycle, it has to be run two more times (three overall) to create 15 carbon molecule that can then be split into three RuBP  The first part of the cycle is called the carbon fixation, the second is reduction and sugar production, and the third is regeneration of RuBP  This pathway is called photorespiration because it consumes O2 and release CO2


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