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Bio Foundations, Chapter 6 Lecture Notes (Week 5)

by: Hannah Kennedy

Bio Foundations, Chapter 6 Lecture Notes (Week 5) 10120

Marketplace > Kent State University > Biological Sciences > 10120 > Bio Foundations Chapter 6 Lecture Notes Week 5
Hannah Kennedy
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These notes cover everything that was discussed on chapter 6 in class. These topics include energy, enzymes, factors affecting enzymes, metabolism, and biochemical pathways.
Biological Foundations Honors
Professor Grampa
Class Notes
Biology, Energy, Enzymes, inhibitors, Activators, biochemical pathways, metabolism, Bio, Biology Foundations
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This 5 page Class Notes was uploaded by Hannah Kennedy on Sunday February 14, 2016. The Class Notes belongs to 10120 at Kent State University taught by Professor Grampa in Spring 2016. Since its upload, it has received 27 views. For similar materials see Biological Foundations Honors in Biological Sciences at Kent State University.


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Date Created: 02/14/16
Copyright ©: Hannah Kennedy, Kent State University 1 Chapter 6 1. Energy = the capacity to do work, 2 types a. Potential energy = the stored energy an object can use to do work b. Kinetic energy = energy of motion; energy currently being used by an object c. Energy can be found in different forms such as heat, sound, light, and  electricity i. Biological energy is obtained from the sun which autotrophs use for  photosynthesis d. Breaking bonds (i.e. C—H bonds) requires a lot of energy i. Ex = storing fatty acids in our fat reserves and using them when  energy is limited because we get energy from their broken C—H bonds e. Redox reactions = oxidation­reaction reactions = when bonds are  broken or formed; when electrons are transferred from one atom to another i. Oxidation = when an atom loses an electron ii. Reduction = when an atom gains an electron 1. Oxidation and reduction always occur together a. Mnemonic: OIL RIG When a reaction is When a reaction is a  an oxidation (O in is a reduction (R in rig) oil) electrons are electrons are gained overall lost overall 2. Thermodynamics a. First law of thermodynamics = states that energy can’t be created or  destroyed; that energy can only change from one form to another i. ex: phase changes, rearranging bonds (ATP) b. second law of thermodynamics = states that the disorder in the universe  = entropy and it is continuously increasing i. the less organized energy is the more stable (i.e. its easier for bricks to collapse then it is for them to stay upright and stacked) 3. Chemical Reactions a. Free energy = G = energy available to do work in any stem i. Can be positive or negative b. Endergonic reactions = (“enter”gonic) = reactions that require an input  of energy; positive     G i. This is not a spontaneous reaction because energy needs to effortfully  put in ii. Occurs when it is beneficial 1. Ex = when a cell puts in ATP for active transport for the  movement of molecules (i.e. there is a good end pay off to  putting in the energy and the effort) Copyright ©: Hannah Kennedy, Kent State University 2 c. Exergonic reactions = “exit” gonic) = reactions that release excess free  energy as heat; negative     G i. This is spontaneous reaction because energy is easily liberated ii. Ex = breaking of phosphate bonds in ATP 4.  ATP = adenosine triphosphate; energy currency of the cell; used for endergonic  reactions a. Adenosine = adenine and ribose b. Naming system: i. Adenosine + 1 phosphate = adenosine monophosphate (AMP) ii. Adenosine + 2 phosphate = adenosine diphosphate (ADP) iii. Adenosine + 3 phosphate = adenosine triphosphate (ATP) c. The phosphate bonds are high energy covalent bonds that are very easily  broken i. Within these bonds there are a lot of strain and tension due to the  negative charges on phosphate being so close to each other 1. This strain makes them easily breakable ii. When broken energy is released and used to power other things in the  cell (i.e. muscle contraction, sodium­potassium pump) d. ATP is easily replenishable and therefore cells don’t have a lot of ATP build­ up; they break the bonds, use the energy, and replace it. 5. Activation energy = the amount of energy needed to initiate a chemical reaction;  can be minimized by a catalyst; known as “the hurdle the reaction needs to  overcome” a. The lower the activation energy, the more stable the reaction b. Catalysts decrease the activation energy by stressing existing bonds (i.e.  rearranging them) and making them easier to break; the reaction is more  likely to occur because of this c. Transition state = the more stable phase in the reaction; the stage in  between the making and breaking of bonds  6. Enzymes = biological catalysts (usually proteins) that increase the rate of a reaction by decreasing activation energy; they are not changed or consumed a. Each enzyme catalyzes only 1 or a few reaction i. Advantage: gives the cell tight and specific control over what it is  doing at any particular time ii. Why we don’t want a multipurpose enzyme: the cell has no backup  plan and no control over what the enzyme is doing b. The location of the enzyme (i.e. the cytoplasm, plasma membrane, and  organelles) is determines by what the mission is of that enzyme i. Ex:  Location Function/Mission Organelles: lysosomes and peroxisomes When enzymes are found here they are in a  protected by a phospholipid bilayer in the  lysosome or peroxisome to help break  Copyright ©: Hannah Kennedy, Kent State University 3 harmful things down Plasma membrane Enzymes here are involved as  transmembrane proteins Cytoplasm Enzymes here catalyze reactions with polar  molecules and make sure reactants and  products don’t enter the cell; they are also  involved in facilitated diffusion here by  helping nonpolar substances through the  bilayer; ex = brush border enzymes c. Substrates = starting materials d. Products = substances formed during the reactions e. Active site = the specific part of the enzyme where the substrate(s) will bind and the reaction will take place i. The bond is temporary and forms an enzyme­substrate complex ii. Enzymes can change the shape of the active site while the substrates  are bound and conform the sit to fit the shape of the substrates 1. At this point the substrates are in close range to the enzyme  and the enzyme can stress bonds, allowing the reaction to take  place more quickly f. Multi­enzyme complexes = complexes that occur when several enzymes  are bound to each other to form a larger molecule and each enzyme catalyzes  sequential reactions of a pathway; “relay race” g. 2 things that allow reactions to happen easier i. When the shape of the substrate is more similar to the active site the  more likely the reaction will be to occur; “lock and key theory” ii. The affinity the substrate has for the active site (if the substrate is  negative then the active site should be positive) 1. The higher the affinity the tighter the bonding strength  between the substrate and the active site 7. Factors affecting enzymes Factor name Effect on enzyme Additional info Temperature The higher the  ­ Optimum temp = the  temperature the faster the  temperature at which our  rate of the reaction until  enzymes function the best;  optimum temperature is  anything higher than this  reached; molecules move  can cause them to lose  more with heat and the  function and denature (i.e.  motion from this stresses  a fever); 98.6°F bonds pH Enzymes have an optimum Exceptions to the 6­8 rule:  pH (6­8) at which they can  pepsin (stomach enzyme  function because enzymes  that prefers its optimum  are sensitive to the  pH at 2.5) and trypsin  Copyright ©: Hannah Kennedy, Kent State University 4 concentration of hydrogen  (enzyme that helps digest  ions proteins that prefers a  basic pH) Inhibitors = binds to and  ­ works to prevent the  In noncompetitive  deactivates an enzyme “turns  making of too much of  inhibition the substrate no  something longer fits into the  it off”; can do this in 2 ways 1. Competitive  ­ prevents the enzyme from allosteric site; this is made  inhibition =  functioning possible by tertiary and  inhibitions in which  quaternary protein  the inhibitor and the  structure shifting so that  substrate bind for the  enzymes cant fit same active site;  reversible 2. Noncompetitive  inhibition =  inhibition in which  inhibitor binds to a  different site than the  substrate = allosteric site and changes the  shape of the active site Activators = binds to and  Allows the enzyme to  Binding of a molecule to  activates an enzyme “turns it  function the allosteric site can also  on”; 2 kinds activate an enzyme 1. Cofactors =  additional chemicals  that are required for a  reaction to occur;  assist the enzyme in  speeding up the  reaction by  manipulating  electrons and  attracting them away  from covalent bonds to weaken them (ex = Zn  and Mn); obtained in  diet 2. Coenzymes = type of  cofactor that are non­ protein organic  (containing­carbon)  Copyright ©: Hannah Kennedy, Kent State University 5 molecules (ex =  vitamins and modified  nucleotides) 8. Metabolism = the sum of all chemical reactions occurring in the organism;  metabolism = anabolism + catabolism a. Anabolism = chemical reactions that use energy to synthesize molecules;  bonds are formed (dehydration synthesis) b. Catabolism = chemical reaction that break down molecules and release  energy; bonds are broken (hydrolysis) 9. Biochemical pathways = series of reactions taking place in sequence; “relay race” a. Each step of a biochemical pathway requires a unique enzyme and typically  happen in one area of the cell b. Negative feedback inhibition = regulation of a biochemical pathway by  controlling the activity of the first step of the pathways i. This is possible because the end product becomes the allosteric  inhibitor of the first enzyme


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