BIOL 213 1st Edition Lecture 6Outline of Last Lecture I. A protein’s function is linked to its structureII. Overview of the levels of protein structureIII. Primary structurea. Amino acid sequenceIV. Secondary structurea. α helices b. β sheets i. antiparallelii. parallelV. Tertiary structurea. Interaction of α helices and β sheetsVI. Quaternary structurea. Multiple polypeptide subunitsi. Identicalii. DifferentVII. Protein foldinga. Defects lead to diseasesVIII. EnzymesThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.a. Lower activation energyOutline of Current Lecture I. Review of protein structure levelsII. Enzymesa. Basic overviewIII. Regulation of Enzymesa. Regulation is essential to a working cellb. Can be positive or negativeIV. Inhibitorsa. Turn an enzyme “off”b. Negative regulationc. Competitive inhibitorsd. Noncompetitive inhibitorsV. Activatorsa. Turn an enzyme “on”b. Positive regulationVI. Phosphorylationa. Add a phosphate group to an amino acid of a proteinb. Changes the structure of the protein, therefore its functionc. Can be negative or positive regulationVII. GTP-proteinsa. GTP turns the G-protein “on”i. Positive regulationb. GDP turns the G-protein “off”i. Negative regulationVIII. Molecules can bind in the right order to cause movementa. Motor proteinsIX. Coordination of regulation of enzymesa. This creates metabolic pathwaysX. Evaluating and graphing enzyme performancea. Graph: substrate concentration vs the rate of substrate consumptionb. Vmax and KM c. Brick wall analogyd. How enzyme regulators affect enzyme performancei. Competitive inhibitors1. Vmax = no change2. KM = increasedii. Noncompetitive inhibitors1. Vmax = decreased2. KM = no changeiii. Activators 1. Vmax = increased2. KM = no changeCurrent LectureI. Review of protein structure levelsa. Primaryi. Amino acid sequenceii. Held together with covalent bonds (peptide bonds) between the amino acidsb. Secondaryi. Small folds within the polypeptideii. Hydrogen bondsiii. α helices and β sheetsc. Tertiaryi. Interaction of α helices and β sheetsii. All bonds are involved1. Covalent2. All weak noncovalentd. Quaternaryi. Multiple polypeptide chains bonding together to form a proteinii. All bonds are involved,1. Covalent2. All weak noncovalentII. Enzymesa. Biological catalysts that are essential to cell biologyb. Lower the activation energy of reactions to increase reaction rate byi. Orienting the multiple substrate molecules so that the reaction can actually occur1. The probability of the substrates meeting randomly in the cell is very low, so the enzymes is there to bring them togetherii. Rearranging the electrons in the substrate(s) to give them partial charges that favor a reaction1. To do this, the enzyme has the opposite charge (of what it wants in the substrate) in the places where it attaches to the substrate inorder to cause the substrate to have a chargeiii. Physically strains the substrate, forcing it into its transition state1. A transition state is where a molecule can be either one thing, or another. It’s like it’s balanced very precariously on the top of a hill2. When a substrate is in its transition state, it’s more likely to go through a reaction (slightly pushing so that it rolls down the hill) than when it’s in its normal state (pushing it up the hill first, and then over the other side)c. Each enzyme binds to a unique ligand/substrated. General sequence of a reaction catalyzed by an enzymei. The ligand/substrate binds to the active/binding site of the enzymeii. This becomes known as the enzyme-substrate complexiii. The reaction which the enzyme catalyzes occursiv. The enzyme-substrate complex is now the enzyme-product complexv. The product has a lower affinity for the enzyme, and vice versa, therefore they detach from each othervi. Allowing the unchanged enzyme to bind to another substrateIII. Regulation of Enzymesa. Enzymes are essential to life, but we can’t just have them running around the cellcatalyzing whatever they want, whenever they want, they have to be regulated, depending on what the cell needsb. Regulation can be positive or negativei. Positive: a molecule binds to an enzyme to turn it “on”ii. Negative: a molecule binds to an enzyme to turn it “off”IV. Inhibitors - negativea. These are molecules that bind to an enzyme to cause it to stop catalyzing reactionsb. They essentially turn the enzyme offi. The addition of inhibitors turns the individual enzyme off, but not the whole population of enzymesii. Some may be inhibited (off), but there are others in the same group that are not inhibited and are therefore still workingc. Competitive inhibitorsi. These bind to the active site of the enzyme so that the substrate and enzyme physically cannot bind together to initiate a reactionii. They compete with the substrate for the active sited. Noncompetitive inhibitorsi. These bind to a different site of the enzymeii. They change the shape (conformation) of the enzyme so that the substrate no longer fits in the active siteV. Activators - positivea. These are molecules that bind to enzymes in order to cause it to start catalyzing reactionsb. They essentially turn the enzyme oni. Like with inhibitors, the addition of activators turns the individual enzymeon, but not the whole population of enzymesii. Some may be activated (on), but there are others in the same group that are not activated and are therefore still not workingc. When they bind to the enzyme, they cause a conformation change of the enzymed. This change in shape allows the enzyme to bind to its substrate and catalyze the reactionVI. Phosphorylation – positive OR negativea. This is a kind of regulation when a protein kinase uses ATP to attach a phosphate group to an amino acid of a proteini. It’s attached by a covalent bondii. Remember that enzymes are a kind of proteinb. This actually changes the (primary) structure of the protein, therefore changing its functioni. Change in primary structure  change in secondary structure  change in tertiary structure  change in quaternary structure  change in functionii. This is seen as a reversible way to change the amino acid sequencec. Phosphorylation can be reversed by the protein phosphatase, which removes thephosphate group, thereby reverting the protein to its original structure/functiond. It can be