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MCDB 310 1st Edition Lecture 1 Outline of Current Lecture II. What is Biochemistry?a. Biomolecules and the elements that make them up III. The chemical foundation of biochemistrya. Carbon and organic moleculesb. Functional groupsIV. Isomerisma. Stereoisomers (configurational and conformational)b. Why is isomerism important in biochemistry?V. Biochemical ReactionsVI. Thermodynamicsa. Gibbs Free EnergyVII. KineticsCurrent LectureI. What is biochemistry?a. Biology is the study of life, and chemistry is the study of how atoms interact with each otherb. Biochemistry is the study of the molecules that function to sustain lifec. Main focus: the cellular and molecular levels of biologyd. All cells in the body are made up of Biomoleculesi. Supramolecular complexes (ie-chromatin, plasma membrane, cell wall) are broken down into Macromolecules(ie-DNA, proteins, cellulose) which are further broken down These 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.into monomers (ie-nucleotides, amino acids, carbohydrates, lipids)ii. Other biomolecules include high energy complexes such as ATPiii. Biomolecules are Organic1. They are made up mainly of carbon (60%), hydrogen (11%), nitrogen (9%), and oxygen(6%)e. Other molecules found in bulk in the body include phosphorus, sulfur, chlorine, sodium, potassium, and calcium i. These elements form salts important in neuron signaling and the kidneys, for examplef. Other trace elements in the body include iron, magnesium, iodine, and zincII. The Chemical Foundation of Biochemistrya. Carbon has 4 unpaired valence electrons i. These form a tetrahedral geometry with bond angles of 109.5 degreesii. Can form single bonds, double bonds, and triple bonds (commonly with other carbons, hydrogens, nitrogens, oxygens, and other organic elements)b. Organic compounds are composed of a covalently bonded hydrocarbon backbone, and can take a linear, branched or cyclic geometryi. This backbone is represented by an R in diagramsc. Functional groups are bonded to this backbone and determine the chemical and physical properties of the compoundi. Functional groups (these should be memorized):1. Involving hydrocarbons:2. Involving Oxygen:3. Involving Nitrogen:4. Involving Sulfur:5. Involving Phosphorus:III. Isomerism: Molecules with the same chemical formula a. Stereoisomers: isomers with the same bond order, but different spatial arrangementsb. Configurational stereoisomers: stereoisomers that can only be created by making or breaking bondsi. Cis and trans isomers1. Cis: similar groups fall on the same side of the carbon/carbon double bond2. Trans: similar groups fall on opposite sides of the carbon/carbon double bonda. Both require a carbon/carbon double bondb. In the body, rapid changes between cis and trans isomers of Retinal (biomolecule found in the retina) lead to a neural pulse and allow humans to seeii. Enantiomers and diastereomers1. Both arise from the presence of an asymmetrical carbon (a carbon bonded to 4 different substituents) called a Chiral Center2. Enantiomers: mirror images of each other, but they can never be super imposed on each othera. Identical physical properties, except their reaction to polarized lightb. Classified as either R or S (dependent on the right hand rule), and all chiral centers on two molecules must be opposite in order for them to be considered enantiomersc. R and S enantiomers can have different chemical and/or biological properties3. Diastereomers: arise from the presence of chiral centers, but are NOT mirror images (not all chiral centers switch configuration)a. Number of stereoisomers possible: 2^(number of chiral centers)b. Like enantiomers, they can have different biological and/or chemical propertiesc. In figure below (an example of diastereomers),a green arrow represents the same configuration and a red arrow represents opposing configurationsc. Conformation Isomers: Stereoisomers that arise from free rotation around a carbon/carbon single bondi. Eclipsed Conformation is less stable than the staggered conformation because of steric hindrance (repulsive forces present between functional groups)d. Why is isomerism important for biochemistry?i. The combination of conformational and configurational isomers determines how biochemical interactionsii. These biochemical interactions determine the structure of biomoleculesiii. The structure of these biomolecules determines their biological functionsiv. Life is the result of the summation of all biological activitiesin the bodyv. Example: glucose must “fit” perfectly into the active site of hexokinase, otherwise this biochemical interaction would not take placeIV. The four categories of Biochemical Reactionsa. Making/Breaking Bonds: dependent on bond strengthi. Bond strength depends directly on differences between the two elements’ electronegativity values (larger difference —> increase bond strength)ii. Bond strength is directly dependent on the number of electrons shared (therefore triple are stronger than double and single bonds)iii. Bond strength is inversely dependent on bond distance (triple bonds are much shorter and therefore much strongerthan single or double bonds)b. Group Transfer Reactions: Nucleophilic (electron rich) group X leaves electrophilic (electron lacking) group A in the presence of a second nucleophilic group Yi. Directly dependent on the strength of the nucleophilic group Y (more electronegative/more lone electron pairs —>stronger nucleophile)ii. Directly dependent on the tendency of the nucleophilic group X to leave (large, stable-when-negatively charged groups = good leaving groups)iii. Example: formation of peptide bonds1. An amine and a carboxylate react to form an amide bond by eliminating a water molecule (hydrogen fromone molecule, and hydroxyl group from the other molecule)a. Note: the hydroxyl group is not a good leaving group, but tRNA bonds to it, making it bulky and causing it to leavec. Redox: Gain and loss of electronsi. Oxidation: gaining “oxygens” (remember: whatever oxygen molecule does, hydrogen will do the opposite)1. Whenever an oxygen is gained, a hydrogen (one proton and one electron) leaves2. Therefore, oxidation is the LOSS of electronsii. Reduction: opposite of oxidation (therefore, electrons are gained)iii. Example: metabolism1. Glucose is oxidized creating carbon dioxide, and electrons are transferred to


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