Physics II- week one notes
Physics II- week one notes CHEM 4712
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This 11 page Class Notes was uploaded by ShayD on Saturday January 16, 2016. The Class Notes belongs to CHEM 4712 at University of Missouri - St. Louis taught by Xuemin Wang in Spring 2016. Since its upload, it has received 9 views. For similar materials see Biochemistry in Chemistry at University of Missouri - St. Louis.
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Date Created: 01/16/16
Dudaie 1 Biochemistry: CH’s 1, 2, and 4 Chapter 1 Introduction to the Chemistry of Life 1. The Origin of Life a. Biological molecules i. All living matter consists of a small number of elements 1. C, H, O, N, P, Ca, and S = 97% ii. Functional groups: 1. b. Complex biological system i. Different monomers (simple) molecules and their various functional groups combine to form a large single molecule called a polymer 1. This increases the chemical versatility Dudaie 2 2. Specific complementation between these functional groups help macromolecules to replicate. ii. Since at first the selfreplicating systems were sloppy and made a lot of mistakes 1. Over time natural selection would favor molecule that made more accurate copies 2. Cell Architecture a. Metabolic reactions in cells i. One of the first advantages created by evolution is the creation of protective boundaries for each cell 1. One theory states that these vesicle were first attached to membranes enclose selfreplicating system= who became the first cells ii. The advantages of compartmentation 1. Provide protection from environmental sources 2. The ability to ,maintain a high concentration of component that would otherwise diffuse away 3. Increased efficiency in polymerization iii. Cells use catalysts: a substance that promotes a chemical reaction without altering itself iv. Reaction require energy v. Specialization in metabolic pathways made it possible for different functional groups work together in a multicellular organism b. Types of cells i. Eukaryotes: which have membrane enclosed nucleus (which encapsulates their DNA) 1. Multicellular as well as unicellular 2. Best characterized as having organelles ii. Prokaryotes which lack a nucleus 1. Compromising various types of bacteria, almost all unicellular iii. Viruses 1. Are much simpler entities that are not classified as living because they lack metabolic apparatus to reproduce outside their own cell Dudaie 3 iv. Organelles 1. Endoplasmic reticulum (ER) site of synthesis of many cellular components 2. Golgi apparatus modifies the ER’s newly synthesized products 3. Mitochondria power house of the cell a. Chloroplasts is in the plants 4. Lysosomes and Peroxisomes a. Specialized functions 5. Vacuoles a. Storage depots 6. Cytoskeleton a. An extensive array of filaments that give the cell shape and ability c. Evolutionary domains: archaea, bacteria, and eukaryotes i. Taxonomy is the science of biological classification 1. Bases on gross morphology 2. Phylogeny= evolutionary history ii. Based on phylogenic relationship are best deduced by comparing polymeric molecules: DNA, RNA, or proteins iii. Archaea include some unusual organisms 1. Methanogens which produce CH 4 2. Halobacteria thrive in concentrated brine solutions 3. Thermophiles inhabit hot springs d. Continue evolutions i. Directed towards a particular goals 1. Random changes that affect the ability of an organism to reproduce under certain conditions ii. Variations among individuals 1. Allow to adapt for particular unexpected changes iii. The past determines the future 1. New structure emerge from preexisting elements 3. Thermodynamics “all life obeys the laws of thermodynamics” That can never be created or destroyed a. The first laws of thermodynamics energy is conserved Dudaie 4 i. A system is defined as the part of the universe that is of interest, such as a reaction vessel or an organism; the rest of the universe is known s the surrounding 1. A system contains an amount of energy (U) a. Energy change of the system is defined as the difference between the heat (q) absorbed and work (w) done by the system on the surrounding ∆ U=Ufinal−Uinitial=q−w b. H, enthalpy H= U+ PV i. A spontaneous process occurs without input of additional energy b. The second law of thermodynamics “Entropy (S) tends to increase” i. The 2 law states that a spontaneous process are characterized by converting order to disorder 1. S= degrees of randomness c. The third law free energy determines the spontaneity process i. Gibbs free energy (G), is the true criteria of spontaneity ∆ G=∆H−T ∆S ii. Types of processes: 1. Exergonic is a process in which expels heat 2. Endergonic is a process in which heat must be inputted Dudaie 5 d. Free energy can be calculated from equilibrium concentration i. The free energy change of a chemical reaction depends on the concentrations of both reactants and products ∆ G°=−RT ln Keq ii. Equilibrium constant 1. Can be calculated from standard free energy C ]D ] Keq= [ ][ ] e. Life obeys thermodynamic laws i. Closed symptoms 1. Can only exchange energy with their surrounding ii. Isolated systems 1. Cannot exchange matter or energy with their surrounding iii. Open systems 1. only exchanges matter or energy with their surrounding Chapter 2 Water 1. Physical properties of water a. Polar molecule i. The oxygen with its unshared electrons carry partial negative charges δ and the hydrogen’s carry a partial positive change δ+ ii. Water molecules form hydrogen bonds Dudaie 6 1. It’s an intermolecular association between the hydrogen and central oxygen atom iii. The ability on water to expand upon freezing and float in water is the reason, there’s life on earth iv. Structure of liquid water is irregular 1. Liquid water consists of rapidly fluctuating three dimensional network of hydrogen bonded H O mo2ecules v. Other weak interactions between biological molecules 1. Non covalent association between neutral molecules a. Van Der Waals forces arise from electrostatic interactions or induced dipoles London dispersion forces b. Hydrophilic substance “water loving” i. Water is said to be the universal solvent c. Hydrophobic effect i. The tendency of water to minimize its contact with hydrophobic molecule ii. A nonpolar molecule can neither accept or donate hydrogen bonds so the water molecules at the surface of the cavity occupied by the nonpolar group cannot hydrogen bond to other molecules in their usual fashion 1. The aggregation of nonpolar groups thereby minimize the surface area and therefore maximizes the entropy of the entire systems. iii. Amphiphilic molecules 1. Most molecules have both polar and nonpolar segments and therefore are simultaneously hydrophobic and hydrophilic Dudaie 7 d. Osmosis i. It is the movement of solvent across the membrane for a region of high concentration to a region of relatively low concentration. 1. Osmotic pressure of a solution is the pressure that must be applied to the solution to prevent the inward flow of water ii. Diffuse 1. Until the concentration of the solute is the same on both sides of the membrane 2. Chemical properties of water a. Water ionizes to form H+ and OH i. Dissociation constant ii. Water is a neutral molecule with a very slight tendency to ionize iii. pH Dudaie 8 H+¿ ¿ H+¿ ¿ 1. ¿ 1 ¿ ¿ pH=−log¿ b. Acids and Bases A−¿ HA+H 2O→H 3O+¿ i. Acid is a substance that can donate a proton 1. Conjugate base is the base form of the acid after it has donated a hydrogen [A] ii. Base is a substance that can accept a proton 1. Conjugate acid is the acid form of the base after it has accepted a hydrogen [H3O] c. Acid dissociation constant i. acid dissociation constant, a , (also known as acidity constant, or acidionization constant) is a quantitative measure of the strength of an acid in solution 1. pK= log K ii. Henderson Hasselbalch equation 1. When the molar concentration of an acid and its conjugate A−¿ ¿ 2. ¿ ¿ pH=pK+log¿ 3. Chapter 4 Amino Acids a. Amino acid structure α amino group, tetrahedral α carbon, α carboxyl, variable R group i. Hydrophobic (Non Polar): everything else 1. Hydrophobic (Non Polar): mostly alkanes R group; rings on proline (cyclobutane ring N as R group), phenylalanine, tryptophan; methionine (thioester S ether) Dudaie 9 ii. Hydrophilic: 1. Polar “Threon the Ty rex hates Seared Gluten Crusted Asparagus => Serine, Cysteine, Tyrosine, threonine, Asparagine, Glutamine a. Neutral: Contains an oxygen; tyrosine (thiol ring); cysteine has sulfhydryl 2. Acid has acid in the name a. Hydrophilic (polar) Hydrophilic (polar) Acidic: carboxylic acid as the R group 3. Basic “His argument is Lysed” => Lysine, Arginine, Histidine a. Hydrophilic (polar) Basic: nitrogen containing R groups NOT tryptophan b. MEMORIZE THESE STRUCTURES and NAMES! Non Polar Polar Neutr al Polar Polar Pola Acidi r Neutr c al Basi Pola r Basi Dudaie 10 c. Dipolar Ions i. Amino acids group bear charged groups of opposites polarity, also called zwitterions d. Peptide bonds link amino acids i. Individual amino acids can be linked together via dehydration 1. They form a CONH bond called a peptide bond ii. Individual amino acids monomeric units are referred to as amino acid residues iii. Variations in the length and the amino acid sequence of polypeptide s are major contributors to the diversity in the shapes and biological functions of proteins e. pK values of Ionizable groups i. the pH at which a molecule carries no net electric charge is known as isoelectric point, pI 1. pI= ½ x (pK+pKi j a. K i d K arj the dissociation constants of the 2 ionizations involving the neutral species 4. Stereochemistry a. Optically active molecules are asymmetric i. Chiral centers 1. A central carbon with a tetrahedral structure that has four different substituents b. Enantiomers i. Non superimposable molecules, there physical and chemical indistinguishable by most techniques 1. Absolute configuration a chiral molecules optical arrangement c. Racemic mixtures i. An equal mixture of each enantiomer 5. Amino acid derivatives a. Protein side chains can be modified Dudaie 11 i. In almost all cases, these unusual amino acids result from specific modifications after a polypeptide chain has been synthesized 1. methylation, phosphorylation, and posttranscriptional modification
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