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Physics II- week one notes

by: ShayD

Physics II- week one notes CHEM 4712

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These notes combine both the class notes and the textbook summery. These notes cover thermodynamics, types of cells, organelles, water's physical properties, water's chemical properties, amino acid...
Xuemin Wang
Class Notes
Thermodynamics, types of cells, organelles, water's physical properties, water's chemical properties, amino acid nomenclature, amino acid properties




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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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