BCHM 307 Week 1 Notes Ch. 1&2
BCHM 307 Week 1 Notes Ch. 1&2 BCHM 30700 - 001
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This 4 page Class Notes was uploaded by Erin VanHoosier on Saturday August 27, 2016. The Class Notes belongs to BCHM 30700 - 001 at Purdue University taught by Stefan Paula in Fall 2016. Since its upload, it has received 66 views. For similar materials see Biochemistry in Chemistry at Purdue University.
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Date Created: 08/27/16
Week 1 Notes Ch. 1&2 Ch. 1 The Chemical Basis of Life What is Biochemistry explains life at the molecular level, using chemistry terms to describe living things. Explains the whole by breaking it into smaller parts (i.e. levels of organization: organism is the whole and organ, cell, organelle, molecules are the smaller parts) Questions of Biochemistry o What are living things made of? o How do organisms gain and use energy? o How does an organism maintain its identity across generations? Biological Molecules Elements found in a living system: C, N, O, H are the main elements Ca, P, K, S, Cl, Na, Mg Bond energies of organic compounds range from ~350-490 kJ/mol o Life requires a certain level of stability and flexibility!!! ***KNOW FUNCTIONAL GROUPS ON TABLE 1-1 in textbook Amine, Alcohol, Thiol, Ether, Aldehyde, Ketone, Carboxylic Acid, Ester, Amide, Imine, Phosphoric Acid ester, Diphosphoric acid ester Four Major Types of Biomolecules: 1 Amino Acids: contain amino group (-NH2) and carboxylic acid group (-COOH) but in ionized forms (NH3+) and (COO-) 2 Carbohydrates: monosaccharides (simple carbs) = (CH2O)n where n is less than or equal to three. a Key to remembering it’s a carbohydrate is the multiple -OH groups 2 Nucleotides: contain five-carbons, nitrogen-containing ring, one or more phosphate groups a i.e. adenosine triphosphate (ATP) 2 Lipids (in the smooth and rough ER): do not have a universal structural formula because very diverse a Poorly soluble Three Major Biological Polymers: Monomers are individual pieces that link together and form polymers. Once linked together, the monomers are known as residues. 1 Proteins (in the smooth and rough ER): polymers of amino acids a Called polypeptides b 20 amino acid building blocks i Linked together to form peptide bonds 1 Three dimensional shape (conformation) depends on AA composition and sequence ii Proteins are the most versatile of all biopolymers due to all the different possible combinations and structures 2 Nucleic Acids (in the chromosomes): polymers of nucleotides a Called polynucleotides i DNA or RNA ii Only made from four different nucleotides iii Phosphodiester bonds are the linkage of two nucleotides iv Have a regular structure 2 Polysaccharides (in the cell wall): contain one or a few types of monosaccharide residues a Little variability in structure, but are fuel-storage molecules in cells due to support b Linked via glycosidic bonds Ch. 2 Aqueous Chemistry Water is about 70% of the mass of most living things o 60% in humans o H20 forms a polar (uneven distribution of charge) covalent bond with a tetrahedral structure o Hydrogen bond forms when the partial negative end of one water molecule connects with the partial positive part of another aka it has a preferred orientation (directionality) Held together through electrostatic force (partial -/partial +) and partial covalent bond Can form up to four hydrogen bonds, but for only a short amount of time because water molecules are constantly moving Therefore, only two strong hydrogen bonds can be formed!!!!!! H+ donors: N-H, O-H, S-H H+ acceptors: N, O, S molecules Hydrogen always bonds with an electronegative atom with a lone pair!!! Other interactions: o Van der Waals Interactions: usually weaker than hydrogen bonds Dipole-dipole interaction is between two strongly polar groups that are not charged o London Dispersion Forces: nonpolar interactions due to temporary separation of charge Only bond when molecules are very close…if too close then van der Waals radii collide and are drawn apart via repulsion forces Water is very high in a….. Dielectric Constant: the measure of a solvent's ability to remove electrostatic interactions between dissolved ions. Glucose is very dilute in human blood (~5mM), but molecules in vivo form a dense mixture rather than a watery soup. Within a cell there is little space between molecules for only a few water molecules to pass by. Cell molecules are coated with water molecules to avoid interactions with each other and to be in a constant liquid state. The Hydrophobic Effect Water fearing/insoluble in water Molecule becomes hydrated when surrounded with water molecules that aren't involved in hydrogen bonding. o Creates a loss of entropy (energy) in the system o If a large number of nonpolar molecules are placed into water, they are hydrated as a group= hydrophobic effect Amphiphilic/Amphipathic= both hydrophobic and hydrophilic parts o Examples: Micelle: polar heads on outside, nonpolar tail on inside and forms a circle Bilayer: polar heads facing outside, nonpolar parts facing inside Vesicle: traps aqueous solution Prevents diffusion down a concentration gradient Acid- Base Chemistry H2O<----> H^+ + OH^- But in reality, the H^+ joins another water molecule to make a hydronium ion H3O^+ Proton jumping involves the rapid H^+ ion bonding from one water molecule to another…this movement is greater than the movement of ions diffusing in water. Acid-base reactions are one of the fastest biochemical reactions K=Kw or the ionization constant of water K= [H^+][OH^-] Kw= 10^-14 Acidic Solution: [H^+] > 10^-7 or 7 Neutral Solution: [H^+]=[OH-] = 10^-7 or 7 Basic Solution: [H^+] < 10^-7 or 7 Adding an acid INCREASES the concentration of H^+ and DECREASE the pH Adding a base DECREASES the concentration of H^+, and INCREASES the pH AND the concentration of OH- Strong Acids: fully dissociate ****KNOW THESE**** HCl, HNO3, H2SO4, KOH, NaOH A pK value describes an acid's tendency to ionize Ions do not dissociate completely, so the equation is expressed via equilibrium Ka: acid dissociation constant o The larger the value of Ka, the more likely the acid will ionize (aka STRONGER ACID) o Need pKa to determine the pH of weaker acids pK=-logKa Conjugate base: proton acceptor in reaction Henderson-Hasselbalch equation: pH=pK + log [A-]/[HA] pH and pK show protonation states pH<3.4 are an acid pH between 3.4 and 9 are neutral pH>9 are basic Buffers Resist changes in pH Made from a weak acid with its conjugate base o The added strong acid combines with conjugate base o The added strong base forms water
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