Soto Biochem 8/27, 9/1, 9/3
Soto Biochem 8/27, 9/1, 9/3 CHEM 351
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This 8 page Class Notes was uploaded by Kayli Antos on Friday September 4, 2015. The Class Notes belongs to CHEM 351 at Towson University taught by Ana Soto in Fall 2015. Since its upload, it has received 139 views. For similar materials see Biochemistry in Chemistry at Towson University.
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Date Created: 09/04/15
Biochemistry Soto Fall 15 0 Water 0 Hydrogen Bonds The valance electrons in oxygen occupy the sp3 hybrid orbital and have a tetrahedron orientation The angle between the owgen hydrogen bonds is 1045 which is slightly less than a perfect tetrahedron which has bond angles of 1095 This is due to crowding from the non bonding orbitals lone pairs on oxygen There is a partial positive charge on hydrogen and a partial negative charge on oxygen because it is more electronegative than hydrogen and this results in an unequal sharing of electrons A hydrogen bond is an electrostatic attraction between the owgen of one molecule and the hydrogen of another Hydrogen bonds are very weak much weaker than covalent bonds They also are very brief only having a lifetime of about 1 20 picoseconds while in liquid form The extended networks of hydrogen bonded water molecules form bridges between solutes which allows molecules to interact with each other over several nanometers without touching Hydrogen bonds are not unique to water They can occur with any hydrogens that are bonded to oxygen nitrogen or fluorine Hydrogens bonded to carbons do not make hydrogen bonds because carbon is not electronegative enough to have a great enough pull on electrons resulting in the needed partial charges The strongest bonds are when all atoms involved are aligned linearly in the same plane Gibbs Free Energy Equation AG AH TAS G Gibbs Free Energy Henthalpy T temperaturein Kelvin S entropy it A negative AG means the reaction is exergonic favorable and will happen when H is negative or S is positive A positive AG means that the reaction is not favorable or spontaneous and will happen when H is positive or S is negative 0 Water As A Solvent Since water is polarized it is a good solvent for charged and polarized molecules Water dissolves salts by hydrating and stabilizing ions which decreased electrostatic interactions between them Water has a high dielectric constant which is the physical property representing the number of dipoles in solvent As salts dissolve in water the entropy increases which makes it easier for more salt to dissolve o Hydrophobic Effect Since quotlike attracts likequot water and nonpolar compounds cannot make energetically favorable interactions These compounds also interfere with the water to water hydrogen bonding All molecules regardless of polarity will interfere with water to water hydrogen bonding but polar and charged molecules compensate for this by forming water soluble interactions When amphipathic molecules those with hydrophilic and lipophilic regions mix with water they form micelles which are the hydrophobic regions clustering together with the polar regions on the outside to maximize interactions with water 0 Van der Waals Interactions The electron clouds of two uncharged atoms in close proximity can influence each other Random variations in the electron cloud of one atom create a brief dipole which induces a brief opposite dipole in the electron cloud of the other atom 39 These dipoles will attract each other bringing the nuclei close These weak attractions are called van der Waals interactions or London Dispersion forces 39 The van der Waals forces bring the atoms closer until their electron clouds repel them 39 At the point where the net attractions are at a maximum the nuclei are said to be at van der Waals contact how close an atom will allow another These distances are unique to each atom o Noncovalent Interactions 39 Are weaker than covalent bonds 39 The four main types van der Waals hydrophobic ionic hydrogen bonding 39 Macromolecules which have a large size and surface area have many sites of potential noncovalent bonding Their native structure is that in which potential weak interactions are maximized The complimentary structure of interacting biomolecules reflect the complementarity of the weak interactions between the molecules 0 Colligative Properties 39 When solutes dissolve in water they can alter some physical properties of water including vapor pressure boiling point freezing point and osmotic pressure 39 These effects are based on the number of particles in solution 0 Ionization Of Water 39 An equilibrium constant is used to describe the ionization of water into hydronium and hydroxide ions K 2 Wk 18x103916 H0 2 KH20 H0H KW 1014 39 In pure water the concentrations of hydroxide ions and hydronium ions are equal 0 Weak Acids And Bases 39 The stronger an acid is the lower its dissociation constant This also corresponds to a larger Ka and smaller pKa value 39 Strong acids and bases are those that dissociate completely in water Weak acids and bases do not 0 pH Titrations 39 When plotting the pH against the amount of strong base added shows the pKa of a weak acid as well as strong acidweak base 39 Before any strong base is added the acid is already slightly ionized 39 When the strong base is added the hydroxide ions from the base combine with free hydronium ions to form water As the hydronium ions are removed from solution the conjugated base is formed 39 When half of the strong base equivalents are added half the acid is dissociated The concentrations of the weak acid and its conjugated base are equal pH pKa 39 As more strong base is added the remaining weak acid is converted to its conjugate base At the end of the titration all protons are lost to hydronium ions 0 Henderson Hasselbalch Equation AT HA I pH pKa log 0 Buffers 39 Conjugate acid base pairs are good buffers when the pH is the pKa i1 39 Some acids have multiple acidic protons and therefore multiple pKas 39 5 steps for working buffer problems Write equilibrium equation Calculate concentrations of acid and conjugate base Convert to moles Add or subtract the change Plug into the Henderson Hasselbalch Equation and calculate the pH 0 Amino Acids Pep tides and Pro z ens 0 Proteins 39 They are the most abundant of the biological macromolecules 39 There are many types of proteins including hormones enzymes transporters antibodies and more 39 Made up of amino acids 0 Amino Acids 39 There are twenty different amino acids commonly found in proteins 39 These twenty are called alpha amino acids because the amino group and carboxyl group are both bonded to the alpha carbon 39 Amino acids differ due to their different side chains R groups 39 The rest of the carbons in the molecule are also labeled using the Greek alphabet beta gamma delta epsilon etc 39 These common twenty are assigned three letter abbreviations and one letter symbols to reference them 39 Chiral amino acids are named using L or D in front of the name to describe the position of the amine group in a Fischer projection while the carboxylate group is on top either on the left or right side of the molecule respectively 0 Amino Acid Classification 39 The twenty common amino acids can be divided into five different classes based on the properties of their R groups Non polar and aliphatic carbon atoms in a chain not an aromatic ring Gly Ala Pro Val Leu Ile Met Aromatic Phe Tyr Trp quot Polar and uncharged Ser Thr Cys Asn Gln quot Positively charged Lys His Arg Negatively charged Asp Glu o Non Polar Aliphatic R Groups 39 Hydrophobic R groups will cluster together to better stabilize the proteins through hydrophobic interactions Name 3 LetterAbbre viation 1 Letter Structure Symbol glycine Gly 3 00 l l3 l l alanine Ala A 0039 H3N H proline Pro P 0039 H3N C H valine Val V 00 H3N H leucine Leu L 90039 H3N iiH isoleucine Ile I COO39 methionine Met M o Aromatic 39 The side chains are non polar The hydrophobic interactions in Tyr and Trp are greater than those in Phe The hydroxyl groups in Tyr and Trp make hydrogen bonds The nitrogen on the Trp indole ring increases polarity Name 3 LetterAbbre viation 1 Letter Symbol Structure phenylalanine Phe F C0039 H3NCH tyrosine Tyr Y tryptophan Trp
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