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VIDA BCHS 3304: Exam 1Tuesday 2/5; SR1 116; 1PM-2:20PM40 multiple choice questions; possibly two bonus point questionsyou need a pencil(s), eraser, and calculatorcovers chapters 1-5; 5 is partial, does not include protein purificationChapter 1

Water vaporH2NH3AtmosphereElectrodeCondenserColdwaterCooled watercontainingorganicmoleculesSample forchemical analysisH2OseaCH44

7Representative Prokaryotes

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Animal Cell89Units of MeasurementLENGTHYou must know and be comfortable using these unitsstandard in science is the meter, mcommon unit in (bio)chemistry is the Angstrom, 1 = 10-10 m = 0.1 nm10 = 10-9 m or 1 nm100 = 10-8 m or 10 nm1000 = 10-7 m or 100 nm10000 = 10-6 m or 1000 nm or 1 m9The Laws of Energy TransformationThermodynamics is the study of energy transformationsA closed system, such as that approximated by liquid in a thermos, is isolated from its surroundingsIn an open system, energy and matter can be transferred between the system and its surroundingsOrganisms are open systems10Thermodynamics First LawThe First Law of ThermodynamicsEnergy (U) is conserved it can be neither created nor destroyedMost biological processes take place under constant pressure (P) and variable volume (V)The Enthalpy (H) of a process is defined as follows: H = U + PV H = U + PV (under constant pressure, the volume will change like the expansion of a gas) The volume changes in biological processes are practically negligible so H U11The Second Law of ThermodynamicsDuring every energy transfer or transformation, some energy is unusable, and is often lost as heatAccording to the second law of thermodynamics: Every energy transfer or transformation increases the entropy (disorder) of the universe12G = Gproducts - Greactants14Gibbs Free Energy (G)The Free Energy (G) change of a spontaneous process is negativeFree energy is defined as follows: G = H TSNormally, we are interested in the change in free energy so the following equation is more useful: G = H TSFor a spontaneous process, G < 0.If the G is < 0, the process is called exergonicIf the G is > 0, the process is called endergonicIf the 0, the process is called equilibrium14

15Equilibrium ConstantsRelationships between concentration and free energy G0 = -RT ln Keq, where G0 is the free energy change in the standard state, R is the gas constant 8.3145 J/K-mol (gas constant will be on the exam)

At equilibrium, G=0 so G0 = -RT ln Keq

16Chapter 2

A hydrogen-bond between two water molecules1819Water of HydrationHydration - to be surrounded by H2O

A polar molecule is hydrated by the partial charge interaction of the water molecule

Multiple hydrogen-bonds increase solubility

Hydrophilic molecules are those that love to be in water

Hydrophobic molecules are those that hate to be in water (remember oil and water dont mix, although they can form some very nice emulsions (salad dressings)) 1920

water molecules form hydrogen-bonds with organic functional groupswater can act as both a hydrogen-bond acceptor and donor (even simultaneously)20Hydrophobic effectHydrophobic effect: The tendency for water to minimize its contacts with hydrophobic moleculesIt is driven by the ordering of water molecules around the hydrophobic molecule, as stated above, to minimize its contactTherefore, water is more ordered around hydrophobic molecules and thus this process is entropically disfavored21

non-polar molecules are hydrated in a different way (i.e. NOT via hydrogen-bonds to the molecule but rather by forming cage-like structures)this results in the hydrophobic effectnon-polar molecules tend to congregate in these water cages2223Aggregation of non-polar molecules in water

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Hypotonic solution(a) Animal cell(b) Plant cellH2OLysedH2OTurgid (normal)H2OH2OH2OH2ONormalIsotonic solutionFlaccidH2OH2OShriveledPlasmolyzedHypertonic solution2425H2O H+ + HO-H+ (proton), HO- (hydroxide), H3O+ (hydronium ion)Recall that K is an dissociation constant, and [A] represent the concentration of species ARecall also that [H2O] is 55.5M by definition but we ignore it since it remains constant, so the equation simplifies to:Ionization of Water

2526H2O H+ + HO-pure water has equal concentrations of H+ and HO-[H+] = [HO-] = (Kw)1/2 = 10-7 M for a neutral solutionTherefore, KW = 10-14 MIf [H+] > 10-7 M, then the solution is acidicIf [H+] < 10-7 M, then the solution is basicIonization of Water!!!!! pH = -log[H+] !!!!!2627Acid-Base ChemistryHA H+ + A-

27Charge of acid/base as function of pH28Acid: If pH < pKa, neutral (0)If pH = pKa, (50% ionized, -0.5)If pH > pKa, charged (-1)Base:If pH < pKa, charged (+1)If pH = pKa, (50% ionized, +0.5)If pH > pKa, neutral (0)29Henderson-Hasselbalch Equationyou MUST know this equationused to compute the pH of a solution of a weak acid (HA) and its conjugate base (A-)

Henderson-Hasselbalch equation29Buffersa substance when in solution will resists changes in pH when only small quantities of a strong acid or strong base are addedany weak acid can act as a buffer if the pH of the solution is near the pK midpoint for the compound (i.e. BY DEFINITION, pH = pK at the midpoint of the titration curve)addition of small quantities of a strong acid or base has little effect on the pH of the solutionread about the blood buffering system, Bb30Chapter 3Nucleotides, Nucleic Acids,and Genetic Informationknow:structure of purines and pyrimidines structure of nucleotides, nucleosidesunderstand how tautomerization affects base pairingstructure of DNA and RNA32

33http://en.wikipedia.org/wiki/Tautomermigration of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond Tautomers and Tautomerizationtautomers are structural isomerstautomers are in equilibrium with one anothersolvents, pH, and temperature can influence which form is more stable

http://en.wikipedia.org/wiki/TautomerTautomers and Tautomerization

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38Chapter 4General propertiesThe backbone of individual amino acids are zwitterionic (i.e. has both a positively charged and a negatively charged group)In addition, some amino acids have ionizable (i.e., charged) side chainsBecause of these ionizable groups (backbone and some side chains), amino acids can have a number of different charge statesThe R group in an amino acid is called the side chainAn amino acid is often called a residue (i.e., an amino acid residue)There are 20 standard amino acids - they all differ in R4040Peptide bonds

As mentioned previously, amino acids can be connected together (i.e. condensed) to form a bigger molecule, now containing two amino acidsThe bond formed is a peptide bond and the molecule is a dipeptide.If we add another amino acid, then we would have a tripeptide4141ClassificationNon-polarGlycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M), Proline (Pro, P), Phenylalanine (Phe, F), Tryptophan (Trp, W)PolarSerine (Ser, S), Threonine (Thr, T), Asparagine (Asn, N), Glutamine (Gln, Q), Tyrosine (Tyr, Y), Cysteine (Cys, C)ChargedAspartic acid (Asp, D, -1); Glutamic acid (Glu, E, -1)Lysine (Lys, K, +1); Arginine (Arg, R, +1), Histidine (His, H, +1)424243Classification

4343

444444

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464646

47474748Non-standard amino acidsPost-translationally modified amino acidsThese transformations are made after the amino acids are already incorporated into a proteinTypical alterations include: hydroxylation, methylation, acetylation, carboxylation, and phosphorylationAddition of PO32- to a Ser, Thr, or Tyr is a common theme in signal transduction

48Chapter 550Four levels of protein structure1. Primary structure1 = Amino acid sequence of the peptide chain(s), the linear order of AAs.Remember from the N-terminus to the C-terminusAbove all else this dictates the structure and function of the protein.

2. Secondary structure2 = Local spatial alignment of amino acids without regard to side chains. Usually repeated structures

Examples: -helix, -sheets, random coil, or -turns50513. Tertiary Structure3 = the 3-dimensional structure of an entire peptide (e.g. folding of secondary structural elements against one another).

Great in detail but vague to generalize. Can reveal the detailed chemical mechanisms of an enzyme.

4. Quaternary Structure4 two or more peptide chains associated with a protein.

Spatial arrangements of subunits.51

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54Cleavage of disulfide bondsPermits separation of polypeptide chainsPrevents refolding back to native structurePerformic acid oxidationCystine (-S-S-) or cysteine (-SH) to Cysteic acid (-SO3-)Methionine to Methionine sulfone, Trp destroyed2-Mercaptoethanol, dithiothreitol, or dithioerythritolKeeps the equilibrium toward the reduced form5455

5556This chart will be on the exam!

5657Edman degradation with Phenyl isothiocyanate, PITCEdman degradation used to automatically sequence the