Review of Lecture 1. Be able to identify the cell components for bacterial, animal, and plant cells and know their functions Properties of water

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1 Review of Lecture 1 Be able to identify the cell components for bacterial, animal, and plant cells and know their functions Properties of water Bulk properties Atomic properties Weak acids and bases Acid dissociation constant, K a ph

2 Clarification Intermolecular interactions are between neighboring molecules from the Latin meaning between Intramolecular interactions are within the molecule from the Latin meaning within or inside

3 Henderson-Hasselbalch Equation Relates ph and pk a of an Acid-Base System HA <===> H + + A - Equilibrium constant, K a K a = [H+] [A-] [HA] Take the log of both sides log K a = log [H+] [A-] [HA] -log [H+] = [A-] = log [H+] + log [HA] -log K a + log [A-] [HA] Substitute ph = pk a + log [A-] [HA] HHE eqn

4 Example of the application of the Henderson-Hasselbalch Eqn. What is the ph of a solution that contains 0.1 M acetic acid (CH 3 COOH) and 0.12 M sodium acetate (Na + CH 3 COO - )? The pk a of acetic acid is 4.76.

5 Say we have 100 ml of the acetic acid/sodium acetate solution and now we add 5 ml of 1M HNO 3. What is the ph?

6 Titration Curves Titration curve is the plot of the ph of a solution as incremental amounts of hyrdoxide ions (or protons) are added.

7 Titration Curve for lactic acid

8 Titration curve for phosphoric acid Polyprotic more than one dissociable proton

9 Study Aids ent/booklist.do

10 Buffers Buffers are solutions that resist changes in ph as acid and base are added Most buffers consist of a weak acid and its conjugate base the plot of ph versus base added is flat near the pk a Buffers can only be used reliably within a ph unit of their pk a

11 Properties of common buffers

12 The bicarbonate blood buffering system respiratory alkalosis (hyperventilation) respiratory acidosis (hypoventilation) The pk a of carboninc acid is 3.77 (at 25 o C) and 3.57 (at 37 o C), but the ph of blood plasma is 7.4 how does this buffer system work?

13 Blood buffering system

14 Overview Properties of water Weak acids and bases Titration curves Henderson-Hasselbalch Eqn Buffers

15 Why do scientists need literature databases?

16 Literature search engines If you want to learn about anything scientific, you can find information through a literature search engine Entrez More biomedical ISI Web of Knowledge OS&Func=Frame&Init=Yes&SID=3DkmCbKpO4ie34P ffok Has biomedical and chemical

17 A few more tools you will use in this class Visualization software Pymol (installed in the chemistry computer lab rm 411) Scientific databases Genes blast, TIGER, and many more Proteins blast, protein structure prediction, and many more Structures : pdb, HIC-Up

18 Pymol

20 DNA and RNA are polymers of nucleotides phosphate nitrogenous base sugar β-glycosidic bond Nucleosides contain a base and a sugar Nucleotides contain a phosphate, base, and sugar

21 Nitrogenous base - Pyrimidines Cytosine (DNA, RNA), Uracil (RNA), Thymine (DNA) ph = 7

22 Nitrogenous base - Purines - Purines Adenine (DNA, RNA) and Guanine (DNA, RNA) ph = 7

23 Properties of Pyrimidines and Purines Keto-enol tautomerism Acid/base dissociations Strong absorbance of UV light

24 Tautomeric pairs for uracil pk a = 9.5 pk a > 8 Keto Enol The aromaticity of the pyrimidine and purine ring systems and the electronrich nature of their OH and NH 2 substituents endow them with the capacity to undergo keto-enol tautomeric shifts

25 Tautomeric pairs for guanine pk a = 9.4 pk a < 5

26 UV Spectra of nucleotides determined by base properties A 260 nm used to quantify nucleic acids pk a = 9.5

27 Nucleosides pentose and a base

29 Structures of the four common ribonucleotides AMP, GMP, CMP, and UMP

30 Beyond the building blocks of nucleic acids

31 Function of Nucleotides Nucleoside 5'-triphosphates are carriers of energy Bases serve as recognition units Cyclic nucleotides are signal molecules and regulators of cellular metabolism and reproduction ATP is central to energy metabolism GTP drives protein synthesis CTP drives lipid synthesis UTP drives carbohydrate metabolism

32 Nucleoside Diphosphates and Triphosphates

33 Phosphoryl and pyrophosphoryl group transfer

34 Energy Reaction Coordinates

35 Coupling ATP Hydrolysis A <====> B Lets say this reaction is thermodynamically unfavorable. ΔG = KJ/mol ΔG = -RT lnk eq = 13, 800 = -(8.31 J/K.mol) (298 K) ln K eq ln K eq = K eq = = [B eq ]/[A eq ] A + ATP<====> B + ADP+ P i A <====> B ATP + H2O <====> ADP + P i A + ATP + H2O <====> B + ADP + P i ΔG = KJ/mol ΔG = KJ/mol ΔG = KJ/mol

36 Coupling ATP Hydrolysis cont ΔG = -RT lnk eq = -16,700 = -(8.31 J/K.mol) (298 K) ln K eq K eq = 850 = [B eq ][ADP][P i ]/[A eq ][ATP] [ADP] =[ATP]=8 x 10-3 M [P i ]=1 x 10-3 M [Beq]/[Aeq] = 850,000 Compared to the uncoupled value of ! Increase by a factor of 10 8

The body has three primary lines of defense against changes in hydrogen ion concentration in the body fluids.

The body has three primary lines of defense against changes in hydrogen ion concentration in the body fluids. ph and Nucleic acids Hydrogen Ion (H+) concentration is precisely regulated. The H+ concentration in the extracellular fluid is maintained at a very low level, averaging 0.00000004Eq/L. normal variations