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Molecules of Life: Biopolymers Dr. Dale Hancock [email protected] Room 377 Biochemistry building Housekeeping • Answers to the practise calculations and a narration are on WebCT. Access these through the lab resources link. • Refresh your browser whenever you go onto WebCT…I am always adding stuff! • The advanced lectures start NEXT week…contrary to your timetable (confusion with bookings, sorry) Housekeeping • There are some concept tests also on WebCT. • I would like you all to do the laboratory calculations, parameters and mole concept tests. • Marks don’t count. They are anonymous. • I will use the results to plan some tutorials. 1 Chemical Bonding Covalent The Hydrogen molecule: the quintessential example of the perfect couple! e- + + e- The Hydrogen molecule: the quintessential example of the perfect couple! 0.74 Å e- + + e- 2 Carbon e- ee- + ee- e- e- ee- + ee- e- The electronic configuration of Carbon 2nd shell 2px 2py 2pz 2s2 1st shell 1s2 3 Carbon as it bonds…. 2nd shell 2s 1st shell 2px 2py 2pz 1s2 Carbon as it bonds…. To maximise bonding options 2nd shell sp3 orbital hybridisation 1st shell 2s 2px 2py 1s2 4 equivalent bonds… ..tetrahedral 2pz Tetrahedral Carbon 4 Chemical Bonding Covalent H-H C-C C-H Chemical Bonding Covalent ionic H-H C-C C-H NaCl Na+ ClIn solution Chemical Bonding Polar covalent Covalent H-H C-C C-H ionic NaCl Na+ ClIn solution 5 Water Chemical Bonding Covalent Polar covalent H-H C-C C-H ionic H-O-H NaCl C=O C-N CO-NH2 C-OH Major Biopolymers Fats or more scientifically lipid has the general formula (-CH2-)n. H2 C H3C C H2 H2 C C H2 H2 C C H2 H2 C C H2 H2 C C H2 H2 C C H2 H2 C C H2 COOH C H2 6 Chemical Bonding Covalent Polar covalent H-H C-C C-H ionic H-O-H NaCl C=O Hydrophobic Non-polar C-N fat CO-NH2 C-OH C-S Major Biopolymers Carbohydrate or hydrated carbon has the general formula (H-C-OH)n. H OH H O HO HO H H H OH OH α−D-glucose Chemical Bonding Carbohydrate Covalent H-H C-C C-H Polar covalent H-O-H ionic NaCl C=O C-N CO-NH2 C-OH 7 Information Biopolymers • • • • • • Nucleic acids: DNA and RNA Protein A variety of monomers The order is important A template is required Processes of copying the template faithfully Information Biopolymers: Nucleic Acids • DNA and RNA • Nucleic acids have a sugar-phosphate backbone which makes them hydrophilic. • The bases, where the variation exists, are quite hydrophobic and buried in the centre of the molecule. • All 4 bases have similar chemical properties Information Biopolymers: Proteins • Made up of 20 amino acids • They differ in their side chain • The amino acid side chains have very different chemical properties, unlike nucleic acid bases. • They can be acidic, basic, polar or hydrophobic. 8 Information Biopolymers: Proteins • The amino acid sequence determines the structure which determines the function. • Proteins make up over 50% of the cell by dry weight. • Proteins give the cell its shape, they form receptors, enzymes, hormones and growth factors, toxins, transporters and antibodies. How do we get from the DNA to the protein? • This is known as the central dogma. • DNA, a very monotonous biopolymer codes for a very diverse class of biopolymers, proteins. • How? The Flow of Genetic Information Replication DNA DNA Transcription RNA Translation Protein 9 Proteins are composed of 20 different amino acids alpha carbon O + H3 N CH O- C Carboxyl group R Amino group Sidechain or R group; there are 20 different ones! Two amino acids combine, by condensation polymerization to form a dipeptide. O O + H3N CH C + H3N + O- CH C O- R2 R1 H2O O + H3N CH R1 C O N CH H R2 C O- Peptide bond Peptide bond resonance O O- N N+ 10 The Peptide Bond • Has 2 resonance structures • Has a polarity (O is δ-ve and N is δ+ve) can form H-bonds • Has a partial double bond character can’t rotate Figure 5.2 Anatomy of an amino acid. Except for proline and its derivatives, all of the amino acids commonly found in proteins possess this type of structure. Figure 5.3 The α-COOH and α- NH3+ groups of two amino acids can react with the resulting loss of a water molecule to form a covalent amide bond. 11 The Coplanar Nature of the Peptide Bond Six atoms of the peptide group lie in a plane! Figure 5.4 Anatomy of an amino acid. Except for proline and its derivatives, all of the amino acids commonly found in proteins possess this type of structure. Amino Acid Side Chains • • • • Hydrophobic, aliphatic and aromatic Polar non-ionic Acidic Basic Aliphatic, hydrophobic e.g. Leucine (leu, L) O H2N CH C OH CH2 CH CH3 CH3 12 Aromatic, hydrophobic e.g. Phenylalanine (phe, F) O H2N CH C OH CH2 Polar non-ionic amino acids e.g. Serine (Ser, S). O H2N CH C OH CH2 OH Acidic amino acids e.g. Glutamate (Glu, E). O H2N CH C OH CH2 CH2 C O OH 13 Figure 4.8 Titration of glutamic acid. Basic amino acids e.g. Lysine (Lys, K) O H2N CH C OH CH2 CH2 CH2 CH2 NH2 Figure 4.8 Titration of lysine. 14 Chirality H H COO- H3N+ R R L isomer CO – R – N spelt in a clockwise direction COO+NH3 D isomer CO – R – N spelt in an anti-clockwise direction Properties of Amino Acids • UV absorbance. – Aromatic amino acids (tyr, phe, trp) absorb ~280 nm • Charge. – Acidic side chains (glu, asp) have a negative charge at pH 7. – Basic side chains (lys, arg and his) have a positive charge at pH 7. Figure 4.15 The ultraviolet absorption spectra of the aromatic amino acids at pH 6. (From Wetlaufer, D.B., 1962. Ultraviolet spectra of proteins and amino acids. Advances in Protein Chemistry 17:303– 390.) 15 Charge • • • • • • Charge is related to pH. pH is the –log10 [H+] in M The “p” denotes power Why use a log measurement? It was designed before calculators Because scientific notation is used and the numbers are ugly! Charge • pH 1 is equivalent to 0.1 M [H+] e.g. 0.1 M HCl. • The maths: 0.1 = 10-1 log100.1=-1-log = 1 • The lower the pH the more [H+] • pH 7 10-7 M [H+] = [OH-] neutral • Kw = [H+]*[OH-] = 10-14 16