Molecules of Life: Biopolymers Dr. Dale Hancock D.Hancock@mmb.usyd.edu.au Room 377 Biochemistry building Housekeeping Answers to the practise calculations and a narration are on WebT. Access these through the lab resources link. Refresh your browser whenever you go onto WebT 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 WebT. 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
hemical Bonding ovalent The Hydrogen molecule: the quintessential example of the perfect couple! + + The Hydrogen molecule: the quintessential example of the perfect couple! 0.74 Å + + 2
arbon + + The electronic configuration of arbon 2 nd shell 2s 2 2p x 2p y 2p z 1 st shell 1s 2 3
arbon as it bonds. 2 nd shell 2s 2p x 2p y 2p z 1 st shell 1s 2 arbon as it bonds. To maximise bonding options 2 nd shell sp 3 orbital hybridisation 2s 2p x 2p y 2p z 1 st shell 1s 2 4 equivalent bonds..tetrahedral Tetrahedral arbon 4
hemical Bonding ovalent H-H - -H hemical Bonding ovalent H-H - -H ionic Nal Na + l - In solution hemical Bonding Polar covalent ovalent H-H - -H ionic Nal Na + l - In solution 5
Water hemical Bonding ovalent H-H - -H Polar covalent H--H = -N -N -H ionic Nal Major Biopolymers Fats or more scientifically lipid has the general formula (- -)n. H 3 H 6
hemical Bonding ovalent H-H - -H Hydrophobic Non-polar fat Polar covalent H--H = -N -N -H -S ionic Nal Major Biopolymers arbohydrate or hydrated carbon has the general formula (H--H) n. H H H H H H H H H H α D-glucose hemical Bonding arbohydrate ovalent H-H - -H Polar covalent H--H = -N -N -H ionic Nal 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 Transcription Replication DNA DNA RNA Translation Protein 9
Proteins are composed of 20 different amino acids alpha carbon Amino group + H 3 N H R - arboxyl group Sidechain or R group; there are 20 different ones! Two amino acids combine, by condensation polymerization to form a dipeptide. + H 3N H - + + H 3N H - R 1 R 2 + H 3N H N H - R 1 H R 2 Peptide bond Peptide bond resonance - N N+ 10
The Peptide Bond Has 2 resonance structures Has a polarity ( 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-h and α- NH 3+ groups of two amino acids can react with the resulting loss of a water molecule to form a covalent amide bond. 11
The oplanar 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 hains Hydrophobic, aliphatic and aromatic Polar non-ionic Acidic Basic Aliphatic, hydrophobic e.g. Leucine (leu, L) N H H H H 3 H 3 12
Aromatic, hydrophobic e.g. Phenylalanine (phe, F) N H H Polar non-ionic amino acids e.g. Serine (Ser, S). N H H H Acidic amino acids e.g. Glutamate (Glu, E). N H H H 13
Figure 4.8 Titration of glutamic acid. Basic amino acids e.g. Lysine (Lys, K) N H H N Figure 4.8 Titration of lysine. 14
hirality H H 3 N+ - R R H +NH 3 - L isomer R N spelt in a clockwise direction D isomer R N spelt in an anti-clockwise direction Properties of Amino Acids UV absorbance. Aromatic amino acids (tyr, phe, trp) absorb ~280 nm harge. 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 hemistry 17:303 390.) 15
harge harge is related to ph. ph is the log 10 [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! harge ph 1 is equivalent to 0.1 M [H+] e.g. 0.1 M Hl. The maths: 0.1 = 10-1 log 10 0.1=-1 -log = 1 The lower the ph the more [H+] ph 7 10-7 M [H+] = [H-] neutral K w = [H+]*[H-] = 10-14 16