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Download Lecture 2 Protein conformation Recap Recap… Proteins
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10/21/10 Recap Proteins….. Lecture 2 Protein conformation – > 50% dry weight of a cell – Cell’s building blocks and molecular tools. – More important than genes – A large variety of functions http://www.tcd.ie/Biochemistry/courses/jf_lectures.php Recap… Proteins are the key functional molecules of life 8 types of protein function 1. Enzymatic 2. Structural 3. Storage 4. Transport 5. Hormonal 6. Receptor 7. Contractile and Motor 8. Defensive – A large variety of shapes and sizes. Proteins 1. Proteins - What are they? And why are they important? 2. The building blocks (aa’s) and how they are connected 3. The hierarchy of protein structure 4. Three-dimensional protein structure 5. How are protein structures determined? 1 10/21/10 Recap… Amino Acid Polymers • Amino acids - Are linked by peptide bonds Peptide bond • Proteins are polymers of amino acids (polypeptides) OH SH CH2 • Amino acids divide into 4 subgroups CH2 H Petide bond is formed by a dehydration reactionCatalytic reaction H N • 20 R groups = 20 aa’s OH CH2 H C C H O N H C C H O OH H (a) N C C H O OH H 2O OH OH CH2 Petide bond - covalent bond (b) • Protein Conformation and Function Polypeptides C C H O Amino end (N-terminus) N H C C H O N C C H O • Sequence of the aa polymer determines the 3D shape of the polypeptide OH Backbone Carboxyl end (C-terminus) • Two models of protein conformation - formed one at a time starting from N-terminus - range from a few monomers to 1000 or more • Specific polypeptides- unique sequence of aa’s Side chains SH Peptide bond CH2 H H H N CH2 Groove Eg. Lysozyme- an enzyme that Breaks down bacterial cell walls by recognizing and binding to specific molecules on the bacteria (a) A ribbon model • Proteins are not just chains of aa’s, they are defined by their shape – interactions between backbone residues and R-groups Groove • A protein’s specific conformation - determines how it functions • eg. Enzyme binds substrate (b) A space-filling model 2 10/21/10 Protein structure Four Levels of Protein Structure • Primary structure – Is the unique sequence of amino acids in a polypeptide HN Amino acid + Gly Pro Thr Gly Thr Gly 3 Amino end subunits Glu CysLysSeu LeuPro Met Val Lys Val Leu Asp AlaVal Arg Gly Ser Pro Ala aa sequence determined by inherited genetic information Glu Lle Asp Thr Lys Ser Lys Trp Tyr Leu Ala Gly lle Ser ProPhe His Glu Ala Thr PheVal Asn His Ala Glu Val Asp Tyr Arg Ser Arg Gly Pro Thr Ser Tyr Thr lle Ala Ala Leu Leu Ser Pro SerTyr Thr Ala Val Val LysGlu Thr AsnPro o c – o Carboxyl end • Secondary structure – Is the folding or coiling of the polypeptide into a repeating configuration – Includes the α helix and the β pleated sheet – Result of Hydrogen bonding between the repeating backbone of a polypeptide Amino acid subunits O H H C C N C N H R R O H H C C N C C N O H H R R R H H C C O C O C N H N H N H O C O C H C R H C R H C R H C R N H O C N H O C O C O C N H N H C C R R N Alpha-helix Beta pleated sheet N O H H O H H R R C C N C C N N C C N R C C R C C OH H OH H O R R O O C H C H H H C N HC C C N HC N N H H C O C C O R R O O R O C H H NH C N C H O C R R H C N HC N H O C β pleated sheet H α helix -Repeated coils or folds in patterns contribute to the overall conformation of a protein 3 10/21/10 Hydrogen bonds Hydrogen bonds • Hydrogen bonds are formed by the attraction between a partial positive charge on the H atom of the amino group and the partial negative charge on the O atom of the peptide bond • Alpha helix - the bonds are formed between repeating atoms on the same polypeptide chain • Hydrogen bonds are formed by the attraction between a partial positive charge on the H atom of the amino group and the partial negative charge on the O atom of the peptide bond R aa C C N O H H • Beta sheets – the bonds are formed between polypeptide chains lying side by side aa H H O N C C aa • Alpha helix - the bonds are formed between repeating atoms on the same polypeptide chain R aa C C ΔN Δ-O H H • Beta sheets – the bonds are formed between polypeptide chains lying side by side H aa aa N Δ- R aa C aa • Hydrogen bonds are formed by the attraction between a partial positive charge on the H atom of the amino group and the partial negative charge on the O atom of the peptide bond R • Beta sheets – the bonds are formed between polypeptide chains lying side by side C Hydrogen bonds • Hydrogen bonds are formed by the attraction between a partial positive charge on the H atom of the amino group and the partial negative charge on the O atom of the peptide bond aa ΔH O R Hydrogen bonds • Alpha helix - the bonds are formed between repeating atoms on the same polypeptide chain aa Δ+ C C ΔN Δ-O H Δ+ ΔH O H N Δ- C R aa HΔ+ C Δ+ aa • Alpha helix - the bonds are formed between repeating atoms on the same polypeptide chain eg keratin • Beta sheets – the bonds are formed between polypeptide chains lying side by side eg. Silk fibrion Individually weak, but strong when repeated R aa aa Δ+ C C ΔN Δ-O H HΔ+ Δ+ ΔH O H N Δ- C C Δ+ aa aa R 4 10/21/10 O Alpha-helix Secondary structure Beta pleated sheet N Up to 60% of a polypeptide chain contains a secondary structure Beta sheet Alpha helix Results from interactions between atoms in the polypeptide backbone β-Sheet α-Helix • C N O of amino acid 1 binds to the H of amino acid 4 • C N O of amino acid on chain 1 binds to the H on chain 2 • 3.6 residues per helical turn • Consists of β-strands - short (5-8 residues) • Right-handed coil • Two types • All H bonds have same orientation – Parallel – Anti-parallel • Most prevalent structure in polypeptide 5 10/21/10 Turns β-Sheet N-Terminus C-Terminus R R R R R R C-Terminus N-Terminus R R • Bends • Usually contain glycine (small R grp=tight U shape) or proline R N-Terminus • 3-4 residues C-Terminus R R R C-Terminus N-Terminus http://www.youtube.com/watch?v=wM2LWCTWlrE Protein structure • Allow proteins to fold into highly compact structures • Larger turns are called loops or bends Tertiary structure – Is the overall three-dimensional shape of a polypeptide ; final shape of a polypeptide – Results from interactions between the side chains of the amino acids Hydrogen bond CH2 CH 2 O H O H 3C H 3C CH CH3 CH3 CH Hydrophobic interactions and van der Waals interactions Polypeptide backbone HO C CH2 CH2 S S CH2 Disulfide bridge O CH2 NH3+ -O C CH2 Ionic bond 6 10/21/10 Tertiary structure • Bonds involved in 3D structure Hydrophobic Van der Waals Hydrogen Bonds Ionic bonds/salt bridges Disulphide bridges Tertiary structure Hydrophobic interactions • Non-polar “R” groups repelled by water • Tend to cluster together • Force themselves into the core of a protein • Stabilise the overall structure water Hydrophobic amino acid Tertiary structure • Van der Waals interactions: occur between hydrophobic non-polar side chains in close contact Tertiary Structure • Hydrogen bonds – between polar side chains • Examples of amino acid side chains that may hydrogen bond to each other: Two alcohols: ser, thr, and tyr. Valine H 3C CH CH3 H 3C CH3 CH Hydrophobic interactions and van der Waals interactions Polypeptide backbone Alcohol (OH) and an acid : asp and tyr Two acids (COO-): asp and glu Alcohol and amine (NH3+): ser and lys Alcohol and amide (NH2): ser and asn 7 10/21/10 Tertiary structure Tertiary structure • Ionic bonds /Salt bridges form between positively and negatively charged side groups • Disulphide bridges form between 2 cysteine residues • result from the neutralization of an acid and amine on side chains. • Disulfide bonds are formed by oxidation of the sulfhydryl groups (-SH) on cysteine. • The final interaction is ionic between the positive ammonium group and the negative acid group. • Different protein chains or loops within a single chain are held together by the strong covalent disulfide bonds. • Any combination of the various acidic or amine amino acid side chains will have this effect. • Eg. Insulin contains important disulphide bridges. Quaternary Structure – Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Quaternary structure Fibrous Trimer of alpha-helical Polypeptide chains Globular Globular protein4 Polypeptide chains/ subunits Primarily alpha-helical β Chains – A variety of bonding interactions including hydrogen bonding, salt bridges, and disulfide bonds hold the various chains into a particular geometry. Iron Heme α Chains – There are two major categories of proteins with quaternary structure - fibrous and globular. Collagen Structure allows for great strength Rigid resistant to stretch Function = connective tissue in skin, bone, tendons, ligaments. 40% of all human protein Hemoglobin 4 polypeptides bind together to form a round globular shape Functions = carries oxygen 8 10/21/10 Hemoglobin Quaternary structure Fibrous Globular insulin Globular proteins are usually round in shape and tend to be a mix of alpha-helical and Beta sheet Beta sheet structure of silk fibroin allows for strength and flexibility Protein structure summary… Protein structure summary… • The conformation of a protein determines its function • Proteins are made of polypeptides which are polymers of amino acids • Amino acid polymers are linked by peptide bonds • The amino acid sequence determines the 3-D shape of the Protein • There are four levels of protein structure http://www.youtube.com/watch?v=iaHHgEoa2c8&feature=related Primary Secondary Ter/ary Quaternary 9