Recap. Lecture 2. Protein conformation. Proteins. 8 types of protein function 10/21/10. Proteins.. > 50% dry weight of a cell

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1 Lecture 2 Protein conformation ecap Proteins.. > 50% dry weight of a cell ell s building blocks and molecular tools. More important than genes A large variety of functions A large variety of shapes and sizes. ecap Proteins are the key functional molecules of life 8 types of protein function 1. Enzymatic 2. Structural 3. Storage 4. Transport 5. ormonal 6. eceptor 7. ontractile and Motor 8. Defensive Proteins 1. Proteins - What are they? And why are they important? 2. The building blocks ( s) and how they are connected 3. The hierarchy of protein structure 4. Three-dimensional protein structure 5. ow are protein structures determined? 1

2 Proteins are polymers of amino acids (polypeptides) 20 groups = 20 s ecap Amino acids divide into 4 subgroups Amino Acid Polymers Amino acids - Are linked by peptide bonds Petide bond is formed by a dehydration reaction- atalytic reaction 2 (a) Peptide bond 2 S 2 2 S Peptide 2 2 bond 2 Side chains Petide bond - covalent bond Backbone (b) Amino end (-terminus) arboxyl end (-terminus) Protein onformation and Function Polypeptides - formed one at a time starting from -terminus - range from a few monomers to 1000 or more Two models of protein conformation Groove Specific polypeptides- unique sequence of s Sequence of the polymer determines the 3D shape of the polypeptide 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 s, they are defined by their shape interactions between backbone residues and -groups A protein s specific conformation - determines how it functions eg. Enzyme binds substrate (b) A space-filling model Groove 2

3 Leu Met Val Lys Val Gly Pro Thr Gly Thr Gly Lys Trp Tyr Leu Ala Gly lle Pro Phe is Glu is Ala Glu Val Ala Thr Phe Val Asn Asp Thr Tyr Thr Ala Val Thr Lys Pro Ala Ala Leu Leu 10/21/10 Protein structure Four Levels of Protein Structure Primary structure Is the unique sequence of amino acids in a polypeptide + 3 Amino end Glu ys Lys Seu Pro Amino acid subunits Leu Asp Ala Val Arg Gly sequence determined by inherited genetic information Glu Lle Asp Gly Pro Thr lle Tyr Ala Arg Arg Tyr Pro o Val Thr Lys Glu c Asn Pro o arboxyl end Secondary structure Is the folding or coiling of the polypeptide into a repeating configuration Includes the α helix and the β pleated sheet esult of ydrogen bonding between the repeating backbone of a polypeptide Alpha-helix Beta pleated sheet Amino acid subunits β pleated sheet α helix -epeated coils or folds in patterns contribute to the overall conformation of a protein 3

4 ydrogen bonds ydrogen bonds are formed by the attraction between a partial positive charge on the atom of the amino group and the partial negative charge on the atom of the peptide bond ydrogen bonds ydrogen bonds are formed by the attraction between a partial positive charge on the atom of the amino group and the partial negative charge on the atom of the peptide bond Alpha helix - the bonds are formed between repeating atoms on the same polypeptide chain Alpha helix - the bonds are formed between repeating atoms on the same polypeptide chain Beta sheets the bonds are formed between polypeptide chains lying side by side Beta sheets the bonds are formed between polypeptide chains lying side by side ydrogen bonds ydrogen bonds ydrogen bonds are formed by the attraction between a partial positive charge on the atom of the amino group and the partial negative charge on the atom of the peptide bond ydrogen bonds are formed by the attraction between a partial positive charge on the atom of the amino group and the partial negative charge on the atom of the peptide bond Alpha helix - the bonds are formed between repeating atoms on the same polypeptide chain Δ + Δ + Alpha helix - the bonds are formed between repeating atoms on the same polypeptide chain eg keratin Δ + Δ + Beta sheets the bonds are formed between polypeptide chains lying side by side Δ + Δ + Beta sheets the bonds are formed between polypeptide chains lying side by side eg. Silk fibrion Individually weak, but strong when repeated Δ + Δ + 4

5 Alpha-helix Beta pleated sheet Up to 60% of a polypeptide chain contains a secondary structure Secondary structure Beta sheet Alpha helix esults from interactions between atoms in the polypeptide backbone α-elix of amino acid 1 binds to the of amino acid residues per helical turn ight-handed coil All bonds have same orientation β-sheet of amino acid on chain 1 binds to the on chain 2 onsists of β-strands - short (5-8 residues) Two types Parallel Anti-parallel Most prevalent structure in polypeptide 5

6 β-sheet Turns -Terminus -Terminus 3-4 residues -Terminus -Terminus Bends Usually contain glycine (small grp=tight U shape) or proline -Terminus -Terminus -Terminus -Terminus Allow proteins to fold into highly compact structures Larger turns are called loops or bends Protein structure Is the overall three-dimensional shape of a polypeptide ; final shape of a polypeptide esults from interactions between the side chains of the amino acids 22 ydrogen bond S S 2 Disulfide bridge Ionic bond ydrophobic interactions and van der Wls interactions Polypeptide backbone 6

7 Bonds involved in 3D structure ydrophobic Van der Wls ydrogen Bonds Ionic bonds/salt bridges Disulphide bridges ydrophobic interactions on-polar groups repelled by water Tend to cluster together Force themselves into the core of a protein Stabilise the overall structure water ydrophobic amino acid Van der Wls interactions: occur between hydrophobic non-polar side chains in close contact Valine ydrophobic interactions and van der Wls interactions Polypeptide backbone Tertiary Structure ydrogen bonds between polar side chains Examples of amino acid side chains that may hydrogen bond to each other: Two alcohols: ser, thr, and tyr. Alcohol () and an acid : asp and tyr Two acids (-): asp and glu Alcohol and amine (3+): ser and lys Alcohol and amide (2): ser and asn 7

8 Ionic bonds /Salt bridges form between positively and negatively charged side groups result from the neutralization of an acid and amine on side chains. The final interaction is ionic between the positive ammonium group and the negative acid group. Any combination of the various acidic or amine amino acid side chains will have this effect. Disulphide bridges form between 2 cysteine residues Disulfide bonds are formed by oxidation of the sulfhydryl groups (-S) on cysteine. Different protein chains or loops within a single chain are held together by the strong covalent disulfide bonds. Eg. Insulin contains important disulphide bridges. Quaternary Structure Is the overall protein structure that results from the aggregation of two or more polypeptide subunits A variety of bonding interactions including hydrogen bonding, salt bridges, and disulfide bonds hold the various chains into a particular geometry. Quaternary structure Fibrous Trimer of alpha-helical Polypeptide chains Globular Globular protein- 4 Polypeptide chains/ subunits Primarily alpha-helical β hains Iron eme There are two major categories of proteins with quaternary structure - fibrous and globular. ollagen Structure allows for great strength igid resistant to stretch Function = connective tissue in skin, bone, tendons, ligaments. 40% of all human protein α hains emoglobin 4 polypeptides bind together to form a round globular shape Functions = carries oxygen 8

9 emoglobin Quaternary structure Fibrous Globular insulin Beta sheet structure of silk fibroin allows for strength and flexibility Globular proteins are usually round in shape and tend to be a mix of alpha-helical and Beta sheet 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 Primary Secondary Ter/ary Quaternary 9

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