Protein Structure Lecture 2 PDF

Protein Structure Dr. Margaret Doherty What are proteins? Proteins are large molecules and they are unstable Proteins are composed of amino acids The properties of a protein depend on the sequence of amino acids Proteins fold into highly organized 3-Dimensional str...

Protein Structure Dr. Margaret Doherty What are proteins? Proteins are large molecules and they are unstable Proteins are composed of amino acids The properties of a protein depend on the sequence of amino acids Proteins fold into highly organized 3-Dimensional structure. This folding pattern is crucial to the function of the protein 4 levels of protein structure Proteins Proteins are composed of one Polypeptides are linear chains or more polypeptides, and of amino acids may contain co-factors After synthesis, the new polypeptide folds The sequence of amino acids spontaneously into its active in a polypeptide is known as configuration and combines its “primary structure” with the other necessary subunits to form an active protein Amino Acids are the building blocks of proteins  Protein Structure Protein primary structure The unique, and specific sequence of amino acids making up an individual chain Joined by Peptide Bonds Translated from mRNA using Genetic Code Synthesis begins at amino end and terminates at carboxyl end Ultimately determines all properties of a protein  Amino Acids Proteins contain 20 common amino acids Each amino acid consists of: – a central carbon atom – an amino group – a carboxyl group – a side [R] chain Differences in side chains (R groups) distinguish the 20 different amino acids  Classification of Amino acids Amino acids are generally grouped according to the various characteristics of their R groups Non-polar (hydrophobic) amino acids Polar (hydrophilic), uncharged amino acids Polar (hydrophilic), charged either positive or negative The variety of side chains allow proteins to have many different properties.  Properties of Amino Acids Hydrophobicity - plays a critical role in determining protein 3D-structure o Hydrophobic or non-polar / functional groups - ‘fear’ water - need to be ‘protected’ from it o In water based environments - hydrophobic groups tend away from water and aggregate together (hydrophobic interactions) o Main contributing factor in determining protein structure  Polarity of Amino Acids Hydrophilic amino acids o Tend to form the outer shell of water soluble proteins. o Interact with water (H2O) to form H-bonds - brings about the dissolution of protein in aqueous solution. Classification of Amino acids Hydrophilic Hydrophobic https://www.youtube.com/watch?v=qBRFIMcxZNM  Amino acids join together to form proteins Many different Amino acids linked In this way, polymers amino acids link together via peptide ranging in size from together to form bonds just a few amino peptides and acids to thousands proteins of amino acids can be created  How are amino acids linked? A peptide bond is a chemical bond that is formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O) Peptide bonds are strong covalent bonds  Peptide Bond o Two amino acids joined = dipeptide o Three AAs joined = tripeptide o Many AAs joined = polypeptide Polypeptide refers to the structure of a single chain.  Polypeptides In addition to the free amino group at the N-terminus and the free carboxyl group at the C-terminus, polypeptides usually contain some amino acids that have ionizable groups on their side chains The charge on the R-group is pH dependent  Properties of Amino Acids The net charge of any amino acid, peptide or protein, will depend upon the pH of the surrounding aqueous environment As the pH of a solution of an amino acid or protein changes so too does the net charge When the net charge of an amino acid or protein is zero the pH will be equivalent to the isoelectric point: pI  pH is of critical importance Changing pH is of critical importance in biochemistry Even a small shift in pH will significantly alter the charges on a protein and may modify its behaviour e.g solubility, stability  Protein Structure 1o : The linear sequence of amino acids and peptide bonds However, these linear chains fold up into remarkably complex tertiary (3D) structures Functional protein Folded structure is stabilised by bonding between amino acids  Protein Structure Peptide Polypeptide Protein Short chain of Long chain of Folded polypeptide chains. Fully amino acids amino acids functional molecule 2-20 amino May contain 1 or acids >20 amino acids more polypeptide chains  Protein Structure 1o : The linear sequence of amino acids and disulfide bonds 2o : Local structures which include, folds, turns, α-helices and β-sheets held in place by hydrogen bonds 3o : 3-D arrangement of all atoms in a single polypeptide chain 4o : Arrangement of polypeptide chains into a functional protein, eg. hemoglobin  Secondary Structures The two most important secondary structures are -helices and -sheets These are both held together by H-bonds between the N-H and the C=O projecting from the main chain  The peptide backbone contains areas of positive and negative charge These areas can interact with one another to form hydrogen bonds Typical shapes that develop from secondary structure are coils (an alpha helix) or folds (beta pleated sheets) Alpha-helix The α helix is a rodlike structure The α helix is stabilized by hydrogen bonds between the NH and CO groups of the main chain The CO group of each amino acid is hydrogen bonded to the NH group of the amino acid  β-sheets The β pleated sheet is stabilized by hydrogen bonds between NH and CO groups in different polypeptide strands, whereas in the α helix the hydrogen bonds are between the NH and CO groups in the same strand β Strand. Hydrogen bonds most often form between the CO and NH groups of adjacent chains — either parallel or antiparallel from different regions of the polypeptide β Sheets  Protein Structure 1o : The linear sequence of amino acids and disulfide bonds 2o : Local structures which include, folds, turns, α-helices and β- sheets held in place by hydrogen bonds. 3o : 3-D arrangement of all atoms in a single polypeptide chain. 4o : Arrangement of polypeptide chains into a functional protein, eg. hemoglobin.  Protein Tertiary Structure Produces the 3D-structure of the amino acid chain 3D-structure - the most stable structure of the molecule in its given environment o Native structure - the biologically active form of the protein o The structure which creates active site which allows the protein or enzyme to perform its designated biological function o Ultimately dictated by protein primary structure and the manner in which the amino acid chain folds to produce the final protein Tertiary Structure Forces Stabilizing Tertiary Structure Very Weak Strong Weak  Protein Structure 1o : The linear sequence of amino acids and disulfide bonds 2o : Local structures which include, folds, turns, α -helices and β-sheets held in place by hydrogen bonds. 3o : 3-D arrangement of all atoms in a single polypeptide chain. 4o : Arrangement of polypeptide chains into a functional protein, eg. hemoglobin.  Protein Quaternary Structure Some proteins are assemblies of two or more chains. The way in which these chains are organized is called the quaternary structure. Hemoglobin consists of 4 subunits There are 2 a chains (identical) and 2 b chains (also identical)  Quaternary structure In these oligomeric proteins, interactions between subunits (which are necessary to protein function) include: hydrogen bonds salt bridges hydrophobic interactions Quaternary structure describes these noncovalent interactions among the subunits Structure of Proteins  Globular & Fibrous e.g. collagen, keratin e.g. haemoglobin, IgG 2º structure does not fold 3º structure normally folds up, form fibres up in a ball not surrounded by hydrophilic R groups point hydrophilic R groups outwards insoluble Hydrophobic R groups point inwards structural functions soluble metabolic functions https://www.youtube.com/watch?v=wvTv8TqWC48  Conclusion Proteins are large unstable molecules built from amino acids. Proteins form secondary, tertiary and sometimes quaternary structures that are stabilised by weak forces which can break up. Any major change to conformation can interfere with the biological activity of the protein