Biomolecules Proteins CLawson 2024 PDF

Proteins Dr Charlotte Lawson School of Pharmacy and Biomedical Sciences [email protected] Where opportunity creates success Learning Outcomes Describe the different functions of proteins in the body Outline amino acid structure Explain how amino acids are arranged into peptides by pepti...

Proteins Dr Charlotte Lawson School of Pharmacy and Biomedical Sciences [email protected] Where opportunity creates success Learning Outcomes Describe the different functions of proteins in the body Outline amino acid structure Explain how amino acids are arranged into peptides by peptide bonds Appreciate that primary, secondary, tertiary and quaternary structure of proteins explains their function Questions? Please use the TEAM! No such thing as a stupid question! If you wondered, then so did someone else! I will post emailed questions on the Team so please save us both a job! If you know the answer to the question, please feel free to post – we are all in this together! Biomolecules Organic molecules that are formed by living organisms – Consists majorly of Carbon, Hydrogen, Oxygen and Nitrogen Four major classes Lipids Proteins Carbohydrates Nucleic acids What are proteins? Proteins are heteropolymers of -amino acids. Proteins are the most abundant and functionally diverse molecules in living systems. Accounts for up to 50% of dry weight of most cells. Out of the many different amino acids in nature, only 20 are commonly found as constituents of mammalian proteins. Main functions of proteins Why are proteins so complex? Some proteins consist of single polypeptides, others have many copies of the same polypeptide (homomeric) or even different polypeptide (heteromeric) Immunoglobulin G Amino acids may be modified. Lipids, carbohydrates, metal ions and other factors can be added. Complexity enables proteins to carry out a myriad of different functions (structural, enzymatic, oxygen carriage, inter and intra- cellular communication, acid-base buffering, etc.) insulin Images from Wikipedia  Amino Acid Three letter One letter Essential Amino Alanine Ala A Arginine Arg R conditional acids Asparagine Cysteine Asn Cys N C conditional Glutamic acid Glu E Glutamine Gln Q conditional Glycine Gly G conditional Histidine His H Essential Isoleucine Ile I Essential Leucine Leu L Essential Lysine Lys K Essential Methionine Met M Essential Phenylalanine Phe F Essential Proline Pro P conditional Serine Ser S Threonine Thr T Essential Tryptophan Trp W Essential Tyrosine Tyr Y conditional Valine Val V Essential Amino acid structure α This structure is common to all but one of the - amino acids (proline) Amino Acids: Atom Naming (Identifying the Carbons in an amino acid) Organic nomenclature: start from one end Biochemical designation: start from -carbon and go down the R-group Additional carbons in the R group commonly designated , , ,  etc.  Amino acids classification Amino acids are classified by R group. The 20 different R groups may be as simple as a H atom (glycine) to a carbon skeleton with various functional groups attached. The physical and chemical characteristics of the R group determine the unique characteristics of a particular amino acid. Amino acid classification Polar/Non-polar Hydrophilic/Hydrophobic Charged +/- Aliphatic Aromatic Acidic Basic Large Small Amino acids with non-polar side chains Hydrocarbon Side-chains Achira l Hydrophobic Non-polar aliphatic amino acid Side-chain bonded to α amino nitrogen Secondary amino acid (imino acid). Cyclic structure induces bends in resulting polypeptide Uncharged polar side chains Hydrophilic Form H- Bonds Formation of disulphide bonds The –SH groups of two cysteines can become oxidized to form a dimer, cystine, which contains a covalent cross-link called a disulfide bond (–S–S–) Disulfide bond helps stabilize many extracellular proteins (Albumin) Acidic side chains Extra Carboxyl group Polar Negative charge Hydrophilic Aspartic Acid (Aspartate) and Glutamic acid (Glutamate) – naming reflects negative charge at pH 7.0 Amides of Aspartate and Glutamate = Asparagine and Glutamine Basic side chains Polar Hydrophilic Positive charge Histidine: Can switch between positive and neutral at physiological pH Often found in enzyme active sites Helps catalyse making and breaking of bonds Amino Acids with Special Properties Name Properties R-group is a Hydrogen Can fit into hydrophobic or hydrophilic environment Glycine (Gly or G) Allows protein backbones of two polypeptide chains to come close to each other Adds flexibility to polypeptide Amino-group is part of ring structure Hydrophobic Proline (Pro or P) Does not interact well in secondary structures Lack of hydrogen bonds Produces kinks or hinges in protein Cysteine Sulfhydryl group (Reactive) (Cys or C) Covalently links to other cysteine residues (Disulfide bridge) Optical properties of -amino acids For all common amino acids (except glycine) - -carbon bonded to 4 different groups -carbon is a chiral centre Optical properties of -amino acids Amino acids that have an asymmetric centre at the α- carbon can exist in two forms designated as D and L, that are mirror images of each other. Optical properties of -amino acids The two forms in each pair are termed stereoisomers, optical isomers or enantiomers. All amino acids found in human proteins are of the L-configuration. Optical properties of -amino acids D-Amino Acids have been found in only a few, generally small peptides (bacterial cell walls) Spectral properties of amino acids Amino acids do not absorb visible light, so they are colourless. Aromatic side chains have a characteristic UV absorption. Wavelength: 280nm (Phe, Tyr, Trp) This allows protein concentration to be spectroscopically estimated. c.f. nucleic acids: 260nm (purine, pyrimidine base) Amino acids modification: new capabilities Post-translational modification Addition of: 1. Hydroxyl –OH 2. Phosphoryl –PO43- 3. Methyl –CH3 4. Acetyl –COCH3 5. Carboxylation –COOH Hydroxylatio n Example: Added hydroxyl groups stabilise collagen fibres (H bonds) Vitamin C deficiency hinders hydroxylation of collagen causing scurvy Methylation E.g. Lysine can be methylated 1, 2 or 3 times at its amino group Histone methylation regulates gene expression N-methyl-lysine is found in myosin, a contractile component of muscle  Carboxylation Example: Prothrombin (a clotting factor) and other Ca2+-binding proteins Vitamin K deficiency hinders carboxylation of glutamate, causing clotting problems and haemorrhage Phosphorylation Protein phosphorylation (and dephosphorylation) is a very important regulatory switch in a wide variety of protein signalling pathways, channels, transporters and enzymes In eukaryotes, proteins may be phosphorylated at: – Serine – Threonine – Tyrosine Uncommon amino acids: important functions There are a number of additional amino acids found in cells but they are not constituents of proteins. Variety of functions (regulating metabolic processes). Intermediates in the biosynthesis of Arginine and in the urea cycle. Amino acids are zwitterions Carboxyl group – weak acid Amino group- weak base At neutral pH amino acids exist as dipolar ions (zwitterions) Ionization At physiologic pH amino acids exist as dipolar ions. Ionization state varies with pH. Acid= proton donator Base= proton acceptor Free or bond amino acids can play the role of a buffer Amino acids are zwitterions Polypeptides are chain of amino acids Amino acids are covalently linked together via peptide bonds. Condensation reaction Peptide Bond  Peptide bond The peptide bond is uncharged at any pH of Cis config physiologic interest. - Peptide bond exhibits partial double-bond character, thus there is no freedom of rotation about the bond the connects the C=O and the N-H of a peptide bond. Not easy to break (it takes very acidic conditions and high temperature- e.g. 100ͦC for 24 hrs). Trans config 95% Polypeptides have polarity POLARITY N terminus C terminus Pentapeptide seryl-glycyl-tyrosyl-alanyl-leucine Ser–Gly–Tyr–Ala–Leu (SGYAL) The size of polypeptides varies significantly Protein structure 1. Primary (1ͦ) - Linear structure (the sequence of amino acid in polypeptide chain) 2. Secondary (2ͦ) - Simple structures resulted from arrangements in space between adjacent amino acids. 3. Tertiary (3ͦ) - Complex 3D shape of the protein. 4. Quaternary (4ͦ) - Arrangement of subunits in multi-polypeptide proteins. Primary structure Linear polymer Simplest protein structure How they are synthesized Knowledge of primary structure of a protein can help predict: - Final 3D structure - Mechanism of action - Associated pathologies Secondary structure Brought about by hydrogen bonding. 2 main types: α helix – Intrachain β sheet – Between strands  α helix Spiral structure, consisting of a tightly packed, coiled polypeptide backbone core. The side chains of the component amino acids extending outward. Stabilized by hydrogen bonds. Each turn of an α-helix contains 3.6 amino acids. Tertiary structure Determined by a variety of interactions between the parts that form secondary structure: - H-bonds - Ionic bonds - Hydrophobic bonds - Disulphide bonds - Van der Waal’s bonds Quaternary structure Assembly of two or more polypeptide subunits. Haemoglobin - four sub-unit oxygen-carrying globular protein - 2 copies of alpha and beta polypeptides Collagen - fibrous protein of three polypeptides that are supercoiled like a rope - structural strength for connective tissue. Loops, turns and bends Turns and bends: shorts segments of amino acids (4 aminoacyl residues) that join two units of secondary structure (2 adjacent strands of an antiparallel beta-sheet). Loops: irregular in conformation, they are regions that contain residues beyond the number necessary to connect adjacent regions of secondary structure. Loops serve key biologic roles. Many loops and bends reside on the surface of the protein, and are thus exposed to solvent. Not all portions of proteins are necessarily Some proteins contain chemical groups Conjugated protein – Proteins that associate with other chemical components. Dynamic Changes Within Proteins Protein structure influenced by the surroundings Conformational changes are key: – For enzymes – For binding – For movement Protein structure can be disrupted Protein denaturation (induces a loss of activity) – pH – Temperature – Chemical e.g. urea Not easily reversed. Summary Proteins are the most abundant and functionally diverse molecules in living systems. There are 20 amino acids; – 9 are essential (not synthesised by mammals);11 are non-essential. Proteins are made up of specific chains of amino acids which are attached by peptide bonds (primary structure) to form a linear peptide chain. Once synthesised, the peptide chain is modified to enable specific protein function (secondary, tertiary, quaternary structure). Individual amino acids can be modified on specific sites and during specific situations which further alters the activity and function of specific proteins (methylation, phosphorylation, addition of other chemicals etc.). Further Reading Moran, Laurence A (2014) Principles of Biochemistry 5th Edition Chapter 16, p307-321 ISBN: 9781292034966 (e-book) Campbell, Neil A (2018) Biology: a global approach 11th Edition, global edition Chapter 5, concept 5.4, p123-126 ISBN: 9781292170442 (e-book) Berg et al., Biochemistry, 8th ed.,Chapters 2, 4.1, 11 and 12 Silverthorn, Human Physiology, 5th ed., Chapter 2, Review section on biomolecules Questions? Please use the TEAM! No such thing as a stupid question! If you wondered, then so did someone else! I will post emailed questions on the Team so please save us both a job! If you know the answer to the question, please feel free to post – we are all in this together!