Amino Acids and Proteins

AMINO ACIDS & PROTEINS 4PY019 – Pharmacy Stage 1 Dr Katherine Karakoula LEARNING OUTCOMES 1. Recognise the chemical structural features of the basic set of 20 amino acids. Essential and non-essential amino acids. 2. Classify the amino acids into neutral, polar, non-polar and charged (negatively and positively charged) on the basis of their side chains. 3. Recognise a variety of types of chemical bonds in the protein structure. 4. Understand the different levels of protein structure. 5. Understand the link between protein structure and function. PROTEINS • Proteins are long chains of polypeptides: chains formed by the condensation/combination of 20 different - amino acids. • Thousands of proteins – provide different functions for living organisms • Polypeptides - may be di-, tri -, etc; up to 10 a.a. • Proteins - longer than 10 a.a. units; ie. MW>10,000 https://d20khd7ddkh5ls.cloudfront.net/amino_acid_chain.jpg PROTEINS ARE… • The most versatile macromolecule in a biological system • Functions include: • • • • • • • • Catalysts (enzymes) Transport and store other molecules (e.g. Oxygen) Tissue structure (e.g. Collagen; most abundant protein in human body) Immune Protection (antibodies) Movement generation (myosin) Growth control Growth factors (cell cycle control proteins) Transmit nerve impulses (cell surface receptors/ ion channels) Gene regulation (transcription factors/repressors) • Enzymes are usually composed of a protein, a vitamin and a trace mineral. • They act as catalysts, allowing reactions to occur more quickly and efficiently. • They can cause two substances to come together making a new structure or can split a compound apart. • An enzyme is not affected by the chemical reactions it allows to take place. PROTEINS AS ENZYMES • Hormones Chemical messengers secreted by endocrine glands in response to altered conditions in the body. Each travels to one or more specific target tissues or organs to elicit a specific response Growth hormone – promotes growth Insulin & glucagon – regulation of blood glucose Thyroxin – regulation of body’s metabolic rate Calcitonin & parathormone – regulation of blood calcium Antidiuretic hormone – regulation of fluid and electrolyte balance And many more…… • Regulation of fluid balance • Dependent edema may be caused when there is too much fluid between cells and not enough hydrophilic protein within the cells. • Acid-base regulation, proteins act as buffers accepting and releasing hydrogen ions thus preventing acidosis or alkalosis. TRANSPORT PROTEINS Copyright 2005 Wadsworth Group, a division of Thomson Learning PROTEINS IN IMMUNITY • Antibodies are giant proteins that bind up specific invaders like viruses or antigens • Antigens are substances that cause the body to produce antibodies. They may include bacteria, allergens, toxins or anything that causes an inflammatory response. OTHER ROLES OF PROTEINS • Source of energy. The brain and nervous system must have glucose. Once the amino group is removed from the protein, the remaining carbon molecules can be used to create energy - 4 Kcal per gram or stored as fat. • Other roles include being converted to other proteins or making neurotransmitters norepinephrine and epinephrine, melanin, fibrin and as precursor to the vitamin niacin. ROLES OF PROTEINS • Other roles include being converted to other proteins or making: • • • • neurotransmitters norepinephrine and epinephrine melanin fibrin precursor to the vitamin niacin. Protein types and functions Role Examples Functions Break down nutrients in food into small pieces that can be readily absorbed Digestive enzyme Amylase, lipase, pepsin Transport Hemoglobin Carry substances throughout the body in blood or lymph Structure Actin, tubulin, keratin Build different structures, like the cytoskeleton Hormone signaling Insulin, glucagon Coordinate the activity of different body systems Defense Antibodies Protect the body from foreign pathogens Contraction Myosin Carry out muscle contraction Storage Legume storage proteins, egg white (albumin) Provide food for the early development of the embryo or the seedling Table modified from OpenStax College, Biology. STRUCTURE OF PROTEINS Proteins exhibit specificity of biologic function, which is a consequence of their unique 3-D structural shape or CONFORMATION In humans, disease states are often related to the altered function of a protein eg DNA mutations Proteins come in many different shapes and sizes. Some are globular (roughly spherical) in shape, whereas others form long, thin fibers. For example, the hemoglobin protein that carries oxygen in the blood is a globular protein, while collagen, found in our skin, is a fibrous protein. Changes in temperature and pH, as well as the presence of certain chemicals, may disrupt a protein’s shape and cause it to lose functionality, a process known as denaturation. Proteins have 4 levels of structural organisation Primary: the sequence of amino acids in a polypeptide chain. Expression of genetic code as protein contains all information required Secondary: The general three-dimensional form of local segments proteins Tertiary: The Sum total of the secondary structure elements - The 3D structure of a protein https://www.thoughtco.com Quaternary: The arrangement of multiple folded protein molecules in a multi-subunit complex PRIMARY STRUCTURE The hormone insulin has two long polypeptide chains, A and B holding together using peptide bonds. The sequence of a protein is determined by the DNA of the gene that encodes the protein. A change in the gene's DNA sequence even by 1 amino acid may lead to a change in the amino acid sequence of the protein - can affect the protein’s overall structure and function. /Primary structure of human insulin (Harfenist and Craig, 1952). EXAMPLE A single amino acid change is associated with sickle cell anaemia -an inherited disease that affects red blood cells. In sickle cell anaemia, one of the polypeptide chains that make up haemoglobin, the protein that carries oxygen in the blood, has a slight sequence change. The glutamic acid that is normally the sixth amino acid of the haemoglobin β chain (one of two types of protein chains that make up haemoglobin) is replaced by a valine. A single amino acid substitution https://cdn.kastatic.org/ka-perseus-images/cd3f3957170cbbc2d70f692522930954402afa2d.jpg Protein Folding Diseases haemoglobin sickle cell anaemia • A single genetic point mutation changes a glutamic acid in the β-globulin chain of haemoglobin into a valine. • The protein changes conformation, exposing a hydrophobic patch that leads to polymerization in individuals homozygous for the genetic mutation. • This reduces the elasticity of red blood cells causing anaemia. Secondary structure It is the general three-dimensional form of local segments of a protein. It refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone (The backbone just refers to the polypeptide chain apart from the R groups). Secondary structure is dependent upon hydrogen bonding and energetically favorable steric conformation: α- Helix β-pleated Sheet Robert Corey Both structures are held in shape by hydrogen bonds, which form between the carbonyl O of one amino acid and the amino H of another. Linus Pauling "for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances” Nobel prize 1954 Both structures are held in shape by hydrogen bonds, which form between the carbonyl O (C=O ) of one amino acid and the amino (–N-) H of another. 1. If the H- bonds form between peptide bonds in the same chain, then HELICAL structures develop 2. If the H-bonds form between peptide bonds in different chains EXTENDED structures form. The α-Helix Rod-like structure with the peptide bonds coiled tightly inside and the side chains extend outwards. Stabilized by hydrogen bonds between N-H and C=O Groups of amino acids 4 residues ahead in the sequence. All the main C=O and N-H Are hydrogen bonded The β-sheet (β pleated sheet) Two or more polypeptide chains (β strands) line up next to each other, forming a sheet-like structure held together by hydrogen bonds Side chains point in opposite directions Parallel β-sheet – chains run in the same direction (H-bonds bind AAs of 1 strand to 2 Aas of the other) Antiparallel β-sheet – chain run in opposite directions (Each AA is bound to 1 other on the Adjacent strand) β-sheets are structurally diverse and important in many proteins prostaglandin synthase Make prostoglandin an autocrine molecule that regulates muscle contraction Tertiary structure The overall three-dimensional structure of a polypeptide is called its tertiary structure. The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein. R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding, hydrophobic/hydrophilic interactions Hydrophobic interactions: in which amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules. Disulfide bonds, covalent linkages between the sulfurcontaining side chains of cysteines, are much stronger than the other types of bonds that contribute to tertiary structure. They act like molecular "safety pins," keeping parts of the polypeptide firmly attached to one another. Tertiary structure of proteins example Formed by : • Hydrophilicity • Hydrophobicity • Hydrogen bonds • Ionic bonds • Disulfide bridges Tertiary structure of proteins X-Ray Crystallography, nuclear magnetic resonance and cryo EM reveal detailed 3D structure of 1000s of proteins Hydrophilic Hydrophobic core Quartenary structure • Many proteins are made up of a single polypeptide chain and have only three levels of structure • However, some proteins are made up of multiple polypeptide chains, also known as subunits. When these subunits come together, they give the protein its quaternary structure. • Examples of a protein with quaternary structure: haemoglobin and DNA polymerase enzyme . • Types of interactions that contribute to tertiary structure: The subunits are held together by hydrogen bonds, ionic bonds, disulphide bridges and van der Waals forces between nonpolar side chains. SUMMARY Image modified from OpenStax Biology's modification of work by the National Human Genome Research Institute. Types of proteins: Proteins are classified into two main categories on the basis of higher levels of structure: Fibrous proteins, which have polypeptide chains arranged in long strands or sheets Globular proteins, which have polypeptide chains folded into a spherical or globular shape. Globular proteins frequently contain multiple types of secondary structure, whereas fibrous proteins typically consist mostly of one type of secondary structure. Fibrous proteins: 1.The structures in which fibrous proteins are present are made stronger or more flexible. 2. All fibrous proteins are insoluble in water because they contain a lot of hydrophobic amino acid residues both inside the protein and on its surface. Examples of fibrous proteins include keratin, collagen, and silk fibroin. Collagen - triple helix formed by three extended protein chains that wrap around one another. Globular Proteins Different polypeptide chain segments (or several polypeptide chain segments) fold back on each other to form a globular protein, which has a spherical shape. Enzymes, transport proteins, motor proteins, regulatory proteins, immunoglobulins, and proteins with several additional activities are examples of globular proteins eg albumin, insulin etc. They are water-soluble. containing two chains: the A- chain consists of 21 residues, and the B-chain has 30 residues. https://encrypted-tbn0.gstatic.com/ Peptide bonds • Each protein consists of one or more polypeptide chains. • Each of these polypeptide chains is made up of amino acids, linked together in a specific order. • The chemical properties and order of the amino acids are key in determining the structure and function of the polypeptide • The amino acids of a polypeptide are attached to their neighbours by covalent bonds known as a peptide bonds. • Each bond forms in a dehydration synthesis (condensation) reaction. During protein synthesis, the carboxyl group of the amino acid at the end of the growing polypeptide chain reacts with the amino group of an incoming amino acid, releasing a molecule of water. The resulting bond between amino acids is a peptide bond Because of the structure of the amino acids, a polypeptide chain has directionality: it has two ends that are chemically distinct from one another. At one end, the polypeptide has a free amino group, and this end is called the amino terminus (or Nterminus). The other end, which has a free carboxyl group, is known as the carboxyl terminus (or C-terminus). PROTEIN DENATURATION Disruption of the weak types of interaction (Hbond, ionic links, hydrophobic interactions, van der Waals forces (van der Waals interactions are important to protein stability and function. function. ) that maintain the 3-D shape of a protein – leading to loss of biological activity. Proteins become “labile” - susceptible to alteration or destruction 1. 2. 3. 4. Extreme temperature Extreme pH High salt concentration Organic solvents(alcohol – ketone bodies at high concentrations AMINO ACIDS – BUILDING BLOCKS OF PROTEINS https://d20khd7ddkh5ls.cloudfront.net/amino_acid_structure.jpg There are 20 amino acids found in the human body (and in all living things). Different types can have different R groups. The R group determines the chemical and physical properties of the overall molecule. Amino Acids The building blocks of proteins Common to all AAs H H2N C COOH R Side chain or R group (Provides functional variation) pH affects the properties of the amino and carboxyl groups Low pH (<2) High pH (>9) H +H H 3N C COOH H2N C R COO- R pH 2-9 H +H COO C N 3 R The isoelectric point At low pH …. Under normal Cellular pH (2-9) Amino Acids are Zwitterions (Dipolar) The structure of an amino acid allows it to act as both an acid and a base. pH 2-9 H +H 3N C COO- R COOH is dissociated and –ve (COO-) NH2 is protonated and +ve (NH3+) Overall charge is neutral An amino acid has both a basic amine group and an acidic carboxylic acid group. There is an internal transfer of a hydrogen ion from the -COOH group to the NH2 group to leave an ion with both a negative charge and a positive charge. Amino acid Structure R: Side Chain Amino acid (pH 2-9) R group is a hydrogen, the zwitterion of glycine has a positive charge on the amine and a negative charge on the carboxylic acid: These are the 20 amino acids commonly used by humans: AMINO ACIDS • Nonessential amino acids • dispensable amino acids can be made within the body • Essential amino acids • indispensable amino acids must be obtained from foods • Conditionally essential amino acids are needed from food sources if the building blocks to make them are not available. https://image.slidesharecdn.com/ AN ESSENTIAL AMINO ACID Phenylalanine is involved in the production of the neurotransmitters norepinephrine and dopamine, which are essential for the proper functioning of the brain and nervous system. Phenylalanine also helps with the production of the pigment melanin, which gives colour to the skin, hair, and eyes. Food: Meat and eggs 4 broad groups: Neutral Non-polar (no charge, no polarity) Neutral Polar (no charge but have a di-pole) Acidic ( -ve charge due to carboxyl group) Basic (+ve charge due to amine group) Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, In Molecular Biology of the Cell; 5th edition, Garland Science: New York, NY, 2008, p. 125-129 (ISBN-13: 9780815341055). All the amino acids – except glycine – possess a chiral carbon. They may exist as either a “right-handed’ or “left-handed” isomer designated “D” or “L”. O Glycine is the simplest and smallest amino acid, with a hydrogen atom as a side chain - its R-group is a hydrogen so it is not bonded to 4 different groups of atoms and will not produce isomers H2N glycine OH PROTEINS • Dipeptide Copyright 2005 Wadsworth Group, a division of Thomson Learning PROTEINS • A tripeptide consists of three amino acids linked together. • When there are three or more amino acids, the protein starts to form three dimensional shapes. Recommended Reading • Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. New York: Garland Science. The Shape and Structure of Proteins. • Berg JM, Tymoczko JL, Stryer L. Biochemistry. New York: W H Freeman. The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure. • Berg JM, Tymoczko JL, Stryer L. Biochemistry. New York: W H Freeman. Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops. • Berg JM, Tymoczko JL, Stryer L. Biochemistry. New York: W H Freeman. Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains. • Cooper GM. The Cell: A Molecular Approach. Sunderland (MA): Sinauer Associates. Protein Folding and Processing. Available from: https://www.ncbi.nlm.nih.gov/books/NBK9843/ • Cooper GM. The Cell: A Molecular Approach. Sunderland (MA): Sinauer Associates. Cell-Cell Interactions. Available from: https://www.ncbi.nlm.nih.gov/books/NBK9851/ • Cooper GM. The Cell: A Molecular Approach. Sunderland (MA): Sinauer Associates. The Central Role of Enzymes as Biological Catalysts. Available from: https://www.ncbi.nlm.nih.gov/books/NBK9921/ • Sanger F. (1959) Chemistry of Insulin: Determination of the structure of insulin opens the way to greater understanding of life processes. Science, 129 (3359), 1340-1344. • Pauling L., Corey R. B. and Branson H. R. (1951) The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A. 37 (4) 205-211. • Pauling L. and Corey R. B. (1951) The Pleated Sheet, A New Layer Configuration of Polypeptide Chains. Proc Natl Acad Sci U S A. 37(5): 251–256. QUESTIONS?