Protein Structure and Function I PDF

Protein structure and function I Amino acids and peptides Objectives Draw the structure of an amino acid Identify amino acids by name, three letter code, structure and properties Describe the ionization of amino acids with changing pH Draw a peptide molecule Describe each level o...

Protein structure and function I Amino acids and peptides Objectives Draw the structure of an amino acid Identify amino acids by name, three letter code, structure and properties Describe the ionization of amino acids with changing pH Draw a peptide molecule Describe each level of structural organisation of proteins Describe the forces involved in the stabilisation of primary, secondary, tertiary and quaternary structure Relate protein structure to biological activity  Amino Acids Are the Building Blocks of Proteins Each amino acid contains a chiral* carbon atom (called the alpha carbon) bonded to -an amino group -carboxyl group -hydrogen atom -side chain, also referred to as R group *proteins contain L amino acids Amino acids are classified according to the character of their R groups. R groups vary in size, shape, charge, hydrogen-bonding capacity, hydrophobic character and chemical reactivity. These factors determine particular properties of a protein such as solubility, flexibility, and polarity. Standard Amino Acids: Names, Abbreviations and Properties  Amino acids are amphoteric: they can act as an acid as well as a base. The amino group is basic and the carboxyl group is acidic. http://www.aqion.de/site/zwitterions In solution, amino acids exist as zwitterions (dipolar ions). In a zwitterion: The amino group has accepted a hydrogen ion, H+, to become NH3+. The carboxyl group has donated a hydrogen ion to become COO-. There is an overall neutral charge. Thus, amino acids are amphiprotic: they can both accept and donate protons (H+) Amino acids can act as buffers due to their amphoteric nature An amino acid molecule will form a cation or anion in response to changes in pH: At low pH, the amino group is protonated (NH3+), and the carboxyl group is not dissociated (COOH). The amino acid is positively charged. As pH increases, the carboxyl group is the first to lose an H+ and the amino acid becomes a zwitterion with a protonated amino group and deprotonated carboxyl group (NH3+ and COO-). At physiological pH, amino acids generally exist as zwitterions. As pH continues to increase, becoming more basic, the NH3+ group loses an H+ to become NH2. Thus, the ion is negatively charged. Amino acids can act as buffers due to their amphoteric nature pKa1 pKa2 pI pKa1 is the pKa of the carboxyl group on the amino acid pKa2 is the pKa of the amino group on the amino acid The isoelectric point, pI, is the pH at which the amino acid will exist as a zwitterion. Different amino acids will have different isoelectric points. At a pH below its pI, an amino acid will exist as a cation. At a pH above its pI, an amino acid will exist as an anion.  Peptide bond formation: a condensation reaction Amino acid 1 Amino acid 2 Dipeptide Peptide: Series of amino acids joined by peptide bonds (also called amide bonds). Chains of small numbers of amino acids are called oligopeptides or simply peptides. Polypeptide: A longer peptide chain. A protein is a long polypeptide chain typically containing 50- 2000 amino acids. Proteins occur naturally and have specific three-dimensional structures under physiological conditions. Each amino acid unit in a peptide/polypeptide is called a residue. Alberts et al. (2002) Detection and quantitation of proteins Biuret reagent provides cupric ions in an alkaline solution. The nitrogen atoms found in peptide bonds form a coloured coordination complex with cupric ions. The higher the number of peptide bonds present (i.e., when the concentration of protein in solution higher), the higher the number of complexes formed with the cupric ions and the greater the intensity of the colour of the complexes. The presence of the complexes formed can be detected by measuring their absorbance at 600 nm.  Organization of protein structure There are four levels of protein structure: Primary: Arises from assembly of polypeptide Secondary: Arises from folding of parts of polypeptide backbone Tertiary: Arises from packing of polypeptide into 3-D shape Quaternary: Arises from interaction between polypeptides Each level of structure is determined by the level preceding it. The organization of polypeptide structure through these levels is responsible for the biological activity of proteins. Primary structure Primary structure is the specific linear sequence of amino acids in a polypeptide By convention, the amino end (N-terminus) is considered the beginning of the polypeptide chain therefore the polypeptide sequence is written starting with the N-terminal residue location of all the covalent bonds in the protein including disulfide bonds The sequence of amino acids making up the primary structure determines the structure, function and general properties of a protein The primary structure is determined by the DNA sequence encoding the protein (gene) Primary structure of human insulin http://jsmith.cis.byuh.edu//inbookstroduction-to-chemistry-general-organic-and-biological/s21-04-proteins.html Secondary structure Secondary structure is the stable conformation adopted by local regions of the amino acid chain, i.e., the folding or coiling of local regions of the amino acid chain Types of secondary structure: A section of the chain forms a/n alpha helix (α helix) beta pleated sheet (β pleated sheet) beta turn (β turn) omega (Ω) loop  Alpha helix A tightly coiled polypeptide backbone with side chains (R groups) projecting outwards Formed due to hydrogen bonds between the CO and NH groups of the polypeptide backbone at regular intervals: The CO group in one amino acid forms a hydrogen bond with the NH group of the amino acid which is found 4 residues ahead in the sequence. Location of atoms and hydrogen The proportion of a protein which consists of alpha helices can bonds in an α helix. (Berg et al., 2002) range from almost none to almost 100%. Beta pleated sheet A beta strand (polypeptide chain) is almost fully extended. A beta sheet consists of two or more β-strands linked by hydrogen bonds between CO and NH groups on adjacent strands of the polypeptide backbone. A broad arrow pointing in the direction of the carboxyl- terminal end is used to depict β strands in a β sheet.  Polypeptide chains can change direction by making reverse turns and loops. Loops and turns do not have regularly repeating (periodic) structures like α helices and β sheets. Tertiary structure Tertiary structure is the overall folding of the polypeptide chain, that is, its final three-dimensional structure. In globular proteins, the final specific folding pattern is determined largely by the hydrophobic effect: In an aqueous environment, a polypeptide chain will fold in such a way that its polar, charged side chains are located on the surface and hydrophobic side chains are buried in the interior of the protein In a non-aqueous environment the polypeptide will fold so that the hydrophobic side chains are on the surface and the polar side chains are on the interior of the protein Alberts et al. (2002) The 3-D shape of a protein is what makes it functional; the protein cannot perform its function in the cell until it takes on its tertiary structure. Forces stabilising the tertiary structure of proteins Quaternary structure Quaternary structure is the specific association of two or more polypeptides to form a multi-subunit complex (oligomer). It is the spatial arrangement of the subunits and the nature of interactions between the subunits Thus it describes the type of subunits number of subunits way in which the subunits interact Haemoglobin The quaternary structure of haemoglobin is formed by the association of two alpha globin and two beta globin polypeptide chains (α2β2 structure). https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Images3/hemoglobn.jpg Forces Driving Quaternary Association Hydrogen Bonding Electrostatic Interactions Van Der Waals Interactions Hydrophobic Interactions  Quaternary structure in action (b) (a) Collagen, the most abundant protein in the human body, is a structural protein which is made strong by its three- stranded rope-like structure. It is found in our An antibody, a protein with a protective function, is cartilage and tendons. able to bind foreign molecules using the two arms of (nigms.nih.gov) its Y-shape. The stem of the antibody sends signals to recruit other members of the immune system. (nigms.nih.gov)  (b) (a) (a) DNA polymerase III is a protein which is able to cinch around DNA due to its doughnut shape. It moves along the DNA strands as it copies the genetic material. (b) Enzymes, proteins which are biochemical catalysts, often contain a groove or pocket to hold the molecule they act upon. Shown here (clockwise from top) are luciferase, which creates the yellowish light of fireflies; amylase, which helps us digest starch; and reverse transcriptase, which enables HIV and related viruses to use infected cells. (nigms.nih.gov)  Structural Comparison of Fibrous and Globular Proteins Fibrous proteins: the main structural material within different tissues fibre-like quaternary structure relatively insoluble in water Globular proteins: have chemical reactivity act as enzymes, transport agents and regulatory messengers generally spherical in shape soluble in water http://ib.bioninja.com.au/standard-level/topic-2-molecular-biology/24-proteins/fibrous-vs-globular- protein.html The biological activity of a protein is determined by the organisation of its structure. Different structural organisation produces proteins which serve different functions. Classification of Some Proteins and Their Functions References Berg, J.M., Tymoczko, J.L. & Stryer, L. 2002. Biochemistry. 5th Edition, WH Freeman, New York. Diagram sources: http://4.bp.blogspot.com/-5mvNWiWq-eo/Uf_etIVuYFI/AAAAAAAAAh0/-cBi5L9uYjM/s1600/Standard%20Amino%20Acids.PNG http://devarchive.cnx.org/resources/55e41e4bb57985547fb168535446840e/Figure_15_01_01.jpg http://geneexpression27.weebly.com/uploads/1/2/6/2/12623644/489510775_orig.gif?170 http://academic.brooklyn.cuny.edu/biology/bio4fv/page/primar.htm http://bio3400.nicerweb.com/doc/class/bio1151/Locked/media/ch05/05_20cKeratin.jpg http://cbm.msoe.edu/teachingResources/proteinStructure/assets/images/tertiaryStructure.jpg http://sites.sinauer.com/animalphys3e/boxex/AnPhys3e-BoxEx-02-01-A-0.jpg http://www.bioinformatics.utep.edu/agriculture/img/betasheet.jpg https://upload.wikimedia.org/wikipedia/commons/thumb/3/3d/1GZX_Haemoglobin.png/600px-1GZX_Haemoglobin.png http://classes.midlandstech.edu/Carterp/Courses/bio110/chap02/Slide22.JPG https://publications.nigms.nih.gov/structlife/chapter1.html http://www.slideshare.net/lizza919/proteins-10306082 http://www.und.nodak.edu/dept/jcarmich/101lab/lab6/lab6.html