Proteins and Amino Acids Vishal Patel CHEM 504 Biochemistry Dr. E. Thornton

Proteins provide structure, catalyze cellular reactions and carry out other tasks. have multiple biological functions classified according to their biological roles.

Types of proteins and their function Enzymes Most varied and specialized proteins with catalytic activity. All chemical reactions of organic biomolecules in cells are catalyzed by enzymes.

Types of proteins and their function Transport Proteins Bind and carry molecules or ions to organs in the blood plasma. Lipoproteins in blood plasma carries lipids from the live to other organs. Two types of catecholamine transport proteins are being characterized: (a) the storage vesicle transporter, which is inhibited by the drug reserpine; and (b) the plasma membrane transporter, which is inhibited by drugs of abuse, such as cocaine. “Molecular properties of the transporters are being determined using radioiodinated reserpine and cocaine photoaffinity labels, purification and cloning, PCR amplication of transporter sequences, and stable expression of transporters in cultured cell lines, such as HeLa, COS, and CHO. The plasma membrane transporters are targets for drugs which are used to treat depression, targets for drugs of abuse, such as cocaine, and may be involved in the etiology of schizophrenia. The sigma receptor is a mammalian protein with multiple putative functions in the brain and the periphery. We have demonstrated that calcium-activiated potassium channels are inhibited by sigma receptors and that these receptors are enriched in cancer cells. Our goal is to identify the natural ligands for the sigma receptor, characterize the binding site, and determine the role of the sigma receptor in intracellular signaling.” (http://images.google.com/imgres?imgurl=http://www.wisc.edu/molpharm/faculty/ruoho/ruohopic.jpg&imgrefurl=http://www.wisc.edu/molpharm/faculty/ruoho.html&h=349&w=385&sz=29&hl=en&start=18&sig2=tsc5tpZFNpqxV0Xvrt0LMQ&tbnid=fXR8rbT7iBI-MM:&tbnh=111&tbnw=123&ei=8FyFRrSaLpuYeMK57PMB&prev=/images%3Fq%3Dtransport%2Bproteins%26gbv%3D2%26svnum%3D10%26hl%3Den accessed 6/29/07)

Types of proteins and their function Nutrient and Storage Proteins Seeds of many plants store nutrient proteins required for the growth of the germinating seedlings. Ovalbumin, the major protein of egg white, and casein the major protein of milk are examples of nutrient proteins.

Types of proteins and their function Contractile or Motile Proteins Some proteins endow cells and organisms with the ability to contract, to change shape, or to move about. Tubulin is the protein from which microtubules are built.

Types of proteins and their function Structural Proteins Many proteins serve as supporting filaments, cables, or sheets, to give biological structures strength or protection. Major component of tendons and cartilage is the fibrous protein collagen, which has very high tensile strength. Ligaments contain elastin, a structural protein.

Types of proteins and their function Defense Proteins Defend organisms against invasion by other species or protect them Immunoglobulin or antibodies, are made by the lymphocytes of vertebrates and can recognize & precipitate or neutralize invading bacteria Fibrinogen and thrombin are blood clotting proteins

Types of proteins and their function Regulatory Proteins Help regulate cellular or physiological activity. The cellular response to many hormonal signals is often mediated by a class of GTP-binding proteins called G proteins.

Amino Acids: Building Blocks of Proteins Every amino acid has the same fundamental structure which consists of a central carbon bonded to an amino group, a carboxyl group & a hydrogen atom.

Example of an Amino Group R Group Carboxyl Group Amino Group Central Carbon

Amino Acids: Side Groups There are 20 different types of amino acids used in making proteins. (You will have a change to study them interactively on the WWW.) The essential structure is the same in all 20 molecules. The 20 molecules differ in the side groups.

Amino Acids: Building Blocks of Proteins A peptide bond is a covalent bond formed. Polypeptides are polymers of amino acids linked together by peptide bonds, with the amino group of one acid joining the carboxyl groups of its neighbor.

Amino Acids: Building Blocks of Proteins

Amino Acids: Building Blocks of Proteins The peptide bond is formed when the OH group from the carboxyl group of one of the amino acids is removed and a hydrogen from the other amino acid is removed. The OH and H bond to from water. The formation of water from the two amino acids is called dehydration synthesis. The covalent linkage that is formed is known as a peptide bond, and the molecule that is formed by the linking of amino acids is called polypeptide.

Proteins are Very Large Molecules Some proteins consist of a single polypeptide chain and others called multisubunit proteins, have two or more. Individual polypeptide chains in a multisubunit protein may be identical or different. If at least some are identical, the protein is sometimes called an oligomers protein and the subunits themselves are referred to as protomers.

Levels of Protein Organization Primary Structure Secondary Structure Tertiary Structure Quaternary structure First we consider empirical clues that amino acid sequence and protein function are closely linked, then describe how amino acid sequence is determined and then outline uses to which the info. Can be put.

Levels of Protein Organization

Primary Structure Covalent bonds between amino acids and is normally defined by the sequence of peptide-bonded amino acids and locations of disulfide bonds. The relative spatial arrangement of the linked amino acids is unspecified.

Secondary Structure Refers to regular recurring arrangements in space of adjacent amino acid residues in a polypeptide chain. There are few common types of secondary structure, the most prominent being the α helix & β conformation.

Tertiary Structure The spatial relationship among all amino acids in a polypeptide. It is the complete 3D structure of the polypeptide.

Quaternary Structure Proteins with several polypeptide chains have one more level of structure referred to at the quaternary structure. Refers to the spatial relationship of the polypeptides, or subunits, within the protein TO REVIEW THE FOUR LELVELS OF ARCHITECTURE IN PROTEINS The primary structure consists of a sequence of amino acids linked together by covalent peptide bonds, and includes any disulfide bonds. The resulting polypeptide can be coiled into an α helix, one form of secondary structure. The helix is a part of the tertiary structure of the folded polypeptide, which is itself one of the subunits tha tmake up the quaternary structure of the multimeric protein.

Let’s sing the protein song. O Little Protein Molecule (Song)

Independent Practice Go to http://biology.clc.uc.edu/courses/bio104/protein.htm Find and make note of the different types of amino acids used in making proteins.

References http://www.beldem.com/library/showimg.asp?tab=BELCategory&fld=CatID&val=1 http://images.google.com/imgres?imgurl=http://www.wisc.edu/molpharm/faculty/ruoho/ruohopic.jpg&imgrefurl=http://www.wisc.edu/molpharm/faculty/ruoho.html&h=349&w=385&sz=29&hl=en&start=18&sig2=tsc5tpZFNpqxV0Xvrt0LMQ&tbnid=fXR8rbT7iBI-MM:&tbnh=111&tbnw=123&ei=8FyFRrSaLpuYeMK57PMB&prev=/images%3Fq%3Dtransport%2Bproteins%26gbv%3D2%26svnum%3D10%26hl%3Den http://www.wisc.edu/molpharm/faculty/ruoho/ruohopic.jpg http://www.lbl.gov/images/PID/dimer.jpg http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/pics/elastin-closed-solv-shell.png http://www-nmr.cabm.rutgers.edu/photogallery/proteins/gif/kst1.gif http://images.google.com/imgres?imgurl=http://www.msg.ucsf.edu/flett/Images_folder/actin.jpg&imgrefurl=http://www.msg.ucsf.edu/flett/Support2.html&h=500&w=500&sz=121&hl=en&start=16&sig2=vsTTR5xfCfTKSEMnVG_i8g&tbnid=WJshzEV1qBSXNM:&tbnh=130&tbnw=130&ei=2GKFRrqOGZuWeOXzxPMB&prev=/images%3Fq%3Dregulatory%2Bproteins%26gbv%3D2%26svnum%3D10%26hl%3Den http://images.google.com/imgres?imgurl=http://academic.brooklyn.cuny.edu/biology/bio4fv/page/prot_struct-4143.JPG&imgrefurl=http://academic.brooklyn.cuny.edu/biology/bio4fv/page/3d_prot.htm&h=1142&w=585&sz=537&hl=en&start=2&tbnid=4gntmshkMPL0BM:&tbnh=150&tbnw=77&prev=/images%3Fq%3DPrimary%2BStructure%2Bof%2Ba%2BProtein%26gbv%3D2%26svnum%3D10%26hl%3Den%26sa%3DG