Chapter 3 BioChem.pdf

MODULE BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE Chapter 3: Proteins and Related Systems – Structures and Functions Proteins Proteins are the most abundant substance, next to water, in nearly all cells (15% of cell’s overall mass). All...

MODULE BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE Chapter 3: Proteins and Related Systems – Structures and Functions Proteins Proteins are the most abundant substance, next to water, in nearly all cells (15% of cell’s overall mass). All proteins contain elements carbon, hydrogen, oxygen, and nitrogen. Having a nitrogen in the chemical structure is what differs proteins from carbohydrates and lipids.Proteins play an enormousvariety of roles: Some carry out the transport and storage of small molecules;others make up a large part of the structural framework of cells and tissues.Muscle contraction, the immune response, and blood clotting are all mediated byproteins.Proteins are naturally occurring, unbranched polymer in which the monomer units are amino acids. Amino Acids–Amino acid is an organic compound that contains both amino (-NH2) group and a carboxyl (-COOH) group. The amino acids found in proteins are always α-amino acids.The amino group is attached to the α-carbon, the carbon next to the carboxylic acid group; hence the name α-amino acid. To the α-carbon of every amino acids are also attached to a hydrogen atom and a side chain (“R” group). More than 700 different naturally occurring amino acids are known, but only 20 of them, called standard amino acids, are normally present in proteins. MODULE BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE Four Categories of Amino Acid: 1. Nonpolar amino acids 2. Polar neutral amino acids 3. Polar acidic amino acids 4. Polar basic amino acids Nonpolar Amino Acids - is an amino acid that contains one amino group, one carboxyl group, and a nonpolar side chain. When incorporated into a protein, such amino acids are hydrophobic, they are not attracted to water molecules. They are generally found in the interior of proteins, where there is limited contact with water. Glycine Alanine Valine Leucine Isoleucine Proline Phenylalanine Methionine Tryptophan Polar Neutral Amino Acids–is an amino acid that contains one amino group, one carboxyl group, and a side chain that is polar but neutral. The side chain of a polar neutral amino acid is neither acidic nor basic. Amino acids in this category are more soluble in water than the nonpolar amino acids; the R group present can hydrogen-bond to water. Serine Cysteine Threonine Asparagine Glutamine Tyrosine Polar Acidic Amino Acid–is an amino acid that contains one amino group and two carboxyl groups, the second carboxyl group being part of the side chain. The side chain of a polar acidic amino acid bears a negative charge; the side chain carboxyl group has lost its acidic hydrogen atom. Aspartic acid and glutamic acid are the two amino acids included in this category. Polar Basic Amino Acid–is an amino acid that contains two amino groups and one carboxyl group, the second amino group being in part of the side chain. The side chain of a polar basic amin acid bears a positive charge; the nitrogen atom of the amino group has accepted a proton. Histidine, Lysine, and Arginine are included in this category. MODULE BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE Peptide and the Peptide Bond Peptides Amino acids can be covalently linked together by formation of an amide bondbetween the -carboxylic acid group on one amino acid and the -amino groupon another. This bond is often referred to as a peptide bond, and the products formed by such a linkage are called peptides. Under proper conditions, amino acids can bond together to produce an unbranchedchain of amino acids. The length of the amino acid chain can vary from a few aminoacids to many amino acids. Peptides are further classified by the number ofamino acids present in the chain. Acompound containing two amino acids is specificallycalled a dipeptide; three amino acids joined together in a chain constitutea tripeptide; and so on. The name oligopeptide is loosely used to refer to peptideswith 10 to 20 amino acid residues, and the name polypeptide is used to refer to longerpeptides.A polypeptide is a long unbranched chain of amino acids. Protein Functions in Human α-Keratin – this protein is found in protective coatings for organisms, and is particularly abundant in nature. It is the major constituent of hair, feathers, wool, fingernails and toenails, claws, scales, horns, turtle shells, quills, and hooves. The structure of a typical keratin is mostly helical. In hair, a pair of keratin molecules coils together and then coils further with another pair to form a protofilament. This protofilament then coils together in groups of four to form microfilaments, which then become the “core” unit in the structure of α-keratin of hair. Introduction of disulfide bridges within the several levels of coiling structuredetermines the “hardness” of an a-keratin. “Hard” keratins, such as those found inhorns and nails, have considerably more disulfide bridges than their softer counterpartsfound in hair, wool, and feathers. Collagen – it is the most abundant of all proteins in humans; it constitutes 30% of total body protein. Collagen is the major structural material in tendons, ligaments, blood vessels, and skin. It is also the organic component of bones and teeth. The structural formation of a collagen is a triple helix, formed when three chains of amino acids wrap around each other to give a rope-like arrangement of polypeptide chain. Glycine and proline are the most dominating presence in a triple helix formation. MODULE BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE Figure 1: Structure of α-keratin Figure 2: Structure of a collagen Hemoglobin – this protein transports oxygen from the lungs to tissue. Haemoglobin is a tetramer, a four peptide subunits, with each subunit also containing a heme group, the entity that binds oxygen. Haemoglobin can transport four oxygen molecules at the same time due to its four heme group. Myoglobin – this protein functions as an oxygen-storage molecule in muscles. Myoglobin is a monomer. It only consist of a single peptide chain and a heme unit, thus only one oxygen molecule can be carried by a myoglobin molecule. Myoglobin has a higher affinity for oxygen than does haemoglobin, thus the transfer of oxygen from haemoglobin to myoglobin occurs readily. Oxygen stored in myoglobin serves as a reserve oxygen source for working muscles when their demand for oxygen exceeds that which can be supplied by haemoglobin. Immunoglobulins – are one of the most important functions of proteins. Immunoglobulins are glycoprotein produced by an organism as a protective response to the invasion of microorganisms or foreign molecules. They serve as antibodies to combat invasion of the body by antigens. Lipoproteins – conjugated protein that contains lipids in addition to amino acids. Its major function is to help suspend lipids and transport them through the bloodstream. Lipids are insoluble in blood because of their non-polar nature. MODULE BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE Four Major Classes of Plasma Lipoproteins: 1. Chylomicrons – transport dietary triacylglycerols from the intestine to the liver and to adipose tissue. 2. Very-Low-Density Lipoproteins (VLDL) – transport triacylglycerols synthesized in the liver to adipose tissue. 3. Low-Density Lipoproteins (LDL) – transport cholesterol synthesized in the liver to cells throughout the body. 4. High-Density Lipoprotein (HDL) – collect excess cholesterol from the body tissues and transport it back to the liver for degradation to bile acids. Protein Classification Based on Shape Fibrous Protein – it is a protein whose molecules have an elongated shape with one dimension much longer than the others. Fibrous proteins have simple, regular, linear structures. Globular Protein – it is a protein whose molecules have peptide chains that are folded into spherical or globular shapes. The folding in such proteinsis such that most of the amino acids with hydrophobic side chains (nonpolarR groups) are in the interior of the molecule and most of the hydrophilic side chains(polar R groups) are on the outside of the molecule. Membrane Protein – protein found associated with a membrane system of a cell. It differs with globular proteins due to its insolubility in water. MODULE BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE For more understanding and knowledge on Proteins, please visit: https://www.youtube.com/watch?v=HSCUAjZQhXI https://www.youtube.com/watch?v=2Jgb_DpaQhM https://www.youtube.com/watch?v=hok2hyED9go Bibliography Mathews, C. K., Van Holde, K. E., Appling, D. R., & Anthony-Cahill, S. J. (2013). Biochemistry 4th Edition. Pearson. Nelson, D. L., & Cox, M. M. (2017). Lehninger Principles of Biochemistry 7th Edition. New York. Stoker, H. S. (2014). Organic & Biological Chemistry 7th Edition. Boston: Cengage Learning.