Palawan State University Chem 4/L Biomolecules PDF

PALAWAN STATE UNIVERSITY College of Sciences CHEM 4/L BIOMOLECULES INTRODUCTION TO BIOMOLECULES Module 1.1 THE CELL & THE BIOCMOLECULES Table of Contents Content Page Learning objectives………………………………………2 Overview……....

PALAWAN STATE UNIVERSITY College of Sciences CHEM 4/L BIOMOLECULES INTRODUCTION TO BIOMOLECULES Module 1.1 THE CELL & THE BIOCMOLECULES Table of Contents Content Page Learning objectives………………………………………2 Overview…….………………………..…………………..3 Initial activity………………….……………………..……3 What is biochemistry………..………………………..….4 The cell…….………….……………………….…….……5 Biomolecules ……………..….…………….….…………6 Energy of the cell …………………………….……..…...7 Linkages in biochemical reaction …………….……..…8 Functional groups ………………..………….………..…9 Evaluation ………………………………….………….…10 Reflection ………………………………….………….…11 References …………………………….….………….…12 2 Page 1 Learning Objectives After going through in this module, you should be able to: ü LO1 Define biomolecules in terms of their structures ü LO2 Identify the key features differentiating eukaryotes and prokaryotes 3 Page 2  Overview What is Biochemistry? Biochemistry deals with living organisms at the molecular level, and includes the most fundamental processes of life (Stryer et al., 2018). An example of this is the flow of information from genes to molecules with functional capabilities. Biochemistry encompasses other fields of science like chemistry, molecular biology, genetics, medicine, and agriculture, among others. The understanding of unexplained phenomena in medicine and other fields are gently influenced by biochemistry. A big contribution of biochemistry is in the elucidation at biochemical level of molecular lesions e.g. cystic fibrosis, hemophilia etc. and clinical diagnostics. A key goal of biochemistry is to explain these phenomena in living organisms in a molecular and organismic level. Later on, it was realized that all organisms have much in common biochemically i.e. organisms are remarkably uniform at the molecular level or the so called unity of biochemistry or unity of life (Stryer et al.). 4 Page 3  Initial Activity How well do you know your cell structure? Draw the cell structure and label the different cell organelles of an animal and give their functions. 5 Page 4  Discussion The Cell Basic building blocks of life Smallest living unit in an organism Grow, reproduce, use energy, adapt, respond to their environment May be an entire organism or one of billions that make up the organism Prokaryotes include bacteria & lack a nucleus or membrane-bound structures called organelles. Eukaryotes include most other cells & have a nucleus and membrane- bound organelles (plants, fungi & animals) 6 Page 6 Discussion 7 Figure 1. Prokaryotes and Eukaryotes features (Tymoczko, Berg and Stryer, 2013) Page 7  Discussion Characteristic Bio-membrane and Organelles Mitochondria Chloroplasts (plastids) Rough Endoplasmic Reticulum (RER) Ribosome Smooth Endoplasmic Reticulum (SER) Golgi Apparatus Lysosomes 8 Figure 1. Prokaryotes and Eukaryotes features (Tymoczko, Berg and Stryer, 2013) Page 8 Discussion There are four biomolecules: 1. Protein 2. Carbohydrates 3. Lipids and fats 4. Nucleic acid 9 Page 9  Discussion Protein A protein folding to its 3D structure is dictated by a sequence of amino acids that constitute the protein. Tymoczko, Berg and Stryer (2013) Membrane proteins embedded (yellow) in membranes and attached (blue) to them, permit the exchange of material and information with the environment. Tymoczko, Berg and Stryer (2013) Page 10  Discussion Carbohydrates Fuels and information molecules. Glucose is the most common fuel sugars and glycogen is the stored glucose in animals. Tymoczko, Berg and Stryer (2013) Page 11  Discussion Lipids and Fats Storage form of fuel and also serve as cell barrier.(One part of a lipid molecule is hydrophilic; the other part is hydrophobic. In water, lipids can form a bilayer, constituting a barrier that separates two aqueous components. Tymoczko, Berg and Stryer (2013) Page 12  Discussion Nucleic Acid The information molecules of the cell. The primary function of nucleic acid is to store and transfer information from the genes to proteins. Tymoczko, Berg and Stryer (2013) A nucleotide (in this case, adenosine triphosphate) consists of a base (shown in blue), a five-carbon sugar (black), and at least one phosphoryl group (red). Page 13  Discussion Energy of the Cell Living cells are inherently unstable. Constant flow of energy prevents them from becoming disorganized. Cells obtain energy mainly by the oxidation of biomolecules (electrons transferred from 1 molecule to another & in doing so they lose energy) This energy captured by cells & used to maintain highly organized cellular structure & functions. How do complex structures of cells maintain high internal high internal order? 1. Synthesis of biomolecules. 2. Transport Across Membranes – Cell membranes regulate the passage of ions & molecules from one compartment to another. 3. Cell Movement – Organized movement is one of the most obvious characteristics of living cells. The intricate & coordinated activities required to sustain life require the movement of cell components. 4. Waste Removal – Animal cells convert food molecules into CO2, H2O & NH3. If these not disposed properly can be toxic. Page 14  Discussion Linkages in biochemical compounds We had reviewed the different functional groups of organic molecules. Functional groups – specific parts of molecules involved in biochemical reactions Linkages between biochemical compounds Page 15  Discussion Functional groups in a single biomolecule Many important biomolecules are polymers Biopolymers - macromolecules created by joining many smaller organic molecules (monomers). Condensation reactions join monomers (H2O is removed in the process). Residue - each monomer in a chain Page 16  Discussion Biochemical reaction Even though thousands of reactions sound very large & complex in a tiny cell: o The number of types of reaction is small o Mechanisms of biochemical reactions are simple o Reactions of central importance (for energy production & synthesis & degradation of major cell components) are relatively few in number. Page 17  Discussion Evaluation Let’s see how much you learn from this lesson! 1. There are several methods in studying the structure and function of cells. Name at least two methods and give an example for each. 2. In the structure below, determine the amount of functional groups and name each. a. cholesterol Page 18  Discussion Evaluation Let’s see how much you learn from this lesson! 2. In the structure below, determine the amount of functional groups and name each. a. chlorophyll Page 19  Reflection Excerpt from Biochemistry by Tymoczko, Berg and Stryer (2013) "One reason that oxygen and hydrogen are so common is the ubiquity of water, or “the matrix of life,” as biochemist Albert Szent-Györgi called it. This tiny molecule—consisting of only three atoms—makes life on Earth possible. Indeed, current belief is that all life requires water, which is why so much effort has been made in recent decades to determine whether Mars had water in the past and whether it still does. The importance of water for life is so crucial that its presence is tantamount to saying that life could be present.” 20 Page 20  References 1. Denniston, K.J., J.J. Topping and R.L. Caret. 2004. General, Organic & Biochemistry. 4th ed. McGraw Hill. 880 pp. 2. Murray, R.K., A.A. Bender, K.M. Botham, P.J. Kennelly, V.W. Rodwell and P.A. Weil. 2012. Harper’s Illustrated Biochemistry. 29th ed. McGraw Hill.818 pp. 3. Tymoczko J.L., J.M. Berg and L. Stryer..2013. Biochemistry (Short course) 2nd ed. Freeman & Company. 862 pp. 4. Ferrier, D.R. 2014. Lippincott’s Illustrated Review: Biochemistry. 6th ed. Baltimore, Walter Klumer Business. 1108 pp. 5. Lehninger, A.L., D.L. Nelson and M.M. Cox. 2014. Lehninger Principles of Biochemistry. 4th ed. New York, Worth Publisher. 1130 pp 21 Page 21