Intro to Biochemistry PDF

Intro to Biochemistry By: Roselita O Natividad Natural Science Department Ateneo de Zamboanga University Define as chemistry...

Intro to Biochemistry By: Roselita O Natividad Natural Science Department Ateneo de Zamboanga University Define as chemistry of the living organism Living organisms are composed of lifeless molecules, when these molecules are isolated and examined individually but when in a living organism, they even support life These lifeless molecules in the living organism conform to all the physical and chemical laws that describe the behavior of matter In addition, these molecules possess extraordinary attributes not shown by any random collection of molecules Living Matter has Several Characteristics Structurally complicated yet highly organized Living organisms extract, transform, and use energy from their environment, usually in the form of either chemical nutrients or radiant energy from the sun Have the capacity for precise self-replication and self-assembly That is …. The molecules in living organisms conformed to all the laws of chemistry but at the same time they interact with each other in accordance with another set of principles referred to as the “Molecular Logic of Life” The molecular logic of life relates nature, function, and interaction of biomolecules The basic goal of biochemistry, therefore, is to determine how these molecules interact with each other to maintain and perpetuate life and ultimately concerned with the wonder of life itself Water Main constituent of Earth's hydrosphere and the fluids of all known living organisms. It is vital for all known forms of life, even though it provides no calories or organic nutrients. Most abundant in living organisms, making up approximately 70% of the weight of most organisms Medium in which the transport of nutrients, enzyme-catalyzed reactions of metabolism, and the transfer of chemical energy occur Properties: Density: 997 kg/m³ or 1 g/cc Boiling point: 100 °C Formula: H2O Molar mass: 18.01528 g/mol Melting point: 0 °C IUPAC ID: Oxidane, Water Structure of Water Composed of two hydrogens and one oxygen Each hydrogen atom is linked to the oxygen by a single covalent bond Oxygen is more electronegative than hydrogen, thus, oxygen bears a slightly negative charge and hydrogen a slightly positive charge resulting to a polar bond Bond angle in water molecule is 104.50 Properties of Water 1) Thermal Properties of Water Acts as an effective modulator of climatic temperature Can absorb and store solar heat and release it slowly Water’s high heat capacity coupled with the high water content found in most organisms, helps maintain an organism’s internal temperature Evaporation of water is used as a cooling mechanism, since it permits large losses of heat An adult human, for example, may eliminate as much as 1200g of water daily in expired air, sweat and urine The associated heat loss may amount to approximately 20% of the total heat generated by metabolic processes Heat of vaporization – energy required to vaporize one mole of a liquid at a pressure of one atmosphere Heat capacity – energy must be added or removed to change the temperature by one degree Celsius 2) Solvent Properties of Water Water’s dipolar structure and its capacity to form H-bonding enable water to dissolve many ionic and polar substances Non-polar molecules are not soluble in water because they lack polar functional groups and thus, cannot form H-bonds *** the reason why water is being called the universal solvent because of the large variety of ionic and polar substances it can dissolve and this is due to the large dielectric constant that water possesses (dielectric constant of a solvent is a measure of its capacity to reduce the attractive force between ions) *** ***the physical and chemical properties of water make it remarkably suitable for its numerous functions in living organisms*** *** non-covalent interactions play a vital role in determining these properties*** Non-covalent Bonding H-Bonds because of the large difference in electronegativity of H and O, the hydrogens of one water molecule are attracted to the unshared pairs of electrons of another water molecule forming H-bond The H-bond describes an electrostatic interaction rather than a covalent bond Act as bridge between water molecule Although weaker than ionic and covalent bonds, hydrogen bonds are stronger than most non-covalent bonds Provide the cohesive forces that make water liquid at room temperature and favor extreme ordering of molecules in ice Has a significant effect on the structure and function of biomolecules Electrostatic interaction Occurs between oppositely charged atoms or group of atoms Significant role in determining the shape and function of biomolecules such as between –COO- and –NH3+ in determining the three-dimensional structure of proteins An important aspect of this interaction in aqueous solution is the hydration of ions Water molecules are polar, thus, they are attracted to charged ions As ions become hydrated, the attractive force between them is reduced and the charged species dissolves in the water Electrostatic interactions between charged groups or polar groups on biomolecules are most significant in water depleted regions since water competes with great success with electrostatic interactions between other groups Hydrophobic interaction When non-polar molecules enter an aqueous environment, H-bonded water molecules attempt to form a cage-like structure around them, this allows the nonpolar molecules to have minimal contact with water Primarily responsible for the structure of membranes and the stability of proteins Other non-covalent interactions are: Dipole-dipole interactions Dipole-induced dipole interactions Induced dipole-induced dipole interactions Bonding property of carbon Can form tetrahedral structure that results to two spatial arrangements, one being the mirror image of the other In the C=C, cis-trans isomerism exists (Cis-trans (geometric) isomerism exists when there is restricted rotation in a molecule and there are two nonidentical groups on each doubly...) * Carbon forms covalent bonds with atoms of carbon or other elements.... Carbon has four valence electrons, so it can achieve a full outer energy level by forming four covalent bonds. When it bonds only with hydrogen, it forms compounds called hydrocarbons. Buffers – solution usually containing an acid and a base, or a salt, that tends to maintain a constant hydrogen ion concentration. Water molecules have a limited capacity to ionize to form H+ + OH- H2O ⎯⎯→ H+ + OH- The H+ ion is one of the most important ions in the biological systems The concentration of H+ ion affects most cellular and organismal processes Also play a major role in processes such as energy generation and endocytosis Because H+ concentration affects living processes, regulating its concentration (pH) is a universal and essential activity of living organisms Living systems regulate H+ concentration by substances that act as buffer A buffer consists of a weak acid and its conjugate base Because of their capacity to combine with H+ ions or to release H+ under different conditions, buffer help maintain a relatively constant hydrogen ion concentration Physiological Buffers Bicarbonate Buffer One of the more important buffers in blood has three components CO2 + H2O ⎯→ H2CO3 Carbonic acid then rapidly dissociates to form H+ and HCO3- H2CO3 ⎯→ H+ + HCO3– Regulated by the kidney if HCO3- decreases, kidney removes H+ from the blood resulting to increase production of HCO3- , H2CO3 is lost in this process but quickly replenish by hydrating CO2 , a waste product of cellular metabolism When excess amount of HCO3- are produced, they are excreted by the kidney (bicarbonate buffer) When acid is added to the body’s HCO3- system, HCO3- decreases and CO2 is formed Since CO2 is exhaled, the ratio of HCO3- to CO2 remains essentially unchanged Therefore … CO2 + H2O ⎯→ H2CO3 ⎯→ HCO3- + H+ Phosphate buffer Consist of H2PO4- / HPO4-2 An important buffer in intracellular fluids Since the normal pH of cell fluids approximately 7.2, an equimolar mixture of H2PO4- and HPO4-2 is typically present H2PO4- ⎯→ H+ + HPO4-2 Protein buffer Composed of amino acids Are significant source of buffering capacity Hemoglobin (oxygen-carrying protein) is the most abundant biomolecule in red blood cells Because of its structure and high cellular concentration, hemoglobin plays a major role in maintaining blood pH The Cell Cells are the structural and functional units of all living organisms A meaningful study of the chemical reactions that underlie the processes of life would only be possible if viewed in different biochemical systems in relation to machineries 1. Nucleus – main center of biochemical system, that is, main center of biosynthesis of nucleic acids: DNA, RNA – called control center – have three regions : nuclear membrane, nucleolus, chromatin Nuclear Membrane Barrier of nucleus Consists of a double phospholipid membrane Contain nuclear pores that allow for exchange of materials with the rest of the cells Nucleoli – packed with ribosomes, rich in RNA and proteins and appears to be active centers of protein and RNA synthesis Chromatin – compose of DNA and proteins – scattered throughout the nucleus – condenses to form chromosomes when cell divides 2. Endoplasmic Reticulum, ER All cells contain ER Constitutes more than half of the total membrane Provides the cells with the mechanism for separating newly synthesized molecules that belong to the cytosol from those that do not Plays a central part in the biosynthesis of molecules used to construct other cellular organelles Rough ER – packed with ribosomes – protein synthesis/RNA synthesis Smooth ER – lipid synthesis 3. Ribosomes Factory site for the manufacture of all cell proteins Transferring of information from DNA to protein synthesis  4. Mitochondria Power house of the cell Site of the oxidation reactions and electron transport chain 5. Lysosomes Principal sites of intracellular digestion Can malfunction and cells will rupture, thus, also called suicide sac For defense 6. Golgi apparatus Packaging plant of the cell/modification of proteins as well as carbohydrates Principal director of mammalian traffic in the cell 7. Cell membrane Controls entry into and out of the cell regulatory *** activity on 1. A One-Page Journal writing on “Life Ceases Without Molecules” Questions 1. Identify the functional groups present in each of the following biomolecules: a. Fatty acids b. Sugars c. Nucleotides d. Proteins 2. The outer boundary of most eukaryotic cells is a cell membrane, while the outer boundary of a prokaryotic cell is a cell wall. How do these structures differ in function? 3. Both peroxisomes and mitochondria consume molecular oxygen. How do their functions differ? 4. What intermolecular force of attraction occurs between the following molecules and ions? a. Water and ammonia b. Lactate and ammonium ion c. Benzene and octane d. Chloroform and diethylether 5. Tyrosine, with the structure given below, is an amino acid. Encircle the part/parts in the molecule that can form H-bonds with water.