Introduction to Biochemistry PDF

Introduction to Biochemistry Water, pH, Acids & Bases, and Buffers Prepared by: John Dale Mateo, MAEd  Learning Objectives Explain the properties of water and why it is essential to life Describe acids & bases and identify B...

Introduction to Biochemistry Water, pH, Acids & Bases, and Buffers Prepared by: John Dale Mateo, MAEd  Learning Objectives Explain the properties of water and why it is essential to life Describe acids & bases and identify Brønsted–Lowry acids & bases Calculate the pH of a solution Describe the role of buffers in maintaining the pH of a solution  Introduction to 01 Biochemistry  Biochemistry It is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes. Biochemical processes or Biochemical pathways Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Biochemistry Much of biochemistry deals with the structures, functions and interactions of biological macromolecules, such as proteins, nucleic acids, carbohydrates and lipids, which provide the structure of cells and perform many of the functions associated with life. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Biochemistry Application 01 Medicine 02 Nutrition 03 Agriculture 04 Research Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only 02 Water  WATER IS AN IDEAL BIOLOGIC SOLVENT ▪ A water molecule is an irregular, slightly skewed tetrahedron with oxygen at its center Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  ▪ The water molecule, H₂O, consists of two hydrogen atoms covalently bonded to an oxygen atom. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Formation of Dipoles ▪A molecule with electrical charge distributed asymmetrically about its structure is referred to as a dipole. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Formation of Dipoles ▪ Due to the difference in electronegativity between oxygen and hydrogen, the shared electrons tend to spend more time closer to the oxygen atom than to the hydrogen atoms. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  ▪ This unequal sharing of electrons creates a polar molecule with a partial negative charge (δ-) on the oxygen atom and partial positive charges (δ+) on the hydrogen atoms. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Formation of Hydrogen Bonds ▪ The partial positive charge on the hydrogen atoms of one water molecule can attract the partial negative charge on the oxygen atom of another water molecule. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  ▪ This attraction forms a hydrogen bond. ▪ Each water molecule can form up to four hydrogen bonds with surrounding water molecules: two through its hydrogen atoms and two through its lone pairs of electrons on the oxygen atom. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  WATER IS AN IDEAL BIOLOGIC SOLVENT ▪ Water's polarity and ability to form hydrogen bonds make it an excellent solvent for biological systems. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  ▪ Water's polarity allows it to dissolve ionic compounds and other polar molecules. The positive end of water molecules can surround negative ions, and the negative end can surround positive ions, effectively separating and dissolving them. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  ▪ Water’s capacity to form hydrogen bonds allows it to interact with a variety of molecules, including proteins, nucleic acids, and other biomolecules, stabilizing their structures and facilitating biochemical reactions. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Importance of Water ▪ Solvent Properties ▪ Temperature Regulation ▪ Transport Medium ▪ Structural Support ▪ Hydration and Homeostasis Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only 03 Acids and Bases  Acids ▪ The term acid comes from the Latin word acidus, which means “sour.” ▪ Swedish chemist Svante Arrhenius was the first to describe acids as substances that produce hydrogen ions (H+) when they dissolve in water. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only For example, hydrogen chloride ionizes completely in water to give hydrogen ions (H+), and chloride ions (Cl-). It is the hydrogen ions that give acids a sour taste, change blue litmus indicator to red, and corrode some metals. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Strong Acids ▪ An acid is strong if it completely ionizes (100%) in water. ▪ Form strong electrolytes. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Bases ▪ Are ionic compounds that dissociate into a metal ion and hydroxide ions when they dissolve in water. ▪ Most Arrhenius bases are formed from Groups 1A (1) and 2A (2) metals, such as NaOH, KOH, LiOH, and Ca(𝑂𝐻)2. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  For example, sodium hydroxide is an Arrhenius base that dissociates in water to give sodium ions (Na+), and hydroxide ions (OH-). A base turns litmus indicator blue and phenolphthalein indicator pink. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Strong Bases ▪ A base is strong if it completely ionizes (100%) in water. ▪ Form strong electrolytes. Examples: LiOH, NaOH, Ca(𝑂𝐻)2 , Mg(𝑂𝐻)2 , KOH Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Brønsted-Lowry Acids & Bases ▪ In 1923, J. N. Brønsted in Denmark and T. M. Lowry in Great Britain expanded the definition of acids and bases. A Brønsted-Lowry Acid is a proton (H+) donor. A Brønsted-Lowry Base is a proton (H+) acceptor. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Brønsted-Lowry Acids & Bases ▪ A free disassociated proton (H+) does not actually exist in water. It undergoes hydration just like other cations because it has a strong attraction to polar water molecules. The hydrated H+ is written as 𝐻3 𝑂 + and called hydronium ion. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only ▪ We can write the formation of a hydrochloric acid solution as a transfer of a proton from hydrogen chloride to water. By accepting a proton in the reaction, water is acting as a base according to the Brønsted–Lowry concept. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only What are the Brønsted–Lowry acid and base? Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Conjugate Acid-Base Pairs ▪ According to the Brønsted–Lowry theory, a conjugate acid–base pair consists of molecules or ions related by the loss or gain of one (H+). ▪ Every acid–base reaction contains two conjugate acid–base pairs because protons are transferred in both the forward and the reverse reactions. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only When the acid HA donates H+, the conjugate base A- forms. When the base B accepts the H+, it forms the conjugate acid BH+. We can write this as a general equation for a Brønsted– Lowry acid–base reaction as follows: Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Now we can identify the conjugate acid–base pairs in a reaction between hydrofluoric acid, HF, and water. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Identify the conjugate acid-base pairs of the reaction below: Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only 04 The pH Scale  The pH Scale ▪ On the pH scale, a number between 0 and 14 represents the [H3O+] for most solutions. ▪ In the laboratory, a pH meter is commonly used to determine the pH of a solution. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Calculating the pH and pOH of Solutions ▪ The pH/pOH scale is a logarithmic scale that corresponds to the [ 𝐻3 𝑂+ ]/[ 𝑂𝐻 − ] of aqueous solutions. ▪ Mathematically, pH/pOH is the negative logarithm (base 10) of the [𝐻3 𝑂+ ]/[𝑂𝐻 − ] 𝒑𝑯 = −𝐥𝐨𝐠[𝑯𝟑 𝑶+ ] 𝐩𝐎𝐇 = −𝐥𝐨𝐠[𝑶𝑯− ] Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Acid and Base Strength ▪ Can be expressed in the equilibrium, Ka pKa = -log Ka pKb = -log Kb Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Calculating the pH of Solutions For example a lemon juice with the [𝐻3 𝑂+ ] = 1.0𝑥10−2 𝑀 has a pH of 2.00. This can be calculated using the pH equation: 𝒑𝑯 = −𝐥𝐨𝐠[𝑯𝟑 𝑶+ ] pH = -log [1.0𝑥10−2 ] pH = - (-2.00) pH = 2.00 Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Calculating the pH of Solutions ▪ Because pH is a log scale, a change of one pH unit corresponds to a tenfold change in [𝐻3 𝑂+ ]. ▪ It is important to note that the pH decreases as the [𝐻3 𝑂+ ] increases. Soln A Soln B Soln C pH = 2.00 pH = 3.00 pH = 4.00 ▪ Soln A has a [𝐻3 𝑂+ ] 10x higher than B & 100x than C. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Calculating the pH of Solutions Determine the pH for the following solutions: 1. [𝐻3 𝑂+ ] = 1.0𝑥10−5 𝑀 2. [𝐻3 𝑂+ ] = 5 𝑥 10−8 𝑀 Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Calculating the pH and pOH of Solutions The [ 𝐻3 𝑂+ ] concentration in a solution is 4.0𝑥10−3 𝑀 (a) What is the pH of the solution? (b)What is the pOH of the solution? Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Calculating the pH and pOH of Solutions The [𝑂𝐻− ] concentration in a solution is 5.3𝑥10−4 𝑀. (a) What is the pOH of the solution? (b)Calculate the pH of the solution. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only 05 Buffers  Buffers ▪ A buffer is a solution that maintains pH by neutralizing added acid or base. Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Buffers ▪ In a buffer, an acid must be present to react with any 𝑂𝐻 − that is added, and a base must be available to react with any added 𝐻3 𝑂+. ▪ However, that acid and base must not be able to neutralize each other. Buffer = Combination of an Acid-Base Conjugate Pair Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Buffers ▪ Most buffer solutions consist of nearly equal concentrations of: Salt Containing Weak Acid Conjugate Base ▪ Buffers may also contain: Salt Containing Weak Base Conjugate Acid Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Buffers Indicate whether each of the following would make a buffer solution: A. HCl, a strong acid, and NaCl B. 𝐻3 𝑃𝑂4 , a weak acid C. HF, a weak acid, and NaF Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Henderson-Hasselbalch Equation Used to calculate the pH of the buffer solution Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Sample Problem What is the pH of a solution consisting of 0.75M 𝐻𝐶2 𝐻3 𝑂2 and 0.50M 𝑁𝑎𝐶2 𝐻3 𝑂2 ? Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Exercise What is the pH of a solution consisting of 0.15mol 𝑁𝐻4 𝐶𝑙 and 1.5mol N𝐻3 ? The Kb of 𝑁𝐻3 is 1.8𝑥10−5 Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Buffers in the Blood ▪ The arterial blood has a normal pH of 7.35– 7.45. If changes in 𝐻3 𝑂+ lower the pH below 6.8 or raise it above 8.0, cells cannot function properly and death may result. ▪ The 𝐶𝑂2 in our body dissolves as carbonic acid, and this weak acid dissociates to give bicarbonate and 𝐻3 𝑂+ Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Buffers in the Blood ▪ In the body, the concentration of carbonic acid is closely associated with the partial pressure of 𝐶𝑂2 Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only  Buffers in the Blood 𝐶𝑂2 𝐻2 𝐶𝑂3 /𝐻3 𝑂+ pH = ACIDOSIS 𝐶𝑂2 𝐻3 𝑂+ pH = ALKALOSIS Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only Prepared by: John Dale Mateo, MAEd For Exclusive Use of USLS Students Only