Biochemistry Notes PDF

## Biochemistry * The application of chemistry in the study of biological processes at the cellular and molecular level. * Basic language of all biological sciences. ### Essential Bio-elements | Bio-elements | Essential Bio-elements | Bio-elements (Theramistic) | | :------...

## Biochemistry * The application of chemistry in the study of biological processes at the cellular and molecular level. * Basic language of all biological sciences. ### Essential Bio-elements | Bio-elements | Essential Bio-elements | Bio-elements (Theramistic) | | :----------------------------------- | :----------------------- | :------------------------- | | **Macro-elements (g/kg)** | | **(Theramistic)** | | - Oxygen (O) | - Nitrogen (N) | - Fluorine | | - Carbon (C) | - Phosphorus (P) | - Lithium | | - Hydrogen (H) | - Sulfur (S) | - Gallium | | - Sodium (Na) | **Trace elements (mg/kg)** | - Vanadium | | - Potassium (K) | - Iron (Fe) | - Nickel | | - Chlorine (Cl) | - Copper (Cu) | - Cobalt | | - Magnesium (Mg) | - Zinc (Zn) | - Selenium | | - Calcium (Ca) | | - Chromium | | **Ultra trace elements (µg/kg)** | | - Molybdenum | | - Selenium | | - Aluminum | | - Cobalt | | - Heavy metals | | - Chromium | | - Arsenic | | - Molybdenum | | - Cadmium | | - Manganese | | - Mercury | | | | - Lead | **Connection: A Two-way street** | Biochemistry | Medicine | | :---------- | :--------------------------------------- | | Nucleic acids | Genetic disease | | Proteins | Anemia, Sickle cell | | Lipids | Atherosclerosis | | Carbohydrates | Diabetes mellitus | **Bio-elements:** * Any chemical element that is found in the molecules and compounds that make up a living organism. * H (59%), O (24%), C (11%), N (4%), P (1%), S (0.1-1%). * **Role:** * **Structural role:** * **Catalytic role:** **Oxidative stress:** is an imbalance of free radicals and antioxidants in the body that leads to cell damage. * **Alzheimer disease** * **Heart disease** * **Accumulation of heavy metals like Lead & Cadmium:** The liver is found to have high levels of heavy metals like Lead & Cadmium in the liver of fish caught from the Tagris river in Baghdad. * **Lithium:** a drug element used for the treatment of Bipolar disorder, called a mood stabilizer. ## Hierarchy of Living Organisms 1. **Creation of monomers:** biomolecules (monosaccharides, fatty acids, amino acids, nucleotides, etc.) 2. **Creation of macromolecules:** (by condensation reactions we release water, H2O). 3. **Creation of supramolecular complex or organelles:** i.e. cell membrane or chromosome. 4. **The assembly of intracellular organelles & the creation of independent cells.** 5. **Creation of tissues, organs and different body systems.** ## **Water** **Significances:** 1. Solvent 2. Temperature regulator 3. Transportation 4. Maintaining pH balance 5. Chemical reactions * Polar molecule * Asymmetrical tetrahedral structure * Unique properties of H2O * ↑ B.P. and vaporization heat * ↑ surface tension * ↑ solubility capability * Forming H.B. with polar compounds. * Is water is acidic or basic? * Water acts as both acid and base, by donating and accepting protons. * Dissociation pH of an aqueous solution: K = 10^-14 at 25° C . * Having strong acid or base significantly dissociates in an acidic or basic environment. * When dissolved in water they completely dissociate into ions. ## Strong Chemical Bonds | Strong Chemical Bonds | Covalent Bonding | | :--------------------- | :----------------- | | Ionic Bond | Due to sharing | ## Weak Chemical Bonds | Weak Chemical Bonds | | | :----------------------------- | :---------------------------------------------------- | | → Hydrogen Bond | Electrostatic (Soft or weak) Bond | | → Vander Waals | Dipole-Dipole force | | → Hydrophobic interactions | Help folding and cell membrane integrity, and maintaining | ## Functional Groups | Functional Groups | | | :---------------- | :-------------------- | | R-OH | (Hydronel) | | R-C=H | (Aldehyde) | | R-C--R | (Ketone) | | R-SH | (sulfhydrid) | | R-NH2 | (Amine) | | R-N-R | (Imine) | | R-C-OH | (carboxyl) | | R-C-NH2 | (Amide) | | R-O-P-O | (Phosphoryl) | ## Chemical Isomers * **Chemical Isomers:** Have the same chemical formula but different structural formulas ### Types of Chemical Isomers * **Structural:** Differ in atom or functional group * **Stereiosomers:** e.g. are cis & trans isomers. **e.g:** Glucose & Fructose ## **pH = -10g[H+]** * **HCI, HNO3, H2SO4** Salution containing weak acids * They don't fully dissociate, only a small fraction split up into ions. * **e.g. Acetic acid**, CH3COOH , **Citric acid**, C6H8O7, **Carbonic acid**, H2CO3 **The term pH was introduced in 1909 by Sorensen:** It is the negative log of H+ ions concentration. **p** is known as power. * **Low pH values** Correspond to **High Conc. of H+ ions** * **High pH values** Correspond to **Low conc. of H+ ions** **Acids:** Proton donor. * **Strong acids:** HCl, H2SO4 * **Weak acids:** Many biochemcials are weak acids. But exception are: * **KOH, NaOH** Strong Base * **Ca(OH)2** Weak base. ## **pH + pOH = 14** * **Kw = Ion product:** Kw = [H+][OH-] = 10^-14 * **Log[H+] + Log[OH-]= 10g10^-14** * **pH + pOH = 14** **To solve:** [OH-] = 4.0x10^-10 **pH + pOH** **pOH = -pH** **pOH = -log[OH-]** **= -log(4.0x10^-10)** **= ( log(4.0) - log(10^-10))** **= -0.60 + 10** **= 0.6 + 4.0** **=3.4** **Now: pH = 14- pOH** **=14 - 3.4** **=10.6** ## pKa * **The pKa of an acid group is the pH at which the protonated and unprotonated species are present at equal concentration.** * **The Henderson-Hasselbalch Equation:** This equation is derived below when a weak acid HA, ionizes as: HA ⇌ H+ + A- The equilibrium constant will be: Ka = [H+][A-] / [HA] * **1: When acid is exactly half neutralized [A] = [HA]** [A-] / [HA]= 1 pH= pKa + log([A-] / [HA]) pH = pKa + Log(1) pH = pKa+0 pH= pKa * **2: When that ratio** **[A-] / [HA] = 100/1 =100/1** pH= pKa + log([A-] / [HA]) pH = pKa + (log(100)) pH = pKa+2 * **3: When ration is (1/10)** [A-] / [HA] = ( 1/10) pH= pKa + log([A-] / [HA]) pH = pKa + Log(0.1) pH = pKa + log(-1) pH = pKa - 1 ## Buffer Solutions & pH Changes * **Buffering** is the ability of weak acids and their conjugate bases to resist the change in pH after the addition of strong acids or base. **Laboratory Buffers:** * **MES (2-N-morpholinoethanesulfonic acid, pKa = 6.1).** * **HEPES:** N-hydroxyethyls piperazine N-2-ethanesulfonic acid. pKa = 7.2 * **Inorganic orthophosphate:** pKa = 7.2 * **Tris (tris [hydroxymethyl] aminomethane)** pKa = 8.3 ### **Assignment # 1:** **What is meant by residue in the Biochemistry?** * It refers to a single unit within a polymer such as amino acids in proteins or a nucleotide in nucleic acids. * Once monomers form a polymer chain, they are called residues. #### Types: 1. **Amino Acid residue:** individual amino acid within a protein after peptide bond formed 2. **Nucleotid residue:** in DNA by phosphoolbester bond ### **Assignment #2:** **Q: Acetic acid = 400mM, Sodium acetate = 400mM, pKa of acetic acid = 4.8, What is the pH?** **PH: pH = pKa + Log(acid/salt)** pH = 4.8 + log(400x10^-3) / (400x10^-3) PH= 4.8+ log(10^3) / 10^3 **pH = 4.8 + 3** So, in a buffer solution **PH will not be changed**. ## **Chapter 12: Distribution of water in Body.** | | | | :-- | :----------------------------------------------------------- | | **Body** | **Inner cell (Intracellular) 65%** | | | **Extracellular 40%** | | **Transcellular Fluids:** | It is a fluid separated from plasma by epithelium | **It includes:** 1. **Synovial** 2. **Peritoneal** 3. **Pericardial** 4. **Intraocular** 5. **Cerebrospinal** ### **Disorder of body water values:** | | | | :-------------------------- | :-------------------------------------------------------------------------------------------- | | **Overhydration (water intoxication)** | Occurs when there is excessive fluid intake. | | **Dehydration** | Refers to the reduction of ECF volume within the vascular system and tissue. | ## **Primary Electrolytes in Body** ### **Sodium: (Na)** * **Maintain the osmotic pressure of ECF:** * **Preserve the electrically neutral state of ECF.** * **Normal concentration in plasma:** = 135-145 mmol/L * **Na reabsorption from nephrons:** almost nearly equal to 99%. * **Sodium Balance:** * **Negative Na balance:** If excretion of Na is greater than intake of Na, it will decrease Na content in ECF, ECF volume, and arterial pressure. * **Positive Na balance:** If excretion of Na is less than intake of Na, then it will increase Na content in ECF, blood volume, that can cause Edema. ### **Edema:** **Types:** 1. **Sodium imbalance** 2. **Diabetes insipidus (DI)** **Causes:** * **Destruction** of neurohypophyseal neurons or **mutation** in AVP (arginine vasopressin or ADH) * **Result:** ↑ Decrease ADH from pituitary ## Diabetes 1. **Neprogenic Lepipidus:** * Decreased response to ADH, or mutation in Aquaporin channels. ### Control of Blood pH * **Types of Potassium imbalance:** * **Addition of weak acid (H2CO3):** Carbonic anhydrase potentially converts HCO3- to CO2. * **Addition of weak base (OH-):** Carbonic anhydrase potentially converts CO2 to HCO3-. ## Potassium Imbalance & Cardiac Function * **Potassium imbalance** should be carefully monitored and corrected to prevent arrhythmias & associated complications. * **If a patient presents with symptoms of bradycardia or tachycardia, it is crucial to evaluate potassium levels as part of a diagnostic process.** ### Chloride * **Normal concentration:** = 99-109 mmol/L * **Present in primary diets of Na & K salts:** * Absorbed & digested in a similar manner to sodium. * Reabsorbed in sweat glands in response to aldosterone. ### Hypochloremia & Hyperchloremia * **Hypochloremia: ** ↑ Blood chloride concentration. Often associated with **hyponatremia**. * **Hyperchloremia: ** ↓ Blood chloride concentration. Often associated with **hypernatremia**. ## Acid-Base Balance * **Homeostasis of H+ ion is critical** * **Phosphate buffer system:** A strong buffer capacity. * **Normal H+ ion in serum:** = 36-44, physiological nanomolar with a pH of **7.35 to 7.45**. * **Come physiological conditions influence H+ ion homeostasis:** ( acidosis & alkalosis) ### Bicarbonate/Carbonic Acid Buffer system: * **Exhibit a weak buffering capacity:** It serves as the most important buffer in the blood. * **Component includes:** a weak acid (carbonic acid) and its conjugate base (bicarbonate). * Under physiological conditions, the concentration of bicarbonate in blood is 20 times greater than that of carbonic acid. ### Protein buffer systems * **Made up of amino acids:** Includes hemoglobin, which works in blood and ISF. * **Carbonyl group gives H+: ** * **Amino group accepts H+: ** Side chains that can buffer H+ are present on amino acids. ### Bone tissue as a buffering system * **Contribute to ↑ of blood pH:** * By absorbing H+ ions and releasing cationic electrolytes * The absorption of cations such as hydrogen by bone leads to the demineralization of bone tissue and ↑ risk of kidney stone formation. * **Can eliminate large amounts of acid:** * **Can conserve and produce bicarbonate ions:** * **Most effective regulator of pH balance:** If kidneys fail, then pH balance fails. ## Respiration Regulation * **Exhalation of CO2:** * **Body pH can be adjusted** by changing rate and depth of breathing. * **CO2 + H2O ⇌ H2CO3 + H+** ## Renal Regulation * **Regulation of H+ ion excretion** in proximal and distal tubule. * **Regulation of bicarbonate reabsorption** in both the renal tubule.