Biotechniques (BMS 34010A) Fall Semester 2023-2024 PDF

Biotechniques (BMS 34010A) Fall semester 2023 -2024 Dr. Tania Tahtouh [email protected] Acids & Bases  Learning outcomes  Distinguish between atoms and elements.  Distinguish between ionic and covalent bonds.  Define isotope and summarize its application in both medicine...

Biotechniques (BMS 34010A) Fall semester 2023 -2024 Dr. Tania Tahtouh [email protected] Acids & Bases  Learning outcomes  Distinguish between atoms and elements.  Distinguish between ionic and covalent bonds.  Define isotope and summarize its application in both medicine and biology.  Describe the properties of water.  Summarize the structure of the pH scale and the importance of buffers to biological systems.  Describe the four classes of organic molecules found in cells.  From atoms to molecules  Matter - anything that has mass and takes up space.  Elements - basic building blocks of matter; cannot be broken down by chemical means.  Over 90% of the human body is made up of only four elements: carbon (C), nitrogen (N), oxygen (O) and hydrogen (H). Carbon (C)  Atom-the basic structural unit of an element. It is the smallest unit of an element that retains the chemical properties of that element.  Atoms consist of three primary particles: protons, neutrons, electrons.  From atoms to molecules  Molecules - atoms bonded together. ▪ Can be made of the same atom or different atoms. That is, O2 , H2O.  Compounds—molecules made of different atoms. ▪ That is, H2O (not O2 ).  Two types of bonds join atoms: ionic bonds and covalent bonds.  Ionic bonding  Atoms are most stable when their outer electron shell, the valence shell, is full.  During an ionic reaction, atoms donate or take on electrons to fill their valence shell.  This results in the formation of positive or negative ions (charged particles). Ionic bond - the attraction between a positive and negative ion. Formation of an ionic bond  Covalent bonding  Each atom contributes one electron to the shared pair.  The electrons spend time in the valence shells of both atoms.  Double covalent bonds share two pairs of electrons; triple covalent bonds share three pairs.  Depicted by one, two, or three straight lines. Covalent bonds - atoms share electrons to fill their valence shells. Covalent bonds  Hydrogen bonds Polarity is a description of how different the electrical poles of a molecule are.  Water is a polar molecule.  Electrons spend more time around the oxygen than the hydrogens, creating a partial negative charge.  Hydrogen bond - attraction between a slightly positive hydrogen to a slightly negative oxygen or nitrogen. ▪ Relatively weak bonds. ▪ Depicted by dotted lines. Hydrogen bonds Water is a Solvent  It dissolves many substances.  Solution—water with dissolved solutes.  Salts dissociate or separate when dissolved in water, facilitating chemical reactions.  Water is a solvent  Polar molecules attract water, so are hydrophilic.  Nonpolar molecules DO NOT attract water, so are hydrophobic. ▪ In nonpolar covalent bonds, the electrons are shared equally (no partial charges).  Acids  Acids are substances that dissociate in water, releasing hydrogen ions (H+). ▪ That is, hydrochloric acid (HCl) is produced by the stomach and aids in digestion.  Bases  Bases are substances that take up hydrogen ions (H+)or release hydroxide ions (OH−). ▪ That is, sodium hydroxide (NaOH) is a strong base.  The pH scale  The pH scale is a measure of acidity or basicity (alkalinity) of a solution. ▪ Ranges from 0 (very acidic) to 14 (very basic). ▪ 7 is neutral - hydrogen ion (H+)concentration is equal to hydroxide (OH−) concentration. ▪ A pH below 7 is acidic (H+ is greater than OH−) and above 7 is basic (OH− is greater than H+). ▪ The concentration of hydrogen ions between each pH number changes by a factor of 10.  Buffers  Buffer - a solution that resists changes in pH when acids or bases are added to it. ▪ Important within the body or in the ecosystem, where pH values need to stay within a narrow range.  Buffers act to establish an equilibrium between a conjugate acid/base pair. Buffers consist of either: ▪ a weak acid and its salt (conjugate base) ▪ a weak base and its salt (conjugate acid)  Buffers can be destroyed by the addition of too much acid or base. Buffer capacity - a measure of the ability of a solution to resist large changes in pH when a strong acid or strong base is added. Biomolecules  Molecules of life  The four major organic molecules in the body: ▪ Carbohydrates. ▪ Lipids. ▪ Proteins. ▪ Nucleic acids.  Each is composed of subunits.  Molecules of life  Dehydration reaction - a type of synthesis  Hydrolysis reaction - the addition of water to chemical reaction that removes water, break macromolecules into their subunits. linking subunits together into macromolecules (large molecules).  Carbohydrates  Used as an energy source.  Simple carbohydrates (monosaccharides) are made of a single sugar molecule: ▪ Glucose. ▪ Fructose. ▪ Galactose.  Carbohydrates  Disaccharides are made of two monosaccharides joined by a dehydration reaction. Sucrose is table sugar Lactose is milk sugar  Carbohydrates  Polysaccharides (complex carbohydrates) - long polymers of glucose subunits. Starch Glycogen Cellulose  Proteins  Amino acids - the subunits of proteins.  Each consists of an amino group, a carboxyl group and an R group. Each amino acid differs in its R group.  Proteins  Polypeptide - three or more amino acids linked together.  Peptide bond - the polar covalent bond between two amino acids.  Shape of proteins  A protein’s 3-dimensional shape is closely linked to its function.  Denaturation - the change in the shape of a protein  Caused by extreme heat or pH.  Disrupts the protein’s function.  Lipids  Lipids are biomolecules that are soluble in nonpolar solvents  Found in the form of: ▪ Triglycerides (fats and oils). ▪ Phospholipids. ▪ Steroids.  Triglycerides  Made of one glycerol and three fatty acids.  Come in two forms: fats and oils ▪ Fats: usually animal origin & solid at room temperature. ▪ Oils: usually plant origin & liquid at room temperature.  Triglycerides are hydrophobic. Emulsifiers are molecules that surround triglycerides and disperse, or emulsify, them.  Phospholipids  Structure is similar to a triglyceride but one fatty acid is replaced by a polar phosphate group.  Have a polar, hydrophilic ‘head’ and nonpolar, hydrophobic ‘tails’.  Are the primary components of plasma membranes.  Steroids - precursor to other steroids like the sex hormones  Lipids made of four fused carbon rings.  Each type differs in the functional group attached to the rings.  Nucleic acids  Polymers of nucleotides composed of: ▪ a phosphate. ▪ a 5 carbon sugar. ▪ a nitrogenous base.  Nucleic acids, concluded: ▪ Deoxyribonucleic acid (DNA) ▪ Ribonucleic acid (RNA) Help regulate enzyme action Nucleotides are commonly identified by ▪ Components of coenzymes their base, since that is the only component ▪ Adenosine triphosphate (ATP) that differs within a nucleic acid. DNA compared to RNA Complementary base pairing Adenine always binds to thymine Cytosine always binds to guanine