MCDB 310 1st Edition Lecture 3 Outline of Last Lecture I. Water and its importance for lifeII. Non-covalent molecular interactionsa. Hydrogen bondsb. Ionic bondsc. Hydrophobic Interactionsd. Van Der Waals focesIII. Amphipathic CompoundsIV. pH, acids, bases, and buffersOutline of Current Lecture II. Protonated vs deprotonated: jargon for proteins, acids and basesII. Physiological buffersIII. Amino acids and proteinsa. Structure of 20 amino acids to memorizeIV. Ionization of amino acidsa. Amino acids with non-ionizable R groupsb. Amino acids with ionizable R groupsV. Formation of peptidesa. Polypeptide structure and function in the bodyCurrent LectureI. Protonated vs Deprotonated: jargon used for proteins, acids, basesThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.a. Remember: pH=pKa when the concentrations of the free acid andconjugate base are equalb. The free acid is called protonated, while the conjugate base is called deprotonatedc. Therefore, pH=pKa when the concentrations of the protonated species is equal to the deprotonated speciesi. pH > pKa —> concentration of deprotonated species is larger than the concentration of the protonated speciesii. pH < pKa —> concentration of the protonated species is larger than the concentration of the deprotonated speciesd. Physiological example: Histidine (an amino acid with a positive charge, protonated, acidic)i. at pH 5 (less than the pKa), the protonated species dominatesii. however, at pH 7 (greater than the pKa), the deprotonated species dominatesII. Physiological buffersa. The pH of the inside of the human body is 7.4b. It is important for the body to remain at or near this pH so that proteins do not denaturec. There are two main buffer systems in the human body: Phosphate buffer and the CO2/bicarbonate bufferi. Phosphate buffer: found in the cytoplasm and extracellular spacesii. CO2/Bicarbonate Buffer: found in plasma (blood), pH is near 7.41. It is not a very ideal buffer (the pKa=6.1 is outside the physiological pH range)2. Made up of 3 separate reactions (therefore, the pKa isthe product of the 3 individual pKas)3. Made up of a dissolution reaction, a hydration reaction, and a dissociation reaction (moving from left to right in above reaction)iii. Because the CO2/Bicarbonate buffer system is not very potent, alternative mechanisms for buffering in blood must be present1. Elimination of H+ by respirationa. Getting rid of CO2 on the products side of this reaction will drive the reaction forward, using up the H+ (acidic) ions and increasing basicity2. Production of H+ via secretion of bicarbonate as urinea. Getting rid of bicarbonate on the products side drives the reaction towards the products, increasing the amount of hydrogen ions produced (increasing acidity)d. Metabolic and Respiratory Acidosis: When the pH of the blood falls below 7.35i. Metabolic Acidosis: 1. Caused by severe diarrhea because the body is secreting bicarbonate at a very rapid rate, producing far more hydrogen ions than needed2. Symptoms: slow, deep breathing (trying to blow off CO2 and increase basicity)3. Cured by giving the patient bicarbonate to drive the reaction backwardsii. Respiratory Acidosis:1. Caused by impaired respiratory function (not breathing off enough CO2, hydrogen ions accumulate)iii. The opposite of acidosis is called alkalosis (when the pH of the blood is above 7.4)iv. Note: respiratory acidosis/alkalosis happens very quickly, whereas metabolic acidosis/alkalosis is much slowerIII. Amino acids and Proteinsa. Proteins are the main agents of biological functionb. Examples of important proteins in the body:i. For Catalysis: DNA Polymerase (vital for DNA replication) and Enolase (necessary in the glycolytic pathway)ii. For nutrient transport: hemoglobin (transports O2 in the blood) and lactose permease (transports lactose across thecell membrane)iii. For physical structure: Collagen (in connective tissue) and keratin (hair, nails, feathers, horns)iv. Motion at the intracellular level: myosin (muscle tissue) andactin (muscle tissue and cell mobility)c. Proteins are linear heteropolymers of amino acids (may have other molecules such as lipids and carbohydrates integrated into them as well)d. Important properties of amino acids:i. Capacity to polymerize into proteinsii. Some are useful as acids/bases (positively/negatively charged)iii. They have varied physical properties that allow for a large range of functionsiv. Their varied structures allow for a wide range of chemicalfunctionse. Structure of all amino acids onlyvary with the side chain (R)i. Common to all amino acids:1. Alpha Carbon (carbon to which 4 substituents are bonded, also a chiral center)2. NH3+: the primary amino group (basic)3. COO-: carboxyl group (acidic)4. Alpha hydrogen: bonded to the alpha carbon5. R group: side chain that differs between the different amino acidsii. All amino acids found in proteins are of the L formation (chirality) and have a tetrahedral geometry as shown in thediagram above1. Exception: Proline, alpha carbon loses tetrahedral geometry because or aromatic ring2. Exception: glycine, because the R group is just another Hydrogen, it is not chiraliii. Naming carbons on amino groups: always start with the alpha carbon and go down the R chain (beta, gamma, etc.)f. 20 Amino Acids (The structures, names, one letter codes, and three letter codes must all be memorized!)i. Non-polar aliphatic R groups (most commonly have hydrophobic interactions, except Glycine):1. Glycine (Gly, G)2. Alanine (Ala, A)3. Proline (Pro, P)4. Valine (Val, V)5. Leucine (Leu, L)6. Isoleucine (Ile, I)7. Methionine (Met, M)ii. Aromatic (All can participate in aromatic stacking-a summation of a few types of secondary bonding):1. Phenylalanine (Phe, F)2. Tyrosine (Tyr, Y)3. Tryptophan (Trp, W)iii. Polar, uncharged (all form hydrogen bonds):1. Serine (Ser, S)2. Threonine (Thr, T)3. Cysteine (Cys, C)-also forms disulfide bonds4. Asparagine (Asn, N)-amide form (CONH2) of Aspartate5. Glutamine (Gln, Q)-amide form(CONH2) of glutamateiv. Positively charged (Basic, can participate in hydrogen bonding and ionic interactions):1. Lysine (Lys, K)2. Arginine (Arg, R)3. Histidine (His, H)-positive charge is only visible when the pH is less than 7 and the nitrogen is protonatedv. Negatively charged (Acidic, participate in ionic bonding andhydrogen bonding):1. Aspartate (Asp, D)2.