BCHM 3050 1st EditionExam # 1 Study Guide Lectures: 1 -10Lecture 1 (January 7)The Effects of BiomoleculesWhat are the five major functional groups that make up the biomolecules, such as nucleic acids, amino acids, and monosaccharaides? Specifically, which of these function groups are in the eachof the three biomolecules mentioned above?Five major functional groups:-OH = Hydroxyl-NH2 = Amino-COOH = carboxylic acid-CO = carbonyl-POOH = Phosphate groupNucleic acids contain:- hydroxyl, amino, carbonyl, phosphate groupsAmino acids contain:- amino group and carboxylic acidMonosaccharaides contain:- hydroxyl and carbonyl groupsLecture 2 (January 9)The Properties and Importance of WaterWhy is water considered the ideal biological solvent? Name five different properties that give water this important role.1.) Partial negative of water attracts other positive ions and partial positive of water attracts other negative ions à Dissociation of solute (ions are surrounded by molecules)2.) CH4 is hydrophobic because it doesn’t normally have partial charges on its atoms (but water can still be used to dissolve it)3.) Cohesion - water molecules remain together because of strong hydrogen bonds4.) Adhesion - water interacts with other surfaces (plays role in capillary action of plants)5.) Surface Tensioni. allows some organisms to be able to walk on waterii. Based on hydrogen bonding of wateriii. Tension of the surface of the water bodyiv. One molecule of water participates in hydrogen bonding with four other moleculesv. Force exerted by the molecules at the surface is weakervi. The pull downwards is stronger than the pull upwardsLecture 3 (January 12)Molarity, Osmotic Pressure, and pH CalculationsWhat is the formula for molarity?Molarity (M) = moles/literWhat is the formula for osmotic pressure?Osmotic pressure: Π = iMRT- Π is the osmotic pressure in atm- i = van 't Hoff factor of the solute.- M = molar concentration in mol/L- R = universal gas constant = 0.08206 L·atm/mol·K- T = absolute temperature in K ( 273.15+ temp in Celcius)How is pH used to measure hydrogen ion concentration?pH = -log[H+]pH + pOH = 14Lecture 4 (January 14)Acids, Bases, and BuffersWhat is the difference between a weak acid and a strong acid?Weak acids dissociate but not completely, while strong acids dissociate completely.What two components make up the ideal buffer?Equal concentrations of a weak acid and its conjugate baseWhat is the Henderson-Hasselbalch Equation?pH = pKa + log [A-/HA]Lecture 5 (January 16)How to Find Isoelectric PointsHow do you find the pI (Isoelectric Point) of acidic amino acids?pI of acidic amino acid = average the pK of the 2 carboxylic acid group (DO NOT take into account the pK of the amino group)How do you find the pI for basic amino acids?For Basic amino acids, pI = (pK-2 + pK-3)/2. Ignore the pK-1 value.Lecture 6 (January 21)Amino Acids and Non Standard Amino AcidsWhat is the difference between an essential amino acid and an non-essential amino acid?Essential – necessary in our diet but our body doesn’t make them so we must ingest themNon-essential – synthesized by the body as break down products How many non-standard amino acids are there? Why are they considered “non-standard”?There are about 300 “non-standard” amino acids. Most are non-protein amino acids. Many are modifications of the standard amino acids. A few are found in proteins. All have “special” biological functionsLecture 7 (January 23)Protein Structure and Torsion AnglesDescribe the difference between primary structure, secondary structure, and tertiary structure of proteins.Primary structure – specific amino acid sequence of the proteinSecondary structure – alpha helix or beta pleated sheet; beta alpha beta is also an example of a supersecondary structure.Tertiary structure – group of secondary structures formed by R group interactions; stabilized by hydrophobic interactions, electrostatic interactions, hydrogen bonds, and covalent bonds.What are the three different types of torsion angles that determine how the protein will look in the end?Phi – refers to the bond rotation between the alpha carbon and the nitrogenPsi – bond rotation between alpha carbon and carbon 1Omega – bond contortion between carbon 1 and other nitrogenLecture 8 (January 26)Protein Folding and Molecular ChaperonesDescribe the steps involved in protein folding.Protein folding cannot occur on its own – requires a lot of energy from the body. It starts with ribosomes translating. Hsp70 attacks the protein à initiates the process of protein with ATP (ATP = energy currency of the body; more ATP molecules means more energy to store). ATP is broken down into ADP, releasing energy to fold the protein. Folded protein handed over to Hsp60 complex (GroEL barrel) àenzymes assist. 7 molecules of ATP are broken down and GroESis added and the lid of the barrel is shut. Folding occurs, organic phosphates are released. Lid comes off and the folded protein in releasedWhat is the role of molecular chaperones? What does “heat shock proteins” refer to?Chaperones surround, guide the proteins and help them to fold. Heat is one form of stress that our body is exposed to easily – chaperones are trained to resist this temp (“heat shock proteins”). Most chaperones are heat shock proteinsLecture 9 (January 28)Fibrous vs. Globular ProteinsWhat are the different functions of fibrous and globular proteins?Fibrous proteins function as structural support systems, while globular proteins function as transport mechanisms.How does the oxygen affinity of hemoglobin and myoglobin differ? Why does this happen?Hemoglobin has a lower affinity to oxygen because it has more oxygen binding sites than myoglobin. This allows for the hemoglobin to release the oxygen to the myoglobin in the tissues. On the other hand, the affinity for oxygen is much higher in myoglobin due to the fact that it has only one oxygen-binding site.Lecture 10 (January 30)The Function of EnzymesWhat is an enzyme? It is a biological catalyst that functions to speed up the rate of a biological reaction, but is not altered or consumed in the reaction. Enzymes are usually proteins, but not always.What is the difference between a substrate and a product? What an active site?Substrates are the substances that enzyme act on, also known as reactants. On the other hand, products are the substances produced by chemical modification of the substrate.The active site is the specific region
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