BCH 361 Exam I Study Guide Spring 2025 PDF

BCH 361 Spring 2025 Exam I Study Guide Chapters Covered: 1. Introduction to biochemistry 2. Water, weak bonds and acid-chemistry 3. Amino acids 4. Peptides & proteins 6\. Basic concepts of enzyme action 7\. Enzyme Kinetics Chapter 1. 1. Organic life forms are distinguished...

BCH 361 Spring 2025 Exam I Study Guide Chapters Covered: 1. Introduction to biochemistry 2. Water, weak bonds and acid-chemistry 3. Amino acids 4. Peptides & proteins 6\. Basic concepts of enzyme action 7\. Enzyme Kinetics Chapter 1. 1. Organic life forms are distinguished from other in-animate matters by their high carbon content. 2. There are four classes of biomolecules a. Protein -- polymers of amino acids. b. Nucleic Acid -- polymers of nucleotides. c. Lipids -- amphipathic molecules d. Carbohydrates -- polymers of monosaccharides. 3. Lipids do not need to polymerize because their amphipathic nature allows them to self-assemble into "bilayers", which can act as barriers separating one cellular compartment from another. 4. What is the central dogma of biology? 5. Unique characteristics of prokaryotic cells include: e. no organelles. f. possess a cell wall. 6. Eukaryotic cells contain the following major organelles: g. Nucleus -- store genetic information. h. Rough ER -- synthesize membrane proteins. "Rough" because their surface is decorated with ribosomes. i. Smooth ER -- fatty acid metabolism. j. Mitochondria -- energy metabolism. Chapter 2. 1. Water molecules are polar. The partially negative oxygen attracts partially positive hydrogens from another water molecule, forming ordered clusters of water molecules. Water can solubilize charged or polar molecules, but not non-polar, hydrophobic molecule. 2. Four types of weak interactions are commonly found in biological systems. a. Hydrogen bonding. Forms between a hydrogen-bearing atom capable of accommodating significant negative charge (H-bond donor) and an electronegative atom (H-bond acceptor). Hydrogen bearing N and O are good H-bond donors. N and O are also good H-bond acceptor. Carbons are not good H-bond donors or acceptors. b. Electrostatic interactions. Attractions between charged molecules. c. Van der waals interactions. Weak forces that take place between non-polar molecules at close distances. Important for non-polar molecules. d. Hydrophobic effect. NOT A FORCE. Manifestation of the entropic effect that maximizes the number of disordered water molecules. 3. Functional groups. Please learn to recognize the following functional groups e. Amino groups. f. Carboxyl groups g. Aldehydes. h. Ketones i. Sulfhydryl j. Phenyls 4. Acid-Base Chemistry k. What is the definition of pH and pKa? l. What is the Henderson-Hasselbach equation? How do you use it? m. Given the pKa of a compound or functional group, can you deduce its protonation state at a specific pH? n. The following terms will be used interchangeably: i. Acid form \ protonated form. ii. Base form \ deprotonated form. o. Given the pKa of a compound and the ratio of its conjugate base to its acid form, can you calculate the pH of the solution? p. The following rules of thumb can be utilized to estimate the protonation state of a compound: iii. If pH is 1 pH unit above pKa, the conjugate base (deprotonated) form dominates. iv. If pH is 1 pH unit below pKa, the acid (protonated) form dominates. v. If pH is equal to pKa, the concentrations of conjugate base and acid are equal. Chapter 3. Amino Acids 1. What is the basic template shared by all amino acids? 2. Can you recognize the correct chirality of an L-amino acid and draw the correct arrangements of the substitutions on the Cα atom? 3. What are the charges of the α-amino and α-carboxyl groups at pH 7.4? Compounds that possess both positive and negative charges on them are called zwitterions. 4. Do you know the names of all 20 amino acids and their three letter abbreviations? 5. Amino acids are classified into four categories. Do you know which amino acids belong in each category? a. Hydrophobic (not including Gly) b. Polar c. Positively charged (basic) d. Negatively charged (acidic) 6. Which amino acid has pKa closest to the physiological pH? 7. Which are aromatic amino acids? Which amino acid is a cyclic amino acid but not an aromatic amino acid? Which amino acid does not have a chiral Cα atom? 8. What are the characteristics of essential and non-essential amino acids? (Essential amino acids usually contain big and complicated side chains, such as branched hydrophobic amino acids, or aromatic amino acids) Chapter 4. Peptides and Proteins 1. Peptide bond -- Amide bond formed between two amino acids through a dehydration reaction that connects α-carboxyl of one amino acid and α-amino of another amino acid. 2. Peptides have polarity. The end with the free α-amino group is called the N-terminus and the end with the free α-carboxyl group is called the C-terminus. 3. Peptide backbone. Three atoms (N-Cα-C) from each amino acid in the peptide are connected through the peptide bond to form a linear chain that extends through the entire peptide. This long linear chain is referred to as the backbone. 4. Disulfide Bridge -- two cysteines can be oxidized to form a sulfur-sulfur bond between them known as the disulfide bridge or disulfide bond. This bond is important in connecting different parts of the protein and connecting different polypeptide chains. 5. Peptide Plane -- The C-N bond in a peptide bond is hindered from rotation due to resonance structures that give the C-N bond characters of a double bond. This means the four atoms Cα-C-N-Cα must lie in the same plane. This is known as the peptide plane. Furthermore, the two Cα atoms must be on different sides of the bond to avoid steric clashes. In this configuration, the peptide bond is said to be in the "trans" conformation. 6. Torsion angles -- There are two types of rotatable bonds in the backbone. Rotation of the N-Cα bond controls the value of the φ angle and rotation of the Cα-C bond controls the value of the ψ angle. 7. Primary structure -- Primary structure refers to the chemical structure of the peptide, ie. its amino acid sequence. 8. Secondary structure -- conformational motifs of short stretches of peptides commonly found in proteins. There are two major types: a. α-helix. Backbone forms a helical structure. i. Stabilized by H-bonds between backbone carbonyl oxygen of one amino acid (residue i) and amide nitrogen of another amino acid that is 4 residues closer to the C-terminus (residue i+4). ii. Very compact, neighboring Cα atoms are only 1.5 Å apart. b. β-sheet. Backbone is almost fully extended. iii. The separation between neighboring Cα atoms is much larger than α-helical structures (3.5 Å). iv. β-sheets always contain two or more strands so that neighboring strands can stabilize one another with H-bonds between backbone carbonyl oxygen on one strand and amide nitrogen on the other. v. The strands in a sheet can be arranged with opposite polarity (anti-parallel, the N-termini are on opposite ends of the sheet) or identical polarity (parallel, the N-termini are on the same end of the sheet) 9. Tertiary structure -- arrangement of secondary structural elements into a compact shape. The main driving force for tertiary structure formation is the hydrophobic effect. 10. Quaternary structure -- Multiple polypeptide chains can come together and form a complex. Chapter 6. Introduction to enzymes. 1. Enzymes are catalysts: a. They change the rate of the reaction, but not its equilibrium (ratio of products to reactants). b. They are not used up in the reactions. 2\. Equilibrium constant of a reaction is determined by the free energy change of a reaction (ΔG). The equilibrium constant is related to ΔG by the following equation: K~eq~=exp(-ΔG/RT), where R is the ideal gas constant and T is temperature in Kelvin. 3. Enzymes are able to speed up the reaction by lowering the energy barrier to reach the transition state (lowering the activation energy). 4. Formation of enzyme-substrate complex is crucial to the efficiency of the enzyme. Weak interactions are the main driving force behind the formation of these complexes. 5. Active site of an enzyme is where the substrate binds and where the reaction is catalyzed. 6. Specificity of enzyme for substrates can be explained by two models. a. The Lock-and-Key model, which stipulates the active site must be perfectly complementary to the substrate. b. The Induced Fit model, which says binding of substrate to the active site will change its shape to produce a better fit for the substrate. 7. Cofactors -- molecules required by enzymes to catalyze the reaction. There are two types: c. Vitamin-based compounds. d. Metals Chapter 7. Enzyme Kinetics 1. What is the Michaelis-Menten equation? What is the definition of the parameters V~max~ and K~M~? 2. What is the value of V~0~ when substrate concentration is equal to K~M~? (half of V~max~) What do the magnitudes of K~M~ tell us about enzymes' affinities for their substrates? 3. Make sure you are comfortable with calculating K~M~ or V~max~ using the Michaelis-Menten equation. 4. What is the Lineweaver-Burk plot? What do the slope, the X-intercept and the Y-intercept represent? You should be able to calculate K~M~ and V~max~ given any two out of the three plot features (X-intercept, Y-intercept & slope). To help you perform the calculations, here are some equations relating V~max~ and K~M~ to the plot features: a. V~max~=1/(Y-intercept) b. K~M~=-1/(X-intercept) c. V~max~=K~M~/slope = -1/(X-intercept\*slope) d. K~M~=V~max~\*slope = slope/Y-intercept 5. How will the Lineweaver-Burk plot change if we change K~M~? V~max~? 6. What are the unique features of allosteric enzymes? There are two of them: e. Binding of molecules at other sites on the protein will affect active site catalysis. f. Change in a single catalytic unit can affect other catalytic units. 7. How does the reaction velocity plot of an allosteric enzyme differ from a Michaelis-Menten enzyme? (hyperbolic vs. sigmoidal) 8. What is the concerted model of allosteric enzyme kinetics? What are the assumptions in the model? g. Enzymes adopt two states: i. T-state, more stable, less active. ii. R-state, less stable, but more enzymatically active, and is stabilized by substrate binding. h. Enzymes form a complex, and conversion of one enzyme from T- to R-state will lead to conversion of other enzymes in the complex also. \ [\$\$\\mathbf{pH = pKa + log}\\frac{\\mathbf{\\lbrack}\\mathbf{A}\^{\\mathbf{-}}\\mathbf{\\rbrack}}{\\mathbf{\\lbrack HA\\rbrack}}\$\$]{.math.display}\ \ [\$\$\\mathbf{K}\_{\\mathbf{\\text{eq}}}\\mathbf{=}\\mathbf{e}\^{\\mathbf{-}\\frac{\\mathbf{\\mathrm{\\Delta}G}}{\\mathbf{\\text{RT}}}}\$\$]{.math.display}\ \ [**V**~**max** ~**=k**~cat~\[**E**\]~**T**~]{.math.display}\ \ [\$\$\\mathbf{K}\_{\\mathbf{M}}\\mathbf{=}\\frac{\\mathbf{k}\_{\\mathbf{- 1}}\\mathbf{+}\\mathbf{k}\_{\\mathbf{2}}}{\\mathbf{k}\_{\\mathbf{1}}}\$\$]{.math.display}\ \ [\$\$\\frac{\\mathbf{1}}{\\mathbf{V}\_{\\mathbf{0}}}\\mathbf{=}\\frac{\\mathbf{1}}{\\mathbf{V}\_{\\mathbf{\\max}}}\\mathbf{+}\\frac{\\mathbf{K}\_{\\mathbf{M}}}{\\mathbf{V}\_{\\mathbf{\\max}}}\\frac{\\mathbf{1}}{\\mathbf{\\lbrack S\\rbrack}}\$\$]{.math.display}\