CHEM 301/ CHEM301 Midterm Examination | Biochemistry – 2026/2027 Academic Year – Questions with Verified Answers and Elaborated Solutions

CHEM 301/ CHEM301 Midterm Examination | Biochemistry – 2026/2027 Academic Year – Questions with Verified Answers and Elaborated Solutions Q: When monosaccharides cyclize, they form: a) enantiomers b) D- and L forms c) ester bonds d) alpha and beta anomers e) chair and boat forms alpha and beta anomers Q: Which of these pairs of carbohydrates are epimers? a) glucose and galactose b) alpha-glucose and beta-glucose c) D-glucose and L-glucose d) cellulose and cellibiose e) glucose and lactose glucose and galactose Q: In DNA and RNA the bases and monosaccharide units are linked to each other by: a) amide bonds b) O-Glycosidic bonds c) N-glycosidic bonds d) acetal bonds e) savings bonds N-glycosidic bonds Q: The aldotetroses have two asymmetric centers and ______ stereoisomers. a) 2 b) 4 c) 8 d) 16 e) 32 4 Q: Which of the following is NOT a common characteristic of most of the fatty acids that are present in the cell membrane? a) they are all highly saturated b) they tend to be liquid at body temperature c) they have relatively higher molecular weights (16-24 carbon atoms) d) they often have even numbers of carbon atoms e) they are often unsaturated or polyunsaturated they are all highly saturated Q: Which process converts unsaturated fats to saturated fats: a) acetylation b) oxidation c) hydrogenation d) hydrolysis e) dehydration hydrogenation Q: The phosphoglycerols do NOT contain _____. a) sphingosine b) phosphate c) choline d) glycerol e) fatty acid sphingosine Q: The saturated fatty acids: a) lower cholesterol levels in humans and prevent atherosclerosis b) some of them cannot be degraded by humans c) they generally need to be provided in the diet d) they are often solid at body temperature and have much higher melting points than the corresponding unsaturated fatty acids e) they are usually not found in triacylglycerol compounds they are often solid at body temperature and have much higher melting points than the corresponding unsaturated fatty acids Q: The lipids in biological membranes are mostly: a) phospholipids and cholesterol b) triacylglycerols and cholesterol c) triacylglycerols and phospholipids d) fatty acids and triacylglycerols e) fatty acids and polyisoprenoids phospholipids and cholesterol Q: Which monosaccharide units are found in DNA? a) glucose b) fructose c) ribose d) 2-deoxyribose e) mannose 2-deoxyribose Q: What generally happens as an enzyme is purified? a) The specific activity decreases b) The turnover number decreases c) The specific activity increases d) The turnover number increases e) The specific activity stays the same the specific activity increases Q: An enzyme with a low Km: a) Has a low turnover number b) Is active at low substrate levels c) Is active only at high substrate levels d) Has a low equilibrium constant e) Has a high energy of activation is active at low substrate levels Q: What does the turnover number tell us about an enzyme and its reaction kinetics? a) How many molecules of product can be formed per second per active site b) Whether the enzyme has a high or low Km c) Whether the enzyme is stable or fragile d) How much product is formed at equilibrium e) Whether the reaction has a high free energy change How many molecules of product can be formed per second per active site Q: The observed Vmax of an enzyme will stay the same when______. a) A noncompetitive inhibitor is added b) An irreversible inhibitor inactivates half the enzyme and leaves the other half fully active c) A competitive inhibitor is added d) The amount of enzyme in a sample is raised e) The amount of enzyme in a sample is lowered a competitive inhibitor added Q: If the movement of a substrate across a membrane is mediated by an active transport protein ____. a) The process will increase in a liner manner with substrate concentration and will not be saturable b) The process will never be concentrative c) The process will not be affected by inhibitors d) The process will not be stereospecific e) The process will be able to concentrate a substrate the process will be able to concentrate a substrate Q: The type of concentrative transport system that uses the downhill flow of an ion to drive the uphill movement of a substrate in the opposite direction is? a) a primary active transport system b) a facilitated diffusion system c) a uniport transport system d) a symport transport system e) a antiport transport system a antiport transport system Q: Integral membrane proteins ______. a) are highly hydrophobic b) never span the membrane c) are relatively easy to remove from the membrane d) usually contain a high percentage of polar and ionic amino acids e) are generally very soluble in water are highly hydrophobic Q: Which is NOT a predominant function of cholesterol? a) Precursor of steroid hormones b) Precursor of bile acids c) Membrane component d) Component of fatty plaques that cause heart attacks and strokes e) Precursor of prostaglandins Precursor of prostaglandins In the presence of a competitive inhibitor: a) The Vmax stays the same and the Km increases b) The Vmax decreases and the Km stays the same c) Both the Km and the Vmax decrease d) The Km increases and the Vmax decreases e) Both the Km and Vmax increase the Vmax stays the same and the Km increases Which base is found in DNA but not in RNA: a) Adenine b) Cytosine c) Uracil d) Guanine e) Thymine thymine In the cofactor FADH2 the oxidation-reduction reactions all take place on the a) adenine b) phosphate c) ribose d) nicotinamide ring e) flavine (isoalloxazine) ring flavine (isoalloxazine) ring In the catalytic triad of chymotrypsin which amino acid is nearest to and interacts with the active site serine? a) threonine b) alanine c) aspartate d) histidine e) glycine histidine Which of the following refers to the relatively stable covalent intermediate in the mechanism of chymotrypsin _________? a) Acyl-enzyme b) Tetrahedral oxyanion c) Delocalized phenyl d) Superoxide acetyl e) Cationic amino acyl-enzyme In the mechanism of chymotrypsin the active site serine acts as? a) An electron acceptor b) A nucleophile c) An cationic reservoir d) A Schiff's base e) A free radical the nucleophile Which statement is NOT true about the binding of substrate and intermediates to an enzyme active site: a) It is reversible b) It can be covalent or noncovalent c) It involves interactions with active site amino acid R groups d) It may not be as tight as the binding of the enzyme to the transition state intermediate e) It is extremely tight with a very strong binding constant and involves a very low energy well it is extremely tight with a very strong binding constant and involves a very low energy well What inorganic ion binds oxygen in the heme cofactor of hemoglobin? a) Mg++ b) Cu+ c) Mn++ d) Zn++ e) Fe++ Fe++ Which of the following statements about catabolic pathways is NOT true? a) Catabolism refers to metabolic pathways that convert complex biomolecules or polymers into simpler products b) catabolic products include carbon dioxide, water and urea c) catabolic pathways are generally oxidative d) highly reduced carbon compounds often yield high amount of energy in catabolic pathways e) compounds with a high content of nitrogen yield a high amount of energy in catabolic pathways compounds with a high content of nitrogen yield a high amount of energy in catabolic pathways Which of the following statement about general metabolism is NOT true? a) Biosynthetic anabolic pathways generally require energy from ATP b) ATP is generated during the catabolism of reduced organic compounds c) NADH is generated during the oxidative catabolism of reduced organic compounds d) NADH is used to produce ATP by the oxidative phosphorylation e) NADPH is used as an oxidizing agent in catabolic pathway NADPH is used as an oxidizing agent in catabolic pathway Which of the following is NOT a common substrate for energy production in catabolic pathways? a) lipids b) carbohydrates c) proteins d) nucleotides e) monosaccharides nucleotides Which is NOT true about hemoglobin and myoglobin? a) Both are heme proteins b) Both bind oxygen c) Hemoglobin is in the blood and myoglobin is in the muscle d) Both exhibit the same oxygen binding curve e) Both have similar amino acid sequences and are derived from the same evolutionary precursors Both exhibit the same oxygen binding curve Which lipoprotein faction contains the highest triacylglycerol content, has the lowest density, and forms the largest particles? a) VLDL b) LDL c) IDL d) HDL e) Chylomicrons chylomicrons Hemoglobin is an allosteric protein and it shows a _______ oxygen binding response. a) Relaxed b) Tight c) Sigmoidal d) Hyperbolic e) Biphasic sigmoidal UNIT 1 Define "biochemistry." the study of the building blocks, or molecules, of life and how these interact in the processes that occur in living organisms. Name the major classes of biomolecules, and identify the atoms most commonly found in each class. - proteins (amino acids) - carbohydrates or polysaccharides (monosaccharides or simple sugars) - lipids (fatty acids) - nucleic acids (nucleotides). Define "metabolic pathway." linked series of chemical reactions occurring within a cellular processes List the 6 elements that make up 99% of living cells CHNO CP carbon, hydrogen, nitrogen, oxygen, calcium, and phosphorus. Identify some applications of biochemistry. medicine (causes and cures of diseases) nutrition (maintain health and wellness, nutritional deficiencies) agriculture (soil and fertilizers) What are the four elements most commonly found in biomolecules? carbon (C), oxygen (O), hydrogen (H) and nitrogen (N) Describe the organization of Eukaryotic Cells and Prokaryotic Cells How does the composition of the earth's crust and living cells differ? The earth's crust is mostly composed of Oxygen, Aluminum, Silicon, and Iron. Living cells are mostly composed of C, H N, O. Two elements found in the earth's crust, Si and Al, are not found in living matter. What is the function of the following organelles? Golgi apparatus, lysosome, ribosomes, mitochondria, cytoskeleton Golgi apparatus - protein assembly and secretion lysosomes - digestion of proteins ribosomes - synthesize proteins mitochondria - synthesize ATP cytoskeleton - provides support and structure to the cell. Where are sugars and fats digested in the cell? Sugars and fats are partially digested in the cytoplasm. They are then transported into the mitochondria, where they are converted into ATP. List the differences between prokaryotic and eukaryotic cells in terms of the following: nucleus internal structures cytoskeleton DNA organization Reproduction Explain DNA difference of prokaryotic and eukaryotic eukaryotic DNA: linear and packaged with histones prokaryotic DNA is circular and negatively supercoiled and is not associated with histones. Explain how the chemical properties of water make it the ideal biological solvent. Water is a universal solvent, Mosaic structure, Hydrogen bonds, Surface tension it is capable of dissolving more substances than any other liquid. It is polar Describe hydrogen bonds (H‑bonds). Dipole-dipole attraction which occurs when a hydrogen atom bonded to a strongly electronegative atom exists in the vicinity of another electronegative atom with a lone pair of electrons Using the concept of H‑bonding, explain how small items that are denser than water (e.g., a fine needle or a water bug) can remain on the surface instead of sinking. hydrogen bonds btwn water molecules, form a lattice of water molecules, which is strong and flexible. Creates a high surface tension. As a result, this molecule at the surface tends to be pulled into the bulk of the liquid and thus minimizes the surface area of a liquid Describe an amphiphilic molecule A chemical compound possessing both hydrophilic (water-loving, polar) and lipophilic (fat loving) properties What is a buffer and why are buffers important? a molecule or molecular system that acts to resist changes in pH (provide or absorb protons as needed). Important in living systems for maintaining homeostasis. Why is pH important for molecules, in particular proteins? Changing charges on biological molecules due to pH changes can affect how these molecules function. Define the terms "acid" and "base." Acid is a substance with protons that can dissociate when dissolved in water. Base is a substance that can absorb protons when dissolved in water. Explain the properties of weak acids and weak bases. Weak acids do not lose protons as readily (H+) and weak bases do not absorb protons readily (OH−) when dissolved in water. Strong Acid = __ Ka, __pKa High Ka, Low pKa Explain pKa, Ka and give an example to illustrate what this value means in terms of acids. The stronger the acid the more protons will dissociate. higher the Ka, the lower the pKa Henderson-Hasselbalch equation pH = pKa + log [A-]/[HA] Equation relating pKa & Ka pKa = −Log Ka pH = −Log [H+] UNIT 2 Define "energy" and "entropy." How does an increase in entropy affect the value of ΔG? Energy - ability to do work Entropy - measure of the amount of energy which is unavailable to do work Entropy increase = decreases free energy Differentiate between oxidation and reduction reactions. Oxidation is the loss of electrons by a molecule (increase in oxidation state). Reduction is the gain of electrons (decrease in oxidation state). Explain the role of phosphorylation in ATP synthesis. Oxidative phosphorylation is the process in which ATP is formed as a result of the transfer of electrons from NADH or FADH 2 to O 2 by a series of electron carriers Compare exergonic, endergonic, and equilibrium reactions. Explain "oxidation", "reduction", "catabolic", and "anabolic" reactions. Oxidation is the loss of electrons by a molecule (increase in oxidation state). Reduction is the gain of electrons (decrease in oxidation state). Catabolic → oxidative → release energy Anabolic → reductive → use energy What is a redox reaction? Why are redox reactions common in biological systems? Chemical reaction that involves a transfer of electrons between two species. An oxidation reduction reaction is any chemical reaction in which the oxidation number of a molecule, atom, or ion changes by gaining or losing an electron Common because they allow the molecules and changes to be conserved within the system. Provide an example of a redox reaction breakdown of glucose in the human body to get ATP for energy involves the oxidation of glucose to carbon dioxide and the reduction of oxygen to water: Glucose (C6H12O6) loses electrons (oxidized) to form carbon dioxide (CO2) and oxygen (O2) is reduced to form water (H2O). In the combustion of wood, oxygen from the air transfers electrons to the carbon in the wood. Is the oxygen being oxidized or reduced? In the combustion of wood, the oxygen is being reduced because it is losing electrons to the carbon in the wood. Is the utilization of glucose to produce ATP catabolic or anabolic? Is synthesis of nucleic acids catabolic or anabolic? The utilization of glucose to produce ATP is catabolic, and the synthesis of nucleic acids is anabolic. What is the role of enzymes in energy coupling? The role of enzymes in energy coupling is to provide energy for the reaction by binding ATP and the other molecules involved in the reaction. Using the ATP for energy and hydrolyzing the ATP to ADP + Pi the enzyme can catalyze the reaction. Describe the two laws of thermodynamics. 1. Energy can be exchanged between physical systems as heat and work. 2. Entropy (disorder) increases in an isolated system Define enthalpy (H) the heat content of a system Define entropy (Delta S) Entropy is a measurement of the molecular disorder in a system Define Gibbs Free Energy and calculate the change in Gibbs Free Energy (ΔG). Gibb's Free Energy is a measurement of thermodynamic potential ΔG = H − TS H is enthalpy (joule), T is temperature (in kelvin), and S is entropy (joule/kelvin). If ΔG is positive... If ΔG is negative... ΔG positive - reaction is unfavourable (endergonic, non‑spontaneous). ΔG negative - reaction is favourable (exergonic, spontaneous). In a biological system, how can reactions be coupled to turn an unfavourable reaction (positive ΔG) into a favourable one (negative ΔG)? (-ΔG) coupled with (+ΔG) but still overall negative therefore spontaneous Demonstrate an understanding of thermodynamic equations. ΔG = ΔG°′ + RT ln([B]b/[A]a) R = gas constant (8.3144598 J mol−1 · K−1) ΔG°′ = −RT ln K Three types of phosphorylation mechanisms in the cell. Glucose Phosphorylation. Protein Phosphorylation. Oxidative Phosphorylation.466 ATP synthase Large protein that uses energy from H+ ions to bind ADP and a phosphate group together to produce ATP Describe the synthesis of ATP by oxidative phosphorylation. The process in which ATP is formed as a result of the transfer of electrons from NADH or FADH 2 to O 2 by a series of electron carriers Steps of the electron transport chain. 1. Proton pumps create an electrochemical gradient (proton motive force) 2. ATP synthase uses the subsequent diffusion of protons (chemiosmosis) to synthesise ATP. 3. Oxygen accepts electrons and protons to form water. Function of the electron transport chain. cluster of proteins that transfer electrons through a membrane within mitochondria to form a gradient of protons that drives the creation of adenosine triphosphate (ATP) Describe the sequence of components of the electron transport chain. Explain why NADH and FADH2 yield different amounts of ATP. NADH produces 3 ATP during the ETC (Electron Transport Chain) with oxidative phosphorylation because NADH gives up its electron to Complex I, which is at a higher energy level than the other Complexes. When Complex I transfers the electron to Complex III, energy is given off to pump protons across the membrane, creating a gradient. The electron moves again to Complex IV and again pumps more electrons across the membrane. Because NADH started with Complex I, it had more chances to pumps more protons across the gradient, which powers the ATP synthase and gives us 3 ATP per molecule of NADH. FADH2 produces 2 ATP during the ETC because it gives up its electron to Complex II, bypassing Complex I. By bypassing Complex I, we missed a chance to pump protons across the membrane, so less protons have been pumped by the time we get to Complex IV. Protons still have been pumped, enough to fuel 2 ATP created by ATP synthase. Define oxidative phosphorylation The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration. Use the "chemiosmotic hypothesis" to explain how the energy from electron transport is "coupled" to ATP synthesis. the action of ATP synthase is coupled with that of a proton gradient. It is the action of the proton gradient that causes a proton motive force that allows ATP synthase to phosphorylate ADP and inorganic phosphate to ATP Explain why aerobic ATP production is much more efficient than anaerobic production. This is because oxygen is an excellent electron acceptor for the chemical reactions involved in generating ATP Identify one advantage of anaerobic glycolysis over aerobic metabolism. Speed (Produces ATP very quickly, but runs out) What is the basis for ATP generation through substrate‑level phosphorylation? ATP is synthesized directly through ADP and a reactive intermediate (a high‑energy phosphate‑containing molecule) How does the generation of a proton gradient contribute to synthesis of ATP in electron transport? provides the energy for ATP synthase to make ATP. What are the three forms/states of ATP synthase and what is the function of each state? Loose (L): binds ADP + Pi Tight (T): squeezes the ADP + Pi together to form ATP Open (O): releases the ATP into the mitochondrial matrix. Why can you not hold your breath indefinitely? You cannot hold your breath indefinitely because humans are aerobes and require oxygen. Without a supply of oxygen, energy metabolism ceases because oxygen is required as the final electron acceptor for the electron transport chain and eventual ATP synthesis. Suppose a patient oxidized NADH regardless of whether ADP was present or not. What symptoms might the patient have? elevated temperature and an inability to sustain prolonged physical exercise. energy that the ETC would normally convert to ATP is lost as heat. Therefore less ATP. Define photophosphorylation. What is the main difference between oxidative phosphorylation (electron transport) and photophosphorylation (photosynthesis)? the synthesis of ATP using light from the sun as a source of energy. Oxidative - biological molecules is source Photo- light is source of energy Why are mitochondria functional only if the inner membrane is intact, while the integrity of the outer membrane is less crucial? Inner membrane keeps the protons out to establish and maintain the gradient used to drive ATP synthase. The only protons allowed to cross the inner membrane via ATP synthase Compare the net ATP input and output of glycolysis and gluconeogenesis. The synthesis of glucose (gluconeogenesis) takes more energy than the utilization of glucose (glycolysis). To have that additional energy, we must eat to provide more fuel and energy through the breakdown (oxidation) of glucose. Why are cells not 100% energy efficient in their energy use? because some reactions may use more energy than they produce How does the amount of ATP in the cell drive the processes of glycolysis and gluconeogenesis? High ATP = gluconeogenesis (synthesis of glucose), requires energy. Low ATP = glycolysis (breakdown of glucose) to provide ATP to the cell. What is a futile cycle? What do they produce? Give an example of an animal process that relies on a futile cycle. two metabolic pathways run simultaneously in opposite directions producing no net effect except heat & ATP loss. thermal homeostasis in brown tissues of young mammals, insect flight muscles for heat, How are muscles able to have stores of energy readily available for use? Explain the mechanism. store creatine phosphate & ADP Becomes creatine and ATP. Explain Creatine phosphate shuttle UNIT 3 Identify the 20 common amino acids. Amino Acid Structure a carboxyl group, amine group, and R group What is the R group in an amino acid basic structure? unique side chain Compare the arrangement of hydrophobic and hydrophilic amino acids in a protein in an aqueous environment to that of a membrane. Aqueous environment - hydrophilic side chains face outside of the protein to interact with water hydrophobic on interior of the protein. Membrane - hydrophobic face the outside where they interact with hydrophobic fatty acids hydrophilic side on inside or any place they can interact with water. Protein Structure As you will see in the final lesson of this unit, a protein depends on its tertiary structure to perform its functions. A mutation in the interior of a given protein inactivated the protein. This mutation is ala → val. A second mutation, ile → gly, restored the activity of the protein. Explain these results. First mutation substituted larger amino acid for smaller one, thus distorting the tightly packed protein interior. The second mutation reversed this change by substituting a smaller amino acid for a larger one. Explain why proline is not common in α-helices, but can be found frequently in collagen. Proline is the least flexible amino acid, too rigid and does not "bend" or fit with other amino acid side chain. Proline found in collagen because of the abundance of glycine which has the smallest side chain. allow for proline to fit into this type of helical structure. Identify the six most abundant amino acids in proteins. The six most abundant amino acids in proteins are: leu - leucine ala - alanine gly - glycine ser - serine val - valine glu - glutamic acid Why it is important to know the protein sequence in addition to the DNA sequence of a particular gene? it reveals information about the protein structure that is not possible with nucleic acid sequencing alone Wool consists of α-keratin. Pure wool sweaters exposed to hot water shrink alarmingly. After shrinkage, it is virtually impossible to stretch the sweater back to its original shape. What do you think is the biochemical cause of this phenomenon? When wool is processed ("spun"), the fibres are teased to an elongated shape. Exposure to steam or hot water will cause the processed fibres to revert to their original, tightly H-bonded α-helices Describe the hydrogen-bonding pattern of an α-helix. The regular coding of an α-helix is caused by H-bonding of the −−C==O group of the first amino acid residue to the −−N−−H group of the fifth amino acid residue. List the two advantages of multiple subunits in proteins. having subunits that are assembled rather than one large polypeptide facilitates repair of a defective protein better manipulation and regulation of the protein. (can make enzyme bigger) Explain how cooperativity between haemoglobin and oxygen is achieved. Hemoglobin binds oxygen by the iron of the heme group in one of the subunits. The heme iron is attached to a histadine side chain. This changes the conformation and allows binding of oxygen Describe the energy and entropy changes that occur during protein folding. increase in conformational stability of the folded protein results in a decrease in free energy. Folded = low-energy, low-entropy Antibodies are proteins that recognize and help to inactivate foreign proteins (called antigens). Why do such antibodies rarely react to denatured proteins? A few antibodies do recognize denatured proteins. How can this occur? Antibodies bind to the surface of an antigen. Therefore, part of the "recognition" is the specific arrangement of amino acids at a particular spot on the surface of an antigen. Denaturation destroys the spatial arrangement of amino acids which form the surface of a protein. antibody may have been raised toward a denatured antigen (lab setting), area of recognition on an antigen may be held together, at least partially, by disulphide bonds. Disulphide bonds are covalent bonds and will not break under the conditions of temperature, pH, solvent, and agitation which will dissociate H-bonds and hydrophobic interactions. What information is provided by comparing the sequences of proteins from different organisms? possible functional differences or binding specificities, whether the protein is a membrane protein or secreted protein, evolutionary relationships between organisms, and conserved regions or sequences, which can be very useful for predictions of protein function. How is a phylogenetic tree constructed? classifying the organisms under study according to similarities (e.g., are they mammals, insects, reptiles, etc.). noting the amino acid sequence of a protein common to all of the organisms. Grouping the organisms according to common alterations in an amino acid sequence. Which side chains normally occur on a protein's interior? On its surface? Typically the nonpolar residues Val, Leu, Ile, Met, and Phe occur most often in the interior. The charged polar residues Arg, His, Lys, Asp, and Glu are located on the protein surface. Uncharged polar side chains, Ser, Thr, Asn, Gln, and Tyr, are typically on the surface, but may be found in the interior of a protein H-bonded to other groups (this neutralizes their polarity). Describe the forces that stabilize proteins. Hydrophobic effect - stabilizes proteins by causing nonpolar groups to minimize their association with water. Electrostatic interactions, such as Van der Waals forces, hydrogen bonding, and ionic associations stabilize proteins by allowing side chains to bond or associate. Chemical cross-linking through the formation of disulphide bonds or by the cross-linking of metal ions to a protein add stability to the folding of the protein. List and describe two functions of proteins. Enzymes – catalyse reactions in the cell. Growth factors – induce growth and differentiation of specialized cells. What is an invariant region and what does in mean in terms of enzymes? section of primary structure that is identical or conserved across all species. For enzymes, this is usually in the catalytic region. What is a prion? infectious protein. causes misfolding of the PrP protein which is found in the brain Describe and draw a peptide bond. bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O) Define primary, secondary, tertiary, and quarternary protein structure. Explain how a comparison of the primary structure of homologous proteins is used to determine both evolutionary relatedness and the importance of the sequence. evolutionarily related proteins are highly likely to share common aspects of function proteins can have very similar structures but be quite diverse in sequence and there is a belief that structurally similar proteins can arise due to either convergent or divergent evolution. Explain why glycine and proline occur at positions where a polypeptide chain makes a reverse turn. proline because its cyclic structure is ideally suited for the beta turn glycine because, with the smallest side chain of all the amino acids, it is the most sterically flexible Describe how X-ray crystallography is used in determining the tertiary structure of a protein. X-ray crystallography can reveal the precise three-dimensional positions of most atoms in a protein molecule because x-rays and covalent bonds have similar wavelength, and therefore currently provides the best visualization of protein structure Demonstrate an understanding of protein denaturation and list the conditions required. refers to the unfolding or disruption of the tertiary and quaternary structures of proteins increased temperature, change in pH, change in solvent, or violent agitation Explain Chou and Fasman's method to predict three-dimensional protein structure. The method is based on analyses of the relative frequencies of each amino acid in alpha helices, beta sheets, and turns based on known protein structures solved with X-ray crystallography. List the major role proteins play in vivo. enzyme (catalysts) Define chromosome & gene chromosome - a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes. gene - unit of heredity which is transferred from a parent to offspring and is held to determine some characteristic of the offspring. Define virus & plasmid virus - submicroscopic infectious agent consists of a nucleic acid molecule in a protein coat. is able to multiply only within the living cells of a host Name the three types of RNA. mRNA - Messenger RNA: Encodes amino acid sequence of a polypeptide. tRNA - Transfer RNA: Brings amino acids to ribosomes during translation. rRNA - Ribosomal RNA: With ribosomal proteins, makes up the ribosomes, the organelles that translate the mRNA. Describe the chemical differences between DNA and RNA, and explain why DNA is the more stable molecule. RNA contains A, U, G, C; DNA contains the nitrogenous bases A, T, G, C. RNA is usually single stranded; DNA is double stranded. Normally the nitrogenous bases in RNA are chemically modified, while those in DNA are not. RNA contains an hydroxyl group at the 2 position of ribose. DNA does not. The presence of a hydroxyl group destabilizes RNA, because the 2′-hydroxyl of ribose is close to a phosphate group in the phosphodiester backbone of RNA. List the functions of DNA and RNA. DNA is responsible for storing and transferring genetic information, while RNA directly codes for amino acids and acts as a messenger between DNA and ribosomes to make proteins What are the four nitrogenous bases Adenine, Thymine, Guanine, Cytosine What difficulties can you see in producing proteins by inserting the mammalian genes into bacterial hosts? The proteins produced by mammalian genes inserted into bacterial hosts will lack sugar groups. This is because bacteria cannot glycosylate proteins like mammalian cells do. Draw the structures of adenine, cytosine, guanine, thymine, and uracil. List and describe the major features of the Watson-Crick model of DNA structure. -two polynecleotide chains that form a double helix structure. -anti-parallel DNA strands -major and minor grooves as a result of the bases on the periphery. -Each base is hydrogen bonded: complementary base pairing. What are the structural differences between DNA and RNA? DNA is double-stranded and RNA is single-stranded. DNA contains deoxyribonucleotides as the pentose sugar is deoxyribose. RNA contains ribonucleotides as the pentose sugar is ribose. The nitrogenous bases in DNA are A-T and G-C, but in RNA they are A-U and G-C, whereby A pairs with uracil instead of thymine. Would you expect DNA and RNA to be water-soluble? Explain. With both an anion (phosphate) and a sugar on every monomer unit, DNA and RNA are readily hydrated Why would you expect RNA viruses to have double stranded RNA? While many RNA viruses are double stranded, not all are. What comments can you make on this latter class of viruses in light of your first answer? RNA viruses have just as great a need to preserve their genomes from generation to generation as other species do. Double stranding would protect the base composition from chemical attack (mutation, destruction, or both), just as duplex DNA is protected. Single strand RNA viruses may mutate faster than duplex RNA viruses; they many have protective protein coats surrounding the RNA; or the RNA may double back on itself to give internal double stranding It was stated that (A + G) always equals (T + C) for duplex DNA. Is this restriction also true for single strands of DNA? Justify your answer. The restriction is true for double stranded DNA because every purine is H-bonded to a pyrimidine. Therefore, the sum of the purines (A + G) must equal the sum of the pyrimidines (T + C). There is no such restriction for each individual strand of DNA. What differences would you expect between a duplex DNA which has more A-T base pairs and a duplex DNA which has more G-C pairs? A and T are joined by two H-bonds, while G and C are joined by three H-bonds. Therefore, the duplex with more G-C pairs will have a higher melting temperature; and it may replicate more slowly. What are the forces that stabilize nucleic acids? What can be used to denature nucleic acids? Can nucleic acids renature? The forces that stabilize nucleic acids are H-bonding. In addition a stabilizing force for DNA is stacking interactions between bases in a strand. Nucleic acids can be denatured by heat (to boiling) and urea. Yes, nucleic acids can renature. Outline the role of the 2′ hydroxyl group in RNA. What is the reason this group is lacking in DNA? The role of the 2′ OH group in RNA is to render it sensitive to degradation so that RNA can send messages and be involved in protein synthesis, but be broken down shortly after. The lack of this group in DNA makes the DNA more stable and resistant to degradation in order to protect the genetic information of the cell. Outline the flow of genetic information in a cell. DNA to RNA to protein. DNA is transcribed to mRNA (transcription) mRNA is then used to make proteins with ribosomes (translation) List and describe the three types of RNA. messenger RNA (mRNA): carries the code for amino acids to make proteins. transfer RNA (tRNA): binds specific amino acids to start protein synthesis. ribosomal RNA (rRNA): binds mRNA and tRNA and associate with proteins in ribosomes which conduct protein synthesis. What is a plasmid small, circular, mobile genetic element that is common in bacteria, used for cloning What is the difference between the α anomer and the β anomer of D-glucose? The α anomer and the β anomer of D-glucose differ in the position of the hydroxyl (OH) group at the anomeric carbon. In the α anomer, the OH substituent of the anomeric carbon is on the opposite side of the ring from the CH2OH group at the chiral centre. In the β anomer, the OH group is on the same side as the CH2OH group. Microorganisms in the gut can hydrolyse the polysaccharides in beans, but not all humans can do so in the process of digestion. How does this fact explain the well-known production of gas that occurs after eating a meal of beans? Microorganisms, after hydrolysing the polysaccharides to monosaccharides, will continue to process the monosaccharides before the host organism can absorb them. The end product of metabolism is frequently a gas, so that metabolism can proceed smoothly. Why does paper (which is composed of unoriented cellulose fibres) lose its strength and structure when wet? Water will penetrate areas of disorder in the cellulose structure. The water molecules will then disrupt some H-bonds by competing with interchain H-bonds. Chemically, how could you hydrolyze chitin to monosaccharides? could hydrolyse chitin to monosaccharides by boiling it with a concentrated base. If cellulose forms such a compact, water-excluding structure, how can ruminants (e.g., cows) hydrolyze it? Time is the key. Continual mechanical processing and exposure to water and enzymes will hydrolyze the cellulose molecule from the outside in. Compare and contrast the and functions of cellulose, chitin, starch, and glycogen. Cellulose and chitin are both structural polysaccharides which mean that they function to provide strength and rigidity. Chitin is the principal structural component of the exoskeletons of invertebrates. Starch is the primary energy reserve for plants. Glycogen is the primary energy reserve for animals. Structure of cellulose, chitin, starch, and glycogen. What common biochemical structure is found in cartilage and hyaluronic acid? Where are cartilage and hyaluronic acid found in the body? Why do they have such different physical properties? Both are glycoproteins Joint lubricating fluid (hyaluronic acid) consists of a gel-like matrix of modified, highly charged polysaccharides. This matrix is more highly hydrated and more flexible than any of the other glycoproteins. Cartilage is the least hydrated and thus the least flexible of the structures. If lysozyme is so effective in cleaving the heteropolysaccharide of the bacterial cell wall, why isn't it used clinically to fight bacterial infection? It kills everything, including host polysaccharides Outline the structure of peptidoglycan. What is the mechanism of penicillin's action on the bacterial cell wall? Penicillin specifically binds to and inactivates enzymes that cross-link the peptidoglycan strands of the bacterial cell wall, thus preventing growing cells from synthesizing the cell wall needed for protection from the hypotonic environment. As a result, the bacterial cells lyse What are the major roles of lipids -main components of membranes -fuel molecules -precursors of hormones and prostaglandins -protective coatings on fur, feathers, fruits, etc. What are the 5 major groups of lipids -fatty acids (building blocks of 2 and 3 below) -triacylglycerols (primary form of energy storage for metabolic activity) -glycerophospholipids (major lipid component of membranes) -sphingolipids (membrane components) -steroids. (component of animal plasma membranes to provide rigitidy) Distinguish between unsaturated and saturated fatty acids Unsaturated fatty acids contain double bonds and saturated fatty acids are fully saturated with hydrogen and therefore do not contain double C==C bonds. As a result saturated fatty acids have the least amount of steric interference and a higher melting point. What is the role of phospholipase? Phospholipases are enzymes that hydrolyze glycerolphospholipids. results in a lysophospholipid, which is a strong detergent capable of lysing cells by disrupting membranes. What are the three types of steroid hormones? What responses do they evoke? glucocorticoids: e.g., cortisol; affect metabolism and inflammation aldosterone: regulates the excretion of salt and water by the kidneys androgens and estrogens: affect sexual development and function. Why is it virtually impossible for phospholipids and membrane proteins to flip-flop within the membrane, while it is relatively easy for these constituents to move laterally? the polar portion of a lipid must pass through the hydrophobic interior of the bilayer to get to the other side. movement is thermodynamically unfavourable Moving within the bilayer would be a little like moving through a field of tall grass. Explain the effect of a detergent on cell membrane structure. Detergents can interact with membrane protein, principally by van der Waals bonds. The hydrophobic portion of the detergent interacts with the protein while the hydrophilic portion of the detergent interacts with water List the six functions of a membrane according to the textbook. -Obtain food for energy for the cell. -Export materials out of the cell. -Maintain osmotic balance. -Create gradients for secondary transport. -Provide an electromotive force for nerve signalling. -Store energy in electrochemical gradients for ATP production (oxidative phosphorylation or photosynthesis). List and describe the four types of membrane proteins. -Integral membrane proteins: embedded in the membrane and pass through the membrane, emerging on each side. -Peripheral membrane proteins: embedded or tightly associated with part of the membrane, but do not project completely through both sides. -Associated membrane proteins: found near membranes, but are not embedded. These proteins may associate through interactions with other proteins or molecules in the lipid bilayer. -Anchored membrane proteins: not embedded in the bilayer, but are attached to a molecule that is embedded in the membrane, typically a fatty acid Distinguish between passive and active transport, and indicate whether energy is required for each of these processes. Passive transport does not require ATP or energy. It is driven by diffusion whereby molecules move from a higher concentration to a lower concentration. Active transport requires energy, ATP as well as other sources (sodium-glucose transporter uses a sodium gradient for the force to transport glucose). Ions are usually transported in active transport. Why is the Na+/K+ ATPase considered to be involved in anti-port transport? The Na+/K+ ATPase transporter is an example of anti-port transport because it transports Na+ ions out (3 atoms) of the cell and K+ (2 atoms) ions into the cell. Define Vitamin and cofactor A vitamin is an organic compound that is essential for normal growth and nutrition. They typically cannot be synthesized by the body and so are required in small quantities in the diet. Cofactor is a non-protein compound or metallic ion that is essential for the activity of an enzyme. Vitamins can be cofactors. UNIT 4 Define "enzyme" and "coenzyme," and explain the relationship between the two. enzyme protein which catalyzes a biochemical reaction Coenzymes exist to make an “active site” more chemically reactive. Describe the six classes of enzymes. Define the terms "activation energy" and "transition state." Activation energy is the reduced energy barrier of a reaction to reach its transition state transition state is the substrate-enzyme activated complex How does a catalyst influence the overall energy of a reaction? How does a catalyst affect the activation energy of a reaction? catalyst does not change the overall energy of a reaction. A catalyst lowers the activation energy of a reaction and helps the reaction proceed so it lowers the activation energy of a reaction. What is the active site of an enzyme? What forces are involved in the interaction between an enzyme and its substrate? Why are covalent interactions not usually involved? active site of an enzyme usually a cleft on the enzyme surface where the substrate binds and is converted to product. The binding forces holding an enzyme and substrate together are ionic, electrostatic, hydrophobic, or a combination of these. Covalent bonds may occur, but are not common because these bonds require more energy and also because it would be harder to release the product and the enzyme would not be able to catalyse another reaction. Distinguish between a coenzyme, a prosthetic group, and a cosubstrate. A coenzyme is molecule that makes the active site of an enzyme more chemically reactive. A coenzyme may be a metal ion or a metal ion complex or a small organic group. A prosthetic groups is a covalently bound coenzyme. A cosubstrate is a noncovalently bound coenzyme. List the six mechanisms of enzyme catalysis. acid-base catalysis, electrostatic or ionic catalysis, metal ion catalysis, proximity and substrate orientation catalysis, covalent catalysis, and transition state binding. Describe a Michaelis‑Menten Graph What is the Michaelis‑Menten equation How are Vmax and KM affected for each of the types of enzyme inhibition: competitive, non competitive, and uncompetitive? Competitive - KM increased, Vmax unaffected. Non‑competitive - KM unaffected, Vmax reduced. Uncompetitive - KM reduced, Vmax reduced. What is suicide inhibition? Give an example. involves irreversible binding of the inhibitor to the enzyme by covalent bonding List the four general mechanisms of enzymatic control. Allosteric control (allosterism) Covalent modification Access to the substrate / substrate-level control Control of enzyme synthesis/breakdown What is feedback inhibition and what type of enzymatic control is it? Feedback inhibition is where a product of a synthetic pathway binds to and inhibits an enzyme early in the pathway to prevent further synthesis of this product if it is not needed. Feedback inhibition is a form of allosteric control What is a zymogen? What kind of enzymatic control operates here? Why is this beneficial? A zymogen is an inactive form of an enzyme. Sometimes enzymes are synthesized in an inactive form and they must be activated by the cleavage of some covalent bonds. This is called covalent modification of enzymes. This is beneficial as a way to control enzymes and keep them off until they are needed. What is a ribozyme? Ribozymes are a special form of enzymes. Unlike most enzymes, ribozymes are not proteins. They are RNAs. A ribozyme is a catalytic RNA capable of cutting RNA (self-splicing). UNIT 5 The synthesis of DNA starts with a primer strand of RNA, which is later excised and replaced with DNA. Why does this mechanism decrease the chance of error? The first few bases to be added during replication have much more steric mobility than bases added to a strand already in place. Therefore, incorrectly paired bases will "fit" better at the beginning of a strand than they will farther along the strand. What is a DNA supercoil? What function or functions does supercoiling perform? Circular DNA (the type found in bacteria) is twisted in one of two ways: the duplex axis is wound as if around a cylinder or the duplex axis is twisted around itself. This is called supercoiling. It gives DNA a more compact shape and provides additional protection to the nitrogenous bases. Distinguish between the "leading" and the "lagging" strand in DNA replication. The leading strand is the 5′ to 3′ strand that is directly replicated in one long piece (continuously). The lagging strand is the 3′ to 5′ strand that primase adds nucleotides to. Suppose an incorrect base was inserted into a daughter strand of DNA and this error was not corrected. Now suppose the daughter strand replicates. Can the error be corrected at this stage? The error cannot be corrected when the daughter strand replicates. The second generation DNA duplex (i.e., the "incorrect" daughter strand plus the partner strand synthesized to complement it) appear perfectly normal to the repair processes, because the base pairing is correct. Why is error control less critical for RNA than for DNA? RNA is a throwaway molecule. It is synthesized on demand. Does proofreading by DNA polymerase eliminate all replication errors? No, the proofreading mechanism of DNA polymerase does not catch all errors in replication. These errors are fixed post‑replication by mismatch repair. How are errors recognized by the mut genes in mismatch repair? New DNA strands are not yet methylated, so the mismatch repair system can distinguish between the old and new strands of DNA. The mut genes detect the new strand and excise the error. What are some causes of DNA damage? What repair system is used to fix this damage and what are the two types of repair? radiation, exposure to dangerous chemicals, and chemical reactions in the cell. repair system: excision repair. there are two types: nucleotide excision repair (NER), for UV damage and chemicals; and base excision repair (BER), for the removal of uracil bases resulting from the deamination of cytosine to uracil. List the 4 major steps with RNA synthesis Recognition, Initiation, Elongation, Termination Is any one σ‑factor unique to one RNA polymerase holoenzyme? No σ factor is unique to one RNA polymerase holoenzyme. The σ‑factor dissociates from the holoenzyme after binding to DNA. The factor can then be picked up by any other core RNA polymerase. Outline the steps involved in transcription (mRNA synthesis). Recognition: RNA polymerase binds to a specific site on DNA in search of at the promoter region. The more tightly RNA polymerase binds to a specific promoter region, the greater the RNA transcription of that gene. Initiation: Two nucleoside triphosphates, complementary to the first two DNA bases in the gene itself, are coupled by RNA polymerase. Elongation: The core enzyme moves rapidly along DNA synthesizing complementary RNA. Termination: When the core enzyme reaches a stretch of DNA rich in adenine residues, it dissociates from DNA, thereby terminating RNA synthesis. The rho factor aids in dissociating RNA polymerase from DNA. Define "repressor." Repressor binds to a DNA promoter region to prevent RNA polymerase from binding Why is it necessary to have repressor proteins to prevent RNA polymerase binding to DNA? Some proteins are only required at infrequent intervals. Repressor proteins keep a gene turned off until a positive factor, which indicates a need for the gene's protein product, is present. How does the presence of lactose affect the lac operon? When lactose is present, it binds to the repressor, which is normally bound to the operator site on the DNA. Binding of lactose to the repressor makes the repressor unable to bind the operator region which overlaps the promoter region for the lac genes. This means that RNA polymerase can now bind the promoter region and transcribe the lac genes, which are needed to utilize the lactose. What are enhancers and silencers? Are these typically eukaryotic or prokaryotic? Enhancers and silencers are regulatory DNA sequences. Enhancers activate transcription by binding transcriptional activators and silencers inhibit transcription of genes by binding to repressors. These are found in eukaryotic organisms. What are the three processing steps for mRNA? - addition of a 7‑methyl guanosine cap to the 5′ end - addition of about 200 A nucleotides (PolyA) tail to the 3′ end - removal of introns by splicing. What is the spliceosome? The spliceosome is a complex of proteins and small RNAs that form small nuclear ribonucleoproteins (snRNPs). These are protein‑RNA enzymes that recognize intron sequences, cut them out, and join the exon sequences together to form a mature mRNA for protein translation. What are the two main steps in RNA splicing? The pre‑mRNA is cut at the 5′ splice site (junction of the 5′ exon and intron) and joined to the branch point sequence in the intron which forms a loop structure. The 3′ splice site is cut, the two exons are joined together, and the intron is released. What is the purpose of alternative splicing? The purpose of alternative splicing is to provide diversity and minimize the number of genes needed to encode proteins. If different introns can be spliced and a variety of exons joined together, a cell can produce many different proteins using fewer genes. A nonsense mutation is one that yields a STOP codon. Such a mutation could be overcome by an altered tRNA. What does this mean? A mutation in the tRNA anticodon can occur so that it is complementary to the STOP nonsense mutation. Malignant tumour cells have a higher dependence on glycolysis than normal cells. Why? Malignant tumour cells grow very fast. The capillary networks that supply oxygenated hemoglobin do not develop as rapidly. Therefore, a malignant tumour will be more successful if its need for oxygen is not great. Why does a mutation in the p53 gene lead to cancer? The p53 gene is a tumour suppressor gene, which means it functions to control cell proliferation that is characteristic of cancer. If p53 is mutated, then there is no mechanism for controlling cell proliferation and tumour growth. The p53 gene activates the transcription of cyclin‑dependant kinase inhibitor (CKI), which binds to Cdk‑cyclin complexes to control the cell cycle. It may also activate the proteins involved in apoptosis as a means to control cell proliferation.