Biology of Amino Acids, Proteins, and Carbohydrates, Exams of Biochemistry

Download Biology of Amino Acids, Proteins, and Carbohydrates and more Exams Biochemistry in PDF only on Docsity! MCB63X Principles of Biochemistry A carbon has its electrons stably distributed into sp3 orbitals. How many different atoms does it likely bond to? - 4 A carbon has its electrons stably distributed into sp2 orbitals and one pi orbital. How many different atoms does it likely bond to? - 3 A carbon has its electrons stably distributed into an sp orbital and two pi orbitals. How many different atoms does it likely bond to? - 2 Most electronegative atoms (in order from least to greatest)? - N O F What is a molecular conformation? - The (potentially flexible) spatial arrangement of atoms around fixed bonds in a molecule What is molecular configuration? - The fixed arrangement of atoms dictated by the bonds of a molecule. What is the metabolic term that describes the synthesis of complex bio-molecules from building blocks? - anabolism What is the metabolic term that describes the breakdown of complex bio-molecules to simple building blocks? - catabolism What is the term for a living organism that extracts energy from sunlight? - Phototroph What is the term for a living organism that extracts energy from chemical molecules? - Chemotroph What are the two major classifications for organisms based on how they obtain carbon? - Autotroph and heterotroph How to autotrophs obtain carbon? - Fixing CO₂ How to heterotrophs obtain carbon? - Eating food Formula for change in Gibbs free energy - ∆G = ∆H - T∆S At equilibrium what is ∆G? - 0 When ∆G is negative? - Forward reaction is spontaneous When ∆G is positive? - Forward reaction is nonspontaneous (backwards reaction is spontaneous) van der waals hydrogen bonds ionic interactions (salt bridge) What makes cysteine unique? - It can form disulfide bonds with itself under oxidizing conditions (extracellular environment). It is also the only naturally L configuration amino acid that is R configuration. What makes glycine unique? - It's R group is just a hydrogen so it isn't chiral. Also, it gives much chain flexibility during protein folding. What makes proline unique? - Although we call it an amino acid, it's actually an imino acid because it's sidechain is covalently linked to its amino group. This makes proline conformationally restrictive during protein folding. What is a protein's primary structure? - The sequence of amino acids What is a protein's secondary structure? - α helices, β sheets, and random loops. What is the peptide bond? - A single bond that connects two amino acids. However, due to resonance, rotation around this bond can't happen. Do peptide bonds prefer the cis configuration or trans configuration? - Trans, except for proline What is a ramachandaran plot? - A plot which shows allowable regions of less steric hinderance dependent on phi and psi angles. Multiple amino acids in sequence in certain regions of the ramachandaran plot can form the elements of secondary structure. What is the periodicity of an alpha helix? - 3.6 residues per turn What stabilizes secondary structure elements? - Hydrogen bonding between carbonyl groups and amide groups. What is tertiary structure? - The arrangement of secondary structure elements within a single polypeptide. What is quaternary structure? - The arrangement of several polypeptides in a protein complex. What is a domain? - Domains are independent folding units within proteins. What is a motif? - a motif made up of several secondary structure elements that assemble in a consistent way. What is a fold? - the arrangement of the secondary structure elements in a domain correspond to a fold. What energies favor protein folding? - hydrophobic effect (water molecules can now interact more with each other when the protein is folded) and enthalpy What energy doesn't favor protein folding? - conformation entropy of chain (reduced conformations in folded state) What is the thermodynamic hypothesis for proteins? - The most thermodynamically stable conformation of a protein is its native fold What is one reason that proteins are able to rapidly adopt their native conformation? - There is a high degree of cooperativity in protein folding. compare and contrast the nucleation condensation and the diffusion collision models of the kinetics of protein folding. - In nucleation condensation, the protein core collapses, bringing sidechains closer together to interact and form the final structure. In diffusion collision, the secondary structure forms first, and then they interact to form tertiary structure. What types of interactions commonly lead to protein aggregation? - hydrophobic interactions What are protein folding chaperones? - They prevent intermolecular hydrophobic interactions while the protein folds. A reaction is at equilibrium when? - there is no net change in the concentration of the reactants (forward and reverse reaction rates are equal). A reaction is spontaneous if... - the product has lower free energy than the substrate. An enzyme increases the rate of a reaction by stabilizing the... - Transition state cyclic glucose predominates at equilibrium. C5 hydroxyl attacks the C1 aldehyde What makes a sugar reducing? - The presence of a open aldehyde group, or open hemiacetal and hemiketal group. What are the linkages present in glycogen? - 1-4 glycosidic linkages for sugars on same chain 1-6 glycosidic linkages for chain branching How is a molecule of glucose added to a glycogen chain? - glucose-6-phosphate is turned into glucose-1-phosphate which is then turned into UDP-glucose (the activated glucose), which is then is appended to the non-reducing end of the glycogen chain by glycogen synthase What is the first step of glycolysis? - Glucose is turned into glucose-6-phosphate by an enzyme known as hexokinase, which uses one ATP. What does phosphoglucose isomerase do? - Turns glucose-6-phosphate into fructose-6-phosphate What is PFK1? - phosphofructokinase, the enzyme which turns fructose-6-phosphate into fructose-1,6- bisphosphate, consuming one ATP in the process. What does aldolase do? - Turns fructose-1,6-bisphosphate into glyceraldehyde-3-phosphate (GAP), which isomerizes with dihydroxyacetone phosphate (DHAP) through triose phosphate isomerase. How many GAPs does one molecule of glucose produce? - Two What is GAPDH? - Glyceraldehyde phosphate dehydrogenase, an enzyme which converts glyceraldehyde-3- phosphate into 1,3-bisphosphoglycerate (reducing NAD+ in the process) PGK is? - phosphoglycerate kinase, enzyme which converts 1,3-bisphosphoglycerate to 3- phosphoglycerate and creates one molecule of ATP PGM is? - phosphoglycerate mutase, converts 3-phosphoglycerate to 2-phosphoglycerate What does enolase do? - Converts 2-phosphoglycerate to phosphoenolpyruvate (PEP) What is the last step of glycolysis? - phosphoenolpyruvate (PEP) is converted to pyruvate by pyruvate kinase, which also makes 1 ATP. What does having a high free energy of hydrolysis mean? - The breaking of the molecule will be highly exergonic. What does having a low free energy of hydrolysis mean? - The breaking of the molecule will be a tiny bit exergonic. What is the coupling of reactions? - Using an exergonic reaction to provide energy to fuel an endogonic reaction. How is coupling constrined in cells? - The reactions need to have a shared molecule and an enzyme that catalyzes both reactions Without NAD+, what would happen to glycolysis? - It would come to a halt How can NAD+ be regenerated? - In aerobic conditions, pyruvate is turned into acetyl-CoA and enters the citric acid cycle and subsequent oxidative phosphorylation (during which the NADH donates it's 2 electrons to the ETC and turns back into NAD+). In anaerobic conditions, fermentation occurs. How does lactate fermentation happen? - lactate dehydrogenase turns pyruvate into lactate, and oxidizes NADH back into NAD+. How does ethanol fermentation happen? - pyruvate decarboxylase turns pyruvate into acetaldehyde, which is then turned into ethanol by alcohol dehydrogenase (and produces NAD+). How does cooperativity affect hemoglobin's (Hb) binding to oxygen? - It results in a sigmoidal binding curve. Hemoglobin binds better to oxygen when oxygen is already on it. This cooperative binding is advantageous because it allows hemoglobin to regulate the release of oxygen during different stages of blood flow ranging from oxygenation to perfusion. Which of the following is the reason that red blood cells cannot completely oxidize glucose to form carbon dioxide? - They lack mitochondria What is the Cori cycle? - It regenerates glucose from lactate generated anaerobically in red blood cells and muscle. It is exogonic and spontaneous. How does one convert between ΔE and ΔG - ΔG = -nF∆E What does a reduction potential measure? - A molecule's relative affinity for electrons (how easily it can be reduced). Higher potentials mean its more likely to be reduced. Electrons will flow from molecules with low reduction potentials to high reduction potentials. What is the final electron acceptor of the ETC in human cells? - O₂ Which statement most accurately describes the function of the Q cycle? - To transfer a single electron to cytochrome c (a single electron carrier) from the double electron carrier QH2 in Complex III of the ETC. Describe the function of complexes I and II in the ETC? - To transfer electrons from universal electron acceptors to coenzyme Q (ubiquinone). Describe ATP synthase subunits and structure - (look at the image) How many molecules of ATP are synthesized per turn of the ATP synthase stalk? - 3 What are ALL the processes promoted by the proton motive force? - ATP synthesis The exchange of ATP and ADP across the mitochondrial inner membrane. The symport of inorganic phosphate and hydrogen into the mitochondrial matrix. What is homotropic allosteric regulation? - The binding of a substrate to one subunit promotes the transition to the R state in other subunits of the enzyme. What is heterotropic allosteric activation? - A small molecule binds the enzyme at a site other than the active site, stabilizing the R state of the enzyme. What are substrate-limited reactions? - Metabolic reactions near equilibrium where the enzymatic activity is governed by how quickly the substrate can be produced. What are enzyme-limited reactions? - Metabolic reactions far from equilibrium where the enzymatic activity is governed by specific effectors. What are the three types of metabolic regulation (from fastest to slowest)? - Allosteric, reversible covalent modification (phosphorylation), and then transcriptional regulation How is PFK1 regulated normally? - Activated by AMP, inhibited by ATP and citrate (citrate actually increases the inhibitory effect of ATP) How is PFK1 regulated in the liver? - In the liver the ATP concentration is always high, hence fructose-2,6-bisphosphate activates PFK1. Describe PFK2? - Phosphofructose kinase 2 converts fructose-6-phosphate into fructose-2,6-bisphosphate. It has both a kinase domain and a phosphatase domain. In part, PFK2 activity is modulated by blood glucose levels (low blood glucose activates the phosphatase domain of PFK1, thereby reducing the fructose-2,6- bisphosphate, subsequently reducing PFK1 activity and glycolysis). What are two isoforms of hexokinase? - M form is found in brain and muscle and has low Km (high affinity for glucose) L form is found in liver and has a high Km (low affinity for glucose) Hence when glucose is low, brain and muscle get priority. Describe the M isoform of hexokinase at high glucose levels. - At high glucose levels, there will be much ATP produced by cells, thereby inhibiting PFK1 and created a backlog of glucose-6-phosphate and fructose-6-phosphate. These molecules, in turn, inhibit M-hexokinase, allowing less glucose uptake into cells and more glucose in the bloodstream for consumption by the liver which aims to convert the glucose into glycogen and stuff. Describe the L isoform of hexokinase at high glucose levels. - At high glucose levels, the L isoform (also known as glucokinase) isn't inhibited by glucose-6- phosphate, and since there's tons of glucose, the liver is able to take it all despite glucokinase having a low Km. Does glucose-6-phosphate/fructose-6-phosphate accumulate in the liver? - No, because they're constantly being shuttled to make glycogen and fatty acids. What three glycolytic enzymes are tightly regulated? - Hexokinase Phosphofructokinase Pyruvate kinase What regulates pyruvate kinase normally? - ATP inhibits it, fructose-1,6-bisphosphate activates it. Since alanine can be converted to pyruvate, alanine inhibits pyruvate kinase. Glucokinase is adapted to a specific physiological need - maintaining blood glucose levels to allow the export of glucose when blood sugar levels are low, and to take up and store excess glucose when blood sugar levels are high. What are the two main mechanisms used by glucokinase to achieve this function? - Glucokinase has a relatively low affinity for glucose. Glucokinase localizes to the nucleus when blood sugar levels are low. What are two main fates of glucose that enters liver cells when blood sugar levels are high? - It is converted into glycogen. It enters fatty acid synthesis via acetyl-CoA. What is the main catabolic fate of fatty acids in the liver? - They undergo β-oxidation and complete oxidation. Why do blood glucose levels tend to stabilize after prolonged starvation? - The brain uses ketones (produced from excess acetyl-CoA by the liver) as a fuel molecule. The muscles tend to oxidize fatty acids Which two pathways are primarily localized to the mitochondria? - β-oxidation TCA cycle Each cycle of beta oxidation yields? - 1 NADH and 1FADH₂ Which anabolic pathway do fatty acids NOT contribute to in the liver? - They contribute to synthesizing new glucose via gluconeogenesis. What are the first two fuel sources that the body uses during fasting? - Glycogen stored in the liver and muscle. Fatty acids stored in the liver.` What is the main fuel molecule that powers skeletal muscle at rest? - fatty acids In conditions of intense physical activity, what are two primary sources of energy for skeletal muscle? - phosphocreatine and glucose What are two unique characteristics of cardiac muscle, relative to skeletal muscle? - Cardiac muscle is much more pH-sensitive than skeletal muscle Cardiac muscle is completely dependent on aerobic respiration (anaerobic respiration can alter pH which is detrimental) What is the primary function of the phosphocreatine system? - To store high energy phosphate groups to regenerate ATP during muscle activity. Which molecule is responsible for transferring high-energy phosphate groups from phosphocreatine to ADP? - CK, creatine kinase What is the relationship between the rate of ATP production and the total energy content of the different fuel sources utilized by muscle? - inverse, vast energy sources have the slowest rate of ATP production What is the main fuel source for cardiac muscle, under essentially all conditions? - fatty acids What are two primary fuel molecules for skeletal muscle under conditions of moderate activity? - fatty acids, glycogen If cardiac muscle is deprived of fatty acids, what are two other fuel molecules that it might utilize? - glucose and lactate What is an important piece of evidence suggesting that fermentation is an important source of energy during high-intensity exercise? - pH levels drop in the blood What are two major functions of the liver in the recovery from exercise? - Eliminating nitrogenous compounds from the breakdown of muscle proteins. Clearing blood lactic acid with the Cori cycle. High blood glucose levels, as encountered after a meal, would likely lead to (hormone-wise) - The release of Insulin from pancreatic β cells. What are two consequences of insulin signaling in the liver? - Glycolysis Glycogen synthesis What are two consequences of insulin signaling in the muscle? - Glycogen synthesis Amino acid synthesis What are two ways in which glucagon signaling differs from adrenaline signaling? - Adrenaline is produced in response to stress, glucagon is produced in response to low blood sugar. Adrenaline promotes muscle glycolysis, glucagon does not (gotta give those muscles energy). Uracil Thymine Nucleoside - Pentose (either ribose or deoxyribose) + nitrogenous base (attached to 1' C on sugar) Nucleotide - Nucleoside + some amount of phosphates (attached to 5' C on sugar) Nucleic acids - Polymers of nucleotides joined by phosphodiester bonds (new nucleotides join at the 3' hydroxyl via a dehydration reaction) What are the primary interactions involved in DNA base pairing? - hydrogen bonds What are the two pathways that nucleotides are produced from? - de novo pathway salvage pathway PRPP - Converted from ribose-5-phosphate (product of the HMP shunt/pentose phosphate pathway) What two molecules are common reactants of de novo synthesis of both inosine monophosphate and uridine monophosphate? - PRPP Aspartate What molecule (or class of molecules) is the source of all of the nitrogens added to the purine ring during de novo purine biosynthesis? - amino acids Uridine monophosphate (UMP) is the precursor to what two molecules? - Uridine diphosphate Uridine triphosphate What steps in purine biosynthesis are inhibited by all of the following molecules: AMP, GMP, and IMP? - The phosphorylation of ribose 5-phosphate to form PRPP by PRPP synthase. The transfer of an amino group from glutamine to C1 of PRPP by Gln-PRPP amidotransferase. What molecule inhibits ATCase activity to regulate the balance of nucleotide pools? - CTP What are the two end purines that are synthesized de novo? - AMP GMP What are the two end pyrimidines that are synthesized de novo - UTP CTP What turns dUMP to dTMP? - thymidylate synthase What enzyme catalyzes these general conversions: ATP + NMP = ADP + NDP - "N"-ylate kinase What enzyme is responsible for the phosphorylation of ADP to form ATP for the vast majority of ATP in a human cell? - ATP synthase What is ATCase? - Catalyzes the first step in the pyrimidine de novo pathway. Describe the general process of de novo purine synthesis? - PPRP is made. Then the nitrogenous base is build directly atop of this molecule. This results in the creation of IMP. IMP can then be turned into adenylosuccinate or Xanthine monophosphate (XMP). adenylosuccinate is then turned into AMP XMP is turned into GMP. ATP is needed for the formation of GMP GTP is needed for the formation of AMP Describe the general process of de novo pyrimidine synthesis? - The pyrimidine ring is first assembled and attached to ribose-5-phosphate given by PRPP. Final product is UMP, which is then turned into UTP, which can be converted into CTP What are the products of reactions catalyzed by ribonucleotide reductase? - Deoxyibonucleotide diphosphates What activates and deactivates ribonucleotide reductase? - ATP activates it