Biochemistry Note-Taking Guide for Amino Acids and Proteins, Exams of Biochemistry

Download Biochemistry Note-Taking Guide for Amino Acids and Proteins and more Exams Biochemistry in PDF only on Docsity! Biochemistry Note-Taking Guide Latest Update 2024 Guaranteed Success **Read This First** - This Note-Taking Guide is meant to be used as you go through each of the Units in Biochemistry. It is only effective when used with course materials, including all of the Essential Reading material in Campbell Biology (), the course videos () and podcasts (), the Learning Check questions, and the Unit Quizzes. We highly recommend that you print out this guide and use it to make your own notes on the course by writing the vocabulary definitions and answering the questions in your own words. We also recommend that you review your notes every day for all Units to keep the course material fresh in your mind even as you learn new material in the course. If there are definitions or questions you are unable to answer on your own, please click here to discover multiple options for working with a Course Instructor . We would love to help you succeed in Biochemistry! {{Click here if you’d like a PDF version }} ***Unit 2: Amino Acids, Peptide Bonds, and Protein Structure*** Pag e Sectio n Vocabulary Key Questions - You should be able to answer these upon completion of the Unit/Section. Please add your own notes as necessary. 12 Amino Acids, Peptide Bonds, and Protein Structure Proteins are all constructed from the same set of 20 amino acids, linked in branched polymers. The bond between amino acids is called A peptide bond, so a polymer of amino acids is called a polypeptide. A protein is a biologically functional molecule made up of one or more polypeptides; each folded and coiled into a specific three-dimensional structure. 13 2.1 Amino Acids: The Building Blocks of Proteins 14 Subtopic: Chemical Elements, Atoms, Electrons Energy Biochemistry Note-Taking Guide page 3 O) bonds Charged have Ionic bonds 17 2.2 Levels of Protein Structure To become functional proteins, polymers of amino acids (polypeptides) must fold and take on a particular shape. Primary – backbone of peptide chain formed by peptide bonds during dehydration reaction Secondary – backbone atoms of peptide chain connected by hydrogen bonds forming Alpha helix or Beta sheets Tertiary – R group interactions via: hydrophobic interactions (weakest), hydrogen bonds, ionic bonds or disulfide bonds (strongest) Quaternary – R group interactions (like above), but with other polypeptide chains 18 Subtopic: Polypeptides and Functional Proteins Polypeptid es Peptide bonds When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can become joined by a dehydration reaction, with the removal of a water molecule. The resulting covalent bond is called a peptide Biochemistry Note-Taking Guide page 4 Bond. This happens during the formation of primary structur e in the peptide chain. 19 Subtopic: Levels of Protein Structure Dehydrati on Hydrolysi s Alpha helix Beta sheet Denaturat ion - Protein Folding: What are the 4 levels of protein structure? List distinguishing features of each. - What bonds make up each level of protein structure and how are they formed? Primary – peptide bonds (a type of strong covalent bond) between monomer amino acids Secondary – hydrogen bonds between polypeptide backbone Tertiary – bonds between R groups (hydrogen/ionic/disulfide bonds, hydrophobic/van der Walls interactions) Quaternary – same as tertiary, but between different polypeptide chains 20 Subtopic: A Protein's Structure Depends on Its Environment Aggregation - What environmental change breaks each type of bond? Heat – 2nd,3rd,4th protein structure and its bonds pH – hydrogen and ionic bonds (2nd, 3rd and 4th structure) chemicals – hydrogen bonds (2nd, 3rd and 4th structure) enzymes – peptide bonds (1st structure) - What type of amino acid side chain leads to protein Biochemistry Note-Taking Guide page 5 aggregation???? Hydrophobic acids tend to aggregate better then hydrophilic Proteins that denature tend to aggregate. These aggregated clumps can’t be broken down and will continue to accumulate until disease occurs 22 2.3 Protein Function and Disease - How do environmental changes affect protein folding? Reducing agent – disulfide bonds pH change – Ionic, hydrogen bonds Salt – Ionic, hydrogen bonds Heat – hydrophobic interactions How do mutations affect protein structure? Biochemistry Note-Taking Guide page 8 Bonds and other weak interactions that stabilize the active shape of the enzyme, and the protein molecule eventually denature. Each enzyme has an optimal temperature at which its reaction rate is greatest. Most human enzymes have optimal temperatures of about 35–40°C. The optimal pH values for most enzymes fall in the range of pH 6–8. Certain chemicals selectively inhibit the action of specific enzymes. Sometimes the inhibitor attaches to the enzyme by covalent bonds, in which case the inhibition is usually irreversible. Many enzyme inhibitors, however, bind to the enzyme by weak interactions, and when this occurs the inhibition is reversible. Toxins and poisons are often irreversible enzyme inhibitors. 31 Subtopic: Enzyme Regulation Allosteric site Competitive inhibitor Non- competitive inhibitor Feedback inhibition - What are the differences between competitive and noncompetitive inhibitors? Some reversible inhibitors resemble the normal substrate molecule and compete for admission into the active site. These mimics, called competitive inhibitors, reduce the productivity of enzymes by blocking substrates from entering active sites. This kind of inhibition can be overcome by increasing the concentration of substrate so that as active sites become available, more substrate molecules than inhibitor molecules are around to gain entry to the sites. Noncompetitive inhibitors do not directly compete with the substrate to bind to the enzyme at the active site. Instead, they impede enzymatic reactions by binding to another part of the enzyme (allosteric site). This interaction causes the enzyme molecule to change its shape in such a way that the active site becomes much less effective at catalyzing the conversion of substrate to product. Biochemistry Note-Taking Guide page 9 - When given an enzyme pathway, be able to analyze that pathway under normal conditions and under inhibition. What molecules increase/build-up or decrease given a specific inhibitor? Allosteric regulation is the term used to describe any case in which a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site. It may result in either inhibition or stimulation of an enzyme’s activity. The binding of an activator to a regulatory site stabilizes the shape that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme. In another kind of allosteric activation, a substrate molecule binding to one active site in a multi-subunit enzyme triggers a shape change in all of the subunits, thereby Biochemistry Note-Taking Guide page 10 Increasing catalytic activity at the other active sites. Called cooperatively, this mechanism amplifies the response of enzymes to substrates: One substrate molecule primes an enzyme to act on additional substrate molecules more readily. Cooperatively is considered allosteric regulation because, even though substrate is binding to an active site, its binding affects catalysis in another active site. Biochemistry Note-Taking Guide page 13 nucleotides complementary to the DNA template strand. The stages of transcription: initiation, elongation, and termination. The DNA sequence where RNA polymerase attaches and initiates transcription is known as the promoter; the sequence that signals the end of transcription is called the terminator. The stretch of DNA downstream from the promoter that is transcribed into an RNA molecule is called a transcription unit . - How do we make proteins? Which type of nucleotide sequence is used and in which direction? How do we read the codon table? Translation is the synthesis of a polypeptide using the information in the mRNA. During this stage, there is a change in language: The cell must translate the nucleotide sequence of an mRNA molecule into the amino acid sequence of a polypeptide. The sites of translation are ribosomes. - What is the relationship between mRNA and tRNA? MRNA carries a genetic message from DNA out of the cell and into the cytoplasm where Ribosome attaches. Here is where Tran comes and transfers a specific amino acid in order to create a polypeptide chain in the translation process. Anticodon on Tran attaches to codon on mRNA. Biochemistry Note-Taking Guide page 14 - How does mRNA splicing allow us to create multiple proteins from a single gene/mRNA? Introns and exons are both found in the pre-mRNA. Introns are sequences of nucleotides that don’t code for protein and are found between exons. Exons are sequences of nucleotides that contain the codons for protein. 41 Subtopic: Control of Gene Expression Splicing Introns Exons Histones Nucleoso mes Methylatio n Acetylatio n Because they don’t code for proteins, introns need to be “cut out” during splicing. Introns usually carry a mutation within, so by cutting those out us decrease the chance of gene mutation. Therefore, introns are considered to be protective. Alternative splicing is cutting out introns and some exons to create different proteins from the same gene. - What factors increase gene expression? What factors decrease gene expression? How do these factors work together to control transcription? Proteins that bind to promote regions and help initiate transcription are called transcription factors Ability to initiate transcription is key in gene expression. Gene expression factor called Activator initiates transcription. When nucleosomes are “tightly packed” gene expression is low, and when “widely spaced” gene expression is high. Biochemistry Note-Taking Guide page 15 Methylation is a chemical marker that is put on histone proteins to cause the nucleosomes to pack tightly together. High methylation=low expression. High acetylation=high expression. 43 4.3 DNA Damage and Repair 44 Subtopic: Mutations Point mutations Nonsense mutations Missense mutations Silent mutations Frame shift mutations Insertion mutations Deletion mutations - You are given a normal and mutated DNA or RNA sequence. What steps will you take to determine the type of mutation that has occurred? Point mutations: (changes to a single letter) Silent mutation is a mutation that doesn’t exert any effect on the protein. Changes a codon w/o changing a protein Missense mutation is a mistake mutation that changes a codon, w/ changes to amino acid Nonsense mutation is a mutation in which no amino acid is produced, only stop codon Biochemistry Note-Taking Guide page 18 ***Unit 5: Myoglobin and Hemoglobin*** Pag e Section Vocabulary Key Questions - You should be able to answer these upon completion of the Unit/Section. 52 Myoglobin and Hemoglobin 53 5.1 Hemoglobin and Myoglobin: Structure and Function Hem et Affini ty - What are the structural differences between myoglobin and hemoglobin? Myoglobin – single subunit protein w/ primary/secondary/tertiary structure contains one home/iron/can bind one O2 Hemoglobin – it is a 4 subunit protein (2 alpha, 2 beta) w/ prim/sec/tart/quit structure contains 4 home/iron/can bind 4 O2 - What are the functional differences between myoglobin and hemoglobin? Myoglobin – found in muscle tissue, stores O2 in muscle, has high O2 affinity Hemoglobin – found in the blood, delivers O2 to body, has Biochemistry Note-Taking Guide page 19 lower O2 affinity - Given the concentration of oxygen (mmHg or tort), what is the saturation of myoglobin? What is the saturation of hemoglobin? Look at the O2 binding curve. 55 5.2 The Dynamic Structure of Hemoglobin 56 Subtopic: Oxygenated versus Deoxygenated Hemoglobin Cooperatively Cooperatively makes other O2 molecules more likely to bind to Hemoglobin if another O2 is already bound to it. It also works in the opposite direction when Hemoglobin reaches tissue that needs to be oxygenated. Myoglobin doesn’t have cooperatively. - What are the structural properties of the tense state of hemoglobin? The relaxed state? Relaxed (R) state has higher affinity for O2 Tense (T) state has lower affinity for O2 Biochemistry Note-Taking Guide page 20 - What causes hemoglobin to change from the tense state to the relaxed state? Shape of hemoglobin changes when O2 attaches Introduction of O2 in the lungs will cause hemoglobin to go from T to R state 57 Subtopic: Modulators of Hemoglobin Function - How does carbon monoxide (CO) affect the structure of hemoglobin? How does it cause poisoning? CO looks very similar to O2 and has 200x greater affinity to attach to Hob. It locks Hob in R state , preventing any O2 to be released by Hob, therefore it increases Hob affinity for O2 - How does 2, 3-BPG (2, 3-DPG) affect the structure of hemoglobin? What is the natural function of 2, 3-BPG? It is produced by RBCs and reduces Hob affinity for O2. It promotes unloading of O2 from Hob by locking Hob in T state , therefore it decreases Hob affinity for O2. 59 5.3 The Bohr Effect The Bohr effect describes pH influence on O2 binding to Hob. Changes in blood pH tell Hob which tissues need more O2. Biochemistry Note-Taking Guide page 23 linkages has Beta linkages (indigestible by humans) - What is the structure and function of ATP? ATP is a nucleotide that consists of three main structures: the nitrogenous base, (adenine), the sugar (ribose), and a chain of three phosphate groups bound to ribose. 69 Subtopic: Glucose Storage Insulin Glycogen (stored glucose) Glycogenesis Glut4 Insulin = promotes synthesis of glycogen when glucose is abundant Glycogen = stored glucose in the form of polymer Glycogenesis = the process of glycogen synthesis, in which glucose molecules are added to chains of glycogen for storage Glycolysis = the breakdown of glucose by enzymes, releasing energy and pyruvic acid. - What are some real-life scenarios that would lead to insulin release from the pancreas? Insulin is released after a meal, or in other words after ingestion of glucose. Biochemistry Note-Taking Guide page 24 - How does insulin help reduce blood glucose levels? How does Glut4 aid in this process? It stimulates body to transport glucose to the cells, as well as glycogenesis. Glut4 is a glucose transporter protein. 70 Subtopic: Tapping Into Glucose Stores Glucagon Glycogenol ysis Glucagon = pancreatic hormone that tell the liver to release glycogen Glycogenolysis = breakdown of glycogen into glucose Gluconeogenesis = creation of new glucose by the liver - What are some real-life scenarios that would lead to glucagon release from the pancreas? Running a marathon, once glucose is needed from the storage - How does glucagon help increase blood glucose levels? It tells the liver to release glycogen 72 6.2 Making ATP 73 Subtopic: Aerobic Metabolism Aerobic metabolism Cellular respiration Glycolysis Citric Acid Cycle Electron Transport Aerobic metabolism = metabolic reaction that requires O2 presence in ATP production. - What are the three pathways of aerobic metabolism? Where in the cell does each pathway take place? Biochemistry Note-Taking Guide page 25 Chain (ETC) NAD+/ NADH FAD/FADH 2 Substrate- level phosphoryla tion Oxidative phosphorylation Glycolysis – in cytoplasm The Citric Acid Cycle – in mitochondrial matrix ETC with Oxidative Phosphorylation – in mitochondrial inner membrane - What molecules are the substrates for each pathway (“ins”)? What molecules are the products for each pathway (“outs”)? How do the products of one pathway become substrates for the next pathway? Look at the picture - How is ATP generated in glycolysis? How is it generated in the ETC? How many ATP are generated in each pathway? Aerobic respiration generates around 30-32 ATP per glucose molecule (2+2+26/28 per cycle). Biochemistry Note-Taking Guide page 28 Most of the energy of a fat is stored in the fatty acids. A metabolic sequence called beta oxidation breaks the fatty acids down to two-carbon fragments, which Enter the citric acid cycle as acetyl CoA. Fats make excellent fuels, in large part due to their chemical structure and the high energy level of their electrons. A gram of fat oxidized by respiration produces more than twice as much ATP as a gram of carbohydrate. 74 Subtopic: Anaerobic Metabolism Anaerobic metabolism Fermentation Gluconeogenesis The Cori Cycle Anaerobic metabolism = metabolic reaction that doesn’t require O2 in ATP production. - What are the two different fates of pyruvate? What factors affect the use of pyruvate by the cell? Pyruvate  Acetyl-CoA if O2 is present Pyruvate  Lactic acid if O2 is not present (fermentation) - What are the three pathways of anaerobic metabolism/the Cori Cycle? Where in the cell does each pathway take place? In which organ or cell type does each pathway take place? Fermentation happens in cytosol. Cori Cycle happens in overworked muscles or RBCs (these cells lack mitochondria) Cori Cycle - What molecules are the substrates for each pathway (“ins”)? What molecules are the products for each pathway (“outs”)? Biochemistry Note-Taking Guide page 29 - What is the role of fermentation in regard to NAD+/NADH? During process of fermentation NAD+ is regenerated, and pyruvate is converted to lactate. Biochemistry Note-Taking Guide page 30 - What are at least 3 different molecules that can be used as substrates of gluconeogenesis? The major substrates of gluconeogenesis are lactate, glycerol, and glycogenic amino acids. - How much ATP is used in gluconeogenesis? What is the net outcome of ATP in The Cori Cycle? Net outcome in the Cori Cycle is -4 ATP. Glycolysis is where 2 ATP and 2 NADH are created, and it is considered a substrate- level phosphorylation. Gluconeogenesis happens in the liver where 6 ATP are lost. Gluconeogenesis has 2 key roles: 1. It prevents acidosis since it consumes lactic acid. 2. It produces glucose that can be used by the peripheral muscle cells. Biochemistry Note-Taking Guide page 33 Type 1 = insulin not produced by the pancreas... Treated w/ supplemental insulin. DKA happens in Type 1 DM. Type 2 = cells not sensitive to insulin. Treated w/ Metformin. Metformin causes decrease in gluconeogenesis  increase in lactic acid in Cori Cycle. Decrease in gluconeogenesis, body uses fats as energy  increases beta-oxidation which causes increase in ketone production. Metformin inhibits complex I of the ETC, preventing the movement of electrons through the chain at a rate sufficient to produce ATP. As a result, the cell is triggered to obtain more glucose from the blood (GLUT4 movement to membrane in muscle cells) and decrease ATP production in the liver cells, therefore inhibiting the liver's ability to make new glucose-gluconeogenesis. Insulin also causes GLUT4 movement to the surface of the cell membrane. Biochemistry Note-Taking Guide page 34 - How can diabetes lead to gyration and AGEs? When the blood contains too much glucose, some of the glucose molecules attach to proteins, a process known as gyration. Gyrated proteins can accumulate in capillaries, disrupting blood flow to a variety of tissues. For example, gyrated Hob is also known as Hob A1c. Advanced gyration end products (AGE) are glucose molecules linked to lipids and proteins. They can cause apoptosis or pathogenic behavior of cells. Gyration Biochemistry Note-Taking Guide page 35 ***Unit 7: Lipids*** Pag e Section Vocabulary Key Questions - You should be able to answer these upon completion of the Unit/Section. 81 Lipids Lipids are hydrophobic molecules, particularly its hydrocarbon chain. Fatty acids are the simplest lipids 82 7.1 Triglycerides Function in Energy Storage 83 Subtopic: Triglyceride Structure Saturated fatty acid Unsaturated fatty acid Triglycerides Cholesterol Phospholipids Micelle - How does the length of a fatty acid affect its melting point and physical state at room temperature? The longer they are the higher melting point. The longer they are, the more solid they are on room temp (solid > 13C atoms). - How do we label the different carbons and bonds in a fatty acid? Alpha, Beta, Omega carbon Alpha, Beta, Omega bond Beta bond is broken up in beta-oxidation Essential fatty acids also have Omega 3/Omega 6 double bonds Biochemistry Note-Taking Guide page 38 of H around the double bonds. Cist = same orientation (more common) Trans = opposite orientation - How can you recognize the structures of triglycerides, cholesterol, and phospholipids? What is each of their functions? Triglycerides contain 3 fatty acid chains and 1 glycerol molecule. They are found in adipose tissue and are main form of energy storage in our bodies. Cholesterol is a steroid that has tetracyclic (4 members) ring. It’s a membrane buffer, helping to maintain the membrane integrity. Cholesterol acts as a fluidity buffer in the membrane to protect the membrane from changes in fluidity. If there is not enough cholesterol in the membrane, the membrane will not be able to adjust to changes in the lipid environment. The lack of cholesterol will allow phospholipids to pack more tightly in the membrane, which will decrease the fluidity. Biochemistry Note-Taking Guide page 39 Micelles are a single layer of phospholipids that form a sphere. They transfer fatty acids, vitamins and cholesterols. 84 Subtopic: Triglyceride Metabolism Adipocyt es Lipases Lipolysis Beta oxidation Ketone bodies Ketoacidosi s MCADD Fatty acid synthesis Oxaloacetate Citrate Lip genesis is the process of generating triglycerides from fatty acids. They can be a combination of saturated and unsaturated fatty acids Fatty acid synthesis happens in the cytosol. Bond between glycerol and fatty acid is called ester linkage. Lipolysis is the breakdown of lipids. - How do we break down a triglyceride? Where in the cell does this take place? What happens to the different components of the triglyceride? Triglycerides are the main source of stored energy. It is broken down to 3 fatty acids and glycerol molecule. Lipase is the enzyme that catalyzes this reaction by breaking down the ester linkages. This process is known as lipolysis. They are primarily digested in the stomach. - How do we break down a fatty acid? Where in the cell does this take place? What are the 3 products of beta oxidation? We break it down in beta-oxidation. Biochemistry Note-Taking Guide page 40 It occurs in the matrix of mitochondria. It produces: 1 Acetyl CoA, 1 NADH, 1 FADH2 Left over Glycerol will enter glucose metabolism pathway. Coenzymes that are needed during beta-oxidation of fatty acids: NAD+, FAD, and coenzyme A Biochemistry Note-Taking Guide page 43 - Which fatty acid metabolism pathways are controlled by insulin? Which are controlled by glucagon? Insulin will store fatty acids in adipose tissue after a meal. Glucagon will free (hydrolysis process) fatty acids during fasting. MCADD is caused by defective enzyme that prevents the breakdown of fatty acids with a hydrocarbon chain of 6-12 C atoms (medium chain fatty acids). MCADD is the most common type of beta- oxidation disorder. By preventing the breakdown, not enough ATP is being made. These individuals have a diet of slow releasing carbs, and they have to eat often as they have no energy reserve in the form of fatty acids. It is critical for an individual with MCADD to avoid situations that would increase fat catabolism, such as fasting, which decreases blood sugar. 86 7.2 Phospholipids Form Cell Membranes Amphipathic The phospholipid bilayer Plasma membrane Glycolipids Glycoproteins - What are the components of the plasma membrane? Phospholipids are the major component. They move from side to through the membrane and are not static. They form a phospholipid bilayer. Phospholipids are amphipathic: hydrophilic head (that is polar) and hydrophobic tail. Phospholipids have 2 fatty acid tails attached to glycerol and a P group. Triglycerides have 3 fatty acid tails attached to glycerol. Biochemistry Note-Taking Guide page 44 - How do cells maintain the fluidity of the plasma membrane when moved to colder or warmer temperatures? Saturated fatty acids create more packed membranes, decreasing the fluidity. Unsaturated fats have kinks which prevents packing, increasing the fluidity. Longer fatty acids have a higher melting point. As the temperature decreases, the membrane remains fluid to a lower temperature if it is rich in phospholipids with unsaturated hydrocarbon tails. Fish in colder climate needs a more fluid membrane to survive. At relatively high temperatures (at 37°C, the body temperature of humans, for example) cholesterol makes the membrane less fluid by restraining phospholipid movement. However, because cholesterol also hinders the close packing of phospholipids, it lowers the temperature required for the membrane to solidify. Thus, Biochemistry Note-Taking Guide page 45 Cholesterol can be thought of as a “fluidity buffer” for the membrane, resisting changes in membrane fluidity that can be caused by changes in temperature. The longer a fatty acid molecule is, the higher its melting point. The more double bonds it has, the lower it’s melting point. What this means for membrane fluidity is this: When it’s warm outside, and we want our membrane not to get too “runny”, we want to make our phospholipids with more saturated, longer chain fatty acids. By contrast, when it is colder, we want to use more shorter-chain and unsaturated fatty acids in our phospholipids to keep our membrane from freezing solid. Glycolipids are lipids attached to sugar Glycoproteins are proteins attached to sugar This is the basis of blood groups: A, B, O 88 7.3 The Structure and Function of Other Lipids Essential fatty acids Eicosanoids Arachidonic acid Chylomicron Steroids have tetracyclic (4 member) ring. It’s a membrane buffer, helping to maintain the membrane integrity. It is a precursor to other hormones, such as sex hormones: estradiol and testosterone. It doesn’t contain fatty acids in its structure. - What does it mean for a nutrient to be essential?