Biochem Note-Taking: Understanding Proteins, Amino Acids, Interactions, Exams of Nursing

Download Biochem Note-Taking: Understanding Proteins, Amino Acids, Interactions and more Exams Nursing in PDF only on Docsity! Biochemistry Note-Taking Guide Latest Update **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*** Page Section Vocabulary Key Questions - You should be able to answer these upon completion of the Unit/Section. Please add your own notes as necessary. Amino Acids, Peptide Bonds, Proteins are all constructed from the same set of 20 amino acids, linked in unbranched polymers. The bond between amino acids is called a peptide bond, so a polymer of amino acids is called a 12 and Protein Structure 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, and Bonds—Optional Review Electrons Energy Covalent bonds 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 Dehydratio n Hydrolysis Alpha helix Beta sheet Denaturati on - 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 Wals 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 aggregation???? Hydrophobic acids tend to aggregate better Biochemistry Note-Taking Guide page 5 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 6 ***Unit 3: Enzymology and Catalytic Mechanism*** Page Section Vocabulary Key Questions - You should be able to answer these upon completion of the Unit/Section. 26 Enzymology and Catalytic Mechanism 27 3.1 Enzyme Action Substrates Products Intermediates Active site Enzyme specificity Induced fit Kinase Phosphatas e - How do enzymes catalyze reactions? Enzymes are specific to one substrate and can catalyze only one type of reaction. In most enzymatic reactions, the substrate is held in the active site by so- called weak interactions, such as hydrogen bonds and ionic bonds. Enzymes are unchanged by the reaction. - How do enzymes affect reaction rate and activation energy? They increase the reaction rate and decrease the activation energy - What are the 4 steps of the enzymatic cycle? 1. Substrate binding 2. Formation of enzyme-substrate complex 3. Product formation and dissociation 4. Enzyme recovery Biochemistry Note-Taking Guide page 9 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 cooperativity, this mechanism amplifies the response of enzymes to substrates: One substrate molecule primes an enzyme to act on additional substrate molecules more readily. Cooperativity 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 11 ***Unit 4: DNA and RNA*** Page Section Vocabulary Key Questions - You should be able to answer these upon completion of the Unit/Section. 36 DNA and RNA 37 4.1 DNA and RNA Structure Gene expression Nucleotides Antiparallel Complementar y - Which nucleotides/bases are used in DNA? Which are used in RNA? Know their abbreviations and their full names. (Example: A is adenine.) DNA: Adenine, Thymine, Cytosine, Guanine Purines: A and G RNA: Adenine, Uracil, Cytosine, Guanine Pyrimidines: T, U and C - Which nucleotides base-pair together to form DNA? To form RNA? DNA: A-T, C-G RNA: A-U, C-G Bases are paired by hydrogen bonds 39 4.2 DNA and RNA Work Together to Make Proteins 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 Nucleosom es Methylation Acetylation Because they don’t code for proteins, introns need to be “cut out” during splicing. Introns usually carry a mutation within, so by cutting them out we 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. 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. Biochemistry Note-Taking Guide page 15 43 4.3 DNA Damage and Repair 44 Subtopic: Mutations Point mutations Nonsense mutations Missense mutations Silent mutations Frameshift 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 16 Frameshift mutations: (change the reading frame/multiple codons) Insertion mutation adds an extra letter to the sequence Deletion mutation deletes a letter from the sequence 45 Subtopic: DNA Repair Pathways Base Excision Repair (BER) Nucleotide Excision Repair (NER) Mismatch Repair Homologous Recombination Non- homologous End-joining What type of DNA damage does each repair pathway fix? BER – single nucleotide NER – several nucleotides MMR – mistakes in DNA replication HR/NHEJ – double stranded breaks - What are the steps each repair pathway takes to fix the damaged DNA? Look at the slides PCR is a procedure used to synthesize copies of DNA. - What are the steps of PCR, including the definitions of each step? Denature – DNA strand separation with heat Anneal – DNA primers base pair to target DNA strands Elongation/Extension – DNA polymerase binds to primers and synthesize new DNA PCR - What are the components of a PCR reaction? Target DNA Heat stable DNA polymerase Nucleotides (dNTP) Biochemistry Note-Taking Guide page 19 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 Cooperativity Cooperativity 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 cooperativity. - 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 Hb. It locks Hb in R state , preventing any O2 to be released by Hb, therefore it increases Hb 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 Hb affinity for O2. It promotes unloading of O2 from Hb by locking Hb in T state , therefore it decreases Hb affinity for O2. 59 5.3 The Bohr Effect The Bohr effect describes pH influence on O2 binding to Hb. Changes in blood pH tell Hb which tissues need more O2. 2,3-DPG binds to hemoglobin stabilizing the deoxygenated, T state of hemoglobin. Biochemistry Note-Taking Guide page 21 60 Subtopic: pH and Hemoglobin Structure pH Proton s Acid Base - What are we measuring when we measure pH? What level of pH is considered acidic? Basic? We are measuring the level of H ion. Level of 7.2 is more acidic. Level of 7.4 is more basic. - What factors change the pH of the blood? How do changes in pH affect hemoglobin’s structure? The change in the level of CO2 and H will change the pH of the blood. 61 Subtopic: pH and Hemoglobin Function Bicarbonate Carbonic anhydrase - How do changes in pH affect the ability of hemoglobin to bind or release oxygen? Higher concentrations of H promote T state of Hb, and vice versa. Carbonic anhydrase catalyzes the reaction that converts CO2 and H2O into HCO3- (bicarbonate) and H+. The H+ produced in this reaction lowers the pH, making it more acidic. CO2 + H2O = HCO3 +H 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 Glycogenolys is 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 Chain (ETC) NAD+/ NADH FAD/FADH2 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? Glycolysis – in cytoplasm The Citric Acid Cycle – in mitochondrial matrix ETC with Oxidative Phosphorylation – in mitochondrial inner membrane Biochemistry Note-Taking Guide page 25 Substrate- level phosphorylati on Oxidative phosphorylation - 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 26 - What are the roles of NADH and FADH2? How is NADH generated in glycolysis? How are NADH and FADH2 generated in the Citric Acid cycle? How does the ETC use NADH and FADH2? NADH/FADH2 carry high energy electrons to pump protons in order to create proton gradient. ETC uses them to bring in the electrons to complex I and II. Proton gradient is a concentration difference between the low concentration of H+ in the mitochondrial matrix and high concentration of H+ in the intermembrane space and is energy source for making ATP. It is a form of stored energy, and this is the energy source for making ATP. - ETC: Which complexes accept NADH and FADH2? What is the role of the electrons in the ETC? What is the role of protons in ATP product? What enzyme ultimately makes ATP? What is the role of oxygen in the ETC? NADH carries 1 highly energetic electron to complex I in ETC, and FADH2 carries 2 lower energetic electrons to complex II in ETC. The role of these electrons is to use their energy in order to pump protons (H+) from the mitochondrial matrix to intermembrane space. H+ is hydrophilic and Inner membrane is hydrophobic, so in order to move H+ across the membrane we need these electrons. O2 has a role of picking up extra electron at the end of ETC. It then converts from O2 to H2O. In a redox reaction, the loss of electrons from one substance is called oxidation, and the addition of electrons to another substance is known as reduction. 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 glucogenic 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. - How are aerobic and anaerobic metabolism the same? How are they different? Which aerobic and anaerobic pathways are controlled by insulin? Controlled by glucagon? Biochemistry Note-Taking Guide page 31 There are two general mechanisms by which certain cells can oxidize organic fuel and generate ATP: aerobic respiration and fermentation. The distinction between these two is that an electron transport chain is used in aerobic respiration but not in fermentation. Fermentation is a way of harvesting chemical energy without using either oxygen or any electron transport chain. Glycolysis oxidizes glucose to two molecules of pyruvate. Glycolysis generates 2 ATP whether oxygen is present or not. The oxidizing agent of glycolysis is NAD+. In aerobic respiration NAD+ is recycled from NADH by the transfer of electrons to the electron transport chain. During lactic acid fermentation, pyruvate (the end product of glycolysis) gets processed into lactate, and NADH is utilized in the reaction. As a result, NADH breaks down to produce NAD+ Biochemistry Note-Taking Guide page 34 - How can diabetes lead to glycation and AGEs? When the blood contains too much glucose, some of the glucose molecules attach to proteins, a process known as glycation. Glycated proteins can accumulate in capillaries, disrupting blood flow to a variety of tissues. For example, glycated Hgb is also known as Hgb A1c. Advanced glycation end products (AGE) are glucose molecules linked to lipids and proteins. They can cause apoptosis or pathogenic behavior of cells. Glycation Biochemistry Note-Taking Guide page 35 ***Unit 7: Lipids*** Page 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 - How do we count the carbons in a full structure of a fatty acid? A structure formula? A zig-zag structure? Biochemistry Note-Taking Guide page 36 Look at the chart There are twice as many H then C atoms, and 2 O2 atoms: C8H16O2 Formula changes for unsaturated fatty acids 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 Ketoacidosis MCADD Fatty acid synthesis Oxaloacetate Citrate Lipogenesis 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. It occurs in the matrix of mitochondria. Biochemistry Note-Taking Guide page 40 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 41 - How do we calculate the amount of acetyl CoA produced from a fatty acid? How do we calculate the number of rounds it takes to break it down completely? How do we calculate the amount of ATP produced? Look at the chart For a 16 C atom fatty acid, 8 acetyl CoA are produced, and it takes 7 rounds to do it. - What happens to the products of beta oxidation after they are produced? Each acetyl CoA produced that enters the CAC can produce 3 NADH and 1 FADH2. Each acetyl CoA produced will produce 14 ATP molecules. Example from above with 8 acetyl CoA will produce 112 ATPs. - How and why are ketone bodies produced? Diabetic ketoacidosis is a severe complication of diabetes. Without enough insulin, the body breaks down fatty acids by the process of beta-oxidation, resulting in excess production of acetyl-CoA that leads to a disproportionate accrual of ketone bodies. - What is the molecule used for fatty acid synthesis? How is this molecule exported from the mitochondria to the cytosol? What is the committed step of fatty acid synthesis? Biochemistry Note-Taking Guide page 44 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? Essential nutrients are compounds that the body can't make on its own, or in enough quantity. These nutrients must come from food - What are the fat soluble vitamins? Biochemistry Note-Taking Guide page 46 Vitamins are essential nutrients. Fat soluble are: A, D, E, K