Understanding Proteins, Amino Acids, and Lipids: Structure, Function, and Metabolism, Exams of Nursing

Download Understanding Proteins, Amino Acids, and Lipids: Structure, Function, and Metabolism and more Exams Nursing in PDF only on Docsity! 1 **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. ***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. 12 Amino Acids, Peptide Bonds, and Protein Structure 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 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 pg. 1 Biochemistry Note-Taking Guide2023//// Biochemistry Note-Taking Guide page 2 Ionic bonds Hydrogen bonds 15 Subtopic: Amino Acid Structure and Chemical Properties Amino Carboxyl Hydrophobic Hydrophilic Disulfide bonds Zwitterions - What is the basic structure of an amino acid? List the 4 groups and describe what they look like. An amino acid is an organic molecule with both an amino group and a carboxyl group. At the center of the amino acid is an asymmetric carbon atom called the alpha carbon. The R group , also called the side chain, differs with each amino acid - How do you identify the 3 different types of side chains: non-polar/hydrophobic, polar, and charged? Hydrophobic has C atom and is not charged (found in protein interior) Polar has S, N, or O atom and is not charged (found in protein exterior) Charged are positively or negatively charged (found in protein exterior) - What kind of bonds do each of the 3 different types of side chains make? Hydrophobic have Hydrophobic bonds (weakest kind of bonds) Polar have Disulfide (S-strongest kind of bonds) or Hydrogen (N, 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 Polypeptide s 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 pg. 2 Biochemistry Note-Taking Guide page 5 bonds, and other weak interactions that stabilize the active shape of the enzyme, and the protein molecule eventually denatures. 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. - 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 pg. 5 Biochemistry Note-Taking Guide page 6 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. pg. 6 Biochemistry Note-Taking Guide page 7 ***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 40 Subtopic: Transcription and Translation Template DNA Coding DNA Replication Transcription RNA polymerase Promoter Transcription factors mRNA Translatio n tRNA Ribosome s Codons Anticodo ns - How do we make complementary DNA (ie coding to template, or template to coding)? Complementary DNA is created codingtemplate strand. DNA exists as a double helix. - How do we make mRNA? Which strand of DNA is complementary to the mRNA? mRNA is created out of template DNA strand only. RNA molecules exist as single strands and are more variable in shape Transcription is the synthesis of RNA using information in the DNA. The two nucleic acids are written in different forms of the same language, and the information is simply transcribed, or “rewritten,” from DNA to RNA. For a protein-coding gene, the resulting RNA molecule is a faithful transcript of the gene’s protein-building instructions. This type of RNA molecule is called messenger RNA (mRNA) because it carries a genetic message from the DNA to the protein-synthesizing machinery of the cell. An enzyme called an RNA polymerase pries the two strands of DNA apart and joins together RNA pg. 7 Biochemistry Note-Taking Guide page 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 47 4.4 PCR and Genetic Testing PCR Primers Denaturati on Annealing Elongation - What are the components of a PCR reaction? Target DNA Heat stable DNA polymerase Nucleotides (dNTP) Primers - How are primers used to assist in a PCR reaction? - How do you calculate the number of copies of DNA produced by a specific number of PCR cycles? Every cycle doubles the amount of DNA - How does PCR compare to normal DNA replication in the cell? RNA primers are used during DNA replication, while DNA primers are used in PCR. PCR uses heat to separate DNA strands. PCR uses heat stable DNA polymerase from bacteria, as normal human polymerase would disintegrate in high heat. pg. 10 Biochemistry Note-Taking Guide page ***Unit 5: Myoglobin and Hemoglobin*** Page 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 Heme Affinit y - What are the structural differences between myoglobin and hemoglobin? Myoglobin – single subunit protein w/ primary/secondary/tertiary structure contains one heme/iron/can bind one O2 Hemoglobin – it is a 4 subunit protein (2 alpha, 2 beta) w/ prim/sec/tert/quat structure contains 4 heme/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 lower O2 affinity - Given the concentration of oxygen (mmHg or torr), 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 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 pg. 11 Biochemistry Note-Taking Guide page - 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. 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 pg. 12 Biochemistry Note-Taking Guide page - 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. ATP Synthase makes ATP, but it needs H+ to flow back from intermembrane space back into mitochondrial matrix. H+ is used to pump the ATP Synthase into converting ADP to ATP. - How do fats and proteins enter aerobic metabolism? Before amino acids can feed into glycolysis or the citric acid cycle, their amino groups must be removed, a process called deamination. The nitrogenous waste is excreted from the animal in the form of ammonia (NH3), urea, or other waste products. pg. 15 Biochemistry Note-Taking Guide page 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”)? - What is the role of fermentation in regard to NAD+/NADH? During process of fermentation NAD+ is regenerated, and pyruvate is converted to lactate. pg. 16 Biochemistry Note-Taking Guide page - 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? 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+ pg. 17 Biochemistry Note-Taking Guide page ***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? Look at the chart There are twice as many H then C atoms, and 2 O2 atoms: C8H16O2 Formula changes for unsaturated fatty acids pg. 20 Biochemistry Note-Taking Guide page - What are the structural differences between saturated and unsaturated fats? How does this affect their melting point and physical state at room temperature? A fatty acid "saturated" (or full) with hydrogens will not include a carbon- carbon double bond between any of the carbons in the fatty tail. This allows the hydrophobic tails to interact closely and create a more solid structure. Conversely, some "unsaturated" fatty acids contain one or more carbon-carbon double bonds along the carbon chain that will cause a bend or kink in the structure. This structural feature prevents unsaturated fatty acids from forming tight interactions, leading to a more fluid state. The general consensus is that saturated fat is more harmful than unsaturated fat. Saturated don’t contain double bonds between C atoms in the hydrocarbon chain. These are mostly solids at room temp and are from animal products. Due to limited interactions between fatty acids, saturated short-chain and medium-chain fatty acids are liquid at room temperature. Unsaturated contain double bonds between C atoms. Mostly liquid at room temp and are from plant products. Monounsaturated vs polyunsaturated depends on 1 vs more double bonds. Cis (bent) vs Trans (straight) configuration depends on orientation of H around the double bonds. Cis = same orientation (more common) Trans = opposite orientation - How can you recognize the structures of triglycerides, cholesterol, and phospholipids? What are 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 member) 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 pg. 21 Biochemistry Note-Taking Guide page membrane, which will decrease the fluidity. pg. 22 Biochemistry Note-Taking Guide page - 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. - 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, pg. 25 Biochemistry Note-Taking Guide page 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? Vitamins are essential nutrients. Fat soluble are: A, D, E, K pg. 26 Biochemistry Note-Taking Guide page - What are the two essential fatty acids and how do we recognize that a fatty acid is essential? Omega 3 and Omega 6 fatty acids are essential, and we recognize them by their double C linkages. Omega-3 CH3CH2CH=CH (CH2) CH=CH (CH2) CH=CH (CH2) CH=CH (CH2)3 COOH Omega-6 CH3 (CH2)4 CH=CH (CH2) CH=CH (CH2) CH=CH (CH2) CH=CH (CH2)3 COOH A double bond between the third and fourth carbon from the omega end (the methyl, or fatty, end) indicates an omega-3 fatty acid, whereas, a double bond between the sixth and seventh carbons from the omega end indicates an omega-6 fatty acid. - How can you recognize the structure of an eicosanoid? What are its functions? How is this affected by aspirin? Eicosanoids are signaling molecules, and have function in: inflammation, pain/fever, BP, blood clotting, reproduction. Arachidonic acid is the precursor to eicosanoid (prostaglandins) and is an essential fatty acid because it contains an omega-6 double bond. ASA and other NSAIDs exert their effects by targeting the production of eicosanoids, a class of lipids that include prostaglandins. Specifically, NSAIDs act on cyclooxygenase (COX) enzymes, and the resulting decrease in prostaglandin production reduces pain and inflammation. ***Unit 8: Review*** 93 Pre-Assessment and Objective Assessment Information pg. 27