Results for "denaturation"

Structural Levels of Proteins and Denaturation

HOMEOSTASIS Maintaining a stable internal environment respond to stimuli Reacting to changes in the environment reproduce and develop Creating new organisms and growing adapt and evolve Changing over time to better suit the environment INDUCTIVE REASONING Making generalizations based on specific observations DEDUCTIVE REASONING Making specific predictions based on general principles Matter Anything that has mass and takes up space elements Substances that cannot be broken down into simpler substances protons Positively charged particles in the nucleus neutrons Neutral particles in the nucleus electrons Negatively charged particles orbiting the nucleus Atomic Number Number of protons in an atom Isotopes Atoms of the same element with different numbers of neutrons Octet Rule Atoms tend to gain, lose, or share electrons to achieve a full outer shell of 8 electrons molecule Two or more atoms held together by chemical bonds compound A substance consisting of two or more different elements IONIC BONDS Bonds formed by the transfer of electrons COVALENT BONDS Bonds formed by the sharing of electrons reactants Starting materials in a chemical reaction products Ending materials in a chemical reaction WATER solvent Dissolves many substances WATER cohesion & adhesion Water molecules stick to each other and other surfaces WATER high surface tension Water's surface resists being broken WATER high heat capacity Water can absorb a lot of heat without changing temperature WATER heat of vaporization Water requires a lot of energy to evaporate WATER varying density Ice is less dense than liquid water acidic solutions Solutions with a pH below 7 basic solutions Solutions with a pH above 7 pH scale Measures the acidity or basicity of a solution buffers Substances that resist changes in pH Organic Molecules Molecules containing carbon carbon The backbone of organic molecules functional groups Chemical groups attached to carbon that give molecules specific properties Macromolecules Large molecules made up of smaller subunits monomers The individual subunits of a polymer polymers Long chains of monomers Dehydration Synthesis Reaction Joins monomers by removing water Hydrolysis Reaction Breaks polymers by adding water Role of Enzymes Speed up chemical reactions Carbohydrates monosaccharides glucose Simple sugars Carbohydrates disaccharides glycosidic bonds Two monosaccharides joined together Carbohydrates polysaccharides starch glycogen cellulose Many monosaccharides joined together LIPIDS Glycerol & Fatty Acids saturated Fatty acids with no double bonds LIPIDS Glycerol & Fatty Acids unsaturated Fatty acids with double bonds PROTEINS Enzymes Proteins that catalyze chemical reactions PROTEINS amino acids peptide bonds The monomers of proteins, joined together PROTEINS protein structure primary The sequence of amino acids PROTEINS protein structure secondary Local folding patterns (e.g., alpha-helices and beta-sheets) PROTEINS protein structure tertiary The overall 3D shape of a single polypeptide PROTEINS protein structure quaternary The arrangement of multiple polypeptides in a protein conformation The 3D shape of a protein denaturation The unfolding of a protein DNA Deoxyribonucleic acid, the genetic material RNA Ribonucleic acid, involved in protein synthesis ATP Adenosine triphosphate, the energy currency of the cell

Enzymes, chemical reaction, denaturation

PROTEIN DENATURATION

lecture 4 - denaturation and annealing of DNA

lecture 5 - denaturation & mutagenesis

Orders of protein structure and protein folding and denaturation

To Investigate The Effect of Heat Denaturation on Catalase Activity

3. Nucleic acids – types and biological role. Chemical composition – structure of nucleotides, chemical bonds. Free nucleotides of biological importance. Features of polynucleotide chains. Watson and Crick model. Primary structure of nucleic acids. Conformation of DNA and of the different types of RNA. Nucleosomes. Histone and nonhistone proteins. Denaturation and renaturation of DNA. Ribozymes, RNA maturation, microRNAs – role in the regulation of gene expression

2. Quaternary structure. Mechanisms maintaining the conformation of proteins. Relation between the structure and the function of proteins – medical importance: defects in receptors (familial hypercholesterolemia, diabetes insipidus); diseases due to impaired conformation (prion disease, Alzheimer’s disease); molecular diseases (sickle cell anemia); defects in the post-translational modification of proteins (scurvy and glycated hemoglobin). Structure of hemoglobin. Isoelectric point, precipitation of protein. Denaturation. Electrophoresis. Methods for protein examination – electrophoresis, chromatography, etc. Electrophoresis of plasma proteins – fractions

1. Standard (Conventional) PCR * Purpose: Basic DNA amplification. * Process: 1. Denaturation: DNA is heated to 94-98°C to separate the strands. 2. Annealing: Primers bind to the target sequence at 50-65°C. 3. Extension: DNA polymerase extends primers at 70-75°C to synthesize new DNA strands. * Applications: Cloning, gene expression analysis, genetic testing. 2. Real-Time PCR (qPCR) * Purpose: Quantifies DNA in real-time during the amplification process. * Process: Uses fluorescent dyes or probes to monitor the amplification in each cycle. * Applications: Gene expression analysis, quantifying pathogens, viral load detection. 3. Reverse Transcription PCR (RT-PCR) * Purpose: Converts RNA into complementary DNA (cDNA) for amplification. * Process: 1. Reverse Transcription: RNA is reverse transcribed into cDNA using reverse transcriptase. 2. PCR Amplification: The cDNA is then amplified using standard PCR. * Applications: Gene expression analysis, RNA virus detection (e.g., HIV, SARS-CoV-2), studying RNA biology. * Note: RT-PCR is critical for studying RNA as it allows researchers to study the transcriptome of a cell or organism. 4. Multiplex PCR * Purpose: Amplifies multiple DNA targets in a single PCR reaction. * Process: Uses more than one pair of primers to target different sequences simultaneously. * Applications: Disease diagnosis (e.g., detecting multiple pathogens), genetic testing, SNP analysis. * Challenges: Primer design and optimization to prevent primer interference. 5. Nested PCR * Purpose: Increases specificity and sensitivity by using two rounds of PCR. * Process: 1. First round: Amplifies a larger fragment. 2. Second round: Uses primers from within the first amplified fragment to increase specificity. * Applications: Low-abundance DNA detection, diagnostics, pathogen detection. 8. Digital PCR (dPCR) * Purpose: Provides absolute quantification of DNA or RNA. * Process: DNA or RNA is partitioned into many individual reactions; results are quantified based on the number of positive reactions. * Applications: Rare mutation detection, precise quantification of low-abundance targets. 10. LAMP (Loop-Mediated Isothermal Amplification) * Purpose: Isothermal amplification technique that does not require thermal cycling. * Process: Uses a set of primers and a strand-displacing DNA polymerase to amplify DNA at a constant temperature (60-65°C). * Applications: Rapid diagnostics, field testing, pathogen detection. 11. Degenerate PCR * Purpose: Amplifies a DNA sequence with degenerate primers, allowing detection of related sequences with unknown or varied nucleotide composition. * Process: Uses primers that contain ambiguous bases (e.g., R = A/G, Y = C/T) to target homologous sequences in related species or unknown genes. * Applications: Amplification of conserved genes across different species, detection of homologous gene families. * Note: Especially useful when the exact sequence of the target gene is unknown or highly variable. 12. Fast PCR * Purpose: Speeds up the PCR process by reducing cycle times. * Process: Optimizes the denaturation, annealing, and extension steps to reduce the overall PCR reaction time. * Applications: High-throughput screening, time-sensitive experiments, rapid diagnostics. * Note: Requires specially formulated polymerases and optimized protocols. 13. Random Amplification of Polymorphic DNA (RAPD) PCR * Purpose: Amplifies random DNA fragments from a genome using short, arbitrary primers, often used for genetic fingerprinting. * Process: A single arbitrary primer is used to amplify random genomic regions, generating a unique pattern of bands that can be analyzed. * Applications: Genetic diversity studies, DNA fingerprinting, phylogenetic studies, population genetics. * Note: RAPD PCR is used when a comprehensive genomic sequence is unavailable and can provide insight into genetic variation. huh

Here are the answers to your biology questions: 1. Definitions: * Metabolism: The sum total of all chemical reactions that occur within a living organism. * Catabolism: The breakdown of complex molecules into simpler ones, releasing energy. * Anabolism: The synthesis of complex molecules from simpler ones, requiring energy input. * Endergonic Reaction: A reaction that requires an input of energy to proceed. * Exergonic Reaction: A reaction that releases energy. 2. Role of Enzymes in Metabolism: Enzymes are biological catalysts that speed up chemical reactions by lowering the activation energy. They bind to specific substrates, forming an enzyme-substrate complex, and catalyze the reaction. This allows metabolic processes to occur at rates compatible with life. 3. Enzyme Activity: * Activation Energy: The minimum amount of energy required for a reaction to occur. * Catalyst: A substance that speeds up a chemical reaction without being consumed in the process. * Active Site: The specific region on an enzyme where the substrate binds. * Denaturation: The loss of an enzyme's shape and function, often due to extreme temperature or pH. * Substrate: The molecule upon which an enzyme acts. * Enzyme-Substrate Complex: A temporary complex formed when an enzyme binds to its substrate. * Suffix -ase: Commonly used to denote enzymes, such as sucrase, protease, and lipase. 4. Oxidation-Reduction Reactions in Cellular Respiration: In cellular respiration, oxidation-reduction reactions involve the transfer of electrons and hydrogen ions. Oxidation is the loss of electrons (and often hydrogen atoms), while reduction is the gain of electrons (and often hydrogen atoms). Energy is released during these reactions and is used to produce ATP. 5. Balanced Equation for Cellular Respiration: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + energy (ATP) 6. Structure of a Mitochondrion: * Outer Membrane: Encloses the mitochondrion. * Inner Membrane: Folded into cristae, increasing surface area for ATP production. * Intermembrane Space: The space between the outer and inner membranes. * Matrix: The fluid-filled space inside the inner membrane, containing enzymes for the citric acid cycle. 7. Glycolysis: Glycolysis is the breakdown of glucose into pyruvate. It occurs in the cytoplasm and produces 2 ATP, 2 NADH, and 2 pyruvate molecules. 8. Citric Acid Cycle: The citric acid cycle, also known as the Krebs cycle, occurs in the mitochondrial matrix. It completely oxidizes pyruvate, producing 2 ATP, 6 NADH, and 2 FADH₂ molecules per glucose molecule. 9. Electron Transport Chain and Oxidative Phosphorylation: The electron transport chain is a series of protein complexes embedded in the inner mitochondrial membrane. Electrons from NADH and FADH₂ are transferred through the chain, releasing energy that is used to pump protons into the intermembrane space. The resulting proton gradient drives ATP synthesis through ATP synthase. 10. ATP and NADH Production: * Glycolysis: 2 ATP, 2 NADH * Citric Acid Cycle: 2 ATP, 6 NADH, 2 FADH₂ * Electron Transport Chain: ~32 ATP (from NADH and FADH₂) 11. Structure and Function of a Dicot Leaf: Dicot leaves are typically broad and flat, with a network of veins. They have a waxy cuticle to prevent water loss, stomata for gas exchange, and mesophyll cells containing chloroplasts for photosynthesis. 12. Structure of a Chloroplast: * Thylakoid: A flattened, disc-shaped sac. * Thylakoid Membrane: The membrane surrounding the thylakoid. * Thylakoid Space: The interior of the thylakoid. * Stroma: The fluid-filled space outside the thylakoids. * Grana: Stacks of thylakoids. 13. Site of Light-Dependent and Light-Independent Reactions: * Light-Dependent Reactions: Thylakoid membrane * Light-Independent Reactions (Calvin Cycle): Stroma 14. Balanced Equation for Photosynthesis: 6CO₂ + 6H₂O + light energy → C₆H₁₂O₆ + 6O₂ * Carbon (C) from CO₂ is incorporated into glucose. * Hydrogen (H) from water (H₂O) is incorporated into glucose. * Oxygen (O) from water is released as O₂. 15. Dual Nature of Light: Light exhibits both wave-like and particle-like properties. As a wave, it has a wavelength and frequency. As a particle, it consists of photons, discrete packets of energy. 16. Light Reactions: Light energy is absorbed by pigments in photosystems I and II, exciting electrons. These electrons are transferred through a series of electron carriers, generating ATP and NADPH. Water is split, releasing oxygen as a byproduct. 17. Calvin Cycle: The Calvin cycle uses ATP and NADPH from the light reactions to fix CO₂ from the atmosphere. CO₂ is incorporated into RuBP, forming 3-PGA. 3-PGA is reduced to G3P, which can be used to synthesize glucose or regenerate RuBP. 18. Role of Photosynthetic Pigments: Photosynthetic pigments, such as chlorophyll a, chlorophyll b, and carotenoids, absorb light energy and transfer it to the reaction center of photosystems. 19. Role of Photosystems: Photosystems I and II are protein complexes containing pigments and electron carriers. They absorb light energy and use it to excite electrons, initiating the electron transport chain. 20. Phases of the Calvin Cycle: * Carbon Fixation: CO₂ is fixed to RuBP, forming 3-PGA. * Reduction: 3-PGA is reduced to G3P using ATP and NADPH. * Regeneration of RuBP: G3P is used to regenerate RuBP, allowing the cycle to continue. 21. ATP, NADPH, and CO₂ Requirements: * To produce 1 G3P molecule: 9 ATP, 6 NADPH, and 3 CO₂ * To produce 1 glucose molecule: 18 ATP, 12 NADPH, and 6 CO₂ I

ENE-1.D = Describe the properties of enzymes. The structure of enzymes includes the active site that specifically interacts with substrate molecules For an enzyme-mediated chemical reaction to occur = the shape & charge of the substrate must be compatible with the active site of the enzyme ENE-1.E = Explain how enzymes affect the rate of biological reactions The structure and function of enzymes contribute to the regulation of biological processes Enzymes are biological catalysts that facilitate chemical reactions (speed up) in cells by lowering the activation energy ENE-1.F = Explain how changes to the structure of an enzyme may affect its function Change to the molecular structure of a component in an enzymatic system may result in a change of the function or efficiency of the system Denaturation of an enzyme occurs when the protein structure is disrupted → eliminating the ability to catalyze reactions Environmental temperatures & pH outside the optimal range for a given enzyme will cause changes to its structure → altering the efficiency with which it catalyzes reactions In some cases, enzyme denaturation is reversible → allowing the enzyme to regain activity ENE-1.G = Explain how the cellular environment affects enzyme activity Environmental pH can alter the efficiency of enzyme activity = including through disruption of hydrogen bonds that provide enzyme structure The relative concentrations of substrates & products determine how efficiently an enzymatic reaction proceeds Higher environmental temperatures increase the speed of movement of molecules in a solution → increasing the frequency of collisions between enzymes & substrates → therefore increasing the rate of reaction Competitive inhibitor molecules can bind reversibly or irreversibly to the active site of the enzyme Noncompetitive inhibitors can bind allosteric sites = changing the activity of the enzyme ENE-1.H = Describe the role of energy in living organisms All living systems require constant input of energy Life requires a highly ordered system & does not violate the second law of thermodynamics Energy input must exceed energy loss to maintain order & to power cellular processes Cellular processes that release energy may be coupled with cellular processes that require energy Loss of order or energy flow results in death Energy-related pathways in biological systems are sequential to allow for a more controlled & efficient transfer of energy A product of a reaction in a metabolic pathway is generally the reactant for the subsequent step in the pathway ENE-1.I = Describe the photosynthetic processes that allow organisms to capture & store energy Organisms capture & store energy for use in biological processes Photosynthesis captures energy from the sun & produces sugars Photosynthesis first evolved in prokaryotic organisms Scientific evidence supports the claim that prokaryotic (cyanobacterial) photosynthesis was responsible for the production of an oxygenated atmosphere Prokaryotic photosynthetic pathways were the foundation of eukaryotic photosynthesis The light-dependent reactions of photosynthesis in eukaryotes = involve a series of coordinated reaction pathways that capture energy present in light to yield ATP & NADPH (power the production of organic molecules) ENE-1.J = Explain how cells capture energy from light & transfer it to biological molecules for storage & use During photosynthesis = chlorophylls absorb energy from light = boosting electrons to a higher energy level in photosystems I & II Photosystems I & II are embedded in the internal membranes of chloroplasts & are connected by the transfer of higher energy electrons through an electron transport chain (ETC) When electrons are transferred between molecules in a sequence of reactions as they pass through the ETC = an electrochemical gradient of protons (hydrogen ions) is established across the internal membrane The formation of the proton gradient is linked to the synthesis of ATP from ADP & inorganic phosphate via ATP synthase The energy captured in the light reactions & transferred to ATP + NADPH = powers the production of carbohydrates from carbon dioxide in the Calvin cycle (which occurs in the stroma of the chloroplast) ENE-1.K = Describe the processes that allow organisms to use energy stored in biological macromolecules Fermentation & cellular respiration = use energy from biological macromolecules to produce ATP Respiration & fermentation = characteristic of all forms of life Cellular respiration in eukaryotes = involves a series of coordinated enzyme-catalyzed reactions that capture energy from biological macromolecules The electron transport chain = transfers energy from electrons in a series of coupled reactions that establish an electrochemical gradient across membranes Electron transport chain reactions = occur in chloroplasts / mitochondria / prokaryotic plasma membranes In cellular respiration = electrons delivered by NADH & FADH2 = passed to a series of electron acceptors (as they move toward the terminal electron acceptor = oxygen) In photosynthesis = the terminal electron acceptor is NADP+ Aerobic prokaryotes = use oxygen as a terminal electron acceptor anaerobic prokaryotes = use other molecules The transfer of electrons = accompanied by the formation of a proton gradient across the inner mitochondrial membrane / the internal membrane of chloroplasts (with the membrane(s) separating a region of high proton concentration from a region of low proton concentration In prokaryotes = the passage of electrons is accompanied by the movement of protons across the plasma membrane. The flow of protons back through membrane-bound ATP synthase by chemiosmosis drives the formation of ATP from ADP & inorganic phosphate known as oxidative phosphorylation in cellular respiration photophosphorylation in photosynthesis In cellular respiration = decoupling oxidative phosphorylation from electron transport generates heat This heat can be used by endothermic organisms to regulate body temperature ENE-1.L = Explain how cells obtain energy from biological macromolecules in order to power cellular functions Glycolysis = a biochemical pathway that releases energy in glucose to form ATP from ADP & inorganic phosphate / NADH from NAD+ /pyruvate Pyruvate = transported from the cytosol to the mitochondrion = where further oxidation occurs In the Krebs cycle = carbon dioxide is released from organic intermediates = ATP is synthesized from ADP + inorganic phosphate & electrons are transferred to the coenzymes NADH + FADH2 Electrons extracted in glycolysis & Krebs cycle reactions = transferred by NADH & FADH2 to the electron transport chain in the inner mitochondrial membranE When electrons are transferred between molecules in a sequence of reactions as they pass through the ETC = an electrochemical gradient of protons (hydrogen ions) across the inner mitochondrial membrane is established Fermentation allows glycolysis to proceed in the absence of oxygen & produces organic molecules (including alcohol & lactic acid = as waste products) The conversion of ATP to ADP = releases energy = which is used to power many metabolic processes SYI-3.A = Explain the connection between variation in the number & types of molecules within cells to the ability of the organism to survive and/or reproduce in different environments. Variation at the molecular level = provides organisms with the ability to respond to a variety of environmental stimuli Variation in the number & types of molecules within cells provides organisms a greater ability to survive and/or reproduce in different environments Kk

PROTEIN DENATURATION BC LAB

M 8: Protein Denaturation (Part 2)

M8: Protein Denaturation (Part 1)

Activity 6: Investigate the effect of heat denaturation on the activity of an enzyme (catalase)

Biochemistry: Unit Test 2 Proteins structure, polymerization and denaturation

Modes of protein denaturation

experiment 2.6- to investigate the effect of heat denaturation on enzyme activity