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Questions and Answers
What is the primary purpose of plasmid vectors in antibiotic-resistant bacteria?
Which of the following describes the action of restriction endonucleases?
What method is primarily utilized for DNA sequencing as described in the content?
What was Kary Mullis's significant contribution to molecular biology?
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How is mRNA used to obtain protein-coding sequences?
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What was a key factor in Buchner's success in demonstrating cell-free fermentation?
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What was a limitation of Pasteur's experiment in fermentation?
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Which strain of yeast did Buchner successfully use for fermentation?
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What is one characteristic of carbon bonding in biochemical molecules?
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Which statement about carbon–carbon bond rotation is true?
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What is the primary function of a genome?
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Which of the following is NOT part of a genome?
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What role do telomeres play in chromosomes?
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What are cloning vectors typically used for in DNA cloning?
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Which enzyme is responsible for covalently linking DNA fragments during DNA cloning?
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What is the purpose of bioinformatics in genomics?
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What is a characteristic of recombinant DNA?
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What are sequence-specific endonucleases used for in DNA cloning?
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What is the role of threonine residues in the antifreeze protein of the yellow mealworm?
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Which type of work does osmotic work refer to in biological systems?
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How does homeostasis differ from equilibrium in biological systems?
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Which statement best describes the energy needs of biological systems?
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What is the primary role of the antifreeze protein in the yellow mealworm during winter?
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Which of the following statements is true regarding exergonic and endergonic reactions?
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What is the main function of ATP in biological systems?
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Which of the following types of work involves the biosynthesis of organic molecules?
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What does a negative value of Gibbs energy (ΔG) indicate about a reaction?
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Which thermodynamic quantity reflects the disorder or randomness of a system?
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What is the standard unit for measuring Gibbs energy change (ΔG)?
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What does it mean when ΔH has a positive value?
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Which statement correctly describes an exergonic reaction?
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What is the relationship between Gibbs energy change (ΔG) and the equilibrium constant (K_eq)?
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How does the presence of water contribute to biochemical reactions?
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What does the term 'mass-action ratio' refer to in the context of Gibbs energy?
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According to the information, what does a reaction with a ΔS < 0 signify?
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Which of the following properties makes water essential for life?
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What does it mean if a reaction has a ΔG of +2.38 x 10^4 J/mol?
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During ATP hydrolysis, what type of reaction occurs?
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Which of the following best describes the significance of hydrogen bonding in water?
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In the context of biochemical reactions, what is the importance of ATP?
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Study Notes
Genome
- Genomic DNA is the genetic material of an organism.
- Consists of DNA or RNA, which includes coding regions, non-coding DNA, and mitochondrial/chloroplast genetic material.
Condensation of Eukaryotic DNA Into Chromosomes
- Occurs when all four subunits of a protein complex bind at the same time, twisting the DNA into a loop.
Telomeres Protect the Ends of Chromosomes From Degradation
- They function to prevent degradation of ends of chromosomes.
Genes Are Regions of DNA that Contain a Coding Sequence for Functional Biomolecules
- Genes are sections of DNA containing sequences that code for functional biomolecules.
Bioinformatics Is Used in Biochemistry to Discover the Function of an Unknown Gene
- Bioinformatics is used in finding the functions of unknown genes.
Bioinformatic Analysis Is Ushering in the Age of Precision Medicine
- Bioinformatics analysis is critical for the development of precision medicine.
The Spread of Infectious Disease Can be Mapped Using DNA Sequencing and Bioinformatics
- Infectious disease spread can be mapped using DNA sequencing and bioinformatics.
Tracking COVID-19: SARS-CoV-2 Coronavirus Mutations
- Genome sequencing and bioinformatics are essential in tracking SARS-CoV-2 mutations.
- Genome sequencing allows for tracking the spread of specific mutations.
Genomic Epidemiology of SARS-CoV-2
- Genomic epidemiology of SARS-CoV-2 relies on the sequencing and analysis of viral genomes.
Restriction Endonucleases Recognize Palindromic Sequences in DNA and Cleave Double-Stranded DNA
- Restriction endonucleases are enzymes that recognize and cleave specific palindromic sequences in DNA.
- They are crucial for DNA cloning and manipulation.
Genomic DNA Cloning Is Based on Methods Collectively Called Recombinant DNA Technology
- Recombinant DNA technology is a broad term referring to techniques used for cloning and manipulating DNA.
Protein-Coding Sequences Can be Cloned Using mRNA That Is Converted to cDNA
- Reverse transcription is used to create a complementary DNA (cDNA) copy of mRNA.
- This cDNA can then be cloned to express the corresponding protein.
The Chain-Termination Method Can be Used to Determine the Sequence of a Region of DNA
- The chain-termination method is a standard method used to determine the sequence of a DNA region.
- It involves using chain terminating dideoxynucleotides during DNA replication, which can then be analyzed to determine the sequence.
The Polymerase Chain Reaction (PCR)
- PCR is a technique used to amplify specific DNA sequences exponentially.
- It is crucial in molecular biology for various applications, including diagnostics, research, and genetic analysis.
Kary Mullis
- Kary Mullis was the inventor of the Polymerase Chain Reaction technique.
- Mullis shared the 1993 Nobel Prize in Chemistry with Michael Smith for his work on PCR.
- While driving in 1983, Mullis conceived the idea of using oligonucleotide primers to copy DNA sequences.
- Mullis received a 10,000bonusfromCetusCorporationfortheinvention,andlaterthecompanysoldthepatentrightstoHoffmannLa−Rochefor10,000 bonus from Cetus Corporation for the invention, and later the company sold the patent rights to Hoffmann La-Roche for 10,000bonusfromCetusCorporationfortheinvention,andlaterthecompanysoldthepatentrightstoHoffmannLa−Rochefor300,000,000.
Louis Pasteur
- Louis Pasteur attempted to demonstrate cell-free fermentation but failed.
- Majority of scientists believed fermentation was a result of a "vital life force", and Pasteur's failure reinforced this belief.
Eduard Buchner
- Eduard Buchner was the first to demonstrate cell-free fermentation.
- Buchner used a mixture of quartz sand and diatomaceous earth to grind yeast, while Pasteur had used ground glass, which made the extract alkaline, inactivating some enzymes.
- Buchner's success came from his use of a 40% sucrose solution as a "preservative", and a different strain of yeast (Saccharomyces cerevisiae).
Chemical Bonding in Biochemistry
- Common carbon bonds in biochemistry are C-C, C=C, C-H, C=O, C-N, C-S, and C-O.
Molecular Geometry of Carbon Atoms
- Carbon atoms can form a maximum of four single bonds, displaying a tetrahedral geometry.
- Rotation around a carbon-carbon sigma (σ) single bond is easy, but rotation around a carbon-carbon pi (π) double bond is not possible without breaking the bond.
Silicon-based Life Forms
- Silicon-based life forms are a theoretical possibility.
- The hypothesis is that silicon could potentially form the basis for life, although the exact structure and properties of such life forms are unknown.
Antifreeze Protein
- The yellow mealworm (Tenebrio molitor) larva contains high levels of an antifreeze protein during winter months.
- This protein prevents ice crystal formation and damage to cell membranes, allowing the larvae to survive low temperatures.
- The protein contains pairs of threonine residues within a повторяющаяся sequence of 12 amino acids, providing hydrogen bonding interactions with water molecules that prevent ice crystal growth.
Energy Conversion in Biological Systems
- All biological processes adhere to the laws of thermodynamics.
- Life requires maintaning a highly ordered steady state called homeostasis.
- Sunlight is the main source of energy for most biological systems
- Exergonic and endergonic reactions are often coupled in metabolism.
- The adenylate system (ATP, ADP, AMP) is responsible for managing many short-term energy needs in biological systems.
Different Types of Energy
- Biological systems utilize different types of energy.
- Kinetic energy is the energy of motion.
- Potential energy is stored energy.
- Chemical energy is stored within chemical bonds.
Different Types of Work
- Energy conversion in living systems is necessary for three types of work: osmotic work, chemical work, and mechanical work.
- Osmotic work maintains solute gradients across biological membranes.
- Chemical work involves biosynthesis (anabolism) and degradation (catabolism) of organic molecules.
- Mechanical work includes muscle contraction in animals.
Sunlight Is the Source of Energy for Almost All Biological Systems
- Sunlight is the ultimate energy source for most living organisms.
- Photosynthetic organisms convert light energy into chemical energy, which is then used by other organisms.
Homeostasis vs. Equilibrium
- Homeostasis is a state of steady internal physical and chemical conditions.
- Equilibrium refers to a state where reactants and products transition between states at equal rates.
- Homeostasis requires energy to maintain, whereas equilibrium does not.
Biological Energy Transformations Obey the Laws of Thermodynamics
- Gibbs energy (G), Enthalpy (H), and Entropy (S) are thermodynamic quantities that describe energy changes in chemical reactions.
- Each thermodynamic quantity has specific units and indicates whether the reaction is releasing or requiring energy.
Gibbs Energy (Free Energy)
- The amount of energy available to do work during a reaction at constant temperature and pressure.
- Exergonic reactions release energy and have a negative ΔG.
- Endergonic reactions require energy and have a positive ΔG.
- The units of ΔG are joules/mole (J mol–1).
One Joule in Everyday Life Is Approximately
- The energy required to lift a small apple one meter straight up (about 102 g).
- The energy released when the apple falls one meter to the ground.
- The energy delivered by a 1-watt solar panel every second.
- The energy released as heat by a person at rest every 1/60th of a second.
- The kinetic energy of a 50 kg human moving very slowly (0.2 m/s or 0.72 km/h).
Enthalpy (H)
- Reflects the heat content of the reacting system.
- Determined by the number and kind of chemical bonds in reactants and products.
- Exothermic reactions release heat and have a negative ΔH.
- Endothermic reactions absorb heat and have a positive ΔH.
- The units of ΔH are joules/mole (J mol–1).
Entropy (S)
- Entropy is a measure of the randomness or disorder of a system.
- If the products of a reaction are more complex and ordered than the reactants, entropy decreases and ΔS is negative.
- If the products are less complex and disordered than the reactants, entropy increases and ΔS is positive.
- The units of ΔS are joules/(mole kelvins) (J mol–1 K–1).
Relationship of the Three Thermodynamic Quantities
- ΔH = ΔG + TΔS or ΔG = ΔH – TΔS (T is in kelvins).
- All spontaneous reactions have ΔGsystem < 0.
- Processes that occur spontaneously result in a decrease in system Gibbs energy and an increase in universe entropy (ΔSuniverse > 0).
Spontaneity of Reactions
- Exergonic processes: ΔGsystem < 0 (Energy-yielding, proceed spontaneously, but may be slow).
- Endergonic processes: ΔGsystem > 0 (Energy-requiring, cannot proceed spontaneously).
Standard Gibbs Energy Change
- Standard state used in chemistry: Temperature of 298 K (25 °C), reactants and products initially at 1 M concentrations (or partial pressures of 101.3 kPa for gases), standard Gibbs energy change = ΔG°.
- Standard state used in biochemistry: [H+] =10–7 M (pH = 7.0), [H2O] = 55.5 M, if Mg2+ is present, then [Mg2+] is constant at 1 mM, standard Gibbs energy change = ΔG°′.
The Relationship Between ΔG°′ and K′eq
- ΔG°′ represents the standard Gibbs energy change at standard conditions.
- K′eq represents the standard equilibrium constant at standard conditions.
- The equation shows the relationship between these two values, where R is the gas constant (8.314 J mol-1 K-1).
Calculation of ΔG°′ (1 of 2)
- This is a numerical example demonstrating how to calculate ΔG°′.
Calculation of ΔG°′ (2 of 2)
- This is the completion of the numerical example demonstrating how to calculate ΔG°′.
Calculating ΔG (1 of 2)
- Equation for calculating Gibbs energy change based on equilibrium constant and prevailing concentrations.
Calculating ΔG (2 of 2)
- Another equation for calculating Gibbs energy change using various factors.
Gibbs Energy Changes (ΔG) Depend on Temperature and the Concentrations of Reactants and Products
- The equation shows a clear relationship between Gibbs energy change (ΔG), standard Gibbs energy change (ΔG°′), temperature, and the concentrations of reactants and products.
Glycolytic Pathway Reaction 4 (ΔG°′ = +23.8 kJ/mol)
- A specific example of a reaction within the glycolytic pathway.
Actual Change in Gibbs Energy (ΔG) for Reaction 4 at 37 °C and Steady-State Concentrations (1 of 4)
- This is a numerical example detailing the calculation of the actual Gibbs energy change for a reaction within the glycolytic pathway.
Actual Change in Gibbs Energy (ΔG) for Reaction 4 at 37 °C and Steady-State Concentrations (2 of 4)
- Continuation of the numerical example, showing how to determine the mass action ratio.
Actual Change in Gibbs Energy (ΔG) for Reaction 4 at 37 °C and Steady-State Concentrations (3 of 4)
- Continuation of the numerical example, showing how to apply the equation to calculate the actual Gibbs energy change.
Actual Change in Gibbs Energy (ΔG) for Reaction 4 at 37 °C and Steady-State Concentrations (4 of 4)
- Completion of the numerical example, showing the calculation of the actual Gibbs energy change in the specific example of the glycolytic pathway reaction.
ATP Is a Carrier of Chemical Energy in Living Systems
- ATP (adenosine triphosphate) is a crucial molecule that acts as a carrier of chemical energy in living organisms.
- It is involved in many cellular processes, including metabolism, biosynthesis, and signaling.
Glutamine Synthesis from Glutamate Is a Two-step Reaction Involving ATP
- Glutamine synthesis is a two-step reaction catalyzed by glutamine synthetase.
- ATP is required for this process and is used to activate glutamate, facilitating the subsequent addition of ammonia to form glutamine.
ATP Hydrolysis Can Provide Energy for Protein Conformational Changes
- The hydrolysis of ATP (breaking down ATP into ADP and inorganic phosphate) releases energy.
- This energy can be used to drive protein conformational changes, allowing proteins to perform their functions.
Adenylate Kinase Plays a Central Role in Maintaining ATP Levels in the Cell
- Adenylate kinase is an enzyme that catalyzes the reversible interconversion of ADP and AMP to ATP.
- This enzyme plays a vital role in maintaining ATP levels within the cell, ensuring that there is sufficient energy available for cellular processes.
ATP, ADP and AMP Concentrations Vary as a Function of Energy Charge
- The energy charge of a cell is a measure of its energy status.
- When ATP levels are high, energy charge is high.
- When AMP levels are high, energy charge is low.
- The cell's energy charge is crucial in regulating metabolic processes.
Balanced Flux Through Catabolic and Anabolic Pathways Maintain the Steady State
- Catabolic pathways break down molecules, releasing energy (usually stored in ATP).
- Anabolic pathways build up molecules, requiring energy (usually provided by ATP).
- A balance between catabolic and anabolic fluxes is necessary to maintain homeostasis and proper cellular function.
Water Is Critical for Life Processes
- Water is crucial for life and constitutes a significant portion of most cells (more than 70% of mass).
- Water's unique chemical properties are essential for many biochemical reactions and processes.
The Unique and Unusual Properties of Water (1 of 3)
- Water exhibits unusually high boiling point (100°C) and melting point (0°C) compared to other similar molecules like hydrogen sulfide (H2S), hydrogen selenide (H2Se), and hydrogen telluride (H2Te).
- This is attributed to the strong hydrogen bonding between water molecules.
The Unique and Unusual Properties of Water (2 of 3)
- Water has a high heat capacity, which is its ability to absorb a large amount of energy before changing temperature.
- This makes water useful for temperature regulation and maintaining a stable internal temperature in organisms.
- Water has high latent heats of fusion and vaporization. It requires a lot of energy to melt ice (fusion) or vaporize liquid water (vaporization). This property of water makes ice a useful coolant and steam a valuable source of heat.
The Unique and Unusual Properties of Water (3 of 3)
- Water is an excellent solvent, thanks to its polarity.
- Water exhibits a high surface tension, enabling water-based organisms to move on water surfaces and contributing to its ability to support life.
- Water becomes less dense as a solid (ice) due to its unique crystal structure, allowing aquatic life to survive in cold environments.
Surface Tension
- Water molecules exhibit strong cohesive forces, resulting in surface tension.
- The cohesive forces arise from strong hydrogen bonding between water molecules.
Water Contains an Oxygen Atom and Two Hydrogen Atoms
- Water molecules are composed of one oxygen atom and two hydrogen atoms.
- The arrangement of these atoms gives water its unique bent structure and polarity.
The Polarity of Water Enables It to Function as Both a Hydrogen-Bond Donor and a Hydrogen-Bond Acceptor
- Due to its bent structure and the electronegativity difference between oxygen and hydrogen, water has two slightly positive hydrogen atoms and one slightly negative oxygen atom.
- This polarity allows water molecules to form hydrogen bonds with each other and with other polar molecules.
- Water molecules in liquid water form and break hydrogen bonds constantly (every 10 ps), contributing to its unique properties.
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