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What is the primary purpose of plasmid vectors in antibiotic-resistant bacteria?

To enhance cell division

To decrease metabolic activity

To restrict gene expression

To facilitate propagation of recombinant molecules (correct)

Which of the following describes the action of restriction endonucleases?

They recognize palindromic sequences and cleave double-stranded DNA. (correct)

They synthesize RNA from DNA.

They enhance DNA replication speed.

They inhibit translation of mRNA.

What method is primarily utilized for DNA sequencing as described in the content?

Gel electrophoresis

DNA hybridization technique

Transcription sequencing

Chain-termination method (correct)

What was Kary Mullis's significant contribution to molecular biology?

Development of the polymerase chain reaction (PCR) Signup and view all the answers

How is mRNA used to obtain protein-coding sequences?

By converting mRNA to cDNA Signup and view all the answers

What was a key factor in Buchner's success in demonstrating cell-free fermentation?

He used a mixture of quartz sand and diatomaceous earth. Signup and view all the answers

What was a limitation of Pasteur's experiment in fermentation?

He ground his yeast with ground glass, making the extract alkaline. Signup and view all the answers

Which strain of yeast did Buchner successfully use for fermentation?

Saccharomyces cerevisiae Signup and view all the answers

What is one characteristic of carbon bonding in biochemical molecules?

A carbon atom can form a maximum of four single bonds. Signup and view all the answers

Which statement about carbon–carbon bond rotation is true?

Rotation around carbon–carbon sigma bonds is easy. Signup and view all the answers

What is the primary function of a genome?

To serve as the genetic material of an organism Signup and view all the answers

Which of the following is NOT part of a genome?

Polysaccharides Signup and view all the answers

What role do telomeres play in chromosomes?

They protect the ends of chromosomes from degradation. Signup and view all the answers

What are cloning vectors typically used for in DNA cloning?

To facilitate the delivery and replication of foreign DNA Signup and view all the answers

Which enzyme is responsible for covalently linking DNA fragments during DNA cloning?

DNA ligase Signup and view all the answers

What is the purpose of bioinformatics in genomics?

To discover the function of unknown genes Signup and view all the answers

What is a characteristic of recombinant DNA?

It includes segments from two or more different sources. Signup and view all the answers

What are sequence-specific endonucleases used for in DNA cloning?

To cut target DNA at precise locations Signup and view all the answers

What is the role of threonine residues in the antifreeze protein of the yellow mealworm?

They form hydrogen bonds with water to inhibit ice crystal growth. Signup and view all the answers

Which type of work does osmotic work refer to in biological systems?

Maintaining varying solute concentrations across membranes. Signup and view all the answers

How does homeostasis differ from equilibrium in biological systems?

Homeostasis maintains steady conditions, while equilibrium has no net change. Signup and view all the answers

Which statement best describes the energy needs of biological systems?

ATP, ADP, and AMP manage short-term energy needs. Signup and view all the answers

What is the primary role of the antifreeze protein in the yellow mealworm during winter?

To prevent damage from ice crystals to membranes. Signup and view all the answers

Which of the following statements is true regarding exergonic and endergonic reactions?

They are often coupled to sustain metabolism. Signup and view all the answers

What is the main function of ATP in biological systems?

To serve as the primary energy currency. Signup and view all the answers

Which of the following types of work involves the biosynthesis of organic molecules?

Chemical work. Signup and view all the answers

What does a negative value of Gibbs energy (ΔG) indicate about a reaction?

The reaction proceeds spontaneously. Signup and view all the answers

Which thermodynamic quantity reflects the disorder or randomness of a system?

Entropy (S) Signup and view all the answers

What is the standard unit for measuring Gibbs energy change (ΔG)?

Kilojoules per mole (kJ/mol) Signup and view all the answers

What does it mean when ΔH has a positive value?

The reaction is endothermic. Signup and view all the answers

Which statement correctly describes an exergonic reaction?

It proceeds spontaneously. Signup and view all the answers

What is the relationship between Gibbs energy change (ΔG) and the equilibrium constant (K_eq)?

A negative ΔG indicates a spontaneous reaction favoring products. Signup and view all the answers

How does the presence of water contribute to biochemical reactions?

Water can donate or accept hydrogen bonds. Signup and view all the answers

What does the term 'mass-action ratio' refer to in the context of Gibbs energy?

The ratio of product concentrations to reactant concentrations. Signup and view all the answers

According to the information, what does a reaction with a ΔS < 0 signify?

The products are more complex and ordered than the reactants. Signup and view all the answers

Which of the following properties makes water essential for life?

Water acts as a universal solvent. Signup and view all the answers

What does it mean if a reaction has a ΔG of +2.38 x 10^4 J/mol?

The reaction requires energy to proceed. Signup and view all the answers

During ATP hydrolysis, what type of reaction occurs?

Exergonic reaction releasing energy. Signup and view all the answers

Which of the following best describes the significance of hydrogen bonding in water?

It allows for high heat of vaporization and surface tension. Signup and view all the answers

In the context of biochemical reactions, what is the importance of ATP?

ATP is a carrier of chemical energy for cellular processes. Signup and view all the answers

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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