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Questions and Answers
What is the significance of the isoelectric point (pI) in amino acids?
What is the significance of the isoelectric point (pI) in amino acids?
Which of the following techniques would be most effective in separating proteins based on their size?
Which of the following techniques would be most effective in separating proteins based on their size?
What is a zwitterion in the context of amino acids?
What is a zwitterion in the context of amino acids?
Which statement about peptide bond formation is true?
Which statement about peptide bond formation is true?
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What property of proteins is primarily utilized in column chromatography for their separation?
What property of proteins is primarily utilized in column chromatography for their separation?
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What defines the equilibrium constant in a chemical reaction?
What defines the equilibrium constant in a chemical reaction?
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How does an increase in temperature generally affect reaction speed?
How does an increase in temperature generally affect reaction speed?
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What is a characteristic of water that makes it essential for life?
What is a characteristic of water that makes it essential for life?
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What is the reason ice floats on water?
What is the reason ice floats on water?
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What does the Henderson-Hasselbalch equation relate?
What does the Henderson-Hasselbalch equation relate?
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Which of the following describes the hydrophobic effect?
Which of the following describes the hydrophobic effect?
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What do weak acids and their conjugate bases do in a buffer solution?
What do weak acids and their conjugate bases do in a buffer solution?
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What happens when water ionizes?
What happens when water ionizes?
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What is one unique feature of living matter that distinguishes it from non-living matter?
What is one unique feature of living matter that distinguishes it from non-living matter?
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Which statement best describes the role of RNA in the origins of life?
Which statement best describes the role of RNA in the origins of life?
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In thermodynamics, what is the significance of Gibbs free energy?
In thermodynamics, what is the significance of Gibbs free energy?
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How do endergonic reactions differ from exergonic reactions?
How do endergonic reactions differ from exergonic reactions?
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What type of system do living organisms represent in thermodynamics?
What type of system do living organisms represent in thermodynamics?
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Which of the following functional groups is characteristic of biological molecules?
Which of the following functional groups is characteristic of biological molecules?
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What is the primary reason why carbon is considered unique and critical to biochemistry?
What is the primary reason why carbon is considered unique and critical to biochemistry?
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What defines the difference between catabolism and anabolism?
What defines the difference between catabolism and anabolism?
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Study Notes
Biochemistry of Life
- Features of living matter include responsiveness, reproduction, growth, and metabolism.
- Life is divided into three domains: Archaea, Bacteria, and Eukarya.
- Basic cell structure consists of a membrane, cytoplasm, ribosomes, and genetic material.
- Unique cellular components include peptidoglycan in bacteria and chloroplasts in plants.
- Energy and carbon sources are crucial for cellular processes, with glucose being a primary input.
- Essential elements for life: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur.
- Carbon's tetravalence allows diverse bonding and compound formation.
- Common functional groups include hydroxyl, carboxyl, amino, and phosphate.
- Cis vs. trans configurations affect molecular shape and function.
- The origin of life theory suggests simple molecules led to complex organic compounds.
- RNA is postulated as the first genetic material due to its ability to store information and catalyze reactions.
- Mutation contributes to the fidelity of information replication and genetic diversity.
- Endosymbiotic theory explains the origin of organelles through symbiotic relationships.
Thermodynamics
- Living organisms adhere to the laws of thermodynamics, particularly energy conservation.
- Energy transformation is fundamental for biological processes.
- Equilibrium refers to a state of balance, while dynamic steady-state indicates constant change.
- Living organisms are open systems, exchanging matter and energy with their environment.
- Metabolism encompasses catabolism (energy-releasing) and anabolism (energy-consuming) processes.
- Gibbs free energy indicates the maximum reversible work; essential for predicting reaction spontaneity.
- Entropy, enthalpy, and temperature influence free-energy calculations.
- Reaction spontaneity is distinct from reaction rate; endergonic reactions require energy, while exergonic reactions release it.
- The equilibrium constant relates to standard free-energy changes, illustrating reaction balance.
- Reaction coupling allows non-spontaneous reactions to occur by associating them with spontaneous ones.
- Biological catalysts (enzymes) lower activation energy, enhancing reaction rates.
Water
- Water is vital for life due to its unique properties and solvent capabilities.
- A water molecule is polar, enabling hydrogen bonds with other molecules.
- Ice is less dense than liquid water due to hydrogen bonding creating a crystalline structure.
- Water's solvent properties lead to interactions with both polar (hydrophilic) and nonpolar (hydrophobic) substances.
- Amphipathic molecules possess both hydrophilic and hydrophobic properties, influencing membrane structure.
- Noncovalent interactions, such as hydrogen bonds and Van der Waals forces, stabilize molecular structures.
- Hydrophobic effects arise when nonpolar substances aggregate to minimize exposure to water.
- Colligative properties, like boiling point elevation and freezing point depression, depend on solute concentration.
- Osmotic pressure is the force generated by water movement across a semipermeable membrane, critical for cell function.
Ionization of Water, Dissociation of Weak Acids, and Buffers
- Ionization of water produces H+ and OH- ions; pure water maintains a neutral pH (~7).
- Proton hopping refers to the rapid transfer of protons between water molecules.
- The ion-product constant (Kw) aids in calculating pH; pH measures hydrogen ion concentration.
- Strong acids fully dissociate in solution; weak acids only partially dissociate.
- Acid dissociation constant (Ka) quantifies weak acid strength, while pKa is its logarithmic form.
- Buffers resist changes in pH by neutralizing added acids or bases, vital for biological systems.
- Henderson-Hasselbalch equation relates pH, pKa, and the ratio of concentrations of acid/base pairs.
Amino Acids, Peptides, and Proteins
- Amino acids consist of an amino group, a carboxyl group, and a variable R-group.
- There are 20 standard amino acids, each with distinct structures and properties.
- Stereoisomer configuration is crucial for protein function; L and D forms exist.
- Amino acids are classified based on R-group characteristics: polar, nonpolar, basic, and acidic.
- Zwitterions are dipolar ions that form at specific pH points, influencing solubility and reactivity.
- Isoelectric point (pI) indicates the pH at which the amino acid carries no net charge; affects mobility in electrophoresis.
- Peptide bonds form between amino acids, releasing water through a condensation reaction.
- Peptides can perform various biological functions, including signaling and catalysis.
Protein Purification and Analysis
- Protein properties such as size, charge, and affinity facilitate separation techniques.
- Column chromatography separates proteins based on size or charge.
- Ion exchange chromatography uses charged resin to attract oppositely charged proteins.
- Size exclusion chromatography discriminates proteins by size during passage through porous media.
- Electrophoresis applies an electric field to separate proteins by size and charge, including SDS-PAGE methods.
- Isoelectric focusing separates proteins based on their isoelectric points.
- 2D electrophoresis combines isoelectric focusing with SDS-PAGE for high-resolution protein analysis.
- The specific activity of a protein indicates its enzymatic activity relative to its total amount.
- Edman's degradation allows sequencing amino acids in proteins, while MALDI-MS gives mass data for analysis.
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Description
Prepare for your Foundations of Biochemistry and Molecular Biology I quiz with this comprehensive study guide. Focus on essential terminology and its application in lectures. Ensure you understand each term's definition and contextual usage for the course.
