Intro and Thermo

Page 9: Types of Cells

• Prokaryotes: Lack a nucleus, smaller, simultaneous transcription and translation.

• Eukaryotes: Larger, membrane-bound nucleus, segregated transcription and translation.

Page 10: Thermodynamics in Biochemistry

• Concepts include: Energy (Enthalpy, Entropy, Free Energy, Equilibrium) and the role of ATP in coupled reactions.

Page 11: Water and Buffers

• Focus on properties of water and the mechanisms and applications of buffers.

• Reference to figures illustrating the molecular structure of water and hydrogen bonding.

Page 12: Amino Acids

• Structure: Basic structure includes an amine group, carboxylic acid group, and variable R group.

• Roles: Vital for protein synthesis and function.

Page 13: Protein Structure and Function

• Understanding purification, sequencing, and the relationship between structure and function in proteins.

• Discussion of protein folding and related diseases.

Page 14: Enzymes

• Definition: Biological catalysts that lower activation energy of reactions.

• Components: Kinetics, mechanisms, and regulation of enzyme activity.

Page 15: Carbohydrates

• Various forms and structures of carbohydrates, including basic sugars and derivatives like glycoproteins and glycolipids.

Page 16: Lipids and Membranes

• Importance of lipids as building blocks of membranes, which maintain cellular integrity.

• Explanation of lipid bilayer properties.

Page 17: Background Knowledge Expectation

• Biology: Basic understanding of cells, proteins, and DNA is needed.

• Chemistry: Knowledge of thermochemistry, bonding, and redox reactions is essential.

Page 18: Review of Previous Courses

• Material from Chem 120 and Chem 123 is expected to be familiar.

• Students should prepare for these topics in quizzes and exams.

Page 19 & 20: Carbon Bonding

• Importance of carbon's ability to form multiple bonds, including single, double, and triple bonds relevant in biochemical processes.

Page 21: Functional Groups in Biochemistry

• Essential to recognize common functional groups and their significance in biochemistry.

• Examples: Amines, alcohols, aldehydes, ketones, carboxylic acids, and others.

Page 22: Important Reaction Types

• Nucleophilic Substitution Reactions: Key reaction mechanism in biochemical processes.

Page 23: Condensation and Hydrolysis Reactions

• Condensation Reaction: Water produced when sugar molecules join.

• Hydrolysis Reaction: Water used to break down sucrose.

Page 24: Isomerization Reactions

• Example: Dihydroxyacetone phosphate to glyceraldehyde 3 phosphate in glycolysis, catalyzed by triose phosphate isomerase.

Page 25: Oxidation-Reduction Reactions

• Key processes in cellular metabolism involving electron transfer, e.g., energy generation in mitochondria.

Page 26: Non-Covalent Interactions

• Types include ionic interactions, dipole interactions, van der Waals forces, and the hydrophobic effect critical in biological systems.

Page 27: Entropy in Solutions

• Discussion on molecular arrangements and entropy relating to solutes in solution across phases.

Page 28: Energy Transfers in Biochemistry

• Topics: thermodynamics, enthalpy, free energy, and equilibrium constants.

Page 29: Reaction Predictions

• Understanding thermodynamics allows predictions about reaction occurrence and direction.

Page 30: Importance of Thermodynamics

• Essential for predicting reaction behavior and understanding biochemical processes.

Page 31: Free Energy in Reactions

• Definition and calculation of free energy; components include enthalpy and entropy.

Page 32: Enthalpy Changes

• Understanding how changes in heat content relate to exothermic and endothermic reactions.

Page 33: Energetically Favorable Processes

• Discussion on spontaneous reactions, including endothermic processes and conditions.

Page 34: Laws of Thermodynamics

• Summary of the three laws of thermodynamics impacting chemical processes.

Page 35: First Law of Thermodynamics

• Reinforcement of energy conservation in chemical reactions.

Page 36: Second Law of Thermodynamics

• Discussion on energy dispersal and systems moving toward maximum entropy.

Page 37: Definition of Entropy

• Explanation of entropy in terms of disorder and energy dispersal throughout processes.

Page 38: Reactivity and Entropy

• Conditions under which reactions may occur spontaneously.

Page 39: Entropy in Phase Changes

• Illustration of how phase changes affect system and surroundings' entropy.

Page 40: Impact of Heat Exchange on Entropy

• Description of how heat transfer influences the spontaneity of reactions.

Page 41: Calculating Entropy Changes

• Formulas relating heat and temperature to entropy changes in reactions.

Page 42: Phase Shift Effects

• How melting and solidification processes affect entropy in systems.

Page 43: Spontaneity Criteria

• Chemical reactions categorized based on entropy changes for the universe.

Page 44: Understanding Spontaneity

• Definition of spontaneity in the context of reaction conditions and energy dispersal.

Page 45: Free Energy Equation

• Key equation exploring free energy changes in relation to enthalpy and entropy.

Page 46: Spontaneity and Free Energy

• Conditions under which reactions can occur spontaneously based on free energy calculations.

Page 47: Considerations for Reaction Occurrence

• A comprehensive understanding of enthalpy, entropy, and concentrations affecting reactions.

Page 48: Spontaneous Reactions in Metabolism

• Insight into metabolic pathways and ATP generation complexity.

Page 49: Free Energy Temperature Dependence

• Exploration of how temperature influences the spontaneity and energy changes in reactions.

Page 50: Examples of Free Energy Calculations

• Step-by-step calculations of free energy changes during common chemical processes.

Page 51: Standard States defined

• Explanation of chemical standard states relevant to biochemistry.

Page 52: Biological Standard State

• Biological conditions that differ from general standard states, impacting free energy calculations.

Page 53: ATP Hydrolysis Energy Values

• Discussion on the hydrolysis of ATP in different biochemical contexts and its relevance.

Page 54: Overview of Biological Processes

• Summary of spontaneity, free energy, and entropy’s role in biological reactions.

Page 55: Free Energy Change Calculations

• Importance of calculating free energy changes for predicting reaction outcomes.

Page 56: Equilibrium and Free Energy

• State of equilibrium as it pertains to changes in free energy during reactions.

Page 57: Free Energy Calculations at Non-Standard States

• Techniques for calculating free energy changes regarding non-standard state conditions.

Page 58: Reaction Quotient in Free Energy

• The relationship between free energy, reaction quotients, and equilibrium constants.

Page 59: Concentration Impact on Free Energy

• How changes in reactant/product concentration impact free energy in reactions.

Page 60: Spontaneous Reaction Considerations

• Summary of conditions affecting spontaneous nature of biochemical reactions.

Page 61: Understanding Free Energy Attributes

• Distinction between favorable and spontaneous free energy values.

Page 62: Free Energy and Reaction Spontaneity

• Adjusting free energy attributes based on reaction conditions and concentrations.

Page 63: Environmental Consideration for Free Energy Calculations

• Free energy calculations reflecting actual reaction conditions in biological systems.

Page 64: Practical Applications of Free Energy Science

• Case studies involving ATP hydrolysis and equilibrium constants.

Page 65: Typical Concentrations in E. coli

• Consideration of metabolic free energy changes based on cellular ATP concentrations.

Page 66: Principles of Reversible Reactions

• Review concepts of reaction reversibility and how it affects free energy versus overall equilibrium.

Page 67: Biological Systems and Entropy

• How living systems maintain order and required energy inputs against entropy principles.

Page 68: Energy Extraction in Biological Systems

• Biological necessity for energy influx to counteract entropy and maintain system order.

Page 69: Calculating Free Energy from Formation Values

• Formula for deriving free energy for reactions based on formation values.

Page 70: Coupled Reactions Overview

• Introduction to the concept of coupling energetically unfavorable reactions with favorable ones.

Page 71: Thermodynamic Favorability in Biochemical Reactions

• Example of coupling glucose phosphorylation reactions with ATP hydrolysis.

Page 72: Concentration Management for Reaction Favorability

• Strategies for maintaining metabolite levels to drive reactions towards favorability.

Page 73: Coupling Unfavorable to Favorable Reactions

• How ATP acts as a common coupling agent to drive thermodynamically unfavorable reactions.

Page 74: Energy Coupling in Metabolic Systems

• Overview of glucose metabolism events coupled with ATP utilization to produce energy.

Page 75: Maximizing ATP Production

• Insights into glucose metabolism leading to ATP synthesis and evaluation of efficiency.

Page 76: Structural Understanding of ATP

• Detailed examination of ATP structure and its ability to provide energy through hydrolysis.

Page 77: Energy from Hydrolysis Reactions

• Discussion on resonance energy effects from ATP hydrolysis contributing to energy release.

Page 78: Explanation of ATP’s Biological Role

• Factors leading to ATP being designated as cellular energy currency.

Page 79: Comparison of Biological Energy Compounds

• Assessment of ATP hydrolysis against alternative energy compounds in terms of free energy.

Page 80: ATP as an Energy Currency

• ATP’s intermediate free energy allows it to efficiently serve in cellular energy reactions.

Page 81: Kinetics Overview

• Importance of reaction kinetics juxtaposed with thermodynamic favorability impacts.

Page 82: Comparison of Reaction Dynamics

• Analysis of the relationship between activation energy and spontaneity of reactions.

Page 83: Impact of Activation Energy on Reaction Rate

• Explaining how high activation energy impacts the speed of thermodynamically favorable reactions.

Page 84: Summary of Key Concepts

• Favorability determined by both enthalpy and entropy with a focus on the universality of increasing entropy.