🔮Chemical Basis of Bioengineering I Unit 8 – Biochemistry and Biomolecules Intro

Key Concepts

• Biomolecules are the fundamental building blocks of life consisting of carbohydrates, lipids, proteins, and nucleic acids
• Structure and function are intimately linked in biomolecules determines their specific roles and interactions within biological systems
• Chemical reactions in living organisms are catalyzed by enzymes highly specific and efficient protein catalysts
• Energy is stored and transferred in biological systems through the breakdown and synthesis of high-energy molecules (ATP)
• Metabolism encompasses all the chemical reactions involved in maintaining life including anabolism (building up) and catabolism (breaking down)
• Laboratory techniques such as chromatography and electrophoresis are used to separate, identify, and characterize biomolecules
  • Chromatography separates molecules based on their physical and chemical properties (size, charge, polarity)
  • Electrophoresis separates charged molecules (proteins, nucleic acids) based on their migration through a gel matrix under an electric field
• Understanding the structure, function, and interactions of biomolecules is crucial for applications in medicine, biotechnology, and bioengineering

Biomolecules Overview

• Carbohydrates are composed of carbon, hydrogen, and oxygen atoms in a 1:2:1 ratio serve as energy sources and structural components
  • Monosaccharides are the simplest sugars (glucose, fructose) and can be linked together to form disaccharides (sucrose, lactose) and polysaccharides (starch, cellulose)
• Lipids are hydrophobic molecules that include fats, oils, waxes, and steroids play crucial roles in energy storage, cell membrane structure, and signaling
  • Triglycerides are the main form of stored energy in animals consist of three fatty acids attached to a glycerol backbone
  • Phospholipids are the primary components of cell membranes have a hydrophilic head and two hydrophobic tails
• Proteins are linear polymers of amino acids folded into specific three-dimensional structures perform a wide range of functions (enzymes, antibodies, transporters)
  • The sequence of amino acids in a protein determines its primary structure which dictates its higher-order structures (secondary, tertiary, quaternary) and function
• Nucleic acids are polymers of nucleotides that store and transmit genetic information in the form of DNA and RNA
  • DNA (deoxyribonucleic acid) is a double-stranded helix that carries the genetic blueprint for an organism
  • RNA (ribonucleic acid) is single-stranded and plays roles in gene expression, protein synthesis, and regulation

Structure and Function

• The structure of a biomolecule determines its function by dictating its shape, interactions, and reactivity
• Proteins have four levels of structure: primary (amino acid sequence), secondary (local folding patterns), tertiary (overall 3D shape), and quaternary (multiple subunits)
  • Secondary structures include alpha helices and beta sheets stabilized by hydrogen bonds between the amino acid backbone
  • Tertiary structure is determined by interactions between amino acid side chains (hydrophobic, ionic, disulfide bonds) and gives proteins their unique shapes
• Enzymes are globular proteins that catalyze chemical reactions by lowering the activation energy barrier
  • The active site of an enzyme is a specific region where the substrate binds and the reaction occurs
  • Enzyme activity can be regulated by factors such as pH, temperature, and the presence of inhibitors or activators
• Nucleic acids have a double helix structure in DNA and a single-stranded structure in RNA
  • The specific base pairing between adenine (A) and thymine (T) or uracil (U), and guanine (G) and cytosine (C) allows for the storage and transmission of genetic information
• Carbohydrates can form complex branched structures (glycogen) or linear chains (cellulose) depending on the specific linkages between monosaccharides
  • The structure of polysaccharides determines their properties and functions (energy storage, structural support)

Chemical Reactions in Biomolecules

• Chemical reactions in living systems are highly regulated and coordinated to maintain homeostasis
• Enzymes are crucial for catalyzing biochemical reactions by providing a specific active site that binds the substrate(s)
  • Enzymes lower the activation energy ($E_a$) of a reaction allowing it to proceed more quickly under physiological conditions
  • The induced fit model suggests that enzymes undergo conformational changes upon substrate binding to optimize the active site for catalysis
• Metabolism involves a complex network of enzyme-catalyzed reactions that break down nutrients (catabolism) and synthesize essential molecules (anabolism)
  • Metabolic pathways are series of linked enzymatic reactions that transform one molecule into another
  • Regulation of metabolic pathways occurs through feedback inhibition, allosteric regulation, and gene expression control
• Redox reactions involve the transfer of electrons between molecules and play important roles in energy production (cellular respiration) and biosynthesis
  • Oxidation is the loss of electrons, while reduction is the gain of electrons
  • Electron carriers (NAD+/NADH, FAD/FADH2) shuttle electrons between reactions in metabolic pathways
• Photosynthesis is a series of light-dependent and light-independent reactions that convert solar energy into chemical energy (glucose) in plants and other photosynthetic organisms
  • The light-dependent reactions occur in the thylakoid membranes and involve the excitation of chlorophyll by light, leading to the production of ATP and NADPH
  • The light-independent reactions (Calvin cycle) use ATP and NADPH to fix carbon dioxide into glucose in the stroma of chloroplasts

Energy and Metabolism

• Energy is the capacity to do work and is required for all life processes
• Adenosine triphosphate (ATP) is the primary energy currency in biological systems
  • ATP consists of an adenosine molecule bonded to three phosphate groups and releases energy when hydrolyzed to ADP (adenosine diphosphate) and inorganic phosphate (Pi)
  • The energy released from ATP hydrolysis is used to drive energetically unfavorable reactions, such as muscle contraction, active transport, and biosynthesis
• Cellular respiration is the process by which cells break down glucose to produce ATP in the presence of oxygen
  • Glycolysis is the first stage of cellular respiration occurs in the cytosol and produces 2 ATP and 2 NADH per glucose molecule
  • The citric acid cycle (Krebs cycle) is the second stage occurs in the mitochondrial matrix and generates 2 ATP, 6 NADH, and 2 FADH2 per glucose molecule
  • Oxidative phosphorylation is the final stage occurs in the inner mitochondrial membrane and involves the electron transport chain (ETC) and chemiosmosis to produce ~34 ATP per glucose molecule
• Fermentation is an anaerobic process that allows cells to generate ATP in the absence of oxygen
  • Lactic acid fermentation occurs in animal muscle cells during intense exercise converts pyruvate to lactate and regenerates NAD+ for glycolysis
  • Alcoholic fermentation occurs in yeast and some bacteria converts pyruvate to ethanol and carbon dioxide and regenerates NAD+ for glycolysis
• Photosynthesis is the process by which plants and other photosynthetic organisms convert solar energy into chemical energy (glucose)
  • The light-dependent reactions occur in the thylakoid membranes and involve the excitation of chlorophyll by light, leading to the production of ATP and NADPH
  • The light-independent reactions (Calvin cycle) use ATP and NADPH to fix carbon dioxide into glucose in the stroma of chloroplasts

Lab Techniques and Applications

• Spectrophotometry is a technique used to measure the absorption of light by a sample at specific wavelengths
  • Spectrophotometry can be used to quantify the concentration of a biomolecule in solution based on its absorbance at a specific wavelength (Beer-Lambert law)
  • Applications include measuring protein concentration (A280), DNA/RNA concentration (A260), and enzyme kinetics (substrate or product absorbance)
• Chromatography is a technique used to separate mixtures of biomolecules based on their physical and chemical properties
  • Size-exclusion chromatography (gel filtration) separates molecules based on their size by passing them through a column packed with porous beads
  • Ion-exchange chromatography separates molecules based on their charge by binding them to a charged resin and eluting with increasing salt concentrations
  • Affinity chromatography separates molecules based on their specific binding to a ligand immobilized on a column (antibody-antigen, enzyme-substrate)
• Electrophoresis is a technique used to separate charged biomolecules (proteins, nucleic acids) based on their migration through a gel matrix under an electric field
  • Polyacrylamide gel electrophoresis (PAGE) is used to separate proteins based on their size and charge
  • Agarose gel electrophoresis is used to separate DNA and RNA fragments based on their size
  • Isoelectric focusing (IEF) separates proteins based on their isoelectric point (pI) by applying a pH gradient across a gel
• Centrifugation is a technique used to separate biomolecules based on their size and density by applying a centrifugal force
  • Differential centrifugation separates organelles and cell components based on their sedimentation rate at different centrifugal forces
  • Density gradient centrifugation separates molecules based on their buoyant density in a gradient medium (sucrose, cesium chloride)
• Microscopy is a technique used to visualize and study the structure of biological samples
  • Light microscopy uses visible light and lenses to magnify samples up to ~1000x
  • Electron microscopy (scanning, transmission) uses a beam of electrons to visualize samples at much higher magnifications (up to ~1,000,000x) and resolution
  • Fluorescence microscopy uses fluorescent dyes or proteins (GFP) to label specific molecules or structures within a sample and visualize them using a specific wavelength of light

Real-World Examples

• Enzymes are used in various industrial processes, such as the production of high-fructose corn syrup (glucose isomerase), cheese (rennet), and biofuels (cellulases)
• Recombinant DNA technology is used to produce human insulin in bacteria for the treatment of diabetes
  • The human insulin gene is inserted into a bacterial plasmid, which is then introduced into E. coli cells
  • The bacteria express and secrete human insulin, which is then purified and used for therapeutic purposes
• PCR (polymerase chain reaction) is a technique used to amplify specific DNA sequences and has applications in forensics, genetic testing, and disease diagnosis
  • PCR uses a heat-stable DNA polymerase (Taq) and specific primers to amplify a target DNA sequence through repeated cycles of denaturation, annealing, and extension
• CRISPR-Cas9 is a gene-editing tool derived from a bacterial adaptive immune system that allows for precise modification of DNA sequences
  • CRISPR-Cas9 uses a guide RNA to target a specific DNA sequence and a Cas9 endonuclease to create a double-stranded break, which can then be repaired by the cell's DNA repair mechanisms
  • Applications include correcting genetic disorders, creating disease models, and modifying crops for improved traits
• Biofuels are renewable energy sources produced from biomass, such as ethanol from corn or sugarcane and biodiesel from algae or waste oils
  • The production of biofuels involves the breakdown of complex carbohydrates (cellulose, starch) into simple sugars by enzymes, followed by fermentation to produce ethanol
• Biosensors are analytical devices that use a biological component (enzymes, antibodies, receptors) to detect and quantify a specific analyte
  • Glucose biosensors use the enzyme glucose oxidase to measure blood glucose levels in people with diabetes
  • Environmental biosensors can detect pollutants, toxins, or pathogens in water, air, or soil samples based on the specific binding or reaction with a biological recognition element

Study Tips and Tricks

• Create a study schedule and stick to it break down the material into manageable chunks and allocate sufficient time for each topic
• Use active learning strategies, such as summarizing concepts in your own words, creating concept maps, or teaching the material to others
• Practice solving problems and answering questions related to the material to test your understanding and identify areas that need improvement
  • Work through practice problems from your textbook, class notes, or online resources
  • Form a study group with classmates to discuss concepts, share ideas, and solve problems together
• Use mnemonic devices or memory aids to help remember key concepts, structures, or pathways
  • For example, the mnemonic "King Philip Came Over For Good Soup" can help remember the taxonomic hierarchy (Kingdom, Phylum, Class, Order, Family, Genus, Species)
• Visualize complex structures or processes using diagrams, illustrations, or animations to better understand and retain the information
  • Sketch out the steps of a metabolic pathway or the structure of a biomolecule
  • Use online resources, such as videos or interactive simulations, to visualize dynamic processes or 3D structures
• Connect new concepts to real-world examples or applications to make the material more relevant and engaging
  • Relate the structure and function of biomolecules to diseases, industrial processes, or everyday experiences
• Take breaks and practice self-care to avoid burnout and maintain a healthy work-life balance
  • Engage in physical activity, hobbies, or relaxation techniques to reduce stress and improve mental well-being
• Reflect on your learning progress and adjust your study strategies as needed
  • Identify your strengths and weaknesses and focus on areas that require more attention
  • Seek help from your instructor, teaching assistants, or tutors if you are struggling with a particular concept or topic