Cell Biology Exam 1 Study Guide PDF

Know key characteristics of life and what there not Order- complex organized structures within cell Sensitivity- reaction to environmental stimuli Reproduction- ability to produce offspring and pass on genetic material Adaptation- long term evolutionary changes in response to the environment Growth...

Know key characteristics of life and what there not Order- complex organized structures within cell Sensitivity- reaction to environmental stimuli Reproduction- ability to produce offspring and pass on genetic material Adaptation- long term evolutionary changes in response to the environment Growth and development- controlled by genetic instructions Homeostasis- regulation of internal conditions, like temp and pH Energy processing- genetic changes over generation Know the cell theory The cell theory: states all living organisms are composed of one or more cells, cells that are the fundamental units of life, and new cells arise only from division of preexisting cells Basic unit of life: cells are the building blocks of all living organism Cell origin; new cells form exclusively through the division of existing cells Know why cells are important Fundamental unit of life: cells are the smallest unit capable of performing all life functions Key functions of cells: intake of nutrients, production of energy, growth and reproduction, response to stimuli Importance: cells form the structure and enable the function of all living organisms Cell biology: study of cell structure, function, and behavior Know composition and energy Cellular composition- all organisms consist of cells Energy use: cells build biological molecules (proteins and fats) Role of cell membranes: maintain separation between intracellular and extracellular environment Forms of energy- kinetic and potential energy Kinetic: movement related energy Potential: stored energy (chemical bonds) ExampleL conversion of potential energy (glucose) to kinetic energy (movement) Know Biological Energy: Metabolism Metabolism: sum total of all chemical reactions that occur in an organism involve energy and occur slowly on their own Cellular metabolism: is comprised of the chemical reactions that occur in living cells These reactions can be divided into catabolic reactions that convert nutrients to energy and anabolic reactions that lead to the synthesis of larger biomolecules Enzyme: catalyst that speed reaction rate Know ATP as an energy source Atp hydrolysis: release energy (-7.3 kcal/mol) for cellular processes Phosphorylation: ATP transfers a phosphate group to other molecules powering cell functions Reaction factors formation of products Energy liberated can drive a variety of cellular processes What speed is energy released? (-7.3 kcal/mol) its fast Atp: acts as a cell storehouse of energy. It enables cells to store energy safely in small packets and release energy for use when needed. ATP; serves to close the gap between energy releasing reactions such as food breakdown and energy-requiring reactions such as synthesis Phosphorylation: ATP is able to power cellular processes by transferring a phosphate group to another molecule. This transfer is carried out by special enzymes that couple the release of energy from ATP to cellular activities that require energy Know Metabolic Diversity energy sources for organisms Lithotrophs: derive energy from inorganic materials Phototrophs: use sunlight for energy Organotrophs: deped on organic molecules Know ecosystems based on lithotrophs Vent fields: sulfur bugs and methane makers that live in mid atlantic ridge vent systems Acid pools: iron bugs that live in copper mines in chile Rock Caverns: sulfur worms and methane makers that live in deep mines and boreholes Know role of mRNA Codons: many RNAs have the information to construct proteins encoded in groups of 3 nucleotides at a time Genetic code and its use is universal in living things Messenger RNA: a type of single stranded RNA involved in protein synthesis Codon: a DNA or Rna sequence of 3 nucleotides that form genomic information encoding a particular amino acid or signaling the termination of protein synthesis (stop signals). There are 64 different codons 61 specify amino acids, 3 are used as stop signs Protein structureL Determined by the amino acid sequence which is determined by the genetic code Genetic code: determines sequence of amino acid in protein chain Codons: what they do in protein synthesis is encode amino acids, start signal, ensure accuracy Start signal: specific codon that starts protein synthesis (AUG) Stop Signal: specific codon that stops protein synthesis (UAA, UAG, UGA) Ensure Accuracy: codons ensure correct sequence of amino acid which is important for proper protein function Know most genes encode proteins Genes encode proteins, which control cell functions. The genes a cell expresses determine what the cell can do. In prokaryotic operons: Structure genes: code for enzymes Promoter, operator, regulatory gene control: structural gene transcription RNA Polymerase and other enzymes: help regulate the process Know Lac operon of e coli The lac operon: is a gene control system in bacteria that turns on to produce enzymes for lactose digestion when lactose is present and stays off when lactose is absent to save energy. Structural genes: in the lac operon of e coli, lac z (code for b-galactosidase) helps break down the lactose Promoter gene: (P) is a dna sequence where RNA polymerase binds to start the transcription Operator gene: (O) is a dna segment where a repressor proteins binds to block transcription when lactose is absent Regulatory gene: the lacl gene produces the repressor protein that controls the lac operons activity RNA polymeraseL enzyme that reads the DNA template and synthesis RNA during transcription Other enzymes: permease (lac Y) help transport lactose into cell What lactose is absent, what happens to lac operon? Know protein regulation of gene expression Direction interaction: transcription factor binds to DNA to turn certain genes or off eg. P53 protein binds to DNA to regulate involved in cell repair or Cell signaling: insulin bind to receptors on a cells surface, triggering a signaling pathway that activates or represses certain genes involved in glucose metabolism Simplified Proteins control genetic information by Directly: binds to DNA or RNA to regulate gene activity Indirectly: using signals to trigger pathway that turn genes on or off Polynucleotides (DNA and RNA): provide the instructions to make proteins from amino acids proteins : are needed to replicate DNA and transcribe RNA Simplified: DNA and Rna store instructions to make proteins but proteins are essential to copy DNA and produce RNA Know evolution has mutation as its root Mutation: in DNA occurs randomly and is the source of differences between individuals and species, they drive evolution and all us to survive and reproduce All mutations are bad Know evolution requirements Traits of individuals within a species: are hereditary More individuals are born than survive and reproduce successfully. Less favorable traits. Not survive that mutation gets wipes out That an individual's traits can help or hinder its ability to survive and or reproduce CFTR gene gets cystic fibrosis Breast cancer is linked to mutations in the Brca1 or Brca 2 gene Benefits from mutations are resistance, increased bone density, etc Know COX 2 gene Overtime mitochondrial genes were lost in eukaryotic cells This happened independently in different cells Modern mitochondrial genomes: contain different genes in different organisms Mt-CO2: variants of this gene have been associated with the mitochondrial complex 4 deficiency, a deficiency in an enzyme complex of the mitochondrial respiratory chain Deficiency is characterized by: L heterogeneous phenotypes ranging from isolated myopathy to severe myopathy to severe multisystem disease affecting several tissue organs Leigh’s disease: mutation of MT-CO2 is also known to cause this which may be caused by an abnormality or deficiency of cytochrome oxidase. COX2 gene is responsible for this Know compartmentalization Cells: are compartmentalized, enclosed of plasma membrane made of phospholipid biliary Membrane separation interferes with the cells and the cells metabolic processes from the outside environments. It allows conditions inside the cell to be different from outside Endosymbiosis theorem: proposes that the mitochondria originated when an ancestral archaeon host engulfed an ancestral bacterial that was not digested and evolved into an organelle Know Eukaryotes have complex compartmentalized cells Eukaryotes: specific cellular functions are compartmentalized into the cell nucleus and organelles surrounded by intracellular membranes Compartmentalization: improves cell functions and dangerous molecules entering inside Know the Scientific Method and order Observe the natural world Develop hypothesis Make predictions based on hypothesis Design experiments to test prediction Do experiments to collect data Is the hypothesis supported? What did you observe? What makes a good hypothesis Know Model organisms E Coli- prokaryote model organism, a rod shaped bacillus g negative bacterium that is used as a model organism. Factors such as its ability to grow fast using cheap media and availability of molecular tools to perform genetic manipulations are favorable for using e coli as a model organisms in molecular genetics Yeast (saccharomyces cerevisiae)- simplest model organism for eukaryotic cell because can grow as both haploids and diploids and can reproduce secually and asexually can study cell cycle from yeast Arabidopsis thaliana: flowing plant model Nematode Caenorhabditis elegans: simple multicellular animal model, powerful experimental organism for a number of traits that facilitate genetic and genomic analysis. Includes the hermaphroditic lifestyle, short 2-3 week lifespan, and small genome which offers an ideal compromise between complexity and tractability. Could be used for studying genetic approaches to understand the aging process, age-related disease, mechanism of longevity and drug screening for compounds that increase lifespan. Has 2 sexes male and hermaphrodite Drosophila melanogaster- model insect, fruit fly, used for biomedical structure, low cost, rapid generation time, easy genetic tools for research, has polytene chromosome structure easy to manipulate Mus musculus: model mammal, the house mouse was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, larger litters, easy to take care of and manipulate, and change in phenotype Homospaeins and mus musculus: with mutations in the same orthologous gene (hit) Know the eyeless gene Homeotic gene: this gene is named for the mutant version. It is a developmental switch Ectopic expression (outside of normaltime. place) causes eyes to be made in unusual places) Know Conservation of developmental genes Pax-6: the fly eyeless gene is the same as this mouse's gene. If defective, the animal lacks eyes. One can be substituted for the other because they are so highly conserved =. Both serves as master switches, regulating all the genes need to form a eye Pax:6- in the brain, this gene s protein is involved in the development of specials group of brian cells that process cells, and can control eye development —------------------------------------------------------------------------------------------------------------------------- Know Capsid vs Capsomere: Capsid: proteins shell that encloses genetic material of virus, protective barrier and delivery system, assembled from multiple capsomeres Capsomere: protein subunits that make up capsid, self-assemble into specific shapes using minimal energy , how are they formed? Know Microtubules why their important and their functions: Components of cytoskeletons in extracellular matrix Made of tubulinL hollow cylindrical structures, alpha and beta tubulin dimers, perform various roles that are vital to cell structure and function. Important for maintaining cell shape. Polymerization and depolymerization: adding or removing tubulin dimers at tehri ends of plus end OrganizationL nucleated and organized by structures like the centrosome in animal cells Functions: Structural support: help maintain shape of cell and resist compression Intracellular transport: serves as tracks for motor proteins kinesin and dynein which transport organelles, vesicles, and cargo Cell division: form mitotic spindle, which is important for segregation of chromosomes during mitosis and meiosis Cilia and flagella movement: key component of cilia and flagella, facilitating movement and fluid flow If something is trying to move but its not in cytoskeleton, it wont move free flowing lost Know cellular energy in metabolism Anabolism: an expensive form of energy consumption allows cells to convert food to energy, without enough energy supply metabolism slows down, impairing growth and repair and leads to cellular disinfection. What is the primary role of anabolic pathway Which ones loses heat and energy Catabolism: breakdown of complex molecules into simpler ones, release energy, exergonic, they release energy as complex molecules are broken down into simpler ones like glucose., fatty acids and amino acids Types of catabolic pathways: glycolysis, citric acid cycle, oxidative phosphorylation, and beta oxidation Glycolysis: breakdown of glucose into pyruvate, making atp and nadh CAC- oxidation of acetyl coa to release electrons and produce high energy carriers (NADH) FADH2) Oxidative phosphorylation: uses NADH and FADH2 to make ATP via etc Beta oxidationL breakdown of fatty acids into acetyl coa for energy production Know importance of catabolism Energy generation: catabolism is the primary source of energy for cellular activities, ensuring survival and function Homeostasis: maintains energy balance by regulating the production and consumption of ATP based on cellular demand Adaptation in times of scarcity, cells prioritize catabolism of stored molecules to meet energy needs Hormonal control: insulin, glucagon and epinephrine Insuline: reduces metabolic activity (inhibits fat break down) Glucagon and epinephrine: promote catabolism during low energy states Feedback mechanisms: atp level regulate catabolic enzyme activity (high atp, inhibits glycolysis, low atp stimulates) Know ultimate energy for most life is the sun Photosynthesis: process of using sunlight as an energy source to build biological molecules P.S: plants take in co2 and add water from the air and soil, in the plant cell water is oxidized and the co2 is reduced, transforms water in o2 and co2 into glucose Main purpose of photosynthesis is to convert energy from the sun into chemical energy that can be used for food. Cellular respiration - occurs in the mitochondria to break down sugar in presence of o2 to release energy in the form of atp. Know energy and thermodynamics in cells Gibbs free energy: this equation explains disorder+heat results from loss of energy Free energy (delta G) depends on total energy in the system and energy lost as heat or to increase disorder Reactions occur spontaneously when: delta g is negative ATP: cells use this to drive reactions with positive delta g by coupling them to highly exergonic reactions (eg ATP hydrolysis) Know spontaneous reactions Spontaneous reactions: occur without the input of external energy (not fast), key factor is the free energy change, why its negative, they release free energy making delta g negative Spontaneous reactions: energy is released during the reaction, eg cellular respiration (breakdown of glucose) driven by thermodynamics Spontaneity: depends on enthalpy, entropy, and temperature This equation determines if reaction is spontaneous Not instantaneous: spontaneous does not mean fast Know exergonic Exergonic reaction - said to occur spontaneously that does not imply that the reaction will take place at an observable rate Know endergonic Endergonic reaction: will not take place on its own without adding free energy or called heat absorbing non spontaneous or an unfavorable reaction, and is a chemical reaction in which the standard change in free energy is positive an an additional driving force is needed to perform this reaction Know enzymes and ribozymes Spontaneous reaction: not a fast reaction Catalyst- an agent that speeds up the rate of the chemical reaction without being consumed during the reaction Enzymes- protein catalysts in living cells Ribozymes- RNA molecules with catalytic properties Know Ea Activation energy: initial input of energy to start reaction, allows molecules to get close enough to cause bond rearrangement, can now achieve transition state where bonds are stretched Common ways to overcome activation energy: Large amounts of heat Using enzymes to lower activation energy Know how enzymes lower activation energy Straining bonds in reactants: t make it easier to achieve transition state Positioning reactants together: to facilitate bonding Changing local environment: direct participation through very temporary bonding Coenzymes and enzyme in relation to activation energy Know Other enzyme terminology Active site- location where reaction takes place Substrates- reactants that bind to active site enzyme -substrate complex: formed when enzyme and substrate bind Prosthetic group: small molecules permanently attached to the enzyme Cofactor: usually inorganic ion that temporarily binds to enzyme Coenzyme: organic molecule that participates in reaction but is left unchanged afterward Know Inhibition Competitive inhibition- molecule binds active site, inhibits ability of substrate to bind, apparent Km increases-more substrate needed Noncompetitive inhibition- lowers Vmax without affecting Km, inhibitor binds to allosteric site, not active site Which inhibits binding to the allosterically like? Know chemical energy to drive metabolism Autotrophs: harvest sunlight and convert radiant energy into chemical energy Heterotrophs: live off of the energy made by autotrophs. Extract energy from food by digestion and catabolism Know cellular respiration Cellular respiration- process that converts the chemical energy in food into usable cellular energy in the form of ATP, atp is produced mainly by the mitochondria Cells get energy by breaking bonds and shifting electrons from one molecule to another Aerobic respiration- final electron acceptor is oxygen Anaerobic respiration- final electron acceptor is inorganic molecule other than oxygen Fermentation- final electron acceptor is an organic molecule Know ATP ATP: energy currency of the cell, used to drive movement, used to drive endergonic movement ATP synthase- most of the atp produced in cells is made by this enzyme, this enzyme is embedded in the membrane and provides a channel through which protons can cross the membrane down their concentration gradient ATp synthesis: is achieved by a rotary motor driven by a gradient of protons What is ATP role Know Glucose catabolism Cells catabolize organic molecules and produce atp in 2 ways: Substrate level phosphorylation and aerobic respiration (in most organisms both are combined) -glycolysis -pyruvate oxidation -krebs cycle -electron transport chain How is atp produced, in what 2 ways Know glycolysis Glycolysis: metabolic pathway that converts glucose into pyruvate to generate ATP. Location: cytoplasm of cells Glycolysis has 2 major phases Energy investment phase (steps 1-5) and energy payoff phase (steps 6-10) Energy investment pases (1-5)- requires atp Energy payoff phase (6-10)- produces ATP and NADH End products: 2 pyruvate molecules, net 2 ATP produced, 2 NADH (electron carriers) S1-phosphorylation of glucose Enzyme: hexokinase, turns glucose to g6p Purpose: traps glucose inside cell and prepares glucose for further break down S2-isomerization EnzymeL phosphoglucose isomerase, turns g6p and f6p Purpose- converts a 6 membered ring of glucose into a 5 membered ring fructose for better cleavage in the later steps S3- second phosphorylation (commitment step, before it was reversible) Enzyme: phosphofructokinase-1 (PFK-1)- phosphorylates fructose Purpose: irreversible step that commits glucose to glycolysis ad is highly regulated enzyme in metabolism S4- cleavage of fructose 1,6 bisphosphate Enzyme: aldolase, splits fructose into 2 sugars that are isomers of each other DHAP and GAAp Purpose: splits the 6 carbon sugar into 2 3 carbon molecules What does this step do S5- isomerization of DHAP enzyme : triose phosphate isomerase, converts DHAP into G3P Purpose: so molecules can continue through glycolysis S6: oxidation and NADH production Enzyme: glyceraldehyde-3-phosphate dehydrogenase, adds a phosphate to g3p Purpose: generates NADH, an electron carrier and adds an inorganic phosphate for atp production S7: ATP generation begins Enzyme: phosphoglycerate kinase, transfers phosphate group to ADP to make ATP and 3-phosphoglycerate This stages net ATP is 0 Purposes: produces first ATP made per glucose and ATP is made via substrate level phosphorylation S8; isomerization Enzyme: phosphoglycerate mutase, rearranges position of phosphate group on the 3 phosphoglycerate molecule to carbon 2 Purpose: prepares the molecule for the next step Mutase: an enzyme that catalyzes the transfer of a functional group from one position on a molecule to another S9: dehydration Enzyme: enolase, removes a molecule of water from 2-phosphoglycerate to make PEP Purpose: creates a high energy phosphate compound What is the enzyme used for the dehydration step and what does it do? S10: ATP generation and pyruvate formation Enzyme: pyruvate kinase transfers a P from PEP to ADP to form pyruvic acid and ATP Purpose: produces another ATP molecule and forms pyruvate, the final product of glycolysis This process is done through substrate level phosphorylation Summary of glycolysis: Key outputs per glucose molecules 2 pyruvate Net 2 atp ( 4 produced, 2 used) 2 NADH Pathways after glycolysis Aerobic (with oxygen): pyruvate enters the mitochondria for the Krebs cycle and oxidative phosphorylation Anaerobic (without oxygen): pyruve undergoes fermentation (lactic acid or ethanol production) What leads krebs cycle and fermentation Know Glycolysis- continue respiration After finishing glycolysis, the cell must continue respiration in either aerobic or anaerobic direction Homolactic fermentation: If a cell able to perfor aerobic respiration is ina situation with no oxygen (like muscles in exertion) it will move inot a type of anaerobic respiration Alcoholic fermentation: yeast are unable to carry out aerobic respiration and will move into a type of anaerobic respiration Know another way to look at stage 1-glycolysis For each molecule of glucose that passes through glycolysis, the cell nets 2 ATP molecules Priming- glucose riming, cleavage, rearrangement Substrate level phosphorylation- oxidation and ATP generation What are the key stages of glycolysis? Know Krebs CA cycle ​Location: ​ Prokaryotic cells – occurs in the cytoplasm. ​ Eukaryotic cells – takes place in the mitochondrial matrix. ​Glycolysis converts glucose into pyruvate, which enters the cycle. ​Oxidizes glucose derivatives, fatty acids, and amino acids. ​Produces carbon dioxide (CO₂) through enzyme-controlled steps. ​The cycle collects high-energy electrons by oxidizing fuels.Produces 8 high-energy electrons, carried by:NADH ​FADH₂ ​These electrons are transported to the electron transport chain for ATP production. What occurs during the first step of the krebs cycle S1: formation of citrate ​ Acetyl-CoA combines with oxaloacetate to form citrate. ​ Catalyzed by the enzyme citrate synthase. ​ Acetyl-CoA donates a 2-carbon acetyl group to oxaloacetate.  ​ A water molecule helps catalyze the reaction. ​ Coenzyme A (CoA) is released, forming citrate. ​ This step initiates the Krebs Cycle and is essential for energy production. ​ Citrate enters the cycle and undergoes further modifications. ​ Prepares molecules for the production of NADH, FADH₂, and ATP. Where does the krebs cycle occur? S2: Formation of Isocitrate: ​ Citrate is rearranged to form its isomer, isocitrate. ​ Enzyme involved: Aconitase. ​ This transformation prepares the molecule for further oxidation in the Krebs Cycle. ​ Water molecule is removed from citrate, causing structural rearrangement. ​ Water is re-added at a different position, shifting the –OH group from the 3' to the 4' position, forming isocitrate. ​ This step creates isocitrate, a key intermediate in the Krebs Cycle. ​ Sets up the next reaction, where isocitrate is oxidized to produce NADH, a crucial step in energy production. What does isocitrate do S3: oxidation of isocitrate to alpha keto glutarate ​ Isocitrate is oxidized to form α-ketoglutarate. ​ Enzyme involved: Isocitrate dehydrogenase. ​ This is an oxidative decarboxylation reaction.  ​ NAD⁺ is reduced to NADH + H⁺, storing high-energy electrons. ​ A carbon dioxide (CO₂) molecule is released, making this the first decarboxylation step in the Krebs Cycle. ​ This reaction prepares α-ketoglutarate for further oxidation and ATP production. ​ Key role: Contributes electrons to the Electron Transport Chain, driving ATP synthesis. Reducing step? S4: oxidation of alpha ketoglutarate to succinyl coA ​ α-Ketoglutarate is oxidized, resulting in the removal of carbon dioxide (CO₂). ​ Coenzyme A (CoA) is added, forming the 4-carbon compound succinyl-CoA. ​ Enzyme involved: α-Ketoglutarate dehydrogenase. ​ NAD⁺ is reduced to NADH + H⁺, capturing high-energy electrons. ​ This reaction is crucial for energy production and the continuation of the Krebs Cycle. ​ Key role: Supplies electrons to the Electron Transport Chain, contributing to ATP synthesis. Know what happens in this step S5: conversion of succinyl coA to succinate ​ Coenzyme A (CoA) is removed from succinyl-CoA, forming succinate. ​ Enzyme involved: Succinyl-CoA synthase.  ​ The energy released is used to generate guanosine triphosphate (GTP) from guanosine diphosphate (GDP) and Pi via substrate-level phosphorylation. ​ GTP can be converted into ATP, contributing to cellular energy production. ​ This step is crucial for ATP synthesis within the Krebs Cycle. Know what enzyme is involved Know gtp can be converted into ATP S6: succinate is oxidized to form fumarate ​ Succinate is oxidized to form fumarate. ​ Enzyme involved: Succinate dehydrogenase. ​ FAD (Flavin Adenine Dinucleotide) is reduced to FADH₂, capturing high-energy electrons. ​ The enzyme catalyzes the removal of two hydrogen atoms from succinate. ​ This reaction contributes electrons to the Electron Transport Chain, aiding ATP production. Know what is oxidized to form what S7: Hydration of fumarate to Malate ​ Fumarate is hydrated to form L-malate. ​ Enzyme involved: Fumarase (Fumarate hydratase). ​ This reaction is reversible and plays a key role in the Krebs Cycle.  ​ A water molecule (H₂O) is added, inserting hydrogen and oxygen back into the substrate. ​ This step continues the rearrangement process, preparing the molecule for the final oxidation step. : Hydration of Fumarate to Malate S7: ​ Fumarate is hydrated to form L-malate. ​ Enzyme involved: Fumarase (Fumarate hydratase). ​ This reaction is reversible and plays a key role in the Krebs Cycle. ​ A water molecule (H₂O) is added, inserting hydrogen and oxygen back into the substrate. ​ This step continues the rearrangement process, preparing the molecule for the final oxidation step. Know what happens in this step and know what formed in this step S8: Oxidation of Malate to Oxaloacetate ​ Malate is oxidized to form oxaloacetate, which restarts the Krebs Cycle. ​ Enzyme involved: Malate dehydrogenase. ​ NAD⁺ is reduced to NADH + H⁺, storing high-energy electrons for ATP production.  ​ This final step completes the Krebs Cycle, regenerating oxaloacetate for another turn. ​ The generated NADH carries electrons to the Electron Transport Chain for further ATP synthesis. Know what step restarts the krebs cycle and what happens to malate in this step, its oxidized ATP Generation in the Krebs Cycle ​ The Krebs Cycle transforms the acetyl group and water into carbon dioxide and high-energy electron carriers. ​ Total ATP Yield: 12 ATP (per acetyl-CoA). ​ 3 NADH → Produces 9 ATP. ​ 1 FADH₂ → Produces 2 ATP. ​ 1 Direct ATP (or GTP) → Produces 1 ATP via substrate-level phosphorylation. ​ Key Role in Cellular Respiration ​ NADH and FADH₂ transfer electrons to the Electron Transport Chain (ETC). ​ The ETC generates the majority of ATP through oxidative phosphorylation. ​ Acetyl-CoA is oxidized through a series of nine reactions. ​ The process occurs in two main steps:  ​ Priming ​ Acetyl-CoA combines with oxaloacetate to form citrate. ​ Citrate undergoes structural modifications to prepare for energy extraction. ​ Energy Extraction ​ NADH and FADH₂ are produced through oxidation. ​ ATP (or GTP) is generated via substrate-level phosphorylation. ​ CO₂ is released, completing the cycle. 2 main steps in krebs cycle Krebs Cycle / Citric Acid Cycle - Summary of Steps 1.​Condensation 1.​Acetyl-CoA combines with oxaloacetate to form citrate. ​2-3. Isomerization ​Citrate is rearranged to form isocitrate. 1.​First Oxidation 1.​Isocitrate is oxidized to α-ketoglutarate, producing NADH and releasing CO₂. 2.​Second Oxidation  1.​α-Ketoglutarate is oxidized to succinyl-CoA, generating another NADH and CO₂ 3.​Substrate-Level Phosphorylation 1.​Succinyl-CoA is converted to succinate, generating ATP (or GTP). 2.​Third Oxidation 1.​Succinate is oxidized to fumarate, producing FADH₂. ​8-9. Regeneration of Oxaloacetate ​Fumarate is converted to malate, then malate is oxidized to oxaloacetate, generating NADH. Key Steps in the Citric Acid Cycle Step 1 Condensation (Formation of Citrate) Acetyl-CoA combines with oxaloacetate to form citrate. Steps 2-3 Isomerization Citrate is rearranged to form isocitrate through cis-aconitate. Step 4 First Oxidation (Production of NADH & CO₂) ​ Isocitrate is oxidized to α-ketoglutarate. ​ NAD⁺ is reduced to NADH, and CO₂ is released. Step 5 Second Oxidation (Production of NADH & CO₂) ​ α-Ketoglutarate is oxidized to succinyl-CoA. ​ NADH and CO₂ are produced. Step 6 Substrate-Level Phosphorylation (ATP/GTP Production) ​ Succinyl-CoA is converted to succinate, ​ generating GTP/ATP. Step 7 Third Oxidation (Production of FADH₂) ( ⭐) ​ Succinate is oxidized to fumarate, reducing FAD to ​ FADH₂. KNOW WHAT HAPEENS AT STEP 7 Step 8 Hydration (Addition of Water) ​ Fumarate is converted to malate with the addition of ​ H₂O. Step 9 Final Oxidation (Regeneration of Oxaloacetate) ​ Malate is oxidized to oxaloacetate, producing ​ NADH. ELECTRON TRANSPORT CHAIN ​The final stage of aerobic respiration, located on the inner mitochondrial membrane. ​The inner membrane has folds (cristae) to increase surface area for efficient ATP production. ​The ETC releases stored energy from NADH and FADH₂ to drive ATP synthesis. ​This process is called oxidative phosphorylation, where ATP is produced using  energy from electron transport and oxygen reduction. ​Key Role of the ETC ​Converts high-energy electrons from NADH & FADH₂ into ATP. ​Oxygen acts as the final electron acceptor, forming water (H₂O). ​Produces the majority of ATP in aerobic respiration. ​ Oxidative phosphorylation occurs in distinct steps: 1.​Proton Pumping & Electrochemical Gradient Electron carriers NADH and FADH₂ transfer electrons to the ETC. Energy from electrons powers proton pumps, creating a proton motive force across the inner mitochondrial membrane. 1.​ATP Synthesis via Chemiosmosis ATP synthase allows protons to diffuse back into the mitochondrial matrix. This diffusion powers ATP synthesis from ADP and Pi. 1.​Oxygen as the Final Electron Acceptor O₂ accepts electrons and protons, forming water (H₂O) as a byproduct. ​ Key Outcome  ​ Major ATP production step in cellular respiration. ​ Efficient use of high-energy electrons for ATP generation. Know the steps for the electron transport Step 1: generating a proton motive 1.​Oxidation of NADH & FADH₂ 1.​NADH and FADH₂ are oxidized, releasing high-energy electrons and protons (H⁺). 2.​Electrons are transferred to the Electron Transport Chain (ETC). 2.​Electron Transfer & Proton Pumping 1.​The ETC consists of transmembrane carrier proteins. 2.​As electrons move through the chain, they lose energy. 3.​This energy is used to pump protons (H⁺) from the mitochondrial matrix into the intermembrane space. 3.​Formation of an Electrochemical Gradient 1.​The accumulation of H⁺ ions in the intermembrane space creates a proton motive force. 2.​This electrochemical gradient is used in the next step to power ATP synthesis. Know what the proton motor force is and what powers ATP synthase enzyme Step Two: ATP Synthesis via Chemiosmosis 1.​Proton Motive Force Drives H⁺ Movement 1.​H⁺ ions move down their electrochemical gradient from the intermembrane space back into the mitochondrial matrix. 2.​Chemiosmosis Facilitates ATP Production 1.​This process is known as chemiosmosis, where ATP synthase allows the controlled diffusion of H⁺ ions across the membrane. 3.​ATP Synthase Generates ATP 1.​As H⁺ ions pass through ATP synthase, the enzyme undergoes molecular rotation. 2.​This movement catalyzes the conversion of ADP + Pi into ATP. Whats the purpose of generating H proton force Step Three: Reduction of Oxygen 1. Removal of De-Energized Electrons 1.​The Electron Transport Chain (ETC) must clear out used electrons to continue functioning.  2.​Without removal, the chain would become blocked, stopping ATP production. 2. Oxygen as the Final Electron Acceptor 1.​Oxygen (O₂) removes de-energized electrons, preventing a buildup. 2.​This allows the ETC to keep accepting new high-energy electrons from NADH and FADH₂. What is the role of oxygen 3. Formation of Water & Proton Gradient Maintenance 1.​Oxygen also binds with free protons (H⁺) in the matrix, forming water (H₂O). 2.​This removal of protons helps maintain the hydrogen gradient, ensuring ATP synthesis can continue. 4. Importance of Oxygen in ATP Production 1.​Without oxygen, the ETC stops functioning, as hydrogen carriers (NADH & FADH₂) cannot transfer electrons. 2.​This results in a halt in ATP production, leading to anaerobic processes instead. Know importance of oxygen and ATP production Summary: Oxidative Phosphorylation 1. Electron Transport & Energy Release NADH & FADH₂ donate high-energy electrons to the Electron Transport Chain (ETC), located in the mitochondrial cristae. As electrons move through the chain, they lose energy, which is transferred to electron carriers. 2. Proton Pumping & Gradient Formation Energy from electron transfer is used to pump H⁺ ions from the matrix into the intermembrane space. This creates an electrochemical gradient, also known as the proton motive force. Know what happens here and where do the ions go 3. ATP Synthesis via Chemiosmosis H⁺ ions diffuse back into the matrix through ATP synthase, generating ATP from ADP + Pi. 4. Oxygen as the Final Electron Acceptor Oxygen binds with electrons and H⁺ ions to form water (H₂O), preventing electron buildup and maintaining the chain’s function. Stage Four: The Electron Transport Chain Electron Transfer NADH and FADH₂ donate high-energy electrons to the ETC located on the inner mitochondrial membrane. Electrons are passed through a series of membrane-associated proteins, releasing energy at each step. Proton Pumping The energy released is used to pump H⁺ ions (protons) from the matrix into the intermembrane space, creating an electrochemical gradient. This proton gradient is crucial for ATP production in the next stage (chemiosmosis). ​Facilitates ATP synthesis by creating the proton motive force. ​Oxygen at the end of the chain accepts electrons and combines with protons to form water. What is the role of NADH and FADH2 Harvesting Energy by Extracting Electrons Glucose Catabolism & Energy Release  1.​The breakdown of glucose occurs through oxidation-reduction (redox) reactions. 2.​These reactions gradually transfer electrons closer to oxygen, releasing energy in the process. Role of NAD⁺ as an Electron Carrier 1.​NAD⁺ (Nicotinamide Adenine Dinucleotide) collects high-energy electrons from glucose. 2.​It transports electrons to the Electron Transport Chain (ETC), where ATP is ultimately generated. What is the role of NAD+ ​Electrons are harvested step-by-step for controlled energy release. ​NAD⁺ plays a crucial role in transferring electrons efficiently. ​Sets up the next stages of cellular respiration (Krebs Cycle & ETC). Regulating Aerobic Respiration Hexokinase Converts glucose → glucose-6-phosphate to maintain low glucose levels in cells. Facilitates passive glucose transport into cells. Phosphofructokinase (PFK) Controls the committed step of glycolysis. ​ Regulation: Upregulated by fructose-6-phosphate and AMP (indicates low energy, needing more ATP). Downregulated by ATP & glucagon (signals high energy state). Pyruvate Kinase Converts PEP → pyruvate, driving ATP production. ​ Regulation: 1.​Upregulated by PEP & fructose-6-phosphate. 2.​Downregulated by ATP (negative allosteric inhibition). What is upregulated and down regulated Catabolism of Proteins and Fats ​When glucose is scarce, proteins and fats serve as alternative energy sources. ​Protein Catabolism ​Proteins are broken down into amino acids. ​Deamination removes the amino group (NH₂), producing ammonia (NH₃) as a byproduct. ​The remaining carbon skeleton is metabolized through the Krebs Cycle or converted into glucose (gluconeogenesis). ​Fat Catabolism (Beta-Oxidation)  ​Lipids (fats) are broken down into glycerol and fatty acids. ​Glycerol can enter glycolysis. ​Fatty acids undergo beta-oxidation, producing Acetyl-CoA, which enters the Krebs Cycle for ATP generation. ​More ATP is produced from fats than carbohydrates, making them an efficient energy source. What is protein and fat catabolism ​Fat Catabolism (Beta-Oxidation) ​Lipids (fats) are broken down into glycerol and fatty acids. ​Glycerol can enter glycolysis. ​Fatty acids undergo beta-oxidation, producing Acetyl-CoA, which enters the Krebs Cycle for ATP generation. ​More ATP is produced from fats than carbohydrates, making them an efficient energy source. Evolution of Cellular Respiration ​degradation  ​glycolysis ​anaerobic photosynthesis ​oxygen-forming photosynthesis ​nitrogen fixation ​aerobic respiration What is the order of this and know it Chloroplasts ​Thylakoid Membranes: Internal membranes in chloroplasts, organized into grana. ​Function: Thylakoid membranes contain pigments for capturing light and producing ATP. ​Photosystems: Clusters of pigments that act as antennas to collect light energy efficiently. What is the function of the different membranes of the chloroplast Two major processes in Photosynthesis Light-Dependent Reactions Occur in the thylakoids of the chloroplast. Capture sunlight using pigments. Convert sunlight into ATP and NADPH for energy. Light-Independent Reactions (Calvin Cycle) Occur in the stroma of the chloroplast. Use CO₂ to build organic molecules. Utilize ATP and NADPH from the light reactions. Know the difference between the two processes Chlorophyll ​Chlorophylls absorb photons through an excitation process. ​Photon absorption excites electrons in the pigment’s ring structure. ​Excited electrons are channeled away through an alternating carbon-bond system. ​Wavelengths absorbed depend on the energy levels available for electron excitation. What is the role of chlorophyll in photosynthesis Light and Reducing Power ​Light-dependent reactions of photosynthesis use light energy to: ​ Reduce NADP to NADPH  ​ Synthesize ATP ​Reducing power from water splitting helps convert CO₂ into organic molecules during carbon fixation. What is the primary function of light dependent reactions The cytochrome complexes of mitochondria and chloroplasts have evolutionarily related proteins in common ​Mitochondria and chloroplasts share evolutionarily related proteins in their cytochrome complexes. ​Descent with modification is a recurring theme in evolution. ​Homologous genes exist due to a common ancestor. ​Comparing the electron transport chains of mitochondria and chloroplasts reveals homologous genes. What is the reason they share proteins ​Summary: CO₂ Incorporation (Calvin-Benson Cycle)  ​The Calvin-Benson cycle is responsible for incorporating CO₂ into organic molecules. ​This process requires a massive energy input. ​For every 6 CO₂ molecules incorporated: ​ 18 ATP and 12 NADPH are consumed. ​Glucose is not directly produced; instead, precursor molecules are formed. Understand this cycle, what does it do The Calvin cycle was determined by isotope labeling methods ​ ¹⁴C-labeled CO₂ was introduced into green algae cultures. ​ Incubation periods varied to track carbon assimilation over time. ​ Two-dimensional paper chromatography was used to separate radiolabeled molecules. ​ Autoradiography helped visualize ¹⁴C-labeled compounds as dark spots on film. ​ Scientists identified the sequence in which labeled molecules appeared. ​ Melvin Calvin was awarded the Nobel Prize in 1961 for this discovery. How is the calcivn cycle determined Summary ​Cellular Energy Harvest ​Cellular Respiration  ​ Glycolysis ​ Fermentation ​ Oxidation of Pyruvate ​ Krebs Cycle ​ Electron Transport Chain ​Evolution of Metabolism ​Photosynthesis ​ Energy harvesting ​ Calvin Cycle Calvin Cycle Know these steps what goes in and out, the three parts, names, Rubisco