DAT Bootcamp High-Yield Biology Notes PDF

 “How Do I Get a Good Bio Score on the DAT?” Bootcamp has multiple ways to study bio based on how you learn best. We have High-Yield Bio Notes, Biology Videos, Bio Bites, question banks, and more. For content review: If you like reading, use these notes. They serve as a concise refer...

 “How Do I Get a Good Bio Score on the DAT?” Bootcamp has multiple ways to study bio based on how you learn best. We have High-Yield Bio Notes, Biology Videos, Bio Bites, question banks, and more. For content review: If you like reading, use these notes. They serve as a concise reference to everything you need to know for the DAT. If you prefer videos, watch the Bio Videos. They cover the same info and incorporate practice questions. Most importantly, you have to practice what you’ve learned. You can practice with the Bio Question Bank and Bio Bites as you progress through biology. The bio practice tests will tie everything together and the performance page will identify areas where you need further studying. If you’re short on time, my #1 recommendation is finishing and reviewing all the DAT Bootcamp practice tests 1-10 and focusing on learning from the explanations. These are the most representative and high-yield questions you’re likely to see on the DAT. Be sure to learn everything in the explanations in the practice tests before you take your DAT. Lastly, I want DAT Bootcamp to be perfect for you. If you have any feedback or questions, please email us at [email protected]! Your feedback is invaluable to improving these notes for future generations of students. Happy studying! 😃 -Dr. Ari and the DAT Bootcamp team © 2025 Bootcamp.com 2  Table of Contents Chapter 1: Molecules and Fundamentals of Biology Chapter 2: Cells and Organelles Chapter 3: Cellular Energy Chapter 4: Photosynthesis Chapter 5: Cell Division Chapter 6: Molecular Genetics Chapter 7: Heredity Chapter 8: Microscopy & Lab Techniques Chapter 9: Plants Chapter 10.1: Circulatory System Chapter 10.2: Respiratory System Chapter 10.3: Immune System Chapter 10.4: Nervous System Chapter 10.5: Muscular System Chapter 10.6: Skeletal System Chapter 10.7: Endocrine System Chapter 10.8: Digestive System Chapter 10.9: Excretory System Chapter 10.10: Integumentary System Chapter 11: Reproduction and Developmental Biology Chapter 12: Diversity of Life Chapter 13: Evolution Chapter 14: Ecology Chapter 15: Animal Behavior © 2025 Bootcamp.com 3 Ch. 1: Molecules and Carbohydrates Fundamentals of Biology Carbohydrates are used as fuel and structural support. They contain carbon, hydrogen, and oxygen atoms (CHO). They can come in the form of Table of Contents monosaccharides, disaccharides, and polysaccharides. Biological Chemistry Monosaccharides are carbohydrate monomers. Carbohydrates Proteins Ribose: A five carbon monosaccharide. Lipids Fructose: A six carbon monosaccharide. Nucleic Acids Glucose: A six carbon monosaccharide. Other Types of RNA Biological Hypotheses and Theories Glucose and fructose are isomers of each other (same chemical formula, different arrangement of atoms). Biological Chemistry Disaccharides consist of two monosaccharides joined Matter: Anything that takes up space and has by a glycosidic bond. It is the result of a dehydration mass. (condensation) reaction. Common examples of Element: A pure substance that has specific disaccharides include sucrose, lactose, and maltose. physical/chemical properties and can’t be broken down into a simpler substance. Polysaccharides contain multiple monosaccharides Atom: The smallest unit of matter that still retains connected by glycosidic bonds to form long polymers. the chemical properties of the element. Molecule: Two or more atoms joined together. Starch: Form of energy storage for plants. Intramolecular forces: Attractive forces that act Glycogen: Form of energy storage in animals. on atoms within a molecule. Intermolecular forces: Forces that exist between Proteins molecules and affect physical properties of the substance. Proteins contain carbon, hydrogen, oxygen, and Monomers: Single molecules that can nitrogen atoms (CHON). These atoms combine to form polymerize, or bond with one another. amino acids, which link together to build Polymers: Substances made up of many polypeptides (or proteins). monomers joined together in chains. Dehydration (condensation) reaction: Creates a Amino acids are the monomers of proteins and have covalent bond between monomers and releases the structure shown below. There are twenty different water. types of amino acids, characterized by a unique Hydrolysis: A reaction that breaks a covalent “R-group”. bond using water. Dehydration Reaction: Proteins Amino Acid Structure Amino Carboxyl Amino Amino acid acid Dipeptide Water R-group side chain © 2025 Bootcamp.com 4 Polypeptides are polymers of amino acids and are Levels of Protein Structure joined by peptide bonds through dehydration Primary structure (condensation) reactions. Hydrolysis reactions break Amino acids Peptide bonds peptide bonds. Protein structure: 1. Primary structure: Sequence of amino acids connected through peptide bonds. Secondary structure 2. Secondary structure: Intermolecular forces between the polypeptide backbone (not R-groups) Alpha helix Beta pleated sheet due to hydrogen bonding. Forms α-helices or β-pleated sheets. 3. Tertiary structure: Three-dimensional structure Hydrogen due to interactions between R-groups. Can create bonds hydrophobic interactions based on the R-groups. Disulfide bonds are created by covalent bonding between the R-groups of two cysteine amino Tertiary structure acids. Hydrogen bonding and ionic bonding Disulfide between R groups also hold together the tertiary Hydrogen linkage structure. bond 4. Quaternary structure: Multiple polypeptide Hydrophobic chains come together to form one protein. interactions Protein denaturation describes the loss of protein Ionic (electrostatic) function and higher order structures. Only the primary interactions structure is unaffected. Proteins will denature as a result of high or low temperatures, pH changes, and salt concentrations. For example, cooking an egg in Quaternary structure high heat will disrupt the intermolecular forces in the egg’s proteins, causing it to coagulate. Protein function Description Storage Reserve of amino acids Signaling molecules that Hormones regulate physiological processes Proteins in cell Receptors membranes which bind to signal molecules Provide strength and Structure support to tissues (hair, spider silk) Antibodies that protect Immunity against foreign substances Regulate rate of chemical Enzymes reactions © 2025 Bootcamp.com 5 Catalysts increase reaction rates by lowering the High-yield biological enzymes: activation energy of a reaction. The transition state is the unstable conformation between the reactants Phosphatase: Cleaves a phosphate group off of a and the products. Catalysts reduce the energy of the substrate molecule transition state. Catalysts do not shift a chemical Phosphorylase: Directly adds a phosphate group reaction or affect spontaneity. to a substrate molecule by breaking bonds within a substrate molecule. Enzymes act as biological catalysts by binding to Kinase: Indirectly adds a phosphate group to a substrates (reactants) and converting them into substrate molecule by transferring a phosphate products. group from an ATP molecule. These enzymes do not break bonds to add the phosphate group. Enzymes bind to substrates at an active site, which is specific for the substrate that it acts upon. Feedback regulation of enzymes occurs when the Most enzymes are proteins. end product of an enzyme-catalyzed reaction inhibits The induced fit theory describes how the active the enzyme’s activity by binding to an allosteric site. site molds itself and changes shape to fit the substrate when it binds. Competitive inhibition occurs when a competitive A ribozyme is an RNA molecule that can act as an inhibitor competes directly with the substrate for enzyme (a non-protein enzyme). active site binding. Competitive inhibitors can be A cofactor is a non-protein molecule that helps outcompeted by adding more substrate. enzymes perform reactions. A coenzyme is an organic cofactor (i.e., vitamins). Inorganic cofactors Noncompetitive inhibition occurs when the are usually metal ions. noncompetitive inhibitor binds to an allosteric site Protein enzymes are susceptible to denaturation. (a location on an enzyme that is different from the They require optimal temperatures and pH for active site) that modifies the active site. function. Noncompetitive inhibitors cannot be outcompeted by adding more substrate. Enzymes catalyze reactions in the following ways: Types of Enzyme Inhibition Conformational changes that bring reactive Uninhibited Enzyme Substrate groups closer. The presence of acidic or basic groups. Induced fit of the enzyme-substrate complex. Active Electrostatic attractions between the enzyme and site substrate. Competitive Enzyme Inhibitor Active site Noncompetitive Inhibitor Enzyme Active Allosteric site site © 2025 Bootcamp.com 6  An enzyme kinetics plot can be used to visualize how Lipids inhibitors affect enzymes. Below are a few terms used to describe the plot: Lipids contain carbon, hydrogen, and oxygen atoms (CHO), like carbohydrates. They have long 1. The x-axis represents substrate concentration [X] hydrocarbon tails that make them very hydrophobic. while the y-axis represents reaction rate or velocity (V). Triacylglycerol (triglyceride) is a lipid molecule with 2. Vmax is the maximum reaction velocity. a glycerol backbone (three carbons and three hydroxyl 3. Michaelis Constant (KM) is the substrate groups) and three fatty acids (long hydrocarbon tails). concentration [X] at which the velocity (V) is 50% of Glycerol and the three fatty acids are connected by the maximum reaction velocity (Vmax). ester linkages. 4. Saturation occurs when all active sites are occupied, so the rate of reaction does not increase Saturated fatty acids have no double bonds and as a anymore despite increasing substrate result pack tightly (solid at room temperature). concentration (causes graph plateaus). Unsaturated fatty acids have double bonds. Double Competitive inhibition: KM increases, while Vmax stays bonds create kinks in the fatty acid chain, preventing the same tight packing and increasing membrane fluidity. Enzyme Kinetics: Competitive Inhibition Phospholipids are lipid molecules that have a glycerol Normal backbone, one phosphate group, and two fatty acid enzyme tails. The phosphate group is polar, while the fatty acids are nonpolar. As a result, they are amphipathic (both hydrophobic and hydrophilic). Furthermore, Reaction they spontaneously assemble to form lipid bilayers. rate Competitive inhibitor: ½ Vmax Vmax stays the same Cholesterol is an amphipathic lipid molecule that is a while Km increases component of the cell membranes. It is the precursor to steroid hormones (lipids with four hydrocarbon rings). It is also the starting material for vitamin D and bile acids. Km Km [Substrate] Lipoproteins allow the transport of lipid molecules in the bloodstream due to an outer coat of Noncompetitive inhibition: KM stays the same, while phospholipids, cholesterol, and proteins. Vmax decreases Waxes are simple lipids with long fatty acid chains Enzyme Kinetics: Noncompetitive Inhibition connected to alcohols. Normal enzyme Carotenoids are lipid derivatives containing long carbon chains with double bonds and function mainly as pigments. Reaction rate Sphingolipids have a backbone with aliphatic (non-aromatic) amino alcohols and have important ½ Vmax functions in structural support, signal transduction, Noncompetitive and cell recognition. inhibitor: ½ Vmax Vmax decreases while Km stays the same Km [Substrate] © 2025 Bootcamp.com 7 Glycolipids are lipids found in the cell membrane with Nucleic acid polymerization proceeds as nucleoside a carbohydrate group attached instead of a phosphate triphosphates are added to the 3’ end of the group in phospholipids. Like phospholipids, they are sugar-phosphate backbone. amphipathic and contain a polar head and a fatty acid chain. DNA is an antiparallel double helix, in which two complementary strands with opposite directionalities Nucleic Acids (positioning of 5’ ends and 3’ ends) twist around each other. Nucleic acids contain nucleotide monomers that build into DNA (deoxyribonucleic acid) and RNA Antiparallel Strands (ribonucleic acid) polymers. Nucleosides contain a five-carbon sugar and a DNA nitrogenous base. DNA strands run parallel to each other, but in Nucleotides contain a five-carbon sugar, a opposite directions nitrogenous base, and a phosphate group. mRNA is single-stranded after being copied from DNA Deoxyribose sugars (in DNA) have a hydrogen at the during transcription. 2’ carbon while ribose five-carbon sugars (in RNA) have a hydroxyl group at the 2’ carbon. Other Types of RNA Phosphodiester bonds are formed through a miRNA (microRNA): Small RNA molecules that can condensation reaction where the phosphate group of silence gene expression by base pairing to one nucleotide (at the 5’ carbon) connects to the complementary sequences in mRNA. hydroxyl group of another nucleotide (at the 3’ carbon) and releases a water molecule as a rRNA (ribosomal RNA): It is formed in the nucleolus by-product. of the cell and helps ribosomes translate mRNA. A series of phosphodiester bonds create the dsRNA (double stranded RNA): Some viruses carry sugar-phosphate backbone, with a 5’ end (free their code as double stranded RNA. OAT Pro Tip: phosphate) and a 3’ end (free hydroxyl). dsRNA must pair its nucleotides, so it must have equal amounts of A/U and equal amounts of C/G. Nucleic Acid Polymerization Phosphate group tRNA (transfer RNA): Small RNA molecule that participates in protein synthesis. 5’ end Nitrogenous base 5’ 4’ 1’ 3’ 2’ Five-carbon sugar Phosphodiester bond Nitrogenous base 3’ end © 2025 Bootcamp.com 8  Biological Hypotheses and Theories The central dogma of genetics states that information is passed from DNA → RNA → proteins. The Universe is approximately 13.8 billion years old. There are a few exceptions to this (e.g., reverse The first cells appeared on Earth approximately 3.5 transcriptase and prions). billion years ago. Central Dogma of Genetics Primordial Earth: DNA RNA 1. Earth’s primordial atmosphere was comprised of inorganic compounds and was a reducing environment (little O2 gas). Protein 2. As Earth cooled, gases condensed, forming the Transcription Translation primordial sea. 3. Simple compounds evolved into more complex organic compounds. Reverse 4. Organic monomers linked into polymers. transcription 5. Protobionts emerged as precursors to cells. 6. Heterotrophic, obligate anaerobic prokaryotes developed. 7. Autotrophic prokaryotes, such as cyanobacteria capable of photosynthesis, formed. This led to oxygen production and accumulation, creating an oxidizing environment (high O2 gas). The RNA world hypothesis is the theory that early life 8. Primitive eukaryotes emerged, supporting the forms relied on self-replicating RNA both to store endosymbiotic theory where membrane bound genetic information and to catalyze chemical reactions organelles (mitochondria, chloroplasts), originally before the evolution of DNA and proteins. free-living, were engulfed by other prokaryotes, leading to a symbiotic relationship. Because RNA is reactive and unstable: 9. More complex eukaryotes and multicellular organisms began to evolve. DNA replaced RNA in how genetic information is stored. Modern cell theory: Proteins largely replaced RNA in catalyzing reactions (ribozymes being a notable exception). 1. All lifeforms have one or more cells. 2. The cell is the basic structural, functional, and The endosymbiotic theory states that eukaryotes organizational unit of life. developed when aerobic bacteria were internalized as 3. All cells come from other cells (cell division). mitochondria while the photosynthetic bacteria 4. Genetic information is stored and passed down became chloroplasts. Evidence for this theory includes through DNA. the similarities between mitochondria and 5. An organism’s activity is dependent on the total chloroplasts: activity of its independent cells. 6. Metabolism and biochemistry (energy flow) occurs They are similar in size. within cells, They possess their own circular DNA. 7. All cells have the same chemical composition They have ribosomes with a large and small within organisms of similar species. subunit. They reproduce independently of the host cell. They contain a double membrane. © 2025 Bootcamp.com 9  High-Yield Roots, Prefixes, and Suffixes Prefix Meaning Example Root Meaning Example Suffix Meaning Example Against Antibiotic -adrena- Adrenal Adrenaline -ase Enzyme Amylase Anti- Ecto- Outside Ectoderm -blast- Formative cell Osteoblast -crine Secrete Exocrine Endo- Inside Endocrine -derma- Skin Endodermis -cyte Cell Adipocyte Relating to Epi- Above Epidermis -enter- Intestine Enterocyte -cytosis Transcytosis cells Producing, Exo- Outside Exocytosis -gastr- Stomach Gastrin -gen Immunogen generating Insufficient, Hypo- Hypoglycemia -glyc- Sugar Glycogen -genesis Formation of Angiogenesis low Excessive, -lytic or Destruction, Hyper- Hyperactive -hem- Blood Hemoglobin Hemolysis high -lysis breakdown Hydroxyl group, Resembles, Intra- Within Intracellular -hydroxyl- Hydroxylation -oid Nucleoid alcohol related to Inter- Between Intermolecular -leuk- White Leukocyte -ose Sugar Glucose Fearing, Mono- One Monomer -lip- Fat or lipid Lipid -phobic Hydrophobic repelling Peri- Around Peripheral -myo- Muscle Cardiomyocyte -philic Attracting Hydrophilic Nucleus, central Development, Poly- Many Polysaccharide -nucle- Nucleus -plasia Hyperplasia part formation Below, Examination, Sub- Subunit -peptid- Protein chain Peptidase –scopy Microscopy under inspection Supra- Above Supramolecular -phag- Eating, swallowing Phagocytosis –stasis Stopping Epistasis Ribose (five-carbon Trans- Across Transduction -ribos- Deoxyribose –trophy Growth Hypertrophy sugar) © 2025 Bootcamp.com 10 Ch. 2: Cells and Organelles Integral proteins are embedded in the phospholipid bilayer. They are amphipathic (contain both hydrophilic and hydrophobic components). Table of Contents Transmembrane proteins, a type of integral protein, traverse the entire bilayer. Integral proteins can Cell Membrane function as receptors in cell signaling. They can also Crossing Cell Membranes function as channels or carrier proteins for transport. Organelles Cytoskeleton Peripheral membrane proteins are found on the Extracellular Matrix surface of the bilayer (inside or outside of the cell) and Cellular Tonicity and Cell Circulation are generally hydrophilic. They can function as Cellular Adaptations receptors or assist with adhesion and cell recognition. Cell Tissues Membrane protein functions: Cell Membrane Receptor: Transmit a signal to a cell. Trigger The cell membrane is a selectively permeable barrier secondary responses within the cell. composed of a phospholipid bilayer with embedded ○ Agonists are molecules that bind to receptors proteins. It regulates the movement of substances in and functionally activate a target. and out of the cell. It also plays a role in cell signaling ○ Antagonists bind and prevent other and communication. molecules from binding, inhibiting production of a response. 1. Phospholipid bilayer: Possesses hydrophilic Adhesion: Attach cells to other things (e.g., other (water-attracting) heads that form the exterior cells) and act as anchors for the cytoskeleton. surfaces and hydrophobic (water-repelling) tails Cellular recognition: Proteins which have that face inward, creating a barrier to most carbohydrate chains (glycoproteins). Used by water-soluble substances. cells to recognize other cells. 2. Membrane proteins: Embedded within the phospholipid bilayer, they facilitate transport, act The fluid mosaic model describes how the as receptors for signaling, and provide structural components that make up the cell membrane can support. move freely within the membrane (“fluid”). 3. Carbohydrates: Attached to proteins and lipids Furthermore, the cell membrane contains many on the extracellular surface, they play key roles in different kinds of structures (“mosaic”). cell recognition, signaling, and adhesion. 4. Cholesterol: Found within eukaryotic cell The fluidity of the cell membrane can be affected by: membranes (absent in prokaryotic membranes), it helps to stabilize membrane fluidity. Temperature: ↑ temperatures increase fluidity while ↓ temperatures decrease it. Cell Membrane Components Cholesterol: Holds membrane together at high Carbohydrates temperatures and keeps membrane fluid at low Peripheral proteins temperatures. Integral proteins Phospholipid Degrees of unsaturation: Saturated fatty acids pack more tightly than unsaturated fatty acids, which have double bonds that may introduce kinks. Cholesterol © 2025 Bootcamp.com 11  Crossing Cell Membranes Cytosis refers to the bulk transport of molecules across the cell membrane. Cells must regulate the travel of substances across the cell membrane. There are three types of transport Endocytosis involves the cell membrane wrapping across the cell membrane: around an extracellular substance, internalizing it into the cell via a vesicle or vacuole. Below are different 1. Simple diffusion: Diffusion of small uncharged forms of endocytosis: molecules (e.g., O2, CO2, H2O) or lipid soluble molecules (steroids) directly across the cell Phagocytosis: Cellular eating around solid membrane, down their concentration gradient objects. (high to low) without using energy. Pinocytosis: Cellular drinking around dissolved 2. Facilitated transport: Channel proteins allow the materials (liquids). diffusion of large (e.g., glucose, sucrose) or Receptor-mediated endocytosis: Requires the charged molecules (e.g., Na+, K+, Cl-) across the cell binding of dissolved molecules to peripheral membrane, down their concentration gradient membrane receptor proteins, which initiates without using energy. endocytosis. 3. Active transport: Substances travel against their concentration gradient and require the Clathrin is a protein that aids in receptor-mediated consumption of energy by carrier proteins. endocytosis by forming a pit in the membrane that Primary active transport uses ATP hydrolysis pinches off as a coated vesicle. This is known as to pump molecules against their concentration clathrin-mediated endocytosis. gradient. For example, the sodium-potassium (Na+/K+) pump sets a membrane potential. Exocytosis is the opposite of endocytosis, in which Secondary active transport uses the energy material is released to the extracellular environment from one molecule moving down its through vesicle secretion. electrochemical gradient to drive the transport of another molecule against its concentration gradient. This requires an energy investment to establish the initial concentration gradient. Active Transport Primary Secondary Na+ Glucose Cotransporter High [Na+] (symporter) Low [glucose] Low [Na+] High ADP [glucose] ATP P © 2025 Bootcamp.com 12  Organelles Cellular Structures Organelles are cellular compartments enclosed by Golgi phospholipid bilayers (membrane bound). They are apparatus Centrioles located within the cytosol (aqueous intracellular fluid) and help make up the cytoplasm (cytosol & Ribosomes Mitochondria organelles). Smooth ER Lysosome Only eukaryotic cells contain membrane-bound organelles. Prokaryotes do not, but they have other adaptations, such as keeping their genetic material in a region called the nucleoid. Vacuoles Peroxisome The nucleus primarily functions to protect and house Cell Nucleolus DNA. DNA replication and transcription (DNA → membrane mRNA) occurs here. Rough ER Nucleus Parts of the nucleus: Ribosomes are not considered to be organelles; they The nucleoplasm is the cytoplasm of the nucleus. work as small factories that carry out translation The nuclear envelope is the membrane of the (mRNA → protein). They are composed of ribosomal nucleus. It contains two phospholipid bilayers (one subunits. inner, one outer). Nuclear pores are holes in the nuclear envelope Eukaryotic ribosomal subunits (60S and 40S) assemble that allow molecules to travel in and out of the in the nucleoplasm and are then exported from the nucleus. nucleus to form the complete ribosome in the cytosol The nucleolus is a dense area responsible for (80S). producing components of ribosomal subunits including rRNA (ribosomal RNA). Prokaryotic ribosomal subunits (50S and 30S) Nucleus assemble in the cytosol and also form complete ribosomes (70S) there. Nuclear envelope Free-floating ribosomes make proteins that function in the cytosol while ribosomes embedded in the rough endoplasmic reticulum (rough ER) make proteins that are sent out of the cell or to the cell membrane. Nucleolus © 2025 Bootcamp.com 13 The rough endoplasmic reticulum (rough ER) is Lysosomes, found in animal cells, are continuous with the outer membrane of the nuclear membrane-bound organelles that contain digestive envelope and is “rough” because it has ribosomes (hydrolytic) enzymes which break down cellular embedded in it. Proteins synthesized by the waste. They also play a role in apoptosis embedded ribosomes are sent into the lumen (inside (programmed cell death). of the rough ER) for modifications (e.g., glycosylation). Afterwards, they are either sent out of the cell or Vacuoles are membrane-bound vesicles typically used become part of the cell membrane. for storage (water, nutrients, waste) or transport. Rough ER Plant cells have large, fluid-filled central vacuoles that help maintain cell rigidity (turgor). Plant cell vacuoles also function similarly to lysosomes in animal cells. Ribosomes Contractile vacuoles actively pump out excess water and are found mostly in single-celled protists. The endomembrane system is composed of the different membranes that are suspended in the cytoplasm within a eukaryotic cell. It is a group of Interconnected organelles and membranes that work together to flattened sacs modify, package, and transport proteins and lipids that are entering or exiting a cell. The components of The smooth endoplasmic reticulum (smooth ER) is the endomembrane system include the nucleus, an extension of the rough ER. Its main function is to rough and smooth ERs, Golgi apparatus, lysosomes, synthesize lipids, produce steroid hormones, and vacuoles, and cell membrane. detoxify cells. Smooth ER The Golgi apparatus has a significant role in the endomembrane system: it receives vesicles from the ER on the cis face that empty proteins and lipids into the lumen of the Golgi. These proteins/lipids undergo Interconnected modifications and are then sorted, tagged, packaged, flattened sacs and distributed as secretory products. (no ribosomes) Peroxisomes perform hydrolysis, break down stored fatty acids, and help with detoxification. These The Golgi apparatus stores, modifies, and exports processes generate hydrogen peroxide, which is toxic proteins that will be secreted from the cell. It is made since it can produce reactive oxygen species (ROS). up of cisternae (flattened sacs) that modify and ROS damage cells through free radicals. Peroxisomes package substances. Vesicles come from the ER and contain an enzyme called catalase, which quickly reach the cis face (side closest to ER) of the Golgi breaks down hydrogen peroxide into water and apparatus. Vesicles leave the Golgi apparatus from the oxygen. trans face (side closest to cell membrane). Golgi Apparatus Lysosomes vs. Peroxisomes Cis face Lysosome Peroxisome H2O2 Digestive Catalase Flattened enzymes sacs O2 Trans face H2O © 2025 Bootcamp.com 14  Mitochondria are the powerhouses of the cell, Cytoskeleton producing ATP for energy use through cellular respiration. Mitochondrial inheritance is maternal, The cytoskeleton provides structure and function meaning all mitochondrial DNA in humans originates within the cytoplasm. from the mother. Mitochondria Microfilaments are the smallest structure of the cytoskeleton and are composed of a double helix made of actin filaments. They are mainly involved in Inward folds cell movement and can quickly assemble and (cristae) disassemble. Below are some of their functions: 1. Cleavage furrow: During cell division, myosin motors and actin microfilaments form contractile rings that split the cell. 2. Cyclosis (cytoplasmic streaming): The flow (or stirring) of the cytoplasm inside the cell. It is driven by forces via actin (microfilaments) and myosin movement, in a manner similar to muscle Chloroplasts are found in plants and some protists. contraction. They carry out photosynthesis. 3. Muscle contraction: Actin microfilaments have directionality, allowing myosin motor proteins to Chloroplasts are a type of plastid. Plastids are pull on them for muscle contraction. double-membraned organelles found exclusively within plant cells and algae, that function in Intermediate filaments are between microfilaments photosynthesis and storage of metabolites. and microtubules in size. They are more stable than microfilaments and mainly help with structural Chloroplast Stacks (granum) support. For example, keratin is an important of flattened intermediate filament protein in skin, hair, and nails. membranes (thylakoids) Microtubules are the largest in size and give structural integrity to cells. They are made of tubulin protein. Microtubules also form centrioles (used in cell division) and are found in cilia and flagella (beating appendages). Cytoskeletal Proteins Centrosomes are organelles found in animal cells Microfilaments containing a pair of centrioles. They act as microtubule organizing centers (MTOCs) during cell division. Centrosomes Intermediate filaments Two perpendicular cylinders Microtubules © 2025 Bootcamp.com 15 Kinesin and dynein are motor proteins that transport Extracellular Matrix cargo along microtubules. The extracellular matrix (ECM) provides extracellular Kinesin mechanical support for cells. Cargo ECM components: Kinesin ADP ATP Proteoglycan: A type of glycoprotein that has a high proportion of carbohydrates. Collagen: The most common structural protein, Microtubule secreted by fibroblasts; organized into collagen fibrils. Microtubule organizing centers (MTOCs) are Integrin: A transmembrane protein that facilitates present in eukaryotic cells and help organize ECM adhesion and signals to cells how to respond microtubule extension. Centrioles are hollow to the extracellular environment (growth, cylinders made of microtubules. Centrosomes apoptosis, etc.). contain a pair of centrioles oriented at 90 degree Fibronectin: A protein that connects integrin to angles to one-another. ECM and helps with signal transduction. Laminin: Behaves similarly to fibronectin. Cilia and Flagella Influences cell differentiation, adhesion, and movement. Cilia are small hair-like projections made of tubulin found only in eukaryotes. They line the outside of Cell walls are carbohydrate-based structures that act eukaryotic cells and function in locomotion of either like a substitute ECM because they provide structural the cell itself or fluids (e.g., cilia remove debris in the support to cells that either do not have ECM, or have a lungs). minimal ECM. They are present in plants (cellulose), fungi (chitin), bacteria (peptidoglycan), and archaea Flagella are longer hair-like structures found in both (non-peptidoglycan polysaccharides). prokaryotes and eukaryotes. Like cilia, flagella also function in locomotion of the cell or fluids (e.g., flagella Peptidoglycan is a polysaccharide with peptide chains. propel sperm). Eukaryotic flagella are composed of This is the primary component of bacterial cell walls. polymers of tubulin. Prokaryotic flagella are The cell wall of archaea is also made of composed of polymers of flagellin (they are not polysaccharides, but does not contain peptidoglycan. microtubules) Cell-matrix junctions (connect ECM → cytoskeleton): Cilia vs. Flagella Cilia Flagella 1. Focal adhesions: ECM connects via integrins to Cell actin microfilaments inside the cell. 2. Hemidesmosomes: ECM connects via integrins to intermediate filaments inside the cell. Fluid Cell-Matrix Junctions Cilia Focal adhesions Hemidesmosomes Flagellum Actin microfilaments Intermediate filaments Sweeping motion Flagellar motion propels the cell ECM ECM © 2025 Bootcamp.com 16  Cell-cell junctions (connect adjacent cells): Cellular Tonicity and Cell Circulation Cell added into 3 different solutions 1. Tight junctions: Form water-tight seals between cells to ensure substances pass through cells and not between them. 2. Desmosomes: Provide support against Hypotonic Isotonic Hypertonic mechanical stress. Connects neighboring cells via Lysis Shrivel intermediate filaments. H2O H2O H2O 3. Adherens junctions: Similar in structure and function to desmosomes, but connects neighboring cells via actin microfilaments. 4. Gap junctions: Allow passage of ions and small Osmosis: Passive movement of water (solvent) across molecules between cells. Formed from a semipermeable membrane from low to high solute transmembrane proteins known as connexons. concentration. Gap junctions are only present in animal cells. Isotonic solutions have the same solute Plant cells contain a few unique cell junctions: concentration as the cells placed in them. 1. Middle lamella: Sticky cement similar in function Hypertonic solutions have a higher solute to tight junctions. concentration than the cells placed in them, causing 2. Plasmodesmata: Tunnels with tubes between water to leave the cell. plant cells. Allows cytosol fluids to freely travel between plant cells. Animal cells shrivel. Cells that have a cell wall (plants, bacteria, fungi, Intercellular Junctions etc.) undergo plasmolysis, the process of the Animal cell junctions Plant cell junctions cell’s cytoplasm shrinking away from the cell wall. Adjacent cell membranes Cell wall Cell Tight Hypotonic solutions have a lower solute and wall junctions Protein of concentration than the cells placed in them, causing membrane complex adjacent water to enter the cell. of one cell cell Open Animal cells swell and can burst (lysis). channel Gap Plant, bacterial, and fungal cells become turgid Closed junctions channel (swollen and firm). Middle Plasmodesmata lamella Connexon Cell Tissues Plaque There are four basic types of tissues: Desmosomes 1. Epithelial tissues are cohesive sheets of cells that Intermediate line internal organs and cover the body. filaments 2. Connective tissues support the structure of the Adherens organism. Sparse connective tissue cells are junctions scattered within an extracellular matrix. Cartilage, Actin microfilaments bone, blood, and adipose (fat) are all types of connective tissue. 3. Muscle tissues function in locomotion (skeletal muscle) and support organ systems (smooth muscle and cardiac muscle). 4. Nervous tissues process and transmit information within the body. Nervous tissue is composed of neurons to send information and various support cells called glial cells. © 2025 Bootcamp.com 17  Adenosine Triphosphate (ATP) Ch. 3: Cellular Energy Phosphate groups Table of Contents Adenine base Biothermodynamics Adenosine Triphosphate (ATP) Ribose Mitochondria sugar Aerobic Cellular Respiration Nucleoside ATP Yield of Aerobic Cellular Respiration Nucleotide Anaerobic Energy Pathways Nucleoside diphosphate Fermentation Nucleoside triphosphate Alternative Sources of Energy Generation ATP is used as cellular energy currency. The bond Biothermodynamics between phosphate groups releases energy upon hydrolysis, resulting in ATP becoming adenosine Laws of thermodynamics: diphosphate (ADP). Because of the additional negatively-charged phosphate group, ATP is less stable 1. Energy cannot be created nor destroyed, but can than ADP. be transformed from one form to another. 2. The entropy (disorder) of the universe is always Reaction coupling is the process of powering an increasing. The combined change in entropy energy-requiring reaction with an energy-releasing (system and surroundings) must be positive. one. It allows an unfavorable reaction to be powered 3. The entropy of a substance at absolute zero is 0. by a favorable reaction, making the net Gibbs free energy negative (-ΔG = exergonic = releases energy + Metabolism refers to all the metabolic pathways spontaneous). (series of chemical reactions) that are happening in a given organism. Catabolic processes involve breaking Mitochondria down larger molecules for energy (less ordered state, increased entropy), while anabolic processes involve Mitochondria are organelles that produce ATP using energy to build larger macromolecules (more through cellular respiration (catabolic process). They ordered state, decreased entropy). have an outer membrane and an inner membrane with many infoldings called cristae. The Q10 (temperature coefficient) is a factor that intermembrane space is located between the outer measures the change in reaction rates for every 10 ºC and inner membranes while the mitochondrial change in temperature. For example, in animals, if matrix is located inside the inner membrane. Q10= 1.5, an increase of 10 ºC in body temperature would increase the metabolic rate of the body by 50%. Mitochondria To break down carbohydrates for energy, cells either Cytosol utilize aerobic cellular respiration (consumes oxygen, more energy produced) or anaerobic Cristae pathways (no oxygen needed, but less energy produced). Mitochondrial matrix Adenosine Triphosphate (ATP) Inner membrane Adenosine triphosphate (ATP) is an RNA nucleoside Inter- membrane triphosphate. It contains an adenine nitrogenous base space linked to a ribose sugar (RNA nucleoside part), and Outer three phosphate groups connected to the sugar membrane (triphosphate part). © 2025 Bootcamp.com 18  Aerobic Cellular Respiration Glycolysis Aerobic cellular respiration is performed to Glucose → 2 ATP + 2 NADH + 2 pyruvate phosphorylate ADP into ATP by breaking down glucose and moving electrons around (oxidation and Glycolysis takes place in the cytosol and does not reduction reactions). Aerobic cellular respiration require oxygen, so it is also used in fermentation. involves four catabolic processes: Substrate-level phosphorylation is the process used 1. Glycolysis to generate ATP in glycolysis by transferring a 2. Pyruvate oxidation phosphate group to ADP directly from a 3. Krebs cycle phosphorylated compound. 4. Oxidative phosphorylation Glycolysis has an energy investment phase and an Glycolysis energy payoff phase: 1. Hexokinase uses one ATP to phosphorylate Glucose glucose into glucose-6-phosphate, which cannot ATP leave the cell (it becomes trapped by the Hexokinase phosphorylation). ADP 2. Isomerase modifies glucose-6-phosphate into Energy investment fructose-6-phosphate. Glucose-6-phosphate 3. Phosphofructokinase uses a second ATP to phosphorylate fructose-6-phosphate into Isomerase fructose-1,6-bisphosphate. This is the key Fructose-6-phosphate regulatory step in glycolysis. 4. Fructose-1,6-bisphosphate is broken into ATP Phosphofructokinase dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P), which are in ADP equilibrium with one another. Fructose-1,6-bisphosphate 5. G3P proceeds to the energy payoff phase so DHAP is constantly converted into G3P to maintain equilibrium. Thus, one glucose molecule will produce two G3P that continue into the next G3P G3P steps. NAD+ NAD+ 6. G3P undergoes a series of redox reactions to produce four ATP through Energy payoff NADH NADH substrate-level-phosphorylation, two pyruvate and two NADH. 2 ADP 2 ADP Since two ATP are used up in the energy investment 2 ATP 2 ATP phase and four ATP are produced in the energy payoff phase, a net of two ATP is produced per glucose molecule within glycolysis. Pyruvate Pyruvate © 2025 Bootcamp.com 19  Pyruvate oxidation Krebs cycle 2 pyruvate → 2 CO2 + 2 NADH + 2 acetyl-CoA 2 acetyl-CoA → 4 CO2 + 6 NADH + 2 FADH2 + 2 ATP Pyruvate dehydrogenase is an enzyme that carries The Krebs cycle is also known as the citric acid cycle out the pyruvate oxidation steps below: or the tricarboxylic acid (TCA) cycle. Like pyruvate oxidation, it also occurs in the mitochondrial matrix 1. Decarboxylation: Pyruvate molecules and the cytosol for prokaryotes. (three-carbon molecule) move from the cytosol into the mitochondrial matrix (stays in the cytosol 1. Acetyl-CoA joins oxaloacetate (four-carbon) to for prokaryotes), where they undergo form citrate (six-carbon). decarboxylation, producing one CO2 and one 2. Citrate undergoes rearrangements that produce two-carbon molecule per pyruvate. two CO2 and two NADH. 2. Oxidation: The two-carbon molecule is converted 3. After the loss of two CO2, the resulting four-carbon into an acetyl group, giving electrons to NAD+ to molecule produces one ATP through convert it into NADH. substrate-level phosphorylation. 3. Coenzyme A (CoA): CoA binds to the acetyl group, 4. The molecule will now transfer electrons to one producing acetyl-CoA. FAD, which is reduced into one FADH2. 5. Lastly, the molecule is converted back into Pyruvate Oxidation oxaloacetate and also gives electrons to produce one NADH. 6. Two acetyl-CoA molecules produce four CO2, six NADH, two FADH2, two ATP. NAD+ NADH Coenzyme A (CoA) Krebs Cycle Acetyl CoA Pyruvate CO2 Acetyl CoA CoA Matrix Oxaloacetate Citrate CO2 NADH Each round of the NAD+ citric acid cycle NADH NAD+ produces: 3 NADH 2 CO2 FADH2 1 FADH2 1 ATP CO2 FAD NAD+ NADH Mitochondria ATP ADP © 2025 Bootcamp.com 20 Oxidative phosphorylation Chemiosmosis goal: Use the proton electrochemical gradient (proton-motive force) to synthesize ATP. Electron carriers (NADH + FADH2) + O2 → ATP + H2O ATP synthase is a channel protein that allows protons The electron transport chain (ETC) and to flow down their electrochemical gradient (from the chemiosmosis (ions moving down electrochemical intermembrane space back to the mitochondrial gradients) work together to produce ATP in oxidative matrix). The spontaneous movement of protons phosphorylation. Oxygen acts as a final electron generates energy that is used to convert ADP into ATP, acceptor and gets reduced to form water. a condensation reaction that is endergonic (requires energy + nonspontaneous = +ΔG). ETC goal: Regenerate electron carriers and create an electrochemical gradient to power ATP production. ATP Yield of Aerobic Cellular Respiration The mitochondrial inner membrane is the location of Aerobic respiration is exergonic (-ΔG). the ETC for eukaryotes while the cell membrane is the location of the ETC for prokaryotes. NADH produces three ATP (NADH from glycolysis produces less). FADH2 produces two ATP. Four protein complexes (I-IV) are responsible for moving electrons through a series of Stage Net products Net ATP yield oxidation-reduction (redox) reactions in the ETC. As 2 ATP (substrate 2 ATP the series of redox reactions occurs, protons are level) pumped from the mitochondrial matrix to the Glycolysis intermembrane space, forming an electrochemical 2 NADH 4-6 ATP gradient. This is the reason the intermembrane space Pyruvate 2 NADH 6 ATP is highly acidic. decarboxylation NADH donates electrons to complex-I, regenerating 2 ATP 2 ATP NAD+. FADH2 donates electrons to complex-II, Krebs cycle 6 NADH 18 ATP regenerating FAD. NADH generates more proton pumping than FADH2. 2 FADH2 4 ATP Total 36-38 ATP Oxidative Phosphorylation Cytoplasm Outer membrane Intermembrane High [H+] space H+ H+ H+ Inner ATP I III IV membrane synthase 4e- II Mitochondrial + matrix NADH NAD FADH2 FAD 4H+ + O2 + 4e- 2 H2O ADP H+ ATP Low [H+] Electron transport chain (ETC) Chemiosmosis © 2025 Bootcamp.com 21  Anaerobic Energy Pathways Types of Fermentation Alcohol fermentation Lactic acid fermentation While aerobic respiration is the most efficient method of energy generation, there are two anaerobic Glucose Glucose alternatives: + 2 NAD 2 ADP 2 NAD+ 2 ADP Glycolysis Anaerobic respiration: Common in many 2 NADH 2 ATP 2 NADH 2 ATP microorganisms. Uses alternative electron acceptors (e.g., sulfate, nitrate) instead of oxygen 2 Pyruvate 2 Pyruvate at the end of an electron transport chain. Fermentation: Common in yeast and human 2 CO2 muscle cells. Creates byproducts while regenerating reactants needed for glycolysis. 2 Acetaldehyde Fermentation 2 NADH NAD + 2 NADH NAD+ Fermentation regeneration regeneration 2 NAD+ 2 NAD+ Fermentation is an anaerobic pathway (no oxygen) 2 Ethanol 2 Lactate that only relies on glycolysis by converting the produced pyruvate into different molecules in order to oxidize NADH back to NAD+. Regenerating NAD+ Types of organisms based on ability to grow in oxygen: means glycolysis can continue to make ATP. Fermentation occurs within the cytosol. The two most Obligate aerobes: Only perform aerobic common types of fermentation are lactic acid respiration, so they need the presence of oxygen fermentation and alcohol fermentation. to survive. Obligate anaerobes: Only undergo anaerobic 1. Lactic acid fermentation respiration or fermentation; oxygen is poison to them. Lactic acid fermentation uses the two NADH from Facultative anaerobes: Can do aerobic glycolysis to reduce the two pyruvate into two lactic respiration, anaerobic respiration, or acid molecules. Thus, NADH is oxidized back to NAD+ fermentation, but prefer aerobic respiration so that glycolysis may continue. because it generates the most ATP. Microaerophiles: Only perform aerobic Lactic acid fermentation is used by muscle cells during respiration, but high amounts of oxygen are periods of intense exercise, when harmful to them. aerobically-produced ATP is quickly depleted and Aerotolerant organisms: Only undergo there is low oxygen availability. Muscle cells will then anaerobic respiration or fermentation, but oxygen default to lactic acid fermentation to produce energy is not poisonous to them. anaerobically to continue to meet demand. Additionally, lactic acid fermentation occurs Microorganism Oxygen Preferences continuously in red blood cells, which lack mitochondria needed for aerobic respiration. Facultative anaerobe Obligate anaerobe 2. Alcohol fermentation Obligate aerobe Microaerophile Aerotolerant Alcohol fermentation, conducted by yeast, uses the [O2] two NADH from glycolysis to convert the two pyruvate into two ethanol. Thus, NADH is oxidized back to NAD+ so that glycolysis may continue. However, this process has an extra step that first involves the decarboxylation of pyruvate into acetaldehyde, which is only then reduced by NADH into ethanol. © 2025 Bootcamp.com 22  Alternative Sources of Energy Generation 2. Fats are mostly present in the body as triglycerides. Lipases are required to first digest Molecules other than glucose, such as other types of fats into free fatty acids and alcohols. carbohydrates, fats, and proteins can be modified to enter cellular respiration at various stages for energy Adipocytes are cells that store fat (triglycerides) and generation. have hormone-sensitive lipase enzymes to help release triglycerides back into circulation as 1. Other carbohydrates mostly enter during lipoproteins or as free fatty acids bound by a protein glycolysis. Glycogenolysis describes the release of called albumin. glucose-6-phosphate from glycogen, a highly branched polysaccharide of glucose. Free fatty acids undergo beta-oxidation to be Disaccharides can undergo hydrolysis to release converted into acetyl-CoA. Beta-oxidation occurs in two carbohydrate monomers, which can enter the mitochondrial matrix of eukaryotic cells and glycolysis. requires an initial investment of ATP. The fatty acid chain is then continuously cleaved to yield two-carbon Glycogenolysis acetyl-CoA molecules and electron carriers NADH and FADH2. Acetyl-CoA enters the Krebs cycle while NADH/FADH2 go directly into the ETC for ATP Digestion production. Glycogen Glucose-6-phosphate Fats are harder to catabolize than carbohydrates as they must undergo beta-oxidation and transport away from fat cells. However, per carbon molecule, fats Carbohydrates are the preferred energy source since contain the most energy. they are easily catabolized and are high yield. 3. Proteins are the least desirable energy source Glycogenesis refers to the reverse process, the because the processes to get them into cellular conversion of glucose into glycogen to be stored in the respiration take considerable energy and proteins liver when energy and fuel is sufficient. Glycogen is are needed for many essential functions in the stored in the liver and muscle cells. body. Beta-Oxidation Fatty acid ATP Coenzyme A (CoA) ADP Fatty acyl CoA (activated) FADH & NAD+ -2C Acetyl CoA β-oxidation cycle FADH2 & NADH Krebs cycle Electron transport chain (ETC) © 2025 Bootcamp.com 23 Ch. 4: Photosynthesis Photosynthesis vs. Cellular Respiration Photosynthesis Table of Contents Net energy input Chloroplast (endergonic) Objective of Photosynthesis Photosynthesis and Cellular Respiration Leaf Structures of Photosynthesis Light-Dependent Reactions of Photosynthesis The Calvin Cycle 6 CO2 6 H2O C6H12O6 6 O2 Photorespiration Carbon Water Glucose Oxygen Alternative Photosynthetic Pathways dioxide Objective of Photosynthesis ATP Net energy output Mitochondria (exergonic) While heterotrophs must get energy from the food Cellular respiration they eat, autotrophs can make their own food. Photoautotrophs take light energy and convert it to Leaf Structures of Photosynthesis chemical energy using photosynthesis. This process originally developed in cyanobacteria. Mesophyll cells: Located between the upper and lower epidermis of leaves. Facilitate gas movement Photosynthesis reduces atmospheric carbon dioxide, within the leaf. Contain chloroplasts. releases oxygen, and creates chemical energy that can be transferred through food chains. Photons (light Chloroplasts: Organelle that carries out energy) are used to synthesize sugars (glucose) in photosynthesis. Found in plants and photosynthetic photosynthesis. algae, but not in cyanobacteria. They are similar to mitochondria and contain the following structures Carbon fixation is the process by which inorganic (outermost to innermost): carbon (CO2) is converted into an organic molecule (glucose). Photosynthesis takes electrons released Structure Description from photolysis (the process of splitting water molecules) and excites them using solar energy. These Outer Outer plasma membrane made membrane of phospholipid bilayer. excited electrons are then used to power carbon fixation. Intermembrane Space between the outer and space inner membranes Photosynthesis and Cellular Respiration Inner plasma membrane made Inner membrane of phospholipid bilayer. Photosynthesis and cellular respiration are reverse processes in terms of their overall reactions: Fluid material that fills the area Stroma inside the inner membrane. Photosynthesis is non-spontaneous and endergonic, The Calvin cycle occurs here. producing glucose after an input of solar energy. A membrane structure within the stroma. Multiple stack up to Cellular respiration is spontaneous and exergonic, Thylakoids form a granum. They are the breaking down glucose to generate energy in the form site of light-dependent of ATP. reactions. Interior of the thylakoid. H+ ions Thylakoid lumen accumulate here, making it acidic. © 2025 Bootcamp.com 24  Light-Dependent Reactions of Photosynthesis 3. The primary electron acceptor sends the excited electrons to the electron transport chain (ETC). The light-dependent reactions occur in the During the redox reactions within the ETC, protons thylakoid membrane and harness light energy to are pumped from the stroma to the thylakoid produce ATP and NADPH (an electron carrier) for later lumen. The electrons are then deposited into use in the Calvin cycle. ATP generated in the photosystem I (PS I). light-dependent reactions is not used to power the 4. Photons excite pigments in PS I, energizing the cell; it is consumed in the Calvin cycle. electrons in the reaction center to be passed to another primary electron acceptor. Photosystems contain special pigments, such as 5. The electrons are sent to a short electron chlorophyll, that absorb photons. Chlorophyll transport chain that terminates with NADP+ absorbs red and blue light and reflects green light, reductase, an enzyme then reduces NADP+ into giving plants their green color. NADPH using electrons and protons. 6. The accumulation of protons in the thylakoid The reaction center is a special pair of chlorophyll lumen generates an electrochemical gradient molecules in the center of these proteins. Chlorophyll that is used to produce ATP using an ATP has a porphyrin ring structure with a magnesium synthase, as H+ moves from the thylakoid lumen atom bound in its center. Photosystem II (P680) and back into the stroma. photosystem I (P700) are used in photosynthesis. Cyclic Photophosphorylation Non-cyclic photophosphorylation is carried out by H+ the light-dependent reactions. Below are the Light Light ADP ATP important steps of this process: ATP 1. Water is split (photolysis), passing electrons to 2e- synthase photosystem II (PS II) and releasing protons into Continuous cycle PS I the thylakoid lumen. 2. Photons excite electrons in the reaction center of PS II, passing the electrons to a primary electron acceptor. 2H2O O2+ 4H+ H+ Non-Cyclic Photophosphorylation Cyclic photophosphorylation: Electrons from PS I are cycled back to the first ETC. This process increases proton pumping across the thylakoid membrane, Chloroplast enhancing ATP production. Electrons bypass NADP+ reductase, so no NADPH is generated. Calvin cycle H+ H+ Chloroplast stroma + Light Light NADP NADPH ADP ATP ATP PS II PS I synthase Thylakoid membrane 2e- 2H2O O2 + 4H+ Thylakoid lumen H+ H+ © 2025 Bootcamp.com 25  The Calvin Cycle Photorespiration The Calvin cycle is made up of reactions known as RuBisCo, in addition to fixing carbon dioxide into light-independent reactions because they do not RuBP, can also cause oxygen to bind to RuBP in a directly use light energy, but can only occur if the process called photorespiration. light-dependent reactions are providing ATP and NADPH. Photorespiration produces two-carbon phosphoglycolate and eventually converts it into The Calvin cycle fixes carbon dioxide molecules that PGA. There is a net loss of fixed carbon in the process enter plant leaves through stomata (pores in the and no new glucose produced. epidermis). It takes place in the chloroplast stroma of plant mesophyll cells. Photorespiration is also called C2 photosynthesis, since a two-carbon molecule is produced. 1. Carbon fixation: Carbon dioxide combines with five-carbon ribulose-1,5-bisphosphate (RuBP) to Hot and dry: Stomata are closed to minimize water form six-carbon molecules, which quickly break loss; oxygen accumulates inside the leaf while carbon down into three-carbon phosphoglycerates (PGA). dioxide is used up. RuBisCo binds oxygen and This reaction is catalyzed by RuBisCo. photorespiration occurs. 2. Reduction: PGA is phosphorylated by ATP and subsequently reduced by NADPH to form glyceraldehyde-3-phosphate (G3P). 3. Regeneration: Most of the G3P is converted back to RuBP. 4. Carbohydrate synthesis: Some o