Aoife's AP Biology Cell, Homeostasis, and Enzymes Test Study Guide PDF

Aoife's AP Biology Cell, Homeostasis and Enzymes Test Study Guide Chapter 6: A Tour of the Cell - Cell is the smallest and simplest unit of life - How does the internal organization of eukaryotic cells allow them to perform the functions of life? ⇒ Internal membranes divide a cell into...

Aoife's AP Biology Cell, Homeostasis and Enzymes Test Study Guide Chapter 6: A Tour of the Cell - Cell is the smallest and simplest unit of life - How does the internal organization of eukaryotic cells allow them to perform the functions of life? ⇒ Internal membranes divide a cell into compartments where specific chemical reactions occur Concept 6.2: Eukaryotic cells have internal membranes that compartmentalize their functions - Cells have two distinct types - prokaryotic and eukaryotic - Bacteria and Archaea consist of prokaryotic cells - Protists, fungi, animals, and plants consist eukaryotic cells - Protist = group of mostly unicellular eukaryotes - Prokaryotic vs Eukaryotic Cells - Same features - They’re both bounded by a selective barrier = plasma membrane - At the boundary of every cell, the plasma membrane functions as a selective barrier that allows passage of enough oxygen, nutrients, and wastes to service the entire cell - All cells have cytosol - the semifluid, jellylike substance of the cytoplasm - All cells have chromosomes - carry genes in the form of DNA - All cells have ribosomes - tiny complexes that make proteins according to instructions from the genes - All cells have cytoplasm - the contents of the cell bounded by the plasma membrane - in eukaryotes, the portion exclusive of the nucleus - Main difference between the two types of cells is the location of the DNA - Prokaryotic cells are characterized by having - No nucleus - DNA and chromosomes in an unbound region called the nucleoid - No membrane-bound organelles - Cytoplasm bound by the plasma membrane - Most of them have cell walls - Eukaryotic cells are characterized by having - DNA in a nucleus that is double bounded by a membranous nuclear envelope - Membrane-bound organelles - Cytoplasm in the region between plasma membrane and nucleus - They’re larger than prokaryotic cells - Plasma membrane - a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell - Ratio of surface area to volume is critical because cells need a larger surface area to volume ratio for efficient exchange of materials through the membranes (this is why cells must be small) - As cell size increases, volume grows more than the surface area ⇒ surface area to volume ratio decreases - Panoramic View of Eukaryotic Cell - A eukaryotic cell has internal membranes that divide the cells into compartments - organelles - The cell’s compartments provide different local environments that support specific metabolic functions, so incompatible processes can occur simultaneously in a single cell - The basic fabric of biological membranes is a double layer of phospholipids and other lipids - Plant and animal cells have most of the same organelles Concept 6.3: The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes - Nucleus - organelle of a eukaryotic cell that contains the genetic material in the form of chromosomes, made up of chromatin - Function of Nucleus: 1. directs protein synthesis by synthesizing messenger RNA (mRNA) that carries information from the DNA 2. mRNA is then transported to cytoplasm via nuclear pores 3. ribosomes translate the mRNA’s genetic message into the primary structure of a specific polypeptide - Some genes are located in the mitochondria and chloroplasts - Nuclear envelope - the double membrane that surrounds the nucleus, perforated with nuclear pores that regulate the entry and exit of molecules with the cytoplasm - The nuclear membrane is a double membrane; each membrane consists of a lipid bilayer - The outer membrane is continuous with the endoplasmic reticulum - Nuclear lamina - netlike array of protein filaments (in animal cells, called intermediate filaments) that lines the inner surface of the nuclear envelope and helps maintains the shape of the nucleus - Both nuclear lamina + matrix help organize the genetic material so it functions efficiently - Within the nucleus, the DNA is organized into chromosomes - cellular structure that carry the genetic information - Each chromosome contains one single long DNA molecule associated with many proteins - Chromatin - the complex of DNA and proteins making up chromosomes - Chromatin condenses to form chromosomes, as cell prepares to divide - Nucleolus - located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis + ribosomal subunit assembly - It contains rRNA genes + ribosomal proteins imported from the cytoplasm - These ribosomal proteins are assembled with rRna into large and  small units of ribosomes in the nucleolus - Then the subunits exit the nucleus through the nuclear pores to the cytoplasm, where a large and a small subunit can assemble into a ribosome - Ribosomes - complexes made of ribosomal RNA and protein - They carry out protein synthesis in two locations - In the cytosol (free ribosomes) - On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes) - Bound and free ribosomes are structurally identical Concept 6.4: The endomembrane system regulates protein traffic and performs metabolic functions - Endomembrane system - collection of membrane-bounded organelles that are related through direct physical contact or by the transfer of membranous vesicles - The organelles include: - Nuclear envelope (discussed in 6.2) - Endoplasmic reticulum - Golgi apparatus - Lysosomes - Various of vesicles and vacuoles - Plasma membrane (discussed in 6.1 + chapter 7) - Vesicles - a membrane-bound sac in or outside a cell - Endoplasmic reticulum (ER) - an extensive membranous network in eukaryotic cells, continuous with the outer nuclear membrane - ER accounts for more than half of the total membrane in many eukaryotic cells ⇒ referring to surface area - ER consists of network of membranous tubules and sacs called cisternae, which forms an internal space of the ER called ER lumen/cisternal space - ER membrane is continuous w/ the nuclear envelope ⇒ allowing direct exchange of materials between nucleus and the ER - Smooth ER - region of ER, where its outer surface lacks ribosomes - Synthesizes lipids - Metabolizes carbohydrates ⇒ breaking them down or putting them together - Detoxifies drugs + poisons  - Stores calcium ions - Rough ER - region of ER, where its surface is studded with ribosomes - Has bound ribosomes, which secrete glycoproteins - proteins covalently bonded to carbohydrates - Distributes transport vesicles - small membranous sac in a eukaryotic cell’s cytoplasm that moves molecules from one part of the cell to another - Secretory proteins depart from the ER wrapped in transport vesicles from a specialized region called transitional ER - Is a membrane factory for the cell - It grows in place by adding membrane proteins + phospholipids to its own membrane - Rough ER + smooth ER both make membrane phospholipids - Golgi apparatus - organelle that consists of flattened membranous sacs called cisternae - Functions - Modifies products of the ER - Manufactures certain macromolecules - Sorts and packages materials into transport vesicles - A golgi stack has a distinct structural directionality - Cis face - the receiving department of the Golgi apparatus; it’s located near the ER - Trans face - shipping department of the Golgi apparatus - How it works - Transport vesicles move membrane from the ER to the Golgi apparatus - A vesicle that buds from the ER can add its membrane + contents of its lumen to the cis face by fusing with a Golgi membrane one that side - Products of ER are usually modified during their transit from the cis region to the trans region of the Golgi apparatus - The trans face makes vesicles pinch off and travel to other sites - Lysosomes - a membrane-enclosed sac of hydrolytic enzymes found in the cytoplasm of animal cells + some protists - Hydrolytic enzymes - enzymes that break down larger molecules into smaller components using water - Lysosomal enzymes work best in the acidic environment inside the lysosomes  - So if a lysosome breaks open or leaks its content, the released enzymes are not very active b/c cytosol has a near-neutral pH - Excessive leakage from a bunch of lysosomes can destroy a cell by self-digestion - Hydrolytic enzymes and lysosomal membranes are made by rough ER and then transferred to the Golgi apparatus for further processing - Lysosomes carry out intracellular digestion (breaking down materials inside a cell) - Phagocytosis - process where cells engulf another cell or large particles - A lysosome fuses with the food vacuole and digests the molecules ⇒ digestion products pass into the cytosol and become nutrients for the cell - Autophagy - a process where lysosomes use their hydrolytic enzymes to recycle the cell’s own organic material - - Vacuoles - large vesicles derived from the ER and the Golgi apparatus - Vacuoles perform a variety of functions in different kinds of cells - Food vacuoles - membranous sac formed when a cell membrane engulfs a food particle, which pinches off to create a membrane bound pocket inside the cell containing food - Fuses w/ lysosomes to digest large particles and cells (phagocytosis) - Found in plants, animals, and protists - Contractile vacuoles - membranous sac that helps move excess water out of certain freshwater protists, thereby maintaining a suitable concentration of ions and molecules inside the cell - Found in protists - Central vacuoles - large membranous sac in mature plant cell hold organic compounds and water + give turgor pressure to plant cells (pushes cytoplasm against the cell wall) - Found in plant cells Concept 6.5: Mitochondria and chloroplasts change energy from one form to another - Both Mitochondria and chloroplasts are organelles that convert energy to forms that cells can use for work - Mitochondria - serves as the site of cellular respiration; uses oxygen to break down organic molecules and synthesize ATP - They have a smooth outer membrane and an inner membrane folded into cristae - folds in the inner mitochondrial membrane - The inner membrane creates two compartments - intermembrane space and mitochondrial matrix - Intermembrane space - narrow region between the inner and outer membranes - Mitochondrial matrix - enclosed by the inner membrane + contains enzymes and substrates for the citric acid cycle + ribosomes + DNA - Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix - Cristae present a large surface area for enzymes that synthesize ATP - Chloroplasts - an organelle found in plants and photosynthetic protists that serves as the site of photosynthesis  - It converts solar energy to chemical energy by absorbing sunlight and using it to drive the synthesis of organic compounds such as sugars from carbon dioxide and water - Chloroplasts contain green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis - Chloroplasts are found in leaves and other green organs of plants and in algae - Structure includes - Thylakoids - membranous sacs that are stacked to form a granum - Function: converts light energy to chemical energy - Granum - stack of thylakoids - Stroma - the internal fluid within the chloroplast, containing the ribosomes + dna - It is involved in the synthesis of organic molecules from carbon dioxide and water - Plastids - family of closely related organelles that includes chloroplasts, chromoplasts, and amyloplasts - They’re found in cells of photosynthetic eukaryotes - Amyloplast - colorless organelle that stores starch (amylose), particularly in roots and tubers - Chromoplast - has pigments that give fruits and flowers their orange and yellow hues - Evolutionary Origins of Mitochondria and Chloroplasts - Mitochondria and chloroplasts have similarities with bacteria - Enveloped by a double membrane - Contain free ribosomes and circular DNA molecules - Grow and reproduce somewhat independently in cells - These similarity led to the Endosymbiont theory - a theory that suggests that an early ancestor of eukaryotic (host cell) engulfed an oxygen-using non photosynthetic prokaryotic cell - The engulfed cell formed a relationship with the host cell,  becoming an endosymbiont (cell living within a cell) - The endosymbionts evolved into mitochondria - At least one of these cells may have then taken up a photosynthetic prokaryote, which evolved in a chloroplast - Peroxisomes - organelles that contains enzymes that transfer hydrogen atoms from substrates and transfer them to oxygen ⇒ producing hydrogen peroxide - It produces hydrogen peroxide and convert it to water Concept 6.6: The cytoskeleton is a network of fibers that organizes structures and activities in the cell - Cytoskeleton - a network of microtubules, microfilaments, and intermediate filaments that extend throughout the cytoplasm and serve a variety of mechanical, transport, and signaling functions - Functions: give mechanical support to the cell and maintain its shape - Involved in types of cell motility/movement - Cell motility requires interaction of cytoskeleton with motor proteins (proteins that interact with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell) - Three types of fibers make up the cytoskeleton - Microtubules - hollow rod composed of tubulin proteins that make up part of the cytoskeleton in all eukaryotic cells and is found in cilia and flagella - Function: - shape and support the cell - serves as tracks along which organelle equipped with motor proteins can move - Guides vesicles from the ER to the golgi apparatus and from the golgi to the plasma membrane - Involved in the separation of chromosomes during cell division - Centrosome - structure in the cytoplasm of animal cells that function as a microtubule-organizing center + important during cell division - It has two Centrioles - structure in centrosome composed of a cylinder of microtubule triplets ⇒ help organize microtubule assembly - Microfilaments (actin filaments) - thin solid rods, twisted double chain of actin protein subunit - Function: acts alone or with myosin (type of motor protein) to cause cell contraction + cell motility  - Intermediate filaments - filaments that are between the size of microtubules and microfilaments - Permanent framework of the cell - Function: provide support and structure for cells - Cilia and Flagella (on the surface of the eukaryotic cell) - Flagella - long, whip-like structures composed of microtubules in a “9+2” pattern - Function - used for locomotion (cells moving around in its environment) - Cilia - shorter, hair-like projections made of the same “9+2” microtubules arrangements - Function - plays a sensory and signaling role (detecting changes in environment and tells them to the cell) - Basal body - structure that organizes the microtubules assembly of a cilium or flagellum; structurally very similar to centrioles - Dyneins - large motor proteins that connects a microtubule doublet to the adjacent doublet - ATP hydrolysis drives changes in dynein shape that leads to bending of cilia and flagella Concept 6.7: Extracellular components and connections between cells help coordinate cellular activities - Cell Wall - an extracellular structure + protective layer external to the plasma membrane in the cells of plants, prokaryotes, fungi, and some protists - Function: protects the plant cell, maintains its shape, and prevents excessive uptake of water - Plant cell walls are made of cellulose fibers embedded in other polysaccharides and proteins - Plant cell walls have multiple layers - Primary cell wall - relatively thin and flexible layer that surrounds the plasma membrane of a young cell - Middle lamella - thin layer between primary walls of adjacent cells ⇒ glues adjacent cells together - Made of stick polysaccharides - pectins - Secondary cell wall (in some cells) - added between the plasma membrane and the primary cell wall that adds more cell protection and support - Extracellular matrix (ECM) - meshwork surrounding animal cells  - ECM is made up of glycoproteins such a collagen, proteoglycans, and fibronectin that are synthesized and secreted by cells - Collagen - forms strong fibers, found extensively in connective tissue and bone - Proteoglycans - large molecule consisting of a small core protein with many carbohydrate chains attached, found in ECM - Fibronectin - help animal cells attach to the ECM - ECM proteins bind to cell surface receptor proteins in the plasma membrane called integrins - Integrins - transmembrane receptor protein w/ two subunits that interconnects the ECM and cytoskeleton - Integrins can transmit signals between ECM and cytoskeleton + helps cells respond to changes - ECM functions - Regulate a cell’s behavior by communicating with a cell through integrins - Influence the activity of gene in the nucleus - Mechanical signaling (when something pushes or pulls on the cell) can occur through cytoskeletal changes ⇒ that trigger the cell to send chemical signals that tell it to do something - Plasmodesmata are channels between adjacent plant cells that connect the cytoplasm of adjacent plant cells, allowing water, small solutes, and some larger molecules to pass between the cells - Cell junction - sites of physical contact for neighboring cells, allowing cells to adhere, interact, and communicate with each other - The three types of cell junctions in animal cells (epithelial tissue) - Tight junctions - membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid - Desmosomes - fasten cells into strong sheets (anchoring junctions) - Gap junctions - provide cytoplasmic channels between adjacent cells (communicating junctions) Concept 6.8: A cell is greater than the sum of its parts - Cells rely on the integration of structure and organelles in order to function Chapter 7: Membrane Structure and Function - Plasma membrane is the boundary that separates the living cell from its surroundings  - The plasma membrane exhibits selective permeability, allowing some substances to cross it more easily than others Concept 7.1: Cellular membranes are fluid mosaics of lipids and proteins - Phospholipids are the most abundant lipid in the plasma membrane - Phospholipids are amphipathic molecules, containing hydrophobic and hydrophilic regions - A phospholipid bilayer can exist as a stable boundary between two aqueous compartments - Fluid mosaic model states that a membrane is a fluid structure with a “mosaic” of various proteins embedded in it - Proteins are not randomly distributed in the membrane - Phospholipids in the plasma membrane can move around drift laterally + rarely a lipid may flip-flop - Temperature - As temperature cools, membranes switch from a fluid state to a solid state - The temperature at which a membrane solidifies depends on the types of lipids - Membranes rich in unsaturated fatty acids (has kinks/bents) are more fluid than those rich in saturated fatty acids - Membranes must be fluid to work properly - The steroid cholesterol has different effects on membrane fluidity at different temperatures - At warm temperature, cholesterol restrains movement of phospholipids - At cool temperatures, it maintains fluidity by preventing tight packing - Evolution of Differences in Membrane Lipid compositions - Different species have different compositions of lipids to help them adapt to their specific environments - Ability to change the lipid composition in response to temperature changes has evolved in organisms that live where temperatures vary - Proteins determine most of the membrane’s specific functions - Peripheral proteins - bound to the surface of the membrane - Integral proteins - penetrate the hydrophobic core - Transmembrane proteins - Integral proteins that span the membrane  - Hydrophobic regions of an integral proteins consists of nonpolar amino acids + coiled in alpha helices - Hydrophilic regions consists of polar amino acids - N-terminus is on the ECM side, C-terminus is on the cytoplasmic side - Six major functions of membrane proteins - Transport - move substances in and out - Enzymatic activity - speed up chemical reactions - Signal transduction - receive and relay signals - Signal molecule binds to receptor protein, and that relays the message to the inside of the cell - Cell-cell recognition - serve as identification tags - Intercellular joining - hooks cells together ⇒ cell junctions - Attachment to the cytoskeleton and extracellular matrix - transmit signals from external to internal - Ex: HIV must bind to the immune cell surface protein CD4 and a “co-receptor” CCR5 in order to infect a cell - - The Role of Membrane Carbohydrates in Cell-Cell Recognition ⇒ important for immune system defense - Cells recognize each other by binding to molecules, often containing carbohydrates, on the extracellular surface of the plasma membrane - These molecules ⇒ glycolipid (membrane carbohydrates covalently bonded to lipid)+ glycoproteins (membrane carbohydrates covalently bonded to proteins) - Carbohydrates on the external side of the plasma membrane vary among species, individuals, and even cell types in an individual - Synthesis and Sidedness of Membranes - Membranes have distinct inside and outside faces - The asymmetrical distribution of proteins, lipids, and associated carbohydrates in the plasma membrane is determined when the membrane is built by the ER and the Golgi apparatus - Secretory proteins, membrane proteins, and lipids are synthesized in ER - Carbohydrates are added to transmembrane proteins ⇒ making them glycoproteins  - Materials are transported in vesicles to the Golgi apparatus - Inside the Golgi apparatus, the glycoproteins undergo further carbohydrate modifications, lipids acquired carbohydrates ⇒ becoming glycolipids - Glycoproteins, glycolipids, and secretory proteins are transported in vesicles to the plasma membrane - As vesicles fuse with the plasma membrane, it secretes the secretory proteins form the cell + positions the glycoproteins + glycolipids on the outside face of the plasma membrane Concept 7.2: Membrane structure results in selective permeability - A cell must exchange materials with its surroundings, a process controlled by the plasma membrane - Permeability of the lipid bilayer - Hydrophobic (nonpolar) molecules can dissolve in the lipid bilayer and pass through the membrane rapidly - Hydrophilic molecules, ions and polar molecules, do not cross the membrane easily - Transport proteins - transmembrane protein that allow passage of hydrophilic substances across the membrane - Channel proteins - type of transport protein that have a hydrophilic channel that certain molecules or ions can use as a tunnel through the membrane - Carrier proteins - type of transport protein that hold on to their passengers and change shape in a way that shuttles them across the membrane - A transport protein is specific for the substance it moves - Aquaporins - channel protein that facilitate the passage of water (osmosis) - Consist of four identical polypeptide subunits - Each polypeptide forms a channel that water molecules pass through, single file, allowing entry up to 3 billion water molecules per second ⇒ makes osmosis faster Concept 7.3: Passive transport is diffusion of substance across a membrane with no energy investment - Diffusion - the tendency for molecules to spread out evenly into the available space - Although each molecule moves randomly, diffusion of a population may be directional ⇒ molecules move from an area where they are in high concentration to an area where they are in low concentration - Dynamic equilibrium is where the concentration of molecules on both sides of a barrier becomes balanced (the molecules are still moving tho) - Substances diffuse down their concentration gradient - a region which the density of a chemical substance increases or decreases - No work must be done + no input of energy to move substances down the concentration (spontaneous process)  - Passive transport - the diffusion of a substance across a biological membrane with no input of energy - Osmosis - the diffusion of water across a selectively permeable membrane - Water diffuses across a membrane from the region of lower solute concentration to the region of higher solute concentration until the solute concentration is equal on both sides of the membrane - Water Balance of the Cells without Cell Walls - Tonicity - the ability of surrounding solution to cause a cell to gain or lose water - Isotonic solution - Solution with equal concentration of solutes compared to the other solution - solute concentration outside the cell is equal to the solute concentration inside the cell - No net water movement across the plasma membrane - Hypertonic solution - solution with a higher concentration of solutes compared to another solution - the solute concentration outside the cell is greater than the solute concentration inside the cell - Water moves out of the cell to try to balance the solute concentrations ⇒ Cell loses water, shrivel, and probably die - Hypotonic solution - solution with a lower concentration of solutes compared to another solution - solute concentration outside the cell is less than the solute concentration inside the cell - Water moves into the cell to balance the solute concentrations ⇒ Cell gains water, swell, and lyse (burst) - In hypertonic or hypotonic environments, organisms that lack rigid cell walls must have other adaptations for osmoregulation - the control of solute concentrations and water balance - Ex: protist Paramecium (hypertonic to its pond water environment) have contractile vacuoles, which is an organelle that functions as a pump to force water out of the cell as fast as it enters by osmosis - Water balance with Cell Walls - Cell walls help maintain water balance  - A plant cell in a hypotonic solution swells until the walls opposes uptake ⇒ cell is now turgid (firm) - If a plant cell and its surroundings are isotonic, there is no net movement of water into the cell ⇒ cell becomes flaccid (limp) - In a hypertonic environment (outside solution has greater concentration), plant cells lose water - Membrane pulls aways from the cell wall, causing the plant to wilt ⇒ this effect is plasmolysis - Facilitated diffusion - passage of molecules or ions down their electrochemical gradient (concentration gradient + charge difference/electrical gradient) across a biological membrane with the assistance of specific transmembrane transport proteins, requiring no input of energy - Transport protein ⇒ Channel proteins + Carrier proteins - Aquaporins facilitate the diffusion of water - Ion channels facilitate the diffusion of ions - Gated channels - type of ion channel that opens or close in response to stimulus Concept 7.4: Active transport uses energy to move solutes against their gradients - Some transport proteins, however, can move solutes against their concentration gradients - Active transport - movement of substance across a cell membrane against its concentration or electrochemical gradient through transport proteins and requiring input of energy - Active transport requires energy, usually in the form of ATP - ATP can power active transport when its terminal phosphate group is transferred directly to the transport protein - Active transport is performed by specific proteins embedded in the membranes - Active transport allows cells to maintain concentration gradients that differ from their surroundings - Type of active transport system - Sodium-potassium pump - transport protein in the plasma membrane of animal cells that actively transports sodium out of the cell and potassium into the cell 1. Cytoplasmic Na+ binds to the sodium-potassium pump 2. Na+ binding stimulated phosphorylation (attachment of a phosphate group to a molecule) by ATP 3. Phosphorylation leads to a change in protein shape,  reducing its affinity for Na+, which is released outside of the cell 4. New shape has a high affinity for K+, which binds on the extracellular side and triggers release of the phosphate group 5. Loss of the phosphate group restores the protein’s original shape, which has a lower affinity for K+ 6. K+ is released; affinity for Na+ is high again, and the cycle repeats - - How Ion Pumps Maintain Membrane Potential - Membrane potential - voltage difference across a membrane - Voltage is created by differences in the distribution of positive and negative ions across a membrane - Two combined forces, collectively called the electrochemical gradient, drive the diffusion of ions across a membrane - Chemical force - the ion’s concentration gradient - Electrical force - the effect of the membrane potential (electrical charge difference) on the ion’s movement - Electrogenic pump - a transport protein that generate voltage across a membrane - Electrogenic pumps help store energy that can be used for cellular work - Sodium-potassium pump is the major electrogenic pump of animal cells - Proton pump is the major electrogenic pump of plants, fungi, and bacteria - They store energy by generating voltage across membranes - Cotransport - it’s when active transport of a solute indirectly drive transport of another substance - The movement of first substance helps the second substance move ⇒ like a free ride  - Ex: plants commonly use the gradient of hydrogen ions generated by proton pumps to drive active transport of nutrients into the cell - Concept 7.5: Bulk transport across the plasma membrane occurs by exocytosis and endocytosis - Small molecule and water enter and leave the cell through the lipid bilayer or via transport proteins - Large molecules, such a polysaccharide and proteins, cross the membrane in bulk via vesicles - Bulk transport requires energy - Exocytosis - it’s when transport vesicles migrate to the membrane, fuse with it, and release their contents outside the cell - Many secretory cells use exocytosis to export their products - Endocytosis - it’s when the cell takes in macromolecules by form vesicles form the plasma membrane - Endocytosis is a reversal of exocytosis, involving different proteins - Three types of endocytosis - Pinocytosis - where large substance or small organisms are taken up by cell (cellular eating) - Phagocytosis - where cell ingests extracellular fluid and its dissolved solutes (cellular drinking) - Receptor-mediated endocytosis - movement of specific molecules into cells by the infolding of vesicles containing proteins with receptor sites specific to the molecules being taken in; enables a cell to acquire bulk quantities of specific substances - Ligand - any molecule that binds specifically to a receptor site of another molecule  - Chapter 8: An Introduction to Metabolism - The living cell is a miniature chemical factory where thousands of reactions occur - The cell extracts energy stored in sugars and other fuels and applies energy to perform work - Some organisms even convert energy to light, as in bioluminescence Concept 8.1: An organism’s metabolism transforms matter and energy - Metabolism - the totality of an organism’s chemical reactions - Metabolism in an emergent property of life that arises from orderly interactions between molecules - Metabolic pathways begin with a specific molecule and ends with a product - Each step is catalyzed by a specific enzyme - - Two different types of metabolic pathways - Catabolic pathways - release energy by breaking down complex molecules into simpler compounds - Hydrolysis is an example of a catabolic reaction - Ex: cellular respiration is the breakdown of glucose in the presence of oxygen - Anabolic pathways -consume energy to build complex molecules from simpler ones - Dehydration synthesis is an example of an anabolic reaction - Ex: synthesis of protein from amino acids - Relationship: Anabolic pathways synthesize complex organic compounds using the energy derived from catabolic pathways - Bioenergetics - the study of how energy flows through living organisms - Energy - the capacity to cause change - Energy exist in various forms ⇒ some of which can perform work - Kinetic energy - energy associated with motion - Heat (thermal energy) - kinetic energy associated with random movement of atoms or molecules - Potential energy - energy that matter possesses because of its location or structure - Chemical energy - potential energy available for release in a chemical reaction - Energy can be converted from one form to another - Thermodynamics - study of energy transformations - In an isolated system (like liquid in a thermos) is unable to exchange energy or matter with its surroundings - In an open system, energy and matter can be transferred between the system and its surroundings - Organisms are open systems - First law of thermodynamics - principle that the energy of universe is constant - Energy can be transferred or transformed, but it cannot be created or destroyed (principle of conservation of energy) - During every energy transfer or transformation, some energy is unusable, and is often lost as heat - Second law of thermodynamics - principle that every energy transfer or transformation increases the entropy (disorder) of the universe - Entropy - measure of molecular disorder - ΔS is negative ⇒ system becomes more ordered (less entropy) - Living cells unavoidably convert organized forms of energy to heat - Spontaneous process - processes that occur without energy input; they can happen quickly or slowly - For a process to occur without energy input, it must increase the entropy of the universe - Biological Order and Disorder - Cells create ordered structures from less ordered materials ⇒ they create new cells + new organelles (that are organized molecules) - Organisms also replace ordered forms of matter and energy with less ordered forms - Ex: turn glucose into water and carbon dioxide - Energy flows into an ecosystem in the form of light and exits in the form of heat - The evolution of more complex organisms does not violate the second law of thermodynamics  - Entropy (disorder) may decrease in an organisms, but the universe's total entropy increases Concept 8.2: The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously - A living system’s free energy - energy that can do work when temperature and pressure are uniform, as in a living cell - The change in free energy (ΔG) during a process is related to the change in enthalpy/ change in total energy (ΔH), change in entropy (ΔS), and temperature in Kelvin units (T) - ΔG = ΔH - TΔS - Only process with a negative ΔG are spontaneous - Spontaneous processes can be used to perform work - Free energy, Stability, and Equilibrium - Free energy - a measure of a system’s instability, its tendency to change to a more stable state - Unstable system (higher ΔG) tend to change in such a way that they become more stable (lower ΔG) - During a spontaneous change, the system’s free energy decreases (negative ΔG) and the stability of a system increases - Equilibrium is a state of maximum stability - Spontaneous process can perform work only when it is moving toward equilibrium - - The concept of free energy can be applied to the chemistry of life’s processes - Exergonic reaction - spontaneous reaction that releases free energy (dG 0) from its surroundings, making the system less stable and have greater capacity to do work - Think about the diver: - he has a lot of potential energy + he’s “unstable” because he has energy that wants to be released - Once he dives, that energy is release, and so he’s in a more stable position with less energy - Reactions in a closed system eventually reach equilibrium, which means it won’t have enough free energy to perform necessary work to maintain life ⇒ cells would die if they reached an equilibrium - Cells are not in equilibrium; they are open systems, experiencing a constant flow of materials - Catabolic pathway in a cell releases free energy in a series of reactions Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions - A cell does three main kinds of work - Chemical work - Ex: the synthesis of polymers from monomers - Transport - Ex: the pumping of substances across membranes against the direction of spontaneous movement - Mechanical - Ex: folding proteins, he contraction of muscle cell - To do work, cells manage energy resources by energy coupling - the use of an exergonic process to drive an endergonic one - Most energy coupling in cells is mediated by ATP - ATP (adenosine triphosphate) - the cell’s energy shuttle - ATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups - The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis - Energy is released from ATP when the terminal phosphate bond is broken  - This release of energy is because the new molecules (ADP and Pi) are more stable (with lower free energy) than the original molecule (ATP) (higher free energy) - So there is a negative free energy change, which indicates the release of energy - How the Hydrolysis of ATP Performs Work - Three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP - In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction - Overall, the coupled reactions are exergonic - ATP drives endergonic reactions by phosphorylation - transferring a phosphate group to some other molecule, such as a reactant - The recipient molecule is now called a phosphorylated intermediate ⬆️ - - Important example - Transport + mechanical work in the cell are also powered by ATP hydrolysis ⬇️⬇️ - ATP hydrolysis leads to a change in protein shape and binding ability - Example  - - The regeneration of ATP - ATP is a renewable resource - The energy from catabolic reaction of the hydrolysis of ATP (exergonic energy releasing process) is absorbed to regenerate ATP by combining ADP and inorganic phosphate group (anabolic reaction) Concept 8.4: Enzymes speed up metabolic reactions by lowering energy barriers - Catalyst - chemical agent that speeds up a reaction without being consumed by the reaction - Enzyme - a catalytic protein - Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction - Activation Energy Barrier - Every chemical reaction between molecules involves bond breaking and bond forming - Activation energy 𝐸𝐴 - initial energy that reactants must absorb in order to start a chemical reaction - Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings - How Enzymes Speed Up Reactions - Enzymes catalyze chemical reactions by lowering the activation energy barrier - Enzymes do not affect the changes in free energy (ΔG) ; instead they speed up reactions that would occur eventually  - - Substrate Specificity of Enzymes - Substrate - the reactant that an enzyme acts on - Enzyme -substrate complex - the temporary complex formed when an enzyme binds to its substrate molecule(s) - The reaction catalyzed by each enzyme is very specific - Active site - the region on the enzyme where the substrate binds - Induced fit - the change in shape of the active site of an enzyme so that it binds more snugly to the substrate - - Catalysis in the Enzyme’s Active Site - In an enzymatic reaction, the substrate binds to the active site of the enzyme - The active site can lower an activation energy barrier by - Orienting substrates correctly - Locally concentrating the reactants (gathering the reactants to a single place, which increases the concentration of reactants) - Straining substrate bonds ⇒ the enzyme applies pressure on the bonds within the substrate, making the bonds weaker and easier to break - Providing a favorable microenvironment - An enzyme might change the pH in its active site sometimes - Covalently bonding to the substrate - Step by Step of Chemical Reactions using an enzyme 1. Substrates enter active site  2. Substrates are held in active sites by weak interactions, like hydrogen bonds 3. Substrates are converted to products 4. Products are release 5. Active site is available for new substrates - An enzyme’s activity can be affected by - General environmental factors, such as temperature, pH, and substrate concentration - Each enzyme has an optimal temperature in which it can function - Up to a point, the rate of an enzymatic reaction increases with increasing temperature because substrates collide with active sites more frequently - Above that temperature, the speed of the enzyme reaction drops sharply because high temperature disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilizes the active shape of the enzyme - Each enzyme has an optimal pH in which it can function - Variations in pH can disturb hydrogen bonding or ionic interactions at the tertiary and quaternary structure of the enzyme, changing the shape of active site - Optimal conditions favor the most active shape for the enzyme molecule ⇒ maintain its best shape so that it can do its function of speeding up reactions - Chemicals that specifically influence the enzyme - Cofactors - non protein molecules or ions that are required for the proper functioning of an enzyme. - Cofactors can be permanently bound to the active site or may bind loosely and reversibly along with the substrate during catalysis - Cofactors may be inorganic (such as metal in ionic form) or organic - Coenzyme - an organic cofactor - Coenzymes include vitamins - Enzyme inhibitors - Competitive inhibitors - inhibitors that are similar to the substrate and bind to the active site of an enzyme, competing with the substrate - Noncompetitive inhibitors - inhibitors that are dissimilar to the substrate and bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective - Examples of inhibitors - toxins, poisons, pesticides, and antibiotics  - - Evolution of Enzymes - Enzymes are proteins encoded by genes - Changes (mutations) in genes lead to changes in amino acid composition of an enzyme - Altered amino acids in enzymes may result in the novel enzyme activity (new function/perform a new reaction of an enzyme) or altered substrate specificity (interact with a new substrate) - Under new environment conditions, certain mutations might be helpful for an organism - Ex: 6 amino acid changes improved substrate binding and breakdown in E. coli Concept 8.5: Regulation of enzyme activity helps control metabolism - If we didn’t regulate enzymes/cell’s metabolic pathways, chemical chaos would happen - A cell regulate enzyme activity by switching on or off the genes that encode specific enzymes (determines whether the cell produces certain enzymes or not) + by regulating the activity of enzymes (ensures that enzymes are active only when needed) - Allosteric regulation may either inhibit (turn off) or stimulate (turn on) an enzyme’s activity - Allosteric regulation - the binding of a regulatory molecule to a protein at one site (regulatory site, NOT the active site!) and affects the protein’s function at another site (the active site) - Most allosterically regulated enzymes are made from polypeptide subunits - Each enzyme exist in two states ⇒ each enzyme has active and inactive forms - The binding of an activator stabilizes the active form of the enzyme - The binding of an inhibitor stabilizes the inactive form of the enzyme  - - Normally, an enzyme oscillates ⇒ it goes back and forth from active to inactive to active to inactive etc. - Cooperativity - a form of allosteric activation, where the enzyme is in its inactive form, and when one substrate molecule binds to one subunit of the enzyme, it causes a shape change in that unit, which then stabilizes the enzyme in its active form just by having that substrate, and then the other active sites can work effectively - Cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different active site - Feedback inhibition - a method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway - Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more products than is needed -  - Another way of regulating enzyme activity is localization (so enzymes are kept where they are needed) - There are structures within the cell that helps organize and bring order to these metabolic pathways - Some enzymes act as structural components of membranes - In eukaryotic cells, some enzymes reside in specific organelles - Ex: enzymes for cellular respiration are located in the mitochondria Practice - In generally, the hydrolysis of ATP drives cellular work by releasing free energy that can be coupled to other reaction ⇒ cell can couple the energy of ATP hydrolysis directly to endergonic process - Much of the suitability of ATP as an energy intermediary is related to the instability of the bonds between phosphate groups ⇒ these bonds are unstable because the negatively charged phosphate group vigorously repel one another and the terminal phosphate group is more stable in water than it is in ATP - A chemical energy is designated as exergonic rather than endergonic when the potential energy of the product is less than the potential energy of the reactants ⇒ the formation of new bonds releases more energy than was invested in breaking the old bonds - Plot of reaction rate against temperature for an enzyme indicates little activity at 10 deg C and 45 deg C, with peak activity at 35 deg C ⇒ low reaction rate at 10 deg C occurs because there is little activation energy available - The environment usually supplies activation energy in the form of heat ⇒ the lower the temperature, the less energy that is available to overcome the activation energy barrier - Competitive inhibitors that bind covalently to the enzyme would be irreversible, and those that bind weakly would be reversible -