adriencleme/openstax_sciq_noformula_split · Datasets at Hugging Face

text stringlengths 2 3.56k	source stringclasses 725 values
cell theory : see unified cell theory	https://openstax.org/books/biology/pages/4-key-terms
cell wall : rigid cell covering made of various molecules that protects the cell, provides structural support, and gives shape to the cell	https://openstax.org/books/biology/pages/4-key-terms
central vacuole : large plant cell organelle that regulates the cellâs storage compartment, holds water, and plays a significant role in cell growth as the site of macromolecule degradation	https://openstax.org/books/biology/pages/4-key-terms
centrosome : region in animal cells made of two centrioles	https://openstax.org/books/biology/pages/4-key-terms
chlorophyll : green pigment that captures the light energy that drives the light reactions of photosynthesis	https://openstax.org/books/biology/pages/4-key-terms
chloroplast : plant cell organelle that carries out photosynthesis	https://openstax.org/books/biology/pages/4-key-terms
chromatin : protein-DNA complex that serves as the building material of chromosomes	https://openstax.org/books/biology/pages/4-key-terms
chromosome : structure within the nucleus that is made up of chromatin that contains DNA, the hereditary material	https://openstax.org/books/biology/pages/4-key-terms
cilium : (plural = cilia) short, hair-like structure that extends from the plasma membrane in large numbers and is used to move an entire cell or move substances along the outer surface of the cell	https://openstax.org/books/biology/pages/4-key-terms
cytoplasm : entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals	https://openstax.org/books/biology/pages/4-key-terms
cytoskeleton : network of protein fibers that collectively maintain the shape of the cell, secure some organelles in specific positions, allow cytoplasm and vesicles to move within the cell, and enable unicellular organisms to move independently	https://openstax.org/books/biology/pages/4-key-terms
cytosol : gel-like material of the cytoplasm in which cell structures are suspended	https://openstax.org/books/biology/pages/4-key-terms
desmosome : linkages between adjacent epithelial cells that form when cadherins in the plasma membrane attach to intermediate filaments	https://openstax.org/books/biology/pages/4-key-terms
electron microscope : an instrument that magnifies an object using a beam of electrons passed and bent through a lens system to visualize a specimen	https://openstax.org/books/biology/pages/4-key-terms
endomembrane system : group of organelles and membranes in eukaryotic cells that work together modifying, packaging, and transporting lipids and proteins	https://openstax.org/books/biology/pages/4-key-terms
endoplasmic reticulum (ER) : series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids	https://openstax.org/books/biology/pages/4-key-terms
eukaryotic cell : cell that has a membrane-bound nucleus and several other membrane-bound compartments or sacs	https://openstax.org/books/biology/pages/4-key-terms
extracellular matrix : material (primarily collagen, glycoproteins, and proteoglycans) secreted from animal cells that provides mechanical protection and anchoring for the cells in the tissue	https://openstax.org/books/biology/pages/4-key-terms
flagellum : (plural = flagella) long, hair-like structure that extends from the plasma membrane and is used to move the cell	https://openstax.org/books/biology/pages/4-key-terms
gap junction : channel between two adjacent animal cells that allows ions, nutrients, and low molecular weight substances to pass between cells, enabling the cells to communicate	https://openstax.org/books/biology/pages/4-key-terms
Golgi apparatus : eukaryotic organelle made up of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution	https://openstax.org/books/biology/pages/4-key-terms
intermediate filament : cytoskeletal component, composed of several intertwined strands of fibrous protein, that bears tension, supports cell-cell junctions, and anchors cells to extracellular structures	https://openstax.org/books/biology/pages/4-key-terms
light microscope : an instrument that magnifies an object using a beam visible light passed and bent through a lens system to visualize a specimen	https://openstax.org/books/biology/pages/4-key-terms
lysosome : organelle in an animal cell that functions as the cellâs digestive component; it breaks down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles	https://openstax.org/books/biology/pages/4-key-terms
microfilament : narrowest element of the cytoskeleton system; it provides rigidity and shape to the cell and enables cellular movements	https://openstax.org/books/biology/pages/4-key-terms
microscope : an instrument that magnifies an object	https://openstax.org/books/biology/pages/4-key-terms
microtubule : widest element of the cytoskeleton system; it helps the cell resist compression, provides a track along which vesicles move through the cell, pulls replicated chromosomes to opposite ends of a dividing cell, and is the structural element of centrioles, flagella, and cilia	https://openstax.org/books/biology/pages/4-key-terms
mitochondria : (singular = mitochondrion) cellular organelles responsible for carrying out cellular respiration, resulting in the production of ATP, the cellâs main energy-carrying molecule	https://openstax.org/books/biology/pages/4-key-terms
nuclear envelope : double-membrane structure that constitutes the outermost portion of the nucleus	https://openstax.org/books/biology/pages/4-key-terms
nucleoid : central part of a prokaryotic cell in which the chromosome is found	https://openstax.org/books/biology/pages/4-key-terms
nucleolus : darkly staining body within the nucleus that is responsible for assembling the subunits of the ribosomes	https://openstax.org/books/biology/pages/4-key-terms
nucleoplasm : semi-solid fluid inside the nucleus that contains the chromatin and nucleolus	https://openstax.org/books/biology/pages/4-key-terms
nucleus : cell organelle that houses the cellâs DNA and directs the synthesis of ribosomes and proteins	https://openstax.org/books/biology/pages/4-key-terms
organelle : compartment or sac within a cell	https://openstax.org/books/biology/pages/4-key-terms
peroxisome : small, round organelle that contains hydrogen peroxide, oxidizes fatty acids and amino acids, and detoxifies many poisons	https://openstax.org/books/biology/pages/4-key-terms
plasma membrane : phospholipid bilayer with embedded (integral) or attached (peripheral) proteins, and separates the internal content of the cell from its surrounding environment	https://openstax.org/books/biology/pages/4-key-terms
plasmodesma : (plural = plasmodesmata) channel that passes between the cell walls of adjacent plant cells, connects their cytoplasm, and allows materials to be transported from cell to cell	https://openstax.org/books/biology/pages/4-key-terms
prokaryote : unicellular organism that lacks a nucleus or any other membrane-bound organelle	https://openstax.org/books/biology/pages/4-key-terms
ribosome : cellular structure that carries out protein synthesis	https://openstax.org/books/biology/pages/4-key-terms
rough endoplasmic reticulum (RER) : region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification and phospholipid synthesis	https://openstax.org/books/biology/pages/4-key-terms
smooth endoplasmic reticulum (SER) : region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates, lipids, and steroid hormones; detoxifies certain chemicals (like pesticides, preservatives, medications, and environmental pollutants), and stores calcium ions	https://openstax.org/books/biology/pages/4-key-terms
tight junction : firm seal between two adjacent animal cells created by protein adherence	https://openstax.org/books/biology/pages/4-key-terms
unified cell theory : a biological concept that states that all organisms are composed of one or more cells; the cell is the basic unit of life; and new cells arise from existing cells	https://openstax.org/books/biology/pages/4-key-terms
vacuole : membrane-bound sac, somewhat larger than a vesicle, which functions in cellular storage and transport	https://openstax.org/books/biology/pages/4-key-terms
vesicle : small, membrane-bound sac that functions in cellular storage and transport; its membrane is capable of fusing with the plasma membrane and the membranes of the endoplasmic reticulum and Golgi apparatus	https://openstax.org/books/biology/pages/4-key-terms
The modern understanding of the plasma membrane is referred to as the fluid mosaic model. The plasma membrane is composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is studded with proteins, some of which span the membrane. Some of these proteins serve to transport materials into or out of the cell. Carbohydrates are attached to some of the proteins and lipids on the outward-facing surface of the membrane, forming complexes that function to identify the cell to other cells. The fluid nature of the membrane is due to temperature, the configuration of the fatty acid tails (some kinked by double bonds), the presence of cholesterol embedded in the membrane, and the mosaic nature of the proteins and protein-carbohydrate combinations, which are not firmly fixed in place. Plasma membranes enclose and define the borders of cells, but rather than being a static bag, they are dynamic and constantly in flux.	https://openstax.org/books/biology/pages/5-chapter-summary
The passive forms of transport, diffusion and osmosis, move materials of small molecular weight across membranes. Substances diffuse from areas of high concentration to areas of lower concentration, and this process continues until the substance is evenly distributed in a system. In solutions containing more than one substance, each type of molecule diffuses according to its own concentration gradient, independent of the diffusion of other substances. Many factors can affect the rate of diffusion, including concentration gradient, size of the particles that are diffusing, temperature of the system, and so on.	https://openstax.org/books/biology/pages/5-chapter-summary
In living systems, diffusion of substances into and out of cells is mediated by the plasma membrane. Some materials diffuse readily through the membrane, but others are hindered, and their passage is made possible by specialized proteins, such as channels and transporters. The chemistry of living things occurs in aqueous solutions, and balancing the concentrations of those solutions is an ongoing problem. In living systems, diffusion of some substances would be slow or difficult without membrane proteins that facilitate transport.	https://openstax.org/books/biology/pages/5-chapter-summary
The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. A positive ion, for example, might tend to diffuse into a new area, down its concentration gradient, but if it is diffusing into an area of net positive charge, its diffusion will be hampered by its electrical gradient. When dealing with ions in aqueous solutions, a combination of the electrochemical and concentration gradients, rather than just the concentration gradient alone, must be considered. Living cells need certain substances that exist inside the cell in concentrations greater than they exist in the extracellular space. Moving substances up their electrochemical gradients requires energy from the cell. Active transport uses energy stored in ATP to fuel this transport. Active transport of small molecular-sized materials uses integral proteins in the cell membrane to move the materials: These proteins are analogous to pumps. Some pumps, which carry out primary active transport, couple directly with ATP to drive their action. In co-transport (or secondary active transport), energy from primary transport can be used to move another substance into the cell and up its concentration gradient.	https://openstax.org/books/biology/pages/5-chapter-summary
Active transport methods require the direct use of ATP to fuel the transport. Large particles, such as macromolecules, parts of cells, or whole cells, can be engulfed by other cells in a process called phagocytosis. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle entirely enclosed by an envelope of plasma membrane. Vesicle contents are broken down by the cell, with the particles either used as food or dispatched. Pinocytosis is a similar process on a smaller scale. The plasma membrane invaginates and pinches off, producing a small envelope of fluid from outside the cell. Pinocytosis imports substances that the cell needs from the extracellular fluid. The cell expels waste in a similar but reverse manner: it pushes a membranous vacuole to the plasma membrane, allowing the vacuole to fuse with the membrane and incorporate itself into the membrane structure, releasing its contents to the exterior.	https://openstax.org/books/biology/pages/5-chapter-summary
active transport : method of transporting material that requires energy	https://openstax.org/books/biology/pages/5-key-terms
amphiphilic : molecule possessing a polar or charged area and a nonpolar or uncharged area capable of interacting with both hydrophilic and hydrophobic environments	https://openstax.org/books/biology/pages/5-key-terms
antiporter : transporter that carries two ions or small molecules in different directions	https://openstax.org/books/biology/pages/5-key-terms
aquaporin : channel protein that allows water through the membrane at a very high rate	https://openstax.org/books/biology/pages/5-key-terms
carrier protein : membrane protein that moves a substance across the plasma membrane by changing its own shape	https://openstax.org/books/biology/pages/5-key-terms
caveolin : protein that coats the cytoplasmic side of the plasma membrane and participates in the process of liquid update by potocytosis	https://openstax.org/books/biology/pages/5-key-terms
channel protein : membrane protein that allows a substance to pass through its hollow core across the plasma membrane	https://openstax.org/books/biology/pages/5-key-terms
clathrin : protein that coats the inward-facing surface of the plasma membrane and assists in the formation of specialized structures, like coated pits, for phagocytosis	https://openstax.org/books/biology/pages/5-key-terms
concentration gradient : area of high concentration adjacent to an area of low concentration	https://openstax.org/books/biology/pages/5-key-terms
diffusion : passive process of transport of low-molecular weight material according to its concentration gradient	https://openstax.org/books/biology/pages/5-key-terms
electrochemical gradient : gradient produced by the combined forces of an electrical gradient and a chemical gradient	https://openstax.org/books/biology/pages/5-key-terms
electrogenic pump : pump that creates a charge imbalance	https://openstax.org/books/biology/pages/5-key-terms
endocytosis : type of active transport that moves substances, including fluids and particles, into a cell	https://openstax.org/books/biology/pages/5-key-terms
exocytosis : process of passing bulk material out of a cell	https://openstax.org/books/biology/pages/5-key-terms
facilitated transport : process by which material moves down a concentration gradient (from high to low concentration) using integral membrane proteins	https://openstax.org/books/biology/pages/5-key-terms
fluid mosaic model : describes the structure of the plasma membrane as a mosaic of components including phospholipids, cholesterol, proteins, glycoproteins, and glycolipids (sugar chains attached to proteins or lipids, respectively), resulting in a fluid character (fluidity)	https://openstax.org/books/biology/pages/5-key-terms
glycolipid : combination of carbohydrates and lipids	https://openstax.org/books/biology/pages/5-key-terms
glycoprotein : combination of carbohydrates and proteins	https://openstax.org/books/biology/pages/5-key-terms
hydrophilic : molecule with the ability to bond with water; âwater-lovingâ	https://openstax.org/books/biology/pages/5-key-terms
hydrophobic : molecule that does not have the ability to bond with water; âwater-hatingâ	https://openstax.org/books/biology/pages/5-key-terms
hypertonic : situation in which extracellular fluid has a higher osmolarity than the fluid inside the cell, resulting in water moving out of the cell	https://openstax.org/books/biology/pages/5-key-terms
hypotonic : situation in which extracellular fluid has a lower osmolarity than the fluid inside the cell, resulting in water moving into the cell	https://openstax.org/books/biology/pages/5-key-terms
integral protein : protein integrated into the membrane structure that interacts extensively with the hydrocarbon chains of membrane lipids and often spans the membrane; these proteins can be removed only by the disruption of the membrane by detergents	https://openstax.org/books/biology/pages/5-key-terms
isotonic : situation in which the extracellular fluid has the same osmolarity as the fluid inside the cell, resulting in no net movement of water into or out of the cell	https://openstax.org/books/biology/pages/5-key-terms
osmolarity : total amount of substances dissolved in a specific amount of solution	https://openstax.org/books/biology/pages/5-key-terms
osmosis : transport of water through a semipermeable membrane according to the concentration gradient of water across the membrane that results from the presence of solute that cannot pass through the membrane	https://openstax.org/books/biology/pages/5-key-terms
passive transport : method of transporting material through a membrane that does not require energy	https://openstax.org/books/biology/pages/5-key-terms
peripheral protein : protein found at the surface of a plasma membrane either on its exterior or interior side; these proteins can be removed (washed off of the membrane) by a high-salt wash	https://openstax.org/books/biology/pages/5-key-terms
pinocytosis : a variation of endocytosis that imports macromolecules that the cell needs from the extracellular fluid	https://openstax.org/books/biology/pages/5-key-terms
plasmolysis : detaching of the cell membrane from the cell wall and constriction of the cell membrane when a plant cell is in a hypertonic solution	https://openstax.org/books/biology/pages/5-key-terms
potocytosis : variation of pinocytosis that uses a different coating protein (caveolin) on the cytoplasmic side of the plasma membrane	https://openstax.org/books/biology/pages/5-key-terms
primary active transport : active transport that moves ions or small molecules across a membrane and may create a difference in charge across that membrane	https://openstax.org/books/biology/pages/5-key-terms
pump : active transport mechanism that works against electrochemical gradients	https://openstax.org/books/biology/pages/5-key-terms
receptor-mediated endocytosis : variation of endocytosis that involves the use of specific binding proteins in the plasma membrane for specific molecules or particles, and clathrin-coated pits that become clathrin-coated vesicles	https://openstax.org/books/biology/pages/5-key-terms
secondary active transport : movement of material that is due to the electrochemical gradient established by primary active transport	https://openstax.org/books/biology/pages/5-key-terms
selectively permeable : characteristic of a membrane that allows some substances through but not others	https://openstax.org/books/biology/pages/5-key-terms
solute : substance dissolved in a liquid to form a solution	https://openstax.org/books/biology/pages/5-key-terms
symporter : transporter that carries two different ions or small molecules, both in the same direction	https://openstax.org/books/biology/pages/5-key-terms
tonicity : amount of solute in a solution	https://openstax.org/books/biology/pages/5-key-terms
transport protein : membrane protein that facilitates passage of a substance across a membrane by binding it	https://openstax.org/books/biology/pages/5-key-terms
transporter : specific carrier proteins or pumps that facilitate movement	https://openstax.org/books/biology/pages/5-key-terms
uniporter : transporter that carries one specific ion or molecule	https://openstax.org/books/biology/pages/5-key-terms
Cells perform the functions of life through various chemical reactions. A cellâs metabolism refers to the chemical reactions that take place within it. There are metabolic reactions that involve the breaking down of complex chemicals into simpler ones, such as the breakdown of large macromolecules. This process is referred to as catabolism, and such reactions are associated with a release of energy. On the other end of the spectrum, anabolism refers to metabolic processes that build complex molecules out of simpler ones, such as the synthesis of macromolecules. Anabolic processes require energy. Glucose synthesis and glucose breakdown are examples of anabolic and catabolic pathways, respectively.	https://openstax.org/books/biology/pages/6-chapter-summary
Energy comes in many different forms. Objects in motion do physical work, and kinetic energy is the energy of objects in motion. Objects that are not in motion may have the potential to do work, and thus, have potential energy. Molecules also have potential energy because the breaking of molecular bonds has the potential to release energy. Living cells depend on the harvesting of potential energy from molecular bonds to perform work. Free energy is a measure of energy that is available to do work. The free energy of a system changes during energy transfers such as chemical reactions, and this change is referred to as âG.	https://openstax.org/books/biology/pages/6-chapter-summary
The âG of a reaction can be negative or positive, meaning that the reaction releases energy or consumes energy, respectively. A reaction with a negative âG that gives off energy is called an exergonic reaction. One with a positive âG that requires energy input is called an endergonic reaction. Exergonic reactions are said to be spontaneous, because their products have less energy than their reactants. The products of endergonic reactions have a higher energy state than the reactants, and so these are nonspontaneous reactions. However, all reactions (including spontaneous -âG reactions) require an initial input of energy in order to reach the transition state, at which theyâll proceed. This initial input of energy is called the activation energy.	https://openstax.org/books/biology/pages/6-chapter-summary
In studying energy, scientists use the term âsystemâ to refer to the matter and its environment involved in energy transfers. Everything outside of the system is called the surroundings. Single cells are biological systems. Systems can be thought of as having a certain amount of order. It takes energy to make a system more ordered. The more ordered a system is, the lower its entropy. Entropy is a measure of the disorder of a system. As a system becomes more disordered, the lower its energy and the higher its entropy become.	https://openstax.org/books/biology/pages/6-chapter-summary
A series of laws, called the laws of thermodynamics, describe the properties and processes of energy transfer. The first law states that the total amount of energy in the universe is constant. This means that energy canât be created or destroyed, only transferred or transformed. The second law of thermodynamics states that every energy transfer involves some loss of energy in an unusable form, such as heat energy, resulting in a more disordered system. In other words, no energy transfer is completely efficient and tends toward disorder.	https://openstax.org/books/biology/pages/6-chapter-summary
ATP is the primary energy-supplying molecule for living cells. ATP is made up of a nucleotide, a five-carbon sugar, and three phosphate groups. The bonds that connect the phosphates (phosphoanhydride bonds) have high-energy content. The energy released from the hydrolysis of ATP into ADP + Piis used to perform cellular work. Cells use ATP to perform work by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions. ATP donates its phosphate group to another molecule via a process known as phosphorylation. The phosphorylated molecule is at a higher-energy state and is less stable than its unphosphorylated form, and this added energy from the addition of the phosphate allows the molecule to undergo its endergonic reaction.	https://openstax.org/books/biology/pages/6-chapter-summary
Enzymes are chemical catalysts that accelerate chemical reactions at physiological temperatures by lowering their activation energy. Enzymes are usually proteins consisting of one or more polypeptide chains. Enzymes have an active site that provides a unique chemical environment, made up of certain amino acid R groups (residues). This unique environment is perfectly suited to convert particular chemical reactants for that enzyme, called substrates, into unstable intermediates called transition states. Enzymes and substrates are thought to bind with an induced fit, which means that enzymes undergo slight conformational adjustments upon substrate contact, leading to full, optimal binding. Enzymes bind to substrates and catalyze reactions in four different ways: bringing substrates together in an optimal orientation, compromising the bond structures of substrates so that bonds can be more easily broken, providing optimal environmental conditions for a reaction to occur, or participating directly in their chemical reaction by forming transient covalent bonds with the substrates.	https://openstax.org/books/biology/pages/6-chapter-summary
Enzyme action must be regulated so that in a given cell at a given time, the desired reactions are being catalyzed and the undesired reactions are not. Enzymes are regulated by cellular conditions, such as temperature and pH. They are also regulated through their location within a cell, sometimes being compartmentalized so that they can only catalyze reactions under certain circumstances. Inhibition and activation of enzymes via other molecules are other important ways that enzymes are regulated. Inhibitors can act competitively, noncompetitively, or allosterically; noncompetitive inhibitors are usually allosteric. Activators can also enhance the function of enzymes allosterically. The most common method by which cells regulate the enzymes in metabolic pathways is through feedback inhibition. During feedback inhibition, the products of a metabolic pathway serve as inhibitors (usually allosteric) of one or more of the enzymes (usually the first committed enzyme of the pathway) involved in the pathway that produces them.	https://openstax.org/books/biology/pages/6-chapter-summary

cell theory : see unified cell theory

https://openstax.org/books/biology/pages/4-key-terms

cell wall : rigid cell covering made of various molecules that protects the cell, provides structural support, and gives shape to the cell

https://openstax.org/books/biology/pages/4-key-terms

central vacuole : large plant cell organelle that regulates the cellâs storage compartment, holds water, and plays a significant role in cell growth as the site of macromolecule degradation

https://openstax.org/books/biology/pages/4-key-terms

centrosome : region in animal cells made of two centrioles

https://openstax.org/books/biology/pages/4-key-terms

chlorophyll : green pigment that captures the light energy that drives the light reactions of photosynthesis

https://openstax.org/books/biology/pages/4-key-terms

chloroplast : plant cell organelle that carries out photosynthesis

https://openstax.org/books/biology/pages/4-key-terms

chromatin : protein-DNA complex that serves as the building material of chromosomes

https://openstax.org/books/biology/pages/4-key-terms

chromosome : structure within the nucleus that is made up of chromatin that contains DNA, the hereditary material

https://openstax.org/books/biology/pages/4-key-terms

cilium : (plural = cilia) short, hair-like structure that extends from the plasma membrane in large numbers and is used to move an entire cell or move substances along the outer surface of the cell

https://openstax.org/books/biology/pages/4-key-terms

cytoplasm : entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals

https://openstax.org/books/biology/pages/4-key-terms

cytoskeleton : network of protein fibers that collectively maintain the shape of the cell, secure some organelles in specific positions, allow cytoplasm and vesicles to move within the cell, and enable unicellular organisms to move independently

https://openstax.org/books/biology/pages/4-key-terms

cytosol : gel-like material of the cytoplasm in which cell structures are suspended

https://openstax.org/books/biology/pages/4-key-terms

desmosome : linkages between adjacent epithelial cells that form when cadherins in the plasma membrane attach to intermediate filaments

https://openstax.org/books/biology/pages/4-key-terms

electron microscope : an instrument that magnifies an object using a beam of electrons passed and bent through a lens system to visualize a specimen

https://openstax.org/books/biology/pages/4-key-terms

endomembrane system : group of organelles and membranes in eukaryotic cells that work together modifying, packaging, and transporting lipids and proteins

https://openstax.org/books/biology/pages/4-key-terms

endoplasmic reticulum (ER) : series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids

https://openstax.org/books/biology/pages/4-key-terms

eukaryotic cell : cell that has a membrane-bound nucleus and several other membrane-bound compartments or sacs

https://openstax.org/books/biology/pages/4-key-terms

extracellular matrix : material (primarily collagen, glycoproteins, and proteoglycans) secreted from animal cells that provides mechanical protection and anchoring for the cells in the tissue

https://openstax.org/books/biology/pages/4-key-terms

flagellum : (plural = flagella) long, hair-like structure that extends from the plasma membrane and is used to move the cell

https://openstax.org/books/biology/pages/4-key-terms

gap junction : channel between two adjacent animal cells that allows ions, nutrients, and low molecular weight substances to pass between cells, enabling the cells to communicate

https://openstax.org/books/biology/pages/4-key-terms

Golgi apparatus : eukaryotic organelle made up of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution

https://openstax.org/books/biology/pages/4-key-terms

intermediate filament : cytoskeletal component, composed of several intertwined strands of fibrous protein, that bears tension, supports cell-cell junctions, and anchors cells to extracellular structures

https://openstax.org/books/biology/pages/4-key-terms

light microscope : an instrument that magnifies an object using a beam visible light passed and bent through a lens system to visualize a specimen

https://openstax.org/books/biology/pages/4-key-terms

lysosome : organelle in an animal cell that functions as the cellâs digestive component; it breaks down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles

https://openstax.org/books/biology/pages/4-key-terms

microfilament : narrowest element of the cytoskeleton system; it provides rigidity and shape to the cell and enables cellular movements

https://openstax.org/books/biology/pages/4-key-terms

microscope : an instrument that magnifies an object

https://openstax.org/books/biology/pages/4-key-terms

microtubule : widest element of the cytoskeleton system; it helps the cell resist compression, provides a track along which vesicles move through the cell, pulls replicated chromosomes to opposite ends of a dividing cell, and is the structural element of centrioles, flagella, and cilia

https://openstax.org/books/biology/pages/4-key-terms

mitochondria : (singular = mitochondrion) cellular organelles responsible for carrying out cellular respiration, resulting in the production of ATP, the cellâs main energy-carrying molecule

https://openstax.org/books/biology/pages/4-key-terms

nuclear envelope : double-membrane structure that constitutes the outermost portion of the nucleus

https://openstax.org/books/biology/pages/4-key-terms

nucleoid : central part of a prokaryotic cell in which the chromosome is found

https://openstax.org/books/biology/pages/4-key-terms

nucleolus : darkly staining body within the nucleus that is responsible for assembling the subunits of the ribosomes

https://openstax.org/books/biology/pages/4-key-terms

nucleoplasm : semi-solid fluid inside the nucleus that contains the chromatin and nucleolus

https://openstax.org/books/biology/pages/4-key-terms

nucleus : cell organelle that houses the cellâs DNA and directs the synthesis of ribosomes and proteins

https://openstax.org/books/biology/pages/4-key-terms

organelle : compartment or sac within a cell

https://openstax.org/books/biology/pages/4-key-terms

peroxisome : small, round organelle that contains hydrogen peroxide, oxidizes fatty acids and amino acids, and detoxifies many poisons

https://openstax.org/books/biology/pages/4-key-terms

plasma membrane : phospholipid bilayer with embedded (integral) or attached (peripheral) proteins, and separates the internal content of the cell from its surrounding environment

https://openstax.org/books/biology/pages/4-key-terms

plasmodesma : (plural = plasmodesmata) channel that passes between the cell walls of adjacent plant cells, connects their cytoplasm, and allows materials to be transported from cell to cell

https://openstax.org/books/biology/pages/4-key-terms

prokaryote : unicellular organism that lacks a nucleus or any other membrane-bound organelle

https://openstax.org/books/biology/pages/4-key-terms

ribosome : cellular structure that carries out protein synthesis

https://openstax.org/books/biology/pages/4-key-terms

rough endoplasmic reticulum (RER) : region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification and phospholipid synthesis

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smooth endoplasmic reticulum (SER) : region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates, lipids, and steroid hormones; detoxifies certain chemicals (like pesticides, preservatives, medications, and environmental pollutants), and stores calcium ions

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tight junction : firm seal between two adjacent animal cells created by protein adherence

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unified cell theory : a biological concept that states that all organisms are composed of one or more cells; the cell is the basic unit of life; and new cells arise from existing cells

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vacuole : membrane-bound sac, somewhat larger than a vesicle, which functions in cellular storage and transport

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vesicle : small, membrane-bound sac that functions in cellular storage and transport; its membrane is capable of fusing with the plasma membrane and the membranes of the endoplasmic reticulum and Golgi apparatus

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The modern understanding of the plasma membrane is referred to as the fluid mosaic model. The plasma membrane is composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is studded with proteins, some of which span the membrane. Some of these proteins serve to transport materials into or out of the cell. Carbohydrates are attached to some of the proteins and lipids on the outward-facing surface of the membrane, forming complexes that function to identify the cell to other cells. The fluid nature of the membrane is due to temperature, the configuration of the fatty acid tails (some kinked by double bonds), the presence of cholesterol embedded in the membrane, and the mosaic nature of the proteins and protein-carbohydrate combinations, which are not firmly fixed in place. Plasma membranes enclose and define the borders of cells, but rather than being a static bag, they are dynamic and constantly in flux.

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The passive forms of transport, diffusion and osmosis, move materials of small molecular weight across membranes. Substances diffuse from areas of high concentration to areas of lower concentration, and this process continues until the substance is evenly distributed in a system. In solutions containing more than one substance, each type of molecule diffuses according to its own concentration gradient, independent of the diffusion of other substances. Many factors can affect the rate of diffusion, including concentration gradient, size of the particles that are diffusing, temperature of the system, and so on.

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In living systems, diffusion of substances into and out of cells is mediated by the plasma membrane. Some materials diffuse readily through the membrane, but others are hindered, and their passage is made possible by specialized proteins, such as channels and transporters. The chemistry of living things occurs in aqueous solutions, and balancing the concentrations of those solutions is an ongoing problem. In living systems, diffusion of some substances would be slow or difficult without membrane proteins that facilitate transport.

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The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. A positive ion, for example, might tend to diffuse into a new area, down its concentration gradient, but if it is diffusing into an area of net positive charge, its diffusion will be hampered by its electrical gradient. When dealing with ions in aqueous solutions, a combination of the electrochemical and concentration gradients, rather than just the concentration gradient alone, must be considered. Living cells need certain substances that exist inside the cell in concentrations greater than they exist in the extracellular space. Moving substances up their electrochemical gradients requires energy from the cell. Active transport uses energy stored in ATP to fuel this transport. Active transport of small molecular-sized materials uses integral proteins in the cell membrane to move the materials: These proteins are analogous to pumps. Some pumps, which carry out primary active transport, couple directly with ATP to drive their action. In co-transport (or secondary active transport), energy from primary transport can be used to move another substance into the cell and up its concentration gradient.

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Active transport methods require the direct use of ATP to fuel the transport. Large particles, such as macromolecules, parts of cells, or whole cells, can be engulfed by other cells in a process called phagocytosis. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle entirely enclosed by an envelope of plasma membrane. Vesicle contents are broken down by the cell, with the particles either used as food or dispatched. Pinocytosis is a similar process on a smaller scale. The plasma membrane invaginates and pinches off, producing a small envelope of fluid from outside the cell. Pinocytosis imports substances that the cell needs from the extracellular fluid. The cell expels waste in a similar but reverse manner: it pushes a membranous vacuole to the plasma membrane, allowing the vacuole to fuse with the membrane and incorporate itself into the membrane structure, releasing its contents to the exterior.

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active transport : method of transporting material that requires energy

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amphiphilic : molecule possessing a polar or charged area and a nonpolar or uncharged area capable of interacting with both hydrophilic and hydrophobic environments

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antiporter : transporter that carries two ions or small molecules in different directions

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aquaporin : channel protein that allows water through the membrane at a very high rate

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carrier protein : membrane protein that moves a substance across the plasma membrane by changing its own shape

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caveolin : protein that coats the cytoplasmic side of the plasma membrane and participates in the process of liquid update by potocytosis

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channel protein : membrane protein that allows a substance to pass through its hollow core across the plasma membrane

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clathrin : protein that coats the inward-facing surface of the plasma membrane and assists in the formation of specialized structures, like coated pits, for phagocytosis

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concentration gradient : area of high concentration adjacent to an area of low concentration

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diffusion : passive process of transport of low-molecular weight material according to its concentration gradient

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electrochemical gradient : gradient produced by the combined forces of an electrical gradient and a chemical gradient

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electrogenic pump : pump that creates a charge imbalance

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endocytosis : type of active transport that moves substances, including fluids and particles, into a cell

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exocytosis : process of passing bulk material out of a cell

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facilitated transport : process by which material moves down a concentration gradient (from high to low concentration) using integral membrane proteins

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fluid mosaic model : describes the structure of the plasma membrane as a mosaic of components including phospholipids, cholesterol, proteins, glycoproteins, and glycolipids (sugar chains attached to proteins or lipids, respectively), resulting in a fluid character (fluidity)

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glycolipid : combination of carbohydrates and lipids

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glycoprotein : combination of carbohydrates and proteins

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hydrophilic : molecule with the ability to bond with water; âwater-lovingâ

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hydrophobic : molecule that does not have the ability to bond with water; âwater-hatingâ

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hypertonic : situation in which extracellular fluid has a higher osmolarity than the fluid inside the cell, resulting in water moving out of the cell

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hypotonic : situation in which extracellular fluid has a lower osmolarity than the fluid inside the cell, resulting in water moving into the cell

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integral protein : protein integrated into the membrane structure that interacts extensively with the hydrocarbon chains of membrane lipids and often spans the membrane; these proteins can be removed only by the disruption of the membrane by detergents

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isotonic : situation in which the extracellular fluid has the same osmolarity as the fluid inside the cell, resulting in no net movement of water into or out of the cell

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osmolarity : total amount of substances dissolved in a specific amount of solution

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osmosis : transport of water through a semipermeable membrane according to the concentration gradient of water across the membrane that results from the presence of solute that cannot pass through the membrane

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passive transport : method of transporting material through a membrane that does not require energy

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peripheral protein : protein found at the surface of a plasma membrane either on its exterior or interior side; these proteins can be removed (washed off of the membrane) by a high-salt wash

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pinocytosis : a variation of endocytosis that imports macromolecules that the cell needs from the extracellular fluid

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plasmolysis : detaching of the cell membrane from the cell wall and constriction of the cell membrane when a plant cell is in a hypertonic solution

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potocytosis : variation of pinocytosis that uses a different coating protein (caveolin) on the cytoplasmic side of the plasma membrane

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primary active transport : active transport that moves ions or small molecules across a membrane and may create a difference in charge across that membrane

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pump : active transport mechanism that works against electrochemical gradients

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receptor-mediated endocytosis : variation of endocytosis that involves the use of specific binding proteins in the plasma membrane for specific molecules or particles, and clathrin-coated pits that become clathrin-coated vesicles

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secondary active transport : movement of material that is due to the electrochemical gradient established by primary active transport

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selectively permeable : characteristic of a membrane that allows some substances through but not others

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solute : substance dissolved in a liquid to form a solution

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symporter : transporter that carries two different ions or small molecules, both in the same direction

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tonicity : amount of solute in a solution

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transport protein : membrane protein that facilitates passage of a substance across a membrane by binding it

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transporter : specific carrier proteins or pumps that facilitate movement

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uniporter : transporter that carries one specific ion or molecule

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Cells perform the functions of life through various chemical reactions. A cellâs metabolism refers to the chemical reactions that take place within it. There are metabolic reactions that involve the breaking down of complex chemicals into simpler ones, such as the breakdown of large macromolecules. This process is referred to as catabolism, and such reactions are associated with a release of energy. On the other end of the spectrum, anabolism refers to metabolic processes that build complex molecules out of simpler ones, such as the synthesis of macromolecules. Anabolic processes require energy. Glucose synthesis and glucose breakdown are examples of anabolic and catabolic pathways, respectively.

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Energy comes in many different forms. Objects in motion do physical work, and kinetic energy is the energy of objects in motion. Objects that are not in motion may have the potential to do work, and thus, have potential energy. Molecules also have potential energy because the breaking of molecular bonds has the potential to release energy. Living cells depend on the harvesting of potential energy from molecular bonds to perform work. Free energy is a measure of energy that is available to do work. The free energy of a system changes during energy transfers such as chemical reactions, and this change is referred to as âG.

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The âG of a reaction can be negative or positive, meaning that the reaction releases energy or consumes energy, respectively. A reaction with a negative âG that gives off energy is called an exergonic reaction. One with a positive âG that requires energy input is called an endergonic reaction. Exergonic reactions are said to be spontaneous, because their products have less energy than their reactants. The products of endergonic reactions have a higher energy state than the reactants, and so these are nonspontaneous reactions. However, all reactions (including spontaneous -âG reactions) require an initial input of energy in order to reach the transition state, at which theyâll proceed. This initial input of energy is called the activation energy.

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In studying energy, scientists use the term âsystemâ to refer to the matter and its environment involved in energy transfers. Everything outside of the system is called the surroundings. Single cells are biological systems. Systems can be thought of as having a certain amount of order. It takes energy to make a system more ordered. The more ordered a system is, the lower its entropy. Entropy is a measure of the disorder of a system. As a system becomes more disordered, the lower its energy and the higher its entropy become.

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A series of laws, called the laws of thermodynamics, describe the properties and processes of energy transfer. The first law states that the total amount of energy in the universe is constant. This means that energy canât be created or destroyed, only transferred or transformed. The second law of thermodynamics states that every energy transfer involves some loss of energy in an unusable form, such as heat energy, resulting in a more disordered system. In other words, no energy transfer is completely efficient and tends toward disorder.

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ATP is the primary energy-supplying molecule for living cells. ATP is made up of a nucleotide, a five-carbon sugar, and three phosphate groups. The bonds that connect the phosphates (phosphoanhydride bonds) have high-energy content. The energy released from the hydrolysis of ATP into ADP + Piis used to perform cellular work. Cells use ATP to perform work by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions. ATP donates its phosphate group to another molecule via a process known as phosphorylation. The phosphorylated molecule is at a higher-energy state and is less stable than its unphosphorylated form, and this added energy from the addition of the phosphate allows the molecule to undergo its endergonic reaction.

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Enzymes are chemical catalysts that accelerate chemical reactions at physiological temperatures by lowering their activation energy. Enzymes are usually proteins consisting of one or more polypeptide chains. Enzymes have an active site that provides a unique chemical environment, made up of certain amino acid R groups (residues). This unique environment is perfectly suited to convert particular chemical reactants for that enzyme, called substrates, into unstable intermediates called transition states. Enzymes and substrates are thought to bind with an induced fit, which means that enzymes undergo slight conformational adjustments upon substrate contact, leading to full, optimal binding. Enzymes bind to substrates and catalyze reactions in four different ways: bringing substrates together in an optimal orientation, compromising the bond structures of substrates so that bonds can be more easily broken, providing optimal environmental conditions for a reaction to occur, or participating directly in their chemical reaction by forming transient covalent bonds with the substrates.

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Enzyme action must be regulated so that in a given cell at a given time, the desired reactions are being catalyzed and the undesired reactions are not. Enzymes are regulated by cellular conditions, such as temperature and pH. They are also regulated through their location within a cell, sometimes being compartmentalized so that they can only catalyze reactions under certain circumstances. Inhibition and activation of enzymes via other molecules are other important ways that enzymes are regulated. Inhibitors can act competitively, noncompetitively, or allosterically; noncompetitive inhibitors are usually allosteric. Activators can also enhance the function of enzymes allosterically. The most common method by which cells regulate the enzymes in metabolic pathways is through feedback inhibition. During feedback inhibition, the products of a metabolic pathway serve as inhibitors (usually allosteric) of one or more of the enzymes (usually the first committed enzyme of the pathway) involved in the pathway that produces them.

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