Chapter 4- Evolutionary Origin of Cells and Their General Features (copy)

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Stage 1

Nucleotides and amino acids were produced prior to the existence of cells.

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Stage 2

  • Nucleotides became polymerized to form RNA and/or DNA, and amino acids became polymerized to form proteins. 

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Stage 3

Polymers became enclosed in membranes

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Stage 4

  • Polymers enclosed in membranes acquired properties that are associated with living cells via chemical selection.

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  • Stage 1: Organic Molecules Formed Prior to the Existence of Cells  

  • The first stage of the origin of life by considering how nucleotides and amino acids may have been made prior to the existence of living cells. 

  • It is believed that early Earth, which was much different from today's, may have been more conducive to the spontaneous formation of organic molecules. 

    • Suggests that organic molecules eventually macromolecules formed spontaneously. 

      • The spontaneous appearance of organic molecules produced what has been called a “primordial soup” which gave rise to living cells.

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Prebiotic Soup

The medium formed by the slow accumulation of organic molecules in the early oceans over a long period of time prior to the existence of life.

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Scientists in the 1950s propostition

  • the atmosphere on early Earth was rich in water vapor (H2O), hydrogen gas (H2), methane (CH4), and ammonia (NH3). This along with atmospheric oxygen (O2) produced a reducing atmosphere because methane and ammonia readily give up electrons to other molecules reducing them. Oxidation-reduction reactions (redox reactions) are required for the formation of complex organic molecules from simple inorganic molecules

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Stanely Miller and Harlod Urey

  • the first scientists to use experimentation to test whether the prebiotic synthesis of organic molecules is possible. 

    • The experimental apparatus was intended to simulate the conditions on early Earth. He used water vapor from a flask of boiling water which rose into a chamber containing hydrogen gas, methane and ammonia 

    • Miller inserted two electrodes into the chamber to simulate lightning bolts, a condenser jacket cooled some of the gasses from the chamber, causing droplets to form that fell into a trap. 

    • In his first experiments he observed the formation of hydrogen cyanide (HCN) and formaldehyde (CH2O). At the end of 1 week of the operation 10-15% of the carbon had been incorporated into organic compounds. Later it demonstrated the formation of sugars, a few types of amino acids, lipids, and bases found in nucleic acids 

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2011 Researchers Analyzation

Samples that Miller had preserved from his experiment, they analyzed the products that were made in the experiment. It was found that 23 different amino acids and 4 amines were also included. 

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Extraterrestrial Hypothesis

  • Scientists argue that sufficient organic molecules may have been present in meteorites material from asteroids and comets that redhead the surface of early Earth.

  • A significant proportion of meteorites belong to a class known as carbonaceous chondrites. These meteorites may contain a substantial amount of organic carbon which includes amino acids and nucleic acid bases. 

    • Scientists have assumed that such a meteorite could have transported a significant amount of organic molecules from outer space to early Earth. 

      • Opponents believe that the materials would have been destroyed by the intense heating that comes with large bodies moving through the atmosphere and colliding with Earth’s surface. 

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Deep Sea-Vent Hypothesis

  • German chemist Gunter Wachtershauser proposed that key organic molecules may have originated in deep-sea vents, cracks in the Earth’s surface where superheated water that contains metal ions and hydrogen sulfide (H2S) mixes abruptly with cold seawater. 

    • These vents release hot, gaseous substances from the interior of the Earth at temperatures in excess of 300 degrees Celsius (572 degrees fahrenheit) 

    • Supporters believe that important molecules have been formed in the temperature between extremely hot vent water and cold water that surrounds the vent. 

  • Worms, clams, crabs, shrimp, and bacteria are found in significant abundance in these areas. These organisms receive their energy from chemicals in the vent not from the sun. 

  • The alkaline hydrothermal deep-sea vent was discovered near mid-ocean ridges in 2000. The synthesis of organic molecules was due to temperature gradients. Researchers have hypothesized that organic molecules and eventually living cells may have been produced from harnessing the energy within the gradients that existed when alkaline vent water mixed with more acidic seawater. 

  • The early oceans are believed to contain more carbon dioxide than now, which could have contributed to the synthesis of organic molecules. 

    • 1.43 billion year old fossils were discovered near ancient deep-sea vents, providing evidence that life may have originated on the bottom of the ocean. 

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Stage 2: Organic Polymers May Have Formed on the Surface of Clay or in Water 

  • Scientists hypothesize that the second stage in the origin of life was a period in which simple organic molecules polymerized to form more complex organic polymers such as DNA, RNA, or proteins. It is assumed that at least 30-60 monomers are needed to store enough information to make a viable genetic system. 

  • Since hydrolysis competes with polymerization, scientists speculate that the synthesis of polymers did not occur in a watery, prebiotic soup but instead took place on a solid surface or in evaporating tidal pools. 

  • In 1951 Irish X-ray crystallographer John Bernal first suggested that the prebiotic synthesis of polymers took place on clay. “Clays, muds, and inorganic crystals are powerful means to concentrate and polymerize organic molecules” 

  • Clay minerals are known to bind organic molecules such as nucleotides and amino acids 

  • During the prebiotic synthesis of RNA, the purine bases of the nucleotides could have interacted with the silicate surfaces of the clay. Cations, such as Mg2+, can bind the nucleotides to the negatively charged surfaces of the clay, thereby positioning the nucleotides in a way that may have promoted bond formation between the phosphate of one nucleotide and the ribose sugar of an adjacent nucleotide.  

  • Studies by Luke Leman, Lesile Orgel, and M. Reza Ghadiri indicates that polymers can also form in aqueous solutions, contrary to the prevalent view.

    • Their work showed that carbonyl sulfide (simple gas) present in volcanic gasses and deep-sea vent emissions, can bring about the formation of peptides from amino acids under mild conditions in water.

    • These results indicate that the synthesis of polymers could have taken place in the prebiotic soup   

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Stage 3: Cell-like Structures May Have Originated When Polymers Were Enclosed by a Boundary

The third stage in the origin of living cells is hypothesized to be the formation of a boundary that separated the polymers, such as RNA, from the environment

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  •  The first non living structures that evolved into living cells

    • Used to describe an aggregate of prebiotically produced molecules and macromolecules that acquired a boundary, such as a lipid bilayer, that allowed it to maintain an internal chemical environment distinct from that of its surrounding. 

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Scientists envision the existence of four key features: 

  • A boundary such as a membrane, separated the internal contents of the protobiont from the external environment

  • Polymers inside the protobiont contained information 

  • Polymers inside the protobiont had catalytic functions 

    • The protobionts eventually developed the capability of self-replication

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Protobionts were not capable of precise self-reproduction like living cells but could divide to increase in number. 

  • Protobionts are thought to have exhibited simple metabolic pathways in which the structures of organic molecules were changed. 

  • Polymers inside protobionts must have gained the catalytic ability to link organic building blocks to produce new polymers. 

    • Over time protobionts became more complex and refined their ability to self-replicate 

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  • A vesicle surrounded by a lipid bilayer

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  • When certain types of lipids are dissolved in water, they spontaneously form liposomes. Lipid bilayers are selectively permeable 

    • Some liposomes can store energy in the form of electrical gradients. Also they can discharge the energy in a neuron-like fashion showing rudimentary signs of excitability, which is characteristic of living cells.

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Martin Haczyc, Shelly Fujikawa, Jack Szostak in 2003

  • Showed that clay can catalyze the formation of liposomes that grow and divide, a primitive form of self-replication. 

    • If RNA was on the surface of the clay, the researchers discovered that liposomes that enclosed RNA were formed. 

    • The experiments showed that the formation of membrane-enclosed vesicles containing RNA molecules is a plausible explanation of the emergence of cell-like structures based on simple physical and chemical properties. 

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Stage 4: Cellular Characteristics May Have Evolved via Chemical Selection, Beginning with an RNA World

  • The majority of scientists favor RNA as the first macromolecule that was found in protobionts. RNA has three key functions 

    • RNA has the ability to store information in its nucleotide base sequence. 

    • Due to base pairing, its nucleotide sequence has the capacity for self-replication. 

      • RNA can perform a variety of catalytic functions. The results of many experiments have shown that some RNA molecules function as ribozymes 

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  • A biological catalyst that is an RNA molecule 

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DNA and Proteins are not as versatile as RNA

  • DNA has very limited catalytic activity, and proteins are not known to undergo self-replication. RNA can perform functions that are characteristic of proteins and, at the same time, can serve as genetic material with replicative and informational functions. 

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Chemical Selection

  • A process that occurs when a chemical within a mixture has special properties or advantages that cause it to increase in amount, it may have played a key role in the formation of an RNA world. 

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Chemical Evolution

  • The process by which a population of molecules changes over time to become a new population with a different chemical composition

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Special properties and chemical selection

  • Scientists speculate that the special properties enabling certain RNA molecules to undergo chemical selection were their ability to self-replication and perform other catalytic functions. 

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RNA World

  • A hypothetical period on primitive Earth when both the information needed for life and the enzymatic activity of living cells were contained solely in RNA molecules 

    • Scientists envisioned that over time mutations occurred in these RNA molecules occasionally introducing new functional possibilities. 

      • Chemical selection would have eventually produced an increase in complexity in these cells. Such as the ability to link amino acids together into proteins and other catalytic roles. 

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Biologists David Bartel and Jack Szotak

  • Conducted the first study on particular functions in RNA in 1993. They obtained a collection of RNA molecules that had catalytic activity that was 3 million times higher than their original random collection of molecules. 

    • The results showed that RNA molecules over time by increasing the proportion of those molecules with enhanced function

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Information Storage

  • Scientists speculated that the incorporation of DNA into cells would have relieved RNA of its role of storing information, thereby allowing RNA to perform a variety of other functions. 

    • If DNA stored the information for the synthesis of RNA molecules, such RNA molecules could bind cofactors, have modified bases, or bind peptides that might enhance their catalytic function. 

    • Cells with both DNA and RNA would have an advantage over those with just RNA so they would have been selected 

      • DNA also is more stable than RNA, the strands are less likely to break spontaneously

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Metabolism and Other Cellular Functions

  • Proteins have vastly greater catalytic ability than do RNA molecules due to the chemical properties of the 20 amino acids. 

  • Proteins can carry out structural roles, and certain membrane proteins are responsible for the uptake of substances into living cells. 

  • RNA molecules can catalyze the formation of peptides bonds and even attach amino acids to primitive tRNA molecules. Modern protein synthesis still includes a central role for RNA in the synthesis of polypeptides. 

    • First mRNA provides the information for a polypeptide sequence. 

    • tRNA molecules act as adaptors for the formation of a polypeptide chain

      • rRNA provides a site for polypeptide synthesis and in the peptidyl transferase center within ribosomes acts as a ribozyme to catalyze peptide bond formation.

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  • A magnification tool that enables researchers to study very small structures such as cells 

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  • An image taken with the aid of a microscope 

    • The first compound microscope (with more than one lens) was constructed in 1595 by Zacharias Jansen of Holland 

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Robert Hooke 1665 Experiment

  • studied cork under a primitive compound microscope he had made. Hooke coined the word cell-derived from the Latin word cellulla meaning small compartment to describe the structures he observed. 

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In microscopy the ability to observe two adjacent objects as distinct from one another; a measure of the clarity of an image

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  • In microscopy, relative differences in the lightness, darkness, or color between adjacent regions in a sample

    • Staining the cellular structure of interest with a dye can make viewing much easier. The application of stains selectively label individual components of the cell, improves contrast. Staining  and colorization are not the same. 

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  • The ratio between the size of an image produced by a microscope and a sample’s actual size 

    • Depending on the quality of the lens and the illumination source, every microscope has an optimal range of magnification before objects appear too blurry to be readily observed. 

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Light microscopes

A microscope that utilizes light for illumination. resolve structures that are as close as .2 micron or micrometer from each other

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Electron microscopes

  • A microscope that uses an electron beam for illumination

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Resolution being improved

  •  the illumination source has a shorter wavelength. In 1931 when Max Knoll and Ernst Ruska invented the first electron microscope. Since the electron beam is much shorter than that of visible light, the resolution of an electron microscope is far better than that of the light microscope. 

    • The resolution limit of an electron microscope is typically around 2 nanometers which is about 100 times better than a light microscope 

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Transmission Electron microscopy (TEM)

  • A type of microscopy in which a beam of electrons is transmitted through a biological sample to form an image of a photographic plate of screen. 

    • To provide contrast the sample is stained with a heavy metal which binds to certain cellular structures such as membranes. THe sample is then adhered to a copper grind and place in a TEM 

      • TEM provides a cross-sectional view of a cell and gives the best resolution compared with other forms of microscopy. However, such microscopes are expensive and cannot be used to view living cells. 

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Scanning Electron microscopy (SEM)

  • A type of microscopy that utilizes an electron beam to produce an image of the three-dimensional surface of biological samples 

    • The sample is coated with a thin layer of heavy metal such as gold or palladium and then is exposed to an electron beam that scans its surface. Secondary electrons are emitted from the sample which are detected and create an image of its three-dimensional surface.

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  • Anything that has mass and takes up space 

    • The matter found in living organisms is composed of atoms, molecules and macromolecules. Each type of cell synthesizes a unique set of molecules and macromolecules that contribute to cell structure 

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  • The ability to promote change or do work 

    • Needed to produce molecules and macromolecules and to carry out many cellular functions

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The molecules and macromolecules that constitute cells are found at specific sites. ALl living cells have the ability to build and maintain their internal organization. Proteins often bind to each other in much the same way as building blocks snap together.

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Protein-protein interactions

  • The specific interactions between proteins that occur during many critical cellular processes

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  • The complete genetic composition of a cell or a species  

    • Each living cell has a copy of that genome. This info is passed from cell to cell and from parent to offspring to yield new generations of cells and new generations of life. 

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  • A unit of heredity that contributes to the characteristics or traits of an organism. At the molecular level, a gene is composed of organized sequences of DNA that produce a functional product, either an RNA molecule or a protein 

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Prokaryotic Cells

Organisms having cells typically lacking a membrane-enclosed nucleus and cell compartmentalization; all members of the domains Bacteria and Archaea.

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One of the three domains of life; the other two are Archae and Eukarya. relatively small, cell sizes are usually range between 1 and 10 ųm in diameter. abundant being found in soil, water and even out digestive tracts; most bacterial species are not harmful to humans and play a vital role in ecology. Some species are pathogenic (can cause disease).

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  • One of the three domains of life; the other two are Bacteria and Eukarya. relatively small, cell sizes are usually range between 1 and 10 ųm in diameter. also widely found throughout the world, although they are less common than bacteria and often occupy extreme environments such as hot springs and deep-sea vents 

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Plasma membrane

  • The biomembrane that separates the internal contents of a cell from its external environment 

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The region of the cell that is contained within the plasma membrane

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A site in a bacterial cell where the genetic material (DNA) is located

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A structure composed of proteins and rRNA that provides the site where polypeptide synthesis occurs

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Cell Wall

 A relatively rigid, porous structure located outside the plasma membrane of prokaryotic, plant, fungai, and certain protist cells; provides support and protection

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  • An outer viscous covering surrounding a bacterium that traps water and helps protect bacteria from drying out. 

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  • Threadlike surface appendages that allow bacteria to attract to each other during conjugation or to move across surfaces

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Relatively long cell appendages that facilitate cellular movement or the movement of extracellular fluids

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  • One of the two categories into which all forms of life can be placed. The distinguishing feature of eukaryotes is cell compartmentalization, including a cell nucleus; includes protists, fungi, plants, and animals 

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A subcellular structure or membrane-bound compartment with its own unique structure and function

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  • A characteristic of eukaryotic cells in which many organelles separate the cell into different regions. Cellular compartmentalization allows a cell to carry out specialized chemical reactions in different places. 

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  • the simplest units of life, the smallest unit that satisfies all of the characteristics of living organisms 

    • The shape, size and organization of cells vary considerably among different species and even among different cell type of the same species 

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Plant Cells

  •  a collection of organelles similar to those found in animal cells. Additional structures found in plant cells but not animals cells include chloroplasts, central vacuole, and cell wall. Laack lysosomes and centrioles

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Liquid-liquid phase separation

  • The phenomenon in which aggregated solutes such as proteins and RNA molecules, separate from the bulk solvent and form a droplet 

    • Proteins and RNA molecules separate from the bulk solvent and form a droplet

      • The droplet has a spherical shape with a measurable surface tension and viscosity  

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Droplet Organelles

  • An organelle that is not surrounded by a membrane but exists as a a droplet formed by liquid-liquid phase separation 

    • The site for rRNA processing and the assembly of ribosomal subunits 

      • The organelles serve two purposes: first molecules are brought close together and can assemble into complexes (ribosomal subunits assemble within the nucleolus). Second the environment within the droplet is chemically different from the surrounding medium which may affect events such as RNA folding

      • Nucleolus is a droplet organelle because it behaves independent of the rest of the nucleus. 

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Multicellular Organism

  • Many organism such as animals and plants are multicellular a single organism is composed of many cells 

    • The cells of a multicellular organism are not all identical (skin cells, neurons, muscle cells)

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Differential Gene Regulation

  • The phenomenon in which the expression of genes differs under various environmental conditions and in specialized cell types. 

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  • The complete complement of proteins that a cell or an organism can make 

  • Certain proteins found in skin cells may not be produced in neurons. Genes can be regulated so that they are turned on only in certain cell types. 

  • Skin cells and neurons may produce the same protein but in different amounts due to gene regulation and to the rates at which a protein is synthesized and degraded 

  • The amino acid sequences of particular protein can vary in skin cells and neurons  

  • Skin cells and neurons may alter their proteins in different ways. After a protein is made, its structure may be changed in a variety of ways. Includes the covalent attachment of molecules such as phosphate and carbohydrates and the cleavage of a protein to a smaller size 

    • The proteomes of cells are largely responsible for producing the traits of organisms, such as the color of the iris of a person’s eye. 

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Surface Area and Volume Are Critical Parameters That Affect Cell Sizes and Shapes 

  • Ostrich eggs are a nearly universal characteristic of cells. Generally large organism obtain their large sizes by having more cells not by having larger cells.  

    • Most types of cell found in an elephant and a mouse are roughly the same size. The elephant has many more cells than a mouse 

    • Cells are small because of the interface between a cell and its extracellular environment

  • For cells to survive their plasma membrane must export waste products. Large cells require a greater amount of nutrient uptake and waste export.

    • The rate of transport of substances is limited by its surface area. (SA/V) (A=4πr2), (V=4/3πr3)

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  • The region of a eukaryotic cell that is inside the plasma membrane and outside the organelles

    • The term cytoplasm refers to the region enclosed by the plasma membrane. This includes the cytosol and the organelles. 

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  • The sum total of all chemical reactions that occur within an organism. Also, a specific set of chemical reactions occurring at the cellular level

    • Often involves a series of steps called a metabolic pathway 

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  • A protein that acts as a catalyst to speed up a chemical reaction in a cell.

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A metabolic pathway that results in the breakdown of larger molecules into smaller molecules. Such reactions are often exergonic

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  • A metabolic pathway that results in the synthesis of cellular molecules and macromolecules; requires an input of energy 

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How to make proteins

  •  amino acids are covalently connected to form a polypeptide, using the information within an mRNA called translation 

    • Translation of information occurs on ribosomes which are found in various locations in the cell. 

      • Some ribosomes float freely in the cytosol, others are attached to the outer membrane of the nuclear envelope or the endoplasmic reticulum membrane and others are found within the mitochondria or chloroplasts 

      • In order for transcription and translation to occur, mRNA leaves the nucleus through nuclear pores. Regulate what molecules go in and out to the ribosomes. 

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  • In eukaryotes, a network of three different types of protein filaments in the cytosol called microtubules, intermediate filaments, and actin filaments 

  • Found primarily in the cytosol as well as in the nucleus along the inner nuclear membrane. 

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  • A type of hollow protein filament composed of tubulin proteins that is part of the cytoskeleton and is important for cell shape, organization, and movement. 

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Intermediate filaments

A type of protein filament of the cytoskeleton that helps maintain cell shape and rigidity

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Actin filament

  • A thin type of protein filament composed of actin monomers that forms part of the cytoskeleton and supports the plasma membrane; plays a key role in cell strength, shape, and movement 

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  • Microtubules: 25 nm 

  • Intermediate filaments: 10nm 

  • Actin Filaments: 7nm 

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  • Microtubules: Hollow tubule 

  • Intermediate filaments: Twisted Filament 

  • Actin Filaments: Spiral filament 

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Protein composition

  • Microtubules: Hollow tubule composed of the protein tubulin 

  • Intermediate filaments: Can be composed of different proteins including keratin, lamin, and others that from twisted filaments

  • Actin filaments: Two intertwined strands composed of the protein actin 

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Common functions

  • Microtubules: Cell shape; organization of cell organelles; chromosome sorting in cell division; intracellular movement of cargo; cell motility (Cilia and flagella) 

  • Intermediate filaments: Cell shape; provide cells with mechanical strength; anchorage of cell and nuclear membranes 

  • Actin filaments: Cell shape; cell strength; muscle contraction; intracellular movement of cargo; cell movement (amoeboid movement); cell division in animal cells 

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  • Microtubules are long, hollow, cylindrical structures about 25 nm in diameter and composed of protein subunits called alpha and beta tubulin. The assembly of tubulin to form a microtubule results in a polar structure with a plus end and a minus end. 

    • Microtubules grow only at the plus end but can shorten at either the plus or minus end. 

    • It can oscillate between growing and shortening phases (dynamic instability)

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Dynamic Instability

  • The oscillation of a single microtubule between growing and shortening phases; important in many cellular activities, including the sorting of chromosomes during cell division. 

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Microtubule-organizing center (MTOC)

A site in a eukaryotic cell from which microtubules grow.

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  • A structure, often near the cell nucleus of eukaryotic cells, that forms a nucleating site for the growth of microtubules; also called the microtubule-organizing center

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  • A pair of structures within the centrosome of animal cells. Most plant cells and many protists lack centrioles 

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Intermediate Filaments

  • Another class of cytoskeletal filaments found in cells of many but not all animal species. 

  • Intermediate filaments proteins bind to each other in a staggered array to form a twisted, ropelike structure with a diameter of approximately 10 nm. Help maintain cell shape and rigidity. 

  • Microtubules and actin filaments readily lengthen and shorten in cells. 

  • Keratins are intermediate filaments in skin, intestinal, and kidney cells, where they are important for determining cell shape and providing mechanical strength. 

  • Keratinocytes are a major constituent of hair, nails, and the surface of your skin. Nuclear lamins form a network of intermediate filaments that line the inner nuclear membrane and provide anchor points for the nuclear pores. 

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Actin Filaments

  • The long thin fibers are approximately 7 nm in diameter. 

  • Microtubules actin filaments have plus and minus ends, and they are dynamic structures in which each strand grows at the plus end by the addition of acting monomers. The assembly process products a fiber composed of two strands of actin monomers that spiral around each other. 

    • Actin filaments play a key role in cell shape and strength. They tend to be highly concentrated near the plasma membrane

    • Actin filament support the plasma membrane and provide shape and strength to the cell 

      • The plus ends grow toward the plasma membrane and play a key role in cell shape and movement.

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a small rodlike structure, about 4–7 nanometers in diameter, present in numbers in the cytoplasm of many eukaryotic cells.

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Motor Proteins

Are a category of proteins that use ATP as a source of energy to promote various types of movements

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  • The site where ATP binds and is hydrolyzed to adenosine diphosphate (ADP) and inorganic phosphate (P1)

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  • The site that bends in response to ATP binding and hydrolysis. This bending is what causes movement to occur 

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  • An elongated region that is attached to other proteins or to other kinds of cellular molecules. Together, the hinge and tail make up a structure called the lever arm. 

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What the head region of a motor protein interacts with?

  • a cytoskeletal filament, a microtubule or actin filament. When ATP binds and is hydrolyzed, the motor protein interacts with the filament in a series of steps. The head of the motor protein is initially attached to a filament. The head detaches from the filament, and binds to another point farther along the filament. 

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Movement of Cargo

  •  The filament is fixed in place and the motor protein moves a cargo from one location to another. 

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Movement of a filament

  • The motor protein is fixed in place. The action of the motor protein moves the filament. 

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Bending of a filament

  • The motor protein and filament are both fixed in place due to linking proteins, so the action of the motor protein causes the filament to bend. 

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Cells and Flagella Allow Cells to Move

  • In certain kinds of eukaryotic cells microtubules and the motor protein dynein work together to produce the bending movements of cell appendages. 

    • Flagella are usually longer than cilia, and they are typically found singly or in pairs. 

  • Both flagella and cilia produce movement by generating bends that move along their length and push backward against the surrounding field. The flagellum of a sperm cell generates bends alternatively in each direction. 

    • Cilia are typically shorter than flagella and tend to cover all of the surface of a cell. 

      • Protists such as paramecia may have hundreds of cilia, which are spaced closely together and bend in a coordinated fashion to propel the organism through the water. 

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The internal structure of eukaryotic flagella and cilia, consisting of microtubules, the motor protein dynein, and linking proteins

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