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Chapter 7

Textbook and Class Notes Collaborated - Week 3 - Unit 2 - Chapter 7 - BIO 1A03
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Department
Biochemistry
Course
BIOCHEM 2B03
Professor
Margaret Fahnestock
Semester
Fall

Description
Bio 1A03 Unit Two: Cell Structure and Function Chapter 7: Inside the Cell 7.1 What’s Inside the Cell?  The cell is the basic unit of structure and function in living organisms  There are two fundamental cell types (according to morphology): Prokaryotic Cells and Eukaryotic Cells Prokaryotic Cells  Archae and Bacteria  Most prokaryotic cells are relatively smaller in size compared to eukaryotic cells  Are structurally simpler in design  Plasma membrane surrounds the cytoplasm, which collectively refers to the contents of the cell  Have few or no subdivisions delimited by internal membranes  Interestingly, recent research has identified membrane bound organelles or cytoskeletons of protein in a few prokaryotic species  Do not contain a nucleus  Figure 7.1, page 126; Prokaryotic Cell  The cell/plasma membrane – consists of a phospholipid bilayer and proteins that either span the bilayer or attach to one side  Cytoplasm – the contents of a cell collectively o Contains high concentration of solutes, in most habitats it is hypertonic relative to the surrounding environment o When it is hypertonic – water enters the cell via osmosis and makes the cell volume expand  Cell wall – tough and fibrous layer that surrounds the plasma membrane; resists pressure from expanding cytoplasm volume; protects the organism and gives it shape and rigidity  Glycolipids – lipids that contain carbohydrate groups  Chromosome – singular, circular, consists of a large DNA molecule associated with a small number of proteins o DNA molecule contains information – contains genes (a segment of DNA that contains the information for building an RNA molecule or a polypeptide) o Proteins provide structural support for the DNA o Found in a localized area of the cell called the nucleoid  Nucleoid is usually found in the center of the cell and typically represents about 20 percent of the cell’s total volume o To fit into the cell, the DNA double helix coils on itself with the aid of enzymes to form the highly compact, “supercoiled” structure – resemble a string that has been held at either end and then twisted until coils back upon itself  Figure 7.3, page 127; Bacterial DNA Supercoiled o Cells may also contain about a hundred, small, usually circular, supercoiled DNA molecules called plasmids  Plasmids contain genes but are physically independent of the main, cellular chromosome  Genes carried by plasmids are not required under normal circumstances; instead they help cells adapt to unusual circumstances (such as the sudden presence of a poison in an environment)  Plasmids can be considered auxiliary genetic elements  Ribosomes – manufacture proteins o Bacterial ribosomes are complex structures consisting of a total of three distinct RNA molecules and over 50 different proteins o These molecular components are organized into two major structural elements, called the large subunit and small subunit  Figure 7.4, page 127; Bacterial Ribosome  Flagella (sing. flagellum) 0 rotate to power swimming in aquatic species o Not all bacterial species have flagella  Photosynthesis – the suite of chemical reaction responsible for converting the energy in sunlight into chemical energy stored in sugars Bio 1A03 o The photosynthetic membranes observed in prokaryotes contain the enzymes and pigment molecules required for these reactions to occur and develop as infoldings of the plasma membrane o In other cases, vesicles pinch off as the plasma membrane folds in o In some cases, flattened stacks of photosynthetic membrane form from the infolded sections of the plasma membrane  Figure 7.4,page 128; Photosynthetic Membrane  Organelles – membrane-bound compartment in the cytoplasm that contains enzymes or structures specialized for a particular function o One type of bacterial organelle is specialized for storing calcium ions o Another type contains crystals of the mineral magnetite, which function like a compass needle to help cells orient themselves in a magnetic field and swim in a directed way  Bacteria and Archae contain long, thin fibers that serve a structural role inside the cell o Protein Fibres – these filaments are essential foe cell division to take place, or they help maintain cell shape; form the bases of the cytoskeleton Eukaryotic Cells  Fungi, Protists, Plants and Animals  Are relatively larger in size compared to prokaryotic cells  Contain a nucleus  Figure 7.6, page 129; Animal and Plant Cells  The large size poses a problem – large molecules cannot diffuse across a large volume quickly o Eg/ ATP is used up on one side of the cell, ATP from the other side of the cell would have to diffuse to that location  solved by compartmentalization  Compartmentalization – offers to key advantages o Incompatible chemical reactions can be separated  Eg/ new fatty acids can be synthesized in one organelle while excess or damaged fatty acids are degraded and recycled in different organelles o The efficiency of chemical reactions is increased  First the substrates required for particular reactions can be localized and maintained at high concentration within organelles  Second, if the substrates are used up in a particular part of the organelle, hey can be replaced by substrates that have only a short distance to diffuse  Third, groups of enzymes that work together an be clustered on internal membranes instead of floating free in the cytoplasm  When the product of a reaction is the substrate for a reaction catalyzed by another enzyme, clustering the enzyme increases the speed and efficiency of a reaction sequence Location of DNA Internal Membranes Cytoskeleton Overall Size and Organelles Bacteria and Archae In nucleoid (not Extensive internal Limited in extent Usually small membrane bound) membranes only in relative to relative to Plasmids also photosynthetic eukaryotes eukaryotes common species Range from 1-10 μm Limited types and in diameter numbers of organelles Eukaryotes Inside nucleus Large numbers of Extensive – usually Most are larger than (membrane bound) organelles found throughout prokaryotes Plasmids extremely Many types of volume of cell Range from 5-100 rare organelles μm in diameter  Nucleus o Surrounded by a nuclear envelope (a double membrane) Bio 1A03  Nuclear Envelope – is studded with pore-like openings, and its inside surface is associated with fibrous proteins that form he nuclear lamina  Nuclear Lamina – a lattice-like sheet that stiffens the structure and maintains its shape o Chromosomes do not float free inside the nucleus – each chromosome occupies a distinct area and is attached to the nuclear lamina in at least one location o Nucleolus – rRNA synthesis and ribosome assembly o Contains chromosomes (chromatin: DNA & histone proteins), which carry the cells genetic information o Figure 7.7, page 130; Nucleus  Ribosomes o Some are present in the cytosol (fluid compartment of the cell’s cytoplasm)  Figure 7.8, page 131 o Eukaryotic ribosomes are composed of RNA and protein o Consists of small (one RNA molecule) and large (three RNA molecules) subunits o When two subunits come together, they form a complex molecular machine that synthesizes proteins o Not enclosed by membrane  Rough Endoplasmic Reticulum (rough ER) o Figure 7.9, page 131; Rough ER o Consists of a network of membrane-bound tubules and sacs o Has ribosomes studded into the cytoplasmic surface of the membranes, where secreted and transmembrane proteins are manufactured o Enzymes, which fold and modify the proteins, are present inside the rough ER’s lumen o From the nuclear envelope, the layers of sacs that make up the ER extend into the cytoplasm o The ribosomes associated with the rough ER are responsible for synthesizing proteins that will be inserted into the plasma membrane, secreted to the cell exterior or shipped to the lysosome o As proteins are being manufactured by ribosomes, they move to the interior of the sac-like component of the rough ER o Rough ER products are destined for transport to various distant destinations – often to the surface of the cell or beyond  Golgi Apparatus o Figure 7.10, page 131; Golgi Apparatus o Products from the rough ER pass through the Golgi apparatus before they reach their final destination o Consists of cisternae (flattened, stacked sacs); processes rough ER’s products o The cis face receives products from the RER; closest to the rough ER and nucleus o The trans face sends products to their destinations; oriented toward the plasma membrane o Micrographs often show vesicles on either side of the Golgi stack, which carry proteins or other products to and from the organelle  Smooth Endoplasmic Reticulum (smooth ER) o Figure 7.11, page 132; Smooth ER o Lacks ribosomes in the cytoplasmic surface of the membranes o Enzymes are present, which are involved in several functions such as lipid synthesis, detoxification of harmful materials, and calcium ion reserves  Endomembrane System – consists of the Golgi Apparatus, lysosomes, and the endoplasmic reticulum  Peroxisomes o Figure 7.12, page 133; Peroxisomes o Are globular, single-membrane bond organelles o Locations of oxidative reactions (remove electrons from atoms and molecules) o Contain catalase, which is an enzyme that detoxifies hydrogen pero2i2e (H O ) by converting it into oxygen and water o Eg/ Liver Cells – peroxisomes oxidize an array of toxins, including ethanol, products are excreted or used in other reactions o Eg/ Enzymes that catalyze oxidation of fatty acids which produces molecules that include acetyl CoA, which is used for the synthesis of important molecules elsewhere in the cell o In plant leaves, glyoxisomes are packed with enzymes that convert one of the products of photosynthesis into a sugar that can be used to store energy for the cell Bio 1A03 o Seeds do not perform photosynthesis and lack glyoxisomes – instead their peroxisomes oxidize fatty acids to yield glucose, which is used in the young plant as it grows  Lysosomes o Figure 7.13, page 133; Lysosomes o Are single-membrane bound organelles o Participate in solid waste processing and the storage of materials o Have an acidic interior, because proton pumps in the lysosome membrane import enough hydrogen ions to maintain a pH of 5.0 o Possess digestive enzymes (acid hydrolases) to breakdown macromolecules  Acid Hydrolases – about 40 different enzymes o Referred to as vacuoles in plants, fungi and certain other groups of cells o Phagocytosis – “eat-cell-act”  Plasma membrane of a cell surrounds a smaller cell or a food particle and engulfs it, forming a structure called a phagosome or food vacuole  This structure is delivered to a lysosome where it is taken in and digested  Figure 7.14a, page 133; Phagocytosis o Autophagy – “same eating”  Damaged organelles are surrounded by a membrane and delivered to a lysosome  There the components are digested and recycled  Figure 7.14b, page 133; Autophagy o Receptor-Mediated Endocytosis  Figure 7.15, page 134; Receptor-Mediated Endocytosis  Begins when macromolecules outside the cell bind to membrane proteins that act as receptors  More than 25 distinct receptors have now been characterized, each specialized for responding to a different macromolecule  Once binding occurs, the plasma membrane folds in and pinches off to form a membrane-bound vesicle called an early endosome  Early endosomes undergo a series of processing steps that include the receipt of digestive enzymes from the Golgi Apparatus and the activation of proton pumps that gradually lower their pH  Early endosomes undergo a gradual maturation process that may lead to the formation of a late endosome and eventually a fully functioning lysosome o Phagocytosis, autophagy, receptor-mediated endocytosis – result; molecules hydrolyzed o Amino acids, nucleotides, sugars and other molecules that result from acid hydrolysis leave the lysosome via transport proteins in the organelle membrane – once in the cytoplasm they can be reused o Not all materials that are surrounded by membrane and taken into the cell end up in lysosomes o Endocytosis – “inside-cell-act”  Any pinching off of the plasma membrane that results in the uptake of material from outside the cell  Can occur in phagocytosis, receptor-mediated endocytosis and pinocytosis o Pinocytosis – “drink-cell-act”  Brings fluid into the cytoplasm via tiny vesicles that form from infoldings of the plasma membrane  The fluid inside these vesicles is not transported to lysosomes, but is used elsewhere in the cell o Most of the macromolecules that collect in early endosomes are selectively removed and used long before the structure becomes a lysosome  Vacuoles o Figure 7.16, page 134; Vacuoles o Found in fungi and plants o Occupy a large portion inside the cell (can take up to 80% of a plant cells volume) o Serves are storage depots for water (maintains the cells normal volume), ions (such as Cl and K ) and proteins o In plant cells, vacuoles may contain pigments or may house noxious substances for chemical defense against herbivores Bio 1A03  Mitochondria o Figure 7.17, page 135; Mitochondria o Sites of ATP production o Possess two membranes (the inner membrane has folds or cristae, the outer membrane is smooth and defines the organelles surface) o Mitochondrial Matrix – solution inside the inner membrane o Most of the enzymes and molecular machines responsible for synthesizing ATP are embedded in the membranes of the cristae or suspended in the matrix o Possess their own mitochondria DNA, produce their own ribosomes o Are capable of dividing independent of cell division  Chloroplasts o Have a double membrane (both inner and outer membranes are smooth) o Inner membrane houses thylakoids (flattened sacs stacked in grana) – contain many of the pigments, enzymes and molecular machines responsible for converting light energy into carbohydrates o Are the sites of photosynthesis o Critical enzymes and substrates are found outside the thylakoids in the stroma o Figure 7.18, page 135; Chloroplasts  Cytoskeleton o Extensive system of protein fibers o Contain several distinct types of proteins and fibers o Gives the cell its shape and structural stability, cytoskeletal proteins are involved in moving the cell itself and in moving materials within the cell  Cell Walls o Cell walls are stiff to protect the cells o In fungi, algae and plant cells o Rods or fibers composed of carbohydrate run through a stiff matrix made of other polysaccharides and proteins o Secondary cell wall – made up of lignin and cellulose fibers  Lignin – forms a branching, cage-like network that is almost impossible for enzymes to attack  Make up most of the material of wood o Figure 7.19, page 135; Cell Wall How Does Cell Structure Correlate with Function  An organelles membrane and its complement of enzymes correlate closely with its function o Table 2, page 137  Cell structure is related to size, the number of organelles, and the types or related to specialized function o Figure 7.20, page 138; Structure Correlated With Function o Pancreatic Cell  Function: Secretes digestive enzyme, specialized for the manufacture and export of digestive enzyme  Structure: Packed with rough ER and Golgi o Testis Cell  Function: Manufactures lipid soluble signals (testosterone)  Structure: Dominated by smooth ER, where processing of steroids and other lipids takes place o Leaf Cell  Function: Absorption of sunlight for the conversion into chemical energy production (photosynthesis)  Structures: Contains hundreds of chloroplasts o Root Cell  Function: Carbohydrate (sugar) storage  Structures: The tuber cell has a prominent large storage vacuole filled with carbohydrate How do the following tools assist in the examination of cells and other organelles?  Light Microscopy and Electron Microscopy Bio 1A03 o Light and electron microscopes o Allow researchers to see cells at increasingly high magnification and increasingly better resolution o Allow biologists to characterize the basic size and shape of organelles and where they occurred in the cell o Limitation – only a “snap shot” of the cell being observed  Differential Centrifugation o Figure 7.21 o Makes it possible to isolate particular cell components and analyze their chemical composition o Based on breaking cells apart to create a complex mixture and then separating components in a centrifuge o The individual parts of a cell can then be purified and studied in detail, in isolation from other parts of the cell o Separates cell components by spinning samples in a solution that allows molecules and other cell components to separate according to their density or size and shape 1. Release the organelles and cell components by breaking the cell apart  Put cell into hypotonic solution  Expose cell to high frequency vibration  Treat cells with a detergent  Grind them up 2. The pieces of plasma membrane broken up quickly reseal to form small vesicles, often trapping cell components inside 3. Ell extract/homogenate – The solution that results from the homogenization step is a mixture of these vesicles, free floating macromolecules released from the cells and organelles 4. When a cell homogenate is placed in a centrifuge tube and spun at high speed, the components that are in solution tend to move outward 5. In response to this outward-directed force, the solution containing the cell homogenate exerts a centripetal (“center-seeking”) force that pushes the homogenate away from the bottom of the tube
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