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BIOL 1000
Julie Clark

Biology: chapter 2 notes Why it matters  Latin name cellulae, meaning ―small rooms‖—hence the origin of the biological term cell.  Robert Brown, an English botanist, noticed a discrete, spherical body inside some cells; he called it a nucleus.  Cells arise only from pre-existing cells by a process of division. Three profound generalizations, which together constitute what is now known as the cell theory: 1. All organisms are composed of one or more cells. 2.The cell is the basic structural and functional unit 
 of all living organisms. 3. Cells arise only from the division of pre-existing 
 cells. 2.1 Basic Features of Cell Structure and Function  Cells carry out the essential processes of life.  Contain highly organized systems of molecules, including the nucleic acids DNA and RNA, which carry hereditary information and direct the manufacture of cellular molecules.  Cells use chemical molecules or light as energy sources for their activities. Cells also respond to changes in their external environment by altering their internal reactions.  Cells duplicate and pass on their hereditary information as part of cellular reproduction.  Some types of organisms, including almost all bacteria and archaea; some protists, such as amoebas; and some fungi, such as yeasts, are unicellular.  Cells is a functionally independent organism capable of carrying out all activities necessary for its life.  In more complex multicellular organisms, including plants and animals, the activities of life are divided among varying numbers of specialized cells.  Organisms are potentially capable of surviving by themselves if placed in a chemical medium that can sustain them.  If cells are broken open, the property of life is lost: they are unable to grow, reproduce, or respond to outside stimuli in a coordinated, potentially independent fashion. 2.1a Cells Are small and are visualized using a microscope  All forms of life are grouped into one of three domains: the Bacteria, the Archaea, and the Eukarya.  Bacteria and archaea were grouped into a single domain: the Prokaryota (prokaryotes); however, this domain is no longer con- sidered to be accurate as recent research has shown that bacteria and archaea are not evolutionarily related.  Humans cannot see objects smaller than about 0.1 mm in diameter. The smallest bacteria have diam- eters of about 0.5 μm (a micrometre is one thousandth of a millimetre).  The cells of multicellular animals range from about 5 to 30 μm in diameter. Your red blood cells are 7 to 8 μm across—a string of 2500 of these cells is needed to span the width of your thumb- nail.  Plant cells range from about 10 μm to a few hundred micrometres in diameter.  To see cells and the structures within them we use microscopy, a technique for producing visible images of objects, biological or otherwise, that are too small to be seen by the human eye (Figure 2.4, p. 28).  The instru- ment of microscopy is the microscope.  The two common types of microscopes are light microscopes, which use light to illuminate the specimen (the object being viewed), and electron microscopes, which use electrons to illuminate the specimen.  Different types of micro- scopes give different magnification and resolution of the specimen.  Resolution depends primarily on the wavelength of light or electrons used to illuminate the specimen: the shorter the wavelength, the better the resolution.  Hence, electron microscopes have higher resolution than light microscopes.  Volume of cell determines how much activity it can do and surface area determines how many substances can travel in and out. By doubling the diameter of the cell, you multiply the volume by 8 but the SA by 4. As a result, there isn't enough exchange between materials for the amount of activity in the cell 2.1b Cells have a DNA – containing central region that is sounder by cytoplasm  All cells are bounded by the plasma membrane, a bilayer made of lipids with embedded protein mol- ecules (Figure 2.6).  The lipid bilayer is a hydrophobic barrier to the passage of water-soluble substances, but selected water-soluble substances can penetrate cell membranes through transport protein channels.  The selective movement of ions and water-soluble mol- ecules through the transport proteins maintains the specialized internal ionic and molecular environments required for cellular life.  The hereditary information is organized in the form of genes—segments of DNA that code for individual proteins.  The central region also contains proteins that help maintain the DNA structure and enzymes that duplicate DNA and copy its information into RNA.  All parts of the cell between the plasma membrane and the central region make up the cytoplasm. The cyto- plasm contains the organelles, the cytosol, and the cytoskel- eton.  The cytosol is an aqueous (water) solution con- taining ions and various organic molecules.  The cytoskeleton is a protein-based framework of filamentous structures that, among other things, helps maintain proper cell shape and plays key roles in cell division and chromosome segregation from cell generation to cell generation.  Cell’s vital activities occur in the cytoplasm, including the synthesis and assembly of most of the molecules required for growth and reproduction and the conversion of chemical and light energy into forms that can be used by cells. 2.1c cells occur in prokaryotic and eukaryotic forms, each with distinctive structures and organization  There are two fundamentally different types of cells: prokaryotic (pro = before; karyon = nucleus) and eukaryotic.  The term prokaryote to describe a unique group of evolutionarily related organisms has fallen out of use by microbiologists as bacteria and archaea are seen as evolutionarily distinct.  The term prokaryotic cell is still used as it refers not to a single group of organisms but rather to a particular cell architecture, that is, one lacking a nucleus.  Within the prokaryotic cell that is a characteristic of both bacteria and archaea, the DNA-containing central region of the cell, the nucleoid, has no boundary membrane separating it from the cytoplasm. 2.2-prokaryotic cells  3 types of prokaryotic cell structures include - rodlike, spherical and spiral  in prokaryotic cells such as bacteria and archae, the DNA is located in the nucleoid (central DNA containing region)  prokaryotic chromosome - single, tangled DNA  In prokaryotes, the DNA is transcribed into mRNA which is then turn into amino acid sequenes thanks to the ribosomal rRNA.  cell walls provide rigidity for the cell prokaryote and the external layer is made of glycocalyx, a polysaccharide layer, that protects the cell and allows attachment with other cells. looseley associated glycocalyx = silme layer whereas strongly associate glycocalyx = capsule  plasma membrane contains system to capture light energy and produce ATP  cytoskeleton in prokaryotes serve similar function to those in eukaryotic cells  flagella help both archae and bacteria move. However, they are different in structure  pili located on cell surface and help them attach to other cells 2.3b The Eukaryotic Nucleus Contains Much More DNA Than the Prokaryotic Nucleoid  The nucleus is separated from the cytoplasm by the nuclear envelope, which consists of two membranes, one layered just inside the other and separated by a narrow space  A net- work of protein filaments called lamins lines and reinforces the inner surface of the nuclear envelope in animal cells.  Lamins are a type of intermediate filament  A nuclear pore complex is a large, octagonally symmetrical, cylindrical structure formed of many types of proteins, called the nucleoporins.  Probably the largest protein complex in the cell, it exchanges components between the nucleus and cytoplasm and prevents the transport of material not meant to cross the nuclear membrane.  A nuclear pore—is the path for the assisted exchange of large molecules such as proteins and RNA molecules with the cytoplasm, whereas small molecules simply pass through unassisted.  A protein or RNA molecule (called the cargo) associates with a transport protein acting as a chaperone to shuttle the cargo through the pore.  The enzymes for replicating and repairing DNA—must be imported into the nucleus to carry out their functions.  A specific protein in the cytosol recognizes and binds to the signal and moves the protein containing it to the nuclear pore complex, where it is transported through the pore into the nucleus.  The liquid or semi-liquid substance within the nucleus is called the nucleoplasm. Most of the space inside the nucleus is filled with chromatin, a combina- tion of DNA and proteins.  eukaryote is distributed among several to many linear DNA molecules in the nucleus. Each individual DNA molecule with its associated proteins is a eukaryotic chromosome.  The terms chromatin and chromo- some are similar but have distinct meanings.  Chromatin refers to any collection of eukaryotic DNA molecules with their associated proteins.  Chromosome refers to one complete DNA molecule with its associated proteins.  A eukaryotic nucleus also contains one or more nucleoli (singular, nucleolus), which look like irregular masses of small fibres and granules  Within the nucleolus, the information in rRNA genes is copied into rRNA molecules, which combine with proteins to form ribosomal subunits.  The ribosomal subunits then leave the nucleoli and exit the nucleus through the nuclear pore complexes to enter the cyto- plasm, where they join on mRNAs to form complete ribosomes.  Genes for most of the proteins that the organism can make are found within the chromatin, as are the genes for specialized RNA molecules such as rRNA molecules. 2.3c Eukaryotic Ribosomes Are Either Free in the Cytosol or Attached to Membranes  Eukaryotic ribosomes are larger than either bacterial or archaeal ribosomes; they contain 4 types of rRNA molecules and more than 80 proteins.  Their function is identical to that of prokaryotic ribo- somes: they use the information in mRNA to assemble amino acids into proteins.  Proteins made on free ribosomes in the cytosol may remain in the cytosol; pass through the nuclear pores into the nucleus; or become parts of mitochondria, chloroplasts, the cytoskeleton, or other cytoplasmic structures.  Proteins that enter the nucleus become part of chromatin, line the nuclear envelope (the lamins), or remain in solution in the nucleoplasm.  Many ribosomes are attached to membranes. Some ribosomes are attached to the nuclear envelope, but most are attached to a network of membranes in the cytosol called the endoplasmic reticulum 2.3d An Endomembrane System Divides the Cytoplasm into Functional and Structural Compartments  Eukaryotic cells are characterized by an endomem- brane system (endo = within), a collection of inter- related internal membranous sacs that divide the cell into functional and structural compartments. The endomembrane system has a number of functions, including the synthesis and modification of proteins and their transport into membranes and organelles or to the outside of the cell, the synthesis of lipids, and the detoxification of some toxins.  The membranes of the system are connected either directly in the physical sense or indirectly by vesicles, which are small mem- brane-bound compartments that transfer substances between parts of the system.  The components of the endomembrane system include the nuclear envelope, endoplasmic reticulum, Golgi complex, lysosomes, vesicles, and plasma membrane.  Endoplasmic Reticulum. The endoplasmic reticulum (ER) is an extensive interconnected network (reticulum = little net) of membranous channels and vesicles called cisternae (singular, cisterna). Each cisterna is formed by a single membrane that surrounds an enclosed space called the ER lumen (Figure 2.12). The ER occurs in two forms: rough ER and smooth ER, each with spe- cialized structure and function.  The rough ER (see Figure 2.12a) gets its name from the many ribosomes that stud its outer surface.  Chemical modifications of these proteins, such as addition of carbohydrate groups to produce glyco- proteins, occur in the lumen. The proteins are then delivered to other regions of the cell within small ves- icles that pinch off from the ER, travel through the cytosol, and join with the organelle that performs the next steps in their modification and distribution.  The smooth ER (see Figure 2.12b) is so called because its membranes have no ribosomes attached to their surfaces. The smooth ER has various functions in the cytoplasm, including synthesis of lipids that become part of cell membranes. In some cells, such as those of the liver, smooth ER membranes contain enzymes that convert drugs, poisons, and toxic by- products of cellular metabolism into substances that can be tolerated or more easily removed from the body.  The rough and smooth ER membranes are often connected, making the entire ER system a continuous network of interconnected channels in the cytoplasm. The relative proportions of rough and smooth ER reflect cellular activities in protein and lipid synthesis. Cells that are highly active in making proteins to be released outside the cell, such as pancreatic cells that make digestive enzymes, are packed with rough ER but have relatively little smooth ER.  The Golgi complex con- sists of a stack of flattened, membranous sacs (without attached ribosomes) known as cisternae.  The complex looks like a stack of cup
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