UNIT 3 – CELL BIOLOGY

THEMES COVERED:

  1. SCIENCE AS A PROCESS: The discovery and early study of cells progressed with the invention and improvement of the microscopes.
  1. EVOLUTION: The matching machinery of all eukaryotic cells evidences a broad evolutionary connection between eukaryotes.
  1. RELATIONSHIP OF STRUCTURE TO FUNCTION: Many of the cell organelles show clear correlation between structure and function.

8. SCIENCE AND TECHNOLOGY, AND SOCIETY: Advances in cancer research depend on progress in our basic understanding of how cells work.

CHAPTER 6 – A TOUR OF THE CELL

OBJECTIVE QUESTIONS:

How We Study Cells

  1. Distinguish between magnification and resolving power.
  2. Describe the principles, advantages, and limitations of the light microscope, transmission electron microscope, and scanning electron microscope.
  3. Describe the major steps of cell fractionation and explain why it is a useful technique.

A Panoramic View of the Cell

4. Distinguish between prokaryotic and eukaryotic cells.

5. Explain why there are both upper and lower limits to cell size.

6. Explain the advantages of compartmentalization in eukaryotic cells

The Nucleus and Ribosomes

  1. Describe the structure and function of the nuclear envelope, including the role of the pore complex.
  2. Briefly explain how the nucleus controls protein synthesis in the cytoplasm.
  3. Explain how the nucleolus contributes to protein synthesis.
  4. Describe the structure and function of a eukaryotic ribosome.
  5. Distinguish between free and bound ribosomes in terms of location and function.

The Endomembrane System

  1. List the components of the endomembrane system, and describe the structure and functions of each component.
  2. Compare the structure and functions of smooth and rough ER.
  3. Explain the significance of the cis and trans sides of the Golgi apparatus.
  4. Describe three examples of intracellular digestion by lysosomes.
  5. Name three different kinds of vacuoles, giving the function of each kind.

Other Membranous Organelles

  1. Briefly describe the energy conversions carried out by mitochondria and chloroplasts.
  2. Describe the structure of a mitochondrion and explain the importance of compartmentalization in mitochondrial function.
  3. Distinguish among amyloplasts, chromoplasts, and chloroplasts.
  4. Identify the three functional compartments of a chloroplast. Explain the importance of compartmentalization in chloroplast function.
  5. Describe the evidence that mitochondria and chloroplasts are semiautonomous organelles.
  6. Explain the roles of peroxisomes in eukaryotic cells.

The Cytoskeleton

  1. Describe the functions of the cytoskeleton.
  2. Compare the structure, monomers, and functions of microtubules, microfilaments, and intermediate filaments.
  3. Explain how the ultrastructure of cilia and flagella relates to their functions.

Cell Surfaces and Junctions

  1. Describe the basic structure of a plant cell wall.
  2. Describe the structure and list four functions of the extracellular matrix in animal cells.
  3. Explain how the extracellular matrix may act to integrate changes inside and outside the cell.
  4. Name the intercellular junctions found in plant and animal cells and list the function of each type of junction.

I. OVERVIEW (The Cell Theory):

  • All organisms are made up of cells
  • Cells are the simplest collection of matter that can live – the basic units of structure and function in living organisms
  • All cells are related by their descent from earlier cells, however, they were modified in may different ways during the long evolutionary history of life

II. MICROSCOPY AND OTHER TOOLS

  1. Light microscope:
  • Visible light is passed through the specimen and then through glass lenses. The lenses refract the light that he image is magnified and projected into the eye or onto a photographic film or digital sensor.

YOU MUST KNOW THE PARTS OF THE MICROSCOPE

  • Two important parameters of light microscopes:
  • Magnification – the ratio of an object’s image size to its real size (to get it, multiply the magnification of the objective lens and the eyepiece) – light microscopes are most effective up to X1000 of magnification
  • Resolution – the measure of the clarity of the image (the minimum distance that still distinguishes two points as separate). The maximum resolution of light microscopes is about 200 nm.
  1. Electron microscope (EM)
  • Focuses a beam of electrons through a specimen or onto its surface and is able to have a resolution of about 0.002 nm.
  • The two basic types of electron microscopes:
  • Scanning electron microscopes (SEM) –excellent to study the surface of the specimen that has to be coated with gold. Provides a three dimensional images of dead specimens.
  • Transmission electron microscope (TM) –Excellent device to study the internal structure of the specimen that must be stained with heavy metals. The specimen also must be dead. Gives two-dimensional images.
  1. Cell Fractionation (Centrifuges)
  • Cell Fractionation – taking cells apart and separate the major organelles from one another by their different densities and size.
  • This procedure is done by centrifuges. Ultracentrifuges are the most powerful ones of these machines that can apply forces that are 1 million times the force of gravity.

III. PROKARYOTES AND EUKARYOTES

  • All cells contain the same general features such as a plasma membrane, cytosol where the organelles are found, chromosomes that carry DNA and all of them have ribosomes to perform protein synthesis.
  • Three structural units are found in every cell:
  • Plasma membrane
  • Nucleus (nucleoid)
  • Cytoplasm
  • Prokaryotes – single celled organisms in which the DNA is concentrated around a nucleoid region but they are lacking a membrane that separates the DNA from the rest of the cell. Many other organelles are also missing. Size: 1-10 μm. Two domains of prokaryotes are Bacteria and Archaea.
  • Eukaryotes – have true nuclei that are bounded by a nuclear envelope. The region between the nucleus and the cell membrane is called cytoplasm (prokaryotes also have it). These cells also have a large number of organelles. Size: 10 – 100 μm.
  • The size differences are the result of the various metabolic requirements. Cells cannot grow larger than the speed of gas exchange and nutrient – waste exchange between the border and the inside of the cell. Organelles’ compartmentalization helps this process in eukaryotes, so they can have a larger cell. The surface to volume ratio is a factor that will limit cell size.

IV. THE NUCLEUS

  • The nucleus contains most of the genes of an eukaryotic cells (some genes are found in the mitochondria and chloroplasts)
  • It is enclosed by the nuclear envelope – a double membrane, each with a phospholipid bilayer and proteins. The envelope also contains pores that are lined with a pore complex of proteins. This complex regulates what enters and leaves the cell.
  • The nuclear side of the envelope is lined by a nuclear lamina (network of protein filaments) that extend inward into the nuclear matrix.
  • Chromosomes – tightly packed DNA are found in the nucleus (46 for humans or 23 pairs, egg and sperm cells have half)
  • Nucleolus – densely stained granules and fibers in the center of a nondividing nucleus that assembles rRNA and its protein components to form the large and small subunit of ribosomes.

V. RIBOSOMES

  • Very small particles that are made up of rRNA and proteins. They are assembled from a small and large subunit.
  • Some ribosomes are free floating in the cytoplasm while others are bound to the nuclear envelope or to the endoplasmic reticulum. Free ribosomes make proteins that function in the cytoplasm, while bound ribosomes make proteins that either are attached to membranes or are packaged into membrane structures.

VI. THE ENDOMEMBRANE SYSTEM

  • Endomembrane system – many different membranes in the cytoplasm of an eukaryotic cell that carry out a wide range of functions. Each membrane is related to the others by either direct contact or by exchange of materials through vesicles
  • This system includes the endoplasmic reticulum, nuclear envelope, Golgi apparatus, lysosomes, vacuoles, and even the cell membrane
  1. The Endoplasmic Reticulum
  • An extensive network of tubules and sacs (cisternae) that is continuous with the nuclear envelope
  • Rough endoplasmic reticulum (RER) – exists as flattened, fluid-filled, membrane sacs that are interconnected. Its appearance is due to the large number of ribosomes on its surface. Almost all of the proteins of the cell are entered through a pore into the lumen of the RER where they are folded into their 3D shape and other nonprotein parts are attached to them. RER also provides catalytic surfaces for some of the chemical activities of the cell. The proteins are than packaged into transport vesicles and moved to various parts of the cell or out of the cells (secretory proteins). The rough ER is also the main membrane factory of the cell where membrane proteins and phospholipids are made.
  • Smooth endoplasmic reticulum (SER) – lacks ribosomes and has a more tubular surface. Participates in synthesis of lipids (oils, phospholipids, sterols), metabolism of carbohydrates, detoxification of drugs and poisons by making them more water soluble so they can be easily flushed through the body. SER is also important in storing calcium ions that are vital for normal nerve and muscle function.
  1. The Golgi Apparatus

  • Vesicles ship many of the products of the endoplasmic reticulum here for further processing. This is the manufacturing, storing and shipping center of the cell. Secretory cells are especially rich in Golgi apparatus.
  • It is made up of a stack of flattened membranous sacs (cisternae) that are surrounded by transport vesicles.
  • The Golgi apparatus has a distinct polarity because of its different molecular composition. The cis face of the apparatus is the receiving end that is located near the ER. Vesicles coming from the ER empty their contents on the cis end.
  • Molecules are modified during their trip from the cis to the trans end of the Golgi apparatus. Molecules that are modified here include carbohydrates, phospholipids and membrane proteins. Also molecular identification tags are frequently added to molecules here.
  • The trans end is the shipping end of the Golgi that gives rise to new vesicles and ship molecules to various other parts of the cell.
  • Some polysaccharides (pectin) that are released by the cell are also made here in the Golgi apparatus.
  1. Lysosomes

  • A lysosome is a membraneous sac of hydrolytic enzymes that an animal cell uses to digest all kinds of macromolecules. These enzymes work best in an acidic environment. Large amount of these enzymes leaking out into the cytoplasm can destroy the cell.
  • Lysosomes carry out intracellular digestion for a variety of reasons:
  • Digest food particles taken in by phagocytosis
  • Break down old cell organelles and recycle some of their components – autophagy
  • Some diseases result when the lysosomes lack hydrolytic digestion enzymes and the cell overcomes with indigestible substances (Tay-Sachs disease)
  1. Vacuoles
  • Plant and fungi cellshave one or several vacuoles.
  • Food vacuoles – formed by phagocytosis
  • Contractile vacuoles –pump excess water out of the cell to maintain stable water and salt balance (unicellular animals can have it as well)
  • Central vacuoles – found in mature plant cells and enclosed by a membrane called tonoplast. The large central vacuole forms from the fusion of smaller vacuoles. Because of the selective permeability of the tonoplast, the vacuole has a different solute composition than the cytoplasm. The central vacuole can act as a storage compartment of organic or inorganic substances, can be a pigment storage place and result in various colors of flowers or can assemble poisons to protect the plant. Their enlargement can grow plant cells.

VII. ENERGY PROCESSING ORGANELLES

  • In eukaryotic cells mitochondria and chloroplasts are the organelles that convert energy to forms that cells can use for work. Both of these organelles are enclosed by a double membrane system and most of their proteins are made by free moving ribosomes that are not attached to the ER or by ribosomes that are inside of these organelles. They both also have their own DNA that program the synthesis of their proteins.
  • Peroxisomes – oxidative organelles that are also not part of the endomembrane system
  1. Mitochondria
  • Found in almost all eukaryotic cells, their numbers correlate to the cell’s level of metabolic activity. They are actively moving and dividing organelles that also change shape easily and frequently.
  • Label and draw the structure by using the figure above
  • The matrix of the mitochondrion contains many different enzymes that are mostly related to cellular respiration including ATP synthase, an enzyme that makes ATP molecules and is imbedded into the inner membrane.
  1. Chloroplasts
  • Part of the family of plastids:
  • Amyloplast – stores starch
  • Chromoplast – stores colored pigments of fruits and flowers
  • Chloroplast – contains the green pigment chlorophyll, photosynthetic enzymes and other molecules that are necessary for photosynthesis.
  • Label and draw the structure by using the picture above
  • The fluid outside the thylacoids contains enzymes, DNA.
  • Chloroplasts are the main organs of photosynthesis.
  • They are also actively moving in the cell, changing shape and divide.
  1. Peroxisomes
  • A single membrane organelle that contains powerful oxidative enzymes that transfer hydrogen from various substances to oxygen and produce hydrogen peroxide.
  • They can break fatty acids down, before the breakdown products enter the mitochondria for cellular respiration, they can detoxify alcohol and other poisons.
  • They contain catalase enzyme that breaks down H2O2 to eventually produce water.

VIII. THE CYTOSKELETON

  • Cytoskeleton is a network of fibers that extend throughout the cytoplasm. It plays a major role in organizing the structures and activities of the cell.
  • It is composed of three kinds of structures:
  • Microtubules
  • Microfilaments
  • Intermediate filaments
  • Functions of the cytoskeleton:
  • Supports the cell and maintains its shape
  • Provides anchorage for many cell organelles and enzyme molecules
  • Involved in many kinds of movements of the cell itself or parts of it. They work together with motor proteins to accomplish this motion
  • They also perform the streaming of the cytoplasm
  • Regulate biochemical processes in the cell
  1. Microtubules
  • Found in the cytoplasm of all eukaryotic cells
  • Hollow rods, 25 nm in diameter and about 200nm – 25 μm in length
  • Their wall is constructed from a globular protein called tubulin that is composed of two different polypeptide chains (dimmers)
  • These tubulin dimmers can be taken apart and rearranged again in a new location in the cell
  • Microtubules shape and support the cell and form tracks to move motor proteins
  • Centrosomes and centrioles – the centrosome is a microtubule organizing center. In the centrosome of animal cells are a pair of centrioles that are each composed of nine triplets of microtubules – these duplicate before the cell divides
  • Cilia (sing. Cilium) and Flagella (sing. Flagellum) – Located outside of the cells, these organelles move the cell or can move substances on the surface of the cell. Found in many unicellular organisms such as Euglena (flagellum) and Paramecium (cilia) or in many cells of multicellular organisms (sperm cells, cells of the oviduct, windpipe etc). Cilia are usually short and there are many of them on the cell’s surface while flagella are fewer but longer. Cilia has a back-and-force motion while flagella has an udulating motion.
  • The ultrastructure of cilia and flagella are the same. They have a core of 9 pairs + 2 single central microtubules that are covered by an extension of the plasma membrane. This arrangement of microtubules is uniform in eukaryotes but different in prokaryotes. Flexible proteins connect the pairs of microtubules to each other like wagon-wheels. The cilium and flagellum are anchored in the cell by a basal body which is identical structurally to the centriole (it enters the egg from the sperm and becomes the centriole of the developing embryo). The protein that extends from one pair of microtubules to the next is called dynein, which is a complex protein with several polypeptide chains. Dynein proteins bend the cilia and flagella microtubules by using ATP and cause the movement of these organelles.

Watch:

  1. Microfilaments
  • Solid rods, about 7 nm in diameter
  • They are built of the globular protein called actin
  • The actin molecules form two long chains that twist together. Some other proteins can form cross bindings between the actin molecules so this way microfilaments can form networks as well.
  • The 3D network of actin filaments help to support the shape of the cell. They also make up the core of microvilli that help to enlarge the cell’s surface for making transport of materials more efficient.
  • Microfilaments also form the contractile structure of muscles where they are connected to a thicker protein called myosin.
  • The contraction of the actin-myosin complex is also important in amoeboid movement (pseudopods) and in cytoplasmic streaming