Cellular Level of Organization PDF

**[CHAPTER THREE]** **Cellular Level of Organization** An Introduction to Cells A. **[Cell Theory]**=developed by three scientists (Schleiden, Schwann, and Virchow) 1. Cells are the building blocks of all plants and animals. 2. All new cells come from the division of pre-existing...

**[CHAPTER THREE]** **Cellular Level of Organization** An Introduction to Cells A. **[Cell Theory]**=developed by three scientists (Schleiden, Schwann, and Virchow) 1. Cells are the building blocks of all plants and animals. 2. All new cells come from the division of pre-existing cells. 3. Cells are the smallest units that perform all vital physiological functions. 4. **Complementarity of Form and Function**=functions are dictated by which subcellular structures are present in the cell. 5. **[Cytology]**=the study of cells. B. Although cells vary widely in size, shape, and function, all of them are the descendants of a single cell: the fertilized ovum. 6. At fertilization, the fertilized ovum -- which is very large -- contains the genetic potential to become any cell in the body. 7. As cellular division occurs, the cytoplasm is subdivided into smaller parcels. These parcels differ from one another because there were regional differences in the position of the cytoplasm at fertilization. 8. The cytoplasmic differences affect the DNA of the cells, turning specific genes on or off. The daughter cells begin to develop specialized structural and functional characteristics. This process of gradual specialization is called **differentiation**. 9. Differentiation produces the specialized cells that form the tissues responsible for all body functions. C. Cells are the smallest living units of life. 10. Our body cells are surrounded by a watery medium known as the **extracellular fluid** or **interstitial fluid** around most tissues. 11. The primary components of the cell are the plasma membrane and the cytoplasm. 12. **[Plasma membrane]**: separates the cell contents, or cytoplasm, from the extracellular fluid. 13. **[Cytoplasm]**: is a general term for the material located between the plasma membrane and the membrane surround the nucleus. A colloid with as consistency that varies between that of thin maple syrup and almost-set gelatin, cytoplasm contains many more proteins than does extracellular fluid. 14. The cytoplasm can be subdivided into: a. **[Cytosol]**: the fluid component of the cytoplasm, also called **intracellular fluid**; may contain inclusions of insoluble materials. b. **[Organelles]**: intracellular structures that have specific functions. There are two types of organelles. i. **[Membranous organelles]** -- isolated from the cytosol by a phospholipid membrane (just as the plasma membrane isolates the cytosol from the extracellular fluid). Includes: mitochondria, nucleus, endoplasmic reticulum, golgi apparatus, lysosomes, and peroxisomes. ii. **[Non-membranous organelles]** -- not completely enclosed by membrane so that all of their components are in direct contact with the cytosol. Includes: cytoskeleton, centrioles, microvilli, cilia, flagella, and ribosomes 1. **The Cell Membrane**: The plasma membrane isolates the cell from its environment and performs varied functions. A. Design of the plasma membrane: 1. **[Phospholipid bilayer]** forms the primary membrane structure. a. It is extremely thin (6-10 nm) and very delicate. b. In each half of the bilayer, the phospholipids lie with their **hydrophilic heads facing outward** and their **hydrophobic tails sandwiched in between**, just as in a micelle. c. The hydrophobic layer in the center of the membrane isolates the cytoplasm from the extracellular fluid. Such isolation is important because the composition of the two fluids is different. 2. **[Proteins]** -- scattered throughout the phospholipid bilayer are two types of proteins that are important to membrane function: a. **[Integral proteins]** are part of the membrane structure and cannot be removed without damaging or destroying the membrane. Most integral proteins pass all the way through the membrane one or more times and are therefore known as transmembrane proteins. Some contain channels or pores through which water and solutes may pass. b. **[Peripheral proteins]** are bound to the inner or outer surface of the membrane and are easily separated from it. Integral proteins greatly outnumber peripheral proteins. c. Functional classes of membrane proteins: i. **Anchoring proteins** -- attach the plasma membrane to other structures and stabilize its position. Inside the cell, membrane proteins are bound to the cytoskeleton. ii. **Recognition proteins** -- detected by cells of the immune system. Enzymes in the plasma membranes may be integral or peripheral proteins. iii. **Receptor proteins** -- bind to specific extracellular molecules called ligands. A **[ligand]** can be anything from a small ion like calcium, to a relatively large and complex hormone. iv. **Carrier proteins** -- bind solutes and transport them across the plasma membrane. v. **Channels** -- are integral proteins containing a central pore (or channel) that forms a passageway completely across the plasma membrane. The channel permits the passage of water and small solutes that cannot otherwise cross the lipid bilayer of the plasma membrane. 3. **[Glycocalyx]** -- layer of superficial membrane carbohydrates. Carbohydrates account for roughly 3% of the weight of the plasma membrane. The glycocalyx is important in cell recognition, binding to extracellular structures, and lubrication of the cell surface. 4. **[Cholesterols]** -- important lipid that helps to stabilize the relatively weak plasma membrane. B. The plasma membrane is a physical barrier that separates the inside of the cell from the surrounding fluids. It is a **selectively permeable** barrier that controls the entry of ions and nutrients (such as glucose), the elimination of wastes, and the release of secretions. C. How Things Enter and Leave the Cell 1. Because the plasma membrane is an effective barrier, the conditions inside the cell are different than the conditions outside the cell. However, the barrier cannot be absolute because cells are not self-sufficient, and their activities must be coordinated. Instead plasma membranes demonstrate **permeability**. a. **[Freely permeable membranes]** = allow any substance to pass without difficulty b. **[Selectively permeable membranes]** = permit the passage of some materials and prevent the passage of others. c. **[Impermeable membranes]** = nothing can pass through. Cells may be impermeable to specific substances, but no living cell has an impermeable membrane. 2. **[Passive transport processes]**=do not require energy because particles are moving down the concentration gradient. d. **[Simple diffusion]**=the movement of solutes through a selectively permeable membrane from an area of high solute concentration to an area of low solute concentration. i. **Solutes** are the dissolved particles in a solution while the **solvent** is the substance that the solutes dissolve into. Remember, water is the universal solvent. ii. There are many factors that influence diffusion rates: **distance, molecule size, temperature, gradient size, electrical forces.** e. **[Facilitated diffusion]**=some molecules are too big to fit through the spaces between the phospholipids and therefore require an integral protein, also known as a carrier protein, to ferry them across the membrane. This type of transport is a carrier-mediated process but DOES NOT REQUIRE ATP. f. **[Osmosis]**=the diffusion of water through a selectively permeable membrane from an area of higher water concentration to an area of lower water concentration. iii. The greater the initial difference in solute concentrations, the stronger the **osmotic flow**. The **osmotic pressure** of a solution is an indication of the force with which pure water moves into the solution as a result of its solute concentration. iv. Both osmosis and diffusion are based on the *osmolarity* of the solution surrounding the cell. **Osmolarity** is the solute concentration of the solution and the effects of the solution on the cell is its **tonicity**. v. Tonicity may have one of three effects on a cell: a. **[Isotonic]**=same solute concentration in the solution than in the cell. (NO NET MOVEMENT resulting in normal animal cell shape) b. **[Hypertonic]**=higher solute concentration in the solution than in the cell. (solvent would MOVE OUT causing animal cells to **crenate**) c. **[Hypotonic]**=lower solute concentration in the solution than in the cell (solvent would MOVE IN causing animal cells to **lyse**) g. **[Filtration]**= "bulk flow" movement of substances because of a *pressure* gradient. 3. **[Active processes]**=do require energy!! h. **[Active transport]**=similar to facilitated diffusion because it too requires carrier proteins however it differs in that it requires ATP and is not dependent on concentration gradients. Therefore, substances can be pumped into and out of the cell regardless of concentration gradients.  Most common example is the sodium-potassium pump. i. **[Secondary active transport]**=by moving sodium across the membrane, energy is stored to pump glucose against its gradient. j. **[Vesicular transport]**=large particles, macromolecules, and fluids are transported across the plasma and intracellular membranes: vi. **[Exocytosis]**=moving substances out of the cell. vii. **[Endocytosis]**=moving substances into the cell. d. **[Phagocytosis]**= "cell eating". e. **[Pinocytosis]**= "cell drinking". **3.2 The Cytoplasm and Cellular organization** A. Membranous organelles 1. **[Endoplasmic reticulum]** -- or ER, is a network of intracellular membranes connected to the nuclear envelope, which surrounds the nucleus. There are two types of ER: rough and smooth. a. **Rough ER** (RER) -- rough because large numbers of ribosomes attach to its surface. Functions as a combination workshop and shipping depot. The RER is the site where newly constructed proteins are chemically modified and packaged for export to the golgi apparatus. b. **Smooth ER** (SER) -- lacks ribosomes; has numerous functions including synthesizing phospholipids and cholesterols, synthesizing steroid hormones, synthesizing and storing glycerides, synthesizing and storing glycogen. 2. **[Golgi apparatus]** -- Composed of five to six flattened discs. Golgi apparatus renews or modifies the plasma membrane, modifies and packages secretions such as hormones or enzymes for release through exocytosis, and packages special enzymes within vesicles for use in the cytosol. There are two types of specialized vesicles formed by the golgi apparatus: a. **Lysosomes** -- special vesicles that provide an isolated environment for potentially dangerous chemical reactions. These vesicles contain digestive enzymes with a wide variety of functions. b. **Peroxisomes** -- special vesicle that breaks down organic compounds and neutralizes toxic compounds generated by the process. These vesicles contain degradative enzymes. 3. **[Mitochondria]** -- the powerhouses of the cell; responsible for ATP synthesis. Mitochondria vary widely in shape, from long and slender to short and fat. All share basic features such as a double-layered membrane. The folded internal membrane is called the **Cristae** and increases internal surface area exposed to the matrix. The **matrix** is the liquid enclosed by the inner membrane. ATP production is a multi-step process called **[Aerobic Respiration]**: a. **Glycolysis** -- glucose molecules are broken down into two molecules of pyruvate. This reaction occurs in the cytoplasm of animal cells and creates two ATP molecules. The pyruvate molecules are absorbed into the mitochondria for steps two and three. b. **Citric acid cycle** -- in the matrix of the mitochondria, a CO~2~ molecule is removed from each pyruvate; the remainder enters the citric acid cycle, an enzymatic pathway that systematically breaks down the absorbed pyruvate remnant into carbon dioxide and hydrogen atoms. Two ATP are produced in this step. c. **Electron transport system** -- The hydrogen atoms are delivered to enzymes and coenzymes of the cristae which catalyze the synthesis of 32 additional ATP. At the end of the process, oxygen combines with the hydrogen atoms to form water molecules. B. Non-membranous organelles 1. **[Cytoskeleton]** -- functions as the cell's skeleton. It provides and internal framework made of protein that gives the cytoplasm strength and flexibility. The cytoplasm of all cells includes microfilaments, intermediate filaments, and microtubules. a. **Microfilaments** -- the smallest of the cytoskeleton elements. These protein strands are generally less than 6 nm in diameter. Typical microfilaments are composed of the protein **actin**. They are common in the periphery of the cell, but relatively rare in the region immediately surrounding the nucleus. b. **Intermediate filaments** -- range from 7 to 11 nm in diameter. These are the strongest and most durable of the cytoskeleton elements. At least 5 types of intermediate filaments are known. c. **Microtubules** -- are the largest components of the cytoskeleton with diameters of 25 nm. Microtubules extend outward into the periphery of the cell from a region near the nucleus called the **centrosome**. 2. **[Centrioles]** -- are cylindrical structures composed of short microtubules. The microtubules form nine *triplets* connected to each other. Two centrioles are located at the centrosome, and the microtubules of the cytoskeleton generally begin at the centrosome and radiate through the cytoplasm. During cell division, the centrioles are associated with the formation of **spindle fibers** which move the strands of DNA to the poles. 3. **[Cilia]** -- long slender extensions composed of microtubules which extend from the cell's surface for the purpose of propelling fluids or solids. The long microtubules of cilia are arranged with nine *doublets* forming a cylinder around a central pair of microtubules. 4. **[Microvilli]** -- finger-shaped extensions of the plasma membrane. A core of microfilaments stiffens each microvillus and anchors it to the cytoskeleton. Microvilli greatly increase surface area of the cell and enhance its ability to absorb nutrients from the extracellular fluid. 5. **[Ribosomes]** -- responsible for protein synthesis and are often attached to endoplasmic reticulum. The more protein a cell synthesizes the more ribosomes it has. A functional ribosome consists of two subunits, one small subunit and one large subunit. **3.3 The Nucleus and DNA replication** A. Function of the Nucleus 1. The nucleus is usually the largest and most conspicuous structure in a cell. The nucleus serves as the control center for cellular operations. 2. A single nucleus stores all the information needed to direct the synthesis of the more than 100,000 different proteins in the human body. This genetic information is coded in the sequence of nucleotides in DNA. 3. By controlling what proteins are synthesized and when, the nucleus determines the structure of the cell and what functions it can perform. 4. Most cells contain a single nucleus, but exceptions exist. A cell without a nucleus cannot repair itself and it will disintegrate within three or four months. B. Structure of the nucleus 1. **[Nuclear envelope]** -- surrounds the nucleus and separates it from the cytoplasm. The nuclear envelope is a double membrane. 2. **[Nuclear pores]** -- account for about 10% of the surface of the nucleus; serve as passageways that permit chemical communication between the nucleus and the cytosol. Proteins at the pores regulate the movement of ions and small molecules, and neither proteins nor DNA can freely cross the nuclear envelope. 3. **[Nucleoplasm]** -- the fluid contents of the nucleus. The nucleoplasm contains the nuclear matrix, a network of fine filaments that provide structural support and may be involved in the regulation of genetic activity. Also contains ions, enzymes, nucleotides, and small amounts of RNA and DNA. 4. **[Nucleoli]** -- a transient nuclear organelle that synthesizes ribosomal RNA. They also assemble the ribosomal subunits. Nucleoli are most prominent in cells that manufacture large amounts of proteins, such as liver, nerve, and muscle cells. 5. **[DNA]** -- stores the instructions for protein synthesis. In the nucleus of cells that are not dividing, DNA strands are loosely coiled around **histones** forming complexes known as **nucleosomes**. Nucleosomes twist to form filaments of **chromatin**. At the beginning of cell division, chromatin becomes more tightly coiled and complex forming a **chromosome**. A constricted region in the middle of the chromosome is called the **centromere**. In human cells, there are 46 chromosomes (23 from the mother and 23 from the father). 4. **Protein synthesis involves DNA, enzymes, and three types of RNA** A. How does a gene, in fact, specify a polypeptide? B. **Genes** are the functional units of heredity. Genes contain all the nucleotides needed to produce a specific protein. The number of nucleotides in a gene depends on the size of the polypeptide represented. C. RNA is necessary because the DNA code is "locked" in the nucleus but the amino acids for constructing proteins are out in the cytoplasm. D. How is RNA different from DNA? 1. RNA contains **ribose** sugar rather than the **deoxyribose** sugar of DNA. 2. RNA contains the bases adenine, guanine, cytosine, and **URACIL** instead of thymine in DNA. 3. RNA is **single-stranded** structure rather than the double-stranded helix of DNA. 4. RNA is **not confined to the nucleus** while DNA is found only in the nucleus of eukaryotic cells. 5. RNA **undergoes significant processing and modification** while DNA is modified only if mutations occur. E. There are three different types of RNA. 1. **[Ribosomal RNA]** (rRNA) combines with already constructed proteins to form the ribosomes where polypeptides are synthesized. 2. **[Messenger RNA]** (mRNA) takes the coded message of a DNA strand out to the cytoplasm and ribosomes for constructing the polypeptides.  The code is written in triplets called **[codons]**. 3. **[Transfer RNA]** (tRNA) transfers the amino acids to the ribosome for addition to the building polypeptide chain.  Possess the **[anti-codons]** for proofreading. F. The formation of proteins involves two main steps: Transcription and Translation 1. **[Transcription]**=DNA serves as a template for the formation of mRNA. a. Transcription begins when **[RNA polymerase]** attaches to a **[promoter]** on the DNA strand causing the DNA helix to unwind and unzip. b. As RNA polymerase moves along the DNA template, complimentary RNA nucleotides pair with the DNA nucleotides of the template strand. c. RNA polymerase adds the RNA nucleotides in the 5' to 3' direction. d. Elongation of the mRNA strand continues until RNA polymerase comes to a **[terminator sequence]** which causes the RNA polymerase to stop transcribing DNA and to release the immature mRNA transcript. 2. mRNA is then processed before leaving the nucleus. a. The introns are removed by **[spliceosomes]**, a complex of enzymes that cut the primary RNA transcript and then rejoin adjacent exons producing a mature mRNA. b. **[Introns]**=non-coding segments of DNA; sometimes called "junk information". c. **[Exons]**=segments of DNA that will eventually be expressed as a polypeptide. 3. **[Translation]**=the mRNA leaves the nucleus through the nuclear pores and enters the cytoplasm where the ribosomes on the rough ER translate the mRNA into a polypeptide chain. This translation involves three steps: a. **[Initiation]**=the ribosome subunits bind to the mRNA strand in the vicinity of a Start Codon.  The **[start codon]** is always the sequence AUG.  The first tRNA binds to the start codon by matching up its **[anticodon]** is carrying a *methionine* and enters the first binding site. b. **[Chain Elongation]=**A second amino acid now enters the second binding site and attempts to match its anticodon to the codon. If it matches, it binds the amino acid it is carrying to the *methionine* of the previous tRNA by a **[peptide bond]**. The ribosome then moves down the strand causing the tRNA in the first site to shift to the second site. This is called **[translocation]**. A third amino acid now enters the newly opened second site and attempts to bind its anticodon to the new codon.  If it matches, it binds its amino acid to the previous two by the formation of a peptide bond. Etc. Etc. Etc. c. **[Chain Termination]=**Elongation continues until the ribosome gets to a codon that signifies the end of the polypeptide chain because no amino acid is specified.  This sequence is called the **[stop codon]**. The polypeptide is enzymatically cleaved from the last tRNA. The polypeptide leaves the ribosome and then takes on its primary, secondary, tertiary and quaternary structure (discussed in chapter 2). 5. **Cell Growth & Division: The Cell Life Cycle** A. **[Interphase]** 1. **G~1~**=the cell grows in volume, performs it normal functions, undergoes protein synthesis, and duplicates its organelles. 8 or more hours in length. 2. **S**= "DNA synthesis". DNA replicates itself. 6-8 hours in length. a. Single-stranded chromosomes form double-stranded chromosomes. b. **[Helicase]** unwinds and unzips the DNA. c. **[DNA polymerase]** binds to the DNA and attaches *complimentary nucleotides* (A always binds to T while C always binds to G). d. The daughter DNA is built continuously on the **leading strand** but discontinuously on the **lagging strand**. e. **Okazaki fragments** produced on the lagging strand are \"glued\" together by **[ligase]**. f. Two daughter strands of DNA are produced with each having half of the original strand. This is known as **[semi-conservative replication]**. g. Each strand of the double-stranded chromosomes is called a **[sister chromatid]**.  The sister chromatids are held together at raised region on the **centromere** called the **[kinetochore]**. 3. **G~2~**=the cell prepares itself for division by making necessary proteins. 2 to 5 hours in length. 4. Some cells enter a stage called **G~0~** where the cell permanently ceases to divide. B. **[M]**= **Mitosis**, or identical nuclear division, occurs in all **[somatic cells]** (body cells) for the purpose of repair and replacement. 1 to 3 hours in length. Sex cells (called gametes) undergo a different process of cell division known as Meiosis. 1. **[PROPHASE]**=three changes characterize this phase. a. Nuclear membrane breaks down. b. Double-stranded chromosomes condense and become visible. c. Spindle fibers form. 2. **[METAPHASE]**= "middle" a. Spindle fibers attached to the kinetochore begin pulling on the chromosome. b. Double-stranded chromosomes line up in the middle of the cell called the **[metaphase plate]**. 3. **[ANAPHASE]**= "apart" a. Chromatids get pulled apart. b. Single-stranded chromosomes migrate to opposite ends of the cell. 4. **[TELOPHASE]**=reverse of prophase. a. Nuclear membrane reforms. b. Single-stranded chromosomes decondense and disappear. c. Spindle fibers break down. C. **[Cytokinesis]**=or cytoplasmic division splits the cell in two. In animal cells [**cleavage** **furrow**] or "pinching in" causes the cytoplasmic division. This process begins as early as anaphase but continues through telophase. The completion of cytokinesis marks the end of cell division. D. **[Daughter Cells]**= two daughter cells are produced and each daughter cell has the same number of chromosomes as the parent cell. The daughter cells are now in G~1~ of interphase and will begin growing and doing their everyday function. E. **Tumor and cancer cells are characterized by abnormal cell growth and division.** 1. **The life span of a healthy body cell can vary from hours to decades depending on the type of cell and the stresses involved.** 2. **Many cells apparently self-destruct after a certain period of time by activating specific "suicide genes" in the nucleus. This genetically controlled death is [apoptosis].** 3. **When rates of cell division and growth exceed the rate of cell death, a tissue begins to enlarge.** 4. **[Cancer] usually begins with a single abnormal cell. Cancer is an illness characterized by mutations that disrupt normal control mechanisms that regulate the rates of cell division. Mutations are permanent changes in the DNA nucleotide sequence and function.** 5. **A tumor, or neoplasm, is a mass or swelling produced by abnormal cell growth and division.** a. **Benign tumors=the cells remain within the tissue of origin and do not spread to other tissues. These tumors seldom threatens an individual's life and can usually be surgically removed it its size and position disturbs tissue function.** b. **Malignant tumors=cells divide very rapidly, releasing chemicals that simulate the growth of blood vessels into the area. The malignant cells then begin to migrate into surrounding tissues and nearby blood vessels. This process -- metastasis -- can produce secondary tumors.**