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1. cell

The human body contains over 200 cell types that all originate from a single fertilized egg cell. Cells differentiate and specialize to perform specific functions. The basic components of cells are the nucleus, which houses the DNA, and the cytoplasm, which contains organelles. The plasma membrane encloses the cell and regulates what enters and exits. Cells communicate through signaling molecules that bind receptors and trigger intracellular signal transduction pathways. Endocytosis and exocytosis allow materials to be transported into and out of cells while maintaining membrane integrity. The nucleus contains DNA and directs cellular activities through gene expression.

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CELL
The human organism presents about 200 different cell types, all derived from the zygote, the single cell formed by fertilization of an oocyte with a spermatozoon.  During their specialization process, called cell differentiation, the cells synthesize specific proteins, change their shape, and become very efficient in specialized functions.  The body's cells can experience both normal and pathological conditions and the same cell type can exhibit different characteristics and behaviors in different regions and circumstances 
CELLULAR FUNCTIONS IN SOME SPECIALIZED CELLS.
 The cell is composed of two basic parts: Cytoplasm and Nucleus.  Individual cytoplasmic components are usually not clearly distinguishable in common hematoxylin-and-eosin–stained preparations.  The nucleus, appears intensely stained dark blue or black.  The cytoplasm is composed of a fluid component, or cytosol, which containes metabolically active structures, the organelles, which can be membranous (such as mitochondria) or non-membranous protein complexes (such as ribosomes and proteasomes).
Membranous organelle Non-Membranous organelle Rough & Smooth Endoplasmic reticulum Ribosomes Mitochondria Centrioles Golgi apparatus Microtubules Peroxisomes Inclusions Lysosomes Cilia - Flagella Vacuoles & vesicles Microvilli
PLASMA MEMBRANE
 The outermost component of the cell, separating the cytoplasm from its extracellular environment, is the Plasma membrane or Plasmalemma.  All eukaryotic cells are enveloped by a limiting membrane composed of phospholipids, cholesterol, proteins, and chains of oligosaccharides covalently linked to phospholipid and protein molecules.  Membranes range from 7.5 to 10 nm in thickness and visible only in the electron microscope.
 With electron microscopy, the plasmalemma and, all other organellar membranes appears a trilaminar structure after fixation in osmium tetroxide.  Because all membranes have this appearance, the 3-layered structure was designated the unit membrane.  Membrane phospholipids, such as phosphatidylcholine (lecithin), consist of two non-polar (hydrophobic or water-repelling) long-chain fatty acids linked to a charged polar (hydrophilic or water-attracting) head group.  Membrane phospholipids are most stable when organized into a double layer (bilayer) with their hydrophobic fatty acid chains directed toward the middle away from water and their hydrophilic polar heads directed outward to contact water on both sides.
 Cholesterol molecules insert among the close packed the phospholipid fatty acids nearly a 1:1 ratio , restricting their movement, and thus modulate the fluidity and movement of all membrane components.  The lipid composition of each half of the bilayer is different.  In red blood cells phosphatidylcholine and sphingomyelin are more abundant in the outer half of the membrane, whereas phosphatidylserine and phosphatidylethanolamine are more concentrated in the inner half.  Some of the lipids, known as glycolipids, possess oligosaccharide chains that extend outward from the surface of the cell membrane and thus contribute to the lipid asymmetry.
 Proteins, are major molecular constituent of membranes, can be divided into two groups. Integral proteins : o Incorporated within the lipid bilayer. o Some integral proteins span the membrane one or more times, from one side to the other, they are called one-pass or multipass transmembrane proteins. Peripheral proteins : exhibit a looser association with one of the two membrane surfaces.
    With freeze-fracture electron microscope studies of membranes show that many integral proteins are only partially embedded in the lipid bilayer and protrude from either the outer or inner surface. Transmembrane proteins are large enough to extend across the two lipid layers and may protrude from both membrane surfaces. The carbohydrate moieties of the glycoproteins and glycolipids project from the external surface of the plasma membrane; they are important components of specific molecules called receptors that participate in important interactions such as cell adhesion, recognition, and response to protein hormones. As with lipids, the distribution of membrane proteins is different in the two surfaces of the cell membranes. Therefore, all membranes in the cell are asymmetric.
     Integration of the proteins within the lipid bilayer is mainly the result of hydrophobic interactions between the lipids and nonpolar amino acids present on the outer region of the proteins. Some membrane proteins are not bound rigidly in place and are able to move within the plane of the cell membrane. unlike lipids, most membrane proteins are restricted in their lateral diffusion by attachment to cytoskeletal components. In most epithelial cells, tight junctions also restrict lateral diffusion of unattached transmembrane proteins and outer layer lipids to specific membrane domains. The mosaic disposition of membrane proteins and the fluid nature of the lipid bilayer and led to the well-established fluid mosaic model for membrane structure.
Functions of plasmalemma :  A selective barrier.  To keep constant the ion content of cytoplasm.  Specific recognition and regulatory functions.
GLYCOCALYX      With the EM the external surface of the cell shows a fuzzy carbohydrate-rich region called the glycocalyx. This layer is made of carbohydrate chains linked to membrane proteins and lipids and of cell-secreted glycoproteins and proteoglycans. The glycocalyx has a role in cell recognition and attachment to other cells and to extracellular molecules. Some ions, such as Na+, K+, and Ca2+, cross the cell membrane by passing through integral membrane proteins. This can involve passive diffusion through ion channels or active transport via ion pumps using energy from the breakdown of adenosine triphosphate (ATP).
ENDOCYTOSIS  Bulk uptake of material also occurs across the plasma membrane in a general process called endocytosis, which involves folding and fusion of this membrane to form vesicles which enclose the material transported.  Cells show three general types of endocytosis. 1. Phagocytosis 2. Fluid-phase Endocytosis 3.Receptor-mediated Endocytosis
Phagocytosis : o o o Certain white blood cells, such as macrophages and neutrophils, are specialized for engulfing and removing particulate matter such as bacteria, protozoa, dead cells, and unneeded extracellular constituents. When a bacterium becomes bound to the surface of a neutrophil, cytoplasmic processes of the cell are extended and ultimately surround the bacterium. The membranes of these processes meet and fuse, enclosing the bacterium in an intracellular vacuole, a phagosome.
PHAGOCYTOSIS
Fluid-phase Endocytosis :  In fluid-phase pinocytosis , smaller invaginations of the cell membrane form and entrap extracellular fluid and anything it has in solution.  Pinocytotic vesicles (about 80 nm in diameter) pinch off inwardly from the cell surface.  In most cells such vesicles usually fuse with lysosomes.
PINOCYTOSIS
Receptor-mediated Endocytosis :  Receptors for many substances, such as low-density lipoproteins and protein hormones, are integral proteins of the cell membrane.  Binding of the ligand (a molecule with high affinity for a receptor) to its receptor causes widely dispersed receptors to aggregate in special membrane regions called coated pits.  The electron-dense coating on the cytoplasmic surface of the membrane is composed of several polypeptides, the major one being Clathrin.  In a developing coated pit clathrin molecules, forming that region of cell membrane into a cage-like invagination that is pinched off into the cytoplasm, forming a coated vesicle carrying the ligand and its receptor.
RECEPTOR-MEDIATED ENDOCYTOSIS
In endocytotic processes, the vesicles or vacuoles produced quickly enter and fuse with the endosomal compartment, a dynamic system of membranous vesicles and tubules located in the cytoplasm near the cell surface (early endosomes) or deeper in the cytoplasm (late endosomes).  The clathrin molecules separated from the coated vesicles recycle to the cell membrane to participate in the formation of new coated pits.  The membrane of endosomes contains ATP-driven H+ pumps that acidify their interior. 
While phagosomes and pinocytotic vesicles soon fuse with lysosomes, molecules penetrating the endosomal compartment after receptor-mediated endocytosis may take more than one pathway.  The acidic pH of early endosomes causes many ligands to uncouple from their receptors, after which the two molecules are sorted into separate vesicles.  The receptors may be returned to the cell membrane to be reused.  The ligands typically are transferred to late endosomes.  Some ligands are returned to the extracellular milieu with their receptors and both are used again.  Late endosomes most commonly fuse with lysosomes for degradation of their contents. 
EXOCYTOSIS In exocytosis a membrane-limited cytoplasmic vesicle fuses with the plasma membrane, resulting in the release of its contents into the extracellular space without compromising the integrity of the plasma membrane.  Often exocytosis of stored products from epithelial cells occurs specifically at the apical domains of cells, such as in the exocrine pancreas and the salivary glands.  The fusion of membranes during exocytosis is a highly regulated process involving interactions between several specific membrane proteins.  Exocytosis is triggered in many cells by transient increase in cytosolic Ca2+. 
 During endocytosis, portions of the cell membrane become endocytotic vesicles; during exocytosis, the membrane is returned to the cell surface.  This process of membrane movement and recycling is called membrane trafficking.  Trafficking and sorting of membrane components occur continuously in most cells and are not only crucial for cell maintenance but also physiologically important in processes such as reducing blood lipid levels.
SIGNAL RECEPTION AND TRANSDUCTION  Cells in a multicellular organism need to communicate with one another to regulate their development into tissues, to control their growth and division, and to coordinate their functions.  Soluble extracellular signaling molecules bind receptor proteins only found on their target cells.  Each cell type in the body contains a distinctive set of receptor proteins that enable it to respond to a complementary set of signaling molecules in a specific, programmed way.
Signaling can take different routes: Endocrine signaling:  the signal molecules (called hormones) are carried in the blood to target cells throughout the body. Paracrine signaling :  the chemical mediators are rapidly metabolized so that they act only on local cells very close to the source. Synaptic signaling :  a special kind of paracrine interaction, neurotransmitters act only on adjacent cells through special contact areas called synapses. Autocrine signaling :  signals bind receptors on the same cell type that produced the messenger molecule.
     Hydrophilic signaling molecules : including most hormones, local chemical mediators (paracrine signals), and neurotransmitters activate receptor proteins on the surface of target cells. These receptors, often transmembrane proteins, relay information to a series of intracellular intermediaries that ultimately pass the signal (first messenger) to its final destination in either the cytoplasm or the nucleus in a process called Signal transduction. One of the intermediary proteins, the G proteins, binds guanine nucleotides and acts on other membrane-bound intermediaries called effectors which propagate the signal further into the cell. Effector proteins are usually ion channels or enzymes that generate large quantities of small second messenger molecules, such as 1,2diacyglycerol (DAG), cyclic adenosine monophosphate (cAMP), and inositol 1,4,5-triphosphate (IP3). The ions or second messengers diffuse through the cytoplasm, amplifying the first signal and triggering a cascade of molecular reactions that lead to changes in gene expression or cell behavior.
MEDICAL APPLICATION Several diseases have been caused by defective receptors.  Pseudohypoparathyroidism and a type of Dwarfism are caused by nonfunctioning parathyroid and growth hormone receptors.  In these two conditions the glands produce the respective hormones, but the target cells do not respond because they lack normal receptors. 
Hydrophobic signaling molecules : such as small steroid and thyroid hormones, bind reversibly to carrier proteins in the plasma for transport through the body.  Such hormones are lipophilic and once released from their carrier proteins, they diffuse directly through the plasma membrane lipid bilayer of the target cell and bind to specific intracellular receptor proteins.  With many steroid hormones, receptor binding activates that protein, enabling the complex to move into the nucleus and bind with high affinity to specific DNA sequences.  This generally increases the level of transcription from specific genes. 
NUCLEUS
The nucleus contains a blueprint for all cell structures and activities encoded in the DNA of the chromosomes .  Nucleus is the site of deoxyribonucleic acid (DNA) replication and transcription of DNA into precursor ribonucleic acid (RNA)molecules.  It contains all of the enzymes required for replication and repair of newly synthesized DNA, as well as for transcription and processing of precursor RNA molecules.  It is enclosed by the nuclear envelope and contains the nuclear lamina, nucleolus, and chromatin 
Nuclear envelope :  The nuclear envelope is a double membrane containing pores that are approximately 90 nm in diameter.  The outer nuclear membrane is continuous with the endoplasmic reticulum.
Nuclear Lamina :  The nuclear lamina is a latticelike network of proteins that include lamins.  Lamins attach chromatin to the inner membrane of the nuclear envelope and participate in the breakdown and reformation of the nuclear envelope during the cell cycle.  Phosphorylation of the lamins, (by lamin kinase) during prophase of mitosis initiates nuclear disassembly into small vesicles.
Nuclear Lamina Functions: Maintenance of nuclear shape Spatial organization of nuclear pores within nuclear membrane Regulation of transcription Anchoring of interphase heterochromatin DNA replication.
Lamina bio.winona.msus.edu/.../ Lec-note/16-new.htm
Nucleolus :  The nucleolus is responsible for ribosomal RNA (rRNA) synthesis and ribosome assembly.  It contains three morphologically distinct zones: • Granular zone—found at the periphery; contains ribosomal precursor particles in various stages of assembly. • Fibrillar zone—centrally located; contains ribonuclear protein fibrils. • Fibrillar center—contains DNA that is not being transcribed.
Nucleolus :  The nucleolus is responsible for ribosomal RNA (rRNA) synthesis and ribosome assembly.  It contains three morphologically distinct zones: • Granular zone—found at the periphery; contains ribosomal precursor particles in various stages of assembly. • Fibrillar zone—centrally located; contains ribonuclear protein fibrils. • Fibrillar center—contains DNA that is not being transcribed.
Chromatin : Chromatin is a complex of DNA, histone proteins, and nonhistone proteins. • DNA—a double-stranded helical molecule that carries the genetic information of the cell.  It exists in three conformations: B DNA, Z DNA, and A DNA. • Histone proteins—positively charged proteins enriched with lysine and arginine residues.  They are important in forming two types of structures in chromatin: nucleosomes and solenoid fibers.  The nucleosomes are the basic repeating units of the chromatin fiber, having a diameter of approximately 10 nm. • Nonhistone proteins—include enzymes involved in nuclear functions such as replication, transcription, DNA repair, and regulation of chromatin function.  They are acidic or neutral proteins.
Chromatin 6 nucleosomes become coiled around an axis, forming a solenoid.
Nucleosome, Solenoid model of chromatin, and chromosome Nucleosome
Forms of Chromatin : • Heterochromatin : highly condensed and transcriptionally inactive.  In a typical eukaryotic cell, approximately 10% of the chromatin is heterochromatin. • Euchromatin : a more extended form of DNA, which is potentially transcriptionally active.  In a typical cell, euchromatin accounts for approximate 90%of the total chromatin, although only about 10% is being actively transcribed.
CYTOPLASM
RIBOSOMES Ribosomes are composed of rRNA and protein. They consist of large (60S) and small (40S) subunits.  Ribosomes are assembled in the nucleus and transported to the cytoplasm through the nuclear pores.  The large ribosomal subunits are synthesized in the nucleolus, whereas the small subunits are synthesized in the nucleus. Polysomes :  Ribosomes often form polysomes, which consist of a single messenger RNA (mRNA) that is being translated by several ribosomes at the same time.  The ribosomes move on the mRNA from the 5' end towards 3' end.  The two ribosomal subunits associate on the mRNA, with the small subunit binding first 
Forms of Ribosomes : Ribosomes exist in two forms: • Free polysomes : are the site of synthesis for proteins destined for the nucleus, peroxisomes, or mitochondria. • Membrane-associated polysomes : are the site of synthesis of secretory proteins, membrane proteins, and lysosomal enzymes.
ENDOPLASMIC RETICULUM The endoplasmic reticulum exists in two forms, rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum (SER).  Rough Endoplasmic Reticulum :  RER is a single, lipid bilayer continuous with the outer nuclear membrane.  It is organized into stacks of large flattened sacs called cisternae that are studded with ribosomes on the cytoplasmic side.  RER snthesize poteins that are destined for the Golgi apparatus, secretion, the plasma membrane, and lysosomes.  RER is very prominent in cells that are specialized in the synthesis of proteins destined for secretion (eg : pancreatic acinar cells). 
ENDOPLASMIC RETICULUM
SMOOTH ENDOPLASMIC RETICULUM
Smooth Endoplasmic Reticulum :  SER is a network of membranous sacs, vesicles, and tubules continuous with the RER, but lacking ribosomes.  SER contains enzymes involved in the synthesis of phospholipids, triglycerides, and sterols
Functions of SER : o o o o Detoxification Reactions : Hydroxylation. Conjugation. Glycogen Degradation and Gluconeogenesis Reactions in Lipid Metabolism Sequestration and Release of Calcium Ions
GOLGI APPARATUS
GOLGI APPARATUS  The Golgi apparatus consists of disc-shaped smooth cisternae that are assembled in stacks (dictyosomes), and associated with numerous small membrane-bound vesicles.  The Golgi apparatus has two distinct faces: • The cis (forming) face is associated with the RER. • The trans (maturing) face is often oriented toward the plasma membrane.  Important in glycosylation, phosphorylation, sulfation, etc. Takes part in synthesis, concentration & storage of secretory products. 
Functions of the Golgi Apparatus : Proteins and Lipids  The Golgi apparatus is the site of post trauslational modification and sorting of newly synthesized proteins and lipids. Glycoproteins  Further modification of the carbohydrate moiety of glycoproteins produces complex and hybrid oligosaccharide chains.  This determines which proteins remain in the Golgi apparatus or leave the Golgi apparatus to become secretory proteins, lysosomal proteins, or part of the plasma membrane.  Two diseases are caused by a breakdown in this process, I-cell disease and hyperproinsulinemia
MEDICAL APPLICATION Hyperprolnsulinemia : Hyperprolnsulinemia is characterized by elevated levels of proinsulin in the serum resulting from the failure of a peptidase to cleave proinsulin to insulin and C-peptide in the golgi apparatus. I-Cell Disease : Phosphorylation of mannose in glycoproteins targets proteins to lysosomes.  Phosphate is added in a two-step sequence of reactions that are catalyzed by N-acetylglucosamine-phosphotransferase and N-acetylglucosaminidases.  A deficiency in N-acetylglucosamine-phosphotransferase results In I-cell dieease .
LYSOSOMES  Lysosomes are spherical membrane-enclosed organelles that are contain enzymes required for intracellular digestion. Lysosomes consist of two forms : •Primary lysosomes have not yet acquired the materials to be digested.  They are formed by budding from the trans side of the Golgi apparatus. •Secondary lysosomes are formed by the fusion of the primary lysosome with the substrate to be degraded and have contents that are in various stages of degradation 
 • Lysosomes contain approximately 60 hydrolytic enzymes. All lysosomal enzymes are acid hvdrolases, with optimal activity at a pH of approximately 5.0. The synthesis of the lysosomal hydrolases occurs in RER.  All hydrolasea are transferred to the Golgi apparatus where they are modified and packaged into lysosomes. 
MEDICAL APPLICATION Glycogen-Storage Disease Type II (Pompe Disease) :  an autosomal recessive disorder that results from the deficiency of acid alpha-glucosidase, a lysosomal hydrolase , is required for the degradation of a small percentage (1-3%) of cellular glycogen.  Because the main pathway for glycogen degradation is not deficient in glycogen-storage disease type II disease, energy production is not impaired, and hypoglycemia does not occur.  However, the deficiency of this enzymatic activity results in the accumulation of structurally normal glycogen in lysosomes and cytoplasm in affected individuals.  Excessive glycogen storage within lysosomes may interrupt normal functioning of other organelles and leads to cellular injury. In turn, this leads to enlargement and dysfunction of the entire organ involved (eg, cardiomyopathy).
RESIDUAL BODIES •Lysosomes containing indigestible compounds are called residual bodies. •The indigestible compounds are usually exocytosed. •The unreleased indigestible compounds in long-living cells appear as lipofuscins or aging pigments.
RESIDUAL BODIES IN LUNG CELLS
AUTOPHAGOSOMES Primary Liposomes fuse with membrane-bound organelles or a portion of cytoplasm to form autophagosomes.  Autolysis occurs when lysosomes rupture and destroy the cell itself. 
PEROXISOMES  Peroxisomes are a heterogeneous group of small, spherical organelles with a single membrane. Functions: Synthesis and degradation of hydrogen peroxide.  Oxidation of very long chain fatty acids (> C24).  Phospholipid exchange.  Bile acid synthesis. 
PEROXISOMES (MICROBODIES )
MEDICAL APPLICATION Peroxisome Deficiency : Several genetic diseases are associated with the impairment or absence of peroxisomes.  These patients fail to oxidize very long chain fatty acids and accumulate bile acid precursors.   The four most common disorders are: • Zellweger (cerebrohepatorenal) syndrome • Neonatal adrenoleukodystrophy • Infantile Refsum disease • Hyperlipopecolaternia
MITOCHONDRIA
MITOCHONDRIA Mitochondria have two membranes , They synthesize adenosine triphosphate (ATP), contain their own doublestranded circular DNA, and make some of their own proteins.  Mitochondria have several compartments : Outer Membrane  The outer membrane is smooth, continuous, and highly permeable.  It contains an abundance of porins, an integral membrane protein that forms channels in the outer membrane through which molecules of less than 10 kD can pass. 
Inner Membrane  The inner membrane is inpermiable to most small ions (Na, K*, H*) and small molecules (ATP, adenosine diphosphate, pyruvate).  The impermeability is likely related to the high content of the lipid cardiolipin.  The inner membrane has numerous infoldings, called cristae.  The cristae greatly increase the total surface area. They contain, enzymes for electron transport and oxidative phosphorylation.  The number of mitochondria arid the number of cristae per mitochondrion are proportional to the metabolic activity of the cells in which they reside.
Mitochondria Two types of cristae: tubular-like and plate-like. Most cells contain mitochondria with plate-like cristae. Steroid secreting cells (eg. Adrenal, gonadal cells) have tubular cristae
Mitochondria Internal membrane contains enzymes for: Oxidative Phosphorylation •electron transport system •oxidative phophorylation systems
Intermembrane Compartment :  The intermembrane compartment is the space between the inner and outermembranes.  It contains enzymes that use ATP to phosphorylate other nucleotides (creatine phosphokinase and adenylate kinase). Matrix :  The matrix is enclosed by the inner membrane and contains: Dehydrogenases : oxidize many of the substrates in the cell (pyruvate, amino acids, fatty acids), generating reduced nicotinamide adenine dinucleotide (NADH) and reduced flavin adenine dinucleotide (FADH,) for use by the electron transport chain and energy generation.
Mitochondria Citric acid cycle Matrix contains enzymes for: •Citric acid cycle for generation of ATP •Dehydrogenases
A double-stranded circular DNA genome—encodes a few of the mitochondrial proteins.  Mitochondrial DNA is always inherited from the mother, resulting in transmission of diseases of enery metabolism.  RNA, proteins and ribosomes—although there is some protein synthesis, most mitochondrial proteins are synthesized in the cytoplasm and are transferred into the mitochondria. Intramitochondrial granule : contain calcium and magnesium. Their function is not known, but it is believed that they may represent a storage site for Calcium. 