Light Microscopy 

• Halogen lamp light source
• condesner lenses
• stage, objective lenses, mirror, occular lens, 
• magnification = objective x occular 

Hematoxylin 

• stain used to identify nucleic acids, nucleus and ribosomes
• stain color is purple/blue
• usually used along with Eosin

Eoisin 

• used in staining
• used to identify protiens and cytoplasm
• pink color
• used in accordance with Hematoxylin 

Periodic Acid- Schiff (PAS)

• acid stain
• used to identify carbohydrates such as glycoproteins and proteoglycans
• this stains magenta or bright pink
• stains glycocalyx, basement membrane

Transmission Electron Microscopy 

(TEM)

• Used to view subcellular structure
• cleared, dehydrated and embedded in epoxy resin
• it is then sectioned on a copper mesh with a diamond knife along with dH20
• enhanced with uranyl acetate and lead citrate
• electrons are then fired at sample.
• if they pass through, appears light on film, if they are blocked, dark - 
• Film also called Charged coupled device

Freeze-Fracture Preparation

• used along with TEM
• cells are first frozen with Liquid Nitrogen
• cells then fractured at hydrophobic layers and are vaccumed and then sahdowed with carbon and platn. 
• organic material is then digested and rest analyzed by TEM

Scanning Electron Microscopy 

• Tissues fixed, dehydrated and coated with gold
• surface is bombarded with electrons which are picked up by a detector and displayed to a CRT
• shows 3D surface of cells or structure bodies

Immunocytochemistry 

• localization of antigens with in cells and tissues based on antigen to antibody pairing 

Glycocalyx

• extracellular polymeric material
• body uses them to identify bad cells
• can be seen as fuzzy coat on external surface of plasma membrane
• "sugar coat"

Clathrin

• plays a major role in the formation of coated vessicles
• transport btw trans-golgi, endosomes and plasmamembrane 
• epsin plays major role in clathrin coat formation
• adaptin also involved
• dynamin(GTPase) pinches off to complete forming coat

Cristae

• inner folds of the mitochondria

Plasma membrane 

• hydrophobic polar fatty acid tails inside, hydrpphylic choline, phosphate, and glycerol heads

Lipid Bilayer Composition

• can contain phosphatidylcholine (PC) or sphingomyelin (SM)
• Cholesterol can also be added (adds thickness to PC but not to SM)
• cholesterol also increases rigidness to the bilayer

Juxtacrine Signalling 

• helps cells perform cellular contact
• uses membrane bound factor and a cytokine receptor
• the cell sending the signal has the factor

G-Protein Cell Signalling

• when activator binds the receptor phosphorylates the GDP on a Gprotein
• this then moves to a secondary enzyme (adynl cyclase)
• this enzyme then activates secondary messengers such as cAMP
• cAMP can activate  PKA which effects transcription

cAMP

• created by Adenylyl clycase burning an ATP to a cAMP
• this then inhibits the regulatory subunit attached to PKA, allowing PKA to become active

Tyrosine Kinase Pathway

• starts out as two seperate receptors
• when activators bind they come together and are phosphorylated by ATP
• this forms a tyrosine kinase complex
• this charged complex can then activate other proteins

JAK-STAT Pathway 

• type of tyrosine kinase signaling
• involves a cytokine receptor
• found in white blood cells and used to regulate immune system
• consists of a receptor, a Janus Kinase and a Singal transducer and activator of transcript (STAT)
• The JAKS recruit STATS when the Tyrosine Complex is activated
• STATS come together to promote transcription of their target genes

Nucleosome

• the combination of DNA and histones
• just a strand of nucleosomes is 11nm
• lightly packed is 30 nm
• can be packed as tightly as 300 to 700nm

Lamins

• specific type of intermediate filament
• coats the surface of nuclear membrane
• helps support the structure of the nucleus 

Nucleolus 

• part of the nucleus that is responsible for transcribing ribosomal RNA and combine it with proteins to make near complete ribosomes
• occupies 25% of the nucleus 
• contains fibrillar centers, dense fibrillar centers and granular components

Mitochondria

• energy production and beta oxidation of long chain fatty acids (this occurs in matrix)
• the more cristae, the more energy a mitochondria can produce
• side chain of cholesterol is removed at the inner mitochondrial membrane (possible step in steroid synthesis)
• has its own ribosomes

Cisterna

• these are the folds of the Rough ER
• contains enzymes, proteins, and ribosomes

microsomes

• not normally present in living cells
• vesicle like artifacts reformed from ER when eukaryotic cells are broken up in a lab
• used to investigate the metabolism of molecules 

Smooth ER

• does not contain ribosomes
• synthesis and breakdown of glycogen
• retoxification of drugs and metabolic waste
• synthesis of steroid hormones
• sarcoplasmic reticulum is a kind of smooth er

Cytoskeleton 

• the scaffolding contains in a cells cytoplasm
• has a variety of functions
• three types: intermediate filaments, microfilaments and microtubles 

*Extracellular Matrix

• extracellular part of animal tissue that usually provides structural support to cells
• includes a variety of things from collagen, to laminin to hyaluronic acid to proteoglycans

Hyaluronic Acid

• not a proteoglycan GAG
• larg chain of sugars w/ no sulfation
• abundant in early embryo (regulates cell behavior)
• resists compressives forces in tissues and joints and is involved in would healing
• the older you get the less you produce
• I.e. joint pain

Proteoglycans

• GAGs linked to core proteins
• binds to secreted proteins and can immobilze them or block their activity
• allows resevoir for delayed release (growth factors)
• protects protein from degredation
• have net negative charge that attracts Na+, causing water to come to ECM through osmosi

Aggrecan

• made up of chondroitin sulfate and keraten sulfate
• MW of 210 KDa
• enforces mechanical support in cartilage, tendons, ligaments and walls of the aorta
• keraten part effects cornea, cartilage, bones and horns of animals

Decorin

• chondroitin sulfate and dermatan sulfate
• involved in regulation of cell cycle
• also helps maintain collagen fibers by not allowing degradation
• has anti-tumor properties and has been shown to repress growth
• KO mice that lack decorin have fragile skin and reduced tensile strength

Syndecans

• extracellular GAGs/intercellular-actin cytoskeleton?
• modulates integrin function
• binds FGFs and presents them to its receptors as well as many other growth factors including epithelial
• helps in wound healing

Collagen

• major protein of ECM
• secreted by connective tissue cells 
• has a triple helix of polypeptides
• most abundant protein in mammals
• usually created by fibroblasts
• many different types of collagen from tendons, to bone, to hair to the basal lamina

Fibrillar Collagen Synthesis

• first pro-α chains are made in ER/Golgi
• it is modified into a pro-collagen tirple helix w. 3 pro-α chain in golgi
• then secreted and the propeptide tails are cleaved
• sequence designates for self assebly into fibril
• fibrils then come together to make a fiber

Basal Lamina

• type IV collagen+ laminin+ entactins+proteoglycan
• this along with reticular lamina make up the basement membrane
• structure and filtering function
• regulate proliferation and differentiation 
• influence cell metabolism
• ECM

Laminin 

• contain alpha and beta chains and are a major part of the Basal Lamina
• different from lamin in nucleus
• influence cell differentiation, migration and adhesion as well as phenotype and survival

Matrix Metalloproteinases

(MMPs)

• degrade ECM
• important for remodeling during embryogenesis, fracture repair and bone absorption
• some bound others secreted
• 20 have autoinhibitory sequence that must be cleaved
• involved in pathological cond(arthritis) and tumor suppression in late stage cancer
• also involved in cell death and receptor cleavage

Adhesive Glycoproteins

• proteins that adhere cells to ECM components
• provide signals for development and tissue repair
• binds to inegrins and has an RGD domain 

Fibronectin

• an adhesive Glycoprotein
• tissue fibronectin as well as soluble fibronectin
• important for neural crest cell migration in developing  embryos
• KO mice die at day 8 of embryo development

Integrins

• receptor for ECM ligands 
• transmembrane protein composed of 2 subunits (alpha and beta) (non covalent bond)
• mediate cell adhesion to ECM
• mainly bind to alpha subunit
• wound healing, migration and differentiation
• active integrin complexs cluster together

Plectin

• giant protein that acts as a link between the three major components of the cytoskeloton
• also links cytoskeleton to junctions that link two cells plasma membranes together
• example of these are desmosomes and hemidesmosomes 

Merocrin Gland Secretion

• normal secretion via exocytosis
• secretory vesicles used
• secretion of primarily proteins and glycoproteins

Apocrine Gland Secretion

• part of the cell breaks away with the product in secretion
• an example is mamory glans and breast milk
• can be both regulative and constitutive 

Holocrine Secretion

• mature cells die and then become secretory product
• cell division replaces lost cells
• an example is the secretion of sebum in sebaceous glands (lubricats and waterproofs skin and hair)

Cytocrine Secretion

• Secretory product transported to the tip of a dendrite or cell process
• this is then phagocytosed by another cell
• an example of this is the secretion of melanin into keratinocytes in skin

COP-Coated Vesicle Formation

• GEF phosphorelates GDP to GTP and GTP interacts with the membrane 
• this interaction brings in the coat and the cargo
• GAP then burns the GTP to finish making the vesicle 

Endosome

• membrane bound compartment inside euk cells
• transport pathway from plasma membrane to lysosome
• major sorting compartment in endomembrane system
• once here can go to lysosome or back to glogli, membrane

Residual Bodies

• holding place for waste products that can not be broken down further
• usually found in long living, active cells like heart tissue

Peroxisome

• breaks down products to yield H₂O₂ 
• has high concentration of enzyme catalase that breaks that down to H20 and O2
• also involved in very long chain fatty acid (also done in mit.), as well as branched chain fatty acid
• 10% of total activity of 2 enzymes in pentose phsophate pathway (makes FA and nucleotide der.)

Zellweger Syndrome

• caused by defects in anyone of 12 genes (PEX genes)
• reduction or abscense of functional peroxisomes
• impaired brain development, craniofacial abnormalities and enlarged liver
• effects bone development and neuroproblems
• abnormal punctate calcification of distal femoral epiphysis

Golgi Complex

• post trans processing of proteins, processing of carbs, addition of sugar, sulfates or phosphoteres 
• synthesis of lipoproteins
• processing of acid hydrolases
• acrosome in sperm
• sorting of proteins
• aids in formation of lysosome(lysosome enzymes leave golgi in vescicle)

Lysosome

• proton pump maintains acididc interior of lysosome
• phagocytosis
• breaks down bone during remodeling
• autophagy (breaks down old organelles)
• endocytosis of LDL and relase of cholesterol

Intermediate Filaments

• strong and durable, resist stretching, resists mechanical stress (rope like)
• extensive network throughout cytoplasm
• nuclear lamina
• ex is keratin filaments in skin

Microtubules 

• plays role in organizing cells
• supportive roles in cells with complex slope 
• mitotic spindle, cilia, flagella, centrioles
• grow from area of cell that contains centrosome

Microfilaments

• also called actin filaments
• thin, flexible and associated with many actin-binding proteins
• microvili, contractile ring, muscle cells

centrosome

• 2 centrioles surrounded by protein called pericentriolar material (PCM)
• regulation of cell cycle progression
• centriole has a 9 triplet arangment

Lipofuscin 

• yellow brown pigment that accumulates with age in cells
• heart muscles, kidneys, neurons, hepatocytes
• composed of lipid-containing residues of lysosomal digestion
• can be linged to muscular degeneration, alzheimers, parkinsons and others

Barth Syndrome

Archondragenesis

• congenital chondrodysplasia (malformation of bones and cartilage)
• small bodies, short limbs and other skeletal abnormalities
• usually born premature, still born, and die shortly after
• caused by defect in microtubles of golgi 

Hunters Syndrome

• GAGs build up in cells throughout the body due to a deficiency or abscence of the enzyme iduronate-2-sulfatase in lysosomes
• can be dwarfs and some have mental problems 

Prophase I Steps

• 5 steps
• lepotene (condensing)
• zygotene (synapsis begins)
• pachytene (synapsis complete; crossing over)
• diplotene (chiasmas become visible)
• diakineseis (nuclear envelope fragments)

Meiotic Nondisjunction

• failure of chromosomes to seperate properly
• this can happen at anaphase 1 where the daughter cells are (n+1)(n+1)(n-1)(n-1)
• It can also happen at anaphase 2 where the daughter cells are (n+1)(n-1)(n)(n)

Robertsonian Translocation

• a acroncentric chromosme has a short arm and a large arm
• in this translocation a short arm of one is exchanged with the long arm of another
• this creates an xtralarge metacentric chromosome and a short fragment that is often lost later in the cell cycle

Trisomy 21

• also known as downsyndrome
• microgenia (shortened jaw)
• neotenization of brain and body(age differently)
• muscle hypotonia (low muscle tone)
• flat and broad facial features
• brushfield spots on iris

microgenia

• shortened jaw length
• found in trisomy 21 (downsyndrome) 
• similar to micrognathia found in trisomy 18 (edwards)

Trisomy 18

• second most common carried to term (Edwards Syndrome)
• microcephaly (small head, brain)
• micrognathia (undersized jaw)
• ocular hypertelorsism ( eyes wider then normal
• rockerbottom feet
• prominent occiput(back of brain enlarged
• kidney malformations
• intestines exposed on outside
• cognitive disorders , hyperactive

Trisomy 13

• Pa taus syndrome
• mental retardation
• polydactylyl (additional fingers)
• microphthalmia (eyes small and close together)
• rocker bottom feet
• holoprosencephaly(halves of brain fail to seperate)

Cri Du Chat Syndrome

• partial deletion of chromosome 5
• cat like cry from malformed larynx
• diffictulty swallowing/sucking
• microcephaly (reduction in head and brain size)
• cognitive, speech and motor delays
• hyperactivity, aggression, and reppetitive movments

Turner Syndrome

• gonadal dysfunction (inactive ovaries)
• only one x chromosome
• amenorrhea (loss of menstral cycle)
• reduced estrogen production
• hypothyroidism
• lognitive deficits

Kleinfelters syndrome

• XXY
• reduced testosterone production
• reduced or malformed testicles
• microorchidism (small testicles)
• gynecomastia
• weaker bones/muscles

Calcium Granule 

• can be found in mitochondria
• participates in apoptosis ( cell death)

Fibrillar Region

• region in nucleolus
• new rRNA attached to ribosome

Granular Region

• in nucleolus
• rRNA becoming a ribosome subunit 

Ischemia

• reduced blood flow to tissue
• a myocyte can adapt to this

Hypotrophy

• change in cell size
• can happen in pregnancy (uterine hypotrophy)
• myocardial hypotrophy (physiological and pathological)
• pathological usually not reversible 

Hyperplasia

• change in cell #
• physiological(temporary usually)
• compensatory(regeneration of liver)
• pathological (prostate enlargement) - caused by testosterone conversion

Atrophy

• partial or total wasting away of any muscle tissue in body
• heart is one example(becomes brown)

Metaplasia

• reversible replacement of one cell type with another
• help cells coup
• normal columnar changed to squamous in smokers
• can be reversed

Necrosis

• pathological process 
• cell swells
• lysosomes ruptures
• triggers host immune system response
• 2 kinds (coagulative and lquefactive necrosis)

Coagulative Necrosis

• ghost like view of cell
• common with myocardial infractions and liver necrosis
• gaps where cells used to be in slides

Liquefactive Necrosis

• where cells  break apart
• release cell content into ECM
• causes a line of inflamation

Apoptosis

• progremed cell death that doesnt cause immune response
• membrane blebs(bumbs form)
• apoptotic bodies formed
• bodies phagocytize 
• intrinsic apoptosis starts with signals from mitochondria
• extrinsic starts from extracellular ligands
• both lead to caspase cascade

Tissue Repair

• increase in fibrin
• coagulation, late inflamation
• proliferation
• remodeling(weeks to months)

Scar Formation

• initial steps occur 
• wound is deeper 
• collagen and elastin used in place of skin cells 
• this becomes scar tissue

Labile Tissue

• continuously being lost and replaced
• epithelial in gastointestinal tract and uterous
• skin cells and endocrine glands
• hematopoetic cells
• older you get the less of these you make

Stable Tissues

• minimal replicative abilities
• proliferate in response to injury or stess
• hyperplasia in liver
• smooth muscle 

Permanent Tissues

• terminally differentiated
• neurons and cardiac myoctes