Histology Lec Prelims PDF

General Histology and Embryology 1st SEM DMD 2 Doc Francis Ian L. Salaver, RMT,MD INTRODUCTION TO HISTOLOGY WHAT IS HISTOLOGY Is the study of tissues, their functions and their arrangement to constitute an organ. WHAT IS A TISSUE...

General Histology and Embryology 1st SEM DMD 2 Doc Francis Ian L. Salaver, RMT,MD INTRODUCTION TO HISTOLOGY WHAT IS HISTOLOGY Is the study of tissues, their functions and their arrangement to constitute an organ. WHAT IS A TISSUE Group of cells with interrelated functions group of cells + extracellular matrix & a group of cells with interrelated functions EPITHELIAL TISSUE provide protection functions for absorption & secretion The cells in the epithelium is tightly packed thus there is no space for blood vessels tightly packed group of cells Avascular = doesn’t have a blood supply CONNECTIVE TISSUE have blood vessels = protects and provides blood supply (oxygen) to the epithelium below the epithelium WHAT IS HISTOLOGY links to other tissues Branch of Anatomy= also known as Microscopic o ex. links epithelial tissue to muscle tissue Anatomy Is the study of tissues, their functions and their MUSCLE TISSUE arrangement to constitute an organ. movement of tissues o makalihok sa stomach 4 BASIC TYPES OF TISSUE NERVOUS TISSUE provides sensation, control, and information Epithelial Tissue processing Connective Tissue o maka feel naa tay ulcer Muscle Tissue Nervous Tissue REAL, RHYSSA SHAYNE P. 1  TRANS: HISTOLOGY IN LABORATORY To study tissues, one must prepare thin and translucent histological sections or tissue slices that can be studied with the aid of a microscope. WHAT IS A TISSUE FIXATION Since cellular decomposition begins immediately after the death of a human/patient, tissues must be fixed to prevent alterations in their structure through decomposition. (TO PRESERVE) o Avoid tissue destruction by digestive enzymes (autolysis) or through bacterial degradation. o Terminate cell metabolism ▪ Glycolysis without oxygen = lactic acid EXTRACELLULAR MATRIX o any area outside the cells o The extracellular matrix is composed of many kinds of ▪ Fibroblasts - cells that secrete matrix proteins ▪ Ground Substance - empty spaces - the matrix of loose connective tissue o (3) Hardens the tissue by cross-linking or denaturing proteins o (4) Kill pathogenic microorganisms such as bacteria, fungi and viruses ▪ Commonly used fixative is formalin DECALCIFICATION Only done in specimens such as bone and calcified tissues Nitric acid Done by successively bathing the specimen in a mixture of ethanol and water from 70% to 100%. (increasing concentration of alcohol) REAL, RHYSSA SHAYNE P. 2  TRANS: Alcohol removes water from tissue. CUTTING AND SECTIONING After the specimen is hardened, it is trimmed into appropriately sized blocks. o Cutting is the removal of excess paraffin The block is then mounted in a microtome and cut with a steel knife. o Sectioning is done with the aid of microtome CLEARING Removal of the dehydrating agent by immersing the specimen in the solvent that the alcohol and embedding medium is miscible Clearing agent are highly volatile (becomes vapor once exposed to heat) Xylene and Toluene MOUNTING Placing cut sections on a slide with adhesives such as pinene or acrylic resins SECTIONS ARE TRANSPARENT EMEDDING After the clearing procedure, the tissue is placed in a melted paraffin in an oven set at 52-60 degree Celsius. The heat causes the clearing agent to evaporate so that the tissue will be filled up with paraffin. STAINING Since paraffin is colorless, staining is a must. Application of color to the tissue to highlight The tissue and paraffin will harden after removal from structures. oven Most used stain: Hematoxylin and Eosin o Plastic resins – makes use of plastic solution o These dyes are water soluble which hardens tissue by cross-linking polymers o Eliminates the need to use oven and paraffin; little tissue distortion REAL, RHYSSA SHAYNE P. 3  TRANS: Hematoxylin and Eosin – Most commonly used stain in histology Hematoxylin- basic dye; usually stains nucleus and RNA-containing portion of cytoplasm Eosin-acidic dye – usually cytoplasmic components and collagen Tissues with negative charges/acids are readily stained with basic dyes – BASOPHILIC o Nucleic acids = nucleus Tissues with positive charges are stained with acidic dyes – ACIDOPHILIC o Mitochondria, collagen, cytoplasm SPECIAL STAINS Feulgen reaction – DNA Periodic acid schiff – Carbohydrates Sudan Black – Lipids Silver stain – reticular fibers FROZEN SECTIONS Fixation is done rapid freezing o Compressed carbon dioxide Sectioning is done thru cryostat, a refrigerated compartment containing microtome Method is rapid Routinely done in hospital to study specimens during surgery Lipids and enzymes are best preserved in this method REAL, RHYSSA SHAYNE P. 4 General Histology and Embryology 1st SEM DMD 2 Doc Francis Ian L. Salaver, RMT,MD CYTOPLASM PART 1 HUMAN CELL CELLS THREE BASIC PARTS Cell Membrane Nucleus Cytoplasm – space between the cell membrane and nucleus o Solid Portion ( Organelles) o Fluid Portion (Cytosol) Cytoplasm = organelles plus cytosol plus INCLUSION BODIES CHARACTERISTICS/ IMPORTANCE OF INCLUSION BODIES CELL MEMBRANE Inclusion bodies are also solid portion ( reason why the boundary of the human cell they are always being compared to organelles) CYTOPLASM Not functional organelle inside the cell membranes o inclusion bodies may or may not be present in the NUCLEUS cell the largest part of the cell located at the center. (they o may or may not be found in cytoplasm are represented in a circular shape) o some of them disappear because the majority of o Nucleolus- the inclusion bodies are stored nutrients or ▪ another spherical found inside the nucleus. stored waste products ORGANELLES It may or may not be present in the cell Most are stored nutrients or cell product They are solid structures of the cytoplasm Lipofuscin, lipid, glycogen functional structures of the cell they act as organs in our body LIPOFUSCIN CYTOSOL liquid portions of the cytoplasm HUMAN CELL UNDER THE MICROSCOPE Lysosome- unique because it contains digestive enzymes. Compound type of microscope- commonly used type o involves in intracellular digestion. of microscope in histology laboratory o the cells in the body can break down fats, Cytoplasm= organelles plus cytosol carbohydrates, and lipids – digestion takes place in our lysosome. o As the lysosome breaks down carbohydrates, fats, and lipids, and damages organelles, the accumulated waste products of the digestion will become LIPOFUSCIN. Yellow Brown pigment is composed of residues of lysosomal digestion. Accumulates through the years. REAL, RHYSSA SHAYNE P. 1  TRANS: “Wear and Tear” pigment= cellular senescence or aging It contains brown pigments which represents LIPOFUSCIN Cell A is older than B because the cell A has the higher amount of LIPOFUSCIN INCLUSION BODIES: GLYCOGEN If the cell has lipofuscin will undergo mitosis o the daughter cells will no longer contain lipofuscin. o As the cell will undergo mitosis, the lipofuscin will disappear. o Lipofuscin will also accumulate cells that are not actively undergoing mitosis LIPOFUSCIN- present in postmitotic cells such as nerves, skeletal muscles, and cardiac muscles Lipofuscin is best demonstrated in organs and - cells that are no longer actively dividing As the glucose enter the cell in undergoes GLYCOLYSIS The product of glycolysis is 2 pyruvate molecule will enter the mitochondria and will become 2 Acetyl CoA Will participate at Citric Acid Cycle will proceed to electron transport chain This is how we convert glucose to AtP We tend to overeating= supply our body a higher amount of glucose that is above required in our body 13,59 REAL, RHYSSA SHAYNE P. 2  TRANS: The storage form of glucose is glycogen The body has its way of adapting to the adapting the presence of excess glucose The excess glucose will be transported by insulin to the muscle and liver so that they can be stored in a form of glycogen. CHARACTERISTICS OF GLYCOGEN Glucose in Vagina (B) the storage form of glucose o Not for storage of energy/glucose stored in skeletal muscles and liver o Stratified Squamos Epithelium /Non keratinized NOT stained with H and E (Hematoxylin and Eosin) o Clear areas in their cytoplasm= Glycogen o It appears like clear areas Requires special stain such as periodic acid Schiff (red) Purpose of storing glycogen of the cell in the lining in the vagina ▪ Because of the bacteria (Lactobacillus Acidophilus) – will convert the glycogen into Hepatocytes- active cells of the liver the lactic acid to promote the acidity environment in the vagina to avoid microorganisms or to protect the vagina from infection) ▪ Lactacyd- prevents infection in vagina INCLUSION BODIES: HEMOSIDERIN The ingestible residue of hemoglobin Also appears brown pigment The breakdown product of hemoglobin Clear areas representing the glycogen Can be normally found in the red pulp of the spleen o Spleen- it is where the red blood cells destroyed Often results from bleeding when red cells and hemoglobin are degraded by macrophages o if the red blood cells will destroyed = the hemoglobin will be degraded = end product is hemosiderin Alveolar macrophage if there is hemorrhages in the alveoli o Found any areas of the body that is hemorrhage or bleeding Cells arranged in a central vein It appears as brown granules PERIODIC ACID SCHIFF REAL, RHYSSA SHAYNE P. 3  TRANS: A spleen o White arrow (white pulp) = rich in lymphocytes or also known as white blood cells surrounded with (Alveoli in microscope) red pulp o Red arrow (Red pulp) = It is where the red blood cells are destroyed If the alveolar spaces will be filled up by red blood cells, the macrophages will try to clear them by ingesting them The yellow color in the right side = macrophages Red pulp o Blue arrow- cytoplasm engulf of red blood cells o Splenic Cords = eaten up and broken down by macrophages = o Splenic Sinuses converted to hemosiderin ▪ Spaces between the red pulp where the red blood cells flow ▪ Too small that the red blood cells needs to be flexible ▪ If the red blood cells damaged = lost its flexibility = stranded to these sinuses = will be eaten by macrophages = the red blood cell will be destroyed = formation of hemosiderin Shows that there is hemorrhage or massive bleeding. INCLUSION BODIES: LIPIDS The blue arrow in the right side pointing to a brown pigment Adipose cells Accumulates through time in adipocytes displacing all organelles and nucleus into periphery. o causes the nucleus to be flattened REAL, RHYSSA SHAYNE P. 4  TRANS: Extracted by solvents during tissue preparation, thus appears a “hole in the cytoplasm” o The hole is previously occupied by the fat Blue Arrow ( Balloon like) = Phospholipids o most abundant component of a cell membrane Yellow Arrow (Yellow Colored structure)= Cholesterol Pink Arrow (Safeguard Structure) = Protein Green Arrow = Carbohydrate The nuclei being flattened, not found at the center but found in the periphery PHOSPOLIPIDS makes up the majority of the bilipid layer of the cell membrane 2 layers of Phospolipids o Head = Phosphate = Hydrophilic= Interact with water or water loving (water attracting phosphate head group) = polar o 2 Tails = 2 fatty acids – Hydrophobic = water fearing (water repelling fatty acids) = nonpolar If the substance has the both hydrophobic and hydrophilic portions, we describe the substance as Melanin found on the basal layer of the epidermis AMPHIPATHIC. Anything brown pigment in the skin/ stratified squamous keratinized HOW ARE THE PHOSPOLIPID ARRANGE IN THE BILIPID LAYER CELL MEMBRANE Since there is water outside the cell, the hydrophilic The outermost boundary of the cell portions is facing the water while the hydrophobic is Regulates passage of molecules in and out of the cell are hidden in the water Bilipid layer DO YOU KNOW THAT PHOSPOLIPIDS TEND TO o 2 layers of lipid MIGRATE FROM ONE PLACE TO THE OTHER? 4 components of cell membrane o Phospolipids o Cholesterol o Proteins o Carbohydrates REAL, RHYSSA SHAYNE P. 5  TRANS: The insulin receptors will bind to the proteins = proteins respond by causing the blue-colored glucose transporter to open = glucose is free to open Glucose will never enter the human cell without insulin If insulin is absent, the glucose will remain in the blood that will caused and diagnosed DIABETIC. What if the membrane is highly fluid? they can change the location of other components of 56:05 the cell membrane o glucose will stay in the blood LIPID RAFTS AS SIGNALING PLATFORMS What will now keep the glucose transporter in place? G-coupled protein composed of 7 transmembrane o The role of the cholesterol is very important proteins and alpha, beta, and gamma protein subunits. CHOLESTEROL Ligands bind to the G coupled receptor which later Cholesterol has a hydrophobic ring cause the activation of the alpha, beta and gamma Hydrophilic hydroxyl group subunits They are both AMPHIPATHIC Signal transduction in lipid rafts occurs more rapidly Inserted among closely packed phospholipids since proteins are found in proximity to each other restricting their movements and thus modulating fluidity and movement of membrane components. PROTEINS How is the Cholesterol arranged in the cell membrane? o Hydrophilic (Hydroxyl group ) located in the area where the phosphate heads of the phospholipids located which are also hydrophilic o Mix along with the hydrophobic fatty acid the furfuse ring of the cholesterol o Purpose of cholesterol ▪ To restrict the movements of the cell membrane ▪ Restrict the movements of phospholipids, keeping the glucose receptors in place Can be divided into ▪ So that the glucose will freely enter o Integral (Transmembrane) proteins ▪ Directly incorporated into the cell membrane LIPID RAFT ▪ Channels, carriers, and transporter o Peripheral Proteins ▪ Exhibits looser association with one of the membranes ▪ Responsible for the shape of the cell and transport of the substances within the cell ▪ They can be responsible for the maintenance of the shape of the cell. Localized region within the plasma membrane that contains high levels of cholesterol and variety of peripheral and integral proteins Area is limited in fluidity thus restricting movement of the proteins which may be involved in cell signaling processes Lipid rafts is abundant in proteins Ankyrin and actin will pull each other using the spectrin causing the bi concave shape of the red cell Hereidtary Spherocytosis = absence of spectrin REAL, RHYSSA SHAYNE P. 6  TRANS: o Ankyrin and actin will not interact with each other and will not form the cell as biconcave concave- shaped o Biconcave shape helps the red blood cells to squeeze into small capillaries o Spherical shape blood cells will have a hard time squeezing themselves into the smaller capillaries = the red blood cells of the people with hereditary spherocytosis will be destroyed in CIRCULATION ▪ Patients with hereditary spherocytosis will have ANEMIA. Endothelial cells- the lining of the blood vessels The green color surrounded by the cell membrane of the neutrophil helps the white blood cells to attached themselves to the wall so that they can easily go out to the blood vessels – CARBOHYDRATES Carbohydrates, glycoproteins, and glycolipids can help cell adhesion Freeze fracture model = developed to study the integral proteins present in the cell membrane o (1)we exposed cells in freezing temperature o (2) strike a force by using a hammer o (3) the force will cause the cell membrane to fracture o (4) the fracture is being created to the hydrophobic portion (fatty acids) of the cell membrane o (5) the membrane will be separated into 2 layers ▪ Extracellular layer (outer part of the cell) ▪ Cytoplasmic Layer (closer to the cytoplasm) o (6) Freeze Fracture Model should be view in ELECTRON MICROSCOPE Prove the presence of integral proteins CARBOHYDRATES Microbe that has been phagocytose by macrophage o Microbe is digested to the cytoplasm of macrophage and the certain portion of the macrophage is loaded in the green color structure that contains carbohydrates o The carbohydrate-containing structure and microbe is together displayed on the surface of the macrophage o After, This macrophage interacts with the Helper T Cell because it will present that portion of the microbe to helper cell. And the T Helper Cell will Can be Glycolipids ( Carbohydrates attached to respond by using the T cell receptor which also phospholipids) or Glycoproteins (Carbohydrates contains carbohydrates attaches to protein) o Carbohydrates will help to cell to cell o Generally found outside the cell membrane interaction o May act as a receptor that participate in cell o The T cell that is being activated by the adhesion and cell-to-cell interaction. macrophage using the carbohydrates will interact o Best example of cell adhesion is CHEMOTAXIS with the B cell. o B cell will transform = a plasma cell (which produce antibodies) REAL, RHYSSA SHAYNE P. 7  TRANS: o Only one of the bacteria will killed by the macrophage o The antibodies killed the 3 other bacteria PASSIVE TRANSPORT (1) Simple Passive o Diffusion o Directly across the cell membrane o Ex. Oxygen and carbon dioxide diffusing across the membrane via Simple Passive Transport (2) Facilitated Passive (With the aid of channels or carriers) o from higher to lower concentrations that will need channels or carriers From higher to lower concentration o the cell will not use energy. No need for energy consumption Channel o allowing the transport of the cell from the area of the higher to lower concentration o doesn’t change its shape Carrier o allowing the transport of the cell from the area of the higher to lower concentration o changes its shape ACTIVE TRANSPORT Requires energy consumption Pumps transport molecules from lower to higher concentration ( against concentration gradient) there is a consumption of ATP requires energy The transport of molecules is against a concentration gradient. REAL, RHYSSA SHAYNE P. 8 LESSON 2- CYTOPLASM PART 2 Facilitated passive transport - the transport of substances from an area of higher concentration to lower concentration with the help of a channel or carrier - In this phase, the membrane stays still. 1. Phagocytes will approach the bacterium Endocytosis (brown colored). - A portion of the cell membrane will engulf the material that should be transported 2. A part of the cell membrane of the phagocyte towards the cytoplasm and that material will invaginate to enclose the bacterium. will be engulfed to the vesicle. 3. Eventually, that portion of the cell membrane Three types of Endocytosis: will detach from the cell membrane and form a vesicle. 1. Phagocytosis - A material that is engulfed and enclosed in TAKE NOTE: the vesicle as a solid particle such as bacteria - Inside the vesicle, there is the internalized or and yeast cells. engulfed bacterium; since the vesicle is the - White blood cells (neutrophils and product of phagocytosis = phagosome macrophages) take up solid materials - Engulfment of bacteria, protozoa, dead - Phagosome is only a vesicle, only a container; it cells and unneeded extracellular does not have the ability to kill the bacterium. constituents. - The phagocytosed material is then enclosed in 4. Phagosome needs to fuse with another a phagosome. organelle which contains digestive enzymes to form Phagolysosomes. - PHAGOSOME + LYSOSOME = PHAGOLYSOSOMES Lysosome - main purpose is to expose the engulfed bacterium to the powerful digestive enzymes 5. Digestion starts after the fusion of the phagosome with lysosome to form phagolysosome. TAKE NOTE: would surround and engulf it and enclose it to - If bacteria enter directly into the cytoplasm, the vesicle. they will likely die within 10 seconds due to the - Binding of ligand/ target molecule to the presence of enzymes that can destroy them. receptor will cause widely dispersed receptors Bacteria need to be enclosed in a vesicle because to aggregate which results to take up the ligand. some produce toxins that can kill phagocytes. 2. Pinocytosis - Also known as cell drinking because the material that is engulfed and enclosed in the vesicle is uid by nature. - Result to the metabolism of the engulfed uid or substance. = another process that is similar to pinocytosis which involves the engulfment of uid but it does not end up getting metabolized. Formation of the vesicle: - Fluid-phase endocytosis - Small invaginations of the cell membrane form and entrap uids which are then enclosed in vesicles. 1. During endocytosis, receptors binding to the target substance accumulates in a speci c region of the membrane. 2. There are other proteins that will aggregate on Transcytosis the cytoplasmic side of the cell membrane = - engulfed transferred to the other side of Clathrin and adaptin the cell (does not result in the metabolism of the engulfed uid or substance. Clathrin and adaptin - responsible for the invagination of the cell membrane causing the formation of the 3. Receptor- mediated endocytosis vesicle. - The material is only enclosed in the vesicle if the material will bind to the receptor ; the star 3. Cause the vesicle to detach from the rest of the shaped material should bind rst to the green cell membrane = Dynamin colored receptors before the cell membrane Dynamin- helps mediate the liberation of the - determine what the cell would do clathrin-coated vesicle from the plasma membrane. endocytose particles - Sort out endocytosed materials 4. Vesicle is transported towards the early endosomes. Two types: 1. Early endosome - found near the cell membrane , rst to interact with the endocytic vesicle 2. Late endosome - found deeper than the early endosome ; receives vesicles originating from the early endosome - Matures into lysosome = pre lysosome 2 Models by paulina 1. Vesicles are formed and it’s coated with 1. The early and late endosomes are di erent clathrin and adaptin. organelles existing on the cytoplasm of the cell. 2. The late endosome is the mature form of the 2. Dynamin is coling around the base of the early endosome. vesicle = it can mediate the release or liberation of the vesicle from the cell membrane. Early endosome — multivesicular body —late endosome — lysosome Endosome - Endosomes facilitate the detachment of - The environment inside these organelles are receptors from their ligands (target molecules). acidi ed by the addition of hydrogen ions. This process allows the vesicle containing the - Once enzymes activated by the acidic ph, receptor to separate and return to the cell lysosome will facilitate intracellular digestion membrane, where it can be recycled to pick up and turnover of damaged organelles. another target molecule = no signi cant change Lysosomes in the surface area of the cell membrane. - site for intracellular and turnover of cellular components. Endocytosis - part of the membrane becomes part of the - Contains di erent powerful digestive enzymes. vesicle / formation of the vesicle - Mature form of late endosome - Destroy and digest the said organelle using the Exocytosis - membrane is returned to the cell surface / same powerful digestive enzymes, the recycling of the vesicle back to the cell membrane Endosome  2. The organelles will be enclosed in a vesicle and the vesicle will be called the AUTOPHAGOSOME which is fused with lysosome. Autophagy (self- eating system) - The process wherein the lysosome is used by the cell to remove its own organelles. 1. enzymes of the lysosomes are produced in the rough endoplasmic reticulum 2. enzymes of the lysosome are still immature and non-functional = transported to the golgi apparatus golgi apparatus = modify, store package and transport proteins and enzymes 3. Inside the golgi the enzymes of the lysosomes are bound to mannose six phosphate. 4. Enzyme and the mano6 phosphate complex will bud o from the golgi to be transported to the early and late endosomes 5. If the mano6 phosphate and the enzyme complex will bind to the mano6 phosphate receptor = cause the early and late endosome to engulf the manocystophosphate and the Mitochondrion / Mitochondria enzyme - powerhouse of the cell - Found almost all the cells in the body except the red cells and its number di er - Has its own set of DNA and RNA - Can only work on medium chain and long chain fatty acids and cannot facilitate the beta oxidation of very long fatty chain acid (18 or more) - 2 membranes : outer and inner membrane - membrane enclosed organelle that functions for the ATP PRODUCTION 1. Unwanted, damage and non-functional - abundant in the following cells: organelles that need to be removed from the 1. Cardiac muscles = need to work every second cell of the day just to help the heart pump out  blood for the blood to circulate through the body Glucose — Glycolysis ( happening in the cytoplasm 2. Cells in the kidney tubules = always of the cell) —- Pyruvate — Acetyl Coenzyme A— functioning to adjust the concentration of Kreb Cycle (NADH & FADH2) — Electron urine and should also reached in mitochondria transport chemiosmosis 3. Sperm Cell = Mitochondria to provide energy to the agellum, enabling the sperm 1. Glucose enters the cell through the action of cell to propel itself forward toward the egg insulin. cell in the fallopian tube; also concentrated 2. Glucose undergoes glycolysis (happens outside un areas in the cell where energy is needed = the mitochondria) in the cytoplasm of the cell midpiece of sperm cell to produce pyruvate. 3. Pyruvate enters the mitochondria and is Intermembrane space converted into Acetyl Coenzyme A - space between the inner and outer membrane 4. Acetyl CoA enters kreb cycle ( mitochondrial matrix ) = products are Cristae FADH2 and NADH - The folded areas inside the inner membrane 5. The acetyl Coenzyme A will participate in the - Associated or found in the mitochondrion kreb cycle / citric acid Cycle. The products of - increase the surface area for energy production the kreb cycle ( FADH2 and NADH) will - Projecting towards the mitochondrial matrix participate or will become part of the electron transport and chemlosmpsis. Matrix / Mitochondria Matrix 6. Once the NADH and the FADH2 will - Space within the inner membrane interact with and the proteins in the electron - contains small circular chromosome of DNA transport chain the matrix will pump out and sets of mRNA hydrogen into the inter membrane space 7. Imbalance distribution of hydrogen so the mitochondrion will cause hydrogen ions to be transported back to the mitochondrial matrix through the protein ATP SYNTHASE. TAKE NOTE: SITE OF GLYCOLYSIS- CYTOPLASM SITE OF KREB CYCLE - MITOCHONDRIAL MATRIX SITE FOR ELECTRON TRANSPORT CHAIN - INNER MEMBRANE OF MITOCHONDRION ATP SYNTHASE - responsible for the synthesis of atp - Everytime hydrogen ions passes through the Atp synthase = production of ATP  releasing chemicals that initiate Nucleus programmed cell death. - Control center of the cell - Contains the DNA 4. Synthesis of reactive oxygen species - reactive oxygen species such as superoxide and hydrogen peroxide can kill bacteria - Electron transport chain are always functioning we need atp constantly - Hydrogen peroxide is potentially damaging to the organelles present in the celll Peroxisomes - contain the enzyme catalyst Endosymbiotic Theory - Break down hydrogen peroxide into water - mitochondria were formerly a separate living so that the hydrogen peroxide will not cause organism. damage to the cell producing the reactive oxygen species 1. A bacterium is engulfed by a human cell. - Are involved in beta oxidation of VERY 2. The bacterium is enclosed in a vesicle via LONG FATTY ACID CHAIN ( 18 or more) endocytosis or phagocytosis. = Acetyl - CoA 3. If the human cell fails to kill the bacterium, and - Synthesis of plasmalogen for the synthesis of the bacterium has survival mechanisms, the myelin sheath vesicle membrane folds inward, with the membrane becoming wrinkled. The vesicle's inner membrane becomes the bacterium's inner membrane, while the vesicle itself becomes the outer membrane. Other functions of the mitochondrion: 1. Synthesis of steroid hormones - derived from cholesterol - Synthesized in the mitochondria of the cell 2. Beta oxidation of fatty acids - for energy production - fatty acids are broken down into the 2- carbon compound acetyl-CoA for energy production. 3. Initiator of apoptosis / cell death - Mitochondria are sensitive to trauma or injury thus can initiate the cell to die by  CYTOPLASM PART 3 What contributes to the differences in our physical traits? Height is greatly influenced by growth hormone: a protein The pigment responsible for the brown color of the skin is melanin: a protein How do we produce the melanin pigment? The synthesis of melanin starts with the phenylalanine amino acid This amino acid will be acted upon by the enzyme phenylalanine hydroxylase, which will be then converted to L-tyrosine. L-tyrosine amino acid will now serve as a substrate for the production of the brown pigment of the skin: Melanin Take note: CONCLUSION: Physical traits are — This chemical reaction was made possible by the enzyme phenylalanine hydroxylase affected by the set of proteins that we — Enzymes are proteins have in our body. — Height : Growth Hormone — Melanin : Phenylalanine Hydroxylase Proteins are made up of a series of Amino Acid Amino acid in a certain protein has a specific sequence, changing or interchanging one amino aid in the sequence will change the protein itself. The sequence of amino acid should be strictly followed If the body has to produce the protein everyday; the body should have a "record" of how to sequence the amino acid to produce the right proteins. The body must have the recipe (GENE) in order to come up with the appropriate proteins GENES > ↳ determines the proper Sequence of AMINO AGD in order to form PROTEINS. -  DNA contains smaller areas/subunits called Genes Genes determine the proper sequence of amino acid to produce specific proteins Specific proteins affect our physical traits DNA is found within the nucleus RIBOSOMES The site for protein synthesis Located within the cytoplasm DNA cannot go out of the nucleus to interact of the ribosome DNA is enclosed within the nucleus in order to protect it from the damaging effect of enzymes of chemicals found within our cytoplasm =>DNA ! Thus TRANSCRIPTION takes may undergo Mutation , place. TRANSCRIPTION In transcription, we unwind the portion of the DNA containing the gene, and we complementarily copy the sequence of the bases in the gene The copied form of the gene is no what we call as the mRNA or messenger RNA These mRNA are the ones who goes out of the nucleus and interact w/the ribosomes to encode the sequence of amino acid to form the specific proteins that is encoded by the gene that was copied in the DNA inside the nudeus. mRNA is synthesized in the nucleus during transcription, where it copies the genetic information from DNA. Once the mRNA is processed and mature, it exits the nucleus and enters the cytoplasm. There, it interacts with ribosomes, which read the mRNA sequence and use it as a template to synthesize proteins by linking together the appropriate amino acids in the sequence specified by the mRNA. Unwinding of the DNA; one of the strands is copied complimentarily (contains the gene important for protein production), thus producing the mRNA These strand goes out of the anchor pone into the cytoplasm I will interact of the large and small units of the ribosome the code copied by the mRNA from the bath will be read and will be translated to the correct sequence of amino and in order to form the correct protein. 2 PROCESSES INVOLVED IN PROTEI PRODUCTION TRANSCRPROT mRNA product : Transcription - synthesis of mRNA by copying the sequence in the genes found in our DNA. It takes place inside the nucleus Translation - the code in mRNA is read and translated into specific sequences of amino acid to produce proteins. It takes D place its within the cytoplasm, in the ribosomes product proteins: ROUGH AND SMOOTH ENDOPLASMIC RETICULUM NUCLEUS have 2 layers of membranes - - the outer nuclear membrane is directly continuous with the Rough ER. B studed w/ Ribosomes making it appear granular/rough Smooth ER-found away from - the - nucleus - devoid of Ribosomes ↑ Reason RER why the is positioned immediately beside the nudeus - ! La RER contains ribosomes which aids in protein synthesis It would be much easier for the mRNA to look for a ribosome once it will go out of the nucleus The foldings within the Rough and Smooth ER-CISTERNAE - - REMEMBER V G foldings within the inner mitochondrial · membrane are CRISTAE · in the case of our ER , we call them as CISTERNAE & RER MITOCHONDRIA OUTER N MEMBRANE INNER. NUCLEOLUS  Take note: All proteins except antibodies are produced in the LIVER Antibodies are produced by the plasma cells of the immune system Hepatocytes of the liver are protein producing cells : thus these cells have abundant number of rough endoplasmic reticulums. Pin ENDOPLASMI ↳ pose cells also abundant in the Liver Fistone particularly in HEPATOCYTES ! the & Every time that we take in ethanol/alcohol, it will be metabolized in the liver to form Acetaldehyde Too much alcohol intake will overwhelm the cytoplasm (cytosol) and will eventually call for backup: the smooth endoplasmic reticulum Some people easily get drunk because they have a less active smooth ER when metabolizing alcohol  DUE TO THE PRESENCE OF ENZYME CYTOCHROME P450 ; INVOLVE IN DRUG METABOLISM Tus PE I , WE CAN CONCLUDE THAT THE SMOOTH ENDOPLASMIC RETICULUM IS CAPABLE Of METABOLIZING DRUGS. SMOOTH ER CAN ALSO STORE CALCIUM IN MUSCLES Smooth Er in the muscles have special names: the Sarcoplasmasmic Reticulum Example: A nerve trying to control a muscle — the nerve releases ACh — the release of ACh ( neurotransmitter ) activated an action potential which actives the sarcoplasmic reticulum of the muscle , releasing the stored calcium resulting in muscle contraction. — during muscle relaxation, the calcium will be restored back into the sarcoplasmic reticulum  The rough Er will send the immature and nonfunctional proteins to another organelle where they will be modify, package, store and transport proteins until they mature and will be functional. - I - GOLGI COMPLEX or GOLSI APPARATS also contains folds called cistern the portion facing the rough ER and receiving due resides containing the immature proteins is called the cis face the portion where the nature proteins buds off to be transported is called the trans face WHAT WILL NOW HAPPEN TO MATURE AFTER IT THE PROTEIN HAS BUD OFF FROM THE GOLGI APPARATS ? Example of Regulated Pathway: Muscle Contraction — arrival of action potential in the post synaptic neuron, causing calcium channels to open and allowing them to go inside — this ions caused the vesicle (ACh) to be released which aids in muscle contraction — the stimulus here is the calcium con  ANTEROGRADE or FORWARD PATHWAY proteins will be synthesized in the ribosomes of the rough endoplasmic reticulum, then it will be transported to the Golgi apparatus ; after the proteins become functional and mature, the proteins will bud off to the trans face of the Golgi apparatus RETROGRADE PATHWAY proteins produced from the rough ER is transported to the Golgi apparatus, after maturation, it will bud of from the trans face, they will be transported back to the rough ER. RER also needs proteins in order to function COP1-mediates retrograte transport decides whether proteins will undergo retrograde COP2-mediates anterograde transport O or anterograde some proteins produced - are misfolded or nonfunctional - - ↳ it will be broken down back into AMINO ACIDS "PROTEASOMES" capable of digesting - proteins  ↳ capable of UBIQUITI recognizing ; a protein present in the of the cell cytoplasm and its key role is to look for misfolded or denatured proteins. MISFOLDED PROTEINS WILL BE CONJUGATED TO UBIQUITN Proteasomes if a protein has ubiquitin conjugated to it it will be targeted by - , CENTRIOLES Functions to produce the mitotic spindle fibers during cell division (mitosis and meiosis) yellow Loblue O TAKE NOTE: The outer membrane of the nuclear envelope is continuous with the rough ER. Outer membrane is also contains ribosomes so that once the mRNA will go out of the nucleus they can be translated in one of these ribosomes. Chromatin is attached to the inner nhclear membrane and what is causing it to be linked to the inner membrane is those blue yellow colored figures those or proteins responsible for anchoring the chromatin to inner membrane called Nucleur Lamina. What portion of the nuclear envelope is Take note: our DNA is enclosed with in associated with nuclear lamina? INNER our nucleus and the main purpose of it NUCLEAR MEMBRANE is to protect the dna from any chemical that can cause it to mutate, but the What is the function of the nuclear lamina? structure within the nucleus still needs It functions to attach the chromatin to the substances that can be found outside inner nuclear membrane the cytoplasm thats why the nuclear envelope should be provided with nuclear pores but this pores must be strict in allowing substances to go in and out of the nucleus it has to be selective because not all substances that will try to enter is beneficial to the nucleus The nuclear pore will allow substances to go in and out of the nucleus through simple diffusion bc small substances have less tendency to cause mutations Nuclear Lamina is found between the chromatin and inner nuclear membrane because it functions to link Recall that proteins are produced in the rough ER or ribosomes but they are initially produced as immature or non functional proteins, these proteins must be transported to the golgi apparatus it functions to modify the proteins and decide where to transport them after In terms of the proteins that are needed by the nucleus the golgi apparatus will modify them by incorporating in their struture Nuclear Localization Signal and the presence of which will allow the protein to go inside the nuclear pore to the nucleus Importin - protein that will identify if the protein has a nuclear localization signal Take note: dna is acidic and it is negatively charged while histones are basic proteins so opposites attract, histones are positively charged so it would be easy for histones to interact with dna Chromosomes and Chromatin are condensed forms of dna and dna was condensed because The main role of the importin is to transport dna was wrapped around histones the protein with the nuclear localization signal through the nuclear pore then to the nucleus, after their entry to the nucleus they will encounter run gpt and the run gpt will cause the alpha subunit of the importin to dissociate from the protein allowing the protein now to be liberated inside the nucleoplasm NLS importin run gpt alpha subunit  Take Note: as the DNA is wrapped around histones they will form what we call “beads on a string” because the nucleusome is described to have beads on a string appearance The DNA will wrap around eight histone molecules and these eight will be referred to as octamer Which among these two would appear darker in a microscope? CHROMOSOME because it is the condensed form of DNA DNA is in the form of chromatin in metabolically active cells but if these cells will undergo cellular division the chromatin further condense and when they do they will now be able to form what we call the chromosomes Chromosomes are actually composed of your dna molecules that are tightly wrapped Take Note: for DNA to be transcribed the around or condensed around histones two strands should be separated so that one strand can be copied to form the mRNA Take note: if the cells are metabolically active and you cannot do that on DNA that is they are not undergoing any form of cellular tightly coiled around histones, the DNA division, the dna must be in a chromatin form must be loosely attached to the histone so and if the cell should undergo mitosis the dna that it would be easy for us to separate the should be condensed to form the two strands and copy one of the strands to chromosomes form the mRNA So what you should expect to see in a Answer is Cell A because it is metabolically metabolically active cell is the chromatin and active and part of the metabolism is to what you’re supposed to see in a cell that is produce proteins supposed to undergo the cell division is the chromosome  The pattern in the hepatocyte is string bead string bead If this is the nucleus of the hepatocyte any light areas would mean that the dna is not wrapped around histones because that portion of the dna should always be transcribed to form mRNA Any light areas could be representing albumin and the dark areas represent the portion of the dna that are not needed by the cell that why it is wrapped around histones There are small areas in the DNA which we call the genes and these genes are the ones responsible for the encoding of proteins Take Note: the portion of the DNA that is actively transcribed should not be tightly coies around histones so therefore that portion of the dna will appear lighter and we refer to it as Euchromatin While the portion of the dna that is not needed by the cell should be tightly coiled around histones therefore it will condense and it will appear darker than euchromatin Take Note: the cells in the body have the same and that is Heterochromatin dna so expect that they have the same sets of genes If the cell your looking at is known to produce proteins expect that the cells would have higher amounts of euchromatin compared to HC so expect that the nucleus of that cell should apper lighter compared to the nucleus of another cell that is not active or does not function to produce protein The nuclei of cells that are active in protein The synthesis appear lighter than the nuclei of spherical cells that do not fuction to produce protein structure we can find inside the nucleus Marginal Chromatin - the dark staining areas that are found near the nuclear membrane Nuclear Associated Chromatin - the chromatin that you can find associated with the nucleus Karyosome - the other heterochromatin that you can find between the marginal Basophilic means they are attracted to basic and the nucleolar associated chromatin dyes such as hematoxylin so expect that the nucleulos will have color dark blue Remember: The function of the ribosomes will interact with the mRNA then the mRNA code is translated to form proteins What is the role of ribosomal rna in protein synthesis?? For ribosomes to be formed you must combine ribosomal rna plus proteins We can never form these ribosomes without rRNA and rRNA is produced by the nucleulos inside the nucleus Imagine, the DNA will be transcribed to form mRNA while the rna is going out of the nucleus, what will assemble the ribosomes so that the mRNA will be translated later on by the riboome is the nucleolus because the nucleolus will produce the mRNA If the cell decides to undergo mitosis it must produce daughter cells with the equal number and type of chromosomes  S Phase is the stage that the cell will duplicate its chromosomes in preparation for another round of mitosis so to have the energy to duplicate its dna or chromosomes the cell in the g1 must gather all the nutrients and materials needed for the dna to be duplicated at the S Phase Cells do not simply jump from g1 to s because the cells mus go through checkpoint because they need to meet some of the requirements which will be checked by checkpoints Take Note: it is not all the time that the cells are dividing because they need to allot some time doing their function  G2 Phase is the last stage of interphase and before the cell is allowed to move from g2 to the actual stage of mitosis the cell has to encounter two checkpoints Checked for its integrity and presence of mutations or damage, you should not allow the damage or mutated dna to be replicated in the S Phase or else mitosis will produce two daughter cells with abnormal or mutated dna Mitosis is the cellular division of somatic cells in the body so these cells are supposed to have 46 chromosomes and these cells are called diploid cells Mitosis will produce two daughter cells and since the number of chromosomes of the daughter cells are similar to the mother cell which is a somatic cell expect that the two daughter cells are diploid