Body Fluid Distribution and Ionic Composition PDF Lecture Notes

Field of Medicine Medicine And Surgery Program Lecture: Chromatin Structure & Cell Cycle Dr.Hidi Azmy El Tahawy Date: 15 / 10 /2024 Let’s think together  Let’s think together DNA length in each cell is about 2m, how is this length compacted in the cell nucleus? ...

Field of Medicine Medicine And Surgery Program Lecture: Chromatin Structure & Cell Cycle Dr.Hidi Azmy El Tahawy Date: 15 / 10 /2024 Let’s think together  Let’s think together DNA length in each cell is about 2m, how is this length compacted in the cell nucleus?  ILOs By the end of the lecture, the student should be able to: 1. Identify eukaryotic chromatin structure. 2. Illustrate the phases of cell cycle. 3. Describe the flow of genetic information.  Chromatin Structure Chromatin is present in non-dividing cells, not visible by light microscope. regularly beaded thread by electron microscope Before cell division, DNA molecules are replicated or doubled. The chromatin is supercoiled in the form of chromosomes. Each chromosome is formed of two identical chromatids.  Chromatin Structure Each Chromatid Consists of: 1- A single DNA molecule. 2- Histone proteins. 3- Non-Histone proteins.  Chromatin Structure 2- Histone proteins: 5 classes of histones (H1, H2A, H2B, H3 & H4) Basic proteins (high content of lysine and arginine) Because of their positive charge, they form ionic bonds with negatively charged DNA. Histones play an important role in DNA supercoiling and regulation of gene expression.  Nucleosome Structure 2- Histone proteins: ▪ Each chromatid is formed of many nucleosomes. ▪ Each nucleosome is formed of 8 histones (histone octomer or histone core) or two copies of each of H2A, H2B, H3 and H4. Around histone octomer, a segment of dsDNA is wound nearly twice (contains average 150 bp).  Nucleosome Structure 2- Histone proteins: ▪ Linker or spacer DNA (contains average 50 bp) connects different nucleosomes like beads on a string. ▪ H1 is attached to linker DNA. ▪ It facilitates packing of nucleosomes into more compact structures. Chromatin Structure  Nucleosome Structure 3- Non-histone proteins: ▪ They interact with the major groove. ▪ Important for the regulation of gene expression. ▪ Responsible for replication and transcription.  Packing of DNA Higher levels of organization: ▪ Nucleosomes can be packed more tightly (stacked) to form a nucleofilament. ▪ This structure assumes the shape of a coil, often referred to as a 30-nm fiber. ▪ The fiber is organized into loops anchored by a nuclear scaffold containing several proteins. ▪ Additional levels of organization lead to the final chromosomal structure. Packing of DNA  Which class of histones facilitate the packing of DNA? H1is attached to linker DNA  Cell Cycle Definition: Events that lead to the completion of cell division & formation of two daughter cells due to mitosis. Stages of Cell Cycle: ▪Mitotic Phase (M) ▪Interphase G1 Phase S Phase G2 phase ▪G0  Cell Cycle Stages of Cell Cycle: ▪ G1 phase: In this phase the cell prepares itself for replication. ▪ S (synthesis) phase: In this phase, the DNA is replicated to produce copies for both daughter cells. ▪ G2 phase: In this phase, new proteins are synthesized and the cell approximately doubles in size preparing itself for mitosis. ▪ M phase (mitosis): In this phase, the maternal nuclear envelope breaks down, paired chromosomes are pulled to opposite poles of the cell, each set of daughter chromosomes is surrounded by a newly formed nuclear envelope, and cytokinesis pinches the cell in half, producing two daughter cells.  Cell Cycle Stages of Cell Cycle: ▪ In embryonic or rapidly proliferating tissue, each daughter cell divides again, but only after a waiting period known as the G1 phase. ▪ In cultured animal cells the entire process takes about 24 hours. ▪ After passing through mitosis and into G1, a cell either continues through another division or ceases to divide, entering a quiescent phase (G0) that may last hours, days, or the lifetime of the cell. ▪ Differentiated cells that have acquired their specialized function and form; remain in the G0 phase (nerve cells). ▪ Stem cells retain their potential to divide and differentiate into any number of cell types. Cell Cycle Cell Cycle  Cell Cycle Regulation & Control of Cell Cycle: ▪There are two key classes of proteins that control the progress of a cell through the cell cycle. ▪They are: The cyclins and Cyclin-dependent kinases (Cdk). Cell Cycle  Cell Cycle Regulation & Control of Cell Cycle: ▪ The cell cycle is initiated by binding of a growth factor to a growth factor receptor on the plasma membrane of the cell. ▪ This leads to autophosphorylation of tyrosine residues in the receptor which becomes an active protein tyrosine kinase that can catalyze phosphorylation of target proteins. ▪ This mediates an intracellular signaling cascade that finally induces the genes producing cyclins. ▪ Cyclins complex with and activate certain CDKs that phosphorylate substrates essential for the passage of the cell from one phase to another.  Cell Cycle Regulation & Control of Cell Cycle: ▪ Animal cells have at least 10 different cyclins (designated A, B, and so forth) and ▪ at least 8 CDKs (CDK1 through CDK8), ▪ which act in various combinations at specific points in the cell cycle.  Cell Cycle Cell Cycle Check Points: ▪ The cell cycle is controlled at a series of checkpoints: that prevent entry into the next phase of the cycle until the preceding phase has been completed.  Cell Cycle Cell Cycle Restriction Point: In the cell cycle, there is a restriction point (in late G1) beyond which the cells become committed to enter the S phase and to complete the cycle independent on the presence of the growth factors. If cultured mammalian cells are removed from medium containing growth factors to one lacking growth factors before they have passed the restriction point, the cells do not enter the S-phase. True or False DNA replication occurs in mitotic phase of the cell cycle. The flow of genetic information Central Dogma ▪ Replication ▪ Transcription ▪ Translation  Summary ▪ Chromatin structure. ▪ Cell cycle. ▪ Central Dogma.  References Lippincott's Illustrated Reviews: Biochemistry, 7th Edition. Chapter 30. Field of medicine Medicine Program Lecture : (body fluid distribution and ionic composition) Dr : (Dr. Mohamed Talal ) Date : 4 / 10 /2022 Introduction ( Patient suffering from Renal Failure = no urine ) 1 2 3 Normal weight 4 43,5 kg Total body water Accounts for 50 – 70 % of body weight. Example: A 70 kg man, calculate his body weight (= 42 liters). Correlates inversely with body fat. Because females have a higher percentage of fat than males, they tend to have less body water  Body fluid compartments: Intracellular fluid (fluid inside the cells) = 2/3 (40 %) Extracellular fluid (fluid outside the cells) = 1/3 (20 %) Plasma (fluid circulating in the blood vessels) = 5 % Interstitial fluid (fluid that bathes the cells) = 15 % Composition of extracellular and intracellular flu Substance ( mEq/L ) Extracellular fluid Intracellular fluid Na+ 140 14 K+ 4 120 Cl- 105 10 HCO3 - 24 10 Intracellular fluid: Major cations K+ Major anions Proteins and organic phosphate Extracellular fluid Major cations Na+ Major anions Cl- and HCO3 - Measuring volumes of body fluid compartment By dilution method Equations  Measuring volumes of body fluid compartment Steps Identification of an appropriate marker substance. Markers for total body D2O  Distrusted wherever water is found water Markers for ECF volume Mannitol  Large molecular weight  Can not cross cell membranes Markers for plasma volume Radioactive  Too large albumin  cannot cross capillary walls ICF and interstitial fluid are determined indirectly Measuring volumes of body fluid compartment Clinical case A man is participating in a research study for which it is necessary to know the volumes of his body fluid compartments. To measure these volumes, the man is injected with 100 mCi of D2O and 500 mg mannitol. During a 2-hour equilibrium period, he excretes 10 % of the D2O and 10% of the mannitol in his urine. following equilibration, the concentration of D2O in plasma is 2.13 mCi/ L and the concentration of mannitol is 32 mg/L. what are his total body water, his ECF volume, and his ICF volume. Measuring volumes of body fluid compartment Clinical case ( the answer ) Measuring the total body water : amount of D2O injected − amount of D2O excreted 𝑐𝑜𝑛𝑐𝑒𝑛𝑡𝑟𝑎𝑡𝑖𝑜𝑛 𝑜𝑓 𝐷2𝑂 𝑖𝑛 𝑝𝑙𝑎𝑠𝑚𝑎 100 −10 = 42,2 L 2.13 Measuring volumes of body fluid compartment Clinical case ( the answer ) Measuring the extracellular fluid : amount of mannitol injected − amount of mannitol excreted 𝑐𝑜𝑛𝑐𝑒𝑛𝑡𝑟𝑎𝑡𝑖𝑜𝑛 𝑜𝑓 𝑚𝑎𝑛𝑛𝑖𝑡𝑜𝑙 𝑖𝑛 𝑝𝑙𝑎𝑠𝑚𝑎 500 −50 = 14,1 L 32 Measuring volumes of body fluid compartment Clinical case ( the answer ) Measuring the intracellular fluid : Total body fluid volume – extra cellar fluid volume 42.2 − 14.1 = 28,1 𝐿 Measuring the total body water : In Body test is a non-invasive body composition analysis that provides a detailed breakdown of your weight in terms of muscle, fat, and water Measuring the total body water : In Body test Preparation for in-body analysis : 1. Do not eat for 3-4 hours before testing 2. Do not exercise for 6-12 hours before testing 3. Ensure access to both feet with removable footwear and socks 4. Avoid putting lotion on hands and feet before testing Measuring the total body water : In Body test analysis 𝑇𝑜𝑡𝑎𝑙 𝑏𝑜𝑑𝑦 𝑤𝑎𝑡𝑒𝑟 ( 𝐿 ) = 𝑏𝑜𝑑𝑦 𝑤𝑖𝑔ℎ𝑡 ( 𝑘𝑔 ) 1 26.5 = 45% 59.1 2 Measuring the total body water : In Body test analysis 𝑇𝑜𝑡𝑎𝑙 𝑏𝑜𝑑𝑦 𝑤𝑎𝑡𝑒𝑟 ( 𝐿 ) = 𝑏𝑜𝑑𝑦 𝑤𝑖𝑔ℎ𝑡 ( 𝑘𝑔 ) 64.2 1 = 47,4% 135.3 2  Body fluid distribution and ionic composition Total body fluid: ( TBW ) Accounts for 50 – 70 % of body weight. Example: A 70 kg man, calculate his total body water? (= 42 liters) Correlates inversely with body fat, thus when body fat is low, the percentage of total body water is higher; when body fat is high, the percentage is lower. Because females have a higher percentage of fat than males, they tend to have less body water. Body fluid compartment: Intracellular fluid (ICF, fluid inside the cells) = 2/3 of TBW (40 %) Extracellular fluid (ECF, fluid outside the cells) = 1/3 of TBW (20 %) o Plasma (fluid circulating in the blood vessels) = 5 % o Interstitial fluid (fluid that bathes the cells) = 15 % Composition of extracellular and intracellular fluid: Substance ( mEq/L ) Extracellular fluid Intracellular fluid Na + 140 14 K + 4 120 Cl - 105 10 HCO3 - 24 10 1  Body fluid distribution and ionic composition Intracellular fluid: Major cations K+ Major anions Proteins and organic phosphate Extracellular fluid: Major cations Na+ Major anions Cl- and HCO3 - Measuring volumes of body fluid compartment: By dilution method amount Volume = 𝑐𝑜𝑛𝑐𝑒𝑛𝑡𝑟𝑎𝑡𝑖𝑜𝑛 amount injected − amount excreted Volume = 𝑐𝑜𝑛𝑐𝑒𝑛𝑡𝑟𝑎𝑡𝑖𝑜𝑛 Steps: Identification of an appropriate marker substance: Markers for total body water D 2O Distrusted wherever water is found Markers for ECF volume Mannitol Large molecular weight Can not cross cell membranes Markers for plasma volume Radioactive Too large albumin cannot cross capillary walls ICF and interstitial fluid are determined indirectly 2  Body fluid distribution and ionic composition Clinical case: A man is participating in a research study for which it is necessary to know the volumes of his body fluid compartments. To measure these volumes, the man is injected with 100 mCi of D2O and 500 mg mannitol. During a 2-hour equilibrium period, he excretes 10 % of the D2O and 10% of the mannitol in his urine. following equilibration, the concentration of D2O in plasma is 2.13 mCi/ L and the concentration of mannitol is 32 mg/L. what are his total body water, his ECF volume, and his ICF volume. 100 −10 Total body water: = 42,2 L 2.13 500 −50 ECF: = 14,1 L 32 ICF = 42.2 – 14.1 = 28.1 L In Body test is a non-invasive body composition analysis that provides a detailed breakdown of the weight in terms of muscle, fat, and water. Preparation for in-body analysis: 1. Do not eat for 3-4 hours before testing 2. Do not exercise for 6-12 hours before testing 3. Ensure access to both feet with removable footwear and socks 4. Avoid putting lotion on hands and feet before testing 3  Body fluid distribution and ionic composition In Body test analysis: Total body water ( L ) body weight ( Kg ) 64.2 1 = 47.4 % 135.3 2 4 Field of Medicine Medicine Program Lecture : (Autonomic Nervous System ) Dr : (Mohamed Talal) Date : 7/10 /2024 Autonomic nervous system Structure and origin : Autonomic nervous system Autonomic nervous system Autonomic nervous system Somatic nervous system Control Involuntary Voluntary Type 2 types One Efferent 2 efferent One Muscle Smooth muscle – cardiac Skeletal muscle muscle Chemical transmitter Acetylcholine Acetylcholine Norepinephrine Autonomic ganglia Present Absent Arise from LHC AHC  Autonomic nervous system Autonomic ganglia :  Autonomic nervous system Autonomic ganglia : Definition: collection of neurons outside CNS Function: acts as distributing center Types: 1. paravertebral ganglia ( lateral ) 2. collateral ganglia 3. terminal ganglia  Autonomic nervous system paravertebral ganglia ( lateral )  present on both sides of vertebral column  relay of sympathetic nervous system  Autonomic nervous system  collateral ganglia :  present midway between spinal cord and viscera.  relay of sympathetic.  relay of parasympathetic.  terminal ganglia :  present near or inside the viscous.  relay of parasympathetic.  Divisions of Autonomic nervous system 1. Sympathetic nervous system. 2. Parasympathetic nervous system. Divisions of Autonomic nervous system 1. Sympathetic nervous system.  Divisions of Autonomic nervous system 2. Parasympathetic nervous system.  sympathetic nervous system Origin : thoracolumbar (LHC of all thoracic and upper 3 lumbar segments)  functions of sympathetic nervous system On head and neck : 1. Eye: pupil dilatation ( mydriasis ) due to contraction of dilator pupillae muscle elevation of upper eyelid ( widening of palpebral fissure ) decrease tear secretion of lacrimal gland 2. Salivary glands: Decreases salivary secretions  functions of sympathetic nervous system On thorax : ( heart and lung ) Heart: increase excitability and rate of conduction +ve inotropic effect ( increase in force of contraction ) +ve chronotropic effect ( increase in heart rate ) vasodilatation of coronary vessels  functions of sympathetic nervous system On thorax : ( heart and lung ) Lung: bronchodilatation ( relaxation of bronchial muscles ). vasoconstriction of pulmonary vessels. Field of Medicine Medicine Program Lecture : (Autonomic Nervous System 2 ) Dr : (Mohamed Talal) Date : 13/10 /2024 functions of sympathetic nervous system on abdomen : Liver: glycogenolysis ( hyperglycemia ). increase metabolic rate. increase fibrinogen synthesis ( limit bleeding ). functions of sympathetic nervous system on abdomen : Pancreas: Stimulates glucagon secretion. inhibits insulin secretion.  functions of sympathetic nervous system on abdomen : Adrenal medulla: secretion of 80% adrenaline – 20% noradrenaline. Adrenaline Noradrenaline Greater effect on : Greater effect on Cardiac contractility ( β1) arterial blood pressure ( VC via α1 ) functions of sympathetic nervous system on abdomen : Gastrointestinal tract: Inhibition ( relaxation ) of wall. contraction of sphincters.  functions of sympathetic nervous system On pelvis : Rectum: (retention of feces) inhibition of wall. contraction of internal anal sphincter.  functions of sympathetic nervous system On pelvis : Urinary bladder: (retention of urine) inhibition of wall. contraction of internal urethral sphincter.  functions of sympathetic nervous system On pelvis : Male genitalia: Ejaculation. Field of Medicine Medicine And Surgery Program Lecture: Structure of Nucleic Acids Dr : George N. B. Morcos Date : 1 / 10 /2024  Let’s think together ▪ How are proteins synthesized? ▪ What is the secret behind the conserved sequence of amino acid in a protein?  ILOs By the end of the lecture, the student should be able to: 1. Describe the flow of genetic information 2. Define nucleic acids 3. Illustrate the basic structural components of a nucleotide 4. Describe the levels of organization of DNA 5. Recognize the mechanism of DNA denaturation.  The flow of genetic information ▪ Replication ▪ Transcription ▪ Translation Nucleotide Structure NITROGENOUS BASES I- Pyrimidines NITROGENOUS BASES II- Purines Nucleoside & Nucleotide  Nucleoside & Nucleotide ✓Nucleosides are formed by connecting C1` of pentose to N-1 of a pyrimidine base or N-9 of a purine base. ✓Nucleotides are formed from nucleosides by esterification of phosphoric acid to the alcohol group at C-5` of the pentose structure. Nucleoside & Nucleotide  How is the genetic characters is transmitted from one generation to another?  Nucleic acids Nucleic acids are polymers of nucleotides. 2 main types of nucleic acids: Deoxyribonucleic acids (DNA) Ribonucleic acids (RNA). Nucleic acids are responsible mainly for storage and transfer of information needed for production of proteins.  Deoxyribonucleic Acids (DNA) ▪ It consists of two strands of polynucleotides ▪ Its structure is described under the following titles Primary, Secondary and Tertiary structures I- DNA Primary Structure  I- DNA Primary Structure ▪ dAMP, dGMP, dCMP and dTMP. ▪ Phosphodiester bonds ▪ Backbone of each DNA strand (5`-P-S-P-S-3`). ▪ The nitrogenous bases are projecting to the inside of the two strands of DNA at right angle. ▪ The sequence of bases determines the coding structure of DNA (genetic information). ▪ Each strand has two terminals; 5` & 3` ▪ The order of nucleotides is always written in 5` to 3` direction, which is the direction of synthesis II- DNA Secondary Structure : Double Helix (dsDNA) II- DNA Secondary Structure : Double Helix (dsDNA) ▪ Watson and Crick proposed a structure for DNA ▪ Double helix ▪ B-form of DNA, ▪ The most common physiological form. II- DNA Secondary Structure : Double Helix (dsDNA) 1- Two antiparallel strands form a right-handed helix ▪ The two strands of DNA are paired to each other and coil around a common axis to form a right-handed helix. ▪ The two strands run antiparallel, that is to say, one runs in the 5` to 3` direction and the other in the 3` to 5` direction. ▪ The double helix of DNA appears much like spiral staircase with 10 base pairs per turn. ▪ From outside of the helix, two grooves are apparent, Major groove & Minor groove ☑Through these grooves many drugs and proteins can make contact with the nitrogenous bases without any need to open the helix. II- DNA Secondary Structure : Double Helix (dsDNA) II- DNA Secondary Structure : Double Helix (dsDNA) 2- Complementary base pairing ▪2 strands are held together by complementary base pairing by hydrogen bonds. ▪Adenine pairs with thymine by 2 hydrogen bonds, ▪Guanine pairs with cytosine by 3 hydrogen bonds. ▪Therefore adenine = thymine & guanine = cytosine bases in DNA. ▪Sequence of the two strands is complementary ▪Sequence of one strand determines the second. ▪This is important during DNA replication. II- DNA Secondary Structure : Double Helix (dsDNA) II- DNA Secondary Structure : Double Helix (dsDNA) 3- Base stacking ▪ The base pairs inside the helix are stacked above each other by hydrophobic interactions. ▪ The stability of the double helix is provided by: The hydrogen bonding between complementary base pairs The hydrophobic interactions of stacked base pairs. II- DNA Secondary Structure : Double Helix (dsDNA)  Structural forms of the double helix ▪ There are three major structural forms of DNA: the B form, described by Watson and Crick in 1953, the A form, and the Z form  The B form of DNA ▪ The B form is a right-handed helix with 10 base pairs (bp) per 360° turn (or twist) of the helix, ▪ The planes of the bases perpendicular to the helical axis. ▪ Chromosomal DNA is thought to consist primarily of B-DNA  The A form of DNA ▪ The A form is produced by moderately dehydrating the B form. ▪ It is also a right handed helix, but there are 11 bp per turn. ▪ The planes of the base pairs are tilted 20° away from the perpendicular to the helical axis. ▪ The conformation found in DNA–RNA hybrids or RNA–RNA double-stranded regions is probably very close to the A form.  The Z form of DNA ▪ Z-DNA is a left-handed helix that contains 12 bp per turn. ▪ [Note: The deoxyribose-phosphate backbone zigzags, hence, the name Z-DNA.] ▪ Stretches of Z-DNA can occur naturally in regions of DNA that have a sequence of alternating purines and pyrimidines (for example, poly GC). ▪ Transitions between the B and Z helical forms of DNA may play a role in regulating gene expression.  The scientists who discovered DNA won the Nobel prize. Do you know how they identified this structure?  Denaturation of DNA ▪ The two strands of the double helix separate when hydrogen bonds between the paired bases are disrupted. ▪ Disruption can occur with Change of pH Heating ▪ Melting temperature (Tm). ▪ Denaturation can be monitored by measuring its absorbance at 260 nm. “Hyperchromicity” [Note: ssDNA has a higher relative absorbance at this wavelength than does dsDNA.] ▪ Cooling of denatured DNA results in renaturation or reannealing. Denaturation of DNA True or False DNA denaturation is reversible.  Summary ▪ Central Dogma. ▪ Nucleotide structure. ▪ 1ry & 2ry structure of DNA. ▪ Structural forms of DNA. ▪ DNA denaturation.  References ▪ Lippincott's Illustrated Reviews: Biochemistry, 7th Edition. Chapter 30.  DR. Amany Abdelfattah Introduction to Histology (Micro-techniques & Microscopy) Histology is the science that study the structure of the cells & tissues using Microscope. The methods used to study cells and tissues include: 1. Micro-techniques 2. Microscopy A- Preparation of thin section B- Staining Paraffin Technique Freezing Technique ❖ Paraffin Technique: - The routine technique for histological preparation during light microscopic studies. - Paraffin wax is used. - It includes the following steps: 1-Obtain 6-Embedding in 7-Cut section. sample paraffin 8- Pick section 2- Fixation 5-Impregnation on slide. 3-Dehydration 4-Clearing 1  DR. Amany Abdelfattah 1) Obtain sample→ small sample from the organ of interest or from patient. 2) Fixation: Put sample of tissue in fixative (e.g. formalin 10%) to prevents putrefaction and autolysis. 3) Dehydration: in ascending grades of alcohol (70%-90%- 100%) to prevent tissue distortion. 4) Clearing: in xylene to replace alcohol, act as paraffin solvent and to make the tissue transparent. 5) Impregnation: infiltration with paraffin wax in the oven to harden tissue 6) Embedding in paraffin: In hard paraffin to obtain a paraffin block to protect tissue & facilitate sectioning. 7) Cut thin sections (5 um thick) by rotary microtome then pick section them on glass slide. ❖ The Freezing: - Freezing of specimen by cryocut. It is characterized by: ✓ Very rapid → rapid diagnosis in operating theatre. ✓ Preserve lipids and enzymes in the tissues→ suitable for histochemistry. B) Staining: As most tissues are colorless, and so can’t be observed clearly by light microscope (L.M.), so, there is a need to use a coloring material to stain the tissue to be examined which is called Stain. There are different types of stains: Acidic Basic Neutral Leishman stain e.g. Eosin (E) Hematoxylin (H) (Methylene blue +Eosin) Stain basic structures Stain acidic structures Two different colours. (cytoplasm) (nucleus) Acidic → basic structures. Acidophilic (pink) Basophilic (blue) Basic → acidic structures. 2  DR. Amany Abdelfattah N.B. H & E is the ordinary histological stain used to examine a section by L.M., it stains the nucleus basophilic (blue), and the cytoplasm acidophilic (pink), as seen in this photo. ❖ Special stains for cell components: 1- Carbohydrates: Periodic acid Schiff’s technique (PAS)→ Magenta color. Best's carmine (for glycogen)→ Red. 2- Lipid: - Frozen sections are used. ✓ Sudan III → Orange. ✓ Sudan black → Black. ✓ Osmic acid → Black. ❖ Other methods of Staining: Vital stain Supravital stain Metachromatic stain Staining of living cells in Staining of living cells in Staining with a color vivo vitro i.e. outside the different from the color body of the dye e.g. phagocytic cells by e.g. mitochondria by e.g. granules of mast injecting Trypan blue. Janus green B. cells are colored red when stained with toluidine blue). 3  DR. Amany Abdelfattah 2. Microscopy. The use of an instrument called the microscope to magnify the image & reveal fine details of the object examined. Types of Microscopes Magnification up to 1000.000 times. Light M. (L.M.) Electron M. (E.M.) Magnification 40, Other types 100, 400, 1000. Transmission (TEM) Scanning ❖ Light (student) microscope: ordinary microscope used in the laboratory to study stained sections. ❖ TEM: used to study the ultrastructure of cells. It differs from L.M. in: - Needs extremely thin sections (0.08 um). - Electron beam is used instead of light for illumination. - The image appears white & black. - Dark components → described as electron dense. - White components → described as electron lucent ❖ Scanning E.M.: give 3D image for the object examined. ❖ Other types: 1- Phase Contrast Microscope: used to study the living or fixed unstained cells. 2- Fluorescence Microscope: used to detect fluorescent substances. 4  Faculty of Medicine Histology & Cell Biology The Structure of the Cell “Part I” By Dr. Amany Abd El Fattah Mohamed Lecturer of Medical Histology & Cell Biology  Learning outcomes ❑ At the end of the lecture, the students will be able to: 1. Enumerate components of the cell. 2. Describe structure of cell membrane. 3. Correlate cell membrane structure to function. 4. Enumerate components of the cytoplasm & classify cell organelles. 5. Describe L.M & E.M of mitochondria. 6. Classify endoplasmic reticulum and describe L.M & E.M of the 2 types.  Learning outcome 1 Enumerate components of the cell.  The structural and functional unit of living body. It consists of: 1. Cell Membrane 2. Cytoplasm 3. Nucleus  To study the cell structure, we use electron microscope (E.M) that has high magnification power. E.M gives pictures that are black and white. Black parts are called electron dense. White parts are called electron lucent.  Learning outcome 2 Describe structure of cell membrane.  Cell Membrane Def.: Membrane surrounds the cell and regulates the passage of materials into or out of it. L.M.: not seen (9-10 nm thick). E.M: trilaminar (outer and inner dark “electron dense” layers and a middle light “electron lucent”). Chemically: formed of lipid, proteins, and carbohydrates in specific arrangement  Lipid Phospholipid Cholesterol Formed of phospholipid molecules, Present between the phospholipid arranged into double layer (bilayer) molecules in the lipid bilayer. Phospholipid molecule Hydrophobic tail Phospholipid Hydrophilic head molecule  Carbohydrate Glycolipids Glycoprotein Project from the external surface as cell coat or glycocalyx.  Proteins Integral Peripheral Incorporated in the lipid bilayer. Not easily extracted. Loosely 2 types: attached to cell Trans-membranous protein membrane. - Large - Completely embedded in the lipid bilayer Easily extracted. - Act as channels. The small type. - Partially embedded in the lipid bilayer.  Learning outcome 3 Correlate cell membrane structure to function.  ❖ Functions of cell membrane: 1. Protect the cell and keep its internal contents 2. Exchange of materials between the cell and its surrounding: A- Endocytosis: entrance of materials into the cell → Phagocytosis: solid material → Pinocytosis: fluids B- Exocytosis: exit of materials from the cell. 3. Cell coat functions : - Adhesion between cells. - Receptors for hormones.  Learning outcome 4 Enumerate components of the cytoplasm & classify cell organelles.  2- Cytoplasm Organelles Inclusion Matrix (Living component) (Non-living component)  Cell Organelles I. Membranous II. Non- membranous Mitochondria. Ribosomes. Endoplasmic Reticulum Centrioles. Golgi Apparatus. Cilia & flagella. Lysosomes. Microtubules. Peroxisome. Microfilaments. Metabolic activities Cytoskeleton I. Membranous Organelles.  Learning outcome 5 Describe L.M & E.M of Mitochondria.  Mitochondria Membranous organelles, provide the cell with ATP (the powerhouse of the cell) → Numerous in active cells as liver cells & muscle. L.M: H&E: acidophilic granules (when numerous). Special stains: - Iron H. → dark blue rods or granules. Histochemical stain: reveal succinic dehydrogenase activity.  E.M: ❑ Double-walled membranous vesicle, formed of: 1.Outer Membrane: smooth & permeable. 2.Inner Membrane: shows cristae (shelf-like projections) & contains respiratory & electron transport enzymes. 3.Matrix: occupies the intra-membranous space, contains the enzymes of Krebs's cycle & mitochondrial DNA and RNA.  Functions of mitochondria: 1-Provide the cell with ATP which gives energy for the different vital activities. 2- They can divide →increase their number.  Learning outcome 6 Classify ER and describe L.M & E.M of the 2 types.  Endoplasmic Reticulum Membranous cell organelle formed of branched tubules. Types: 2 types: rER (rough) sER (smooth)  rER sER - Protein synthesizing cells e.g. - Lipid synthesizing cells e.g. liver, Site plasma cell, pancreas suprarenal cortex. Not seen as a reticulum (cause L.M - Not seen. basophilia of cytoplasm). - Parallel flattened tubules. - Communicating narrow tubules. E.M. - Rough surface (ribosomes). - Smooth surface (no ribosome) -Segregation of proteins - Lipid synthesis. Function -Initial glycosylation of protein - Detoxification of toxic substance - Protect cytoplasm from enzym. - Muscle contraction (store Ca+).  Summary and wrap up The cell is the building block of living body. It is formed of cytoplasm & nucleus. Cytoplasm contain membranous and non membranous organelles. Mitochondria is the powerhouse of the cell. ER has two types: rough & smooth.  References or further readings Junqueira's Basic Histology Text & Atlas (16th ed.). https://www.youtube.com/watch?v=RKmaq7jPnYM  Dr. Amany Abdelfattah Structure of the Cell The cell is the structural and functional unit of living tissues. It consists of: I. Cell Membrane II. Cytoplasm III. Nucleus N.B.: - To study the cell structure, we use electron microscope (E.M.) that has high magnification power. - E.M gives pictures that are black and white. - Black parts are called electron-dense. - White parts are called electron-lucent. I. Cell Membrane: The membrane surrounds the cell and regulates the passage of materials into or out of it. L.M.: not seen (9-10 nm thick) E.M.: trilaminar (outer and inner dark “electron dense” layers and a middle light “electron lucent”). Chemical Structure: It is formed of lipids, proteins, and carbohydrates in specific arrangement. A) Lipids: 2 types: Phospholipids Cholesterol Formed of phospholipid molecules, Present between the phospholipid arranged into a double layer (bilayer). molecules in the lipid bilayer. Each molecule has a hydrophilic head directed outwards and a hydrophobic tail directed inwards.  Dr. Amany Abdelfattah B) Carbohydrates: Glycolipids Glycoprotein CHO linked to lipids of cell membrane CHO linked to proteins of cell membrane Project from the external surface as cell coat or glycocalyx. C) Proteins: Integral proteins Peripheral proteins Incorporated in the lipid bilayer. Loosely attached to cell Not easily extracted. membrane. 2 types: Easily extracted. Trans-membranous protein - Large - Completely embedded in the lipid bilayer - Act as channels. The small type. - Partially embedded in the lipid bilayer. Functions of cell membrane: 1. Protect the cell and keep its internal contents 2. Exchange of materials between the cell and its surrounding: A- Endocytosis: entrance of materials into the cell → Phagocytosis: solid material → Pinocytosis: fluids B- Exocytosis: exit of materials from the cell. 3. Cell coat functions: - Adhesion between cells. - Receptors for hormones. II. Cytoplasm It is formed of: 1- Cell organelles: living components, essential for the life of the cell. 2- Inclusions: Non-living component, not essential for the life of the cell. 3- Matrix.  Dr. Amany Abdelfattah 1. Cell Organelles. Membranous. Non- Membranous. Mitochondria. Ribosomes. Endoplasmic Reticulum Centrioles. Golgi Apparatus. Cilia. Lysosomes. Microtubules. Peroxisome. Microfilaments. They are important for metabolic They are important for cell cytoskeleton. activities inside the cell. A. Membranous Organelles. Mitochondria ❖ Membranous organelles, provide the cell with ATP (the powerhouse of the cell). They are numerous in active cells such as liver cells & muscle. ❖ L.M: ✓ H&E: acidophilic granules (when numerous). ✓ Special stains: Iron H. → dark blue rods or granules. ✓ Histochemical stain: reveal succinic dehydrogenase activity. ❖ E.M: double-walled membranous vesicle, formed of: 1. Outer membrane: smooth. 2. Inner membrane: shows cristae (shelves-like projections) & contains all respiratory and electron transport enzymes. 3. Matrix: contains the enzymes of Krebs’s cycle & mitochondrial DNA and RNA. ❖ Function: 1-Provide the cell with ATP which gives energy for the different vital activities. 2- They can divide →increase their number.  Dr. Amany Abdelfattah Endoplasmic Reticulum ❖ Membranous cell organelle formed of branched tubules. ❖ Types: 2 types: 1. rER (rough). 2. sER (smooth) rER sER L.M Not seen as a reticulum (cause - Not seen. basophilia of cytoplasm). E.M - Parallel flattened tubules. - Communicating narrow tubules. - Rough surface (ribosomes). - Smooth surface (no ribosome). Site - Protein synthesizing cells e.g. - Lipid synthesizing cells e.g. liver, plasma cell, pancreas suprarenal cortex. Function -Segregation of proteins - Lipid synthesis. -Initial glycosylation of proteins. - Detoxification of toxic substances - Protect cytoplasm from - Have a role in muscle contraction enzymes. (store Ca+2). Golgi Apparatus ❖ A membranous organelle that plays a role in secretory functions of the cell (prominent in protein-synthesizing cells). ❖ L.M: ✓ H&E: negative Golgi image (pale area in deep basophilic cytoplasm). ✓ Special stain: Silver → brown fibrillar network. ❖ E.M.: 1.Golgi stack: 4-10 saccules, with 2 surfaces (mature” trans” face, immature “cis” face). 2.Micro-vesicles, present at the immature face & contain proteins from rER.  Dr. Amany Abdelfattah 3. Macro-vesicles, present at the mature face & contain modified proteins that may be excreted as secretory product or remain in cytoplasm as lysosome. ❖ Functions of Golgi apparatus: 1. Modifies, concentrate, segregate and packe the secretory proteins. 2. Sorting out proteins and regulates their distribution. 3. Maintain integrity of cell membrane. Lysosomes ❖ Membranous organelles, contain acid hydrolases for intra-cytoplasmic digestion (suicide bags) → numerous in phagocytic cells. ❖ L.M: ✓ H&E: not seen. ✓ Histo-chemically: for acid phosphatase activity. ❖ E.M: 2 types: Primary lysosomes Secondary lysosomes Size Small spherical vesicles Larger vesicles Core Homogenous electron dense Heterogenous electron dense Function not engaged in intra-cytoplasmic engaged in intra-cellular digestion digestion Types of Secondary lysosomes: Heterolysosome Autophagosome Formation 1ry lysosome fuses with a 1ry lysosome fuses with dead or phagosome. nonfunctioning organelle. Fate After digestion: 1. Nutrients (reused by the cell). 2. Residual body →expelled out of the cell. -In long-lived cells, such as heart and nerve cells, residual bodies can accumulate as lipofuscin pigment (wear and tear pigment). N.B.: Deficiency of any of lysosomal enzymes → accumulation of materials inside the cell interfering with cellular functions → lysosomal storage diseases e.g Gaucher's disease.  Dr. Amany Abdelfattah Peroxisomes ❖ Membranous organelles contain oxidases that form H2O2 and catalase enzyme which converts H2O2 ® H2O+O2 ❖ L.M: ✓ H&E: not seen. ✓ Histochemically: for catalase activity. ❖ E.M.: ✓ In human, small membranous vesicles contain a homogenous granular electron-dense core. ✓ In rodents, contain a more electron-dense crystalline core called nucleoid (rich in uricase enzyme). ❖ Function: 1. Segregate the developing H2O2 and protect the cell from its damaging effect. 2. Play a role in lipid metabolism (oxidation of long chain fatty acids). 3. Formation of bile acids.  Dr. Amany Abdelfattah B. Non-Membranous Organelles. Ribosomes Non-membranous organelles, important for protein synthesis. L.M: ✓ H&E: cytoplasm containing a large number of ribosomes is stained basophilic. E.M: electron-dense granule, composed of 2 subunits (formed of rRNA &protein). - May be held together by mRNA-forming polyribosomes. ❖ Types: Free Ribosomes. Attached Ribosomes. - Scattered in the cytoplasm. - To the outer surface of (rER). - Produce protein used inside the - Produce protein for export or cell. lysosomal enzymes.  Faculty of Medicine Histology & Cell Biology The Structure of the Cell “Part II” By Dr. Amany Abd El Fattah Mohamed Lecturer of Medical Histology & Cell Biology  Learning outcomes ❑ At the end of the lecture, the students will be able to: 1. Describe L.M & E.M of Golgi apparatus. 2. Describe L.M & E.M of the lysosome. 3. Describe L.M & E.M of peroxisome. 4. Enumerate non membranous organelles. 5. Describe L.M & E.M of the ribosome.  Learning outcome 1 Describe L.M & E.M of Golgi apparatus.  Golgi Apparatus Membranous organelle, plays important role in secretory functions of the cell (prominent in protein-synthesizing cells) L.M: H&E: negative Golgi image (pale area in deep basophilic cytoplasm) Special stain: * Silver: brown fibrillar network. Negative Golgi image  E.M: 1. Golgi stack: 4-10 saccules, with 2 surfaces * Immature “cis” face. * Mature “trans” face. 2. Micro-vesicles, at the immature face, contain proteins coming from rER. 3. Macro-vesicles, at the mature face, contain modified proteins that may be excreted as secretory products or remain in the cytoplasm as lysosomes.  Functions of Golgi apparatus: 1. Modifies, concentrate, segregate and pack the secretory proteins. 2. Sorting out proteins and regulating their distribution. 3. Maintain the integrity of the cell membrane.  Learning outcome 2 Describe L.M & E.M of lysosome.  Lysosomes Membranous organelles, contain acid hydrolases for intra- cytoplasmic digestion (suicide bags) → numerous in phagocytic cells. L.M: H&E: not seen. Histochemically: for acid phosphatase activity.  E.M: Types: 2 types: Primary lysosomes Secondary lysosomes Size Small spherical vesicles Larger vesicles Core Homogenous electron dense Heterogenous electron dense not engaged in intra- engaged in intra-cytoplasmic Function cytoplasmic digestion digestion ✓ Types of Secondary lysosomes: Heterolysosome Autophagosome Formation 1ry lysosome fuse with 1ry lysosome fuse with phagosome. dead or non-functioning organelle. Fate - After digestion: 1. Nutrients (reused by the cell). 2. Residual body →expelled out of the cell. -In long-lived cells, as heart and nerve cells, residual bodies can accumulate as lipofuscin pigment (wear and tear pigment).  Clinical hint Deficiency of any of lysosomal enzymes → accumulation of materials inside the cell interfering with cellular functions → lysosomal storage diseases e.g Gaucher's disease.  Learning outcome 3 Describe L.M & E.M of peroxisome.  Peroxisomes Membranous organelles contain oxidases that form H2O2 and catalase enzyme which converts H2O2 → H2O + O2. L.M: H&E: not seen. Histochemically: for catalase activity.  E.M: ❖ In human, small membranous vesicles containing a homogenous granular electron dense core. ❖ In rodents, contain more electron dense crystalline core called nucleoid (rich in uricase enzyme).  Functions of peroxisomes: 1. Segregate the developing H2O2 and protect the cell from its damaging effect. 2. Play a role in lipid metabolism (oxidation of long chain fatty acids). 3. Formation of bile acids. Non-membranous Organelles  Ribosome Non-membranous organelles important for protein synthesis. L.M: H&E: cytoplasm containing large number of ribosomes is stained basophilic.  E.M: ▪ Electron dense granule, composed of 2 subunits. ▪ May be held together by mRNA forming polyribosomes.  Types: Free Ribosomes Attached Ribosomes Scattered in the cytoplasm. To the outer surface of (rER). Produce protein used inside the Produce secretory proteins or cell. lysosomal enzymes.  Summary and wrap up Golgi is important for the secretory function of the cell. Lysosomes & peroxisome contain important enzymes. Ribosome is the factory for protein synthesis. Field of Medicine Medicine And Surgery Program Lecture : Introduction Dr : Moataz maher Date : / / Introduction to Medical Biochemistry & Protein Chemistry What’s your expectations from studying Biochemistry & Molecular Biology Objectives: By the end of this lecture the student will be able to: 1. Identify the importance of Biochemistry in Medicine. 2. Recognize the major biomolecules in living organisms. 3. Recognize the types of living cells and cell compartments. 4. Describe the chemical structure of proteins.  1. What is Biochemistry? Biochemistry = chemistry of life. Living organisms contain thousands of molecules (simple & complex). These molecules are complicated and highly organized (proteins, DNA, RNA, carbohydrates, and lipids) Biochemistry is the study of these biomolecules function, interaction, synthesis and degradation inside the living cell. Living organisms can a. extract b. Store ENERGY c. Use  Principle Areas of Biochemistry Structure and function of biological macromolecules Metabolism – Anabolic and catabolic processes. Molecular Biology – How life is replicated? – How protein synthesis is regulated?  Role of Biochemistry in Medicine Several diseases have a molecular basis, so Biochemistry enables us to Understand the chemical processes involved in such conditions. Diagnosis and follow up of diseases. It is a guide to discovery of therapy and apply it to diseases. In nutrition: The nutrients value of food material can also be determined by biochemical tests. For maintenance of health, optimum intake of many chemicals like vitamins, minerals, essential fatty acids is needed  Nutritional imbalance leads to disease.  2. Biomolecules The human body is composed of: - Major elements (C, H, N, O, P, S). These elements are major components of important biomolecules, such as proteins, nucleic acids, polysaccharides and lipids. - Less abundant: Na, Mg, K, Ca, Cl - Trace elements: Mn, Fe, Co, Cu, Zn. The major components of the body are water (60%). The others include proteins (17%), fat (14%), carbohydrates (1.5%) and minerals (6%).  2. Biomolecules - Large biomolecules are polymers (Greek: poly + meros, many + parts) - They are derived from monomers (Greek: mono + meros, single + part)  What are the different types of cells? Extract differences between these cells  3. Types of Cells The cell is the fundamental unit of biologic activity. Living cells fall into 2 broad categories: - Prokaryotes - Eukaryotes In Greek “before the nucleus” In Greek “true nucleus” a. Single-celled organisms (such as a. contains a well-defined nucleus bacteria) surrounded by a nuclear b. It lacks nuclei and other membrane organelles b. can be single celled, such as c. It has only one membrane yeasts, or multicellular, such as “Plasma membrane” animals and plants  Prokaryote Cell Simplest No organelles No nucleus No membrane bound organelles DNA uncomplexed by histones  Eukaryote Cell More complex – Contain organelles – Has a nucleus More DNA – Has to be folded – Contains histones  Differences between Prokaryotes & Eukaryotes Organelle Prokaryotes Eukaryotes Nucleus No definite nucleus; DNA Present present but not separated from the rest of the cell Cell membrane Present Present Mitochondria None: enzymes for oxidation Present are on plasma membrane Endoplasmic None Present reticulum Ribosomes Present Present  Summary of Cell Organelles of and Their Functions Organelle Function Nucleus Location of main genome; site of most DNA and RNA synthesis Mitochondria Site of energy-production reactions; has its own DNA Endoplasmic Rough: synthesis, folding and reticulum modification of proteins. Smooth: synthesis of phospholipids and cholesterol.  Cell organelles and their functions (cont.) Golgi Cell post office. apparatus Involved in secretion of proteins to their cellular target Lysosomes contain hydrolytic enzymes responsible for breakdown of different molecules Peroxisomes Breaks down H2O2 and other products that can damage the cell components Cell membrane Separates the cell contents from the outside world Where can we find proteins?  4. Chemical structure of proteins Proteins are the most abundant macromolecules in living cells. All proteins contain the elements carbon (C), hydrogen (H), oxygen (O) and nitrogen (N). Most proteins contain about 1% of the element sulfur Certain specialized proteins contain other elements such as phosphorus (found in milk).  Amino Acids (The structural unit of proteins)  Amino acids are the building block of proteins.  All proteins are made of a long chain of amino acids linked together by peptide bonds and other bonds forming a polypeptide chain.  All proteins are made up of one or more polypeptide chains.  All proteins in all species are formed from the same set of 20aminoacids.  Amino Acids (The structural unit of proteins)  Amino acids contain both an amino group and a carboxyl group.  α-Amino acid is an amino acid in which the amino group is on the carbon adjacent to the carboxyl group.  Protein Nomenclature Peptides 2 –50 amino acids Proteins >50 amino acids Three letter code: –Met-Gly-Glu-Thr-Arg-His Single letter code: –MGETRH  Types and functions of proteins Role Examples Functions They are catalysts, meaning that they speed the reactions up 1. Enzymes Amylase, - Digestive enzymes break down nutrients in food lipase, pepsin into small pieces that can be readily absorbed - All chemical reaction of the body are catalyzed by enzymes 2. Transport Hemoglobin Carry substances throughout the body in blood (e.g. molecules, ions…) Actin, 3. Structure collagen, Build different structures keratin 4. Receptors Mediate chemical, electrical and hormonal stimuli  Types and functions of proteins Role Examples Functions 5. Hormones Insulin, Coordinate the activity of different body systems glucagon 6. Defense Antibodies Protect the body from foreign pathogens 7. Contraction Myosin Carry out muscle contraction - Albumin - Serve as biological reserves of metal ions and 8. Storage amino acids - Ferritin - A protein that stores iron in the liver - Biochemistry is of chemistry of life. - The major biomolecules in different organisms. - There are two forms of living cells eukaryotes and prokaryotes. - Introduction to Proteins structure and function.  Introduction to Biochemistry link https://www.youtube.com/watch?v=9MfGXc2qKXo&list=PLluIsqNl4jcqXszPTyKWVYmSfT00E qx8q Field of Medicine Medicine And Surgery Program Lecture : Amino acid chemistry Dr : Moataz maher Date : 10 /2024 Objectives: By the end of this lecture, the student will be able to: 1. Recognize the general properties of amino acids. 2. Identify the role of amino acids and proteins as buffers. 3. Identify the amino acids that share in protein synthesis and classify them according to their structure.  1. Amino Acids Properties ▪ Amino acid (aa.) is a compound that contains both an amino group and a carboxyl group. ▪ a-Amino acid is an amino acid in which the amino group is on the carbon adjacent to the carboxyl group. carboxyl group R-group attached to the α- Carbon can be a hydrogen or amino group other small organic groups (e.g., —H, — CH3 , —CH2OH, ….). a-carbon side chain  1. Amino Acids Properties ▪ All naturally occurring protein amino acids (aa.) are α – amino acids. ▪ There are 2 forms of aa. (L & D form) ▪Human body only synthesizes and use L- amino-acids. ▪ All L-amino acids have their amino group toward the left.  1. Amino Acids Properties Isomerism (optical activity): - Amino acids contain asymmetric carbon (carbon atom with 4 distinct groups) or chiral carbon. - Chirality is the ability of a molecule to rotate the plane of polarized light either to the right When a beam of plane polarized (dextrorotatory) or to the left (levorotatory), light is passed through a solution of also known as optical activity. an amino acid it will rotate the light either to right or to left. - All aa. are optically active except glycine. Why????  1. Amino Acids Properties Amphoteric properties: – Amino acids have both basic and acidic groups. They are ionized in different ways in solution, depending on the pH of solution. – In acid media they act as base (+) & in alkaline media they act as acid (-) Leucine in different pH. (Buffer activity of aa).  1. Amino Acids Properties Isoelectric point: - The pH at which aa is electrically neutral [=carries equal positive and negative charge] and does not move toward cathode or anode when subjected to electrical field → at this pH it can precipitate. This is the isoelectric point.  2. Amino acids and proteins as buffers A solution with a high hydrogen ion concentration has a low pH (acidic) A solution with a low hydrogen ion concentration has a high pH (alkaline). Buffers: are compounds that correct a change in a solution pH that occur in response to the addition of alkali or acid to this solution. Proteins have the most buffering effect due to their high concentration in the blood. Proteins contains basic and acidic groups, which act as H+ acceptors or donors, if H+ is added or removed. Protein buffering effect is mediated as follows: COOH (acid) of amino acid can lose H+ (COO-) NH2 (amine) of amino acid can gain H+ (NH3+).  3. Amino Acid Classification ▪ Each of the 20 a-amino acids found in proteins can be distinguished by the R-group substitution on the α-carbon atom ▪ They can be classified by one of three methods: 1. Chemical classification: based on the number of amino groups vs carboxyl group (basic, NH2 higher), (acidic, COOH higher) or (neutral, equal NH2 and COOH) 2. Biological classification: based on whether they can be synthesized in the body of not (essential or non-essential) 3. Metabolic classification: based upon the fate of AA. in the body (glucogenic, ketogenic or both)  3a. Chemical Classification 1. Aliphatic Amino acids can be classified according to the properties of the R 2. Aromatic group, in particular their polarity 3. Sulfur containing [tendency to interact with water at 4. Polar/Non polar physiological pH (~ 7.4). 5. basic/acidic/Neutral - nonpolar and hydrophobic (water- insoluble) - polar and hydrophilic (water-soluble).  3a. Chemical Classification - Aliphatic amino acids: have no ring structure - Aromatic amino acids : contain an aromatic ring (benzene or phenol ring) -Phenylalanine. -Tyrosine. - Heterocyclic amino acids :contain other ring structure -Tryptophan. -Histidine. -Proline. 3a. Chemical Classification  3a. Chemical Classification Aliphatic (OH containing) Sulfur containing: Methionine, Non polar Cysteine, polar  3a. Chemical Classification Cystine consists of two disulfide-linked cysteine residues  3a. Chemical Classification Acidic Amino Acids Contain 2 carboxyl groups Negatively charged at physiological pH  3a. Chemical Classification Basic Amino Acids: They are hydrophilic and positively charged at physiological pH Histidine – imidazole ring, only amino acid that functions as buffer in physiologic range. Lysine - diamino acid Imidazole Arginine - most basic amino acid ring  3a. Chemical Classification Polar Amino Acids By polarity its is meant solubility in water. Polar side groups (R), are hydrophilic in nature. - Amino acids with polar R groups: Their R groups can form hydrogen bond with water. They include: Hydroxy- aa (OH containing) : e.g Serine, threonine, tyrosine SH- amino acid: cysteine. Acidic aa.: aspartate and glutamate Basic aa.: lysine, arginine, and histidine  3b. Biological Classification (Essential/Non-Essential Amino Acids) 1. Essential: there are 8 essential aa. in normal growth and they can not be synthesized in our body so they must be supplied in diet (Isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine) 2. Non-essential: These are amino acids that can be synthesized in the body  3b. Biological Classification (Essential/Non-Essential Amino Acids) 3. Histidine and arginine are semi-essential aa.: They are formed in the body at a rate enough for adult but not for growing individuals.  Define the biological value of proteins Proteins are classified according to their content of essential aa. into: 1. High biological value proteins that contain all essential aa. They are mostly proteins of animal origin e.g. milk proteins, egg proteins, meat and liver proteins. 2. Low biological value proteins that don’t have at least one essential aa. They are usually of plant origin.  3c. Metabolic Classification 1. Ketogenic amino acids During its catabolic pathways, it only forms acetyl CoA that can give rise to fat. examples Leucine and Lysine 2. Glucogenic amino acids During its catabolism, it gives rise to one of the glucose precursors that can be transformed to glucose. 3. Mixed amino acids (glucogenic and ketogenic)  3. Amino Acids Classification (Uncommon Amino Acids) In addition to the 20 common amino acids, proteins may contain aa. created by modification of aa. already incorporated into a polypeptide. Examples: Hydroxyproline, a derivative of proline, and hydroxylysine, derived from lysine. Both are found in collagen, a fibrous protein of connective tissues.  4. Amino Acids with important products ✓ Tyrosine: the precursor of thyroid hormones, adrenaline, noreadrenaline and melanin pigments. ✓ Tryptophan: the precursor of nicotinic acid, serotonin (neurotransmitters) and melatonin (regulate sleep rhythm). ✓ Histidine: the precursor of histamine (vasodilator & chemical mediators of inflammation). ✓ Hydroxylysine: present only in collagen ✓ Cystine: is derived from cysteine aa. and enters in the structure of Keratin (a hair protein).  SUMMARY - Amino acids are the building block of protein. - Amino acids have the following features: They are L- amino acids They are mostly optically active They are amphoteric - Amino acids and proteins act as blood buffers. - Amino acid are classified according to their chemical, biological and metabolic characters.  Test link: https://www.khanacademy.org/test-prep/mcat/biomolecules/amino-acids-and-proteins1/e/amino- acids-and-proteins-questions Reference: – Lippincott's Illustrated Reviews: Biochemistry, 5th Edition. Chapter 1, pp 1-5 Best wishes Field of Medicine Medicine And Surgery Program Lecture : Protein chemistry 1 Dr : Moataz maher Date :10/ 2024 Objectives: By the end of this lecture the student will be able to: 1. Define the peptide bond and illustrate how a peptide bond is formed. 2. Identify biologically active peptides 3.Classify proteins according to their shape, chemical structure and function.  Proteins and peptides are the same. True /False Peptides and proteins are polymers of amino acids.  1. Peptides/ peptide bond formation A peptide consists of two or more amino acids linked by peptide bonds. The bond between the α- carboxyl group of one amino acid and the α-amino group of another aa. with release of H2O (dehydration reaction). Peptide bonds are not broken by conditions that denature proteins, such as heating.  1a. Peptide Bond The peptide chain has two ends - One end containing an amino group to the left of the chain (N-terminus) - The other contains a carboxyl group to the right of the chain (C-terminus) - Each component amino acid in a polypeptide is called a “residue”  1b. Types of peptides Peptides are classified according to the number of amino acids in the chain into: a. Oligopeptides (contain 2-10 amino acids) Dipeptide: a molecule containing 2 amino acids joined by a peptide bond Tripeptide: a molecule containing 3 amino acids joined by peptide bonds b. Polypeptide: a macromolecule containing many amino acids (up to 50) A polypeptide that contains more than 50 amino acids is known as a protein. Proteins consist of one or more polypeptides.  2a. Biologically active Peptide Name Function Amino Acid Sequence Glutathione (3aa) Antioxidant + acts as cofactor in enzymatic Glu-Cys-Gly reactions (help detoxify chemicals) Thyrotropin releasing Hypothalamic hormone Glu-His-Pro Hormone [TRH] (3aa) (regulates release of thyroid hormones) Angiotensin II (8aa) Increases blood pressure Asp-Arg-Val-Tyr-Ile-His-Pro- (acts on the adrenal gland) Phe Bradykinin (9aa) Hypotensive/Vasodilator Arg-Pro-Pro-Gly-Phe-Ser-Pro- (acts on smooth muscle) Phe-Arg Oxytocin (9aa) Uterus-Contracting Hormone Cys-Tyr-Ile-Gln-Asn-Cys-Pro- (also stimulates lactation) Leu-Gly  2b. Biologically active Polypeptides ✓ Insulin (30 aa and 21 aa) - pancreatic hormone, needed for carbohydrates metabolism, 2 polypeptide chains ✓ Glucagon (29 aa) - pancreatic hormone, opposes action of insulin ✓ Corticotropin (or Adrenocorticotropic hormone (ACTH) (39 aa) – secreted from the anterior pituitary gland hormone in response to stress. It stimulates adrenal cortex to produce glucocorticoids like cortisol.  3. Protein classification 3a. Based on their chemical structure: 1.Simple proteins: They are composed of only amino acid residues. 2.Conjugated proteins: They are combined with non-protein part. e.g. Nucleoprotein, Phosphoprotein, Lipoprotein, Metalloprotein…. 3.Derived proteins: They are derivatives or degraded products of simple and conjugated proteins. e.g. peptones, peptides.  3. Protein classification 3a. Based on their chemical structure (Conjugated proteins):  3. Protein classification 3b. Based on their shape (Axial Ratio): Axial ratio = ratio of length over width 1. Fibrous protein: 2. Globular protein: - Axial ratio more than 10 - Axial ratio not more than 4. - Polypeptides arranged in long strands - They are compactly folded and or sheets. coiled into spherical or globular - Water insoluble [due to high content form. of hydrophobic amino acid]. - Water soluble - Strong but flexible - e.g. Albumin, Globulin, - e.g. Keratin, Elastin, Collagen. Hemoglobin, Histones.  3. Protein classification (Fibrous proteins) 3b1. Collagen: Collagen in Greek means –Kolla= “glue”, and -gen =“producing”. As boiling of the skin and tendons of horses [or other animals] resulted in glue formation. Collagen is the most abundant protein in mammals, making 25% to 35% of the whole-body protein content. - It can be converted into gelatins by boiling. - It is found predominantly in various connective tissues in the body [mostly in fibrous tissues such as tendons, ligaments, and skin]. - Collagen is a glycoprotein and contains two types of carbohydrate- glucose and galactose. The carbohydrate part forms glycosidic bond with the hydroxylysine residues.  3. Protein classification (Fibrous proteins) 3b1. Collagen: - Collagen is very rich in glycine (~33% ), proline, hydroxyproline, hydroxylysine (21%) and alanine (11%). - Hydroxylation of proline and lysine are post- translational reactions and require the co-factors [ferrous ion, and vitamin C]. - The amino acid sequence in collagen is a repeating tripeptide unit: (Gly-X- Y). Glycine occurs every third residue while X and Y can be any amino [mostly X positions are proline and Y positions are hydroxyproline].  3. Protein classification (Fibrous proteins) 3b1. Collagen: - The basic structural unit of collagen is tropocollagen. - The tropocollagen subunit consists of three separate polypeptide chains [triple helix]. - There are different types of collagen (~19) and over 90% of the collagen in the human body is type I.  3. Protein classification (Fibrous proteins) 3b1. Collagen: Disorders of Collagen: (1) Scurvy: It is a nutritional disorder caused by a deficiency of vitamin C. This vitamin is important for hydroxylation reactions of lysine and proline (by the enzymes lysyl hydroxylase and prolyl hydroxylase). Defect in hydroxylation causes loss of collagen stability. The formed tropocollagen is unstable and easily degraded. (2) Osteogenesis imperfecta: It is a genetic disorder resulting into fragile bones with skeletal deformities (bone that easily bend and fracture]. The common cause is mutation resulting into replacement of glycine by another bulky amino acid, affecting the triple helix formation. Scurvy:  3. Protein classification (Fibrous proteins) 3b2. Elastin: – It is similar to collagens but cannot be converted to gelatins by boiling. – Elastin is present with collagen in connective tissues and it is the major component of elastic fibers. – Elastin fibers are highly stretchable and has high elasticity, so elastic fibers allow tissues to expand and contract. Tissues rich in elastic fibers include the aorta and other vascular connective tissues, various ligaments and the lungs. – Elastin gives these tissues the property of stretching without tearing (e.g. blood vessels contract in response to the changes in intravascular pressure; the lungs stretch with inhalation and return to their original shape with each exhalation).  3. Protein classification (Fibrous proteins) 3b2. Elastin: - The basic subunit of elastin is tropoelastin. - It is rich in proline and lysine, but contains little hydroxyproline.  3. Protein classification (Fibrous proteins) 3b3. α-keratin: - It is the key structural element making up hair, nails, horns, claws, hooves, and the outer layer of skin. - It is rich in cysteine residues with high percentage of covalent disulfide bonds giving strength to keratin fibers.  3. Protein classification 3c. Based on their Function: Proteins serve in many roles in the body: They act as structural components such as keratin of hair and nail, collagen of bone. They have catalytic function acting as enzymes for almost all reactions in the body They transport important molecules in blood, e.g. oxygen and carbon dioxide by hemoglobin. They have regulatory function as many proteins are hormones and receptors. They are involved in blood clotting through thrombin, fibrinogen and other protein factors. They act as the defense against infections by means of antibodies. Actin, myosin act as contractile protein important for muscle contraction  SUMMARY A peptide consists of two or more amino acids linked by peptide bonds. Peptide bond is formed between the carboxyl group of one amino acid and the amino group of another. Biologically active peptides perform important function in the body [e.g. glutathione and hormones like insulin and glucagon] Protein are classified according to their chemical structure [simple, conjugated and derived], their shape [fibrous & globular] and their function.  Reference: – Lippincott's Illustrated Reviews: Biochemistry, 7th Edition. Chapter 2, pp 45- 47, Chapter 4, pp 134- 158. Best wishes Field of Medicine Medicine And Surgery Program 1– Anatomical Terminology (A) Prof. Usama Hussein Date : 30 / 9 /2024 ILOs: by the end of this lecture, you will be able to: 1. Define Anatomy & its subdivisions. 2. Depict the anatomical position & its importance 3. Differentiate between anatomical planes 4. Explain terms of positions 5. Define various movements 6. Explain anatomical nomenclatures Anatomy is …. The science which studies the structure of the body and the relations of its different parts to each other. Greek: Ana = apart - Tome = To cut  SUBDIVISIONS OF ANATOMY 1. Macroscopic (Gross) A- Regional anatomy B- Systemic anatomy 2. Microscopic (Histology) 3. Developmental anatomy (Embryology) 4. Living anatomy (Surface, Radiologic & Endoscopic) 5. Surgical (clinical) anatomy 6. Comparative anatomy 7. Artistic anatomy 4  True or False Comparative anatomy is the study of gender differences? Endoscopic anatomy is a type of living anatomy 5 anatomical position  anatomical planes anatomical axes (single : axis) vertical axis anterior middle line Sagittal plane posterior middle line transverse axis (median) (median) antero-posterior axis  True or False In the anatomical position, the palms are in the resting position? The median plane divides the body into right & left similar parts? The coronal plane divides the body into anterior & posterior equal parts The supine position is used for incising an abscess in the back? 9 anatomical terms  anatomical terms. deep - internal superficial - external plantar  anatomical terms. deep - internal superficial - external plantar  anatomical terms. deep - internal dorsal superficial - external plantar  anatomical terms. deep - internal superficial - external plantar central peripheral median lateral... medial  True or False The terms proximal & distal are used in the limbs The terms medial and lateral are absolute terms The terms palmar and dorsal are used in the hand and foot Field of Medicine Medicine And Surgery Program 2 – Skin and Fascia Prof. Usama Hussein Date : 7 / 10 /2024 ILOs: by the end of this lecture, you will be able to: 1- Differentiate between thin skin & thick skin 2- Define various lines of skin 3- Describe the characters and functions of superficial and deep fascia  Skin and Fascia skin fascia  Skin and Fascia (largest organ of body keratin 2m square) stratified epithelium connective tissue cutaneous functions: nerves 1- protection hair follicles 2- barrier 3- sensation sebaceous glands 4- secretion cutaneous 5- Vitamin D blood vessels : arteries and veins 6- nails and hair sweat glands  Skin Types Thin skin Thick skin Most body Palm & sole Thin keratin Thick keratin Hairs Hairless Extended Modular Program 5 Hairs are also absent in some thin skin areas e.g.: 1. Sides of fingers and toes 2. Lips and nipple skin creases Langer’s lines wrong right 7 Which incision will heal better? 8  Skin and Fascia superficial fascia (subcutaneous tissue) Fatty tissue  Skin and Fascia Devoid of fat in: 1. Eyelids 2. Auricle 3. Scrotum 4. Penis 5. Clitoris 6. Beneath the nipple superficial fascia 1-binds skin to deep fascia gently 2-heat insulation 3-food and energy store 4-forms body contours 5-medium to vessels and nerves  1 2 3 Which sites have no subcutaneous fat? 4 Extended Modular Program 11  Skin and Fascia deep fascia it invests deeper structures and binds them together assists muscle action and venous return absent in certain regions, e g., in the face, scalp and anterior abdominal wall.  deep fascia bone skin compartment muscle muscle intermuscular septum compartment superficial fascia limits spread of infection and cancer aponeurosis retinaculum  can u predict the functions of the deep fascia? 1. It invests the deeper structures and binds them to bones. 2. It gives attachment to muscles. 3. Protection, e.g., the palmar aponeurosis of the hand. 4. Formation of intermuscular septa. 5. Limits spread of infection and cancer. 6. Fixation by forming retinaculae. 15 Field of Medicine Medicine And Surgery Program 3 A – Cartilage and Bone Prof. Usama Hussein Date : 11 / 10 /2024 ILOs: by the end of this lecture, you will be able to: 1- Classify bones according to position, shape, structure & development 2- Describe structure of long bone and bone growth 3- Classify cartilage according to position, shape and structure  SKELETON Cartilages Bones Joints  Cartilage (chondro) chondrocytes embedded in dense martix features : 1- dense 2- elastic 3- avascular (nourished by diffusion from perichondral vessels) perichondrium ( contains the blood vessels ) according to the nature of the matrix , there are 3 types of cartilage  according to the nature of the matrix , there are 3 types of cartilage clear matrix 1- hyaline cartilage without fibres costal cartilage developing fetal skeleton  according to the nature of the matrix , there are 3 types of cartilage 1- hyaline cartilage matrix full of collagenous 2- white fibrocartilage fibres (strength) symphysis inter- vertebral disc pubis  according to the nature of the matrix , there are 3 types of cartilage 1- hyaline cartilage 2- white fibrocartilage matrix full of elastic 3- yellow elastic cartilage fibres (flexibility) tip of nose auricle laryngeal cartilages  BONE (ossa ) Hard Vascular Unflexible osteocyte periosteum calcified matrix  tissue which is not a bone center of ossification ossification ( bone formation )  center of ossification on top of on top of membrane of cartilage connective tissue intra-membranous cartilaginous ossification ossification intra-membranous ossification cartilaginous ossification the rest of body bones Functions of bones 1- support 2- movement 3- formation of blood cells 4- protection 5- storage for Ca , ph Are bones living or dead tissue ? Why? 15 axial skeleton peripheral skeleton Bones of upper limb Bones of lower limb  axial skeleton peripheral skeleton skull Bones of upper limb hyoid bone sternum ribs Bones of lower limb vertebral column  7 cervical vertebrae vertebral column 12 thoracic vertebrae 5 lumbar vertebrae sacrum 5 sacral vertebrae coccyx 3-5 coccygeal vertebrae 32 - 34  shoulder region arm elbow forearm wrist hand thumb fingers  clavicle shoulder girdle scapula humerus ulna radius 1 8 carpal bones 5 metacarpal bones thumb 14 phalanges (phalanx) hip region thigh leg knee ankle foot leg toes big toe  hip bone pelvic girdle sacrum pelvis femur thigh patella tibia fibula leg  7 tarsal bones 5 metatarasal bones 1 14 phalanges toes Big toe  frontal bone maxillary bone. scapula pneumatic bones. bones of skull vault. Humerus, ulna, radius,…... bones of skull base carpal and tarsal bones Field of Medicine Medicine And Surgery Program 3 B – Bone (cont.) Prof. Usama Hussein Date : 10 / 10 /2024 ILOs: by the end of this lecture, you will be able to: 1- Classify bones according to position, shape, structure & development 2- Describe structure of long bone and bone growth 3- Classify cartilage according to position, shape and structure  compact bone outer parts of bone cancellous ( spongy ) bone inner parts of bone  compact bone outer parts of bone cancellous ( spongy ) bone inner parts of bone ms. attachment endosteum periosteum medullary cavity ( bone marrow cavity ) 1- periosteal arteries 2- nutrient artery 3- muscular arteries cartilage to be long bone diaphysis primary center of ossification 5-6 W of pregnancy Birth epiphysis secondary centers of ossification after birth epiphyseal cartilage  articular epiphysis cartilage epiphyseal cartilage muscles bone marrow diaphysis cavity endosteum periosteum metaphysis  Growth of long bone in length in width  growth in width proliferation sub-periosteal deposition of bone new bone Functions of periosteum 1- muscle attachment 2- blood supply of bone 3- growth in width 4- healing of fracture  Growth in length growing end epiphyseal cartilage less growing end new bone growing end to the elbow we go nutrient a. from the knee we flee  applied anatomy amputation