Archive for the ‘ Case 2 (Cell Structure) ’ Category

Case 2: Obj 4,5,6,7,8


Case 2: Obj 1,2,3

Pc- Physical and Chemical Characters of urine

Physical Characters of urine


-1200 – 1500  ml/day

-physiological increase

  • Excess water intake
  • A high salt diet
  • A high protein diet

-Physiological decrease

  • Excess sweating
  • High temperature
  • Muscular Exercise

-Pathological variations


  • Diabetes mellitus
  • Diabetes insipidus
  • Chronic renal failure
  • Conne’s syndrome (hyperaldosteronism)
  • Cushing syndrome (hypercortisonemia)
  • Thyrotoxicosis


  • Burns, diarrhea, vomiting, and hemorrhage
  • Acute renal failure
  • Acute glomerulonephritis
  • Acute hepatic failure


  • Acute renal failure
  • Obstructive lesion e.g calculi
  • Neurological lesions of urinary bladder


-It is amber yellow due to the presence of certain pigments e.g urochrome, urobilin, and uroerythrin

-Variations in the color of urine

  • Pale yellow in case of polyuria (due to dilution of pigments)
  • Deep yellow in the case of oliguria (due to concentration  of pigments)
  • Reddish in case of hematuria
  • Orange brown in case of hemolytic jaundice
  • Greenish brown in case of obstructive, and hepatocellular jaundice
  • Black in case of melanoma ,and alkaptonuria


-The fresh urine has a characteristic aromatic odor (due to volatile aromatic acids)

-On standing ,it takes the odor of ammonia

-Variations in the odor of urine

  • Offensive odor : in case of pyuria
  • Acetone odor : in case o Ketosis (e.g D.M)
  • Burnt sugar odor : in case of maple syrup urine disease


-Fresh urine has a slightly acidic PH (6)

-High protein diet makes the urine more acidic

-Excess citreous fruits, and vegetables make the urine more alkaline

5.Specific gravity:

-It depends on the total amounts of solids , mainly Na Cl, urea ,proteins, and sugar

-It decreases in case of polyuria

-It increases in case of oliguria


-Normal fresh urine is clear

-Causes of turbid urine :

  • Pyuria
  • Hematuria
  • Bacteruria
  • Chyluria
  • Crystaluria

Chemical Characters of urine

-Normal urine contains about 50 gm of solids dissolved  in about 1.5 liter of water .

The main organic solid are :

  • NPN .
  • Proteins .enzymes ,hormones , and , vitamins .
  • Sugars .
  • Organic Acids .

1) Non protein nitrogenous substances ( NPN):

  1. Urea
  2. Uric acid
  3. Creatine
  4. Creatinine
  5. Ammonia
  6. Amino acids

1- Urea :

-It is the metabolic end product of   protein metabolism

-Formation : by urea cycle of the liver .

-Excretion in urine :  15 – 35 gm /day .


2- uric acid :

-It is the metabolic end product of purine catabolism .

-Excretion in urine : 300 – 700 mg / day .

-Gout .

3.   Creatine :

-It is formed of 3 amino acids .

-It is directly proportional to muscle mass (present as creatine  phosphate )

-Excretion in urine : less than 50 mg / day

4.  creatinine :

-It is formed from creatine phosphate .

-It is a renal function test .

-Excretion in urine : 0.8 – 2.0 gm / day

5. Ammonia :

-It is appears in urine as :

  • NH3 ( from deamination of amino acids ).
  • NH4 ( by action of glutaminase on glutamine received  by the kidneys from  other tissues

-This is significant to maintain acid  base balance in the case of acidosis

6.Amino acids :

-They  appear in urine in 2 forms :

  1. Free  ( 20 % )
  2. Conjugated   ( 80 % ) e.g  .
  • Hippuric acid
  • Phenyl Acetyl Glutamine
  • ß-Mercupturic Acid

-Amino aciduria

2) Sugars :

-Small amount of glucose ( not exceeding 150 mg /day  are excreted daily .

-Small amount of lactose , pentoses . and glucuronic  acid are excreted daily

3) Organic Acid :

  1. Oxalic Acid .
  2. Lactic Acid .
  3. Citric Acid .
  4. Short chain fatty acids .
  5. Hippuric  Acid  .
  6. Aromatic Acid

The main inorganic solids are :

  • Sodium .
  • Potassium .
  • Chloride .
  • Sulfate .

Sodium , potassium, chloride ( mainly from food )

and sulfur ( from sulfur containing amino acids,

and   sulfur   containing   vitamins )   are   mainly

excreted in urine .

N . B :

Abnormal constituents of urine :



L3-Structure of The Cell


  • The structural and functional unit of life.
  • The smallest unit that display the characteristics of life, i.e. reproduction, metabolism, response to stimuli
  • formed of a complex structure called protoplasm.

Cell Characteristics

•Plasma membrane

  • selectively permeable boundary between cell and environment

•Genetic material ( Nucleus )

  • single molecule of DNA in prokaryotes
  • double helix of  DNA  in eukaryotes


  • everything between plasma membrane and nuclear compartment
  • fills cell interior

Generalized Eukaryotic Cell

Picture1Prokaryotic Cells




(Plasmalemma or Plasma Membrane)

•outer limiting membrane

•surrounds the cell

•regulates the passage of materials into or out of the cell.


•It is very thin to be resolved.


•three layers (trilamellar)

•outer and inner dark (electron dense) layers

•A middle light (electron lucent) layer



  • phospholipid bilayer
  • proteins embedded in, and attached to, the inner (intracellular) and outer (extracellular) surfaces



•Repository for genetic material

•Usually single / some cells several / RBC none


1.Nuclear Envelope (membrane)

a.Phospholipid bilayer with nuclear pores – protein gatekeepers

b.  Controls what enters/leaves the nucleus

— things only go in or out by passing through

•      protein channels, which are selective • Usually proteins going in and RNA going out

c.   Encloses all the chromosomes


= all the chromosomes, which are long strands of the molecule DNA

— DNA regulates all cell activities, yet never      leaves the nucleus; how is this possible?

–produces RNA, short messenger molecules

that exit through nuclear pores

–RNA carries instructions out into the  cytoplasm


a.  compartment in the nucleus where ribosomes

are assembled

b.  ribosomes are then moved out into cytoplasm

through nuclear pores

c.  ribosomes and RNA work together outside

the nucleus, to build all the proteins in the cell



  1. Cell organelles
  2. Cell inclusions
  3. Cell matrix


•living components in the cytoplasm

•essential for life of the cell

•perform specific functions inside the cell.

Types of Cell Organelles

1- membranous cell organelles

2- non membranous cell organ

1-Membranous Cell Organelles

•surrounded by a unit membrane

•important for the metabolic activity in the cell.


2.Golgi apparatus


4.endoplasmic reticulum (smooth and rough)


6.coated vesicles

2-Non-membranous cell organelles

•not surrounded by unit membrane

•important as a cyto-skeleton of the cell




4.cilia and flagella

1) Mitochondria

-Mitochondrion = “thread granule”

-(power house of the cell)

a.  energy is taken from sugar, stored ATP

b.  requires oxygen to make  (aerobic metabolism)

c.  contained within double membrane

-Localization of the Mitochondria in the Cell

At sites of high-energy requirement in the cell:

  1. apical part in ciliated cells
  2. basal part in of protein synthesizing cells
  3. between myofibrils in skeletal muscle.

Picture92) Ribosomes

•non-membranous cell organelles

•Ribosomes = site of protein synthesis

–assembled in the nucleolus

–exported into the cytoplasm

•Ribosomes are RNA-protein complexes composed of two subunits that join and attach to messenger RNA

Picture10Types of ribosomes:


  • unbound in the fluid cytoplasm
  • produce proteins for use in the cell


  • attached to the (ER)
  • produce proteins for export, or for the plasma membrane

3) Endoplasmic Reticulum (ER)

•= “within the cytoplasm network”, a system of tubes and sacs formed by membranes (an enclosed space)

•Largest internal membrane

•Composed of Lipid bilayer

•Serves as system of channels from the nucleus

•Functions in storage and secretion

•Types of ER

  • Rough ER – studded with ribosomes

–modifies proteins produced by ribosomes

  • Smooth ER – few ribosomes

–doesn’t modify proteins

–functions in

lipid synthesis

drug  detoxification

carbohydrate metabolism

Picture114) Golgi apparatus

-collection of Golgi bodies

•collect, package, and distribute molecules synthesized at one location in the cell and utilized at another location

•Front – cis , Back – trans

•Cisternae – stacked membrane folds

Picture12Picture13Picture145) Vesicles

  • Lysosomes

•membrane-bound vesicles

•containing digestive enzymes – from Golgi

  • Microbodies

•enzyme-bearing, membrane-enclosed vesicles.

•Peroxisomes – contain enzymes that catalyze the removal of electrons and associated hydrogen atoms

Picture156) Cytoskeleton

Network of protein fibers

•supporting cell shape

•anchoring organelles

•Cytoskeleton Components

  1. Microfilament
  2. Intermediate Filament
  3. Microtubule

Picture181-Thin filaments

•Actin micro-filaments (6-7 nm)

  • contractile filaments
  • inter-act with myosin


  • micro-villi
  • cleavage furrow
  • muscles


2-Thick filaments

•myosin (12-16 nm).

•thicker than thin filaments


•In muscle in association with actin filaments forming the myofibrils.

3- Intermediate Filaments

•Tough, insoluble protein fibers with high tensile strength.

•The most stable of the cytoskeletal elements

•Act like internal ‘guy wires’ to resist pulling forces on the cell Important for diagnosis of the tumor

•They are not capable of producing contraction.

1.Desmin filaments


3.Vimentin filaments


5.Glial filaments


•They are pipe-like structure

•unfixed length

•uniform diameter.

• formed of a protein molecule; tubulin


All over the cytoplasm.


1- component of the cytoskeleton supporting, maintaining and stabilizing the shape of the cell.

2- maintain the asymmetrical shape of the cell.

3- the main structural component of cilia, flagella and centeriole.

4- guiding tracks for transporting material and organelles.



The centrosome

  • It is a specialized zone of the cytoplasm
  • contains two centerioles oriented at right angle to each other.

Picture22The Centeriole

  • It is a non-membranous cell organelle
  • important for cell division.


• in juxtanuclear position  in association with Golgi apparatus


•non living materials in the cytoplasm.

•products of metabolism or substances that are taken inside the cell from its surrounding.


1- Stored food.

2- Pigments.

3- Crystals.

1-Stored food

a)Carbohydrates (glycogen granules)

1- alpha glycogen particles

2- beta glycogen particles

b) Fat:

•small droplets large globules


•coloured substances • seen in the cell without staining.

a) Exogenous pigments:

  1. Lipochromes pigments
  2. Dust
  3. Minerals
  4. Tattoo marks

b) Endogenous pigments:

  1. Haemoglobin and its Derivatives
  2. Melanin
  3. Lipofuscin pigment


L2-Physiology of Kidney

Kidneys–as waste removal

– Bean shaped organs, about the size of your fist

– Located near the middle of your back, just below the rib cage

– Sophisticated reprocessing machine

– Processes about 180 liters of blood to give about 1.5 liters of waste products and extra water every day that is essential for homeostasis

Picture1Cross section of a kidney


– Every kidney has about a million nephrons

– Each nephron is formed of two  parts:

1-The Malpigian corpuscle, which consists of:

  1. The Bowman’s capsule
  2. Tuft of capillaries called the glomerulus

2-The renal tubule, which consists of 3 parts:

  1. The proximal convoluted tubule
  2. The loop of Henle
  3. The distal convoluted tubule


Urine Formation

Mechanism of urine formation

-Renal blood flow is about 1300 ml /min from which 125 ml is filtered/min by the glomeruli GFR

-Urine formation occurs by 3 different  nephron mechanisms acting on the GF:

  1. filteration
  2. reabsorption
  3. secretion.

1)Renal Corpuscle (Glomerulus)

-Glomerular filteration is the first step of urine formation

-The glomeruli act as ultrafilter to the plasma (very fine sieve), that allow the passage of substances having small molecular weight and prevent those of colloidal size.

-The filteration membrane is a 3 layers barrier:

  1. The capillary endothelium
  2. Basement membrane
  3. Podocytes

Picture4Picture5Mechanism of glomerular filteration

-Glomerular filteration is an inactive process.

-The glomerular membrane acts as a passive membrane.

-No active transport of materials takes place in that membrane.

-The driving force for filteration is the high hydrostatic pressure in the glomerular capillaries.


-It is the appearance of protein in urine, particularly albumin.

-Normally, no proteins appear in urine.

-Causes may be:

pre-renal, e.g. Bence-Jonesproteins

renal, e.g. damage of the glomerular membrane as in cases of nephritis.

post-renal e.g.cystitis, renal stones.

2)Renal Tubules

-The renal tubules receive about 180 liters  per day (125 ml/m x 60 x 24) by filteration.

-The renal tubules reabsorb about 178.5 liters daily and secrete other materials in urine

-The renal tubules consist of 3 portions:

  1. PCT (Proximal Convulated Tubules)
  2. Loop of Henle
  3. DCT (Distal Convulated Tubules)

-The tubular fluid pours in the collecting ducts.


1-It is the only part of the renal tubule where absorption of the following nutrients occurs:

  • Glucose
  • Amino acids

Failure of absorption of any of these nutrients, leads to its excretion in urine.

2-About 70% of sodium ions are reabsorbed by an active process.

3-Almost all potassium ions are reabsorbed in this part

4-Passive reabsorption of the anions Cl-, HCO3- occurs in this part along with the reabsorbed Na+ and K+

5-Obligatory water reabsorption: About 70% of the filtered water

6-Back diffusion of urea in this part following water reabsorption.

7-Secretion of several metabolic waste products as uric acid and creatinine, foreign substances, and drugs e.g. penicillins.

1)Functions of the PCT

Picture82)Functions of Loop of Henle

-The loops of Henle are concerned with the production of concentrated or diluted urine.

-The U-shaped structure of these loops allows them to constitute a countercurrent system. Fluids passes inward and outward closely parallel to each other and in an opposite direction

-These loops are responsible for the development of high osmolality in the renal medullary interstitium. This is essential for urine concentration

Picture9Medullary Gradient

Picture10Picture113)Functions of DCT

In this part of the renal tubule, the final adjustment of urine occurs according to body needs:

-urine volume


-Electrolyte content

Regulation of urine volume

-The main regulator of water in urine is the antidiuretic hormone (ADH).

-The ADH is secreted when the crystalloid osmotic pressure increases, when plasma volume decreases, and in certain emotions, pain, and drug intake.

-Urine volume increases in hydration and decreases in dehydration.

Mechanism of action of ADH

-ADH increases the permeability of the DCT by opening of the aquaporins present in there walls.

-Now, water absorption occurs passively by the effect of renal medullary hypertonicity

Lack of ADH-Diabetes insipidus

The walls of the DCT become impermeable to water, so most of fluid delivered to DCT is lost in urine.

-Urine volume/day is 15-20 liters


-Urine is very diluted

Regulation of electrolyte excretion in urine

In the DCT, sodium ions reabsorption continues by an active ionic exchange mechanism i.e. in exchange with either K+ or H+.

The process is controlled by the Aldosterone hormone

Regulation of pH of urine

The pH of urine is changeable so that to keep the pH of blood constant. It varies from 4.5 in severe acidosis to 8 in severe alkalosis.

Mechanism of pH regulation

1- By getting rid of several acid metabolites e.g. lactic, carbonic, phosphoric and keto acids.

2-The renal tubules absorb the alkali reserve (NaHCO3) which helps to maintain the blood pH constant.

Picture12Kidney – Contd.

In addition to removing wastes, your kidneys release three important hormones:

Erythropoietin or EPO, which stimulates the bone marrow to make red blood cells

Renin (REE-nin), which regulates blood pressure

The active form of vitamin D, which helps maintain calcium for bones and for normal chemical balance in the body

Juxtaglomerular Apparatus



Basic Info

žIt is the functional unit of the kidney. žEach kidney contains about one million nephron. žAfter age 40 the number of functioning nephrons decreases by about 10%.

It consists of:

1-Renal corpuscles.

2-renal tubules:

  • —Proximal convoluted tubule.
  • —Loop of henle.
  • —Distal convoluted tubule.


1) Renal corpusles

It is formed of:

1-Bowman’s capsule: is doubled walled spherical  cup shaped like structure

It is the dilated blind end of the renal tubule

2-Glomerulus: It is a tuft of capillary which are surround by the Bowman’s capsule.

3-Glomerular membrane: (formed of three layers)

—The endothelium of glomerular capillaries —A basement membrane —The epithelium of Bowman’s capsule.


Renal Blood Supply


JuxtaGlomerular Apparatus


It  consists of 3 cell types:

Macula densa cells

  • Present at the zone between ascending loop of Henle &DCT.
  • It detects the fall of NaCl leading to renin release.

Juxta-glomerular cells

  • —Located at the wall of afferent arterioles —
  • Respond to wall stretch —
  • Forms &secretes renin

Mesangial cells

  • Interstitial cells act as link between the other 2 types of cells

Function of renin

  • Conversion plasma angiotensinogen to angiotensinI (AI)
  • AI→Angiotensinǁ (Aǁ) by ACE
  • Function of Aǁ:
  1. VC → ↑BP
  2. ↑ aldosterone secretion from supra-renal cortex
  3. ++ secretion of ADH
  4. ++ thirst sensation
  5. ++ Na reabsorption from PCT

The Glomeruli Functions

  • Glomerular filtration is the first step in urine formation
  • It is a passive process
  • The glomeruli act as a semi permeable membrane
  • They filter all the constituents of plasma except the colloids(protein &fat)
  • About 700 ml of plasma passes through the kidney per minute only 125 ml are filtered
  • Factors favoring glomerular filtration
  1. The high pressure in the glomerular capillaries (it is the only capillary in the body that lie between two arteries
  2. Large surface area of the glomerular capillary
  3. High permeability of the glomerular membrane due to the presence of pores

2)Renal Tubules

General Functions

1-Reabsorption: It is the transport of substances from the lumen of the tubules to the blood stream.

2-Secretion: It  is the transport of substance into the tubular lumen. The most important secreted substance include creatinine ,uric acid  H ions &foreign substance.

3-Synthesis: NH3 that play a role in acid base balance.

Proximal convoluted tubule


  1. It is the only part where reabsorption of glucose, amino acids and phosphate take place by an active process.
  2. Phosphate reabsorption is controlled by parathyroid hormone.
  3. About 70-75% of Na ions are reabsorbed by an active process.
  4. Passive reabsorption of70-75% of water secondary to Na K glucose & amino acids

Loop of Henle

  • žIt is a U shaped consisting of descending &ascending limbs
  • žIt is concerned with the production of diluted or concentrated urine
  • žThe structure of loop of henle allow them to constitute a counter current system
  • žThis system in which the inflow and outflow passes parallel to each other and in opposite direction.


How concentrated urine is produced?
  • AT the descending loop of henle:
  1. The walls are highly permeable to water & poorlypermeable to solutes
  2. As a result the tubular fluid becomes hypertonic in the medullary inter stetium.
  • AT the ascending loop:
  1. The walls are highly permeable to solutes & less permeable to water
  2. It is the responsible for creating graded hyper osmolarity


Distal convoluted tubules

This segment  is responsible for:

1 –Final adjustment of urine volume.

  • Water reabsorption determine  the volume of urine.
  • It is under the control of anti diuretic hormone (ADH).

2- Regulation of PH &electrolytes.

  • Na is reabsorbed in exchange with either H ions or K ions
  • It is under aldosterone hormone.

S1/Case 2 – The Structure of Cells


  1. Understand the structure and function of the kidney
  2. Understand glomerular filtration , tubular reabsorption and secretion
  3. Understand the component parts of a cell
  4. Know about the different types of electromagnetic radiation
  5. Understand how cells interact with insoluble molecules in their immediate environment
  6. Be able to discuss membrane transport mechanisms