Renal clearance

Renal clearance is a measurement to determine the functional status of the kidney. By definition clearance is the volume of plasma from which a substance is completely removed through excretion by the kidney in a given amount of time (usually a minute). For example, the  urea is 75 ml/min. This means that the kidney removes all of the urea in 75ml of plasma in one minute. 

Every minute approximately 625 ml of plasma flows to the kidney. This is the renal plasma flow. Some of the fluid leaves the kidney in the plasma while some leaves the kidney as urine. There are only two ways for a substance to end up in the urine: either it is filtered at the glomerulus and then not reabsorbed from the tubules, or the substance is not filtered but is secreted by the peritubular capillaries into the tubules. In either instance, the substance ends up in the collecting duct and is excreted into the urine.

Figure- showing the structure and function of a nephron

Of the 625 ml/min of plasma that goes to the glomerulus, 125 ml/min is filtered into Bowman’s capsule forming the filtrate (The rate of filtration is known as the Glomerular filtration rate- GFR). The remaining 500 ml/min enters into the peritubular capillaries. Of the 125ml/min filtered, almost all of the water in this fluid is reabsorbed back into the blood. The composition of the filtrate in Bowman’s capsule is identical to the composition of the plasma except that the filtrate has no or very little amount of proteins.

Any substance, which is freely filtered by the glomerulus and is neither reabsorbed nor secreted, ends up in the urine.Thus all the plasma that gets filtered is cleared of that substance(that is, all the substance in the filtrate gets excreted) while the substance that that is not filtered (and thus remains in the plasma) is not excreted.Since clearance is defined as the volume of plasma ‘cleared’ of a substance in1 min, the clearance for that substance would be 125 ml/min. This means that out of the 625 ml of plasma that come to the kidney in one minute, 125 ml (the fraction that is filtered) has all of the substance removed from it in that minute, the other 500 ml (the fraction that is not filtered) keeps it as there is no way for the substance get into the urine as it is not secreted.

The GFR is typically recorded in units of volume per time, e.g., millilitres per minute ml/min. 

The compound inulin is cleared in the same way as mentioned above. All of the plasma that is filtered is cleared of inulin so that if one has to measure the clearance of inulin, it would be equal the amount of plasma filtered in a minute, the glomerular filtration rate.Therefore, the clearance of inulin is equal to the glomerular filtration rate, the volume of plasma filtered in one minute. Inulin is not a normal metabolite of the body; it is in fact administered to determine the functional status of the kidney

The clearance of any other substance is not similar to clearance of inulin. For example-Glucose, like inulin, is freely filtered. Thus glucose is present in Bowman’s Capsule. However, glucose does not appear in urine because glucose is completely reabsorbed as it passes through the tubules. Inulin is not reabsorbed. This means all of the glucose that comes to the kidney is saved and leaves the kidney in the plasma and that no glucose is excreted into the urine. The clearance of glucose is therefore 0ml/min as no plasma has its glucose removed as it passes through the kidney.This would be true for any substance that is completely reabsorbed. Hence if the clearance of Tryptophan (an amino acid) is 0 ml/min, it can be inferred that Tryptophan must be completely reabsorbed (as long as it is freely filtered).

Taking the example of another substance, Paraamino Hippuric acid (PAH), It is freely filtered, not reabsorbed and is completely secreted by the kidney. Thus all of the PAH entering the kidney ends up in the urine, both the PAH that is filtered and that that is not filtered.This means that all the plasma entering the kidneys would be cleared of PAH. Since the renal plasma flow is about 625 ml/min in a ‘normal’ kidney, the clearance of PAH must be 625 ml/min. Therefore, the PAH clearance is equal to the renal plasma flow. PAH clearance is used to determine whether the kidneys have an adequate plasma flow.

Now, if the clearance of a substance is 625ml/min, this would suggest that the kidney completely secretes this substance(that is, the kidney ‘treats’ this substance the same as PAH which is known to be completely secreted). Using similar logic, a clearance value of 125 would suggest that the kidney neither reabsorbs nor secretes the substance and a clearance value of 0 suggests that the kidney completely reabsorbs the substance (assuming that the substance is freely filterable in the glomerulus).

The urea clearance has been measured to be 75ml/min. What does the kidney ‘do’ with urea (does it reabsorb, secrete or neither)? Well if urea is completely reabsorbed, its clearance should be like that of glucose (0 ml/min) and if urea is not reabsorbed at all (and not secreted), its clearance should be 125 ml/min. Since the value of urea clearance is 75 ml/minute, which means urea is partially reabsorbed. Note that the common belief concerning kidney function is that it removes urea from the blood yet the nephron partially reabsorbs urea! Thus urea clearance is not a true predictor of Glomerular filtration rate as is Inulin clearance.

In clinical practice, however, creatinine clearance or estimates of creatinine clearance based on the serum creatinine level are used to measure GFR. Creatinine is produced naturally by the body (creatinine is a break-down product of creatine phosphate, which is found in muscle). It is freely filtered by the glomerulus, but also actively secreted by the peritubular capillaries in very small amounts such that creatinine clearance over estimates actual GFR by 10-20%. This margin of error is acceptable, considering the ease with which creatinine clearance is measured.Unlike precise GFR measurements involving constant infusions of inulin,creatinine is already at a steady-state concentration in the blood, and so measuring creatinine clearance is much less cumbersome.

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Chemistry Of Proteins-3

1. Why are amino acids called as Amino acids?

(Since they have an amino group and an acid group i.e. Carboxyl group which is ionized at the physiological p H and behaves as a proton donor and is thus an acid)

 2- What is meant by primary amino acids?

(Those amino acids which have a genetic information on the DNA for their synthesis are called as Primary or standard amino acids)

3- What is the linkage between the amino acids in a peptide?

(The amino acids are linked together by a peptide bond which is an anhydrous linkage between the amino acids)

4- Name the amino acids which are derived or modified after translation but are not incorporated in to the tissue proteins.

 (Homocysteine, GABA, Argino succinic acid, Ornithine, Citrulline, etc)

5- Define Denaturation

 ( It is the loss of secondary , tertiary or quaternary structure( if present ) of a protein on exposure to heat, UV light, acids, alkalies, heavy metal salts or even by vigorous shaking, the primary structure is left intact)

6-What is meant by a complete protein, give an example of a complete protein?

( A Complete protein contains all the essential amino acids in an appropriate amount  required for growth, repair and maintenance of body weight.  Example -Egg protein)

7- Give an example of a protein with axial ratios >10:1

(Fibrinogen, keratin, collagen )

8-How many amino acids can be accommodated in one turn of alpha helix?

(3.4 amino acids)

 9- What are chaperones?

 (These are the proteins which participate in the proper folding of the proteins)

10- What is the defect in “transmissible spongiform encephalopathies’?

(These are included under the category of Prion’s diseases and are fatal neurodegenerative diseases characterized by spongiform changes, astrocytic gliomas, and neuronal loss resulting from the deposition of insoluble protein aggregates in neural cells. The protein aggregates are formed of misfolded proteins.)

11-What is the difference between a homodimer and a heterodimer?

(Homodimer contains two copies of the same polypeptide chain, while in a heterodimer the polypeptides differ)

12-What are amphipathic helices?

(The alpha helices having predominantly hydrophobic R groups on one side of the axis of the helix and predominantly hydrophilic ones on the other side are called amphipathic helices)

13-All the amino acids except——- have a chiral centre.

 (Glycine)

14-What is meant by isoelectric  p H ?

 ( It is the p H at which amino acid carries no net electrical charge)

15-Proteins contain only D-amino acids, for which a left handed alpha helix is by far the more stable,  thus only left-handed helices are present in proteins. True or false?

 (False –Proteins contain only L-amino acids, for which a right-handed alpha helix is by far the most stable, and only right-handed alpha helices are present in proteins)

16-Give examples of metalloproteins-

( Alcohol dehydrogenase, glutamate dehydrogenase, Xanthine oxidase  etc. are the examples of metalloproteins

17-Give examples of non standard amino acids which are incorporated in to tissue proteins.

( Hydroxy proline, hydroxy lysine )

18– What is meant by zwitterion ?

( It is the form of amino acid present at its isoelectric p H,  both positive  and negative charges are there but the net charge is zero)

19-Name an indole ring containing amino acid-

(Tryptophan

20- Name the peptides which act as gastro intestinal hormones-

( Secretin, pancreozymin and cholecystokinin)

21- Name the amide group containing amino acids

(Asparagine, Glutamine)

22- What are derived proteins ?

(Proteoses, peptones and peptides etc, the product of digestion and denaturation are called as derived proteins )

23- Give two examples of antibiotic peptides

(Polymyxin, Penicillin, etc )

24-What is the difference between cysteine and cystine ?

( Two cystine residues are joined together by a disulfide bridge to from cystine )

25- What are histones? 

( Histones are simple proteins which can bind with DNA to form nucleoproteins, generally they are rich in basic amino acids like Arginine and lysine )

26- Which amino acid disrupts the alpha helical structure of the proteins ?

( Proline and hydroxy proline )

27- Name the components of Glutathione

(Glutamic acid, cysteine and glycine )

28- Name two proteins with a quaternary structure

( Immuno globulins, Hemoglobin, CPK , LDH etc )

29- What are brain peptides ?

( Met encephalin and Leuencephalin)

30- Name a Phospho protein

(Casein, Ovovitellin)

31-What is the product formed after decarboxylation of an amino acid ?

( Amines are formed after decarboxylation of amino acids- like Tryptamine, histamine Tyramine etc)

32-Name the sulphur-containing amino acids-

(Cysteine, cystine and Methionine)

33-Choose the aromatic amino acid out of the following-

Arginine, Histidine, lysine and Tyrosine —— (Tyrosine)

34-Choose an amino acid that does not participate in the alpha helical formation-

Methionine, tryptophan, serine, cysteine——

( Tryptophan )

 35- Millon’s reaction is specific for——- ?        

( Tyrosine )

36- Out of the followings which amino acid is not present in the proteins?

β- Alanine, Histidine, Glycine                    

(β- Alanine)

 37- Name a peptide which acts as a smooth muscle relaxant

( Bradykinin)

38-   What is the nature of prosthetic group in Ceruloplasmin ?

(Copper- It is metalloprotein)

 39- What is a nutritionally poor protein ?Give an example-

( A protein which lacks many essential amino acids is called a poor protein, E.g.- Gelatin

 40- Which protein is abundantly present in hair?     

(Keratin )

41-What is the significance of Biuret test?

 ( It is for the detection of proteins and peptides. Dipeptides and amino acids do not give this test positive, more than two peptide bonds are required for this test to be positive )

42- What is the nature of casein, the milk protein?

( It is a Phospho protein- A conjugated protein)

 43- What is the axial ratio in fibrous proteins?

 ( > 10:1)

 44- In proteins the alpha helical and beta pleated sheet structures are examples of-

Primary, secondary or tertiary structure ?            

( Secondary)

 45- Name an Imidazole ring containing amino acid 

(Histidine)

46- Name a peptide  hormone which prevents diuresis –

( ADH)

47 What is the basis of using raw egg for heavy metal poisoning ?

( Egg protein binds with heavy metal to form metal proteinate complex, which is water-soluble and is excretable, else heavy protein binds with tissue proteins to cause damage)

48- The tertiary structure of a protein describes sequence of amino acids- true or false ?

( False- Tertiary structure describes the folding of the protein )

49- Give two examples of haemoproteins.

(Hemoglobin, Myoglobin, Cytochromes, Catalase, Peroxidase and Tryptophan Pyrrolase)

50-  In a protein the disulphide bridges can be broken by–

 ( Reduction )

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Chemistry Of Proteins-2

1- What is the nature of a prosthetic group in a lipoprotein?

 (Lipoprotein is a conjugated protein with lipid as a prosthetic group)

 2- What is the significance of Sakaguchi test?

 (This test is undertaken for the detection of Arginine)

 3- What is the distance traveled per turn in an alpha helix?

 (0-54 nm)

 4- Name an imino acid.

 (Proline, hydroxy proline)

 5-Choose the chromo protein out of the followings-

 Collagen, Keratin, hemoglobin                       

 (Hemoglobin)

 6-Carbonic anhydrase is an example of simple or conjugated protein?

 (It is a conjugated protein, with metal as th prosthetic group)

 7- Name a peptide which acts as an artificial sweetener.

 (Aspartame)

 8- Name the agents which can bring about denaturation of proteins

 (Heat, acids, alkalis, heavy metal salt, UV light, vigorous shaking etc)

 9- Name a tripeptide which acts a reducing agent in the tissues.

 (Glutathione)

 10- Name a peptide which acts as vasoconstrictor

 (Angiotensin-II)

 11- Name the amino acid which is deficient in pulses

 (Methionine)

 12- Choose the odd one out- Collagen, Elastin, Keratin, Histones

 (Histones- The rest three are scleroproteins)

 13- Name two nano peptides

 (Oxytocin, Vasopressin)

 14- Name two globular proteins

 (Hemoglobin, Myoglobin)

 15-Which test should be undertaken for the detection of cysteine in a protein solution?

 (Lead acetate test)

 16-What is the nature of peptide bond- Single, double or partial double bond ?

(Partial double bond)

 17- Out of all the primary amino acids which amino acid gives yellow color on Ninhydrin test?                  

 (Proline and hydroxy proline )

 18- Histamine is formed from Histidine by-

 Deamination, decarboxylation or transamination

 (Decarboxylation)

 19- Name two non alpha amino acid

 (GABA, beta Alanine, Delta amino Levulinic acid)

 20- Choose the odd one out-

 Aspartic acid, lysine, Arginine, Cysteine                   

 (Cysteine- Amino acid with uncharged side chain at physiological p H

 21- Choose the odd one out-

Tyrosine, Tryptophan, Threonine                   

 (Tyrosine- non essential Amino acid from the nutritional perspective or threonine if considered non aromatic amino acid)

 22- Name a purely ketogenic amino acid             

 (Leucine)

 23- Name a peptide used as an anticancer drug            

 (Bleomycin)

 24- Name the defense proteins                                     

 (Complement, immunoglobulin)

 25- Choose the odd one out- Silk fibroin, Hemoglobin, Carbonic anhydrase

 (Hemoglobin- The rest are proteins with beta pleated sheet

 26- The proteins with a carbohydrate content > 10 % are called as Mucoproteins- True or false?         

 (True)

 27- The most abundant amino acid in keratin?             

 (Cysteine)

 28- The most abundant amino acid in Collagen—-?      

 (Glycine)

 29- Xanthoproteic test does not specify for—- ?

 Tyrosine, Tryptophan, Serine               

 (Serine)

 30- Give the characteristics of a peptide bond in one line-

 (Rigid, partial double bond, Trans and stable)

31-Name the branched chain amino acids 

 (Valine, Leucine, iso Leucine)

 32-Choose the hydrophobic amino acid out of the followings-

 Aspartic acid, Arginine, Serine, Isoleucine

 (Isoleucine)

 33-Which amino acid acts as Methyl group donor?

 (Methionine)

 34- What is the difference between Deamination and Transamination?

(Deamination is the removal of amino group of the amino acid while Transamination is the transfer of amino group from one  donor amino acid to an acceptor keto acid for the formation of a new amino acid)

 35- Out of the 20 amino acids which amino acids participate in the formation of phosphoproteins

 (Serine and Threonine)

 36- Formation of carbamino compound for the transportation of carbon dioxide is a property of amino group, carboxyl group or both groups?

 (Amino group)

 37- Hopkins Cole test is a confirmatory test for which amino acid?

 (Tryptophan)

 38- How many peptide bonds are there in a tripeptide?

 (Two)

 39- The alpha helix is right or left handed?         

 (Right handed)

 40- What is the direction of hydrogen bonds in the beta pleated sheet structure?

 (Perpendicular to the axis)

 41-What is the direction of beta pleated sheets in flavodoxin?

 (Parallel)

 42-Name the most abundant protein in mammals        

 (Collagen)

 43-Name a defect in the primary structure responsible for the causation of a disease

 (Sickle cell disease)

 44-What is the defect in Alzheimer disease?

 (Protein misfolding leading to formation of insoluble protein aggregates)

 45-What is the isoelectric p H of casein?

(4.6)

 46- What is the effect on the solubility of a protein upon denaturation?

 (Solubility decreases upon denaturation)

 47- Name the lipo proteins of biological significance

 (Chylomicrons, VLDL, LDL, HDL)

 48- Which amino acid is lacking in cereals?

 (Cereals lack Lysine)

 49- Which amino acid forms disulphide linkages between two polypeptide chains in oligomeric proteins?                       

 (Cysteine)

 50- Which peptide is used in clinical practice to induce uterine contractions?

 (Oxytocin)

------------------------------------------ Best Wishes: Dr.Ehab Aboueladab, Tel:01007834123 Email:ehab10f@gmail.com,ehababoueladab@yahoo.com ------------------------------------------

Chemistry of Proteins-1

1-Give an example of reversible denaturation

(Denaturation of Ribonuclease by urea)

 2. Give example of a circular peptide.

(Gramicidin S)

 3-What is the difference between Salting in and Salting out?

(Salting in is addition of a pinch of salt to increase the solubility of a protein, while salting out is addition of excess of salt to precipitate it out)

4. Name the proteins containing alpha helical structure predominantly.

(Hemoglobin, Myoglobin etc)

5. Name the super secondary structures

(Greek key, beta meanders, Beta alpha beta)

6. Name the respiratory proteins

(Hemoglobin, Myoglobin, cytochromes)

 7. What is the class of Zein protein?

(Poor protein- it lacks Tryptophan and Lysine)

 8. Name the contractile proteins 

( Actin, Myosin, flageller proteins)

 9-What are the features of isoelectric pH?

(Decrease in solubility, electric charge, Electrophoretic migration, loss of biological activity)

 10-What is the basis of protein precipitation by organic solvents?

(Decrease in dielectic constant of the medium)

11-What is the difference between flocculum and coagulum?

(Flocculum is a reversible state of denaturation while coagulum is a an irreversible state of denaturation)

12-What are the forces that stabilize the alpha helical structure?

(Hydrogen and Vander waals forces mainly)

13-What is the basis of cauterization by silver nitrate during surgery to control bleeding?

(Silver nitrate is a heavy metal salt and by causing precipitation of proteins seals the oozing points of the blood vessels)

14-What is meant by a domain?

(Domain is a term used to denote a compact globular functional unit of a protein)

15-Why is Glutathione called a pseudo peptide?

(In glutathione instead of alpha carboxyl group, the gamma carboxyl participates in the peptide bond formation)

16-Covalent forces stabilize the tertiary structure in a protein- True or false?

(False- the non covalent forces stabilize the tertiary structure in a protein)

17- Which tests should be carried out for the detection of Tryptophan in a given solution?  

(Xanthoproteic and Hopkins Cole test)

18- Which amino acids contribute towards ionic interactions?

(Positively charged amino acids like Arginine , Lysine and negatively charged amino acids like Aspartic acid and Glutamic acid)

19- Which protein is precipitated by full saturation with Ammonium sulphate?

(Albumin)

20- What is the relationship of amount of salt required and the molecular weight of a protein?

(More the molecular weight and lesser is the amount of salt required by the protein and vice versa)

21-What are the functions of proteins?

(Nutritive, buffering, defense, viscosity, osmotic pressure, enzymes, hormones etc)

22-Name mono amino dicarboxylic acids

 (Aspartic and Glutamic acid)

 23-Name heterocyclic amino acids

 (Tryptophan and Histidine)

 24-Name the 21st and 22 nd amino acid

 (Seleno cysteine and Pyrrolysine)

 25-Which amino acids are involved in forming N- Glycosidic linkages?

 (Asparagine and Glutamine)

26-Name the semi essential amino acid

(Arginine and Histidine)

27-Which amino acid acts as the precursor of vitamin Niacin?

 (Tryptophan)

28-Name the amino acids with a non polar side chain

(Alanine, Valine, Leucine Isoleucine, Methionine, Phenyl Alanine)

29-Which protein structure determines the relationship of amino acids which are 3-4 residues apart ?

 (Tertiary structure)

30-Which test will be negative for a protein lacking tryptophan ?

 (Hopkins cole test)

 31-Name the essential amino acids

( Valine, Leucine, Isoleucine, lysine, Phenylalanine, Methionine and Threonine)

 32-Which amino acid is optically inactive ?

(Glycine)

 33-Which amino acid is abundantly present in prolamines ?

(Proline)

 34-Which protein is mostly found attached to DNA?

(Histone)

 35-Name the amino acids which are both glucogenic as well as ketogenic

(Isoleucine. Phenyl Alanine, Tyrosine and Tryptophan)

35-Name a specific test for the detection of alpha amino acids

(Ninhydrin test)

 36-Name a  specific test for the detection of cysteine

(Lead acetate test)

37-Covalent bond is formed at which level of protein’s structural organization?

(Primary structure)

38-Name the peptide hormones

 (ACTH, TRH, FSH, Glucagon, PTH, ADH, Oxytocin, Secretin, Pancreozymin, Cholecystokinin)

 39-What is the effect on the biological activity of a protein when exposed to UV light ?

 ( It will lose its biological activity since it will be denatured)

 40-Give two examples of protein misfolding causing disease?

 ( Prion’s and Alzheimer disease)

41-What is the class of casein ?

 (Class 1- complete protein) 

42-What are the forces that stabilize quaternary structure of a protein ?

 (Mainly non covalent)

 43-Which amino acid acts as the best buffer of the plasma?

 (Histidine)

 44-What will be the product of decarboxylation of Tyrosine?

 (Tyramine)

 45-Why can’t albumin and majority proteins acquire the native configuration upon denaturation?      

 (Chaperones and other proteins assisting proper folding are not there)

 46-What are Beta bends?

 (Short loops to turn the direction of the beta sheets?

 47-What are the forces that stabilize the beta bends?

 (Hydrogen and electrostatic)

 48-Name a peptide to regulate the volume of urine excreted?

 (ADH)

 49-Which protein is present in the tendons and cartilages? 

(Collagen)

 50-Name the storage proteins

 Ferritin, ceruloplasmin)

------------------------------------------ Best Wishes: Dr.Ehab Aboueladab, Tel:01007834123 Email:ehab10f@gmail.com,ehababoueladab@yahoo.com ------------------------------------------