Archive for October, 2006

Clinical biochemistry

Friday, October 20th, 2006

important to evaluate the health status of individual

once blood clotted, remaining liquid phase is serum

activity of serum enzyme depend on
enzyme conct, rather of enzyme synthesis, rate of enzyme clearance,biological factors ie age.


ALT = alanine aminotransferase
ALP = alkaline phosphatatse
AST = aspartate aminotransferase
CK = creatine kinase
GGT = gamma glutamyltransferase
LDH = lactate dehydrogenase
LIP = lipase
OCT = ornithine carbomoyltransferase
GLDH = glutamate dehydrogenase

liver receive 1.5L/min of blood , damage to liver result
a range of enzyme released intoblood
disturbance of blood chemistry chnage in total bilirubin
reduced blood level of albumin and globulins

Liver function test- abnormalities may caused by
direct damage to hepatocytes
damage of biliary system
specific disease such as tumours


serum AST and ALT tend to change in parallel with ALT more specific and sensitive marker of hepatic function.

ALP alkaline phosphatase rise when active bone formation, pregnancy and damage of bile duct epithelium, intestinal dysfunction.

both obstruction and hepatocellular liver disease result increased free and conjugated bilirubin

bilirubin is degradation product of haem due to haemoglobin breakdown
free biliburin take up by liver hepatocyte and conjugated to glucuronic acid, leave liver via bile duct to bowel. reduced to urobilinogen colourless and urobilin color in both intestinal bacteria. colorless urobilinogen are excreted in faeces.in liver disease ,urobilinogen may be excreted in urine.


increase in serum bilirubin may caused by
increased RBC turnover
liver disease

when excess 1mg/dL result jaundice yellow skin and passage to brain cause kernicterus in which bilirubin deposit in lipid rich basal ganglia of the brain.

Diagnosis of MI based on
physical exam, ECG changes, elevation of serum enzymes

CK creatine kinase, AST: aspartate aminotrasnferase, LDH: lactate dehydrogenase

Ck dimer of 2 part M muscle and B brain. brain CK is almost enitrely BB.
heart 60% MM and 40 % MB

serum CK is virtually MM except after MI ,MB isenzyme increases.

lactate dehydrogenase LDH
tetramer of 4 subunit H, M
LDH 1/LDH2 increase with CK-MB = SIGNIFICANT OF MI

AST - aspartae aminotransferase
elevated 1-4 days after MI
Prolonged elevation due to hepatic damage

Kidney function test

GFR glomerular filtration

assessment of GFR could be achieved by infusing a suitable tracer into blood and recording its rate of appearance in the urine.

hyperamylasemia : high level of plasma amylase activity in blood
pancreatic oedema to severe necrosis and haemorrhage of the organ allows the release of pancreatic enzyme (amylase,lipase,and protease)
occur when pancreatic disease such as acute/chronic pancreatitis, non-pancreatic abdominal such as local surgery and intestinal obstruction. renal insufficiency and burns

electrophoresis : migration of charged particle under the influence of an electric field .
cellulose acetate is the most common electrophoresis used for analyzing plasma protein such as fibrinogen, albumin and globulins.

albumin is major protein abt 60 % of plasma protein. albumin is the major determinant of plasma osmotic pressure. albumin bind with various ligands such as calcium, free fatty acids, steroid hormones, and some drug like aspirin.

liver disease px, low albumin coz body produce insufficient albumin
during nephrotic syndrome , level of albumin decrease .

malnutrition, decrease in albumin level during kwashiorkor. not enuff protein for liver to make new albumin. human lack of albumin will exhibit moderate odema which is called analbuminemia.

metabolism of nucleic acid

Friday, October 20th, 2006

nucleic acid = polynucleotide = nucleotide = nucleoside = sugar + base

all 4 N atoms of purine from amino acids
2 from glutamine, 1 from aspartate, 1 from glycine
all 5 C atoms come from
2 glycine, 2 tetrahydrofolate , 1 co2

de novo biosynthesis of purine in liver

PRPP = inosine 5 monophosphate IMP = adenylsuccinate = adenosine AMP
                                                       = Xanthosine 5 phosphate XMP =guanosine GMP

salvage reaction
conversion of purine to mononucleotides
require less enrgy compare to de novo biosynthesis

adenine + PRPP = AMP + PPi 
guanine + PRPP = GMP + PPi
hypoxanthine + PRPP = IMP + PPi

adenosine + ATP = AMP+ ADP
guanosine + ATP = GMP + ADP

biosynthesis of pyrimidine simpler because one ring simple structure

1 mole glutamine,ATP,CO2,aspartate = OMP = UMP uridine monophosphate

salvage reaction :
thymidine + ATP =TMP + ADP
uridine + ATP = UMP + ADP
cytidine + ATP = CMP + ADP
orotic acid + PRPP = OMP + PPi

differences . for pyrimidine, PRPP is added first to form OMP
no branch in de novo, precursor diff

ribonucleoside diphosphates reduced to 2-deoxyribonucleoside diphosphate in all organism
NADPH Is reducing agent

majority nucleotide form by de novo or salvage are ribonucleotide reductase

cancer chemotherapy = inhibit formation of dTTP thus DNA cancer cells cause its death

catabolism of pyrimidine

CO2     NH3    beta alanine      beta-aminoisobutyrate

end product for
thymine : CO2, NH3, beta aminoisobutyrate
cytosine: CO2, NH3, beta alanine

Disorder,overproduction cause by

deficiency of urea cycle enzyme ornithine transcarbamoylase
high nitrogen food
drug effect
type 1 orotic aciduria

treatment of orotic aciduria
uridine/cytidine increase UMP production
UMP inhibit CPS ll  thus attenuating orotic acid production

catobolism of purine

adenosine = inosine = hypoxanthine = xanthine = uric acid

guanosine = guanine = xanthine = uric acid

disorder of purine metabolism

gout cause by excess PRPP and deficiency HGPRT, renal disorder lead to accumulation of uric acid

big toe, inflammatory , pain, stiffness, swelling.
diagnosis: uric acid cyrstal, blood test , urine test

treatment: NSAIDs, corticosteroids, allopurinol

lesch-nyhan , deficiency of HGPRT cause increase production of uric acid, accumulation os stones and gout . bite off fingertips and part of lips.

von gierke , increase PRPP

hypouricemia cause by xanthine oxidase deficiency

Metabolism of lipid

Friday, October 20th, 2006

food contain lipid transport as chyloromicrons in intestine

undergoes digestion with the aid of bile acid and pancreatic lipase

give fatty acid and glycerol : provide energy, synthesize brain and nerve tissue, energy reserve


activated form of fatty acid is acyl-coA
           oxidation               hydration         
         2nd oxidation          cleavage
acyl-coA -  trans beta-enoyl-coA - beta-hydroxyacl-coA   - beta-ketocyl-coA - acyl-coA

odd number fatty acid - propionyl coA - succinyl coA - krebs cycle

ketone bodies@substances related to acetone produces when an excess of acetyl-coA arises from beta-oxidation

this condition occur when not enough oxaloacetate available to react with large amount of acetyl-coA that could enter citric acid cycle.

occur wif diabetic patiens, starvation(keep fit), high intake lipid low intake carbohydrate

formation of ketone bodies
1 acetyl coA  = acetoacetylcoA = acetoacetate = beta hydroxybutyrate + acetone

biosynthesis of cholesterol

acetyl coA 2C= 3-hydroxyl-3-methylglutaryl-coA ( HMG-CoA)   = mevalonate 6 C =
isoprene isopentenyl pyrophosphate (IPP) 5C= squalene  30C= cholesterol 27C

Chylomicrons 90% triacyglyceride = food, exogenous
lipoprotein = endogenous

VLDL= 60% triacyglyceride
IDL = 40% triacyglyceride
LDL = 50 % cholesterol
HDL = protein 25%  transport cholesterol back to liver

VLDL not mature form = IDL = LDL  mature form

cholesterol can be converted to
manufacture bile acid
precursor of vitamin D
manufacture of steroid hormones

bile acid synthesis is the only mechanism for the elimination of the excess cholesterol
bile acid = emulsifying agent
solubilise cholesterol preventing ppt of cholesterol in gallbladder

hypercholesterolimia : high blood cholesterol

plaque: narrowing of blood vessel  cause blood clot cause stroke or death

avoid , take poly.mono unsaturated oils .
mevastatin & lovastatin = inhibit HMG-CoA reductase
cholestyramine resin = interrupt enterohepatic circulation of bile acid
sitisterol = block absorption of cholesterol from GI tract
probucol = increase LDL catabolism
nicotinic acid = inhibit adipose tissue lipolysis

Metabolism of carbohydrate

Friday, October 20th, 2006

catabolism: breakdown of molecule to get energy
anabolism: synthesis of compounds needed by the cells

glycogenesis: glucose - glycogen
glycogenolysis: glycogen - glucose

glycolysis: glucose - pyruvic acid
aerobically - pyruvic acid’
Glucose - glucose -6- phosphate - fructose -6- phosphate - fructose 1,6 -biphosphate-
glyceraldehyde-3-phosphate - pyruvate


glucose + 2ADP +  2NAD+  + 2Pi  = 2 PYRUVATE + 2 ATP + 2NADH + 2H+

anaerobically - lactate
anaerobically: glucose + 2ADP + 2Pi = 2 lactate + 2ATP + 2H20

alcoholic fermentation by yeast: glucose +2ADP +2Pi = 2 ethanol + 2CO2 + 2ATP +2H20

gluconeogenesis: all mechanism responsible for converting non carbohydrate for glucose or glycogen
major substance: gluconeogenic amino acids, lactate, glycerol, propionate

it meet the need of body for glucose supply when carbohydrate is not available in sufficient amt from diet

clear the product of metabolism of other tissue from the blood eg lactate, glycerol, propianate

disorder
- fructose-1.6-biphosphatase deficiency cause lactic acidosis
- glycosuria
- hypoglycemia
- type 1 diabetes mellitus


deficiency

von gierke’s disease : deficiency of glucose-6-phosphatase
andersen’s disease : absence of branching enzyme
hers’s disease : deficiency of liver phosphorylase
cori’s disease : absence of debranching enzyme

metabolism of amino acids&proteins

Friday, October 20th, 2006

protein - amino acids - amphibolic pathway :
either undergoes catabolic to give CO2 + H20
OR  anabolic pathway to giv protein, carbohydrate


Transamination
glutamate = alpha-ketoglutarate    NH3+ group replaced by ketone group

muscle generate more than 50 % total pool of amino acids

it release mostly glutamine and alanine to blood

in liver, glucose production from alanine higher than other amino acids
alanine - pyruvate - glucose

aspartate synthesis :  oxaloacetate - aspartate   
by enyzme aspartate aminotransferase

Deamination

oxidative: amino acid to alpha-keto acid
l-glutamate - alpha ketoglutarate    by glutamate dehyrogenase
NAD+   -  NADH

Decarboxylation
tyrosine - tyramine

urea cycle - to avoid ammonia intoxication, synthesised in liver 
transported to kidney for excretion
90% of urinary nitrogen is urea

urea cycle disorder" carbomyl phosphate synthase 1 deficiency" hyperammonaemia type 1
ornithine transcarbamoylase deficiency: hyperammonaemia type ll
citrullinaemia: elevated citrulline levels in urine and plasma

impaired ability to convert phenylalanine to tyrosine
defects in phenylalanine hydroxylase
defects in dihydrobiopterin biosynthesis/reductase ( rare but severe)

alternative metabolite produce ie phenylpyruvic acid cause mental retardation

maple syrup urine disease
reduced of alpha keto acid decarboxylase
maple syrup odour to urine
must remove leu,ile,valine from diet.

albinism : tyrosine hydrolase absent
white hair , pink skin , photophobia coz lack of eye pigment


nearly all product of digestion of carbohydrate , fat and protein are
metabolised to acetyl-coA b4 final oxidation to CO2 in citric acid cycle

amino acids

- lactic acid - acetyl coA - krebs cycle - electron transport chain -ATP

- urea cycle - urea - urine 90%

             

                                    GLYCOLYSIS
glucose - glucose -6-phosphate  - pyruvid acid - acetyl coA - krebs cycle -
                                   GLUCONEOGENESIS
             electron transport chain - ATP


fatty acid - acetyl coA - krebs cycle - electron transport chain - ATP

Electron transport chain
in mitochondria H removed from substrate by dehydrogenase, donate their E- to ETC which transfer them oxygen reducing it to H20.cytochrome oxidase passes electons to O2 which require 4 H+ to reduce O2 completely to two H20.

ENERGY released in ETC is used for oxidative phosphorylation of ADP to ATP which takes place in the inner mitochondrial membrane.

ETC can be inhibited by
ET inhibitors prevent E- pass from 2 carrier to next carrier/complex
eg: rotenone,antimycin, cyanide, azide anion, malonate
uncoupling agents eg 2,4-DNP, FCPP
oxidative phosphorylation inhibitor : eg oligomycin : bind ATP synthase block proton channel

Amino Acids

Thursday, October 19th, 2006

AA classfied by polarities : polar, non polar, acidic , basic

aliphatic group: alanine, glycine, isleucine, leucine, valine

hydroxyl : serine, threonine

sulphur: cysteine, mathionine

acidic: aspartic acid, asparagine, glutamic acid, glutamine

basic: arginine, histidine, lysine

aromatic: phenylalanine, tyrosine, tryptophan

pI is the midway btw pK values on either side of isoelectric species with net charged 0
isoelectric point: + and - charge equal

acid below pI  COOH remain, NH3+     charge = +1 
base above pI  COOH = COO-    NH3+  = NH2      charge = -1
at isoelectric point charge = 0

essential aa = cannot be synthesised in human , must supplu from diet
leu,lle,lys,trp,met,his,arg,phe,val,thr

non essential aa = can synthesise in body
gly,ala,ser,asn,gln,pro,asp,glu,cys,tyr

Protein & peptide

Thursday, October 19th, 2006

dipeptide = 2 aa
tripeptide = 3 aa
tetrapeptide , pentapeptide so on

amino acids link by peptide bond/amide bond to form polypeptide chain

classes of peptides: ribosomal peptides, non ribosomal peptides, digestive peptides

dipeptide eg l-aspartyl-l-phenylalanine  200x sweeter than sugar

tripeptide  eg gamma -glutamyl-l-cysteinylglycine / glutathione it is scavenger for oxidizing agent that are harmful to organism

pentapeptide , 2 pentapeptide found in brain are enkephalins eg leucine and methione enkephalin.natural analgesic

protein: made up of more than 1 polypeptide
functions: carriers, structural, catalytic, defense system, hormones


primary structure: order in which amino acids are linked together
secondary structure: arrangement in space of the atoms in the backbone of the polypeptide chain alpha helix and beta plated sheet hydrogen bonded arrangement are the most important secondary structure
tertirary structure: 3D arrangement of all atoms in protein including side chain and prosthetic group
quaternary structure: arrangement of subunit with respect to one another


alpha helix : rodlike involve only 1 polypeptide chain
beta sheet: H-bond can be formed btw diff part of single chain that is doubled back on itself or btw diff chain

eg collagen

tertiary structure: 3d arrangement of all atoms in molecules.

myoglobin: eg of globular protein
8 alpha helical regions and no pleated sheet regions.

quaternary: consist more than 1 polypeptide chain
eg dimers, trimers, tetramers  eg insulin


as a result of these non covalent interaction subtle changes in structure ar one site on a protein molecule may cause drastic change in properties at a distant site. this property = allosteric


denaturation
pH
heat
detergents eg urea, SDS


Hemoglobin   tetramer : 2 alpha chain 2 beta chain
heme group same in hemoglobin and myoglobin
both bind oxygen reversible

1 molecule of hemoglobin can bind 4 molecules of oxygen
binding of o2 is cooperative in hemoglobin meaning to say, after bind 1st, second o2 is easier to bind.
oxygen binding curve in myoglobin is hyperbolic
hemoglobin is sigmoidal

Enzyme

Thursday, October 19th, 2006

all enzyme = globular protein
biocatalyst = increase rate of reaction
highly specific to substrate

1.oxidoreductase = redox
2.transferase = group transfer
3.hydrolases = hydrolytic reaction
4.lyases = group to double bonds
5.isomerase = isomerisation
6.ligases = condensation

D-hexose-6-phosphotransferase    2.7.1.1   
2= class of enzyme, 7= subclass, 1= subsubclass,1 = specific enzyme

some enzyme need coenzyme for full activation

lock and key model
substrate and enzyme has complementary shape

induced fit model
shape of active site not exact complementary of shape of substrate
after binding, comformational change in shape of active site

types of catalytic mechanism

nucleophilic substitution , subtance seek positive charge
acid-base catalysis , donation or acceptance of proton
metal ion catalysis, metal ions is electron acceptor and complexed to substrate

low substrate conc, adding of substrate increase rate
high   ll                            ll                   little increase of rate coz reach maximum rate

increase temperature in crease rate
pH affect both ionic state and conformation

Km= michaelis constant - conct of substrate that produce half-maximal velocity
when conct Substrate very much less than Km, initial velocity depon in subs conct
   ll                                             greater ll                 ll                    is maximal
   ll                             equal to  Km                            ll                      half maxima

enzyme inhibitors

substrate analog , product of reaction, alternative substrate, substrate at high conct

competitive:  inhibition at active site V max unchanged, but Km increased
non competitive: inhibition at site other than active site , Km unchanges but Vmax decreased
irreversible: poisons eg heavy metal Hg2+  increase in sub conc do not relieve this inhibition

mixed inhibitor: inhibitor bind to enzyme and ES

BI-BI reaction = 2 substrate + 2 products
cleland nomenclature
ordered bi-bi sequential ordered : substrate A, then B , A induces conformation change that aligns residues essential for binding B
ping pong BI-BI : substrate , then product release , then substrate then second product released.

methanol bind to ethanol dehydrogenase, produce formaldehyde cause harmful effect, thus by increase conct of ethnaol, more ethanol will compete wif methanol and bind to enyzme ,thus reverse the effect of poisoning.

AG-1284 inhibitor for HIV protease , thus inhibit producing of new cell

Lipid

Thursday, October 19th, 2006

insoluble in water
soluble in  non polar solvent

simple = fats`and waxes
complex = phospholipid and glycolipid
precursor and derived lipids

source of energy
storage energy in adipose tissue
thermal n electical insulator
cellular constituent in cell membrane


fatty acid   saturated anoid, no double bond, zigzag
                unsaturated , enoic , double bond , u shape


has carboxyl hydrophilic
non polar tail hydrphobic , thus it is amphiphilic

lauric acid = coconut
palmitic acid = palm oil
stearic acid = animal fats
oleic acid = olive oils
arachidonic acid = liver fats

Triacylglycerols
ester of alcohol gylcerol with 3 fatty acids by ester bonding, can break down by lipases
main storage form of fatty acids
storage form of energy
hydrophobic
neutral fat

phospholipid    glycerol + phosphate ( hydrophilic head)+ fatty acid( hydrophobic tail)

plasmanogen , similar to phospholipid except fatty acid group at carbon 1 of glycerol contain either an o-alkyl or 0-alkenyl ether
platelet activating factor

sphingolipids
composed of backbone sphingosine which derive itself from glycerol

4 classes of glycosphingolipids
cerebrosides
sulfarides
globosides
gangliosides

functions of phospholipids
main lipid constituent of cell membrane
cardiolipin is major lipid of mitochondrial membranes
phosphotidylinositol is precurosr of second messenger

lysophospholipid = intermediate in metabolism of phosphoglycerol
plasmologens = 10% of phospholipid of brain and muscle
sphingomyelins = brain and nerve tissue
glycolipid = nerve tissue and cell membrane

STEROIDS

Bile acid
Adrenocortical hormone
sex hormone
D vitamins
cardiac glycosides
sitosteroids
alkoloids

Carbohydrate

Thursday, October 19th, 2006

(CH20 ) n

alpha anomer, at 1st carbon, OH facing down
beta anomer , at 1st carbon, OH upward

ketose= C=0
aldose CH=O

stable ring of monosaccharide, 5 ring is furanose, 6 is pyranose

D  OH group on the right
OH group on the left

Monosaccharide : simplest sugar
colourless, soluble in h20, crystalline solid,
eg , 5 c = pentose: ribose, xylose, ribulose,xylulose
      6c = hexose : glucose, galactose, fructose

Disaccharide : water soluble, sweet tasting, crystalline solid, yield 2 monosaccharide via hydrolysis, glycosidic bond 1.4

sucrose = glucose + fructose cane sugar
lactose = glucose + galactose  milk sugar
maltose = glucose + glucose

OLIGOSACCHARIDE : POLYMER contain a small no of component of sugar. component of glycoproten or glycolipid. eg raffinose, maltodextrins, cellodextrins

Polysaccharide : polymers made up of many monosaccharide, insoluble in h20 no sweet tasting. large ,  branched or linear

energy storage and structural material.
starch: amylose + amylopectin, food and enery storahe
glycogen: highly branced , storage in liver n muscle
cellulose: structural component of cell wall, insoluble
inulin: polymer of  fructose as food storage
chitin: important structural of invertebrate

Reducing sugar: sugar with ketone or aldehyde group
sucrose not coz no aldehyde group available for bonding .
consist glucose and fructose joined by glycosidic bond