Biochemistry UW notes

: The lac operon is regulated by 2 mechanisms

negatively by binding of the repressor protein to the -1
operator locus
positively by cAMP- CAP binding upstream from the -2
.promoter region
Constituve expression of the structural genes of the lac
operon occurs with mutations that impair the binding of
the repressor protein (lac I) to its regulatory sequence in
.the operator region

Niemann- pick D. type A, autosomal recessive disorder,

most common in ashkenzi jew. Present with HSM and
progressive hypotonia and MR. the cause is deficiency of
sphingomyelinase enzyme. Which in normal individuals is
.responsible for leaving sphingomyelin
Sphingmyelin accumulates in phagocytes > foamy
.histiocytes > which accumulates in liver and spleen
Deposition in retina > cherry red macular spot (similar to
.tay-sachs) death usually occurs before age 3
Polyol pathway : Aldose reductase converts glucose into
sorbitol during the first step in the polyol pathway of
glucose metabolism. Sorbitol cannot readily cross cell
membranes and is therefore trapped inside the cells. If the
enzyme sorbitol dehydrogenase is also present in the cell,
.it can convert sorbitol into fructose
This pathway is most active in the seminal vesicle. The
lens also contains significant levels of sorbitol
dehydrogenase which become overwhelmed in the setting
of hyperglycemia. Other tissues such as retina , renal
papilla and Schwann cells, have much less sorbitol
dehydrogenase activity. This increase the osomotic

pressure and facilitates the influx of water into the lens

cells leading ti the development of hydropic lens fibres
that degenerate. > lens opacification and cataract
formation. In addition, oxidative stress resulting from
depletion of NADPH contributes to cataract formation and
.other diabetic complications

Sickle cell anemia is the most common inherited blood D.

HbS the non-polar amino acid valine replaces the charged
polar amino acid glutamate at the position 6 of the beta
chain. This results in alteration of a hydrophobic part of
the beta chain that fits into a complementary site on the
alpha chain. The altered structure results in aggregation of
Hb molecules under anoxic conditions. HbS polymers form
fibrous strands that reduce red blood cell membrane
.flexibility
Sickling is promoted by conditions associated with low
oxygen levels, increased acidity or low, slow blood
volume, high 2,3 DPG. Sickled cells are not flexible enough
to pass through the microvasculature. By impeding blood
flow through these vascular beds, the sickled cells cause
microinfarcts in tissues and painful vasooculsive crises in
.the bone

:Primary genital herpes simples tx

Acyclovir( nucleoside analogs) during primary episode
reduce duration of viral shedding ,time of lesional healing ,
.constituational symptoms, and local pain
In infected host cells, acyclovir is converted into acyclovir
monophosphate, principally via virus encoded thymidine
kinase. Cellular enzymes then convert the monophosphate
into acyclovir triphosphate into the viral DNA chain, viral
.DNA synthesis is terminated

So these nucleoside analogs are incorporated into newly

replicated viral DNA and ultimately terminate viral DNA
.chain synthesis
Vitamin A can be of benefit in tx of measles infection ,
.reduce time for recovery, from pneumonia and diarrhea

Fabry's disease (angiokertoma corporis diffusum) which

result from an inherited deficiency of alpha-galactosidase
A
Cermide trihexoside accumulates in tissues >
.hypohidrosis, acroparesthsia and angiokertomas
Acroparesthesia is episodic, often debilitating burning
neuropathic pain in the extremities. Angiokeratomas :
punctuate dark, red, non-blanching macules and papules
.that classically occur between umbilicus and the knees
Without enzyme replacement therapy > progressive renal
.failure and death
Ubiquitin is a protein that undergoes ATP dependant
attachement to other proteins labeling them for
degradation. These modified proteins enter the
proteasome and are degraded into small peptides.
Impairment of the ubiquitin-proteasome system can
contribute to the development of neurodegenerative
.disorders including parkinson's and Alzheimer's

As a consequence of aging, fine skin wrinkles appear

secondary to the decreased synthesis and net loss of
dermal collagen and elastin.(decrease collagen fibrils )

Thyroid hormones bind to receptors situated inside of the

nucleus. Receptors for several steroid hormones

(glucocortioids, mineralocorticoids, androgens, estrogens )

are usually initially present in the cytoplasm , although
.they do migrate to the nucleus once activated

DNA can be damaged in a number of ways ( spontaneous

mutation, chemical reactions , UV light , ionizing radiation)
:through the following mechanisms
depurination of DNA and base excision repair -1
formation of thymine dimmers (UV light ) -2
breaks in DNA chains, and oxidative damage (ionizing -3
radiation)
cross-linkage, intercalation, alkylation (chemical. -4
Pharmacologic)
The DNA repair mechanism utilized by cells for bas
.alterations is called bas exicion repair
Specific glycosylases cleave these altered DNA bases from
.the parent DNA molecules
This leaves an empty sugar phosphate site called a basic
.site, or apurinic-apyrimidinic site (AP)
An endonuclease then cleaves the 5 end of the AP site
before a lyase enzyme completes the removal of the AP
site from the DNA by removing the sugar phosphate group
.at the 3' end
DNA polymerase then fills the gap with the correct sugar
phosphate base, which is finally joined to the strand by
.ligase

In the oxidative portion of the HMP shunt, glucose-6phosphate is converted to ribulose -5-phosphate, this
result in formation of 2 molecules of NADPH (a reducing

molecules) the oxidative portion of HMP shunt is most

active in tissues responsible for reductive biosynthesis
such as liver and adrenals because certain enzymes
involved in fatty acid, cholesterol, steroid synthesis and
.also drug metabolism, require NADPH as a co-factor

:Important metabolic pathways for glucose

glycolysis and the krebs cycle (TCA) cycle are used to -1
generate ATP. Glucose is first metabolized to pyruvate
during glycolysis, and then pyruvate is converted to
acetylcoA, which enters the TCA cycle
glycogenesis stores glucose for later use via formation -2
of the glucose polymer glycogen from glucose-1phosphate
HMP shunt generates pentose sugars and NADPH -3

The breast milk content of vit D and K is typically

insufficient for the nutritional needs of the newborn.
Vitamin K is given IM at birth to prevent hgic disease in
newborn. Exclusive breastfed infants may develop vit D
.deficiency due to lack of sunlight exposure

N-acetylglutamate is an essential activator of carbamoyl

phosphate synthase I(which catalyze the reaction of co2+
ammoniaNH4+ATP > carbamoly phosphate). Nacetylglutamate is formed by the enzyme Nacetylglutamate synthetase from the precursors acetyl.coA and glutamate

The collagen molecule consists of 3 polypeptide alpha

chains held together by hydrogen bonds to form a rope
.like triple helix structure
Ehlers-Danlos $ group of rare D, defect in the synthesis of
collagen > overflexible joints , over elastic skin and fragile
tissues susceptible to bruising, wounding and
.hemarthrosis
Commom mutations leading to EDS phenotypes include
deficiency of lysyl-hydroxylase and pro-collagen peptidase
.enzymes responsible for collagen synthesis
$ Fibrillin-1 defect > Marfan

Homeobox : a highly conserved DNA sequence , usually

about 180 nucleotides in length, a gene containing
homeobox is called a homeobox gene. Homeobox genes
typically code for DNA binding transcription factors which
alter the expression of genes involved in morphogenesis
Morphogenesis: is the proper formation and placement of
tissues organs and structural elements of the body.
Homeobox were initially described in Drosophila where
mutations of these genes caused limbs and appendages to
.develop in the correct locations

HbF : fetal Hb, synthesis in fetal liver at 10-12 weeks of

gestation , then by spleen then finally bone marrow as
maturation progress
HbF : 2 alpha and 2 gamma
HbA2: 2 alpha and 2 delta
Hb Gower : zeta 2 and epsilon 2
Hb Bart : 4 gamma > hydrops fetalis and death in utero

G6PDH deficiency is a defect in HMP shunt that impairs

glutathione reduction due to failure to produce NADPH.
.Glutathione reducatse deficiency causes similar picture

Ascorbic acid L activation of prolyl and lysyl hydroxylase

precursors , both of which are necessary for the
hydroxylation of procollagen. As collagen contains
considerable hydroxyproline, the quantity and quality of
collagen produced is dramatically impaired by any
.reduction in available ascorbic acid

The nitrogen atoms in the urea are derived from NH3 and
aspartate in the urea cycle. Remember that carbamoyl
phpsphate synthetase I is the rate limiting enzyme in the
urea cycle reaction and is activated by N-acetylglutmate

Growth factors can stimulate cell proliferation by altering

the expression of certain genes. This requires the use of
signal transduction systems that can transfer the signal to
: the nucleus. Examples
Ras- MAP kinase pathway -1
PI3K/AKt?mTOR pathway -2
Inositol phospholipid pathway-3
cAMP pathway -4
.JAK/STAT pathway -5
The Ras-MAP kinase pathway starts with
Growth factor ligand bind to receptor tyrosine kinase,
causing auto phosphorylation of the receptor then

Phospotyrosine produced in this reaction interacts with a

.number of proteins , leading to RAS activation
RAS (inactive) contains GDP while the active form is bound
.to GTP
Activated RAS begins a phosphorylation cascade starting
.with activation of RAF kinase
This results in the activation of MAP kinase, which enters
the nucleus to influence gene transcription
The RAS protein exist in a balance between its active and
inactive forms. Inactive GDP-containing, Ras is activated
by a signal originating from the receptor tyrosine kinase.
Active (GTP-containing) RAS is inactivated by GAP
( GTPase activating protein) , which induce hydrolysis of
GTP into GDP. Mutation of RAS can lead to an inability to
split GTP , the resultant permanently activated RAS
.stimulates cell proliferation and can lead to cancer

tRNA is one of the non coding RNA composed of between

74-93 nucleotides. Specific molecules of tRNA transfer
certain amino acid residues to the growing polypeptide
chain during translation. The tRNA molecule functions by
recognizing the 3 base codon on the mRNA molecule
being translated through its anticodon region, which
.contains complementrary bases
: Structure of tRNA
the acceptor stem : created through the bas pairing of 5 -1
terminal nucleotides with the 3 terminal nucleotides , the
CCA tail hangs off the 3 end with the amino acid bound to
the 3 with the amino acid bound the 3 terminal hydroxyl
group. tRna is loaded with appropriate amino acid through
the process of aminoacetylation which catalyzed by
aminoacyl tRNA synthetase. The acceptor stem helps to

mediate correct tRNA recognition by the proper aminoacyl

.tRNA synthetase
A 3CCA tail is added to the 3 end of tRNA as a -2
posttranscriptional modification in eukarotes and in most
prokaryotes. In some prokaryotic tRNAs the tail region is
directly transcribed from the genome. Tail help recognize
.tRNA and its presence is necessary for protein translation
The D arm , facilitaes correct tRNA recognition by the -3
.proper aminoacyl tRNA synthetase
The anticodon arm contains sequence which are -4
complementary to the mRNA codon and is read in the 3 to
5 direction. During translation , the ribosome complex
.selects the proper tRNA based on its anticodon sequence
The T arm, contains the TYC sequence that is necessary -5
for binding of tRNA to ribosomes. The TYC sequence refer
to the presence of thymidine , pseudouridine, and
cystidine residues in this arm of tRNA. tRNA is the only
.RNA species that contains the nucleoside thymidine

Because DNA synthesis can occur in 5>3 direction , one

daughter strand is made continuously toward the
replication form (leading strand ) and the other
synthesized discontinuously in a direction away from the
replication form (lagging strand). With more and more
.segments added

Porphyria : deficiency of any of the enzymes responsible

for porphyrin synthesis, clinical manifestation of porphyia
result from accumulation of precursors of porphyrins in the
.blood and tissues , urine

Heme is synthesized in liver for use in cytochrome P450

enzyme system while heme in bone marrow , is generated
.for Hb use
Acute attacks van be caused by : drugs like barbiturates ,
Phenobarbital , griseofulvin, and phyentoin. Also alcohol
and low caloric diet can induce an acute attack of
.porphyria
Decreasing hepatic concentration of heme > causes
increase in hepatic ALA synthase activity and leads to >
increased formation of delta aminolevulinic acid and
.porphobilinogen
These intermediates are responsible for the acute
abdominal pain, and neurologic symptoms observed in the
.disease
ALA dehydratase and ferrochelatase are inhibited by
. lead

Translation of mRNA template proceeds in the 5 to 3

.direction
Because complementary sequences align in antiparallel
fashion, during translation tRNA anticodons will be
oriented in the opposite 3 to 5 direction
All 3 prokaryotic DNA polymerases have proof reading
activity and remove mismatched nucleotides via 3 to 5
exonuclease activity. Only DNA polymerase I has 5 to #
exonuclease activity which is used to excise and replace
RNA primers and damaged DNA sequences
The sequence of amino acids in a growing polypeptide
chain is dictated by the interaction of the mRNA codon
with the tRNA anticodon. tRNA that is mischarged with the
incorredt amino acids, and not corrected by aminoacyl
tRNA synthetase proofreading, will incorporate the wrong

amino acid into the growing polypeptide chain , as there is

.no amino acid proodreading during protein translation

Gout occurs with increased frequency in patients with

activating mutations involving phosphoribosyl
pyrophosphate synthetase due to increased production
.and degradation of purines

Colchicines is useful in the acute management of gout as

it inhibits neurtrophil chemotaxis and phagocytosis by
preventing microtubule formation

The symptoms of difficulty in swallowing (dysphagia and

disfigured fingernails (spoon nails or koilonychias are
.specific for iron deficiency anemia

Dietary fructose is phophorlyated in the liver to F1P and is

rapidly metabolized because it bypasses PFK-1 , the major
rate limiting enzyme of glycolysis. Other sugars (glucose ,
galactose , mannose ) enter glycolysis prior to PFK-1 and
.as a result are metabolized more slowly

Protons dissociate from amino acide when th pH exceeds

the pKa associated with each given proton
Norepinephrine and dopamine produced by both the CNS
and PNS. Epinephrine > chiefly produced by adrenal
.medulla
Phenylalanine > tyrosine by phenylalanine hydroxylase
Then tyrosine >dopa by tyrosine hydroxylase
Then dopa >dopamine by dopa decarboxylase

Dopamine > norepinephrine by dompamine B.hydroxylase

The conversion of NE to epinephrine occurs in adrenal
medulla where an enzyme called phenylethanolamine-Nmethyltransferase (PNMT). Cortisol increase transcription
.on this enzyme

Vit K essential co-factor for the hepatic microsomal

carboxylase that converts glutamyl residues into gammacarboxyglutamates. This step is essential for the
functionality of clotting factors VII, IX, X because it allows
for the creation of calcium binding sites that interact with
.the phospholipid surface to ultimately generate thrombin
Anti-coagulants protein C and S require carboxylation of
glutamates for activation , so vit K deficiency > bleeding
.diathesis
: People with vit K deficiency
Malaborption $, broad spectrum antibiotics that destroy
intestinal flora, neonates , those with generalized liver
disease
Tx: Coumadin

After 12-18 hrs of fasting , gluconeogensis is the principal

source of blood glucose. The intial step of
Gluconeogenesis involves the conversion of pyruvate to
.oxaloacetate and oxaloacetate to phosphoenolpyruvate

.Glycogen is broken down by > glycogen phosphorylase

Phosphorylase kinase is the enzyme responsible for the
.phosphorylation of glycogen phophorylase

Phosphoprotein phosphatase catalyzes its

.dephosphorylation
Phosphorylase kinase is phosphorylated by protein kinase
A in response to increased cAMP (which increase due to
binding of epinephrine and glucagon to Gs protein coupled
receptors. (in liver )
Phosphrylation of phosphorylase kinase by protein kinase
> activation
While phosphorylation of glycogen synthase by protein
.kinase A > inactivation
Phosphorylase kinase activity can also be increased
through the direct allosteric binding of ca ions. Ca increase
the catalytic activity of both the phophorylated and
.dephophorylated forms of phosphorylase kinase
In liver NE can promote glycogenlysis through Gq pathway
.mediated Ca influx

The affinity of HbF to o2 is much higher than that of HbA ,

cuz HbF does not bind effectively to 2,3 DPG, because of
presence of serine instead of charged histidine at the
normal 2,3 DPG binding sit. 2,3 DPG normally binds or
form ionic bonds with the 3 beta subunits of HbA

:The glutamate glutamine cycle

Glutamate is released by neurons during
neurotransmission and taken up by astrocytes and
. converted to glutamine
Glutamine is released by astrocytes and taken up by
neurons where it's either converted to alpha ketoglutrate
.for krebs cycle or to glutamate as a neurotransmitter

Ammonia toxicity results in > depletion of glutamate and

alpha ketoglutrate during the process of ammonia
.detoxification
Hyperammoniemia > increase conversion of glutamate
into glutamine by glutamine synthetase within astrocytes.
The resulting increase of glutamine leads to
hyperosmolarity and mitochondrial dysfunction , causing
astrocytic swelling and impairment , also decrease total
brain glutamate stores , impairing excitatory
.neurotransmission
So in nutshell : hyperammonemia can lead to depletion of
alpha ketoglutrate > inhibition of krebs cycle. Excess
ammonia also depletes glutamate , an excitatory
neurotransmitter, and causes accumulation of glutamine ,
.resulting in astrocyte swelling and dysfunction

Aldolase B deficiency causes hereditary fructose

intolerance. This disease manifest after introduction of
fructose into the diet with vomiting and hypoglycemia
about 20-30 minutes , after fructose ingestion. Infants
.present with failure to thrive , jaundice and hepatomegaly

Ethanol : for every equivalent of ethanol metabolized to

acetaldehyde by alcohol dehydrogenase and then to
acetate by aldehyde dehydrogenase , two equivalents of
NAD are reduced to NADH
The high intracellular ration of NADH to NAD favors
conversion ofpyruvate to lactate and oxaloacetate to
.malate., and inhibit gluconeogensis
So low glucose intake , coupled with alcohol induced
inhibition of gluconeogensis and baseline low glycogen
stores all contribute to alcohol induced hypoglycemia in
.alcoholics and binge drinkers

Exposure to radiation including therapeutic and palliative

radiation therapy, induces DNA damage through DNA
double-strand fractures and the formation of oxygen free
.radicals

Hypoxia induced lactic acidosis is caused by a low activity

of pyruvate dehydrogenase (oxidative phosphorylation
.pathway ) and a high activity of lactate dehydrogenase

Amino acids with 3 titratable protons include histidine,

arginine , lysine , aspartic acid , glutamic acid , cysteine
.and tyrosine

Maple syrup urine disease (MSUD) a disorder characterized by defective

breakdown of branched chain amino acids (leucine, isoleucine and valine ).
Degradation of these amino acids first involves transamination to their
respective alpha ketoacid, which are subsequently metabolized by enzyme
.complex referred as branched chain alpha ketoacid dehdrogenas
Clinically : neurotoxicity, sweet odor of urine much like burned caramel ,
can be life threatening if untreated, but diatery restriction of branched
.chain amino acids can lessen the severity of symptoms
Branched chain alpha ketoacid dehydrogenase , and pyruvate and alpha
ketoglutrate dehydrogenase requires several co-enzymes : thiamine
pyrophosphate (TPP) , lipoate , Coenzyme A , FAD , NAD ) Tender Loving
.Care For Nancy

: Causes of lactic acidosis

Enhanced metabolic rate (seizures, and exercise )

Reduced oxygen delivery, decreased oxygen utililization (cyanide

poisoning )
Diminished lactate catabolism (hepatic failure or hypoperfusion)
Enzymatic defects in glycogenolysis or gluconeogenesis
Lactic acidosis : anion gao metabolic acidosis that results from
overproduction and or impaired clearance of lactic acid. Occurs in septic
shock because of tissue hypoxiawhich results in impaired oxidative
phosphorylation and the shunting of pyruvate to lactate following
glycolysis. Hepatic hypoperfusion also contributes to the buildup of lactic
.acid, as the live is the primary site of lactate clearance

The prokaryotic 16S rRNA sequence is found in the 30S ribosomal subunit.
The 16S rRNA contains a sequence complementary to the shine dalgarno
sequence on mRNA. Binding of these 2 complementary sequences is
necessary for intiation of protein translation. Once mRNA is bound to the
30S ribosomal subunit, an intiator tRNA binds to the AUG start codon, the
.50S ribosomal subunit joins the complex and protein synthesis begins

Elastin : similar to collagen , composed of non-polar amino acids, glycine,

alanine and valine. Also contains proline and lysine , however few of these
.are hydroxlyated
: Difference between collagen and elastin
very few proline and lysine residues are hydroxylated in elastin -1
whereas triple helix formation is the basis of the collagen molecule, -2
.elastin does not form triple helices
triple helix formation in collagen is initiated by hydroxylation, -3
glycosylation and interchain disulfide bridges at the C-terminus of
procollagen molecule. These modification do not occur in elastin
Elastin plasticity and ability to recoil upon release of tension is attributable
to a unique form of desmosine crosslinking between four different lysine
resideues on four different elastin chains. This crosslinking is accomplished
.by the action of extracellular lysyl hyroxylase

Homocystinuria : the most common inborn error of methionine metabolism

caused by deficiency of cystathionine synthetase , an enzyme that
requires pyridoxine (vit B6) as a cofactor. Clinically : patients present at 310 yrs with ectopia lentis , MR, marafnoid habitus, and osteoporosis .

thromboembolis complications are the major cause of morbidity and

.mortality in these patients

Catabolism of isoleucine , valine , threonine , methionine , cholesterol and

odd-chain fatty acids leads to formation of propionic acid. Which is then
.converted to methylmalonic acid by biotin-dependent carboxylation
Isomerization of methylmalonly CoA forms succinyl CoA which
subsequently enters the TCA cycle. Defects in this isomerization reaction
lead to the development of methylmalonic acidemia. This generally results
.from deficiency of vit B12 dependent enzyme methylmalonate mutase

In lesch-Nyhan $ there is deficiency of HGPRT, which result in failure of

purine salvage. This results in increased degradation of guanine and
hypoxanthine bases into uric acid, thereby causing hyperuricemia.
Excessive levels of PRPP also develop as PRPP is a substrate used by
HGPRT during purine salvage and it accumulates when there is deficiency
of the enzyme. PRPP is created by PRPP synthetase during 1 st step of de
.novo purine synthesis
Phosphoribosyl pyrophosphate amidotransferase acts upon PRPP to form
phosphoribosylamine in the 1st committed step of de novo purine
synthesis , therefore its activity will be increased in lesch-Nyhan $
.secondary to the increased PRPP concentrations

Glucose is the most important stimulatoe of insulin release. Glucose enters

beta cells by facilitated diffusion using GLUT-2. Glucose >glycolysis > citric
.acid cycle > generates ATP
A high ATP to ADP ratio within beta cells causes the closure of potassium
(KATP) channels. This closure occurs when ATP binds to the regulatory
subunit of KATP. When closed beta cells depolarize which results in the
opening of voltage dependent ca channels. High intracellular ca then leads
.to insulin release
Defects in KATP channel gene result in type 2 DM
So ATP is the regulatory substance that stimulates KATP channel closure in
.insulin-producing pancreatic beta cells
Smooth ER contains enzymes for steroids and phospholipid biosynthesis.
All steroid-producing cells (cells in the adrenals , gonads, liver ) contain a
.well developed smooth ER

Receptors for cortisol are located within the cytoplasm and are
translocated to the nucleus after binding to cortisol. In the nucleus the
cortisol receptor complex binds to the hormone responsive elements,
.causing an alteration in the transcription of target genes

Southern blotting is a technique used to detect DNA mutations. Briefly the

:process involves the following steps
.DNA extraction from the individual's cells -1
.restriction endonuclease digestion of the DNA sample into fragments -2
.Gel electrophoresis to separate the various sizes of DNA fragments -3
DNA probe (a single-stranded segment of radiolabeled DNA -4
.complementary to the gene of interest) to identify the target gene
Once the gene of interest is identified by the DNA prbe , various family
.members southern blots can be compared

: Phosphoinositol system
a-adrenergic, M1, M3 cholinergic, V1, H1 , oxytocin, angiotensin II , TRH
.and GnRH receptors
:The signal transduction pathway proceeds through the following steps
binding of a ligand to its cell surface receptor causes the exchange of -1
GDP to GTP on the a-subunit of Gq-protein associated with the receptor.
The activated a-subunit undergoes a conformational change and exposes
.a phospholipase C (PLC) activating site
after activation PLC hydrolyzes PIP2 into DAG and IP3 -2
DAG is able to directly stimulate protein kinase C but the major -3
activator of PKC is increased intracellular Ca that occurs due to IP3
mediated release of intracellular Ca stores from ER. Protein kinase C is the
major effector molecule in this pathway it directly modulates the activity
of other proteins via phosporylation

Alkaptonuria is a relatively benign disorder of tyrosine metabolism, it's

autosomal recessive disorder in which deficiency of homogentisate
oxidase blocks the metabolism of phenylalanine and tyrosine at the level
of homogentisic acid, therpy preventing the conversion of tyrosine to
.fumarate

BH4 is a co-factor used by hydroxylase enzymes in the synthesis of

tyrosine, Dopa, and serotonin, as well as nitric oxide. Serotonin is
synthesized from tryptophan and the intial step in this reaction is
.catalyzed by enzyme uses BH4 as a cofactor
Enzyme dihydrobiopterin reductase deficiency causes defective
regeneration of BH4 and is an uncommon cause of phenylketonuria (PKU)

Delta-aminolevulinate synthetase catalyzes the rate limiting reaction in

the heme biosynthetic pathway. Glycine and succinyl CoA are combined in
this intial reaction of heme synthesis to form delta ALA. In the second
reaction catalyzed by delta aminolevulinate dehydratase, the two
molecules of ALA condense to form porphobilinogen. In the final steo of
heme synthetic pathway Iron Fe is incorporated into protoporphyrin IX in a
.reaction catalyzed by ferrochelastase to form heme
The enzyme delta ALA dehydratase, which contains zinc and
ferrochelatase are inactivated by lead. Thus in lead poisoning delta ALA
and protoporphyrin IX accumulate and the production of heme is
decreased leading to microcytic hypochromix anaemia secondary to lack
of Hb

The nucleolus the dark intranuclear body visible both by light microscopy
.and electron microscopy is the site of ribosomal RNA synthesis

Glycolysis unidirectional enzymes are : hexokinase , PFK1, and pyruvate

.kinase
Gluconeogenesis enzymes L pyruvate carboxylase , PEP carboxykinase ,
.fructose 1,6 bisphosphatase and glucose 6 phosphatase
Fructose 2,6 bisphosphate helps control the balance between
gluconeogensis and glycolysis by inducing PFK1 and inhbiting fructose 1,6
bisphosphatase. So high levels of fructose 2,6 bisphosphate inhibit
.gluconeogensis and promote glycolysis
By inhibiting gluconeogensis > this will also lead to a decrease in
conversion of alanine to glucose (alanine to pyruvate > glucose ) ,
because gluconeogensis utilizes pyruvate derived from alaine as a
.gluconeogenic substrate

Fructose 6 phosphate > fructose 2,6 bisphosphate by a bidirectional

enzyme (PFK-2 which converts F6P to F2,6BP)
. Fructose 2,6 bisphosphate > fructose 6 phosphate by 2,6 bisphosphatase
Glucagon cause phosphyrlation of this enzyme leading to activation of
.phosphatase and inactivation of kinase
Insulin causes dephosphyrlation and activation of kinase and inactivation
.of phosphatase
Thus insulin increases the level of fructose 2,6 bisphosphate causing
.allosteric upregulation of the enzyme PFK 1 and augment glycolysis

The insulin receptor is a tetrameric structure consisting of two alpha and

two beta subunits the alpha subunits are extracellular and they provide
the binding site for insulin. The beta subunits are intracellular and contain
tyrosine kinase domains that are activated when insulin attaches to the
alpha subunits. A series of downstream signaling is then triggered starting
with autophosphorylation of IR. This is a prerequisite for activation of the
receptor's tyrosine kinase and also for interaction with other molecules
particularly IRS -1 (insulin receptor substrate)
TNF-alpha is a proinflammatory cytokine that induce insulin resistence
through the activation of serine kinase , which then result in
phosphorylation of IRS-1 serine residues. This inhibits IRS-1 tyrosine
phosphyrlation by insulin . phosphrylation of serine residues in the beta
subunit of insulin receptors also hunders downstream signaling, resulting
.in resistence to the normal action of insulin
Phosphorylation of threonine has similar effects. Catecholamines,
glucocorticoids and glucagon can also induce insulin resistance by the
same mechanism. And intracellular fatty acids are suspected of increasing
.serine kinase activity as well

The hepatitis C virus is genetically unstable because it lacks proofreading

3>5 exonuclease activity activity in its RNA polymerase and its envelop
glycoprotein contains a hypervariable region prone to frequent genetic
.mutation

Thiazide diuretics cause hypercalcemia by increasing the distal tubular

reabsorption of filtered Ca. the increased serum Ca levels result in
suppression of parathyroid hormone which distinguishes the side effect
from primary hyperparathyroidism

Brown pigment stones typically arise secondary to infection of the biliary

tract, which results in the relase of beta-glucuronidase by injured
hepatocytes and bacteria. The presence of this enzyme contributes to the
hydrolysis of bilirubin glucuronides and increases the amount of
.unconjugated bilirubin in bile

The nucleolus is the site of ribosomal subunit maturation and assembly.

RNA polymerase I synthesizes the vast majority of rRNA from within the
.nucleolus

Vita A overuse can result in intracranial hypertension, skin changes and

.hepatosplenomegaly

Niacin (vit B3) can be synthesized endogenously from tryptophan. A

deficiency of this vitamin results in pellagra, which characterized by
.dermatitis , diarrhea, and dementia

The hydroxylation of proline and lysine residues in collagen helps it attain

its maximum tensile strength. This process occurs in the rough
endoplasmic reticulum and requires vitamin C as a cofactor. Collagen
strengthen the blood vessel wall, so impaired collagen synthesis resulting
from vitamin C deficiency can lead to fragile vessels predisposing to
.gingival bleeding , ecchymosis , petechia

When mRNA is first transcribed from DNA , it's unprocessed form called
pre-mRNA or heterogeneous nuclear mRNA (hnRNA), several processing
steps are required before finalized mRNA molecules can leave the nucleus
including 5- capping and poly A tail addition and intron splicing.
Cytoplasmic P bodies play a role in mRNA translation regulation and mRNA
.degradation

Alanine is the major amino acid groups are transferred to a-ketoglutrate to

form glutamate. Glutamate is then processed in the liver to form urea , the
primary disposal form of nitrogen in humans. Free ammonia is also
.excreted into the urine by the kidney for regulation of acid-base status

Alanine and glutamine play an important role in transporting nitrogen

throughout he body . glutamine is produced by most body tissues and is
catabolized primarily by the gut and kidney for maintenance of cellular
metabolism and acid base regulation, respectively. A significant portion of
the glutamine used by these tissues is converted to alanine and released
into the circulation. Alanine is also released by skeletal muscle during
protein catabolism as part of the glucose alanine cycle that helps remove
excess nitrogen. Alanine is then transported to the liver where it serves as
a vehicle for nitrogen disposal and as a source of carbon skeletons for
.gluconeogenesis
In the liver alanine is transaminated by alanine aminotransferase to
pyruvate with amino group being transferred to a-ketoglutrate to form
glutamate. Almost all aminotransferase enzymes use a-ketoglutrate as the
amino group acceptor. Glutamate is metabolized by enzyme glutamate
dehydrogenase which liberates free ammonia and regenerates a.ketoglutrate . ammonia then enters urea cycle
Alanine is the major amino acid responsible for transferring nitrogen to the
liver for the disposal. During the catabolism of proteins, amino groups are
transferred to a-ketoglutrate to form glutamate. Glutamate is then
processed in the liver to form urea , the primary disposal form of nitrogen
in humans. Free ammonia is also excreted into the urine by the kidney for
.regulation of acid bas status

DNA polymerase III is the primary enzyme responsible for synthesis of

.daughter DNA strands
DNA polymerase I functions chiefly to replace the RNA primers with DNA
segments
DNA polymerase I : has a 5 3 exonuclease activity that can remove RNA
primers and damaged DNA segments
DNA polymerase I and III has proofreading function from 35
Primase : DNA depenent RNA polymerase that incorporates short RNA
primers into the replicating DNA
Multiple origins of replication make eukaryotic DNA synthesis quick and
effective despite the large size of the genome compared to that of
.prokaryotic organisms

In patients with essential fructosuria metabolism of fructose by hexokinase

to fructose 6 phosphate is the primary method of metabolizing dietary
.fructose, this pathway is not significant in normal individuals

.Lacoste > galactose and glucose by lactase

.Galactose > galactose 1 phosphate by galactokinase
Galactose 1 phosphate+ UDP glucose > glucose 1 phosphate +
.UDPglalactose by galactose 1 phosphate uridyltransferase
UDP galactose > UDP glucose by UDP galactose 4 epimerase
UDP galactose can be converted to lactose by lactoe synthase within
mammry gland
Galactosemia is caused by deficiency of GALT (type1) , galactokinase (type
2) or UDP glucose-epimerase (type 3) . excess galactose > converted to
galactitol by aldose reductase

Glycine is the most abundant amino acid in the collagen molecule. It

occurs in at least every 3rd amino acid position, the amino acid formula of
collagen is Gly-X-Y

The PI3K/Akt/mTOR pathway is an intracellular signaling pathway that is

important for cellular proliferation. This pathway is typically activated
when a growth factor binds to its receptor tyrosine kinase, causing
autophophyrlationof tyrosine residues within the receptor. These residues
activates the phosphoinositide 3-kinase (PI3K) which then phosphrylates
PIP2 found in the plasma membrane to PIP3. This leads to activation of
protein called Akt ( or protein kinase B) , a serine/threonine specific
protein kinase. AKt activates mTOR ( mammalian target of rapamycin)
which translocates to the nucleus to induce genes involved in cell
survival , antiptosis, angiogenesis. mTOR activation is inhibited by PTEN
(phosphatase and tensin homolog) a tumour suppressor protein that
removes the phosphate group from PIP3
This pathway is highly active in many cancer cells as a result of
mutations causing increased activity of PI3K or AKt or loss of function of
PTEN. Mutations involving certain growth factor receptors can also
enhance activity. Several drugs targeting this pathway have shown benefit
.in treating certain cancers

Cysteine becomes an essential amino acid in patients with homocystinuria

as defective enzyme cystathionine synthetase produces the substrate
.used by cystathionase for the endogenous production of cysteine

The classic galactosemia results from deficiency of galactose 1 phosphate

uridyl transferase , this defect is the most common cause of galactosemia.
.Clinically : vomiting , lethargy , and failure to thrive

Glycogenolysis
Glycogen phosphorylase : shorten the glycogen chain by cleaving a1,4
glycosidic linkages . this occurs until only 4 residues are remaining.these
remaining glucose residues before a branch point are referred to as limit
.dextrins
The 1st debrancher enzyme work on a1,4 : removes outer 3 residues and
.transfer them to the main a1,4 chain
The 2nd debrancher : amylo-a-1,6 glucosidase , cleaves a1,6 glycosidic
.bond at the branch point and liberate a free glucose molecule
Cori disease : debranching enzyme deficiency includes hypoglycemia ,
.hypertriglyceridemia, ketoacidosis and hepatomegaly
Transketolase and transaaldolase carry out the non-oxidative reactions of
HMP shunt . some cells do not use the oxidative phase reaction to produce
NADPH, but all cells can synthesize ribose from fructose-6-phosphate
.using the non-oxidative reactions
The HMP shunt is responsible for NADPH, which is used as reducing agent
in cytosol, rather as a source of energy for ATP synthesis in the electron
.transport chain
The HMP shunt is also responsible for the production of ribose 5.phosphate needed for the synthesis of nucleotides

Leptin is protein hormone produced by adipocytes in proportion to the

quantity of fat stored. Leptin acts on the arcuate nucleus of the
hypothalamus to inhibit production of neuropeptide Y, which a potent
appetite stimulant (decrease appetite) and stimulate production of
proopiomelanocortin (POMC) in the arcuate nucleus. Alpha-melanocytestimulating hormone (alpha-MSH) is produced by cleave of POMC and
.inhibits food intake
Mutation in the leptin gene or receptor result in hyperphagia and profound
.obesity

The Gibbs free energy change ^G describes both the direction in which
chemical reaction will tend to proceed as well as the concentration of
.reactants and products that will be present at equilibrium

Go denotes the change in free energy that accompanies the formation of ^

.one mole of the product
If the free energy of the products is lower than that of the substrates, the
sign of ^Go will be negative > indicating that the reaction favors product
formation. (spontaneous reactions)
If the free energy of the substrates is lower than that of the products , the
sign of ^Go will be positive, indicating that the reaction favors substrate
.formation

Ultraviolet rays damage DNA through the formation of thymine dimmers ,

by forming an abnormal covalent bond between adjacent thymine
.residues
Secondary to this covalent bond > transcription and replication can not
proceed normally. These thymine dimmers can be removed by the action
of ultraviolet-specific endonucleases. This enzyme causes nicks at
damaged sites that are later excised by the 5' to 3' exonuclease activity of
DNA polymerase, which also synthesizes new DNA in the place of the
.damaged DNA. Lack of repair > xeroderma pigmentosum

Fibrillin -1 is a major componenet of microfibrils that form a sheeth around

elastin fibres. Microfibrils are abundantly present in blood vessels,
periosteum and the suspensory ligaments of the lens. Fibrillin in the
extracellular space acts as a scaffold for deposition of elastin extruded
.from connective tissue cells
Defects in fibrilin casues marafan's syndrome : 1- long thin extremities ,
.loose joints , long fingers
ocular abnormalities , dislocation of lens (ectopia lentis ) -2
C.V.S abnormalities including ascending aortic aneurysm, aortic -3
.dissection , mitral valve prolpase

Cyanide poisoning : cyanide binds to a variety of iron containing enzymes,

the most important of which is the cytochrome a-a3 complex. This
complex is critical for ETC during oxidative phosphorylation. By binding to
this molecule, minute amounts of cyanide can inhibit aerobic metabolism
.and rapidly result in death
Clinically : flushing , tachypnea, headache , N/V. labs: severe lactic
acidosis in conjunction with lessened difference between arterial and
venous o2 content ( venous blood is still higky oxygenated )

Tx : antidote is nitrites. Nitritis are oxidizers and act primarily in cyanide

poisoning by inducing the formation of methemoglobin. This occurs when
ferrous iron in Hb is oxidized to ferric iron. Methemoglobin cannot carry
oxygen but it does have high affinity for cyanide. Methemoglobin can bind
and sequester cyanide in blood, thereby keeping the poison away from
.mitochondrial enzymes where cyanide exerts its toxic effects
Sodium sulfate is also used for cyanide , it combines with it to form less
.toxic thiocyanate which is excreted in the urine

Amatoxins are found in a variety of poisonous mushrooms and are potent

inhibitors of RNA polymerase II (halting mRNA synthesis ) . clinically :
symptoms starts 6-24 hour after ingestion and include abdominal pain ,
vomiting , and severe cholera like diarrhea that may contain blood and
mucus. Severe poisoining can lead to heptic and renal failure. Dx: urine
.testing for a-amantinin can confirm

Beta- oxidation of fatty acids involves the sequential removal of two

carbon units from the fatty acid chain by oxidation at B-carbon postion.
This process occurs within mitochondria. To transport a fatty acyl-CoA from
the cytosol into mitochondria the cell must first form the fatty acylcarnitine intermediate. This reaction is catalyzed by Carnitine
acyltransferase I on the outer surface of the inner mitochondrial
membrane. After the fatty acyl-carnitine molecule is transported into the
mitochondria, carnitine acyltrasferase II on the inner mitochondrial
membrane catalyzes the regeneration of the fatty acyl-CoA molecule and
.free carnitine. This known as the caarnitine shuttle
Carnitine deficiency reduces the ability of fatty acids to enter the
.mitochondria for beta oxidation
Beta-oxidation of fatty acids produces acetyl CoA, a precursor of
acetoacetate (one of the 3 primary ketone bodies). Carnitine deficiency
.thus causes decreased formation of acetoacetate

Galactitol accumulates in lens of patients with galactosemia and causes

osmotic damage to cataract formation. Galactitol is formed from excess
.circulating galactose in galactosemia by aldose reductase

tRNA is the smallest subtype of cellular RNA. The 3' end is the site of
amino acid binding. The opposite side of molecule contains the anticodon
.loop, which recognizes a specific codon on the mRNA molecule

G- protein is heterotrimer consist of a, B, and gamma , associated with

intracellar domains of cell membrane associated receptors. The alpha
subunit of the inactivated G-protein is bound to GDP. Upon activation of
the receptor , the alpha subunit undergoes a conformational change and
GDP is released. Subsequent binding of GTP then allows for the
dissociation of the alpha subunit from the remainder of the G-protein
complex. There are multiple subtypes of alpha G-proteins , each with
different secondary effects. A specific alpha subunit known as Gs (present
in the glucagon, TSH, PTH complexes ) activates adenylate cyclase when
released from the G-protein complex. Once formed from ATP, cyclic AMP
activates a family of enzymes known as the cAMP dependent protein
.kinase
Protein kinase A phosphorylates specific serine or threonine residues in
some enzymes , thereby leading to their activation or deactivation. Protein
kinase A also phosphrylates several proteins that bind to regulatory
.regions of genes on the DNA molecule itself
So protein kinase A is primarily responsible for the intracellular effects of
the G-protien adenylate cyclase second messenger system. Some
hormone receptors that use this mechanism include the TSH, glucagon,
.PTH, and beta adrenergic receptors

Thiamine deficiency is associated with infantile and adult beriberi, as well

.as wernicke-korsakoff syndrome , in alcoholics
Infantile beriberi : between 2-3 months and include a fulminant cardiac
syndrome with cardiomegaly , tachycardia , cyanosis , dyspnea and
.vomiting
Adult beriberi: dry or wet. Dry : a symmetrical peripheral neuropathy
accompanied by sensory and motor impairments, especially of the distal
.extremities
Wet beriberi include neuropathy and cardiac involvement ( cardiomegaly ,
.myopathy , CHF, peripheral edema , tachycardia)

DNA polymerase I has 5' to 3' exonuclease activity in addition to its 5 to 3

polymeraase and 3' to 5' exonuclease activities. This 5' to 3' exonuclease
activity is used to remove the RNA primer (which initiates DNA
.polymerization ) and to remove damaged DNA

hCG is produced by malignant testicular tumours , particularly

nonseminomatous germ cell tumours, which can secrete very high levels
of hCG. The alpha subunit of hCG, TSH, LH and FSH are identical , and the
beta subunits of hCG, and TSH share significant sequence homology.
Because of this structural similarity , hCG can bind to the TSH receptor
(although with much lower affinity than TSH). As a result very high
circulating levels of hCG can over stimulate the thyroid gland causing
.paraneoplastic hyperthyroidism

Mitochondrial DNA (mtDNA) is the most common non-nuclear DNA found

in eukaryotic cells. It resembles prokaryotic DNA and is maternally
derived. Mutations involving mtDNA or nuclear DNA that codes for
mitochondrial proteins can cause variety of mitochondrial disorders
.including Leigh and MELAS
mtDNA codes for about 14 proteins and ribosomal and transfer RNA
needed for mitochondrial protein synthesis. Each mitochondrion contains
1- 10 copies of maternally derived mtDNA. This DNA exist as small circular
.chromosome

Hb C is caused by a missense mutation that results in glutamate residue

being substituted by lysine in the beta globin chain. This results in an
overall decrease in negative charge for Hb molecule. The speed of Hb
movement during gel electrophoresis is Hb A > Hb S > Hb C
Hb S is abnormal type of Hb, in which a nonpolar amino acid (valine )
replaces a negatively charged amino acid (glutamate) in the beta globin
chain. This replacement decrease the negative charge on Hb S molecule
.which causes Hb S to move more slowly toward the anode
Similarly , Hb C has a glutamate residue replaced by lysine in the beta
globin chain. Because lysine is a positively charged amino acid , Hb C has
even less total negative charge than Hb S and moves even more slowly
toward the anode. Both Hb C and Hb S result from missense mutations , a
type of mutation in which a single base substitution results in a codon that
.codes for a different amino acid
Patients with Hb S in both beta chains , and those with Hb C have Hb C in
both beta chain , patients with SC have 1 Hb S and 1 Hb C allele and will
.have 2 Hb bands on electrophoresis
Patients with Hb C are typically asymptomatic and often have mild
.hemolytic anemia and splenomegaly

PCR : amplify small segments of DNA by repeated replication . the

sequence amplified can be a gene , gene segment , or non coding
segment. Unlike other cloning techniques , PCR is carried out in vitro and
does not require a living organism. A synthetic primer is used to start the
reaction , and a thermostable DNA polymerase facilitates the DNA
: polymerization. The five materials needed to perform PCR are
DNA template this is the region of DNA to be amplified -1
two primers : 25-35 base sequence complementary to the regions -2
flanking the target DNA to be amplified. Pcr does not require that the
sequence of the target DNA to be known the flanking sequences must be
.known in order to make the primers
DNA polymerase : the enzyme that replicates the target DNA -3
.Deooxy nucleotide triphospahtes : to build the new DNA strands -4
: PCR steps
denaturing : separation of target DNA -1
annealing : primers combine with the denatured single stranded -2
flanking ends of the target DNA when temp. lowered
Elongation : DNA polymerase elongates the DNA starnds in 5' to 3' -3
direction
So PCR requires primers that are complementary to the regions of DNA
flanking the segment to be amplified. Thermostable DNA polymerase ,
deoxynucleotide triphosphates , and the target DNA template strand are
.also necessary

Folate derivatives are crucial in the synthesis of DNA and in the conversion
.of Vit B12 to one of its co-enzymes forms
Thymidylate synthase catalyze methylation of dUMP to dTMP while
.converting methyleentetrahydrofolate to dihydrofolate
.This is the only denovo pathway for dTMP production
DNA synthesis is impaired when a deficit of methyltetrahydrofolate
develops. One of the common consequences of reduced DNA synthesis is
megaloblastosis . there is salvage oathway using thymidine kinase that
normally accounts for 5-10 % of dTMP synthesis , therefore activation of
this pathway with thymidine supplementation can partially compensate for
.diminished d TMP synthesis

The biologically active form of pantothenic acid is coenzyme A , which

binds with oxaloacetate in the first step of the TCA cycle to form citrate
then succinyl CoA
Coenzyme A is an essential cofactor in numerous acetylation reactions. It's
also important in the synthesis of vitamin A , D , cholesterol , steroids ,
.Heme A , fatty acids , amino acids , and proteins
The panthotheic acid is actively transported into cell and then undergoes
.ATP dependent phosphorylation which transform it to coenzyme A
Deficiency : paraesthesis and dysthesias (burning feet syndrome ) and GIT
.distress

Lynch $ autosomal dominant disease caused by defective DNA mismatch

nucleotide repair. The mismatch repair system involves several genes
including MSH 2 and MLH 1 which code for components of the human
MutS and MutL. Mutations in these 2 genes account for around 90 % of
$ cases of Lynch
Mismatch repair begins with MutS detecting a mismatch on the newly
created daughter strand, which is distinguished from the parent by
occasional nicks in the bonds. MutL is then recuriy=ted and resulting
complex slides along DNA molecule until 1 of the daughter strand nicks is
encountered. Then exonuclease ! is loaded onto and activated by the
repair complex. Then the daughter strand degraded backward past the
intial mismatch point , leaving a variable gap of single stranded DNA that
is stabilized by ssDNA- binding protein. The complex then dissociates while
DNA polymerase delta loads at the 3' end and begins synthesizing a new
daughter strand segment. Finally DNA ligase I seals the remaining nick to
.complete the repair process

Biotin acts as a co2 carrier on the surface of the carboxylase enzyme ,

which encompasses the enzymatic subtypes acetyl-CoA carbylase ,
pyruvate carboxylase , propionyl carboxylase , and beta-methylcrotonyl
. CoA carboxylase
Ex. Pyruvate carboxylase convert pyruvate to oxaloacetate. In biotin
deficient individuals , the level of pyruvate rises and the pyruvate is
.coverted to lactic acid instead
Another ex. Propionyl CoA carboxylase conver valine to succinyl CoA. In
biotin deficient , th epropionyl CoA builds up and in instead metabolized
.into surplus of odd chain fatty acids
Deficiencies : poor diet, excessive raw egg white consumption, and
.congenital disorders of biotin metabolism

Xeroderma pigmentomsum : enzymatic disorder, autosomal recessive .

clinically : photo sensitivity , poikiloderma, hyper pigmentation in sun
exposed areas and also possess a markedly increased risk of developing
.skin cancers
Telomerase is a reverse transcriptase enzyme (RNA dependant DNA
polymerase ) that adds TTAGGG repeats to the 3' end of DNA strands at
the terminal end of chromosomes the telomere region. It synthesizes
single stranded DNA using a single stranded RNA as a template
Stem cells have a very long telomeres and active telomerase , but with
every cell division the length of telomeres progressively shortens.
Terminally differentiated adult somatic cells have a very short telomeres.
Critical shortening in telomere length is though to be one signal for
programmed cell death. Cancer cells are immortal because these cells
.contine to divide withought aging and shortening of their telomeres
Thus telomerase is a potential target for tx of cancers. Syndrome of
premature aging such as Bloom $ are associated with shortened
.telomeres
Stem cells are undifferentiated cells that have the potential to differentiate
into other cell types . 2 types : embryonic and adult stem cells . Adult
stem cells are thought to be present in most tissues where they are
responsible for replacement of dead cells present in most tissues where
they are responsible for replacement of dead cells. Ex. The epidermis ,
. bone marrow

Pyridoxine (B6) is an essential co-factor for the transamination and

.decarboxylation of amino acids and for gluconeogensis
Transamination reactions typically occur between an amino acid and an aketo acid. The amino group is transferred to the a-keto acid from amino
.acid and the a-keto acid thereby becomes an amino acid
Ex. Oxaloacetate (a-keto acid) reacts with glutamate (amino acid ) to form
aspartate (the resulting amino acid ) and a-ketoglutrate (the resulting a.keto acid)
Transaminases are the enzymes that catalyze transamination and
.pyridoxal phosphate (vit B6) serves as an essential cofactor

In prokaryotic mRNA the intiation codon AUG also codon for methionine is
locates 6-10 bases downstream from a genetic sequence known as the
shine Dalgarno element, which recognizes complmentary sequence in the

16 rRNA and the 30 S small ribosomal subunit. The Shine Dalgarno

.element is unique to prokaryotes
Binding of the 30 S ribosomal subunit to mRNA ans N formylated
methionine tRNA forms the prokaryotic intiation complex , facilated by the
intiation factors IF1, IF2 , If 3. The energy for this reaction is obtained
through the hydrolysis of GTP , which also brings the 50S ribosomal
subunit to intiation complex resulting in formation of the 70 S ribosomal
unit
Streptomycin : binds the 30 S ribosomal subunit and distorts its structure ,
impairing the intiation of protein synthesis and inhibition of formation of
.intiation complex
Chloramphenicol : peptidyl transferase is a compoenent of the 50S
ribosomal subunit necessary for the transfer of amino acid from A to the P
!site and for the formation of peptide bonds , chloramphenicol inhibits it
During elongation ribosomes move in 5' to 3' direction on the m RNA
molecule in a process known as the translocation. The antibiotics
.clindamycin and erythromycin both inhibit this translocation step
.Tetracycline interfere with binding of aminoacyle tRNA to the A site

Type I collagen synthesis : begins with collagen a-chain translation in the

cytosol . the a hydrophobic signal sequence at the N- terminus directs the
ribosome to the RER. In RER : cleavage of the signal sequence and
.hydroxylation and glycosyaltion of certain residues
Intrachain disulfide bonds then form at the N and C terminus globular
.regions, helping stabilize them
Special interchain disulfide bonds also form at the C terminus between 3
pro-a-chains for triple helix formation
.The resulting procollagen molecule then undergoes exocytosis
N and C terminus non helical regions are cleaved from the triple helix by
procollagen peptidase forming tropocollagen. Tropocollagen subunits then
self assemble into collagen firbrils that are subsequently crosslinked by
.lyslyl oxidase
Ehlers- Danlos $ : caused by mutations affecting the collagen genes or the
enzymes such as lysyl hydroxylase or procollagen peptidase. In the case
of EDS due to procollagen peptidase deficiency , impaired cleavage of the
procollagen N and C termini causes the formation of more stable collagen
that does not properly cross link with other collagen molecules this results
.in joint laxity , loose skin and easy bruisability

Extracellular peptidase cleave disulfide rick terminal extensions from

procollagen molecule. This results in formation of water insoluble triple
helical collagen subunits (tropocollagen) that self assemble and undergo
crosslinking by lyslyl oxidase to for mature collagen firbrils. Impaired
cleavage of procollagen causes the formation of more soluble collagen
.that does not properly crosslink with other collagen molecules

The liver takes up indirect (unconjugated bilirubin through a passive

process utilizing an organic anion transpoting polypeptide (OATP). It
secretes direct (conjugated ) bilirubin into the biliry syatem through active
transport by a specific ATP binding cassette protein known as MRP2 .
inhibition of this energy dependanet transport protein prevents conjugated
bilirubin from being excreted into the biliary system, comjugated bilirubin
can still exit the hepatocyte by passive diffusion through the basolateral
OATP. Thus inhibition of the canalicular active organic anion transporter
.results in an isolated conjugated hyperbilirubinemia

The Kozak sequence plays a role in the initiation of translation. A mutation

three bases upstream from the start codon (AUG) in this sequence is
.associated with thalassemia intermedia
Thalassemia intermedia : a form of beta thalassemia that is clinically less
severe than beta thalassemia major. Hypochromic microcytic anaemia is
the classic lab finding , anisopoikilocytosis, target cell formation , tear drop
., and or Heinz bodies

After binding to 1 oxygen molecule, the oxygen affinity of other heme

molecules increases, this heme-heme interaction is responsible for the
.characteristic sigmoid shape of the oxygen hemoglobin dissociation curve
Myoglobin is a monomeric protein and the primary oxygen storing protein
in skeletal and cardiac muscle tissue, it's only found in the blood stream
.after muscle injury
The partial pressue of oxygen at which 50 % of myoglobin molecules are
oxygen saturated is only 1 mm Hg, which is much lower than the P50 of
Hb (26 mmHg). Myoglobin also has only a single heme group and so does
not experience heme-heme interactions , therefore its oxygen dissociation
.curve is hyperbolic
The individual subunits of the Hb molecule are structurally analogous to
myoglobin. If separated , the monomeric subunits will demonstrate a
.hyperbolic oxygen dissociation curve similar to that of myoglobin

G3P> 1,3BPG by G3p dehydrogenase , and this enzyme uses NAD

.dependent oxidation and in this reaction NAD is converted into NADH
Under aerobic conditions : NAD is converted to NADH in the TCA cycle and
NADH in then converted back to NAD in the ETC as the energy in the
.NADH is utilized to synthesize ATP
In anaerobic glycolysis NAD is regenerated from NADH when pyruvate is
.converted to lactate by lactate dehydrogenase
In strenuously exercising muscle, glycolysis can be inhibited by limited
.regeneration of NAD from NADH

Wernicke syndrome manifests with the triad of : ophthalmoplegia, ataxia,

.and confusion
Foci of hge and necrosis in the mamillary bodies and periaqueductal gray
matter. This condition occurs due to chronic thiamine deficiency, a
.condition common with alcoholism
Thiamine (vitB1) participate in a number of reactions of glucose
:metabolism. It is a cofactor for the following enzymes
Pyruvate dehydrogenase : converts pyruvate into acetylcoA -1
a-ketoglutrate dehydrogenase : enzyme for citric acid -2
Transketolase : enzyme of hexose monophspate pathway. It converts -3
pentoses to G3P
Thiamine deficieny leads to decreased glucose utilization which is
especially pronounced in CNS if a patient with chronic thiamine deficiency
is given a glucose infusion without thiamine supplementation, acute
cerebral damage occurs. An increase in erythrocyte transketolase levels
. after thiamine infusion is diagnostic for thiamine deficiency

The brain , kidney , cardiac muscle and skeletal muscle can all
.utilizeglucose and or ketones for energy
Ketone bodies yield energy when they are converted to acetyl CoA.
Erythrocytes cannot use ketone bodies foe energy because they lack
.mitochondria
The liver cannot also utilize ketone bodies for energy because it lacks the
enzyme succinyl CoA-acetoacetate CoA transferase (thiophorase) which is
.required to convert acetoacetate to acetoacetyl CoA

Glucose is the major stimulant of insulin secretion. After glucose enters

the beta cells , it is metabolized by glycolysis , followed by citric acid
cycle, which results in the generation of ATP molecules. A high ATP to ADP
ratios within the beta cells results in the closure of potassium (KATP)
channel , which causes insulin secretion by opening the coltage
.dependanet Ca channel
In the beta cell of the pancreas , the forst enzyme in the glycolytic
pathway is glucokinase, glucokinase converts glucose to glucose 6phosphate. Glucokinase has a much higher Km (10 mmol) than
hexokinase (0.5 mmol). Further more glucokinase is less sensitive ti
.allosteric inhibition by its product, glucose ^ phosphate
An increase in serum glucose leads to increased metabolism of glucose
within the beta vells , ultimately leading to insulin secretion by the
formation of ATP. The conversion of glucose to glucose 6 phosphate by
.glucokinase is crucial and rate limiting
Glucokinase defects result in one of the types of maturity onset diabetes.
Inactivating mutations of the glucokinase gene lead to a decrease in the
enzyme's function causing decrease in the metabolism of glucose , lesser
. ATP formation and diminished insulin secretion
Glucokinase is a glucose sensor within the pancreatic beta cells ,
inactivating muatations in the enzyme result in mild hyperglycemia than
.can be exacerbated by preganancy

Ornithine transport into mitochondria is essential for urea formation as

ornithine is needed to combine with carbamoly phosphate with the
mitochondria to form citrulline in the second step of urea cycle. Urea cycle
defects cause neurological damage primarily due to the accumulation of
.ammonia. Protein restriction would improve this condition

Beta oxidation , ketogenesis , TCA cycle , parts of Urea cycle (carbamoly

phosphate synthetase 1 and ornithine transcarbamoylase ) and pyruvate
carboxylation all occur exclusively within the mitochondria. All of the
.reactions of the pentose phosphate pathway occur in the cytoplasm

Proteins in ingested food exist as polypeptides and require hydrolysis to

dipeptides, tripeptides and amino acids for absorption. Hydrolysis of these
polypeptides is accomplished by proteolytic enzymes as pepsin and
trypsin. These enzymes are secreted as the inactive proenzymes
pepsinogen and trypsinogen from the stomach and pancrease,
respectively. Trypsin in turn activates other proteolytic enzymes including

chymotrypsin, carboxypeptidase and elastase. Activation of trypsinogen to

trypsin is achieved by enteropeptidase ( or enterokinase) an enzyme
.produced in the duodenum
Enteropeptidase deficiency results in defective conversion of the
proenzyme trypsinogen to the active enzyme trypsin. Clinically : diarrhea,
.growth retardation and hypoproteinemia

In order for a child to have sickle disease both parents must be carriers.
The carrier status of prospective parents can be established by
.hemoglobin electrophoresis

Maturing erythrocytes lose their ability to synthesize heme when they lose
their mitochondria. Mitochondria are necessary for the first and final 3
steps of heme synthesis. Erythrocytes utilize the iron-containing heme to
form hemoglobin , the major oxygen carrying molecule in the body.
.Hepatocytes use heme in the microsomal cytochrome p 450 system

In hartnup disease the intestinal and renal absorption of tryptophan is

defective . tryptophan is an essential amino acid and a precursor for
nicotinic acid, serotonin, and melatonin. The clinical manifestation of
hartnup disease are due to the malabsorption of tryptophan, resulting in
.niacin vit B3 deficiency, because niacin is synthesized from tryptophan
Photosensitivity and pellagra like skin rashes, neurologic involvement >
ataxia. Lab: aminoaciduria, restricted to the neutral amino acids(alanine,
serine , threonine , valine, leucine, isoleucine , phenylalanine , tyrosine ,
tryptophan , and histidine). The urinary excretion of proline,
hydroxyproline, and arginine remains unchanged and this important
finding differentiates hartnup disease from other causes of generalized
aminoaciduria such as fanconi syndrome. Tx with nicotinic acid or
nicotinamide and a high protein diet generally results in significant
.improvement of symptoms

Acid maltase deficiency leads to glycogen accumulation within lysosomal

vesicles. Clinical manifestations of this disease include hepatomegaly,
cardiomegaly , macroglossia, hypotonia , and mental retardation in its
.most severe form

Receptors are divided into : steroid , ion channels, enzyme linked , G.protein linked

Enzyme linked are proteins that span the cell membrane , extruding an
extracellular terminal that binds to the corresponding growth factor. Once
bound, the receptor protein configuration is changed , which triggers a
cascade of events. So of the enzymes linked receptors are enzymes
.themselves and some activates enzyme present in the cytosol
: Difference
Receptor

Structure

Signaling pathway

Examples

With intrinsic
enzyme activity
( receptor tyrosine
kinase )
Extracellular domain
( binds the growth
factor )
Transmembrane
domain
Cytosolic domain
( enzyme )
MAP kinase
Receptor
autophosphorylates
and triggers
phosphrylation of Ras
protein
Growth factor
receptor : EGF, PDGF,
..FGF, etc

Without intrinsic
enzyme activity
(tyrosine kinase
associated receptor)
Extracellular domain
Transmembrane
domain
Cytosolic domain
( lacks enzymatic
activity )
JAK/STAT
Receptor activates
Janus Kinases which
phosphrylate STATs
(signal transducers and
activators of
transcription)
Receptors for cytokines
, growth hormone,
prolactin , IL-2 , colony
.stimulating factors

Arginase deficiency: arginase is an enzyme of the urea cycle , that

produce urea and ornithine from arginine. Underdiagnosed condition ,
missed as cerebral palsy. Tx: low protein diet , devoid of arginine.
Synthetic protein made of essential amino acids results in dramatic
.decrease in plasma arginine and improvement of neurological symptoms

In gluconeogeneiss , glucose is formed from pyruvate derived from

lactate , glycerol and glucongenic amino acids. Ppyruvate > oxaloacetate
in mitochondria by pyruvate carboxylase, the activity of which is increased
.by acetyal CoA
Oxaloacetate > malate by malate dehydrogenase > malate shuttled out to
cytosol > converted back to oxaloacetate by cytosolic malate
.dehydrogenase. Cytosolic oxaloacetate > PEP by PEP carboxykinase

So acetyal CoA is an important allosteric activator of gluconeogensis that

.acts by increasing the activity of pyruvate carboxylase

Propionyl CoA is derived from amino acids (valine , isoleucine , threonine ,

methionine , cholesterol , and odd- chain fatty acids leads to the formation
of propionic acid, which is then converted to methylmalonic acid by biotin
.dependent carboxylation
Methymalonic acid > succinylCoA by isomerase which then enters the
.TCA
Deficiency of propionyl CoA carboxylase > propionic academia > propionyl
CoA accumulates > poor feeding , vomiting , hypotonia , lethargy ,
.dehydration and anion gap acidosis

Methionine and tetrahydrofolare are formed when methyl-tetrahydrofolate

donates a methyl group to homocysteine. The conversion of homocysteine
to methionine requires the cofactor B12 (cobalamin)
In vit B12 deficiency tetrahydrofolate cannot be regenerated. Folate
.metabolism is consequently impaired
Defective DNA synthesis and megaloblastic anaemia is seen in both Vit
B12 and folate deficiency. Homocysteine levels are elevated in both
conditions as well. Elevated homocysteine is a risk factor for arterial and
.venous thrombosis
Vit B 12 is alone responsible for conversion of methylmalonyl CoA to
succinyl CoA. Thus in vitamin B 12 deficiency methylmalonly COA are
elevated. The result is the incorporation of non-physiologic fatty acids into
neuronal lipids. This contributes to the neurologic dysfunction in vit B 12
.deficiency as well
Homocysteine is elevated in both folic acid and vit B12. Deficiency
Methylmalonyl CoA is elevated only in vit B 12 deficiency