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Biochemistry PDF
Biochemistry PDF
Biochemistry PDF
BIOCHEMISTRY:
for a run through revision
This book has been published on good faith that the material provided by
author(s) is original. Every effort is made to ensure accuracy of material,
but the publisher, printer and author will not be held responsible for any
inadvertent error(s). In case of anydispute, all legalmattersto be settled under
Gorakhpur Jurisdiction only.
No cast-iron guarantee is given that this book is totally free from errors of any kind.
If there are errors, they are inspite of our best efforts. The author or the publisher will
not be responsible for these unintended errors.
ACKNOWLEDGEMENT
Although language is the most eloquent vehicle of human expression, yet on the
occasion one finds it difficult to express a feeling appropriately. It is not easy to
formulate in words the feeling of gratitude which I have for many individuals,
who made individual contributions in enabling me to bring this book to
completion.
Firstandforemost I thankthe Almighty for thispricelesslifeandfor bestowing
upon his blessings to help me carry out this work with lots of courage and sheer
determination.
Thank you doesn’t seem sufficient for my loving husband Jaspreet Singh whose
invaluable presence is constant source of myhappiness and has always endowed
me with strength to face challenges in life. Without his relentless support, this
book would have never been materialized.
Words are insufficient to verbalise my deep sense of gratitude and regards to
my parents, who soulfully provided me the sincere encouragement, endless
patience, emotional and financial support and inspiration throughout my work
and lifting me uphill this phase of life. Special and heartiest thanks to my in laws
for all the support as my parents and encouraging me.
This book would never have been complete without my son Divaahaan who
sacrificed his mother’s time and let me to compose this book.
It is an extraordinary joy to thank my assistant Dimple Nagpal whose
constructive criticism, deep interest and intellectual acumen were instrumental
in accomplishing this book.
I would like to thank Roffers Publications for their efforts and inputs and in
providing me a platform in bringing out thebook.
Finally the credit goes to all my students, who have been the actual inspiration
for the composition of this particular book.
PREFACE
Biochemistry, both a life science as well as a chemical science, is the foundation for
understanding all biological processes. Over the last few decades, a vast information has
been gathered on the subject. It is for sure a standout amongst the most troublesome subjects
as studying and understanding this vast subject is an uphill task for the students. Even after
the students are almost aware about the subject, this subject requires revision.
Keeping all facts in mind, this pocket book aims to enable you to make this tedious work
relatively easy for the students providing the main points to be covered for any entrance
exam containing MCQ type questions on biochemistry. Also the basic theme of the book is
to keep it concise and straightforward.
This book comprises 8 chapters. The first chapter CONCEPTS IN BIOCHEMISTRY
contains the overview of biochemistry and forms the base of student and helps them to
interlink and relate these concepts with other chapters.
The highlights of each topic have been refined and fine tuned to stimulate the learning
process among the students. Several tables and figures are added for the elementary learning.
This book is a time saving hack and comprehends last minute revision notes.
The book is primarily designed for those preparing for various P.G. entrance tests, AIIMS,
AIPGMEE, PGI JIPMER and all India entrance exams and also for undergraduate and
postgraduate medical biochemistry students. This book serves as a ready made source for
MCQ preparation.
In order to score well in these exams, this pocket book is a perfect source for the high time
revision. I have done much justice to providing the best brief knowledge by adding tables,
figures and homophones. I wish you gain maximum from it and develop your concepts.
To help you develop a deeper understanding of the subject, you can have an access to videos
through mobile app “Biochemistry by Dr. Smily Pruthi” in google play store.
Good luck for your coming examinations. Genuine doubts are always welcome. You can be
in touch with me for any doubt at my Facebook group.
ENZYME CLASSIFICATION
Enzyme Code or Commission Number 1 is Oxidoreductase.
Enzyme Code or Commission Number 2 is Transferase.
Enzyme Code or Commission Number 3 is Hydrolase.
Enzyme Code or Commission Number 4 is Lyase.
Enzyme Code or Commission Number 5 is Isomerase.
Enzyme Code or Commission Number 6 is Ligase.
Isomerases are enzymes which interconvert various isomers into each other.
Molecular formula is not changed when Isomerase work.
Dehydrogenase means removal of Hydrogen means Oxidation.
A person on fat free, carbohydrate rich diet continues to grow obese because of
formation of Endogenous Fat, which is transported in the form of VLDL.
VLDL transports Endogenous Fat from Liver to Peripheral Tissues.
CHAPTER
CARBOHYDRATE
CHEMISTRY 2
CARBOHYDRATE CHEMISTRY
Hydroxy group always gives polarity and has high tendency to bind Phosphate.
Aldehyde group is always present at C-1.
Keto group is always present atC-2.
Molecular formula of Carbohydrates is(CH2O)n where n = number of Total Carbons.
n
Total number of Isomers possible = 2 , where n = number of asymmetric carbons.
If all the four valancies of carbon are occupied by different atoms or groups of atoms,
then the carbon is Asymmetric.
If any two, three or four valancies of carbon are occupied by same atoms or groups
of atoms, then the carbon is Symmetric.
Functional carbon in case of Carbohydrates (aldehyde or keto) is Symmetric,
But only in Linear configuration. In cyclic configuration functional carbon is
Asymmetric.
Any compound having asymmetric carbon will show both Optical and Structural
Isomerism.
Carbohydrates and Amino Acids have asymmetric carbon so both Structural and
Optical Isomerism present.
Molecules which have Same molecular formula and Different structure are known
as Structural Isomers.
Molecules which have Same molecular formula and Different optical properties are
known as Optical Isomers.
Structural Isomerism is of four types functional isomerism, enantiomerism,
Epimerism and Anomerism.
Number of asymmetric Carbons in Ketoses are one less the number in aldoses.
The only carbohydrate with zero asymmetric carbon is Di Hydroxy Acetone
(DHA).
Parent alcohol of Carbohydrates Glycerol.
Parent carbohydrate D-Glyceraldehyde.
Simplest carbohydrate D-Glyceraldehyde.
Functional Isomerism - Functional group different (ald or keto).
Enantiomerism - different -H and -OH orientation around the penultimate carbon.
Enantiomerism, also known as -D and -L isomerism, also known as mirror images
of each other.
Enantiomer of carbohydrate abundant in Body/Nature/Plasma/Cell Always D
form Or For Carbohydrates, it is always ‘D’ form which is abundant.
Enantiomer of Amino Acid abundant / abundant in Proteins/ synthesized in our
body L form.
Enantiomer of a Free Amino Acid in body Both D and L form exists.
6 : Carbohydrate chemistry
CHAPTER
CARBOHYDRATE
METABOLISM 3
GLYCOLYSIS
Glucose
Hexokinase ATP
1 ADP
Glucose 6-phosphate
2 Phosphoglucose
isomerase
Fructose 6-phosphate
3 Phosphofructo- ATP
kinase-1 ADP
Fructose 1,6-bisphosphate
4 Aldolase-A
Triose
5 phosphate Glyceraldehyde
Dihydroxyacetone isomerase
phosphate 3-phosphate
(2 molecules)
Glyceraldehyde +
2 NAD + 2P1
6 3-phosphate +
2 NADH+ 2H
dehydrogenase
1,3-Bisphosphoglycerate
(2 molecules)
Phosphoglycerate 2 ADP
7 kinase 2 ATP
3-phosphoglycerate
(2 molecules)
Phosphoglycero-
8 mutase
2-phosphoglycerate
(2 molecules)
9 Enolase
Phosphoenolpyruvate
(2 molecules)
Pyruvate 2 ADP
10 kinase 2 ATP
NADH NAD
Pyruvate Lactate
(2 molecules) (2 molecules)
11 Lactate Dehydrogenase
(anaerobic)
12 : Carbohydrate Metabolism
LINK REACTION
Cytosol Mitochondrion
T RANSPORT PROTEIN
+
(Pyruvate-Proton NAD+ NADH +H
CO2
Symport)
Pyruvate enters Mitochondria via Pyruvate Proton Symport present in the Inner
Mitochondrial Membrane
Link reaction enzyme is Pyruvate Dehydrogenase complex (PDH complex)
PDH complex is a Multienzyme containing three components:
1) E1-Pyruvate Dehydrogenase or Pyruvate Carboxylase
2) E2-Dihydro Lipoyl Transacetylase
3) E3-Dihydro Lipoyl Dehydrogenase
PDH complex and TCA both requires five coenzymes – Vitamin B1, B2, B3, B5 and
Lipoic acid
Deficiency of these Vitamins (B1, B2, B3, B5) leads todecreased energyproduction
and CNS problems as Brain cells depend upon this Aerobic reaction
Allosteric Inhibition of PDH occurs by Acetyl CoA, NADH and ATP
PDH is active in Dephosphorylated state and Dephosphorylation is done by Insulin
Arsenate inhibits the enzymes requiring Lipoic Acid as coenzyme such as PDH
complex
Deficiency of PDH complex is the most common biochemical cause of Congenital
Lactic Acidosis.
Beri-Beri causes Lactic acidosis
Link reaction is irreversible.
TCA CYCLE
Acetyl CoA
Malate Oxaloacetate
Citrate synthase
dehydrogenase
NADH
NAD
Malate Citrate
Fumarase Aconitase
Fumarate Isocitrate
FADH NAD
Succinate Isocitrate
dehydrogenase FAD dehydrogenase
NADH
CO2
Succinate -ketoglutarate
GTP NAD
GDP
NADH
Succinyl -ketoglutarate
thiokinase Succinyl-CoA dehydrogenase
CO2
TCA known as Tricarboxylic Acid Cycle as Citrate and Isocitrate are Tricarboxylic
Acids.
Kreb’s cycle name is by name of scientist ‘Hans Adolf Krebs’.
TCA is also called Citric Acid cycle as first compound formed is Citrate which is a
Prochiral molecule.
Prochiral Molecules are those which can be converted from Achiral to Chiral in a
single step.
Citrate inhibits Glycolysis and activates Fatty Acid Synthesis.
Four steps involved in Oxidation-Reduction (Enzymes involved are Isocitrate
Dehydrogenase, α-KG Dehydrogenase, Succinate Dehydrogenase and Malate
Dehydrogenase.
Two steps involved in Oxidative Decarboxylation (Isocitrate DHase and α-KG
DHase).
Oxaloacetate (OAA) is regarded as First Substrate and Carrier of TCA and not
Acetyl CoA.
Oxaloacetate has a Catalytic role in TCA.
Acetyl CoA is not the intermediate of TCA and is never Glucogenic.
Aconitase always acts on the part of Citrate derived from Oxaloacetate.
Flouroacetate is Non Competitive Inhibitor of Aconitase.
Flourocitrate is Competitive Inhibitor of Aconitase.
Aconitase/Aconitate Hydratase belongs to Lyase category and is exceptionally an
Iron-Sulphur Protein.
α-KG Dehydrogenase is a Multi Enzyme Complex similar to PDH complex and
requires same five coenzymes (TPP, Lipoic Acid, FAD, CoA, NAD)
α-KG Dehydrogenase is not regulated by Phosphorylation or Dephosphorylation.
Enzymes catalyzing Dehydrogenation without Decarboxylation do not require
Metallic ions for their activity (Mg2+, Mn2+).
Substrate level Phosphorylation Step : Conversion of Succinyl CoA to Succinate
by Succinyl CoA Synthetase/ Succinate Thiokinase (produce both ATP & GTP but
ATP is predominant) GTP is produced in Liver and Kidney during Starvation for
PEPCK enzyme of Gluconeogenesis.
There is only one Substrate Level Phosphorylation step in TCA.
All enzymes of TCA lies in Mitochondrial Matrix Except Succinate Dehydrogenase
(located in Inner Mitochondrial Membrane).
Succinate Dehydrogenase isa Flavoprotein Enzyme in which FAD act as Hydrogen
Acceptor and is inhibited byMalonate.
Succinate Dehydrogenase is involved in TCA & ETC.
Fumarate Hydratase/Fumarase and Aconitase are Lyases.
One Acetyl CoA gives 10 ATPs in TCAcycle (9 by Oxidative Phosphorylation/ETC
and 1 by SLP).
Anaplerotic Reactions are those reactions which replenish TCAintermediates.
Most important Anaplerotic reaction is Pyruvate to Oxaloacetate conversion by
Pyruvate Carboxylase.
Two CO2 in TCA are derived from the Carbons of Oxaloacetate.
Irreversible steps of TCAare Citrate Synthase & α-Ketoglutarate Dehydrogenase.
16 : Carbohydrate Metabolism
There are three Rate Limiting Enzymes in TCA depending on various complex
conditions in body : Citrate Synthase, Isocitrate Synthase & α-Ketoglutarate
Dehydrogenase
WARBURG’s EFFECT
SHUTTLES
Transportof NADH from Cytoplasm to Mitochondria occurs with the help of two
Shuttles namely Malate Shuttle and Glycerol Phosphate Shuttle.
NADH cannot cross Inner Mitochondrial Membrane (IMM). So Shuttles are used to
transport NADH from Cytoplasm to Mitochondria.
NADH Shuttles (Malate Shuttle and Glycerol Phosphate Shuttle) are only used by
those Pathways which occur in Cytoplasm.
+
NAD Glycerol-3P FAD
Cytoplasmic Mitochondrial
glycerol-3-P DH glycerol-3-P DH
+
NADH+H DHAP FADH
2
Glycerol-3-Phosphate Shuttle
Malate Shuttle takes NADH from Cytoplasm and delivers NADH in the
Mitochondria.
Glycerol Phosphate Shuttle takes NADH from Cytoplasm and delivers FADH2 in
the Mitochondria.
Glycerol Phosphate Shuttle is a shorter shuttle and is a quick source of ATPs and is
ATP Citrate Lyase breaks Citrate to Oxaloacetate and Acetyl CoA in Cytoplasm.
NADH is the main starting material for ETC, also sometimes FADH .
2
NADH enters ETC and gives 2.5ATPs.
or Cytochrome b/c1.
Complex IV is also known as Cyt C Oxidase or Cytochrome a/a3 (Prosthetic
Group-Cu).
Complex IV is the only Electron Carrier in which Haem Iron has an available
coordination site that can directly react with O 2.
Complex V has twounits:
of 1 ATP each.
+
Complex IV transfers 2H , so it is responsible for production of 0.5 ATP.
When ETC starts from FADH2, FADH2 gives electrons to Succinate Dehydrogenase,
which further gives to Complex II and then to CoQ.
Complex II does not form anyATP.
In ETC, Oxidation and Phosphorylation are coupled i.e. they always occur together.
Translocase.
Malonate (3C) is inhibitor of Complex II of ETC, Succinate Dehydrogenase of TCA
cycle and CPT-I (Carnitine Palmitoyl Transferase-I) of β-Oxidation of Fatty Acids.
Rotenone and Phenobarbitone inhibits Complex I of ETC.
GLUCONEOGENESIS
Occurs in both (2) Pyruvate
2 ATP
Mitochondria and Pyruvate carboxylase
2 ADP
Cytoplasm (starts from
Mitochondria) (2) Oxaloacetate
2 GTP
Organs: 90% in Liver PEP Carboxy Kinase
2 GDP
(predominant) and 10% in
Kidneys. (2) PEP
Gluconeogenesis occur
during Fasting/Starvation (2) 3-Phosphoglycerate
and in Diabetes Mellitus 2 ATP
Phospho Glycerate Kinase
Firststepof Gluconeogenesis
2 ADP
is conversion of Pyruvate to (2) 1,3-Bisphosphoglycerate
Oxaloacetate by Pyruvate NADH + H
+
Carboxylase enzyme +
NAD
(Anaplerotic reaction).
Fructose-1,6-bisphosphate
Acetyl CoA is veryimportant
Allosteric Activator of P1 Fructose1,6 bisphosphatase
Pyruvate Carboxylase.
Fructose-6-phosphate
Oxaloacetate produced in
Mitochondria gets converted
to Malateby Mitochondrial Glucose-6-phosphate
Malate Dehydrogenase as P1 Glucose-6-Phosphatase
Oxaloacetate cannot cross
IMM. Glucose
in Gluconeogenesis.
Instead of Pyruvate Kinase in Glycolysis, Enzymes used in Gluconeogenesis are
Total Glucogenic Amino Acids = 18 (13 are purely Glucogenic and 5 are in both
category).
So only 2 Amino Acids can never form Glucose. Rest 18 can form Glucose
Mostly 3-C containing compounds are Good Substrates for Gluconeogenesis e.g.
Pyruvate, Lactate, Alanine.
Link Reaction (Pyruvate Dehydrogenase complex) is inhibited during Fasting,
so excess of Pyruvate which is not entering into Link Reaction is used up for
Gluconeogenesis.
If Fructose 2,6 Bisphosphatase is active, Glycolysis decreases.
GLYCOGEN
HMP is the minor pathwayfor oxidation of Glucose but a major source for NADPH.
NADPH produced in HMP is needed for Reductive Biosynthesis or to counter the
damaging effects of Oxygen Radicals.
No ATP is generated but CO2 is produced in HMP.
HMP has 2 phases: Oxidative phase (irreversible) and Non-Oxidative phase
(reversible).
In cells with greater need for NADPH than Ribose-5-P, both Oxidative and Non-
Oxidative Phase occurs.
In cells with greater need for Ribose-5-P than NADPH, only Non-Oxidative Phase
occurs.
Oxidative Phase synthesize NADPH.
Non-Oxidative Phase synthesize Ribose-5-Phosphate.
Heptose keto sugar formed in HMP shunt is Sedoheptulose-7-P.
Glucose-6-P dehydrogenase (G-6-PD) catalyzes the conversion of Glucose-6-P to
6-Phosphogluconate.This is the Rate Limiting step, first Commited step and also the
Regulatory step of HMP.
NADPH is a potent Competitive Inhibitor of Glucose-6-P dehydrogenase.
Insulin upregulates the expression of gene for Glucose-6-P dehydrogenase
Pathways which do not produce ATP are HMP, Uronic Acid Pathway and RL shunt,
Synthesis of Ketone Bodies, α-Oxidation of Fatty Acids & Oxidation of VLCFA
(Very Long Chain Fatty Acids).
NADPH is produced from : HMP (major source), Malic enzyme and Cytosolic
Isocitrate Dehydrogenase.
In Oxidative Phase, 2 molecules of NADPH, 1 molecule of CO2 and 1 molecule of
Ribulose-5-P is formed per Glucose-6-P moleculeoxidized.
Products of HMP from three molecules of Glucose-6-P are 6 NADPH, 3 CO2 , 2
molecules of Glucose-6-P and one Glyceraldehyde-3-P.
Transketolase requires TPP (derivative of Vitamin B1) and Mg .
++
Galactose Metabolism
Galactose Metabolism, Fructose Metabolism and
Gluconeogenesis uses the enzymes of Glycolysis
so that energy is not wasted to make different
enzymes for many pathways occuring in the cells.
Source of Galactose is Lactose (milk and milk
products).
Galactose also obtained by Lysosomal
Degradation of Glycoproteins and Glycolipids.
Galactose
ATP
Mg2+ Galactokinase
ADP
Block in
Galactose galactosemia UDPGIc
1-phosphate
Galactose Uridine
+
1-phosphate NAD diphosphogalactose
uridyl transferase 4-epimerase
Glucose
1-phosphate UDPGal
Carbohydrate Metabolism : 27
Fructose Metabolism
Fructose Metabolism takes place Fructose
mainly in Liver. ATP
Fructose entry into cells is Insulin Fructokinase
ADP
Dependent.
Fructose ingestion does not lead to Fructose-1-Phosphate
Insulin release. Aldolase B (fructose-1-P
aldolase)
Fructose is most Lipogenic sugar.
Fructose gets rapidly metabolized as
DHAP
it bypasses PFK-1 step (rate limiting Glyceraldehyde
ATP
step). Triose kinase
Fructose is more sweet than ADP
Glucose.
Glyceraldehyde
Substrate for Aldolase A and -3-Phosphate
Aldolase C is Fructose 1,6
Enters Glycolysis
Bisphosphate.
Osmotic stress
Aldose Sorbitol
reductase dehydrogenase
Glucose Sorbitol Fructose
+
N A DP H N A DP N AD+ NADH
GSSG GSH
Glutathione
reductase
CHAPTER
ENZYMES 4
ENZYMES
Enzymes are High Molecular Weight, Highly efficient and specialized Proteins,
which catalyze the Biochemical Reactions.
Enzymes increase the Rate of the Reaction, without being changed in the overall
process.
All enzymes are Proteins except
Ribozyme.
Enzymes are Substrate Specific,
Stereospecific and Thermolabile.
Active Site is made up of Binding
Sites (usually two) & Catalytic Site.
Active site (A.S) is Flexible and not
Rigid.
The A.S of enzyme is formed of Amino Acids which may be placed at long distances
on the Primary Structure, but are brought nearer to each other by 3-D Conformation
of Enzyme.
Induced Fit Theory – Active Site is flexible, when substrate approaches active site
then there is conformational change which induces the active site to fit the substrate.
For any Thermodynamically Favourable Reaction, the Free Energy of the Product is
lower than that of Substrate.
Amount of ΔG tells that a reaction is Thermodynamically Favourable or not.
Negative ΔG (ΔG<0) Thermodynamically Stable Reaction.
Positive ΔG (ΔG<0) Thermodynamically Unfavourable Reaction (i.e. energy
required).
ΔG=0 Reaction is at Equilibrium (i.e. freely reversible).
30 : Enzymes
Enzyme decreases the Activation Energy as well as Time required by the Reaction.
Enzyme does not affect Free Energy or Equilibrium of the Reaction.
Activation Energy
++
All Carboxylases need Mg .
Cytoplasmic SOD require Copper but Mitochondrial SOD requires Manganese.
Isoenzymesarephysicallydistinct formofEnzymeswhichcatalyse sameBiochemical
Reaction.
Isoenzymes may be present in same/differenttissues.
Lactate Dehydrogenase (LDH) is a Tetramer made up of two subunits, H and M.
LDH-1 (HHHH) is present in Heart.
LDH-2 (HHHM) is present in Blood (WBC). So known as Functional Plasma
Enzyme.
In a Normal person, LDH-2>LDH-1.
LDH-1 >LDH-2 in Myocardial Infarction (known as Flipped ratio of LDH).
Creatine Kinase (CK) has two subunits : B (Brain) and M (Muscle).
CK-1 (BB) is present in Brain.
CK-2 (MB) is present in Heart.
CK-3 (MM) is present in Skeletal Muscles.
LDH-1 and CK-1 has maximum Electrophoretic Mobility.
LDH-5 and CK-3 has least Electrophoretic Mobility.
CK-2 is raised in MI after 4-6 hours.
AST/SGOT is raised in MI after 6-8 hours.
LDH-1 is raised in MI after 8-10 hours.
Earliest Marker for MI Myoglobin but it is Non Specific.
Last Marker to rise in MI LDH.
Most Specific Marker for MI = Troponin I > Troponin T.
First Marker to fall in MI Myoglobin.
Second Marker to fall in MI CK-MB.
Last Marker to fall in MI LDH.
IMA(Ischemia Modified Albumin) New Marker for Acute Myocardial Ischemia.
Isoenzymes of Hexokinase are of four types (Type I, II, III, IV) and Type II being
most abundant and overexpressed in Cancerous Cells.
Hexokinase IV is known as Glucokinase.
All Serine Proteases have Catalytic Triad (presence of three Amino Acids at active
site) of Histidine, Serine and Aspartate.
32 : Enzymes
5. Isomerases
Racemase interconvert L & D stereoisomers
Mutase transfer groups b/w atoms within a molecule
Epimerase interconvert epimers
6. Ligase
Synthetase link 2 molecules via an ATP-dependent reaction
Carboxylase use CO2 as a substrate
Exceptions :
1) Nitric Oxide Synthase is an Oxidoreductase
2) Glycogen Synthase and Citrate Synthase Transferase
3) ATP synthase Hydrolase
Oxygenases directly incorporate O2 into the substrate.
AllHydroxylases are Mono-Oxygenases (Exceptions: Proline Hydroxylase and
Lysyl Hydroxylase are Dioxygenases).
Mono-Oxygenases are known as Mixed Function Oxidases as they incorporate one
[O] into the Substrate and other [O] into H2 to make H2O.
Examples of Dioxygenases are Homogentisate Dioxygenase, Tryptophan Pyrrolase.
Hydroxylase EC Number 1
Hydrolase EC Number 3
Hydratase EC Number 4
Phosphatase is Hydrolase
K that [S] (substrate concentration) at which Velocity of reaction is half of V .
m max
Km is Michaelis MentonConstant.
Km isSignature of Enzymeandisinverselyproportional toAffinitybetweenEnzyme
and Substrate.
Km is characteristic of an enzyme and its particular substrate, and reflects the Affinity
of Enzyme for that Substrate.
Small Km means a High Affinity i.e. low concentration of substrate is needed to
attain half of Vmax.
34 : Enzymes
Amino Acids ionize to give negative charge on Carboxy group and positive charge
on Amino group and the Net Charge is zero, hence known as Zwitter-Ion or
Ampholyte.
pI is Isoelectric pH that pH at which Zwitter ions exist.
At pI (Isoelectric pH), a protein will precipitate.
basic acidic
group H group H
+H N
H2N C COOH 3 C COO
R R
amino acid zwitterion
All Amino Acids are L-α-Amino Acids, which are present in Proteins. But in body,
Free Amino Acids are present (i.e. those which are not in proteins), which can be L
or D or α/β/Y.
Amino Acid abundant in Protein L-form.
Amino Acid abundant in Body L-form.
Amino Acid present in Protein always ‘L’ form and always α.
Amino Acid present in Body Both ‘L’ and ‘D’ forms.
38 : Amino Acids
( given by codon UAG) respectively. These two Amino Acids are formed by
modification of Stop Codons which is a Co-Translational Modification.
22 Amino Acids are encoded by DNA i.e. they are not formed by Post Translational
Modifications.
Pyrrolysine
NH2
O
X OH
N
H
N O
Lysine NH2
OH
H2 N
OH SH SeH
H H H
O O O
H2N H2N H2N
OH OH OH
Arginine Histidine
O O
H2 N CH C OH H2N CH C OH
CH2 CH2
CH2
N
CH2
NH
NH
C NH
NH2
- - -
COO COO COO
+ + +
HN
3 C H H 3N C H H 3N C H
CH CH H C CH3
H3C CH3 CH CH2
H3C CH3 CH3
Valine Leucine Isoleucine
Maple Syrup Urine Disease (MSUD) is Autosomal Recessive disease in which there
is a defect in the Oxidative Decarboxylation step (in the catabolism of Branched
Chain Amino Acids).
Enzyme defect in MSUDis branched chain α-Ketoacid Dehydrogenase/ Branched
Chain α-Keto Acid Decarboxylase (Multi enzymecomplex).
Clinicalfeatures of MSUD are Burnt Sugarlike Odour Of Urine, Ketosis, Vomiting,
Feeding Problems, Mental Retardation, Abnormal Muscle Tone
If MSUD is not treated , then Coma or Death may occur.
Patients with rare Thiamine Dependent Variant of MSUD give response when large
Biochemistry of Phenylketonuria
Tyrosine is used for the synthesis of Catecholamines, Thyroid Hormone and the
pigment Melanin.
Amino Acids : 43
Albinism (milky white skin, white hair, red eye color) is absence of pigment
Melanin from skin, hair and eyes. Enzyme deficient is Tyrosinase (an Oxidase and
Cu required).
Oculo Cutaneous Albinism associated with defects in Vision and Photophobia.
In Vitiligo, enzyme Tyrosinase is normal but there is lack of Melanoblasts in
regional areas.
Alkaptonuria is associated with defects in Catabolism of Tyrosine and
Phenylalanine.
Alkaptonuria (Autosomal Recessive) is part of Garrod’s Tetrad.
Benedict’s Test is positive in Alkaptonuria due to Homogentisic Acid which is
Reducing in nature.
Fresh urine of Alkaptonuria patients is normal color.
But urine on long standing turns black due to oxidation of Homogentisic Acid.
Amino Acid Transporter – Failure to absorb Tryptophan from Intestine and also
reabsorb it from Kidneys.
Massive Aminoaciduria (mainly Tryptophan) without a corresponding increase in
Plasma Amino Acid level is characteristic of Hartnup’s Disease.
Mutation of Hartnup’s Disease is on gene SLC6A 19.
In Carcinoid Syndrome, Tryptophan used to form excess Serotonin, so Tryptophan
All Basic Amino Acids (Histidine, Arginine, Lysine) and Acidic Amino Acids(
Aspartic Acid, Glutamic Acid) are Polar.
Arginine is Glucogenic (Catabolic End Product – α-Ketoglutarate).
COO C CH2
CH2
H2N O
COO C
H2N O
NH2 OH NH2
Cysteine Methionine
Alanine.
Amino Acids which cannot form Glutamate and cannot undergo transamination are
Proline, Hydroxy- Proline, Lysine and Threonine.
Glucose– Alanine cycleisalsoknownas Cahill cycle – Transport of ammonia from
Muscles to Liver – occurs in Fasting Muscles.
Hyperammonemia Type I & Hyperammonemia Type II are most severe Urea Cycle
defects as ammonia is present in inorganic form which is highly toxic.
Arginine is the first line treatment of Urea Cycle Disorders but it is contraindicated
in Hyperargininemia.
Sodium Benzoate and Phenylbutyrate are Ammonia Scavenging Agents.
Deficiency of enzyme Arginosuccinate synthetase leads to Citrullinemia Type I.
Defect in Citrin Transporter (transports aspartate) leads to Citrullinemia Type II.
Phenyl Butyrate is more effective than Sodium Benzoate in treating Urea Cycle
disorders.
Increased Gluconeogenesis from Amino Acids increase Ureaformation.
Protein foods
Dipeptidases and Tripeptidases: Cleaves Di and Tri peptides into their individual
Amino Acids, which are absorbed.
Primary Structure: Sequence of Amino Acids joined by Peptide bonds.
α-helix is Rigid and Right handed - Only Interchain Hydrogen bonds present.
β-sheet has both Interchain and Intrachain Hydrogen bonds – fully extended chain
– may be parallel or anti- parallel.
Tertiary Structure: Single fully folded Functional Polypeptide chain.
Quaternary Structure: More than one fully folded Functional Polypeptide chains.
Mass Spectrometry.
Tandem Mass Spectrometry, also known as MS/MS or MS in the first stage of
2
CHAPTER
LIPIDS 6
LIPID BIOCHEMISTRY
Fatty Acid consists of a Hydrophobic Hydrocarbon Chain (Non-Polar) and a
Hydrophilic Carboxyl Group(Polar) whichisionized at pH 7. In case of Long Chain
Fatty Acids, the Non Polar Portion is predominant. In case of Short Chain Fatty
Acids, the Polar Portion is predominant.
Terminal Methyl Group in a Fatty Acid is called ω-carbon (omega).
ω-6 Essential Fatty Acids are Gamma-Linolenic Acid (18 C, 3 Double bonds),
Linoleic acid (18 C, 2 Double bonds), Arachidonic Acid (20 C, 4 Double bonds).
Most essential Fatty Acid is Linoleic Acid.
α-Linolenic Acid is the precursor of ω-3 category.
Linoleic Acid is the precursor of ω-6 category.
Cervonic Acid / Docosa Hexaenoic Acid (DHA) has 22C and 6 double bonds.
DHA is important for Brain development in Children and decreased amount leads
to increased risk of Retinitis Pigmentosa. DHA is present in high concentration in
Sperm, Retina, Cerebral Cortex. Constant source of DHA is Breast Milk.
Lipotropic Factors are the factors which are required for the synthesis of
Phospholipids. E.g. Essential FAs, Choline, Methionine. Their deficiency leads to
Fatty Liver.
Cholecystokinin is a Peptide Hormone which is released from Duodenum and
Jejunum in response to Lipid and Protein diet. This hormone helps Gall Bladder to
contract and also cause Pancreas to release it secretions.
Humans cannot introduce double bonds beyong Δ9 (delta 9) position.
Antioxidants are added in oils to prevent Rancidity (Hydrolytic cleavage of double
bond leading to formation of Short Chain Fatty Acids & Aldehydes).
LIPOPROTEINS
Lipids present in Lipoproteins are TGs, Phospholipids, Free Cholesterol
(unesterified) and Cholesterol Ester. TGs and Cholesterol Ester are neutral or totally
Non-Polar and lies in the core. Cholesterol and PLs are Amphipathic Lipids and lie
towards the periphery.
Proteins present in Lipoproteins are known as Apo Lipoprotein s or Apoproteins
and are synthesized in RER and Golgi Apparatus. They are Apo A-I, A-II, Apo B-48,
Apo B-100, Apo C-I, C-II, C-III and Apo E.
Lipoprotein s are Chylomicrons, Chylomicron remnant, VLDL (Very Low Density
Lipoproteins), VLDL remnant or IDL (Intermediate Density Lipoprotein s), LDL
(Low density Lipoproteins) and HDL (High density Lipoproteins) in the order of
increasing Density.
Density is directly proportionalto Percentage of Proteins andinverselyproportional
to TG Content and Size.
HDL has maximum density, so smallest size, has minimum TG content and
maximum Proteins.
In circulation, HDL donates Apo C and Apo E to Chylomicron and VLDL so that
they are converted to Chylomicron remnant and VLDL remnant.
Chylomicrons are largest insize.
Lipoprotein Lipase enzyme is synthesizedby Adipose Tissues, Cardiacand Skeletal
Muscles. This enzyme is activated byInsulin.
Chylomicrons carry Exogenous Lipid (or Exogenous TGs) from Intestine to
Peripheral Tissues.
Chylomicron remnant is degraded in Liver.
Lipids : 57
Endogenous fats are synthesized by Liver and transported in the form of VLDL. So,
VLDL transports endogenous TGs or Endogenous Lipids from Liver to Peripheral
Tissues.
Cholesterol is transported to Peripheral Tissues by LDL.
HDL takes Cholesterol from Peripheryto Liver: also known as Reverse Cholesterol
Transport.
HDL converts Cholesterol to Cholesterol Ester with the help of enzyme LCAT
(Lecithin Cholesterol Acyl Transferase). Apo A-I activates LCAT. LCAT transfers
FA from Lecithin (PL) to cholesterol. Lecithin after losing Fatty Acid becomes
Lysolecithin.
Main Ligand for LDL-Receptor is Apo B-100 and minor Ligand is Apo E.
Ligand for HDL-Receptor is ApoA-I.
Ligand for Chylomicron remnants & VLDL remnants is Apo E.
Apo C-I and Apo C-II activate Lipoprotein Lipase.
Apo C-III inhibits Lipoprotein Lipase.
Apo A-I activate LCAT.
Apo A-II inhibits LCAT.
HDL (cardioprotective) is known as α-Lipoprotein or Lipoprotein -A.
Deficiency of HDL leads to Tangier’s Disease.
LDL is known as β-Lipoprotein and is increased in DiabetesMellitus.
VLDLisknownasPre- β-Lipoprotein.
IDLisknownas Broadβ-Lipoprotein.
Lipoprotein ‘a’ has a structure similar to Plasminogen, so it interferes with
activation of Plasminogen to Plasmin, leading to Intravascular Thrombosis.
Therefore, it is associated with increased risk for Cardiovascular diseases. It contains
LDL and Apo ‘a’.
Lipoprotein A or HDL preventAtherosclerosis.
Lipoprotein ‘a’ causes Atherosclerosis (as it contains LDL).
Insulin enhances the action of Lipoprotein Lipase but only in the capillary beds of
Adipose tissue.
Hormone Sensitive lipase is activated by Glucocorticoids, Glucagon, Epinephrine,
Nor-Epinephrine, Dopamine and Growth Hormones.
HDL has maximum Electrophoretic Mobility.
LIPID METABOLISM
FA synthesis is an Anabolic pathway and occurs in Fed state and activated by Insulin
hormone.
Major site of Fatty Acid synthesis is Liver.
FA synthesis occurs in Cytoplasm.
Acetyl CoA (produced in Mitochondria) is the starting material for Fatty Acid
Synthesis.
RLE of Fatty Acid synthesis is Acetyl CoA Carboxylase (adds CO2 to Acetyl CoAto
make Malonyl CoA).
Malonyl CoA is the activated form in Fatty Acid Synthesis.
Main enzyme of FA synthesis is FattyAcid synthase complex/ Palmitate synthase
complex.
Fatty Acid synthase complex is a Multienzyme complex consisting of 6 enzymatic
activities: Ketoacyl synthase, Malonyl-Acetyl Transacylase, Hydratase, Enoyl
Reductase, Ketoacyl reductase and Thioesterase/Deacylase.
Lipids : 59
Malonyl Dehydratase
Enoyl Releasing
transacylase
enzyme
Acetyl reductase Ketoacyl
transacylase
reductase
Ketoacyl
synthase
ACP Thioesterase
4`-phospho-
Cys pantetheine
SH Subunit SH
SH division SH
Cys
4`-phospho-
pantetheine
Ketoacyl
synthase
Thioesterase
ACP Acetyl
Malonyl transacylase
Ketoacyl Enoyl transacylase
reductase Dehydratase
reductase
Fatty Acid Synthase Complex is a dimer consisting of two subunit and each subunit
attached to Acyl Carrier protein (has SulThydryl group with Phosphopanetheine).
Malonyl-Acetyl Tranacylase enzyme is involved in the loading of Acetyl CoA (2C)
and Malonyl CoA (3C).
Palmitic Acid / Palmitate is the first Fatty Acid synthesized denovo after 7 cycles of
Fatty Acid Synthesis.
Synthesis of one Palmitate requires 14 NADPH.
Cofactors required for Fatty Acid Synthesis are NADPH, Biotin & ATP.
Malate in Cytoplasm gets converted to Pyruvate by Malic enzyme which is a minor
source of NADPH.
Citrate Shuttle
60 : Lipids
Odd Chain Fatty acids can form Glucose (as they form Propionyl CoA) but Even
Chain Fatty Acids cannot.
β-oxidation of VLCFA occurs in Peroxisomes upto Octanoyl CoA, Rest in
Mitochondria.
Zelleweger Syndrome/ Cerebro-Hepato-Renal Syndrome occurs because of the
accumulation of Polyenoic Acids in Brain (containing >C22).
Zellweger Syndrome is the most severe Peroxisomal Biogenesis Disorder.
Cholesterol Synthesis occurs in all tissues. Acetyl CoA is starting material and
NADPH is used for Reductive Biosynthesis. ATP is also used.
First two steps in Cholesterol Synthesis are same as those in KB synthesis but
CHAPTER
MOLECULAR 7
CHEMISTRY & METABOLISM OF NUCLEOTIDES
Nucleic Acid is polymer of Nucleotides.
Nucleotide = Nitrogenous base + Sugar +
Phosphate.
Nucleoside = Nitrogenous base + Sugar.
requires Molybdenum.
Allopurinol is the Suicide Inhibitor of Xanthine Oxidase.
Molecular : 65
DNA is Helical (right handed) and the two strands are Antiparallel.
DNA is made up of four Nitrogenous bases : Adenine (A), Thymine (T), Guanine
(G) and Cytosine (C).
B-DNA and A-DNA are Right Handed whereas Z-DNA is Left Handed.
B-DNA is the major DNA in cells.
Z-DNA has a function in regulation of Gene Expression, particularly in GC sequence
(alternating Purine-Pyrimidine).
Gene Expresssion = Transcription +Translation.
Thymine (T) is present instead of Uracil (U) in DNA to prevent Mutations.
Cytosine gets converted to Uracil (by removal of amino group) very spontaneously
in DNA, by enzyme Cytosine Deaminase.
Main difference between DNA and RNA is Sugar i.e always Deoxyribose in DNA
and its always Ribose in case of RNA.
Chargaff’s Rule: Adenine must pair with
Thymine and Guanine with Cytosine with
weak Hydrogen bonds. The number of
Purines (A+G) is equal to the total number
of Pyrimidines (C+T) but the number
of (A+T) is not equal to (G+C), it can be
variable.
Nucleosomes = DNA +Proteins.
Histone Proteins have positive charges because they are rich in Basic Amino Acids
(Lysine, Arginine).
Due to opposite charge on DNA and Histone Proteins, they get tightly bound
forming Nucleosomes.
If DNA is separated from Histone, then it is free or is transcriptionally active.
PTMs(Post Translational Modifications) of Histones: These are reversible covalent
modifications in which N-terminal of Proteins is modified by adding or removing a
group and helps in regulation of GeneExpression.
Various ways of Histone Modifications are: Acetylation, Phosphorylation,
Methylation, ADP Ribosylation, Mono-Ubiquitylation and Sumoylation.
Molecular : 67
i.e. X and Y.
Homologous Chromosomes
are Chromosome Pairs (one
from each parent) that are
similar in Length, Gene Position,
and Centromere location.
The position of genes on each
Homologous Chromosome is
exactlysame, however, the genes
may contain differentalleles.
high frequency during each round of Mitosis. So Tumor Cell gives a different Genetic
Fingerprint than the host cell.
Variable number of Tandem repeats/VNTRs are also known as Mini-Satellites and
the repeat size is 15-70 base pairs.
Mitochondrial DNA: same like Prokaryotic
DNA i.e. Circular double stranded and no
Introns present.
Mitochondrial (DNA/mtDNA) is
synthesized by γ-Polymerase (gamma).
mtDNA has high rate of Mutation as
compared to Nuclear DNA.
mtDNA contains 16500 base pairs and 67
DNA Recombination or
Recombination DNA
Molecular Cloning is the
insertion of DNA fragments
to produce new Nucleotide
+
sequence arrangements.
70 : Molecular
Types of DNARecombination:
Homologous Recombination (HR)
Site Specific Recombination (SSR) or Non-homologousrecombination
Transposition
Site Specific Recombinase are the enzymes that catalyze DNA Exchange (direction
sensitive) between Short Target Site sequences (30- 40 nucleotides.) that are specific
to each Recombinase.
Examples of Site Specific Recombinase are CRE Recombinase, λ Phage encoded INT
protein , Yeast FLP Recombinase
CRE/Lox Recombinase associates specifically with the Lox P locus.
Transposition is highly specialized form of recombination in which a segment of
DNA moves from one location to another, either on the same chromosome or a
different chromosome.
Transposable Elements are known as Jumping Genes as these are DNA sequences
that can move from one chromosome locus toanother.
There are two types of TransposableElements:
Transposons
Retrotransposons
Transposons move by means of DNA Intermediate.
Retro Transposons move by means of an RNA Intermediate.
Small Scale Mutations (Micro Alteration) or Gene Mutation are Point Mutations,
Insertions and Deletions.
Point Mutations involve Transition and Transversion.
Transitions - Pyrimidine to Pyrimidine or Purine to Purine
Transversions - Pyrimidine to Purine or Purine to Pyrimidine
Each Aminoacid has morethan one codons, isknown as Degeneracyor Redundancy.
Point mutations are of three types namely Silent, Missense and Non Sense Mutations.
In Silent Mutation, Primary Structure of Protein always remain the same. Codon is
replaced by another codon which codes for same Amino Acid.
Silent Mutations occur due to Degeneracy of Codons (codon is changed but Amino
Acid is not changed). So Degeneracy prevents Mutations.
In Non Sense Mutation, Primary Structure of Protein will be changed, as there will
be premature Termination of Protein Synthesis due to introduction of Stop Codon.
In Missense Mutation, a Codon is replaced by another Codon coding for a different
Amino Acid.
Trinucleotide Repeat Expansion: a sequence of three bases that is repeated in
tandem will become amplified in number, so that too many copies of the triplet
occur.
Diseases due to Trinucleotide Repeat Expansion:
Hungington Disease
Fragile XSyndrome
Unbalanced Translocation.
In Robertsonian Translocation, there is joining of long arms of two chromosomes.
The tiny short arms are usually lost.
Aneuploidy is abnormal Chromosome Number. It can be Trisomy (three
chromosomes instead of two) or Monosomy (one chromosome).
DNA REPLICATION
Central Dogma of Molecular Biology: Theflow of information from DNAto RNA
and then to Proteins.
Reverse Transcription is the synthesis of DNA from RNA by enzyme RNA
Dependent DNA Polymerase.
Reverse Transcription occurs in Retroviruses such as HIV virus, Transposons and
Telomerase.
DNA Replication and Synthesis of Histones occurs in S-phase of Cell Cycle.
DNA Replication is Semi-Conservative in nature (one parental strand is conserved
each time).
Prokaryotes have one Origin of Replication (ori) while Eukaryotes have multiple
ori sites.
Ori is AT rich sequence and can be separated easily.
Topo-Isomerases cut and reseal DNA and relieves Positive Supercoiling without the
use of ATP and gain energy from the cleavage of Phosphodiester Bonds.
Type I Topo-Isomerases cut onestrand.
of two separated strands as they have high affinity for single strand and also protect
from Nucleases attack. These are not Enzymes.
RPA (Replication Protein A) In Eukaryotes, for prevention of Reannealing.
If any of the four substrates i.e dATP, dGTP, dCTP, dTTP is not available, DNA
synthesis stops.
DNA Polymerase I remove RNA Primers from both Leading and Lagging strand.
DNA Polymerase I has Polymerase (5’3’ Polymerase) activity and 3’5’
Exonuclease (Proofreading Activity) & 5’3’ Exonuclease Activity.
Klenow Fragment is a fragment of DNA Polymerase Iwhich has 5 3’ Polymerase
(TTAGGG)n.
Telomeres provide structural support to the Chromosome, prevent attack by
Telomerase is not a Ribozyme because this RNA is not used as enzyme. It is used as
a template for DNA synthesis.
Telomerase is RNA Dependent DNA Polymerase or Reverse Transcriptase.
Telomerase activity increases in Cancer and decreases in Aging.
Proofreading and DNA repair both are done by DNA Polymerase II in Prokaryotes.
Most Repairs occur in G1 phase of Cell Cycle. But Mismatch Repair occurs in G2
phase.
DNA Repair is done mainly by β-polymerase in Eukaryotes.
ε-polymerase has a minor role in DNA repair. Also has role in Leading Strand
Comparisonof prokaryoticandeukaryotic
DNA polymerase
E. coli Eukaryotic Function
I Remove primer and fill the gap
II Remove primer and fill the gap
β DNA repair
γ Microchondrial DNA synthasis
Ethidium, Actinomycin, Mitomycin are the inhibitors that directly interact with
DNA.
rRNA
tRNA
mRNA is the most Heterogenous RNA, synthesized in Nucleolus.
mRNA.
Bacterial/ Prokaryotic Ribosome: 70S comprising larger subunit 50S (5s, 23s
Gene.
Ribozyme means RNAactas Enzyme.
TypesofRNAPolymeraseinEukaryotes:
Type I – synthesize all rRNA except 5s rRNA
Type II – synthesize mRNA, mi-RNA, inc-RNA, few snRNA, snoRNA
Template Strand Strand where gene is present, also known as Anti-Sense/ Non-
Coding/ Minus strand.
Non Template Strand also known as Sense/ Coding/ Plus strand.
RNA Polymerase first binds with the Promoter Region (helps in initiation but
promoter region is not transcribed).
TATA box in Prokaryotes known as Pribnow Box present at -10 position on DNA
(10 base pairs upstream to the transcription startsite).
Molecular : 77
TATA box in Eukaryotes known as Hogness box present at -25 position on DNA
(25 base pairs upstream to the Transcription Start Site).
Upstream.
Substrate for Elongation step in Transcription is Ribonucleotide Triphosphates.
Two high energy Phosphates used to add one Ribonucleotide.
Termination of transcription may be Rho-dependent (ρ) or Rho-independent.
Rho-dependent Termination requires ρ-protein and uses ATP and Helicase activity.
It releases the RNA at Termination Site.
Inhibitors of Transcription are Actinomycin D, Rifamycin and α-Amanitin.
also known as RNA processing. These are Cap at 5’end, removal of Introns/ Splicing
and Tail at 3’end.
7-Methyl Guanosine Cap is added at 5’end of mRNA by Guanylyl transferase by
unusual 5’5’ Triphosphate Linkage.
Methyl group isdonatedbySAM byenzyme Guanine 7 methyltransferase (occurs
in cytoplasm).
Alternate Splicing and RNA Editing are exceptions to One Gene One Protein
theory.
Cap facilitates the initiation of Translation and stabilizes mRNA by preventing it
from attack by 5’ Exonucleases.
78 : Molecular
OPERON MODEL
Operator is a site on DNA that regulate the activity of the Gene by binding a Protein
known as Repressor.
Inducer can bind to Repressor and can remove Repressor from Operator site leading
to Gene Activation. Inducer is Lactose in Lac Operon.
Operon means a complete unit operating on itself. It has the capability to activate or
inhibit the Genes.
Operons are found in Prokaryotes.
O-site : Operator lies downstream to Promoter.
CAP site : lies Upstream of Promoter. CAP-cAMP Complex (trans acting protein)
binds here.
Lac Operon Genes are activated if glucose decreases in the environment of E.Coli
and if Lactose is present.
Molecular : 79
Lac I (Inhibitory) is a House Keeping Gene i.e. always active and has its own
Promoter.
Lac I produces Repressor Tetramer (a trans acting factor).
Lac Z codes for β-Galactosidase – breaks Lactose to Galactose and Glucose.
Lac Y codes for Permease – Facilitate permeation of Lactose into the cell.
Lac X codes for Transacetylase - Acetylates Lactose.
TRANSLATION
Codons are Nucleotide Triplets (3 nucleotides make 1 codon).
4 Nucleotide Bases used to produce three base Codons i.e. A, U, C, G.
Total number of Codons possible =64.
STOP Codons : UAA, UAG, UGA – do not code for any Amino Acid.
Methionine and Tryptophan have only 1 Codon i.e. do not show degeneracy.
Genetic Code is Unambiguous : each Codon is specific for its Amino Acid e.g. AUG
will always Code for Methionine.
Genetic Code is Universal i.e well conserved during evolution with only slight
differences.
Genetic Code is Non-Overlapping and Commaless.
There is Antiparallel binding between Codon and Anti-Codon in tRNA.
Wobble Hypothesis: Movement of first base of Anti-Codon can occur to allow non-
traditional base pairing with the last base of Codon. This movement is called Wobble,
which allows single tRNA to recognize more than one Codon.
Ribosomes are spherical bodies made up of RNA and Proteins. They are not
considered Organelles as they are Non-Membranous.
Mitochondria contain their own Ribosome (55s) and their own unique circular
dsDNA.
mRNA is translated in 5’3’ direction and Proteins are synthesized from Amino
terminal to Carboxy terminal.
Activation of Amino Acids or Charging of tRNA to make Aminoacyl tRNA is done
Hydroxy-Proline a derived Amino Acid does not require Amino Acyl tRNA
Synthetase.
Initiation Codon is AUG which Codes for Methionine in Eukaryotes and N-Formyl
Methionine in Prokaryotes.
Polymerase.
Pfu is used in conjunction with Taq Polymerase to obtain fidelity of pfu with the
when mixed with Manganese ions and thus can be used for the Amplification of
RNA to cDNA. It also has Polymerase activity.
Quantitative Flourescent PCR (QF-PCR) use STRs to detect Aneuploidy.
PCR is specific, simple, sensitive, flexible, rapid and relatively inexpensive technique
which amplifies DNA from low quantities and can work on damaged DNA.
PCR has many applications such as Structural Analysis, DNA Typing, Disease
Complex Translocations.
FISH tells Gene location on a Chromosome.
84 : Molecular
Conventional Karyotyping, FISH and CGH are cytogenetic techniques for Detection
of Mutations.
Down Syndrome : 3 copies of Chromosome 21
Edwards Syndrome : 3 copies of Chromosome 18
PatauSyndrome : 3 copies of Chromosome 13
FISH, RT-PCR, QF-PCR, MPLA are the methods for the detection of Specific
Chromosomal Aneuploidy.
Sperm Sorting (Microsort Method) – separate X-bearing (larger in size & has
more DNA) & Y-bearing sperms to be used for Artificial Insemination or In-Vitro
Fertilization.
Sanger’s Reagent is 1-Fluoro 2,4 Dinitro Benzene, used in DNA Sequencing.
Hybridomas are cells which are engineered to produce a specific Antibody in huge
numbers, or used as source of DNA or RNA for Gene Cloning, Sequencing or Gene
Manipulations.
RNA INTERFERENCE
RNA Interference/Gene Knock Down/Silencing Technique is a biological
phenomenon by which RNA molecules inhibit Translation.
Gene Knock Down - means Gene is present but its function is suppressed.
Gene Knock Out - means Gene isdeleted.
Micro RNA binds to 3’ end of target mRNA to inhibit Gene Expression.
Drosha workswithDGCR8 , alsoknownas PASHA. It cuts primary microRNA to
form pre-micro RNA.
Dicer cut pre-microRNA to form dsRNA (around 20 Nucleotides in length).
ss micro RNA combines with Proteins to form RISC (RNA-induced Silencing
Complex).
RISC can bind to the target mRNA and can just suppress it or degrade it by enzyme
Slicer/Argonaute/Ago.
siRNA (Silencing or small interfering RNA) is synthesized from cytoplasmic RNA
(e.g. tRNA or viral RNA) and can bind anywhere on the target mRNA.
CHAPTER
MISCELLANEOUS 8
in lysosomes.
Pompe’s disease is the only Glycogen Storage Disease which is a Lysosomal Storage
Vitamins those are necessary for Neurological Function are Thiamine, Pyridoxine
and Cobalamine.
Micronutrients required for Bones are Vitamin D (for Calcium Absorption),
Haem contains Fe .
+2
Albumin transports Most Steroids, T3, T4, Fat Soluble Hormones, Unconjugated
Bilirubin, Calcium, Magnesium and manydrugs.
Normal A/G ratio is 1.2-1.6.
Alpha- Feto Protein transports Long Chain Fatty Acids & Bilirubin.
H2O2 is not a free radical but it can generate Free Radicals. Precursor of all ROS is
Superoxide Radical.
MDA is not considered the Marker of Lipid Peroxidation.
FOX Assay – (Ferrous oxidation in Xylenol) is for the measurement of Free Radicals.
Lipids are most susceptible for Free Radical Damage (known as Lipid Peroxidation).
Peroxidase.
Diabetic situation isalmost samelike Fasting or Starvation Increasedβ-oxidation
Protein Precicipation can be done byHeat, Strong Mineral Acids, HeavyMetal Salts
used).
90 : Miscellaneous
Alport Syndrome.
Type VII Collagen (present at the junction of Dermis & Epidermis) is defective in
Epidermolysis Bullosa.
Fish Odour Syndrome/Trimethyl Aminuria - a rare Metabolic Disorder due to
Cognomen
Name Other Name
Sarcosine N-Methyl Glycine
Betaine Trimethyl Glycine
Choline Trimethyl Ethanolamine
Carnosine β-Alanyl Histidine
Anserine Carnosine on methylation
Homo Carnosine GABA + Histidine
Melatonin Acetyl Methyl Serotonin
Serotonin 5-OH Tryptamine
Ethanolamine Serine on Decarboxylation
Β-Mercapto Ethanolamine Cysteine on Decarboxylation
Creatine
Cysteine Cystine
Taurine
Glutathione
Creatinine
Histidine FIGLU
Histamine
Tryptophan Melanin
Catecholamines (Epinephrine,
Norepinephrine, Dopamine)
Thyroxine
Tyrosine Serotonin
Melatonin
Niacin
Homophones in Biochemistry
D and L Structural Isomers (Enantiomers
d and l Optical Isomers (Dextro-rotatory and Levo-
rotatory)
Racemic Mixture Equal d + l present(opticallyinactive)
Racemase Enzyme Enzyme which converts D and L (name
Racemase is misnomer)
Dextrin Hydrolytic Product of Starch
Dextran Branched, HMW Homopolysaccharide made up
of α-Glucose (used as Plasma Volume Expander)
Dextrose Solution of Glucose
Lactose Made up of Galactose + Glucose (Presentin
Lactulose Milk)
Made up of Galactose + Fructose (usedas
Laxative)
Lactate Dead end of Glycolysis, Produced in Anaerobic
Glycolysis
Lactase Enzyme which breakdown Lactose
(Disaccharide)
Lectin Carbohydrate Binding Proteins, which play a role
in Recognition and Attachment
Pectin Polysaccharide, acting as a Soluble Dietary Fibre
Lignin A complex organic polymer, which is the major
Insoluble Dietary Fibre
Insulin Hormone, secreted from β-Islet cells of Pancreas
Inulin A Homopolysaccharide, made up of β-Fructose,
also Ideal substance for GFR
Fructose1,6 Bisphosphate Involved in Glycolysis
Fructose1,6Bisphosphatase Involved in Gluconeogenesis
94 : Miscellaneous
Mucopolysaccharidosis (MPS)
Disease Name Enzyme Deficiency Substrate Accumulated
I H-Hurler α-L-Idouronidase *DS+#HS
(Autosomal Recessive)
I S-Scheie α-L-Idouronidase *DS
(Autosomal Recessive)
II Hunter Iduronate Sulfatase *DS+#HS
(X-linked Recessive)
VI Maroteaux Lamy Aryl Sulfatase B *DS
(Autosomal Recessive)
*DS – Dermatan Sulfate, #HS – Heparan Sulfate
Miscellaneous : 95
Hyperlipoproteinemias
Disease Name Enzyme Deficiency Substrate Accumulated
Type I/Familial Lipoprotein Lipase or Chylomicrons
Hyperchylomicronemia Apo C-II VLDL
(Autosomal Recessive) TGs (Triglycerides)
Type II-α/Familial Absent or Defective Cholesterol
Hypercholesterolemia LDL-Receptors or Apo LDL
(Autosomal Dominant) B-100
Type II-β/Familial Unknown defect VLDL
Hyperlipoproteinemia LDL
TGs
Cholesterol
Type III/ Dysbeta- Apo E Chylomicron remnant
Lipoproteinemia/ Broad VLDL remnant/IDL
Beta Disease TG
(Autosomal Recessive) Cholesterol
Sphingolipidoses
Disease Name Enzyme Deficiency Substrate Accumulated
Neimann-Pick Disease Sphingomyelinase Sphingomyelin
(Autosomal Recessive)
Gaucher’s Disease β-Glucosidase/ Glucosyl Ceramide
(Autosomal Recessive) Gluco-cerebrosidase
Krabbe’s Disease β-Galactosidase Galactosyl Ceramide
(Autosomal Recessive)
Fabry’s Disease α-Galactosidase Ceramide Trihexoside
(X-linked Recessive)
Farber’s Disease Ceraminidase Ceramide
(Autosomal Recessive)
Tay Sach’s Disease Hexosaminidase A GM2 Ganglioside
(Autosomal Recessive)
Sandhoff’s Disease Hexosaminidase A&B GM2 Ganglioside
(Autosomal Recessive)
Metachromatic Aryl Sulfatase A Cerebroside Sulfate
Leukodystrophy
(Autosomal Recessive)
GM1 Gangliosidosis β-Galactosidase
96 : Miscellaneous
Table of Vitamins
Name Active Form Function Deficiency Special Features
Vitamin B1/ TPP Oxidative Beri-Beri RBC
Thiamine (Thiamine decarboxylation Wernicke- transketolase
Pyrophos- reactions Korsakoff activity to be
phate) Transketolase Syndrome determined for
Phosphorylation biochemical
of chloride assessment of
channel in brain deficiency
Vitamin B2/ FMN Electron transfer (Rare) For detecting
Riboflavin/ FAD Riboflavinosis deficiency, RBC
Warburg Dermatitis glutathione
Yellow Angular reductase is
Enzyme Stomatitis assessed
Cheliosis Endogenously
synthesized by
bacterial flora
Vitamin B3/ NAD+ Electron transfer Pellagra Tryptophan
Niacin/ NADP+ (Diarrhea, synthesizes it
Nicotinic Dementia, 60mg
Acid/ Dermatitis, tryptophan
Nicotinamide Death) synthesizes 1mg
of Niacin
Vitamin B5/ Coenzyme Acyl carrier (Rare) Contains
Pantothenic A TCA Burning Feet β-Alanine in its
Acid ACP Haem synthesis Syndrome structure
Present in
CoA and Acyl
Carrier Protein
(ACP)
Vitamin B6/ PLP Transamination (Rare) Deficiency can
Pyridoxine/ (Pyridoxal Simple Neurological be induced by
Pyridoxam- Phosphate) Decarboxylation Manifestations Isoniazid
ine/ Trans- Epileptic
Pyridoxal Sulfuration convulsions in
infant
Miscellaneous : 99
Table of Minerals
Mineral Major Functions Deficiency
Sodium Na+/K+ ATPase pump Hyponatremia-
Major Extracellular Cation Excess Sodiumloss
excitability
Cofactor for enzymes e.g.
Pyruvate Kinase
Chloride Formation of HCl in stomach Hypochloraemia-
Regulation of osmotic pressure of Severe vomiting
Respiratory Acidosis
Metabolic Alkalosis
excitabilty
Miscellaneous : 101
certain enzymes
ENERGETICS
Number of ATPs in Anaerobic Glycolysis = 2 ATPs/glucose.
Number of ATPs in Aerobic Glycolysis = 7 ATPs/Glucose.
ATPs formed by Substrate Level Phosphorylation in Glycolysis are 4 ATPs.
ATPs formed by Oxidative Phosphorylation (ETC) in Glycolysis are 5 ATPs.
Number of ATPs in RBCs are never more than 2 , but it can be less than 2 if it is RL
(Rapaport Leubering) shunt.
Link reaction gives 5 ATPs (as 2 NADH produced) from two Pyruvate. From one
Glucose, two Pyruvate are obtained.
One Glucose on complete breakdown or complete oxidation = 32.
One Glucose in a Cancerous Cell gives 2 ATPs (Warburg’s effect).
One Acetyl CoA = 10 ATPs.
One Palmitic Acid (16 C) =106.
One Stearic Acid (18 C) = 120.
2 pyruvate to glucose 4 ATP & 2 GTP used.
2 lactate to glucose 4 ATP & 2 GTP used.
2 alanine to glucose 4 ATP & 2 GTP used.
IMAGE BASED
104 : Image Based
Organelles of a cell
Benedict’s Test
Blue solution Green / yellow ppt Orange red ppt Brick-red ppt
No sugar present Traces of sugar Moderate amount Large amount sugar
present sugar present present
Powder puff/hedge hog shaped crystals of Sun flower shaped maltosazone crystals
lactose as viewed under the microscope as viewed under the microscope
Albinism
Gaucher’s cell
Reilly bodies
Reilly bodies, also known as Alder-Reilly bodies are found in many mucopolysaccharidosis
e.g. Hurler disease & Maroteaux-Lamy syndrome. The picture shows a neutrophil with
highly lobulated nucleus. They sometimes resemble toxic granulations, but reilly bodies are
not related to infecti on and are not transient in nature. These are metachromatic granules,
surrounded by a clear zone. These are present in the cytoplasm of all leukocytes including
neutrophils.
108 : Image Based
Enzymes