BIOCHEMISTRY medpgnotes
BIOCHEMISTRY
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1 GENERAL BIOCHEMISTRY
CONTENTS GENERAL BIOCHEMISTRY .............................................................................................................................................. 6
GENERAL FEATURES OF BIOCHEMISTRY ................................................................................................................... 6
STUDIES ..................................................................................................................................................................... 6
BONDS ....................................................................................................................................................................... 6
PH AND BUFFERS ...................................................................................................................................................... 7
ENERGY ..................................................................................................................................................................... 7
PATHYWAYS IN CYTOSOL AND MITOCHONDRIA ...................................................................................................... 7
CARBOHYDRATES .......................................................................................................................................................... 8
EPIMERS AND ENANTIOMERS ................................................................................................................................... 8
STRUCTURE OF CARBOHYDRATES............................................................................................................................. 8
GLUCOSE TRANSPORTERS ....................................................................................................................................... 10
CORI CYCLE .............................................................................................................................................................. 10
GLUCOSE ................................................................................................................................................................. 10
GLYCOLYSIS ............................................................................................................................................................. 12
ACETYL COA ............................................................................................................................................................ 13
KREB’S CYCLE .......................................................................................................................................................... 13
GLUCONEOGENESIS ................................................................................................................................................ 15
GLYCOGENOLYSIS .................................................................................................................................................... 15
ELECTRON TRANSPORT CHAIN ................................................................................................................................ 16
HMP SHUNT ............................................................................................................................................................ 17
GLUCOSE 6 PHOSPHATE DEHYDROGENASE DEFICIENCY ........................................................................................ 18
FRUCTOSE METABOLISM ........................................................................................................................................ 18
LACTOSE METABOLISM ........................................................................................................................................... 19
GENERAL FEATURES OF GLYCOGEN STORAGE DISORDERS .................................................................................... 19
VON GIERKE’S DISEASE ........................................................................................................................................... 20
DISORDERS OF GALACTOSE METABOLISM ............................................................................................................. 20
SUBSTRATE LEVEL PHOSPHORYLATION .................................................................................................................. 21
LIPIDS .......................................................................................................................................................................... 21
FATTY ACIDS ............................................................................................................................................................ 21
SYNTHESIS OF FATTY ACIDS .................................................................................................................................... 23
OXIDATION OF FATTY ACIDS ................................................................................................................................... 24
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GENERAL FEATURES OF LIPOPROTEIN .................................................................................................................... 24
LIPOPROTEIN LIPASE ............................................................................................................................................... 24
CHYLOMICRON ........................................................................................................................................................ 25
LDL........................................................................................................................................................................... 25
VLDL ........................................................................................................................................................................ 26
HDL .......................................................................................................................................................................... 26
APOPROTEIN ........................................................................................................................................................... 27
CHOLESTEROL ......................................................................................................................................................... 27
HYPERCHOLESTEROLEMIA ...................................................................................................................................... 28
XANTHOMA ............................................................................................................................................................. 28
ABETALIPOPROTEINEMIA ....................................................................................................................................... 29
BILE ACIDS ............................................................................................................................................................... 29
KETONE BODIES ...................................................................................................................................................... 29
STARVATION ........................................................................................................................................................... 30
AMINOACIDS ............................................................................................................................................................... 30
GENERAL FEATURES OF AMINOACIDS .................................................................................................................... 30
PROLINE .................................................................................................................................................................. 32
VALINE ..................................................................................................................................................................... 32
LEUCINE................................................................................................................................................................... 32
ARGININE ................................................................................................................................................................ 32
HISTIDINE ................................................................................................................................................................ 32
GLYCINE ................................................................................................................................................................... 33
ALANINE .................................................................................................................................................................. 33
PHENYLALANINE ..................................................................................................................................................... 33
TYROSINE ................................................................................................................................................................ 33
TRYPTOPHAN .......................................................................................................................................................... 34
CYSTEINE ................................................................................................................................................................. 34
METHIONINE ........................................................................................................................................................... 34
HOMOCYSTEINE ...................................................................................................................................................... 34
ASPARTATE .............................................................................................................................................................. 35
GLUTAMATE ............................................................................................................................................................ 35
GLUTAMINE ............................................................................................................................................................ 35
LYSINE ..................................................................................................................................................................... 35
GLUTATHIONE ......................................................................................................................................................... 36
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CREATININE ............................................................................................................................................................. 36
GENERAL FEATURES OF DISORDERS OF AMINOACID METABOLISM ...................................................................... 36
PHENYLKETONURIA................................................................................................................................................. 36
MAPLE SYRUP URINE DISEASE ................................................................................................................................ 37
MULTIPLE CARBOXYLASE DEFICIENCY .................................................................................................................... 37
HARTNUP DISEASE .................................................................................................................................................. 38
ALKAPTONURIA ....................................................................................................................................................... 38
AMMONIA ............................................................................................................................................................... 38
UREA ....................................................................................................................................................................... 39
GLUTAMATE DEHYDROGENASE .............................................................................................................................. 39
DISORDERS OF HEME SYNTHESIS ............................................................................................................................ 40
PORPHYRIN AND PORPHYRIA ................................................................................................................................. 40
PROTEINS AND ENZYMES ............................................................................................................................................ 41
STRUCTURE OF PROTEIN ......................................................................................................................................... 41
DETERMINATION OF PROTEIN STRUCTURE ............................................................................................................ 42
GLYCOPROTEINS ..................................................................................................................................................... 43
PROTEOGLYCAN ...................................................................................................................................................... 44
TYPES OF PROTEIN .................................................................................................................................................. 44
ESTIMATION OF PROTEINS ..................................................................................................................................... 44
DENATURATION OF PROTEINS ................................................................................................................................ 44
SEPARATION OF PROTEINS ..................................................................................................................................... 45
GENERAL FEATURES OF ENZYMES .......................................................................................................................... 46
OXIDASE .................................................................................................................................................................. 46
OXYGENASE ............................................................................................................................................................. 46
DEHYDROGENASE ................................................................................................................................................... 46
HYDROLASE ............................................................................................................................................................. 47
TRANSFERASE.......................................................................................................................................................... 47
LIGASE ..................................................................................................................................................................... 47
LYASE ....................................................................................................................................................................... 47
HOLOENZYME ......................................................................................................................................................... 47
TRANSAMINATION .................................................................................................................................................. 47
SERINE PROTEASE ................................................................................................................................................... 48
ENZYME INHIBITION ............................................................................................................................................... 48
ENZYME REGULATION............................................................................................................................................. 48
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RIBOZYMES ............................................................................................................................................................. 49
ISOENZYMES ........................................................................................................................................................... 49
COMPONENTS OF ENZYMES ................................................................................................................................... 49
COENZYMES AND COFACTORS FOR ENZYMES ........................................................................................................ 50
INFORMATIONAL MACROMOLECULES ....................................................................................................................... 50
PURINE METABOLISM ............................................................................................................................................. 50
PYRIMIDINE METABOLISM ...................................................................................................................................... 51
STRUCTURE OF DNA ................................................................................................................................................ 51
HISTONE .................................................................................................................................................................. 53
MITOCHONDRIAL DNA ............................................................................................................................................ 54
TELOMERASE ........................................................................................................................................................... 54
REPLICATION OF DNA ............................................................................................................................................. 54
GENETIC CODE ........................................................................................................................................................ 55
INTRONS AND EXONS.............................................................................................................................................. 56
MUTATION .............................................................................................................................................................. 56
REGULATION OF DNA.............................................................................................................................................. 57
GENERAL FEATURES OF TRANSCRIPTION ............................................................................................................... 57
RNA POLYMERASE ................................................................................................................................................... 58
POST TRANSCRIPTIONAL MODIFICATION ............................................................................................................... 58
SPLICING .................................................................................................................................................................. 59
rRNA ........................................................................................................................................................................ 59
mRNA ...................................................................................................................................................................... 59
tRNA ........................................................................................................................................................................ 59
MICRORNA .............................................................................................................................................................. 60
RIBOSOMES ............................................................................................................................................................. 60
TRANSLATION ......................................................................................................................................................... 60
POST TRANSLATIONAL MODIFICATION .................................................................................................................. 62
PROTEIN FOLDING .................................................................................................................................................. 62
INBORN ERRORS OF METABOLISM ............................................................................................................................. 63
GENERAL FEATURES OF INBORN ERRORS OF METABOLISM .................................................................................. 63
TAY SACH’S DISEASE................................................................................................................................................ 63
GAUCHER’S DISEASE ............................................................................................................................................... 64
NIEMANN PICK DISEASE .......................................................................................................................................... 64
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5 GENERAL BIOCHEMISTRY
KEY TO THIS DOCUMENT
Text in normal font – Must read point.
Asked in any previous medical entrance
examinations
Text in bold font – Point from Harrison’s
text book of internal medicine 18th
edition
Text in italic font – Can be read if
you are thorough with above two.
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6 GENERAL BIOCHEMISTRY
GENERAL BIOCHEMISTRY
GENERAL FEATURES OF BIOCHEMISTRY
Presence of 2 extra pairs of electrons on the oxygen in water molecule results in
Electronegative charge on water molecule
Monoprotic acids Formic acid, Acetic acid, Nitric acid
Diprotic acid Carbonic acid, succinic acid, glutaric acid Tripotic acid Citric acid Crystal Molecules are arranged in same conformation and
same orientation
Farnesyl diphosphate is used in synthesis of Ubiquitin, Dolichol, Cholesterol
Shell formation in Mollusc Biomineralisation
Most accurate method of blood creatine estimation Jaffe method
STUDIES
Bioinformatics deals with Economics
Oldest and widely used bioinformatics database
Genbank, uniport, protein database
Bioinformatics is associated with Computer science, statistics, mathematics, engineering
Biotechnology is used for Viral vaccine production, To cure genetic disorder, Genetic crop, Gene production, Complete collection of gene copies of one organism
Study of structure and products of gene Genomics
Study of multiplication of proteins in disease process is called
Proteomics
Study of multiplication of proteins in a disease process Proteomics
Techniques used for protein expression proteomics study include
Gene array chips, two dimensional electrophoresis
BONDS
Drugs interact with their receptor sites by Ionic bonds
Strongest bond Electrostatic
Covalent bond Electrons have opposite spin
Weakest Bond Vander wall forces
Force NOT involved in antigen antibody reactions Covalent bond
NOT a force acting in enzyme substrate complex Vander walls
High energy phosphate bond (produce ATP on hydrolysis)
Creatine phosphate, Carbomyl phosphate. ATP,GTP,UTP, Co A derivatives
High energy compound on hydrolysis yield high standard free energy
Phosphoenolpyruvate
NOT a high energy bond substance CoA
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Component making carbon bond of a molecule least polar
Carboxyl
PH AND BUFFERS
In a solution, concentration of H+ is 1*10^-6 moles/litre. pH of the solution
6
Number of pKa values possessed by Orthophosphoric acid
3
Buffering capacity of a buffer is maximum at pH equal to
pKa
High pKa lowers its Acidic nature A buffer that is most effective at a pH of about 4.5 Acetate buffer
Blood buffers Bicarbonate, Plasma proteins, Hemoglobin
Buffering capacity of Interstitial fluid is greatest by Bicarbonate
Most powerful extracellular buffer Bicarbonate Most important buffer in RBC H2Co3 + NaHCO3
Most important buffer in ECF Bicarbonate
Intracellular buffer Phosphate
ENERGY
Energy required for basal metabolism 1 kcal/hour/kg of body weight
Difference between reversible and irreversible reaction Work done
Entropy Measure of randomness in a system
Entropy in biological system does NOT increase because It is a open system
Largest reserve of energy in body stored as Adipose tissue
Adipose tissue lacks Glycerol 3 kinase Main source of energy derived from Glycogen
Specific dynamic action is Energy expanded on consumption of food
Best source of energy Lean meat
Energy emitted following absorption of EM radiation Phosphorescence
Heart at rest utilizes Fatty acid
Metabolism in brain Fatty acids are NOT utilized in starvation, Ketone bodies are used during starvation, 60% of total energy is obtained in resting state, Has no stored energy
Descending order of energy Fat > alcohol > carbohydrate
PATHYWAYS IN CYTOSOL AND MITOCHONDRIA
Creatine Phosphokinase is both Mitochondrial and Cytoplasmic
Pathway occurring both in mitochondria & cytosol Heme synthesis, Gluconeogenesis, Urea cycle
De novo fatty acid synthesis Cytosol
Glycogenesis occurs in Cytosol Glycolysis occur in Cytosol
Pathways occurring in mitochondria Beta oxidation of fatty acids, citric acid