Transcript Document

THE NUCLEIC ACIDS
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Friedrich Miescher in 1871
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Isolated what he called nuclein from the nuclei of
pus cells
Contain phosphates
Nuclein was shown to have acidic properties,
1889 Altman called it as nucleic acid
© 2007 Paul Billiet ODWS
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Watson & Crick (1953)
Structural model for DNA (Nobel prize 1962)
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STRUCTURE OF NUCLEIC ACID
Nucleoproteins
H2O
NA
+ Protein
H2O
Nucleotides
Nucleosides
+ H3 PO4
2 purine bases +
2pyrimidine bases +
A pentose sugar
© 2007 Paul Billiet ODWS
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Purine base or Pyrimidine base
Pentose Sugar
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Nucleosides
Two components
1. Pentose Sugar - Ribose
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or
2-Deoxyribose
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Nucleosides contd…
2. Heterocyclic Nitrogenous base
 Substituted Purine or Pyrimidine
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Purine nucleosides
Base
O
H
sugar
Adenine
H
Nucleoside
β - Glycosidic link
Adenosine
2-deoxyadenosine
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Base
O
sugar
4
3
2
Pyrimidine nucleosides
5
2
6
1
4
3
5
4
2
1
6
1
H
Thymine
H
5
4
3
3
6
2
1
5
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β - Glycosidic
link
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Ribose – thymine & 2-deoxy-uracil not found
among the hydrolytic products of natural NA
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Nucleotides
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1.
2.
3.
Three components
Pentose sugar
Heterocyclic Nitrogenous base
Phosphate group
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Base
Phosphate
H3PO4
+
P
O
O
sugar
Nucleoside
sugar
Base
Nucleotide
Nucleotides are phosphate esters of nucleosides
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O
HO
P
Phosphoric acid
OH
OH
O
HO
- H2O
Adenosine
P
OH
Adenosine monophosphate
(a ribonucleotide)
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O
O
HO
P
HO
P
OH
OH
OH
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Thymidine
2
5
Thymidine monophoshate
(a deoxyribonuxleotide)
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Nucleic acids
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Very high molecular weight polynucleotides
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Important biopolymers of cells
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Responsible for biosynthesis of proteins and
transmission of hereditary character.
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Nucleic acids
P
P
G
G
P
P
C
C-5’ – C-3’
P
C
Phosphodiester linkage
P
C
C
P
P
A
A
P
P
T
T
P
P
T
Nucleotides
Biological properties are determined by
the sequence of bases
T
Polynucleotide or
Nucleic acid
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Two types
Ribonucleic acid (RNA)
Deoxyribonucleic acid (DNA)
 Sugar unit – Ribose
 Sugar unit – Deoxyribose
Nitrogenous bases – Adenine,
Guanine (purines)
+
Cytosine, Uracil (Pyrimidines)
Nitrogenous bases – Adenine,
Guanine (purines)
+
Cytosine, thymine (Pyrimidines)
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Structure of RNA
Single stranded
Some portions aquire double
helical pattern
A-U
G-C
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Types of RNA
1.
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mRNA or template RNA
Single stranded
Some degree of coiling: no base pairing
Most stable & heterogeneous in size
Mol mass: 30000-50000
Free state in cyttoplasm or associated with ribosomes
5% of total cellular RNA
Carries genetic information from chromosomal DNA
to ribosomes for protein synthesis
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2. tRNA or soluble RNA
Single stranded
 Bending and looping to clover leaf pattern
 Smallest polymeric form of RNA
 Mol mass: 25000
 70-100 neucleotide units
 Occurs in cytoplasm
 15% of total cellular RNA
 Carry specific AA from AA pool of cytoplasm
to ribosome
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3. rRNA
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Single stranded
High degree of coiling; double helical
regions
Highest mol mass: 1.2x 106
Most abundant (80%)
Present in ribosome
Provide correct orientation to mRNA
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Structure of DNA
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Sugar- deoxy ribose
Bases: A, G …..purine
T, C ….. Pyrimidine
Two polynucleotide chains: Double helical
A :T… 2 H bonds
G:C…..3 H bonds
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Two strands: complementary but not identical
A T G C T T A C
T A C G AA T G
Diameter 20Ao Avg distance between two adj.
base pairs= 3.4 Ao
10 base pairs / turn
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Biological functions
1. Replication
2. Protein synthesis
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Biological functions
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1. Replication
DNA Contain genetic information as specific base
sequence
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Protein synthesis
Genetic code: Genetic information for protein synthesis :
sequences of bases in DNA
Message in A G C T language
Message Read, translated & expressed
Two steps
 Transcription
 Translation
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1. Transcription
Transcribing genetic information from DNA to mRNA
Process
• Unwind DNA helix
• One acts as template for synthesis of mRNA
• Build-up of complementary nucleotides along template DNA
strand : enzyme RNA polymerase
• According to Base pairing principle
DNA : A C G T
mRNA: U G C A
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• DNA return to its original double helical structure
mRNA diffuses from nucleus to cytoplasm
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2. Translation
Transferring the transcribed information from mRNA to
polypeptide chain to get specific protein
Process
 Cytoplasm : mRNA attached to rRNA –protein combination
and genetic code deciphered
 Triplet of base along mRNA codes particular AA: codon
Eg: GGA : glycine
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All 20 AA have triplet code
 Transcribed code in mRNA read by tRNA
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tRNA looped structure
On one of its loops it carries a triplet of bases;
anticodon
One of its trailing end AA ( AA pool)is
attached through high energy ester bond
catalyzed by aminoacyl-tRNA synthetase
tRNA transport AA to the correct site of
mRNA on ribosome particles
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tRNA Structure
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tRNA line up on mRNA through H bonding
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Each codon on mRNA is matched by its
complementary tRNA anticodon
Eg: mRNA codon:
GGC
tRNA anticodon: C C G glycine
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AA linked through peptide bonds form
polypeptide chain (protein) catalyst: peptide
synthetase
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Protein released from ribosome
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Genetic Code
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AA sequence of proteins is predetermined in DNA
which is transcribed to mRNA
Genetic Code: The nucleotide base sequence of DNA
that specifies the AA sequence of protein
4 bases of mRNA code for all 20 AA in polypeptide
chains of various
If one base for one AA; 41 = 4: only 4 AA can be
specified
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2 base for 1 AA; 42 = 16 doublet codes; 16 AAs
can be specified
3 base for 1 AA; 43= 64 triplet codes; more than
sufficient for 20 AAs
Only 20 AAs but 64 triplet codes
More than one code for some AAs
Some combinations are not code for AAs
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Codon: Each triplet of bases strung consecutively along
mRNA molecule that codes for particular AA
Codon
Sense codon
Non-sense
codon
Non-sense codon: stop or termination codon: signals the
termination of protein synthesis
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64 Codon
61Sense codon
3 ( UAA, UAG,
UGA)
Tryptophan (UGG) & methionone (AUG) : 1 codon each
Others : many codons
Sense codon which code for same AA: degenerate or synonymous
codon
Eg: GGU, GGC, GGA, GGG code glycine
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Mutation
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Alteration in the sequence of nucleotide bases of
DNA molecule
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Can ocuurs spontaneously or brought about by
external agents
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Lead to abnormal changes in DNA replication &
the defect may pass along to the next generation as
an inherited factor
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Mutation (contd…)
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Lead to production of protein with altered AA sequence:
affect biological activities and lead to abnormalities and
deseases
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Possibility for the development of cancerous cells
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Causes: some chemicals Hydroxylamine NH2OH
high energy radiations (x-rays, gamma rays)
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Disrupt some bonds in DNA molecule and will re-form in
another sequence\
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Thymine dimerisation
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28-10-2013
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Enzymes
Biological catalysts
Reactions are successful, efficient and high rate
1860: Louis Pasteur detected enzymatic activity in living
cells- ferments
1878: Friedrich Kuhne introduce the term Enzyme = ‘in
yeast’
1897; Edward Buchner extracted enzyme from yeast cells
1926: James B. Summer isolated an enzyme in pure
crystalline form (urease)
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Enzymes
> Biological catalyst
> Catalyze biochemical reactions in the cells
> Capable of acting independently of the cells
> Highly specialized class of proteins
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N H2CONH2 + H2O …….> 2NH3 + CO2 (urease)
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C12H22O11 + H2O ……> 2 C6H12 O6 ( maltase)
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Biochemistry : enzymology
Living cells require thousands of different enzymes to
catalyse the metabolism of carbohydrates, fats, proteins, etc
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Endoenzymes: eg:- Respiratory enzymes
Exoenzymes: eg:- digestive enzymes
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Chemical nature of enzymes
 Chemically high molecular mass globular proteins
Simple protein enzyme: molecular structure are made
up of α- aminoacid units only
Eg:- pepsin, trypsin amylase, etc
Conjugated protein enzyme: contain a non-protein part
with protein part
Protein part: Apoenzyme
Non-protein part: co-factor
Apoenzyme + co-factor = holoenzyme
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Chemical nature of enzymes
Neither cofactor nor apoenzymes can be active
 Only combination can show catalytic activity
 Cofactor: bridge between Apoenzyme and substrate
 If cofactor firmly bound to apoenzyme: Prosthetic
group
Eg: Fe-porphyrin combination in cytochrome
Fe – heme combonation
 Cofactor : inorganic moeity(Mg2+, Ca2+, Zn2+.etc) :
activator
or organic moeity ( B- vitamin)- coenzyme
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General characteristics
A. Functional
1. Efficient: Increase the speed up to 10 million times that of
uncatalyzed reactions
2. Unalterability
3. Small quantity
4. Speed up the attainment of equilibrium, but not alter the
position
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5. Specificity: Choosy about substrate
Eg: Urease: hydrolysis of urea
Alcohol dehydrogenase: dehydrogenation of
primary alcohols
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B. Condition characteristics (Factors influencing enzyme action)
1. pH: optimum pH- at which catalytic efficiency will
become maximum
 for most enzymes optimum pH around 7
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gastric enzyme pH around 2
2. Temperature: Optimum temp.: maximum catalytic
activity
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Animal enzyme: 35- 45oC
 Plant: 40- 60oC
 High temp. activity lost due to denaturation
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3. Susceptibility to the action of enzyme regulators
Regulators
Inhibitors
Activators
Increase the catalytic activity of
enzymes
Eg: Zn 2+ : alcoholic dehydrogenase
Mn 2+ or Co 2+ : arginase
Decrease or destroy the catalytic activity of
enzymes
Eg: Ag+,, Hg2+, Pb2+,etc: urease
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4. Dependence on substrate concentration
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© 2007 Paul Billiet ODWS
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Theory of enzyme catalysis
1. Michaelis-Menten Theory
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Koshland’s Induced fit hypothesis
Active site: flexible and elastic
Substrate induces some configurational
changes in active site
New configuration perfectly matching
with that of substance
The active site is reverts to its original
configuration after the product is detached
from the enzyme
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Koshland’s Induced fit hypothesis
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PART IV
CELLULAR ENERGETICS &
METABOLISM
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Biochemical reactions
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Anabolism:
Simple molecules + Energy .…> macromolecules
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Catabolism
Macromolecules ……> simple molecules + energy
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Anabolism + catabolism = metabolism
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CELLULAR ENERGETICS: Thermodynamics
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Gibbs- Helmoltz eqn: ∆G = ∆ H -T ∆ S
Feasible (spontaneous) : ∆G = -ve
∆G = -ve : exergonic reactions (Catabolism)
Eg: step wise degradation of sugar … CO2 + H2O
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∆G = +ve : endergonic reactions (anabolism)
Eg: amino acids ….> peptides
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Coupled reactions
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If ∆ G +ve , coupled with reactions having large & -ve ∆
G so that net ∆ G –ve : coupled reactions
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Coupling is a fundamental mechanism of bioenergetics
All energy requiring processes proceed by coupling
A ……> B ; ∆ G > 0 (endoenergetic) ----- (1)
P……> R ; ∆ G < 0 (exoenergetic) ------(2)
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(1)
+ (2)
P
R+E
∆ G = (∆ G1 +∆ G2) < 0
A+E
B
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Not direct
Two taking place at different time & at different place in the
cell
Link between exo- and endo-energetic reactions
Adenosine TriPhosphate
Energy released first used to generate ATP
ATP on hydrolysis
ADP + Energy
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Store and transport the energy of catabolic
reactions
Anabolic reactions taking place at proper site,
time and rate
ATP: Nucleotide
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Oxidation
Food
ADP + P
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ATP
ADP
E
Products + E
ATP
ADP + P ΔG = -31 kJ/mol
AMP + P
ΔG = -28.5 kJ/mol
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Not a long term storage form of energy
Consumed at a high rate : stock in the cell is very
small
As it is being used up, it has to be replenished: need
energy
Phototrophs (algae, plants, some bacteria) use solar
energy: photosynthesis
Chemotrophs ( eg; S-bacteria, nitrifying bacteria)
use chemical energy from oxidation of inorganic
compounds
heterotrophs (humans animals, etc) consume
biomolecules produced by photoptrophs
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Biological role
 Reservoir of chemical bond energy
 Link between endergonic & exergonic reactions
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hydrolysis
ATP
ADP + Energy(cell functions:
muscle movement, uptake of nutrients, etc)
Indispensible for the transport of substances across
the cell membrane
Energy source of all cellular reactions: universal
energy currency of the cell
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Metabolism
o
o
o
o
o
o
molecular processes by which living system acquire
and utilize energy needed for life processes
Aggregate of biosynthetic and biodegradative
processes
Anabolism
Catabolism
Coupling reaction
ATP
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Energy need for the synthesis of ATP
 Catabolism of carbohydrates, lipids and proteins
 Before synthesis of ATP, nutroients have to be digested and
absorbed into body/ body fluid
Digestion: breakdown of ingested complex foodstuff into simple
molecules by hydrolysis\
 Small molecules can be absorbed through the walls of
alimentary canal into body luids and used for metabolism
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Carbohydrate: simple sugars
Lipids: fatty acids
Proteins:AA
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METABOLISM OF LIPIDS
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Digestion …..> fatty acids
Metabolism of lipidS = catabolism of fatty acids
First stage: β-oxidation
fatty acid cycle (spiral)
Catalyzed by a set of enzymes : fatty acid oxidases
1st stage : fatty acid cycle’
2nd stage: Krebs cycle
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Fatty acid cycle (spiral)
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NAD+ and FAD : oxidizing agents, reduced to NADH &
FADH2
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Under cytochrome series NADH & FADH2
and FAD + ATP: electron transport chain
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Most of the associated energy is released & stored in this
stage of lipid metabolism
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β-oxidation + Krebs cycle +
electron transport chain)
NAD+
(stearic acid )
147 ATP molecules
45% stored energy + 55% dissipated as heat
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METABOLISM OF PROTEINS
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1.
2.
Proteins:AA
1st step: elimination of amino group: α-keto acid
Two group transfer reactions
Oxidative deamination
Transamination
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Oxidative deamination
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AA is converted to keto acid by NAD+ or FAD:
amino acid oxidases
NH2 …..> NH3 …….> Urea (excreted)
Significant for Glutamic acid: α-ketoglutaric acid
is an intermediate in Krebs cycle
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Transamination
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AA and α-keto acid mutually exchange their NH2 and
CO groups
Catalyzed by transaminases having coenzyme;
pyridoxal phospahte
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Pyruvic acid converted into acetyl coenzymeA, then degraded
through Krebs cycle
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Aspartic acid …….> oxaloacetic acid
COOH- CHNH2- CH2-COOH …..> COOH – CO CH2-COOH
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All AA can make their way to the Krebs cycle
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2nd stage: Krebs cycle and electron transport chain
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Deaminated moeity oxidised to CO2 + H2O + ATP
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Wilkins & Franklin (1952): X-ray
crystallography
© Norman Collection on the History of Molecular Biology in Novato, CA
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