Nutritional Biochemistry-1

Prepared by-
Mohammad Asadul Habib
Lecturer,
Department of Food Technology and Nutrition Science
Noakhali Science and Technology University
Rationale of this course

• Should be aware about the biochemical mechanisms associated with

the macronutrients, dietary fiber and enzymes in food biochemistry.
• Nutritional biochemistry introduces the structural and functional
characteristics of macronutrients (carbohydrates, lipids and proteins),
dietary fiber and enzymes in food that are consumed by humans.
• This course will aware about influence of nutritional biochemistry on
diet therapy and practicum subjects
Objectives of this course
1. Explain the biochemical absorption and metabolic function of
macronutrients, dietary fiber and enzymes
2. Describe the role of nutrients in the optimal functioning of key
biochemical pathways in the body
3. Integrate biochemical mechanisms with a coherent argument for the
use of nutrient supplementation and food therapy for maintaining and
promoting health and wellbeing through optimal biochemical pathway
functions
Different Methods of Degradation of Amino
Acids
Amino acid structure and its
classification
• An amino acid contains both a carboxylic group and an amino
group. Amino acids that have an amino group bonded directly to
the alpha-carbon are referred to as alpha amino acids.
• Every alpha amino acid has a carbon atom, called an alpha
carbon, Cα ; bonded to a carboxylic acid, –COOH group; an
amino, –NH2 group; a hydrogen atom; and an R group that is
unique for every amino acid.
Classification based on structure
1.Amino acids with aliphatic side chains : These are monoamino monocarboxylic acids. This group
consists of the most simple amino acids—glycine, alanine, valine, leucine and isoleucine.
2.Hydroxyl group containing amino acids : Serine, threonine and tyrosine are hydroxyl group
containing amino acids. Tyrosine—being aromatic in nature—is usually considered under aromatic
amino acids.
3.Sulfur containing amino acids : Cysteine with sulfhydryl group and methionine with thioether group
are the two amino acids incorporated during the course of protein synthesis.
4.Acidic amino acids and their amides : Aspartic acid and glutamic acids are dicarboxylic monoamino
acids while asparagine and glutamine are their respective amide derivatives. All these four amino
acids possess distinct codons for their incorporation into proteins.
4.Basic amino acids : The three amino acids lysine, arginine (with guanidino group) and histidine
(with imidazole ring) are dibasic monocarboxylic acids. They are highly basic in character.
5.Aromatic amino acids : Phenylalanine, tyrosine and tryptophan (with indole ring) are aromatic amino
acids.
6. Imino acids : Proline containing pyrrolidine ring is a unique amino acid. It has an imino group ( NH),
instead of an amino group ( NH2) found in other amino acids. Therefore, proline is an -imino acid.
7.Heterocyclic amino acids : Histidine, tryptophan and proline.
Classification of amino acids
based on polarity :
Amino acids are classified into 4 groups based on their polarity. Polarity is important for protein
structure.
1.Non-polar amino acids : These amino acids are also referred to as hydrophobic (water
hating). They have no charge on the ‘R’ group. The amino acids included in this group are —
alanine, leucine, isoleucine, valine, methionine, phenyl- alanine, tryptophan and proline.
2.Polar amino acids with no charge on ‘R’ group : These amino acids, as such, carry no
charge on the ‘R’ group. They however possess groups such as hydroxyl, sulfhydryl and amide
and participate inhydrogen bonding of protein structure. The simple amino acid glycine (where
R = H) is also considered in this category. The amino acids in this group are—glycine, serine,
threonine, cysteine, glutamine, asparagine and tyrosine.
3.Polar amino acids with positive ‘R’ group : The three amino acids lysine, arginine and
histidine are included in this group.
4.Polar amino acids with negative ‘R’ group : The dicarboxylic monoamino acids— aspartic
acid and glutamic acid are considered in this group.
 Nutritional classification of amino
acids :
1. Essential or indispensable amino acids :
The amino acids which cannot be synthesized by the body and, therefore, need to be
supplied through the diet are called essential amino acids.

Arginine, Valine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenyla- lanine,

Threonine, Tryptophan.
A.V. HILL, MP., T. T. useful codes are H. VITTAL, LMP; PH. VILLMA, TT, PVT TIM
HALL and MATTVILPhLy.]
The two amino acids namely arginine and histidine can be synthesized by adults and
not by growing children, hence these are considered as semi–essential amino acids
(remember Ah, to recall). Thus, 8 amino acids are absolutely essential while 2 are
semi-essential.

2. Non-essential or dispensable amino acids : The body can synthesize about 10

amino acids to meet the biological needs, hence they need not be consumed in the
diet. These are—glycine, alanine, serine, cysteine, aspartate, asparagine, glutamate,
glutamine, tyrosine and proline.
Amino acid classification based on
their metabolic fate :
The carbon skeleton of amino acids can serve as a precursor for the
synthesis of glucose (glycogenic) or fat (ketogenic) or both.
1. Glycogenic amino acids : can serve as precursors for the
formation of glucose or glycogen. e.g. alanine, aspartate, glycine,
methionine etc.
2. Ketogenic amino acids : Fat can be synthesized from these
amino acids. Two amino acids leucine and lysine are exclusively
ketogenic.
3. Glycogenic and ketogenic amino acids : The four amino
acids isoleucine, phenyl- alanine, tryptophan, tyrosine are pre-
cursors for synthesis of glucose as well as fat.
 Properties of amino acids
The amino acids differ in their physico– chemical properties which
ultimately determine the characteristics of proteins.
Physical properties
1.Solubility : usually soluble in water and insoluble in organic solvents.
2.Melting points : melt at higher temperatures, often above 200°C.
3.Taste : Amino acids may be sweet (Gly, Ala, Val), tasteless (Leu) or bitter
(Arg, Ile). Monosodium glutamate (MSG; ajinomoto) is used as a flavoring
agent in food industry, and Chinese foods to increase taste and flavor.
4.Optical properties : All the amino acids except glycine possess optical
isomers due to the presence of asymmetric carbon atom. Some amino acids
also have a second asymmetric carbon e.g. isoleucine, threonine. The structure
of L- and D-amino acids in comparison with glyceraldehyde has been given
5.Amino acids as ampholytes : Amino acids contain both acidic ( COOH) and
basic ( NH2) groups. They can donate a proton or accept a proton, hence
amino acids are regarded as ampholytes.
 Zwitterion or dipolar ion
Zwitter ion (or dipolar ion) is a hybrid molecule
containing positive and negative ionic
groups.
•The amino acids rarely exist in a neutral form with
free carboxylic ( COOH) and free amino ( NH2)
groups. In strongly acidic pH (low pH), the amino
acid is positively charged (cation) while in strongly
alkaline pH (high pH), it is negatively charged
(anion). Each amino acid has a characteristic pH
(e.g. leucine, pH 6.0) at which it carries both
positive and negative charges and exists as
zwitterion.
Isoelectric pH
Isoelectric pH (symbol pI) is defined
as the pH at which a molecule exists
as a zwitterion or dipolar ion and
carries no net charge. Thus, the
molecule is electrically neutral
• Leucine exists as cation at pH below 6
and anion at pH above 6. At the
isoelectric pH (pH = 6.0), leucine is
found as zwitterion. Thus the pH of
the medium determines the ionic
nature of amino acids.
Chemical properties
The general reactions of amino acids are mostly due to the presence of two functional groups
namely carboxyl ( COOH) group and amino ( NH2) group.
Reactions due to COOH group
1.Amino acids form salts ( COONa) with bases and esters (COOR) with alcohols.
2.Decarboxylation : Amino acids undergo decarboxylation to produce corresponding
amines.

3. Reaction with ammonia : The carboxyl group of dicarboxylic amino acids reacts with
NH 3 to form amide
Aspartic acid + NH 3 ⎯→ Asparagine
Glutamic acid + NH 3 ⎯→ Glutamine
Reactions due to NH2 group
4. The amino groups behave as bases and combine with acids (e.g. HCl) to form
salts ( NH+Cl–).
5. Reaction with ninhydrin : The -amino acids react with ninhydrin to form
a purple, blue or pink colour complex (Ruhemann’s purple).
Amino acid + Ninhydrin ⎯→ Keto acid + NH 3 + CO 2 + Hydrindantin
Hydrindantin + NH 3 + Ninhydrin ⎯→Ruhemann’s purple

Ninhydrin reaction is effectively used for the quantitative determination of

amino acids and proteins. (Note : Proline and hydroxyproline give yellow
colour with ninhydrin).
6. Color reactions of amino acids : Amino acids can be
identified by specific color reactions .
7. Transamination : Transfer of an amino group from an
amino acid to a keto acid to form a new amino acid is a very
important reaction in amino acid metabolism .
8. Oxidative deamination : The amino acids undergo
oxidative deamination to liberate free ammonia.
 Structure of proteins
• The sequence of a protein is determined by the DNA of the
gene that encodes the protein (or that encodes a portion of the
protein, for multi- subunit proteins).
• A change in the gene's DNA sequence may lead to a change in
the amino acid sequence of the protein. Even changing just
one amino acid in a protein’s sequence can affect the protein’s
overall structure and function.
• To understand how a protein gets its final shape or
conformation, we need to understand the four levels of
protein structure: primary, secondary, tertiary, and quaternary
Primary Structure
• The simplest level of protein structure, primary structure is
simply the sequence of amino acids in a polypeptide chain.
• The hormone insulin has two polypeptide chains A, and B. The
sequence of the A chain, and the sequence of the B chain can be
considered as an example for primary structure.
 Secondary structure
• secondary structure, refers to local folded structures that form within a
polypeptide due to interactions between atoms.
• The most common types of secondary structures are the α helix and the β pleated
sheet. Both structures are held in shape by hydrogen bonds, which form between the
carbonyl O of one amino acid and the amino H of another.
 Tertiary structure
• The overall three-dimensional structure of a polypeptide is called its tertiary structure. The
tertiary structure is primarily due to interactions between the R groups of the amino acids that
make up the protein.
• Important to tertiary structure are hydrophobic interactions, in which amino acids with nonpolar,
hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids
on the outside to interact with surrounding water molecules.
• Also, Disulfide bonds, covalent linkages between the sulfur- containing side chains of cysteines, are
much stronger than the other types of bonds that contribute to tertiary structure
 Quaternary structure
• When multiple polypeptide chain subunits come together, then the
protein attains its quaternary structure.
• An example for quaternary structure is hemoglobin. The hemoglobin
carries oxygen in the blood and is made up of four subunits, two
each of the α and β types.
 TRANSAMINATION, DEAMINATION AND
DECARBOXYLATION
• Protein metabolism is a key physiological process in all forms of life
• Proteins are converted to amino acids and then catabolized
• The complete hydrolysis of a polypeptide requires mixture of
peptidases because individual peptidases do not cleave all peptide
bonds
• Both exopeptidases and endopeptidases are required for complete
conversion of protein to amino acids
Amino acid metabolism
• The amino acids not only function as energy metabolites but also used as
precursors of many physiologically important compounds such as heme,
bioactive amines, small peptides, nucleotides and nucleotide coenzymes.
• In normal human beings about 90% of the energy requirement is met by
oxidation of carbohydrates and fats. The remaining 10% comes from
oxidation of the carbon skeleton of amino acids.
• Since the 20 common protein amino acids are distinctive in terms of their
carbon skeletons, amino acids require unique degradative pathway.
Amino acid metabolism
• The degradation of the carbon skeletons of 20 amino acids converges to just seven metabolic
intermediates namely.
i. Pyruvate
ii. Acetyl CoA
iii. Acetoacetyl CoA
iv. alfa-Ketoglutarate
v. Succinyl CoA
vi. Fumarate
vii. Oxaloacetate

• Pyruvate, alfa-ketoglutarate, succinyl CoA, fumarate and oxaloacetate can serve as precursors for
glucose synthesis through gluconeogenesis. Amino acids giving rise to these intermediates are
termed as glucogenic.
• Those amino acids degraded to yield acetyl CoA or acetoacetate are termed ketogenic since
these compounds are used to synthesize ketone bodies.
• Some amino acids are both glucogenic and ketogenic (For example, phenylalanine, tyrosine,
tryptophan and threonine.
Catabolism of amino acids
• The important reaction commonly employed in the breakdown of an
amino acid is always the removal of its alpha-amino group. The
product ammonia is excreted after conversion to urea or other
products and the carbon skeleton is degraded to CO2 releasing
energy. The important reaction involved in the deamination of amino
acids is
• i. Transamination
ii. Oxidative deamination
iii. Non oxidative deamination
Transamination
• Most amino acids are deaminated by transamination reaction
catalysed by aminotransferases or transaminases.
• The a-amino group present in an amino acid is transferred to an a-
keto acid to yield a new amino acid and the a-keto acid of the original
amino acid.
• The predominant amino group acceptor is a-keto glutarate.
Glutamate's amino group is then transferred to oxaloacetate in a
second transamination reaction yielding aspartate.
Glutamate + oxaloacetate → -ketoglutarate + aspartate
pyridoxal phosphate
Transamination
Transamination is an exchange of functional groups between any amino acid (except lysine, proline, and threonine) and an α-
keto acid. The amino group is usually transferred to the keto carbon atom of pyruvate, oxaloacetate, or α-ketoglutarate,
converting the α-keto acid to alanine, aspartate, or glutamate, respectively. Transamination reactions are catalyzed by specific
transaminases (also called aminotransferases), which require pyridoxal phosphate as a coenzyme. In an α-keto acid, the carbonyl
or keto group is located on the carbon atom adjacent to the carboxyl group of the acid.
Oxidative Deamination

In oxidative deamination, amino groups are removed from amino acids,

resulting in the formation of corresponding keto acids and ammonia.
The reaction catalysed by a flavo protein may be represented as
follows:
• Oxidative deamination is stereospecific and is catalyzed by L- or D-amino acid oxidase. The initial
step is removal of two hydrogen atoms by the flavin coenzyme, with formation of an unstable α-
amino acid intermediate.
• This intermediate undergoes decomposition by addition of water and forms the ammonium ion
and the corresponding α-keto acid: L-amino acid oxidase occurs in the liver and kidney only.
• This is an intermediate of the citric acid cycle, serves as a link between the metabolism of this
amino acid and that of the carbohydrate. Some organisms metabolize aspartic acid to acetic acid,
ammonia and CO2.
Non-oxidative Deamination
• Nonoxidative deamination is a type of deamination reaction in which the removal
of the amine group occurs without proceeding through an oxidation reaction.
• However, this type of deamination reactions liberates ammonia, producing the
corresponding α-keto acids. Significantly, the hydroxyl amino acids which bear
one or more hydroxyl groups undergo nonoxidative deamination.
• Also, these amino acids are not involved in protein synthesis. Some of these
hydroxyl amino acids are serine, homoserine, and threonine
Amino acid metabolism
alpha keto gulteric acid Glutaric acid
The glucose-alanine cycle is used primarily as a
mechanism for skeletal muscle to eliminate nitrogen
while replenishing its energy supply. Glucose
oxidation produces pyruvate which can undergo
transamination to alanine. This reaction is catalyzed
by alanine transaminase, ALT (ALT used to be
called serum glutamate-pyruvate transaminase,
SGPT, this is different from the transaminase
SGOT). Additionally, during periods of fasting,
skeletal muscle protein is degraded for the energy
value of the amino acid carbons and alanine is a
major amino acid in protein. The alanine then enters
the blood stream and is transported to the liver.
Within the liver alanine is converted back to
pyruvate which is then a source of carbon atoms for
gluconeogenesis. The newly formed glucose can
then enter the blood for delivery back to the muscle.
The amino group transported from the muscle to the
liver in the form of alanine is converted to urea in
the urea cycle and excreted.
Urea Cycle 1.Synthesis of carbamoyl phosphate
Carbamoyl phosphate synthase I (CPS I) of
:

mitochondria catalyses the condensation of

NH4+ ions with CO2 to form carbamoyl phosphate.
2. Formation of citrulline : Citrulline is
synthesized from carbamoyl phosphate and
ornithine by ornithine transcarbamoylase.
Ornithine is regenerated and used in urea cycle.
3. Synthesis of arginosuccinate : Arginosuccinate
synthase condenses citrulline with aspartate to
produce arginosuccinate.
4. Cleavage of arginosuccinate : Arginosuccinase
cleaves arginosuccinate to give arginine and fumarate.
Arginine is the immediate precursor for urea.
Fumarate liberated here provides a connecting link
with TCA cycle, gluconeogenesis etc.
5. Formation of urea : Arginase is the fifth
and final enzyme that cleaves arginine to yield
urea and ornithine. Ornithine, so regenerated,
enters mitochondria for its reuse in the urea
cycle.
Interrelation between Urea and TCA cycle
• 1. The production of fumarate in urea cycle is the
most important integrating point with TCA cycle.
Fumarate is converted to malate and then to
oxaloacetate in TCA cycle. Oxaloacetate undergoes
transamination to produce aspartate which enters
urea cycle. Here, it combines with citrulline to
produce arginosuccinate. Oxaloacetate is an
important metabolite which can combine with acetyl
CoA to form citrate and get finally oxidized.
Oxaloacetate can also serve as a precursor for the
synthesis of glucose (gluconeogenesis).
• 2. ATP (12) are generated in the TCA cycle while ATP
(4) are utilized for urea synthesis.
• 3. Citric acid cycle is an important metabolic pathway
for the complete oxidation of various metabolites to
CO2 and H2O. The CO2 liberated in TCA cycle (in the
mitochondria) can be utilized in urea cycle
DNA stands for
•Deoxyribonucleic acid
DNA Structure
 DNA consists of two molecules that are arranged into a
ladder-like structure called a Double Helix.

 A molecule of DNA is made up of millions of tiny

subunits called Nucleotides.

 Each nucleotide consists of:

1. Phosphate group
2. Pentose sugar
3. Nitrogenous base
Nucleotides

Phosphate

Nitrogenous
Base

Pentose
Sugar
Nucleotides
 The phosphate and sugar form the backbone of the
DNA molecule, whereas the bases form the “rungs”.

 There are four types of nitrogenous bases.

Nucleotides

A T

Adenine Thymine

C G

Cytosine Guanine
Nucleotides
 Each base will only bond with one other specific base.

Adenine (A)
Thymine (T) Form a base pair.

Cytosine (C)
Guanine (G) Form a base pair.
 Base-Pair Rule
Adenine <==> Thymine

Guanine <==> Cytosine

The sides of the DNA

ladder are phosphate &
sugar held together
by hydrogen bonds
DNA Structure
 Because of this complementary base pairing, the order
of the bases in one strand determines the order of the
bases in the other strand.
A T

C
G
T A

C
G

A T

G C

T A
Base Pair Rule
DNA Structure
 To crack the genetic code found in DNA we need to
look at the sequence of bases.

 The bases are arranged in triplets called codons.

AGG-CTC-AAG-TCC-TAG
TCC-GAG-TTC-AGG-ATC
DNA Structure
 A gene is a section of DNA that codes for a protein.

 Each unique gene has a unique sequence of bases.

 This unique sequence of bases will code for the

production of a unique protein.

 It is these proteins and combination of proteins that

give us a unique phenotype.
RNA/ TRANSCRIPTION /
TRANSLATION
 RNA
▪ RNA: ribonucleic acid
▪ Carries out protein synthesis
▪ Differences from DNA:
▪ different sugar (ribose)
▪ single strand
▪ different base
▪ no thymine
▪ URACIL instead
3 Types of RNA:
• Messenger RNA: (mRNA)
carries nucleotide
sequence from nucleus to
ribosome
• Transfer RNA: (tRNA) picks
up amino acid in
cytoplasm and carries
them to ribosome
• Ribosomal RNA:
(rRNA)found in ribosome,
joins mRNA and tRNA;
forms protein
DNA Replication
DNA replication is the process by which DNA makes a
copy of itself during cell division.
1.The first step in DNA replication is to ‘unzip’ the double
helix structure of the DNA molecule.
2.This is carried out by an enzyme called helicase which
breaks the hydrogen bonds holding the complementary Bases
of DNA together (A with T, C with G).
3.The separation of the two single strands of DNA creates
a ‘Y’ shape called a replication ‘fork’. The two separated
strands will act as templates for making the new strands
of DNA.
4.One of the strands is oriented in the 3’ to 5’ direction
(towards the replication fork), this is the leading strand.
The other strand is oriented in the 5’ to 3’ direction (away
from the replication fork), this is the lagging strand. As a
result of their different orientations, the two strands are
replicated differently:
Leading Strand:
Leading Strand:
4.A short piece of RNA called a primer (produced by an
enzyme called primase) comes along and binds to the end
of the leading strand. The primer acts as the starting point
for DNA synthesis.
5.DNA polymerase binds to the leading strand and then
‘walks’ along it, adding new complementary
nucleotide bases (A, C, G and T) to the strand of DNA in
the 5’ to 3’ direction.
6.This sort of replication is called continuous.
Lagging strand:
Lagging strand:
4.Numerous RNA primers are made by the primase
enzyme and bind at various points along the lagging
strand.
5.Chunks of DNA, called Okazaki fragments, are then
added to the lagging strand also in the 5’ to 3’ direction.
6.This type of replication is called discontinuous as the
Okazaki fragments will need to be joined up later.
 https://www.youtube.com/watch?v=TNKWgcFPHqw

8.Once all of the bases are matched up (A with T, C with

G), an enzyme called exonuclease strips away the
primer(s). The gaps where the primer(s) were are then
filled by yet more complementary nucleotides.
9.The new strand is proofread to make sure there are no
mistakes in the new DNA sequence.
10.Finally, an enzyme called DNA ligase seals up the
sequence of DNA into two continuous double strands.
11.The result of DNA replication is two DNA molecules
consisting of one new and one old chain of nucleotides.
This is why DNA replication is described as semi-
conservative, half of the chain is part of the original DNA
molecule, half is brand new.
12.Following replication the new DNA automatically
winds up into a double helix.
Steps involved in DNA translation https://youtu.be/5bLEDd-PSTQ
There are three major steps in translation: initiation, elongation, and
termination. These steps are briefly discussed below:
1. Initiation
Small ribosomal subunits bind to mRNA. The initiator tRNA which is
equipped with the anticodon (UAC) also binds to the start codon
(AUG) of the mRNA. The resulting large complex forms a complete
ribosome and initiates protein synthesis.
2. Elongation
Following initiation, a new tRNA-amino acid complex enters the
codon next to the AUG codon. If the anticodon of the new tRNA
matches the mRNA codon, base pairing occurs and the two amino
acids are linked by the ribosome through a peptide bond. If the
anticodon does not match the codon, base pairing cannot happen
and the tRNA is rejected. Then, the ribosome moves one codon
forward making space for a new tRNA-amino acid complex to enter.
This process is repeated several times until the entire polypeptide
has been translated.
3. Termination
As the ribosome moves along the mRNA, it encounters one of the
three stop codons for which there is no corresponding tRNA.
Terminator proteins present at the stop codon bind to the ribosome
and trigger the release of the newly synthesized polypeptide chain.