BIO462

CHAPTER 2:
AMINO ACIDS & AMINO ACIDS
BIOSYNTHESIS
 LEARNING OUTCOMES

 Explain general features of amino acids.

 Categorize the amino acids.
 Understand zwitterion of amino acids.
 Describe nitrogen cycle, amino acid biosynthesis and urea
cycle.
AMINO ACIDS

 Basic structure:
 Carbon (α)
 Carboxylic acid group
 R-group side chain
 Amino group
AMINO ACIDS – BUILDING BLOCKS OF PROTEINS
AMINO ACIDS

 There are 20 common amino acids

 R-group classification
 Polar, non-polar, acidic and basic

 Determines properties of amino acid

COMMON AMINO ACIDS
 All are α-amino acids
 The amino and carboxyl are connected to the same
carbon
 Differ by the other substitutes attached to the α
carbon, called the side chain (R), with H as the
fourth substituent
 Proline is a five membered secondary amine, with
N and the C part of a five-membered ring
NOTATION FOR 20 STANDARD AA
Three-Letter One-Letter
Amino Acid Symbol Symbol
Alanine Ala A
Arginine Arg R
Asparagine Asn N
Aspartate Asp D
Cysteine Cys C
Glutamate Glu E
Glutamine Gln Q
Glycine Gly G
Histidine His H
Isoleucine Ile I
Leucine Leu L
Lysine Lys K
Methionine Met M
Phenylalanine Phe F
Proline Pro P
Serine Ser S
Threonine Thr T
Tryptophan Trp W
Tyrosine Tyr Y
Valine Val V
CLASSIFICATION OF AMINO ACIDS

 Classify by structure of R (side chain)

 Nonpolar amino acid
 Polar, neutral/uncharged amino acid
 Acidic amino acid
 Basic amino acid
NONPOLAR AMINO ACIDS
 Hydrophobic - neutral
POLAR AMINO ACIDS
 Hydrophilic, neutral/uncharged
ACIDIC AMINO ACIDS
 Negatively charged
BASIC AMINO ACIDS
 Positively charged
Aromatic Amino Acids
Sulphur-containing amino acids
 CHIRALITY

The mirror-image objects cannot be superimposed on one another but

are related are said to be chiral.

Amino acid has a chiral carbon atom except for glycine

 PROTEINS – AMIDES FROM AMINO ACIDS

 Amino acids contain a basic amino group and an acidic

carboxyl group
 Joined as amides between the -NH2 of one amino acid
and the -COOH to the next amino acid
 Chains with fewer than 50 units are called peptides
 Protein: large chains that have structural or catalytic
functions in biology
Amino Acids Can Join Via Peptide Bonds

LO
Amino Acids Can Join Via Peptide Bonds
 ZWITTERION

 At a certain pH known as the isoelectric point (pI), an amino acid has no net
charge, because the number of protonated ammonium groups and
deprotonated carboxylate groups are equal.

 The ions produced at the pI have both positive and negative charges and are
known as zwitterion.
ZWITTERION OF AMINO ACIDS
 In neutral solution, the COOH is ionized and the NH 2 is
protonated
 The resulting structures have “+” and “-” charges 
zwitterion (dipolar ion)
 A zwitterion is a compound with no overall electrical
charge, but which contains separate parts which are
positively and negatively charged
 ZWITTERION OF AMINO ACIDS
 In acidic solution, the -COO- part of the zwitterion
picks up a hydrogen ion (an overall cation)
 ZWITTERION OF AMINO ACIDS
 In basic solution, the hydrogen ion is removed from
the -NH3+ group (an overall anion)
ZWITTERION OF AMINO ACIDS
 At a pH less than value of the pI, the amino acid is
protonated and has a +ve charge
 At pH greater than the pI, the amino acids is
deprotonated and has –ve charge
 AMINO ACIDS AS A BUFFER
 Amino acids have
pseudo-buffer
action
TITRATION OF AMINO ACID

 When an amino
acid is titrated, its
titration curve
indicates the
reaction of each
functional group
with hydrogen ion.
TITRATION CURVE OF GLYCINE
 indicates that amino acid has two
regions of buffering. So there are two
stages in titration of glycine
 At midpoint of any titration, the pH is
equal to pKa of the protonated group
being titrated.
 At the midpoint in the 1st stage of
titration of glycine, the pH is 2.34 thus
its COOH group has pKa of 2.34.
 At the midpoint of second stage of
titration of glycine, the pH is 9.60 which
is equal to pKa for NH3 group.
AMINO ACIDS BIOSYNTHESIS
AMINO ACID BIOSYNTHESIS
 AMINO ACID BIOSYNTHESIS
 A matter of synthesizing the appropriate α-keto acid
carbon skeleton, followed by transamination with
glutamate
 The amino acid can be classified according to the source
of intermediates for the α-keto acid biosynthesis
 E.g: the amino acid Glu, Pro, Arg are all members of α-
ketoglutarate family because they are derived from
citric acid cycle intermediate, α-ketoglutarate
 Serine family

Aromatic family

Aspartate family

Pyruvate family

Glutamate family

COMMON FEATURES IN AMINO ACID BIOSYNTHESIS

How do amino acid synthesized?
 Involved glutamate and glutamine (amino acids) – central
importance in the process
 Glutamate arise from α-ketoglutarate (reduce amination)
 Glutamine from glutamate (amidation)
 TRANSAMINATION
 Glutamate or glutamine can be used as an amino
group donor in the amino acid biosynthesis
 The reactions involve transfer of the amino group
(transamination) to a central metabolite to make
the required amino acid
 The transfer of amino group is catalyzed by enzyme
called amino-transferases
 All amino acids with exception of lysine and
threonine participate in transamination
 TRANSAMINATION REACTIONS
 In this process the α-amino group is transferred from an α-
amino acid to an α-keto acid ， and the α-amino acid forms an
α-keto acid. In the meantime, the α-keto acid converts to a new
amino acid.
 Transamination reactions are reversible

Transaminase /
aminotransferase

donor acceptor product

MECHANISM OF ACTION OF AMINOTRANSFERASES

 All aminotransferase require the coenzyme pyridoxal

phosphate
 Act by transferring the amino group of an amino acid to
the pyridoxamine phosphate.
 Pyridoxamine form of the co-enzyme then reacts with
an α-keto acid to form an amino acid and regenerates
the original aldehyde form of the coenzyme
 OXIDATIVE DEAMINATION
 Result in liberation of the amino group as free ammonia.
 An amino acid is converted into the corresponding keto
acid by the removal of the amine functional group as
ammonia and is replaced by the ketone group
 Occurs under aerobic conditions in all tissues but
especially in the liver and kidney
 Produce:
1) α-keto acids = can enter the pathway central
2) ammonia = source of nitrogen in urea synthesis
 OXIDATIVE DEAMINATION
 Glutamate is a unique as it is the only amino acid that under
goes rapid oxidative deamination (others AA : low activity)
 Glutamate formed by transamination reactions is deaminated
to α-ketoglutarate
 Glutamate dehydrogenase (NAD+ is coenzyme)
TRANSPORT AND DETOXICATION OF AMMONIA

 Ammonia has to be
transported to liver
 Glutamine is the
major transport
form
 Glutamine serves
as a source of
amine groups for
biosynthesis
NITROGEN CYCLE, UREA CYCLE
MAJOR PATHWAYS FOR ‘N’ ACQUISITION

 The principal inorganic forms of N are in an oxidized

state
 N (atmosphere)
2
 NO - (soil and ocean)
3

 Thus, N acquisition must involve reduction of the

oxidized forms (N2 and NO3-) to NH4+
 Nearly all of this is in microorganisms and green
plants.
 Animals gain N through diet.
 OVERVIEW OF ‘N’ ACQUISITION
 Nitrate assimilation – reduction of nitrate to ammonium
 Occurs in two steps:

1. 2e- reduction of nitrate to nitrite

2. 6e- reduction of nitrite to ammonium
 Nitrate assimilation accounts for 99% of N acquisition by
the biosphere

 Nitrogen fixation – formation of ammonium from nitrogen

gas
 involves reduction of N in prokaryotes by nitrogenase
2
NITROGEN CYCLE
 NITROGEN CYCLE
 Organic nitrogenous compounds are formed by the
incorporation of NH4+ into carbon skeletons.
 Ammonium can be formed from oxidized inorganic precursors
by reductive reactions:
 nitrogen fixation reduces N to NH +;
2 4

 nitrate assimilation reduces NO3- to NH4+.

 Nitrifying bacteria can oxidize NH4+ back to NO3- and obtain
energy for growth in the process of nitrification.
 Denitrification is a form of bacterial respiration whereby
nitrogen oxides serve as electron acceptors in the place of O2
under anaerobic conditions.
 DISPOSAL OF NH3
 NH3 is very toxic and must be detoxified and
excreted from the body
 Fish: NH3
 Mammals: Urea
 Birds: Uric acid

UREA
 UREA CYCLE
 Urea = major disposal form of amino group
derived from amino acid.
 Account for about 90% of the nitrogen-

containing components of urine

 Urea produce by liver, transport in the blood to

kidney for excretion in the urine

UREA CYCLE
 UREA CYCLE
 Overall reaction:
O
||
2 NH3 + CO2   H2N–C–NH2 + H2O

• Energy required (3 ATP)

• Urea diffuses from liver cells to body fluids
• Excreted by the kidneys
 SYNTHESIS OF UREA

 Urea formation is basically confined to the liver

 5-step Urea Cycle
4

3
2

 Linked to citric acid cycle through fumarate

Step 1:  Carbamoyl phosphate formation from
ammonium ion, carbon dioxide and ATP

 Carbamoyl phosphate synthetase

 Liver cell mitochondrias
 Utilizes 2 ATP
Step 2:  Formation of citrulline from ornithine and
carbamoyl phosphate

 Ornithine
transcarbamoylase
 Liver mitochondria
 Citrulline passes from
mitochondrial
membrane to cytosol
Step 3:  Formation of arginosuccinate from citrulline
and aspartate

 Argininosuccinate synthetase
 Requires 1 ATP
Step 4:  Formation of arginine and fumarate from
arginosuccinate
 Argininosuccinase
 Liver and kidney of mammals
 Fumarate is metabolised in Citric Acid Cycle (thus aspartate
could be regenerated)
Step 5:  Hydrolysis of arginine to form ornithine and
urea

 Ornithine regenerated, urea produced

 Urea excreted (N rich, excelent solubility,
harmless
END OF THIS CHAPTER