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

L
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 NH2 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

 aa essential – not produced by the body

- consumed in the diet
 aa non-essential – produced by the body
- not consumed in the diet
 excess dietary aa :
• stored – converted to common metabolic
intermediates
• excreted

aa Breakdown, synthesis, utilization

 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)
Amino acid breakdown

Deaminat
ion
 amino group removal – converted to ammonia (NH3)
and others
 Glutamate – product of most deamination reaction
 Involved 3 type of processes :
 Transmination
 Oxidative deamination
 Other deamination mechanism
 TRANSAMINATION
 Glutamate or glutamine can be used as an amino
group donor in the amino acid deamination
 The reactions involve transfer of the amino group to
a central metabolite to make the required amino
acid
 The transfer of amino group is catalyzed by enzyme
called amino-transferases @ transaminases
 All amino acids with exception of lysine and
threonine participate in transamination
-Amino Acid


 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
 The generic transamination-
aminotransferase reaction
involves the transfer of the α-
amino group of glutamate to
an α-keto acid acceptor.

 The transamination of
oxaloacetate by glutamate to
yield aspartate and α-
ketoglutarate
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 = nitrogen gas (atmosphere)
2
 NO - = nitrate (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.

 Nitrogen
assimilation

Formation of organic nitrogen compounds like amino acids

from inorganic nitrogen compounds present in the
environment.

Organisms like plants, fungi and certain bacteria that

cannot fix nitrogen gas (N2) depend on the ability
to assimilate nitrate or ammonia for their needs.
 Nitrogen fixation

Nitrogen fixation is a process by which nitrogen in

the Earth's atmosphere is converted into ammonia
(NH3) or other molecules available to living organisms.

Atmospheric nitrogen or molecular dinitrogen (N2) is

relatively inert : it does not easily react with other
chemicals to form new compounds.
 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 – reduction of nitrogen gas to form

ammonium
 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 NO - to NH +.

3 4

 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 O 2
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