PROTEIN METABOLISM

1. Biosynthesis and degradation.

2. Deamination of Amino Acids
3. Transamination of Amino Acids
4. Decarboxylation of Amino Acids

Dr. Rahil Razak Bhat

V.B.C. SKUAST-Kashmir
Organized
Controlled
Boosted
 METABOLISM AND ITS PURPOSE
• Total chemical reactions taking place in living system.
METABOLISM is all the chemical reactions taking place
inside a cell.
A metabolic pathway is a multistep sequences of enzyme-
catalyzed reactions.
> Metabolic pathways are tightly regulated and highly
integrated.
• Pathways that regenerate a component are called
cycles.
• Comprises of Anabolism and catabolism. Energy
Production
• Catabolism: oxidative breakdown of complex molecules
into simpler ones, often releasing energy in the process.
• Usually exergonic, Waste
Eliminatio
Building
Blocks
n
• The key purposes of catabolism are:
 METABOLISM AND ITS PURPOSE
• Anabolism: This involves the synthesis of complex molecules from
simpler ones and typically consumes energy. The primary purposes of
anabolism include:

Growth and
Pathways : Linear, cyclic, spiral. Repair

● Amphibolic Pathways: For example: Krebs cycle is

mainly a catabolic cycle, but with some anabolic
features, e.g., part of Krebs cycle is used for the
synthesis of glucose from amino acids,
Therefore, Krebs cycle is amphibolic. Anabolism
Energy Storage
● Fate of metabolism: energy generation and Maintaining
Homeostasis:

synthesis of biomolecules
 METABOLISM AND ITS PURPOSE
• Characteristics of Metabolic pathways:
• Irreversible
• Every one has a committed step
• Specific cellular location.
• Highly regulated
like substrate concentration, allosteric regulation, requires external
cellular signals.
• Metabolic pathways involve enzyme catalyzed reactions like: 5
Oxidation-reduction rxn, C-C make break bonds, group transfer, internal
rearrangements, isomerizations & elimination rxn, free radical rxns
 SUMMARY OF METABOLISM
• metabolism serves as the biochemical engine of life, providing energy,
building blocks, and the means to eliminate waste in living systems.
• It allows organisms to grow, repair, respond to environmental changes,
and carry out all the functions necessary for survival and reproduction.
• Metabolism is a highly regulated and tightly controlled process that
adapts to the specific needs of an organism and its environment.

Find the answer?

What is feed back inhibition and feedback repression.?
IMPORTANCE OF PROTEINS TO ANIMAL
HEALTH
Transport Functions:
Enzyme Structural Functions:
Support and Strength,
blood gasses
catalysis Muscle Contraction Transport, Nutrient
Transport

Storage Functions: Nutrient Storage, Energy

Reserves Immune
Regulatory Functions: Gene Functions:
Expression, Antibodies
Hormonal Functions:
Cellular Communication: Cell Signaling, Transport and Storage of Molecules: Ion
Channels, Storage Proteins
Metabolic Functions: Metabolic Enzymes, Self Defense Mechanisms: Toxins and Venom, Blood
Clotting:
 FATE OF PROTEIN METABOLISM
• Body protein synthesis
• Peptide biosynthesis (Oligopeptides: from12-to 20 AAs),
• Synthesis of NPN compounds: Creatinine, urea, ammonia etc
• Synthesis of : Glucose, new amino acids, Ketone bodies.
• To generate energy during starvation conditions when fat depots are
exhausted.
• How does the body regulate protein synthesis and degradation?
• What is the significance of protein turnover in maintaining
cellular health?
• How do cells recycle amino acids?
• What happens to excess dietary protein in the body?
• What is the impact of protein metabolism on overall metabolism
and energy balance?
• How do different types of dietary proteins affect metabolism and
health?
• What are the consequences of protein deficiency or excess in the
diet?
HORMONES OF PROTEIN METABOLISM

Insulin

Glucagon

Growth hormone

Cortisol

Insulin like growth

hormone
Protein Biosynthesis
 BIOSYNTHESIS OF PROTEINS

Making Proteins

Step 1: Transcription
 BIOSYNTHESIS OF PROTEINS
• How are proteins synthesized in cells?
• The translation of coded genetic information from DNA via mRNA into the
amino acid sequences of proteins involves the orderly interactions of over
100 different macromolecules. There are four broad steps in the synthesis
of a protein:
• Activation of amino acids
• Initiation of the synthesis of the polypeptide chain
• Elongation
• Termination
• What is the role of ribosomes in protein synthesis?
 BIOSYNTHESIS

Proteins are manufactured (made) by the ribosomes

 BIOSYNTHESIS
Making a Protein—Transcription
• First Step: Copying of genetic information from DNA to RNA called
Transcription
Why? DNA has the genetic code for the protein that needs to be
made, but proteins are made by the ribosomes—ribosomes are outside
the nucleus in the cytoplasm.
DNA is too large to leave the nucleus (double stranded), but RNA can
leave the nucleus (single stranded).

Part of DNA temporarily unzips and is used as a

template to assemble complementary
nucleotides into messenger RNA (mRNA).
BIOSYNTHESIS
 BIOSYNTHESIS
• mRNA then goes through the pores of the nucleus with the DNA code
and attaches to the ribosome.
EUKARYOTIC TRANSCRIPTION

Nuclear
Cytoplasm
pores
DNA

Transcription
RNA
RNA
Processing
mRNA G AAAAAA G AAAAAA

Export
Nucleus
 BIOSYNTHESIS OF PROTEINS

Making Proteins

Step 2: Translation
 BIOSYNTHESIS OF PROTEINS
Making a Protein—Translation
• Second Step: Decoding of mRNA into a protein is called Translation.
• Transfer RNA (tRNA) carries amino acids from the cytoplasm to the
ribosome.
• These amino acids come from the food we eat.
Proteins we eat are broken down into individual
amino acids and then simply rearranged into new
proteins according to the needs and directions of
our DNA.
• These Amino acids also come from degraded
body proteins
 PROTEIN
SYNTHESIS
AMINE H O ACID
Alanine Serine
H N C OH H O H O
C
H N C OH H N C OH
ANYTHING R H
H C H C
Amino Acid C H C H
H H HO H

H2O H O H O
H N C N C OH
H C H C
C H C H
H H HO H
 BIOSYNTHESIS OF PROTEINS
• A series of three adjacent bases
in an mRNA molecule codes for
a specific amino acid—called a Amino acid
codon.

• Each tRNA has 3 nucleotides

that are complementary to the
codon in mRNA.

• Each tRNA codes for a different

amino acid.
Anticodon
 BIOSYNTHESIS OF PROTEINS

• mRNA carrying the

DNA instructions
and tRNA carrying
amino acids
meet in the ribosomes
Amino acids are joined
together to make a
protein.
BIOSYNTHESIS OF PROTEINS
 PROTEIN TURNOVER
• Protein turnover refers to the replacement of older proteins as they are
broken down within the cell. Different types of proteins have very
different turnover rates, depending on their particular function.
• Half life of a given protein in different organs and species is generally
similar.
• Rapid turn over of some proteins implies their relative instability.
• The rate of hydrolysis of a protein can be inversely related to the stability
of its tertiary structure. As a result misfolded and unfolded proteins
are quickly degraded.
• Structural proteins such as collagen tend to have long half-life periods (in
the range of years), while enzymatic protein have a shorter life span
to adapt to the metabolic requirements of the body.
• Once the protein have been hydrolyzed and amino acids recycled, these
amino acids are added to the amino acid pool for further utilization.
The relative rates of protein synthesis and degradation — protein turnover — determine the size
of the free amino acid pools available for the synthesis of new proteins and for other essential
functions. For example, the synthesis of new proteins to mount an immune response is supported
by the net degradation of the proteins in the body.
 DEGRADATION OF PROTEINS
Amino acid degraded Catabolic end product

Alanine, Serine, Cysteine, Glycine, Threonine Pyruvic acid

Leucine Acetyl CoA

Phenylalanine, Tyrosine Leucine, Lysine, Tryptophan Aceto acetic acid

Methionine, Isoleucine valine Succinyl CoA

Arginine, Proline, Histidine, Glutamine, Glutamic acid α- Ketoglutaric acid

Asparagine, Aspartic acid Oxaloacetate

Phenylalanine, Tyrosine Fumarate

Amino Acids pool: Animal body cannot store amino acids. If the amino acids in the
amino acid pool are not used for biological processes, they are degraded and the nitrogen
excreted in the urine as urea.
 DEGRADATION OF PROTEINS

Ubiquitin-
Lysosomal
proteasom
degradation
e mediated

Endosome-
Autopha
 UBIQUITINATION
• Ubiquitination, also known as ubiquitylation, is a process that involves
attaching ubiquitin to a target protein.
• Ubiquitin is a small protein found in almost all tissues of eukaryotic
organisms. The process of ubiquitination is essential for protein
homeostasis, which is the rapid removal of unwanted or damaged proteins.
• Ubiquitination is a tightly regulated, highly specific, and ATP-dependent
biological process. It is carried out by a complex cascade of enzymes. The
first step in ubiquitination is the activation of ubiquitin by the E1 enzyme.
The E1 enzyme hydrolyses ATP and adenylates the C-terminal
glycine residue of ubiquitin. The E1 enzyme then links this residue to the
active site cysteine of E1.
• Ubiquitination can involve the covalent attachment of one
(monoubiquitination) or more (polyubiquitination) ubiquitin monomers. The
process most commonly binds the last amino acid of ubiquitin (glycine 76)
to a lysine residue on the substrate.
• Ubiquitination can occur in the mitochondrial matrix and on the
cytosolic side of the ER membrane.
UBIQUITINATION AND PROTEIN DEGRADATION

• Ubiquitination of proteins is the

process of tagging the target
protein by ubiquitin protein which
is to be degraded.
• Ubiquitination involves the three
proteins:

1. Ubiquitin –activating enzyme

(E1)
2. Ubiquitin-conjugating
enzyme (E2)
3. Ubiquitin-protein ligase (E3).
 AMINO ACID SYNTHESIS
S. ANIMAL No. of EAAs Main EAA
N
O
1 Poultry 10 GLYCINE
2 Human 9 -
3 Pig 8 LYSINE
4 Rat and fish 10
5 Cattle/buffalo/sheep/goat 0 *SHEEP
=METHIONIN
CAT* = TAURINE
 AMINO ACID SYNTHESIS
• STEPS OF AMINO ACID SYNTHESIS

• Reduction of N2 into NH4+

• Incorporation of AMMONIUM ION (Nitrogen) into AMINO ACIDS biomolecules.

• Source of amino group to amino acids via transamination

• Glutamate and glutamine entry into the system

• Synthesis of amino acids via their metabolic precursors

 AMINO ACID SYNTHESIS
2. Incorporation of AMMONIUM ION (Nitrogen) into AMINO ACIDS
biomolecules.

a-ketoglutarate is key acceptor

of Ammonium ion.

GDHases fixes nitrogen as NH4+

*Glutamate dehydrogenase is present in all organisms. In eukaryotes this is minor

pathway and occurs in mitochondria. This enzyme is unusual. This reaction is known as
REDUCTIVE AMINATION of a-keto acids. Deamination of glutamate leads to formation of
a-ketoglutarate k/a oxidative deamination.
The second reaction is AMIDATION of glutamate carried out by glutamine synthetase
which is also present in all organisms and is driven by ATP hydrolysis.
 3.TRANSAMINATION OF AMINO
ACIDS
• This is major pathway for
the amino acid formation
in cells.
• Transfer of amino group
from amino acid to keto
acid by
aminotransferases
/transaminases is known
as transamination. All
transaminases require
pyridoxal phosphate
coenzyme.
3.TRANSAMINATION OF AMINO
ACIDS
 CARBON SOURCES OF AMINO ACIDS
• Glutamate family:
glutamate

glutamine

a-
ketoglutarate
proline

arginine
 CARBON SOURCES OF AMINO
ACIDS
2. Aspartate family:

Aspart OXALOA
ate CETATE

Methio
Lysine
nine
 CARBON SOURCES OF AMINO ACIDS
• Serine family:

serine

Gycerate
-3-
phospha
te

cysteine glycine
 CARBON SOURCES OF AMINO ACIDS

4. Pyruvate family:
a v
l a
a
l
n
i i
n n
e e

pyruvate

l i
s
e o
u l
e
c u
i c
i
n n
e e
 CARBON SOURCES OF AMINO ACIDS
5. AROMATIC FAMILY
 CARBON SOURCES OF AMINO ACIDS
6. Histidine family:

C Source:
 2.DEAMINATION OF AMINO
• Oxidative deamination is a metabolic process that converts
ACIDS
amino acids into a more usable form.
• During this process, amino groups are removed from amino
acids, resulting in the formation of keto acids and
ammonia. The ammonia is then neutralized into urea through
the urea cycle.
• Oxidative deamination occurs mostly in the liver and kidney. It
is catalyzed by enzymes.
• Removal of NH3 by glutamate dehydrogenase,α- ketoacids
liberated enter the central pathway of energy metabolism,
and ammonia, which is a source of nitrogen in urea synthesis.
• It involves the use of NADPH as energy source while as
 2.DEAMINATION OF AMINO
ACIDS
Amino acids whose catabolism yields pyruvate
or one of the inter- mediates of the citric acid
cycle are termed glucogenic. These inter-
mediates are Substrates for gluconeogenesis and,
therefore, can give rise
to the net formation of glucose in the liver and
kidney.

Amino acids whose catabolism yields either aceto

acetate or one of its precursors (acetyl CoA or acetoa
cetyl CoA) are termed ketogenic. Acetoa cetate is one
of the ketone bodies, which also include 3-
hydroxybutyrate and acetone. Leucine and lysine
are the only exclusively ketogenic amino acids found
in proteins. Their carbon skeletons are not substrates
for gluconeogenesis and, therefore, cannot give rise
to the net formation of glucose
 AMMONIA TRANSPORT OF
AMMONIA

•Ammonia from all tissue.

•Toxic
•Ammonia to liver
•Glutamine and Cahill cycle
•Urea cycle to urine
 GLUTAMINE AS TRANSPORTER OF
AMMONIA FROM PERIPHERAL TISSUES

•Glutamate is collector of NH3 of all amino

acids: oxidative deamination
•Purine, pyrimidine, oxidative deamination
generate ammonia
•This ammonia combines with glutamate to
synthesize glutamine

NH3 + a-KGT
Urea
Cycle Oxidative deamination (GDH)

NH3 +Glu

Blood
Liver Mitochondria
More important for brain Glutaminase
• Alanine glucose cycle (Cahill Cycle)
• Important in muscle tissue
• Branched chain amino acids in muscles generate pyruvate
• Glucose also generate pyruvate
• Amino groups of amino acids are also donated to glutamate
• Therfore the load of pyruvate and glutamate increases and undergo
transamination leading to alanine formation.
CAHILL CYCLE
 UREA CYCLE
• Alanine and glutamine are the major transporters of nitrogen in the
blood.
• Urea formation takes place in liver
• Urea is the major disposal form of amino groups derived from amino acid
pool.
• Comprises of major 5 reactions , first 2 in mitochondria and remaining in
cytosol.
• Synthesis of one molecule of urea needs
3 mol. of ATP
1 mol of ammonium ion
1 mol of α – amino nitrogen of aspartate.
UREA CYCLE
 CPS-I CPS-II
• Cellular location: mitochondria • Cytosol
• Pathway involved: Urea cycle • Pyrimidine synthesis
• Source of nitrogen: ammonia • Γ-amide group of glutamine
• Activator: n- acetylglutamate • Activator: PRPP
• Inhibitor: UTP
Overall stoichiometry of the urea cycle
Aspartate + NH3 + CO2 + 3 ATP + H2O → urea + fumarate + 2 ADP + AMP + 2 Pi + PPi