Protein Synthesis

• The various steps involved in the process of protein

synthesis are;
• Formation of RNA by DNA
• mRNA carries the message to cytoplasm for type of
protein to be synthesized
• tRNA transfers amino acids to ribosomes
• Ribosomes are the source of protein synthesis
(anabolism)
• Protein synthesis takes place at about 50
seconds/protein (fast!!)
• Amino acids serve dual purpose for synthesis of
protein as well as they are catabolized for energy
Protein structure is determined by the genetic
code in your DNA. The section of DNA that codes for one
protein is called a gene

A gene is a section of
DNA that determines
the 10 sequence of amino
acids in a protein.

Therefore, the gene

determines the shape
and therefore, the
function of the
protein it codes for.
 Central Dogma in Biology

one gene
one type
of protein
one function
in the cell
 Transcription
(Trans = across, cription = to write)
Also called protein synthesis, the coded message of a gene
on DNA has specific instructions on how to make each
particular protein that our bodies need

The instructions from a gene are copied DNA mRNA

from DNA to messenger RNA (mRNA) in

the nucleus A
U
Then, the mRNA moves through the
T
nuclear pores and into the cytoplasm A
where the proteins are made. C
G
Main players in protein synthesis are
G
DNA, mRNA, tRNA, rRNA, Ribosomes, C
and enzymes
 General Process
Step 1: Helicase unwinds the DNA (starting at the
promoter).
Step 2: Complementary RNA base pairs attach to
form the mRNA strand

Step 3: RNA polymerase forms the RNA sugar-

phosphate backbone and checks for mistakes
Step 4: The RNA detaches & leaves the nucleus, & the
DNA winds up back
The process of making mRNA is
called TRANSCRIPTION
 Translation
• • The mRNA code is made up of groups of three
nucleotide bases known as codons.
• Each codon codes for a specific amino acid. E.g. AGC for
Serine, UGC for cysteine
• It takes 3 nucleotides on the mRNA to code for 1 a.a.
We must code for 20 different amino acids and there
are only 4 letters (nucleotides, AUGC) in the alphabet
For two nucleotides, there are only 16 possible codes
(42). However, for three nucleotides there are 64
possible codes (43), and that is enough to code for the
20 amino acids.
mRNA codon chart
• A tRNA molecule is a small piece of RNA that has a
specific amino acid attached to it. The tRNA also has a
special sequence of 3 nucleotide bases known as an
anticodon, There is at least one type of tRNA for each
of the 20 amino acids. As the correct amino acids are
. brought to the ribosome by the tRNAs, ribsomes
position them and they are joined together via
dehydration synthesis in the presence of enzyme called
peptidyl transferase to form the protein that the
original DNA coded for.
• Normal sequence of AAs is; Methionine---Cysteine---
Glycine---Alanine---Stop
Which codes for
methionine

Terminator codons are UAA, UAG, or UGA. None of

these have a matching tRNA anticodon, so when no
more tRNA’s attach, the ribosome, protein, and
mRNA detach from each other
Summary of the Protein Synthesis
What if something goes wrong during
translation?
Answer: MUTATION
• A change in the nucleotide
sequence of DNA
• When the bases (‘letters’) change, the wrong
amino acids are used to make the protein.
• The protein will NOT be able to do its job, it
means that there is change(mutation) in
codon(position of bases).
• Mutations are of two types
• 1: Chromosomal
• 2: Gene mutations
1. Chromosomal mutations: a mutation of all or part of
a chromosome.
This usually involves MANY GENES, and therefore,
MANY PROTEINS.
Example: Down’s syndrome.

2. Gene mutations: a mutation that occurs within a

gene at some point along a chromosome. This
mutation is only a change of 1 or a few ‘letters’
(nitrogenous bases).
It usually only affects ONE GENE, and therefore,
ONE PROTEIN.
Example: Sickle cell anemia.
 Digestibility of protein and biosynthesis

• Some food (especially vegetables) are deficient in

some essential amino acids hence digestibility vary
– Rice: thr & lys are low
– Maize: lysine is low
• Hence digestibility vary with protein quality
– High if full mixture of essential amino acids are
present
• If one amino acid is missing, then proteins contain
that amino acid cannot be made
– cannot make ½ a protein! It’s all or none
– Compromises pool of the other amino acids
 Digestibility and bioavailability
• Dietary protein quality is determined by its
bioavailability to the animal

• “Bioavailability” is not simply digestibility, it also

includes assimilation and incorporation of the AA into
protein

• The most common index of protein bioavailability is

apparent protein digestibility (APD)

• APD = % of protein not rejected as feces

 Protein Digestibility
• APD depends upon degree of purity of proteins involved,
therefore protein can be;
• Purified: gelatin, casein, soy-isolate
• Semi-purified: hi-pro soybean meal, glutens
• Practical: fish meal, squid meal, peanut meal, rice bran,
etc.
• Contrary to popular beliefs, animal protein is not more
“digestible” than plant protein
• Digestibility really is determined by level of purification
and degree of interaction (competition for absorption
sites) between one nutrient and another. Hence
digestibility also depends on following factors.
• Factors: salinity (indirect), size/age (indirect)
 Amino Acid Digestibility
• Apparent amino acid digestibility (AAAD) is directly
related to protein digestibility
• Proteins vary in APD, but amino acids don’t in terms of
AAAD (proteins compete with other nutrients, AA’s
don’t)
• Amino acids are typically absorbed in the gut (fish) and
midgut/midgut gland (shrimp)

• For amino acids there are 6 transport mechanisms : 1)

neutral AA’s (mono’s), 2) basic (diamino’s), 3) acidic
(dicarboxylic’s), 4) aromatics, 5) alanine and 6) glycine
Protein Metabolism
1. Pathways of Amino Acid Degradation
• Only 10-15% energy (Human body) get from AA than
that obtained from active glycolysis and fatty acid
oxidation
• 20 catabolic pathways converge to form only six major
products which enter citric acid cycle
• From here Carbon skeletons are diverted to
gluconeogenesis or ketogenesis or completely oxidized
to CO2 and H2O
• Leu, Lys, Trp, Phe, Ile, Tyr, Thr are degraded entirely
to acetoacetyl-CoA and/or acetyl-CoA can yield ketone
bodies in liver where acetoacetyl-CoA is converted to
acetoacetate and then to acetone and β-hydroxy
butyrate these are called ketogenic amino acids
• Those degraded to pyruvate, a-ketoglutarate,
succinylCo-A, fumarate and/or oxaloacetate can be
converted to glucose and glycogen, they are called
glucogenic AAs
• Trp, Phe, Tyr, Thr and Isoleu are both ketogenic and
gluconeogenic
• Leucine is exclusively ketogenic and is very common in
proteins, its degradation makes a substantial
contribution to ketosis under starvation conditions
 Entry of AAs in TCA Cycle

3..
• Several Enzyme Co-Factors play
Important Roles in AA Catabolism

• Like transamination reactions requiring pyridoxal

phosphate, another common type of reaction in AA
catabolism is one-carbon transfer which usually involve
one of the three co-factors, biotin(transfer C (CO2) in
its most oxidized state, tetrahydrfolate (intermediate
oxidized state or sometimes as CH3) or S-
adenosylmethionine transfers methyl groups

• It is normally involved in the metabolism of every cell of

the human body, especially affecting DNA synthesis and
regulation, but also fatty acid synthesis and energy
production.
• In tetrahydrofolate vit B12 (cobalamin) in the form of
methylcobalamin is used as methyl donor
• Deficiency of B12 results in pernicious anemia or
megaloblastic anemia with presence of large immature
precursors of RBCs in bone marrow called megaloblasts

• RBCs decline and replaced by smaller number of

abnormally large erythrocytes called macrocysts
• No vit B12, no tetrahydrofolate, no folate, no production
of thymidine which is required for DNA synthesis hence
no DNA synthesis so no RBC production
28
29
 Fate of –NH2 removed during deamination

• Amine groups are channeled into urea

– Synthesized from aspartate and glutamate’s amine
groups in the urea cycle
– Ammonia the main excretory product in fishes and
is excreted and released in water from gills
through concentration gradient
– Ammonia is quite toxic and is converted into urea
in higher vertebrates which is less toxic
• Urea cycle only occurs in the liver
• Ammonia is toxic to animals
• Terminal stages of ammonia intoxication in humans are
comatose state accompanied by cerebral edema and
increased cranial pressure which might be potential
depletion of ATP in brain cells
• Ammonia readily crosses blood brain barrier and results in
loss of neurons, altered synapse formation and general
defect in cellular energy metabolism
• High levels of Ammonia increases glutamine concentration
which acts as osmotically active solute in brain astrocytes
(which provide nutrients, support and insulation for neurons)
• This triggers an uptake of water in astrocytes to maintain
osmotic balance leading to swelling of cells and brain
leading to coma
 UREA CYCLE
•If not reused for the synthesis of new AAs or other
nitrogenous products, amino groups are channeled into single
excretory end product
•Most aquatic species such as the bony fishes are ammonotelic
excreting amino nitrogen as ammonia
•Toxic ammonia is simply diluted in the surrounding water
• Terrestrial animals require pathways for nitrogen excretion
that minimize toxicity and water loss
•Most terrestrial animals are ureotelic excreting amino
nitrogen in the form of urea
•Birds and reptiles are uricotelic excreting amino nitrogen as
uric acid
•In ureotelic organisms ammonia deposited in mitochondria of
hepatocytes is converted to urea in urea cycle
• Urea is produced from Ammonia in Five
Enzymatic steps

• Urea cycle begins inside liver mitochondria but three of

the subsequent steps take place in cytosol
• First amino group to enter the urea cycle is derived from
Ammonia in mitochondrial matrix
• Liver also receives some ammonia via portal vein from the
intestine
• Whatever the source is NH4+ generated in liver
mitochondria is immediately used together with CO2(as
HCO3-) produced by mitochondrial respiration to form
carbamoyl phosphate in matrix
• This ATP-dependent reaction is catalyzed by carbamoyl
phosphate synthetase I which is different from cytosolic
II form used in pyrimidine biosynthesis
• Carbamoyl phosphate which functions as an activated
carbamoyl group donor now enters the urea cycle
• Urea cycle has 4 enzymatic steps
• 1: Carbamoyl phosphate donates its carbamoyl group to
ornithine to form citrulline with the release of Pi in the
presence of Ornithine transcarbamoylase
• Ornithine is not one of the 20 common AAs but it is key
intermediate in nitrogen metabolism
• It is synthesized from glutamate in 5 step pathway
• Ornithine plays a role resembling that of oxaloacetate in
the citric acid cycle accepting material at each turn of
urea cycle
• Citrulline produced in the first step of urea cycle passes
from mitochondria to the cytosol
• The next two steps bring in the second amino group
• Source is aspartate generated in mitochondria by
transamination and transported into the cytosol
• A condensation reaction between the amino group of
aspartate and ureido(carbonyl) group of citrulline forms
argininosuccinate
• This cytosolic reaction catalyzed by argininosuccinate
synthetase requires ATP and proceeds through citrullyl-AMP
intermediate, Argininosuccinate is then cleaved by
argininosuccinase to form arginine and fumarate
• Fumarate is converted to malate before entering
mitochondria to join the pool of citric acid cycle
intermediates,
• Cytosolic enzyme arginase cleaves arginine to yield urea and
ornithine
ornithine
transcarbamoylase
Formation of carbamoly phosphate and
Arginino-succinate
Molecular weight of ATP 507g and urea is 60g, production
of this amount of urea takes 1521g of ATP
 Amino Acid Assimilation
• “Assimilation” is not transport, it involves the appearance
of AA’s in various tissues (blood, hemolymph, muscle, etc.)
• Amino acid Toxicity/antagonism
• Toxicity/antagonisms are result of dietary imbalances in
EAA
• When one EAA is fed in excess it can also increase the
requirement for another, structurally-similar EAA
• Toxicity = overfeeding of one EAA and negative effects
not mitigated by increasing other EAA
• Antagonism = one EAA regulates uptake of another
• LEU/ILE in catfish
• LYS/ARG in shrimp