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Tishk International University Faculty of Science Department of Medical Analysis General and systemic Biochemistry Protein Dr. Rundk A. Hwaiz Grade 2-Fall 2020-2021 Dr. Rundk A. Hwaiz Lec2

Protein - Lecture Notes - TIU - Lecture Notes

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Bild 1Nutritional classification:
1- Essential amino acids: These amino acids can’t be formed
in the body and so, it is essential to be taken in diet. Their
deficiency affects growth, health and protein synthesis.
2- Semiessential amino acids: These are formed in the body
but not in sufficient amount for body requirements especially
in children.
amino acids: valine, isoleucine, lysine, leucine, arginine*,
histidine*, methionine, tryptophan, threonine, phenyl alanine
*= arginine and histidine are semiessential
3- Non essential amino acids: These are the rest of amino acids
that are formed in the body in amount enough for adults and
children. They are the remaining 10 amino acids.
Metabolic classification: according to metabolic or
degradation products of amino acids they may be:
1- Ketogenic amino acids: which give ketone bodies . Lysine
and Leucine are the only pure ketogenic amino acids.
2- Mixed ketogenic and glucogenic amino acids: which give
both ketonbodies and glucose.
include the rest of amino acids.
These amino acids by catabolism yields products that enter in
glycogen and glucose formation.
Amphoteric properties of amino acids: that is they have both
basic and acidic groups and so can act as base or acid. Neutral
amino acids (monobasic, monocarboxylic) exist in aqueous
solution as “ Zwitter ion” i.e. contain both positive and
negative charge.
amino acid units (residues) that are linked together through the
formation of amide bonds (peptide bonds) from the amino
group of one residue and the carboxylate of a second
A peptide or polypeptide has two different ends. The amino
terminal (N-terminal) is the amino group while the
carboxyl terminal (C-terminal) is the carboxyl group. The
order of amino acids from N-terminal to C-terminal is the
primary structure of the protein.
In a peptide, the amino acids are written from left to right
with the (NH3+) group on the left and (COO-) group on the
The left hand amino acid is called the N-terminus and the
right hand amino acid is called the C-terminus.
peptide: the name given to a short polymer of amino
acids joined by peptide bonds; they are classified by the
number of amino acids in the chain.
dipeptide: a molecule containing two amino acids joined
by a peptide bond.
joined by peptide bonds.
amino acids joined by peptide bonds.
protein: a biological macromolecule, consisting of
one or more polypeptide chains. Consist of
polypeptides with more than 50 A.A.
• Write three-letter abreviations and names of tripeptides that
could form from two glycine and one alanine.
Glycine glycine alanin Gly-Gly-Ala
Glycine alanine glycine Gly-Ala-Gly
Alanine glycine glycine Ala-Gly-Gly
What is the possible tripeptides formed from one each of
leucine, glycine and alanine?
1. Protein primary structure is the linear sequence of amino
acids in a peptide or protein.
2. The amino acids in the primary structure are held
together by covalent bonds, which are made during the
process of protein synthesis.
A peptide or polypeptide has two ends. The amino terminal
(N-terminal) is the amino group (on the first amino acid in the
chain) while the carboxyl terminal (C-terminal) is the carboxyl
group on the last amino acid in the peptide.
The order of amino acids from N-terminal to C-terminal is the
primary structure of the peptide or protein.
Secondary structure
2. The structure allows hydrogen bonds between the amide
proton and the carbonyl acid in the peptide bond to be
3. The hydrogen bond is formed between the amide proton
of an amino acid and the carbonyl acid of the other amino
1. A β-strand is an extended structure.
2. Two or more β-strands may be adjacent to each other,
thereby forming a β-sheet which is held together with
hydrogen bonds between the amide proton in one β-
strand and the carbonyl acid in another β-strand.
Tertiary structure
1. The final structure that a protein forms depends on which
amino acids are included in the primary structure. Through
the hydrophobic effect, the protein is folded so that unpolar
amino acids are placed inside the protein without contact
with the surrounding water. By folding, polar side chains
will be placed on the surface, making the protein water-
ionic bonds, van der Waals interactions and disulfide
bonds between the amino acid side chains.
Quarternary structure
have an additional structural level. The quaternary structure
describes how these individual parts relate to each other in
to properly fold a protein.
2. If you destroy the structure and denture the protein (with
heat, acid or otherwise) while reducing all the disulfides,
you get a completely unfolded protein chain. If you then
lower the temperature or remove the agent that caused
the denaturation, the protein will be folded back to its
normal structure.
Native Structure
("aprons"), is necessary for the folding to occur properly and
for the protein to become functional.
CHAPERONES are special proteins which only helps
proteins to fold into correct conformation, The chaperones
need energy to carry out the process. ex. heat shock protein (hsp)
A real protein
The oxygen we breathe is transported with the blood bound to
the protein hemoglobin which brings it to the various tissues
that need the oxygen. On the way back to the lungs,
hemoglobin takes with it the carbon dioxide formed during
energy conversion. We have two proteins that take care of
oxygen: myoglobin that can store oxygen and hemoglobin
that transports it.
1. Hemoglobin consists of 4 polypeptides, or two pairs of
subunits. Each subunit contains a heme group that can bind
2. By putting together several subunits, you get a protein that
has a cooperative ability to bind oxygen. This property is
very valuable to us because it makes hemoglobin readily
bind to oxygen in the lungs and at the same time it binds
much worse when hemoglobin enters the tissue and
therefore easily loosens.
of the functions within the cell.
• Proteins are large biological molecules that serve
diverse functional and structural roles within cells.
• Proteins are synthesized during the translation
covalently linked by peptide bonds.
• Proteins have four basic levels of structure. However,
proteins must fold correctly in order to function