Download 2- Proteins

2- Proteins
Many Structures, Many Functions
1. A polypeptide is a polymer of amino acids connected in a specific sequence
2. A protein’s function depends on its specific conformation
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2-Proteins
 Their functions include structural support, storage, transport of
other substances, intercellular signaling ‫اإلشارات بين الخلوية‬, movement,
and defense against microbes.
 Some proteins works as enzymes in the cell that regulate
metabolism ‫ األيض‬by accelerating ‫ تسريع‬chemical reactions.
 Humans have tens of thousands of different proteins, each with
their own structure and function.
 All protein polymers are constructed from ‫ تتركب من‬the same set of
20 monomers, called amino acids.
 Polymers of proteins are called polypeptides ‫ببتيدات عديدة‬.
 A protein consists of one or more polypeptides folded and coiled
into a specific conformation
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- They are Polymers of amino acids (constructed from 20 amino
acids) (to form Polypeptides).
- These components include a hydrogen atom, a carboxyl group, an
amino group, and a variable ‫ متغيرة‬R group (or side chain).
H
H
General Formula
of the Amino
Acid:
N
Amino
group
H
C
R
O
C
OH Carboxyl
group
Side chain
- The side chain R links with ‫ ترتبط بـ‬different compounds
- Differences in R groups produce the 20 different amino acids.
- The physical and chemical characteristics ‫ صفات‬of the R group
determine ‫ تحدد‬the unique characteristics of a particular amino acid.
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Amino acids ‫األحماض األمينية‬
1.
Hydrophobic: the amino acids that have hydrophobic R groups
(non-polar).
2-
Hydrophilic: the amino acids that have polar R groups, making
them hydrophilic.
3- Ionized: the amino acids with functional groups that are charged
(ionized) at cellular pH (7). So, some R groups are bases, others are
acids.
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Fig. 5.15, Page 72
Amino acids
1.
Hydrophobic: the amino acids that have hydrophobic R groups
(non-polar).
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Fig. 5.15, Page 72
2-
Hydrophilic: the amino acids that have polar R groups, making
them hydrophilic.
3- Ionized: the amino acids with functional groups that are charged
(ionized) at cellular pH (7). So, some R groups are bases, others are
acids.
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Fig. 5.15, Page 73
Peptide bonds
Peptide bond formed between the carboxyl group of one amino acid
and the amino group of the other by dehydration.
H
N
H
H
O
H
H
C
C
N
C
OH H
R
Peptide bond
Peptide
O
C
R
OH
Dehydration
Polypeptide (Protein)
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Page 73, Fig. 5.16
•
•
•
•
•
Amino acids are joined together when a dehydration reaction removes a
hydroxyl group from the carboxyl end of one amino acid and a hydrogen
from the amino group of another. The resulting covalent bond is called a
peptide bond.
Repeating the process over and over ‫ عدة مرات‬creates a long polypeptide chain.
– At one end is an amino acid with a free amino group the (the N-terminus)
and at the other is an amino acid with a free carboxyl group the (the Cterminus).
The repeated sequence (N-C-C) is the polypeptide backbone.
Attached to the backbone are the various R groups.
Polypeptides range in size from a few monomers to thousands.
Fig. 5.16, Page 73
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Levels of Protein Structure
• The folding ‫ إلتفاف‬of a protein from a chain of amino acids
occurs spontaneously ‫ذاتيا‬.
• There are three levels of structure:
primary ‫أولى‬, secondary ‫ثانوى‬, and tertiary ‫ ثالثى‬structure,
are used to organize the folding within a single
polypeptide.
• Quaternary ‫ رباعى‬structure arises when two or more
polypeptides join to form a protein.
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1. Primary structure:
It is a single polypeptide
chain of amino acids.
–
Lysozyme, an enzyme that
attacks bacteria, consists of a
polypeptide chain of 129
amino acids.
–
A slight change ‫ تغيير طفيف‬in the
primary structure can affect a
protein’s conformation and
ability to function.
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Fig. 5.18, Page 75
• Sickle cell disease ‫المنجلية‬:
an abnormal hemoglobin because of a single amino acid
substitution ‫تغيير‬.
– These abnormal hemoglobins crystallize, deforming ‫ يُكسر‬the red blood
cells and leading to clogs ‫ إنسداد‬in tiny blood vessels.
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Fig. 5.19, Page 75
2- The secondary structure:
Results from hydrogen bonds at regular intervals ‫ على أبعاد متساوية‬along
the polypeptide backbone.
A. Coils ‫( الحلزونى‬α helix)
are typical shapes
that develop from
secondary structure
B.
Folds (β pleated sheets)
‫الشيت ال ُمجعد‬. Composed
of several parallel αhelix
coils attached by H bonds
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Fig. 5.20, Page 76
An example for folds (beta pleated sheets) ‫الشيت ال ُمجعد‬:
Is the structural properties of silk because of the presence of so
many hydrogen bonds makes each silk fiber stronger than steel.
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Fig. 5.21, Page 77
• Tertiary structure:
is determined by a variety of interactions among ‫ خالل‬R groups
and between R groups and the polypeptide backbone.
– These interactions include hydrogen bonds among polar
areas, ionic bonds between charged R groups, and
hydrophobic interactions and
Van der Waals interactions among
hydrophobic R groups.
• While these three interactions
are relatively weak, disulfide
bridges, strong covalent bonds
that form between the
sulfhydryl groups (SH) of
cysteine monomers, stabilize
the structure.
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Fig. 5.22, Page 77
4- The quaternary structure:
Results from the aggregation ‫ تجمع‬of two or more
polypeptide chains.
A. Collagen is a fibrous protein of three polypeptides that
are supercoiled, and function in connective tissues.
A. Hemoglobin is a
globular protein
with two copies
of two kinds
of polypeptides
(2α and 2β).
Collagen
Fig. 5.23, Page 78
Hemoglobin
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The 4 forms of protein
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Fig. 5.24, Page 79
Denaturation of protein ‫فرد البروتين‬
• It is the change of protein’s conformation in response to ‫إستجابة لـ‬
the physical and chemical conditions.
• For example, alterations ‫ تغيير‬in pH, salt concentration,
temperature, or other factors can denature ‫ يفرد‬a protein.
– These forces break the hydrogen bonds, ionic bonds, and disulfide
bridges that maintain the protein’s complicated shape.
• Some proteins can return to their original shape again after
denaturation, but others cannot.
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‫فرد البروتين ‪Denaturation of protein‬‬
‫فرد‬
‫مفرود‬
‫إعادة إلى طبيعته‬
‫‪18‬‬
‫‪Fig. 5.25, Page 79‬‬
Hydrophobic (non-polar R group)
Amino
acids
Hydrophilic (polar R group)
Ionized (charged functional groups)
Peptides
Primary
structure
Secondary
structure
Single chain
of amino acids
H bonds
e.g. Lysozyme
Coils &
Folds
e.g. silk
Polypeptides
Tertiary
structure
1- Hydrophobic
Interaction
(Van der Waals
interaction);
Proteins
Quaternary
structure
two or more
polypeptide
chains
2- H bonds;
e.g. Collagen
3- Ionic bonds;
& Hemoglobin
4- Di-sulfide
bridges;
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