Download Proteins

Proteins
IUG, Fall 2012
Dr Tarek Zaida
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Amino Acids, Peptides, and Proteins
• Proteins are naturally occurring polymers
composed of amino acid units joined one to
another by amide (or peptide) bonds.
• Spider webs, animal hair and muscle, egg
whites, and hemoglobin (the molecule that
transports oxygen in the body to where it is
needed) are all proteins.
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• Peptides
• Are oligomers of amino acids that play
important roles in many biological processes.
• For example, the peptide hormone insulin
controls our blood sugar levels,
• Thus, proteins, peptides, and amino acids are
essential to the structure, function, and
reproduction of living organisms.
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Amino Acids
• The amino acids obtained from protein
hydrolysis are α-amino acids.
• That is, the amino group is on the α-carbon
atom, the one adjacent to the carboxyl group.
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• With the exception of glycine, where R is H, αamino acids have a stereogenic center at the
α-carbon.
• All except glycine are therefore optically
active.
• They have the L configuration relative to
glyceraldehyde.
• Note that the Fischer projection, used with
carbohydrates, is also applied to amino acids
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• The following table lists the 20 α-amino acids
commonly found in proteins.
• The amino acids are known by common
names.
• Each also has a three-letter abbreviation
based on this name, which is used when
writing the formulas of peptides, and a oneletter abbreviation used to describe the amino
acid sequence in a protein.
• The amino acids in the following table are
grouped to emphasize structural similarities.
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• Of the 20 amino acids listed in the table, 12
can be synthesized in the body.
• The other 8, those with names shown in a
blue color and referred to as essential amino
acids, cannot be synthesized by adult humans
and therefore must be included in the diet in
the form of proteins.
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The Amphoteric Nature of Amino Acids
• Amino acids are amphoteric.
• They can behave as acids and donate a proton
to a strong base, or
• they can behave as bases and accept a proton
from a strong acid.
• These behaviors are expressed in the following
equilibria for an amino acid with one amino
and one carboxyl group:
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Zwitterion
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The isoelectric Point
• If placed in an electric field, the amino acid will
therefore migrate toward the cathode (negative
electrode) at low pH
• and toward the anode (positive electrode) at high
pH.
• At some intermediate pH, called the isoelectric
point (pI), the amino acid will have a net charge
of zero.
• It will be unable to move toward either electrode.
• Each of the amino acids has a characteristic
isoelectric points
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Essential & Nonessential Amino Acids
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Peptides
• Amino acids are linked in peptides and
proteins by an amide bond between the
carboxyl group of one amino acid and the αamino group of another amino acid.
• Emil Fischer, who first proposed this structure,
called this amide bond a peptide bond.
• A molecule containing only two amino acids
joined in this way is a dipeptide:
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A dipeptide
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Write out the abbreviated formulas for all
possible tripeptide isomers of:
1. Leu—Ala—Met
2. Gly—Ala—Ser
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A spider’s Web
A spider’s web is a device built by the spider to trap prey. Spider silk, a protein, is the main component of
the web. Silk is composed largely of β-sheets, a fundamental unit of protein structure. Many proteins
have β-sheets; silk is unique in being composed all most entirely of β-sheets.
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Protein Three-Dimensional Structure
composed of primary, secondary, and tertiary structures
• Functioning proteins are not simply long
polymers of amino acids.
• These polymers fold to form discrete threedimensional structures with specific biochemical
functions.
• The amino acid sequence is called the primary
structure.
• Three-dimensional structure resulting from a
regular pattern of hydrogen bonds between the
NH and the CO components of the amino acids in
the polypeptide chain is called secondary
structure.
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• The three-dimensional structure becomes more
complex when the R groups of amino acids far
apart in the primary structure bond with one
another.
• This level of structure is called tertiary structure
and is the highest level of structure that an
individual polypeptide can attain.
• However, many proteins require more than one
chain to function.
• Such proteins display quaternary structure, which
can be as simple as a functional protein consisting
of two identical polypeptide chains or as complex
as one consisting of dozens of different polypeptide chains.
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1. The Primary Structure of Proteins
• The number and sequence of the amino acids
in the protein chain.
• Primary structure is stabilized by peptide
bonds.
• A slight change in the amino acid sequence
(replacement of an amino acid with another),
may change the entire protein.
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2. Secondary Structure
• Polypeptide chains can fold into regular
structures.
• Two types of secondary structure elements:
1. α-helix
2. β-sheet
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1. α-helix
• Is a coiled structure stabilized by intrachain
hydrogen bonds.
• Each turn of the helix contains a bout 3.6
amino acids.
• Hair & wool are examples
of protein with helical
structure, both contain
keratin.
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(A) A ribbon depiction shows the –carbon atoms and side chains (green).
(B) A side view of a ball-and-stick version depicts the hydrogen bonds (dashed
lines) between NH and CO groups.
(C) An end view shows the coiled backbone as the inside of the helix and the
side chains (green) projecting outward.
(D) A space-filling view of part C shows the tightly packed interior core of the
helix.
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β-sheet
• Beta sheets are stabilized by hydrogen bonding
between polypeptide strands instead of a single
polypeptide strand,
• The β-sheet is composed of two or more
polypeptide chains called β-strands.
• A β-strand is almost fully extended rather than
being tightly coiled as in the α-helix.
• The distance between adjacent amino acids along
a β-strand is approximately 3.5 Å, in contrast with
a distance of 1.5 Å along an α-helix.
• The side chains of adjacent amino acids point in
opposite directions.
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Examples of proteins
with β-sheet are
protein in silk (fibroin),
and proteins that bind
fatty acids
The structure of a β-strand. The side chains
(green) are alternatively above and below
the plane of the strand. The bar shows the
distance between two residues
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Tertiary Structure
• The specific folding and bending of the coils
into specific layers or fibers.
• This level of structure is the result of interactions between the R groups of the peptide
chain.
• It is the tertiary structure that gives proteins
their biological activity.
• Tertiary structure is stabilized by several types
of bonds.
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Types of Bonds that stabilize tertiary structure
1.
2.
3.
4.
Hydrogen bonds
Disulfide bridges
Hydrophobic interactions
Salt bridges between positively & negatively
charged groups within the protein.
5. Nonpolar amino acids are folded on the
inside of the protein, and polar amino acids
are on the outside where they react with
water to form polar group interactions.
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Quaternary Structure
• It occurs when a protein has at least 2 units
combine together to form a complex.
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The α2β2 tetramer of human hemoglobin.
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Percent Composition
• Average percentage of nitrogen in protein is
16%.
• 16% Nitrogen = 1/6 of protein content.
• Protein is the major food containing nitrogen.
• Chemists can determine the amount of
protein present in food substance by determining the amount of nitrogen present.
• Calculation of protein in food can be done by
multiplying the weight of nitrogen by 6 and
converting it to a percentage of the total.
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• % protein in food = grams of Nitrogen x 6
• Example:
• If 100 g of food yield 4 g of nitrogen on
chemical analysis. Calculate the % protein in
the sample?
• Since the amount of nitrogen in protein is 1/6
of the total amount of protein,
• Then the amount of protein present in food is:
4g Nitrogen x 6 = 24
24 g protein in 100 g sample food; meaning
24%
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Classification of Proteins
• Proteins can be classified into three classes:
1. Simple protein
2. Conjugated proteins
3. Derived proteins
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 Simple proteins:
they give amino acids or their derivative
(polypeptides) upon hydrolysis
 Conjugated proteins:
they give amino acids and other compounds
(non protein compound) upon hydrolysis
 Derived proteins:
Are produced from simple or conjugated proteins
upon chemical action or enzyme on proteins.
As derived proteins one can consider proteoses,
peptones, polypeptides, tripeptides, and
dipeptides.
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Classification Of Proteins According To Solubility
• Simple proteins are classified according to
their solubility in various solvents and also as
to whether they are coagulated by heat.
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Classification Of Proteins According To Composition
• Conjugated proteins can be classified into
different types:
1. Nucleoproteins: (nucleic acid/ chromosomes)
2. Glycoproteins: (carbohydrates/ mucin in
saliva)
3. Phosphoproteins: (Phosphate/ casein in milk)
4. Chromoproteins: (Chromophore/ hemoglubin,
cytochrome)
5. Lipoproteins: (lipids/ fibrin in blood)
6. Metalloproteins: Metals/ ceruloplasmin
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Classification Of Proteins According To Function
According to their biological function, proteins can be classified
into various classes:
1. Structural proteins:
Collagen (in connective
tissues), keratin (in hair).
2. Contractile proteins:
Myosin, actin (muscle
contaction)
3. Storage proteins:
Ferritin (storage of iron)
4. Transport proteins:
Hemoglobin (transfers
oxygen)
5. Hormones:
Insulin ( metabolism of
carbohydrates)
6. Enzymes:
Pepsin (digestion of
proteins)
7. Protective proteins:
gamma-globulin (antibody
formation)
8. Toxin:
Venoms (poisons)
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Classification Of Proteins According To Shape
1. Globular proteins:
• Folded into a shape of ball.
• Are soluble in water or form colloidal dispersions.
• Examples: Hemoglobin, Albumin, globulins
2. Fibrous proteins
• Consists of parallel polypeptide chains that are
coiled and stretch out.
• Are insoluble in water.
• Examples: collagen, fibrin, myosin.
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Properties of Proteins
• Proteins have two characteristic properties:
1. Colloidal Nature
2. Denaturation
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1. Colloidal Nature
• When proteins are in water, they form a colloidal
dispersion.
• Due to this property, proteins will not pass
through a membrane.
• This is very important because proteins present in
bloodstream can not pass through the capillaries
& should remain in blood-stream.
• Therefore there should be no protein in the urine.
• So if there is a protein in urine, it indicates that
there is a damage in the kidney membranespossibly nephritis.
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2. Denaturation
• Unfolding & rearrangement of secondary and
tertiary structure of a protein without
breaking the peptide bonds.
• A denatured protein loses its activity
• If denaturing conditions are mild, protein will
restore their active structure if these
conditions of denaturing are reversed.
• If denaturation is drastic, the process is
irreversible; the protein will coagulate or
precipitate from solution.
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Factors or Reagents Causing Denaturation
1. Alcohol
- It causes irreversible denaturation.
- 70% alcohol is used to disinfect bacteria
because of its ability to coagulate proteins.
- Alcohols form hydrogen bonds, that compete
with original hydrogen bonds
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2. Salts of heavy metals
HgCl2 (mercuric chloride) and AgNO3 (silver
chloride) cause irreversible denaturation by
disrupting salt bridges & disulfide bridges.
3. Heat
- If heat is gentle, protein will denature
reversibly.
- If heat is vigorous, protein will denature
irreversibly by disrupting several types of
bonds.
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• Examples:
1.Egg-white coagulates on heating.
2. In bacteria heat destroys & coagulates
proteins, hence in hospitals, the sterilization of
instruments and clothing for use, need high
temperature.
3. Determination of proteins present in urine
can be done by heating a sample of urine
which will cause the coagulation of any protein
present.
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4. Alkaloidal Reagents (tannic acid & picric acid)
- Both form insoluble compounds with proteins.
They denature proteins irreversibly by disrupting salt bridges and hydrogen bonds.
5. Radiation
UV & X-ray cause coagulation of proteins.
They denature proteins irreversibly by
disrupting the hydrogen bonds and hydrophobic bonds.
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6. pH
Changing the pH will disrupt hydrogen bonds
and salt bridges causing irreversible
denaturing. (H2SO4, HCl, HNO3).
7. Oxidizing & reducing agents
- Bleach (chlorine), nitric acid, both oxidizing
agents.
- SO32- (sulfites) & oxalates are reducing
agents. Both denature proteins by disrupting
disulfide bridges.
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8. Salting out:
- The vast majority of proteins are insoluble in
saturated salt solutions and precipitate out
unchanged.
- It is possible to separate proteins from other
proteins in a mixture by placing the mixture in
a saturated solution of (NH4)2SO4, Na2SO4 or
NaCl.
- The protein is precipitated out and removed
by filtration.
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