Download Molecules, Genes, and Diseases Session 2 Protein Structure and

Molecules, Genes, and Diseases
Sun 23/2/2014
Session 2
Protein Structure and Folding
Dr. Mona A. Rasheed
Structure of Session 2
Lecture 3:
Protein Folding and Function
8:00 – 8:50
Lecture 4:
Oxygen Transport Proteins
(Hemoglobin & Myoglobin)
8:50 – 9:40
Work Session 1
10:00 – 12:00
MGD Session 2, Protein Structure & Function
Learning Outcomes
At the end of this session you should be able to:
1. Describe what is meant by the primary, secondary,
tertiary and quaternary structure of proteins.
2. Describe the types of bonds and forces involved in
protein structure.
3. Explain the key features of the two major secondary
structure elements of proteins (α-helix and β -sheet).
4. Explain the physiological roles of myoglobin and
haemoglobin.
MGD Session 2, Protein Structure &
Function
Learning Outcomes
5. Contrast the oxygen-binding properties of myoglobin and
haemoglobin and explain why haemoglobin is most suited to its
role as an oxygen transporter.
6. Describe the major structural differences between oxygenated
and deoxygenated haemoglobin and the molecular basis of
cooperativity.
7. Describe the effects of CO2, H+, 2’3bisphosphoglycerate and
carbon monoxide on the binding of oxygen by haemoglobin, and
the physiological significance of these effects.
8. Appreciate that mutations in globin genes can give rise to
diseases such as sickle cell anaemia or thalassemia.
MGD Session 2, Protein Structure & Function
Proteins
• Proteins are the primary structural and functional
polymers in living systems.
• Only 20 amino acids are coded by DNA to appear in
proteins.
• Proteins are synthesized as a sequence of amino acids
linked together in a linear polyamide (polypeptide)
structure, but they assume complex three-dimensional
shapes in performing their function.
MGD Session 2, Protein Structure & Function
Proteins
• The linear sequence of the linked amino acids
contains the information necessary to generate
a protein molecule with a unique threedimensional shape.
• The complexity of protein structure is best
analyzed by considering the molecule in terms
of four organizational levels, namely , primary,
secondary , tertiary , and quaternary.
MGD Session 2, Protein Structure & Function
Proteins
• Many proteins also contain modified amino
acids and accessory components, termed
prosthetic groups.
• A range of chemical techniques is used to
isolate and characterize proteins by a variety of
criteria, including mass, charge, and threedimensional structure.
MGD Session 2, Protein Structure & Function
Levels of protein structure
MGD Session 2, Protein Structure &
Function
PRIMARY STRUCTUR E OF PROTEINS
• The sequence of amino acids in a protein is called the
primary structure o f the protein .
• Understanding the primary structure of proteins is
important because many genetic disease s result in
protein s with abnormal amino acid sequences , which
cause improper folding and los s or impairment o f
normal function.
• The primary structures of the normal and the mutated
protein s are known, this information ma y be used to
diagnose or study the disease .
MGD Session 2, Protein Structure & Function
PRIMARY STRUCTUR E OF PROTEINS
• The bonds responsible for the stabilization of
primary structure is only the peptide bonds.
• Peptide bond s are not broken by heating or
high concentrations of urea.
• Prolonged exposure t o a strong acid or base at
elevated temperatures is required t o hydrolyze
these bonds.
MGD Session 2, Protein Structure & Function
Secondary Structure of Proteins
• The polypeptide backbone forms regular
arrangements of amino acids that are located
near to each other in the linear sequence.
• These arrangements are termed the secondary
structure of the polypeptide .
• The α-helix, β-sheet , and β-bend are examples
o f secondary structures.
• Collagen helix , another example o f secondary
structure , will discussed in the future.
MGD Session 2, Protein Structure & Function
Alpha Helix
• The Alpha Helix Is a Coiled Structure
Stabilized by Intra- chain Hydrogen Bonds.
• Essentially all a helices found in proteins are
right handed.
• Hydrogen-Bonding Scheme For an a helix. In
the a helix, the CO group of residue n forms a
hydrogen bond with the NH group of residue
n+ 4
MGD Session 2, Protein Structure &
Function
Alpha Helix
MGD Session 2, Protein Structure &
Function
Alpha Helix
MGD Session 2, Protein Structure &
Function
Alpha Helix
Amino acids per turn
Each turn o f a n α-helix contains 3.6 amino acids, and has a
0.54nm pitch. Thus , amino acid residues spaced three or four
apart in the primary sequence are spatially close together when
folded in the α-helix.
Amin o acids that disrupt an α-helix :
• Proline.
• Large numbers of charged amino acid.
• Large numbers of amino acids with bulky side chains, such as
tryptophan , or amino acids, such as valine or isoleucine, that
branch at the β-carbon .
MGD Session 2, Protein Structure &
Function
β- Sheet
1. An Antiparallel β Sheet.
Adjacent β strands run in opposite directions. Hydrogen
bonds between NH and CO groups connect each amino
acid to a single amino acid on an adjacent strand,
stabilizing the structure.
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Structure of a β - Strand. The side chains (green)
are alternately above and below the plane of the
strand
1. An Antiparallel β Sheet.
2. A Parallel β Sheet
Adjacent β - strands run in the same direction. Hydrogen
bonds connect each amino acid on one strand with two
different amino acids on the adjacent strand.
3. Reverse Turn:
The CO group of residue i of the
polypeptide chain is hydrogen bonded
to
the NH group of residue i + 3 to
stabilize the turn
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Reverse Turn
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Tertiary structure
• The overall 3-dimensional structure of a protein is
referred to as the tertiary structure. This involves
folding up of the secondary structures so that amino
acids far apart in the primary sequence may interact.
• Larger proteins (~200 amino acids or greater) tend to
have distinct domains. These are regions of the
polypeptide that have distinct structures and often serve
particular roles (e.g. ligand binding, interaction with
other proteins etc.)
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Tertiary structure
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Bonds involved:
Hydrogen bonds
Van der Waals
Hydrophobic interactions
Covalent (disulphide) bonds
Ionic interactions
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Protein folding
• Interactions between the side chains o f amino
acids determine how a long polypeptide chain
folds into the complex three-dimensional
shape o f the functional protein .
• Protein folding, occurs within the cell in
seconds to minutes
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Role o f chaperones in protein folding
• The information needed for correct protein
folding is contained in the primary structure of
the polypeptide.
• Why most proteins when denatured (see
below) do not take up again their native
conformations under favorable environmental
conditions?
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Role o f chaperones in protein folding
• One answer to this problem is that a protein
begins to fold in stages during it s synthesis ,
rather than waiting for synthesis o f the entire
chain to be totally completed.
• In addition, a specialized group o f proteins,
named "chaperones," are required for the
proper folding of many species of proteins.
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Quaternary structure
• Many proteins consist of more than 1 polypeptide
chain. The polypeptide chains may be identical
(homomeric proteins) or different (heteromeric
proteins).
• The arrangement of these subunits in such proteins
is referred to as the quaternary structure.
• The same types of bonds, that involved in tertiary
structure, are involved in Quaternary structure.
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Globular and fibrous proteins
• Proteins can be categorised into 2 major
groups depending of their higher order
structure: globular or fibrous.
• Most enzymes and regulatory proteins inside a
cell tend to be globular proteins whereas
fibrous proteins tend to provide structure,
support and protection.
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Protein Denaturation
• The loss of protein structure sufficient to cause
the loss of function is known as denaturation.
• Denaturation is brought about by breaking the
bonds that hold that maintain the protein’s
tertiary and secondary structure.
• Denaturing agents include heat, organic
solvents, mechanical mixing, strong acids or
bases , detergents, and ion s of heavy metals
such as lead and mercury.
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Role of b -Mercaptoethanol in Reducing
Disulfide Bonds. Note that, as the disulfides are
reduced, the b-mercaptoethanol is oxidized and
forms dimers
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Reduction and Denaturation of
Ribonuclease
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