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Proteins
• Proteins account for about 50 percent of the organic material in the body (17 percent of the body weight), and they play critical roles in almost every physiological process.
• Proteins are composed of carbon, hydrogen, oxygen, nitrogen, and small amounts of other elements, notably sulfur. They are macromolecules, often containing thousands of atoms.
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Physiologic Roles of Proteins
• Structural Proteins
– keratin, collagen, and elastin. • Keratins strengthen protective coverings such as hair, quills, feathers, horns, and beaks. • Collagens and elastin provide support for connective tissues such as tendons and ligaments.
• Antibodies ‐ defend the body from antigens (foreign invaders).
• Contractile Proteins ‐ actin and myosin are used in force development in all types of muscle
Physiologic Roles of Proteins
• Enzymes – catalysts for biochemical reactions. – Enzymes lower the activation energy and make biological reactions proceed at a higher reaction rate. – To function, an enzyme must come into contact with reactants, which are called substrates in the case of enzyme‐mediated reactions. – The substrate becomes bound to the enzyme, forming an enzyme‐
substrate complex, which then breaks down to release products and enzyme.
Physiologic Roles of Proteins
• Hormonal Proteins ‐ are messenger proteins which help to coordinate certain bodily activities
Physiologic Roles of Proteins
• Receptor Proteins – interact with specific chemical messengers thereby allowing cell to communicate with its external environment
– Locations
• Cell membrane
• Cytoplasm
• Nuclear Membrane
– A molecule which binds noncovalently to a receptor is called a ligand
• Autocrine agent, paracrine, endocrine (hormone), neurocrine (neurotransmitter), neurohormone
• drug, toxin
Many physiologic phenomenon are based on interactions between ligands and protein binding sites
on both enzymes and receptors
• A ligand is any molecule or ion that is bound to a protein by one of the following forces: (1) Electrical attractions between oppositely charged ionic or polarized groups on the ligand and the protein (2) Weaker attractions due to hydrophobic forces between nonpolar regions on the two molecules (3) These types of binding do not involve covalent bonds and are generally reversible.
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Terminology
• The region of a protein to which a ligand binds is known as a binding site. • A protein may contain several binding sites, each specific for a
particular ligand, or it may have multiple binding sites for the same ligand. • Typically, the binding of a ligand to a protein temporarily changes the conformation (tertiary shape) of the protein.
– When this happens, the proteins’ physiologic activity changes
• Enzyme Protein Catalyzes a reaction
• Transport Protein moves something across cell membrane
• Receptor Protein activates a signaling pathway 7
Protein‐Binding Sites
LIGAND
charges and shape are complementary between BINDING SITE
and LIGAND
PRIMARY STRUCTURE
of BINDING SITE
PROTEIN BINDING SITE
FOR THE LIGAND
BENT AND
FOLDED IN
TO 3o
FUNCTIONAL
SHAPE
(CONFORMATION
)
Lock and Key Binding
Receptor Site‐Ligand Binding: Chemical Specificity
• In order for two proteins to bind, they must be close enough together to make bonds, so the charges and the shape must be complementary to have strong binding. • The ability of a protein binding site to bind with specific ligands is known as chemical specificity: – binding site shape and charge determines the type of chemical that can be bound.
• In order to bind properly proteins must have the right conformational shape.
• Some sites only bind one ligand while others can bind many ligands. This is why the shape of the proteins and drugs are so important. The more sites a drug binds to, the higher the chance
of unwanted side‐effects. 10
Chemical Specificity
Protein Binding: Affinity
• The strength of ligand‐protein binding is a property of the binding site known as affinity. • The affinity of a binding site for a ligand determines how likely it is that a bound ligand will leave the protein surface and return to its unbound state. – Binding sites that tightly bind a ligand are called high‐
affinity binding sites
– Binding sites that weakly bind the ligand are low‐affinity binding sites.
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Affinity
Protein Binding: Affinity
• Different proteins may be able to bind the same ligand—that is, may have the same chemical specificity—but may have different affinities for that ligand. • For example, a ligand may have a negatively charged ionized group that would bind strongly to a site containing a positively charged amino acid side chain, but would bind less strongly to a binding site having the same shape but no positive charge. • Affinity has great importance in physiology, because when a protein has a high affinity binding site for a ligand, very little of the ligand is required to bind to the protein. • For example, a therapeutic drug may act by binding to a protein; if the protein has a high affinity binding site for the drug, then only very small quantities of the drug are usually required to treat an illness. This reduces the likelihood of unwanted side effects.
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Binding Site Saturation
• An equilibrium is rapidly reached between unbound ligands in solution and their corresponding protein‐binding sites. • The term saturation refers to the fraction of total binding sites that are occupied at any given time.
• When all the binding sites are occupied, the population of binding sites is 100 percent saturated. When half the available sites are occupied, the system is 50 percent saturated, and so on. • The percent saturation of a binding site depends upon two factors: (1) the concentration of unbound ligand in the solution, and (2) the affinity of the binding site for the ligand.
Saturation
Competition for Binding Sites
• Specificity is not perfect
– Two ligands in equal concentration compete for a binding site
– One with the strongest affinity will reach saturation first
Competition
Competition for Binding Sites
– Examples of competition
• LDH and PDH compete for Pyruvate
– If LDH has higher affinity, Lactate will be formed – If PDH has higher affinity, Acetyl CoA will be formed
– Once LDH is saturated, PDH can get Pyruvate
• Oxygen and Carbon Monoxide compete for hemoglobin binding site
– Carbon monoxide poisoning occurs because it wins due to higher affinity for binding site
» Is not displaced at cell, so eventually all Hb is HbCO
rather than HbO2
Regulation of Binding Site Activity
• Proteins have multiple binding sites for different ligands
• The activity at one can be altered by activity at a second
– ALLOSTERIC MODULATION: non covalent bonds formed between modulator and allosteric site alters binding site
– COVALENT MODULATION (covalent bond formed between phosphate and protein alters affinity for ligand at binding site
Allosteric Modulation
• Allosteric modulation occurs when a protein has two binding sites and the binding of a protein to one of the sites alters the shape of the other.
• One binding site on an allosteric protein, known as the functional (or active) site, carries out the protein’s physiological function. • The other binding site is the regulatory site. The ligand that binds to the regulatory site is known as a modulator molecule, because its binding allosterically modulates the shape, and therefore the activity, of the functional site.
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Allosteric Modulation
Covalent Modulation
• Covalent modulation is the covalent bonding of charged chemical groups bind covalently to some of the protein’s side chains.
– The most common type is the addition of a phosphate group. This is called phosphorylation
• Phosphorylation (adding) and dephosphorylation
(removing) require specifc enzymes.
– A kinase enzyme that adds the phosphate group to another protein.
– A phosphatase is an enzyme that removes the phosphate group from a protein
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Covalent Modulation