L4 - Roles of Proteins

objectives

Understandings:

• Proteins are polymers of 2-amino acids, joined by amide links (also known as peptide bonds).
• Amino acids are amphoteric and can exist as zwitterions, cations and anions.
• Protein structures are diverse and are described at the primary, secondary, tertiary and quaternary levels.
• A protein’s three-dimensional shape determines its role in structural components or in metabolic processes.
• Most enzymes are proteins that act as catalysts by binding specifically to a substrate at the active site.
• As enzyme activity depends on the conformation, it is sensitive to changes in temperature and pH and the presence of heavy metal ions.
• Chromatography separation is based on different physical and chemical principles.

Applications and skills:

• Deduction of the structural formulas of reactants and products in condensation reactions of amino acids, and hydrolysis reactions of peptides.
• Explanation of the solubilities and melting points of amino acids in terms of zwitterions.
• Application of the relationships between charge, pH and isoelectric point for amino acids and proteins.
• Description of the four levels of protein structure, including the origin and types of bonds and interactions involved.
• Deduction and interpretation of graphs of enzyme activity involving changes in substrate concentration, pH and temperature.
• Explanation of the processes of paper chromatography and gel electrophoresis in amino acid and protein separation and identification.

Guidance:

• The names and structural formulas of the amino acids are given in the data booklet in section 33.
• Reference should be made to alpha helix and beta pleated sheet, and to fibrous and globular proteins with examples of each.
• In paper chromatography the use of Rf values and locating agents should be covered.
• In enzyme kinetics Km and Vmax are not required.

The role of Proteins

• When a polypeptide chain folds into a three-dimensional shape, it can now play a role in metabolic processes.
• Some proteins are structural components of cells, tissues and organs, while other proteins, known as enzymes, act as chemical messengers, transport molecules or biological catalysts.
• Proteins can also be an energy source for consumers when other forms of energy, like carbohydrates, are not available.

Shape of Proteins

• The shape of the protein will determine its function in biological processes.
• There are two main classes of protein shapes - globular and fibrous.
• There are also protein shapes that are classified as 'disordered', which are those that lack a definite three-dimensional shape.

Globular Proteins

• Globular proteins are those that are more spherical in shape, as determined by their tertiary structure and the intermolecular forces between R groups.
• They tend to dissolve well in aqueous solutions due to the presence of polar R groups on the exterior of the protein and the nonpolar R groups on the interior.
• Globular proteins typically act as chemical messengers (hormones), catalysts (enzymes) and transport molecules, since they are small and can dissolve well in the cytoplasm and bloodstream, which are aqueous solutions.
• Globular proteins are sensitive to high temperatures, which can cause the intermolecular forces holding the shape to weaken, denaturing (unfolding) the protein.

Fibrous Proteins

• Fibrous proteins, also known as scleroproteins, consist of long linear bundles of polypeptide chains that are bonded covalently to one another or held together by disulfide bridges (also a covalent bond) or by hydrogen bonds.
• Fibrous proteins are generally not soluble in aqueous environments due to the presence of exposed R groups that contain a variety of polar and nonpolar functional groups.
• Fibrous proteins generally form the basis of structural elements in an organism, due to their strength, or storage proteins.
• Fibrous proteins are less sensitive to high temperatures, compared to globular proteins, as fibres are held together by covalent bonds, rather than intermolecular forces.

Proteins as Enzymes

• One very important role of some globular proteins is as enzymes.
• Enzymes are biological catalysts that increase the rate of a reaction by providing an alternate pathway with lower activation energy.
• For some biological processes, the reaction would not even occur without the action of an enzyme.
• Most biological processes require a catalyst as a means of controlling timing or frequency of the reaction.
• Low levels of an enzyme or an incorrectly folded enzyme can result in certain biological functions not occurring correctly.
• Enzyme names often end in '-ase' with the beginning of their name referring to the reaction they catalyse.
• For example, lactose, a type of sugar found in dairy products, is broken down by the enzyme lactase.

• Enzymes can work as homogeneous catalysts.
• When homogeneous, they are in the same phase as the other species in the reaction, which is aqueous for most biological processes.
• Homogeneous catalysts generally provide a surface for the reaction to take place, helping with the orientation of the species involved.
• The enzyme's shape allows for the interaction with other specific compounds, referred to as substrates, fitting together like a key into a lock, known as the 'lock and key' model.
• Many catalysts play a role in the synthesis or decomposition of a substance.
• The shape of the substrate is complementary to the active site of the enzyme, forming a temporary complex during which the chemical reaction takes place.
• The active site and substrate must fit correctly in order for the reaction to be catalysed.
• The presence of an incorrect substrate or a mistake in the protein folding for the enzyme will result in the reaction not taking place.

• An alternate model to explain the function of enzymes is the 'induced fit model'.
• It has been proposed that some enzymes function by changing their shape once the substrate binds to the active site.
• Since globular proteins are folded and held together by intermolecular forces, they can exhibit some flexibility in their shape.
• This means that substrates that seem to be a different size or a different shape than the active site will be able to fit.

Measuring Enzyme Activity

• Studying the effect of an enzyme on a chemical reaction can be difficult, since the absence of an enzyme often means that no reaction will occur.
• The concentration of the enzyme, substrate and even external factors of temperature and pH can influence the performance of an enzyme and the rate of the chemical reaction.
• Enzyme studies, known as enzyme assays, are often performed under simulated biological conditions to maintain the concentrations, temperature and pH that the enzyme would typically be performing in.
• Changing any of these factors can result in the increase or decrease of the enzyme's activity.
• Enzyme activity, like any Rate of Reaction experiment, can be measured by the decrease in the concentration of the reactants (the substrate) or in the increase in the concentration of the products, measured generally by mol l-1 s-1.

Concentration

• The rate of reaction can be compared by analysing the initial rate of product formation over time.
• In a graph of concentration versus time, the rate of reaction is expressed by the slope of the tangent line early in the rate of reaction.
• The concentration of the enzyme will directly affect the rate of the chemical reaction, since more of the enzyme is present to catalyse the reaction.

• The concentration of the substrate does not have the same effect on the rate of the reaction.
• When the substrate concentration is relatively lower than the concentration of the enzyme, the rate of reaction will increase as substrate concentration approaches the level of concentration of the enzyme.
• When the substrate concentration is relatively higher than the concentration of the enzyme, there is not enough of the enzyme to catalyse the reaction, so the rate of reaction approaches a maximum.

Temperature

• Temperature can also interfere with the performance of an enzyme.
• The rate of a reaction generally increases with temperature.
• However, since enzymes are globular proteins, heat can easily disrupt the intermolecular forces, causing the enzyme to denature (change its shape).
• A denatured enzyme cannot perform its function, since the shape of the active site will no longer be the same.
• Many organisms have temperature control systems to maintain body temperature in order for enzymes to perform optimally.

pH

• The pH of the aqueous environment can also affect enzyme activity as changes in pH can also cause denaturing of the enzyme.
• For many enzymes, the aqueous environment they are performing in has a pH that is close to neutral, but some enzymes, such as those in the stomach responsible for digestion, must perform in pH ranges that are outside neutral.
• Significant changes to pH can cause the amino acid residues with acid-base activity to gain or lose protons, changing the shape and interactions with other amino acid residues.
• The pH of an aqueous environment can be maintained by the action of a buffer system.

Heavy Metal Ions

• The presence of certain heavy metal ions also affects the performance of an enzyme.
• Some heavy metal ions have the ability to bind to an enzyme, just like a non-competitive inhibitor, causing a decrease in the activity of the enzyme.
• Common heavy metal ions include lead(II) and mercury(II), which bind to a variety of enzymes, causing immediate and long-term health effects.
• For example, lead and mercury ions are both neurotoxins, since they can cause permanent damage to the brain.
• Silver, lead, mercury and copper ions can form a bond with the thiol (-SH) group on cysteine amino acid residues.
• Their presence then causes a change in the shape of the enzyme, resulting in a decrease of function. Since the bond is covalent, the binding of the heavy metal to the enzyme is strong and permanent.