F334 - The Thread of Life

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Rates of Reaction

Rate of reaction = change in concentration of reactant or product / time taken

Rate equation

For the general reaction:

A + B → products

The rate equation would be, rate = k[A]^m[B]^n where:

[A] and [B] are the initial concentrations of reactants A and B

k is the rate constant for the reaction at a specified temperature

m is the order of reaction with respect to reactant A

n is the order of reaction with respect to reactant B

(n+m) is the overall order of the reaction

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Rates of Reaction

Reaction Mechanisms

The slowest step in a multi-step reaction is called the rate-determining step. The rate equation for a reaction tells us which particles are involved in the rate-determining step. 

For example:

(CH3)3CBr + OH- → (CH3)3COH + Br-

rate = k[(CH3)3CBr]

The reaction is first order with respect to 2-bromo-2-methylpropane and zero order with respect to hydroxide ions. 

This means that the rate-determining step only involves 2-bromo-2-methylpropane.

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Optical Isomerism

Stereoisomers are molecules that have the same molecular formula and also have their atoms bonded in the same order, but these atoms are arranged differently in space. There are two types of stereoisomers- E/Z isomers, and optical isomers.

For a molecule to exhibit optical isomerism, it must have a chiral carbon centre. Molecules with a chiral centre have non-superimposable mirror images.

There are two ways in which optical isomers behave differently from each other.

- Optically active molecules rotate the plane of plane-polarised light in different directions. One isomer (the L- isomer) rotates the light anti-clockwise, while the other isomer (the D- isomer) rotates the light clockwise.

- Optical isomers behave differently in the presence of other chiral molecules. For example, the different smells of oranges and lemons are due to the two optical isomers of the molecule limonene interacting with the chiral receptors in your nose.

Some chemical reactions produce a 50:50 mixture of D- and L- optical isomers- called a racemic mixture.

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Amino Acids and Proteins

Amino acids are bifunctional molecules- they contain both a -COOH (carboxyl) group and a -NH2 (amino) group.

Apart from glycine, all α-amino acids (all four functional groups attached to the same carbon)) can exhibit optical isomerism as they have four different functional groups attached to the central carbon atom.

Amino acids can act both as weak acids and weak bases. The -COOH group donates H+ ions, while the -NH2 group accepts H+ ions. Amino acids can exist in three different ionic forms, depending on the pH of the solution they are in.

In acidic conditions, the NH2 group is protonated forming NH3+.

In basic conditions, the COOH group is deprotonated forming COO-.

An ion can have both a positive and a negative group at the same time, called a zwitterion.

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Amino Acids and Proteins

Forming dipeptides, polypeptides and proteins

Two amino acids can join together to form a dipeptide. The NH2 group of one amino acid reacts with the COOH group of another amino acid, forming a secondary amide group or a peptide link.

When several amino acids join together like this, a polypeptide is formed.

Proteins are naturally occuring condensation polymers formed when many amino acids join together.

                     

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Proteins

The structure of proteins

Primary structure: The order in which amino acids join together (determined by base sequence of DNA)

Secondary structure: When a polypeptide chain forms an alpha helix or beta sheet (occur as a result of hydrogen bonding)

Tertiary structure: The folding of a polypeptide chain to give it a unique shape. 

There are four types of interaction responsible for maintaining tertiary structure:

- instantaneous dipole- induced dipole bonds between non-polar side chains

- hydrogen bonds between polar side chains

- ionic bonds between ionisable side chains

- covalent bonds

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Proteins

Hydrolysis of peptides/proteins

Reagents and conditions for hydrolysis:

- moderately concentrated (sulfuric/hydrochloric) acid OR

- moderately concentrated base

- heat under reflux

Under acidic hydrolysis conditions, the NH2 groups are protonated to form NH3+, whereas in basic hydrolysis conditions, the COOH deprotonates to form COO-.

The amino acids produced by peptide hydrolysis can be identified using thin-layer chromatography and the use of ninhydrin as a locating agent.

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Enzymes and Atom Economy

Enzymes are metabolic catalysts.

They have a high specificity for a given substrate. All enzymes have active sites where the tertiary structure of the enzyme is complementary to its substrate. The substrate can weakly bind to the surface of the active site. This may weaken bonds in the substrate or slightly alter its shape, allowing a reaction to occur. After the reaction, the products can leave the active site and the process is repeated.

Any changes to the shape of the active site- such as disruption of hydrogen bonds on heating, or disruption of ionic interactions through changes in pH- will result in the enzyme becoming denatured, and losing its activity.

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Enzymes and Atom Economy

Enzyme-catalysed reactions

At low concentrations of substrate, the rate equation is: rate = k[E][S].

There are plenty of active sites for the substrate to bind to- so doubling the substrate concentration doubles the rate of reaction. Making the reaction first order with respect to the substrate.

At high concentrations of substrate, the rate equation is: rate = k[E].

This is because all of the active sites on the enzymes have become saturated. The reaction becomes zero order with respect to the substrate.

Enzymes in industry

Enzymes are used increasingly as catalysts in industry because:they are specific- they can 'select' a particular substrate from a feedstock containing a mixture of reactants, they work effectively at low temperatures- this helps to reduce the energy costs of an industrial process, they work well in an aqueous environment- this reduces the need for organic solvents, which can be flammable and damaging to the environment, they can often convert reactant to product in a one-step reaction- this increases the percentage atom economy of the process.

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