Biochemistry - Syllabus Statements B.2 (part 1)

B.2 Part 1 - Proteins

B.2 is quite long, so I will split the post up into 2-3 parts.

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Proteins

Proteins are polymers of 2-amino acids, joined by amide links (also known as peptide bonds).

WHAT ARE PROTEINS?

Proteins are the main building blocks of human tissue. They make up muscles, skin, hair, fingernails and more less obvious things like enzymes.

WHAT'S THE CHEMISTRY?

All amino acids have a common structure, they have a carboxylic acid group, and an amine group. The 'R' group which you're hopefully familiar with from organic chemistry, determines which amino acid it is. There are 20 different naturally occurring amino acids, the simplest of which is glycine where the R group is just H. This R group be anything though.

This diagram will be discussed more below (zwitterions), don't worry if it's confusing

This R group vastly affects the properties of the amino acid.

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Zwitter Ions

Amino acids are amphoteric and can exist as zwitterions, cations and anions.

Application of the relationships between charge, pH and isoelectric point for amino acids and proteins.

Amino acids are amphoteric because of the general structure discussed above. All amino acids have a carboxylic acid group (acidic) and an amine group (basic). This makes amino acids amphoteric because they can react with both acids and bases.

LOW PH

In a low pH situation, the amine group reacts with H+ to form a cation.

​HIGH PH

At a high pH, the carboxylic acid group reacts with OH- to form an anion.

ZWITTERIONS

Zwitterions (Zwitter ions) are when a molecule is both an anion and a cation at the same time. This can occur with amino acids. At a certain pH, amino acids have both a H3N+ group, and a COO- group.

The pH at which this zwitterion occurs is called the Isoelectric point (pI). Every amino acid has it's own isoelectric point, which is dependant on the R group. An acidic R group leads to a lower pI and a basic R group leads to a higher pI.

An extra COOH group in the R group leads to a low pI

Only a H for the R group leads to a pI of 6

Several NH and NH2 groups in the R group leads to a high pI

At a pH higher than that of the isoelectric point, a cation will form and at a pH lower than the isoelectric point, an anion will form.

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Effect of the R group on amino acid properties

Explanation of the solubilities and melting points of amino acids in terms of zwitterions.

MELTING POINT

As you will have learnt in topic 4, melting points are dependant on Intermolecular Forces (IMFs). An R group with a large amount of intermolecular forces will cause the amino acid to have a high melting point. This syllabus statement is basically a repeat of what has already been learnt in topic 4.

SOLUBILITY

Same as above. A more polar R group will be more soluble, just like you learnt in topic 4.

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Protein structures

Protein structures are diverse and are described at the primary, secondary, tertiary and quaternary levels.

Description of the four levels of protein structure, including the origin and types of bonds and interactions involved.

PRIMARY STRUCTURE

This is a protein's one dimensional structure. This is just looking at the sequence of amino acids that are joined to each other.

SECONDARY STRUCTURE

This is looking at proteins on a broader level. Protein chains can fold or coil depending on intramolecular forces in the protein chain. There are two types of secondary structures that proteins can form (besides straight chain).

ALPHA HELIX

Basically a cool looking spiral shape. This is caused by intermolecular forces between different sections of 1 chain that forces the protein into a helix shape. It's usually drawn as a ribbon so that it's helix structure is more easily seen.

BETA PLEATED SHEET

The beta pleated sheet occurs when 2 or more chains (or parts of chains) 'line up' due to intermolecular forces and form a sheet

TERTIARY STRUCTURE

This is an even broader look at a protein. In 1 protein, there's likely to be sections that have an alpha helix structure, and some sections with a beta sheet structure. Looking at the protein chain as a whole is looking at it's tertiary structure.

This diagram shows the tertiary structure of this protein, which has a mixture of alpha helices and beta sheets.

QUATERNARY STRUCTURE

An again broader view of proteins. The tertiary structure looked at only one protein chain. The quaternary structure could have multiple chains bonded together. A common example of this is haemoglobin, which has 4 protein chains bonded together.

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Effect of shape on function

A protein’s three-dimensional shape determines its role in structural components or in metabolic processes.

GLOBULAR PROTEINS

Haemoglobin is an example of a globular protein. Globular proteins usually have complex tertiary and quaternary structures, and are usually somewhat spherical. Because of their complex structure, they are more heat sensitive. The protein chain in a globular protein usually has it's polar R groups exposed, and is therefore more soluble in water.

​FIBROUS PROTEINS

​Fibrous proteins have little or no tertiary or quaternary structures at all, and form long fibres. This structure makes them much 'stronger' than globular proteins. Their polar R groups are not exposed like in globular proteins, making them insoluble. Examples of fibrous proteins would be  in hair, skin and bones, where insolubility and structure are needed.

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Part 2 coming soon

As in as soon as I learn it...