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Proteins Notes

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Bioc hemistry - Lecture 4 (08/02/2018)
Amino Acids

The central dogma of molecular biology describes how information encoded in DNA which can self-replicate, flows first to RNA and then to Protein.

The key point here is that information encoded on a linear DNA sequence is translated into
RNA and then a linear protein sequence.
DNA's role includes the storage of information but proteins are the workhorses of the cell with hundreds of functions in which a variety of Chemistry is necessary.

Proteins are therefore composed of not 4 like DNA, but 20 different amino acids.

Protein Functions

 A large group of proteins is responsible for carrying out the chemistry in the cell, these proteins are called enzymes.
 Catalase for example, breaks down hydrogen peroxide.

Transport and Carrier Proteins
 Other proteins specialise in the transport of specific molecules such as lipids or oxygen, such as

Channels and Pores
 The transport of molecules across membranes is enabled by protein channels pumps and pores, such as aquaporin's.

Structural Proteins
 The internal structures shape and support of cells is organised by structural proteins including actin and tubulin of the cytoskeleton or collagen in the connective tissue.

 All active movement in the cell is done by motor proteins, mainly Myosin, Kinesin and Dynein,
this includes specialised cells such as the Cilia.

Gene Expression
 The control of gene expression is also in the hands of proteins including the large class of protein transcription factors.

 Many hormones and almost all hormone receptors are proteins as well.
 It is proteins which relay and amplify hormones and other signals in the cell. 

 Proteins have many functions in defence, such as antibodies or the antimicrobial defence peptides which bind to lipid membranes and form pores in them.

 Many proteins act as adhesives, including Fibrinogen in blood clotting, spider silk and muscle byssus.

The Amino Acids

In order to perform all these varied functions of proteins a sufficiently large collection of amino acids are required.

Proteins are synthesised from 20 different amino acids.

Basic Structure of Amino Acids
All amino acids that are incorporated into proteins have this basic structure:

An Amino group.
A Carboxyl group.
One of 20 different side chains (R-group).

The centre also has a Carbon atom with a single
Hydrogen atom covalently bound.

This type of an amino acid is called an alpha amino acid, and the Carbon atom that carries both the carboxyl group and the amino group is called the alpha Carbon atom.

It's called the alpha Carbon atom as it uses the old numbering system where the Carbons could be labelled: α, β, γ, δ.

Under normal conditions of the cell, amino acids carry both a positive and a negative charge, and this feature is called a Zwitterion.

Titration Curve

The titration curve of an amino acid shows the two pKa values of the ionisable groups.

At pH 1.0 the amino acid is fully protonated.
At pH 2.2 the pKa value of the α carboxyl group is reached, which is now around 50% ionized.
At pH 7.0, both the carboxyl group and the amino groups are ionised (in its Zwitterion state). 

At pH 9.0 the pKa value of the amino group is reached and it begins to lose its protons at around 50% ionisation.

The α Carboxyl groups of amino acids are all relatively strong amino acids and have pKa values between 1.8-2.6.
Similarly the pKa values of the α amino groups are all between 9-10.

Stereochemistry of Amino Acids

All of the amino groups except 1 have an important property that comes from the tetrahedral alpha carbon. Whenever this is the case there are 2x possible arrangements of the amino acids as they can form mirror images of each other (Enantiomers).

There is no way to convert one arrangement into the other merely by rotating bonds.
From this the molecule is addressed as Chiral as it asymmetric.

Hence amino acids are available in 2 different configurations which are mirror images of each other.
These have all the same connections of atoms but their arrangement differs.

These are called Stereoisomers, and if these stereoisomers are exact mirror images of each other then they are referred to as Enantiomers.

The isomers can be classed into Lisomers (Left) and D-isomers (Right).

Only L amino acids are incorporated into Proteins.

The only amino acid which cannot form an Enantiomer is Glycine as it has 2 bound hydrogen atoms to the C alpha which makes it not chiral.

Fisher projections

To indicate which conformation the residues have, the
Fisher projection can be used. 

In the L amino acids through the Fisher projections the amino group is pointed left and in D
amino acids the amino group is pointing right with the R group facing down and the Carboxyl group facing up.

This is how the nomenclature began.

These projections specifically display the stereochemistry surrounding the amino acid.

Amino Acid groups by their Chemical
The chemical properties Amino acids have include:

Acidic, Amides.

Aliphatic Amino Acids

Aliphatic means the side chains are non-aromatic hydrocarbons,
Aliphatic Amino Acids are hydrophobic.

These include Glycine, Alanine,
Aline, Leucine and Isoleucine.

Valine, Leucine and Isoleucine are known as branched amino acids.


Proline contains a Heterocycle (pyrrolidine).

Much less hydrophobic than Aliphatic Amino Acids.

The t=rotation around the N-Cα bond is restricted due to the ring structure.

Aromatic Amino Acids 

The aromatic amino acids have alternating (conjugated)
double bonds with delocalised π electrons.
The Hydrophobicity of these amino acids varies widely, as Phenylalanine is highly hydrophobic and Histidine is highly hydrophilic.
Histidine is interesting as it is a weak acid with a pKa of 6.0.

Hydroxyl (Alcohol) Amino Acids

These amino acids are Polar.

Their Hydroxyl groups engage in hydrogen bonding as hydrogen donors and acceptors.

These hydroxyl groups can also form phosphate esters in protein phosphorylation, which has a fundamental role in signalling within cells.

Amino Acids containing Sulphur

Cysteine is essentially the Sulphur analogue of
Serine and has similar properties, such as the ability to form weak hydrogen bonds.

Cysteine is a much stronger acid than Serine however, with a pKa of 8.3.

The thiolate ion plays many roles in catalytic reactions and is ionisable.
Cysteine can be joined by oxidation in order to form disulphide bonds, and this is very important in stabilising many extracellular proteins, including Insulin.

Methionine is relatively hydrophobic and is always the first amino acid in protein biosynthesis.

Acidic Amino Acid

Acidic Amino acids form salt bridges and polar interactions with water through Hydrogen bonding.

The Side chains of the Aspartate and Glutamate are weaker acids than the Alpha Carbon groups with the
(Asp) and 4.1 (Glu).

Amides of Acidic Amino Acids

pKa of both = 3.9 

The amides of the Acidic Amino acids are acidic or basic or ionisable, but are highly polar.
These are strong Hydrogen donors and acceptors and are typically found on the surfaces of proteins.

Basic Amino Acids

Lysine and Arginine are very strong bases as the N atoms with free electron pairs are very good proton acceptors (basic).

Side chain pKa = 10 (Lys) and 12.5 (Arg).

Things to remember:

General structure of amino acids.
Principle of chirality.
Acid base chemistry (α-amino and carboxyl group and side groups).
Recognise structures.
Chemical Property of Amino Acids

Amino Acids







Alcohols (Hydroxyl)




Acidic Amino Acids


Amides of Acidic Amino Acids



Arginine Biochemistry - Lecture 5 (12/02/2018)

Proteins: Primary and Secondary Structures

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