proteins

what are they?

• A protein is a large macromolecule  

• Perform an enormous range of functions within the body  

• Catalysing chemical reactions – enzymes  

• Transporting molecules – transporter  

• Forming channels – ion channels  

• Providing structural support – cytoskeletal proteins  

• Producing movement- motor proteins  

• Regulating gene expression – transcription factors  

 

amino acids

• An amino acid has a basic structure of amino group (nitrogen,2 hydrogens), side chain (r) and carboxyl group  

Amino acids can be classified by their side chains 

• Non polar – hydrophobic  

• Polar – hydrophilic  

• Acidic – negatively charged at the physiological pH 

• Basic – positively charged at the physiological pH  

These characteristics affect where they are in the protein and how they affect how the protein folds 

R groups of each amino acid:  

• Glycine is the simplest amino acid – r group is just a hydrogen atom  

• Valine – branched hydrocarbon r group  

• Phenylalanine – ringed structured r group  

How are amino acids joined together:  

• Amino acids are connected by peptide bonds  

• These form between the carboxyl group of one amino acid and the amino group of another amino acid (positive/negative)  

• This reaction releases a molecule of water – this is a condensation / dehydration reaction   

• A dipeptide forms after this reaction  

• This can be repeated many times to form a long polypeptide chain 

• These polypeptide chains have direction – n-terminus to c-terminus  

• Writing our amino acids from n to c terminus  

• The peptide bonds formed between the chain are covalent bonds so they're strong and stable   

Protein structure:  

 

• Proteins have different level of structure: primary, secondary, tertiary and quaternary 

• Primary – sequence of amino acids forming a polypeptide chain 

• Secondary- local folding goes on

• Tertiary - more 3D folding of the protein

• Quaternary- interaction of multiple subunits in proteins

Primary structure:

• Primary sequence is the specific order of amino acids in a polypeptide chain

• Chain of codons that generates the chain of amino acids in their basic form

• One change of the amino acid in the primary sequence can cause a huge effect on protein structure

Secondary structure:

• econdary structure refers to the local folding patterns of the polypeptide backbone

• There are two main shapes that take place due to the hydrogen bonding between the peptide backbone

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• Directly controlled by the amino acid sequence therefore indirectly controlled by gene sequence

  

Alpha helix:

• Spiral structure with aa tightly packed polypeptide backbone core

• Side chains extend outwards

• Stabilised by the hydrogen bonding with the carboxyl oxygen and amide hydrogen

• 3.6 amino acids per turn

• Mostly found in globular proteins

 

Favourable amino acids in an alpha helix:

• Methionine (M)

• Alanine (A)

• Arginine ( R )

• Lysine (K)

• Leucine (L)

Their side chains are relatively small and simple, preventing steric clashes

Alanine (A) – Small and structurally uncomplicated

• Alanine is one of the best α-helix-forming amino acids.

• It has a small methyl (-CH₃) side chain.

• The small size means there is very little steric interference between the side chain and the protein backbone.

• This allows the backbone to adopt the regular geometry required for an α-helix.

• Alanine does not have a bulky or highly constrained side chain, so it can fit comfortably within the helical structure.

• Its small side chain also allows neighbouring amino acids to pack together without causing significant clashes.

• Overall: Alanine strongly favours α-helix formation because its small, simple side chain causes minimal steric hindrance.

Leucine (L) – Flexible hydrophobic side chain

• Leucine is generally a favourable amino acid for α-helix formation.

• It has a large, branched hydrophobic side chain.

• Although its side chain is larger than alanine's, it is flexible enough to avoid interfering with the backbone.

• The side chain extends away from the backbone, leaving the backbone relatively free to form the α-helical structure.

• Leucine's hydrophobic side chain can also contribute to hydrophobic interactions with other residues within a protein.

• Its structure does not impose strong restrictions on the backbone angles needed for an α-helix.

• Overall: Leucine favours α-helices because its flexible side chain can accommodate the helical backbone geometry without causing major steric clashes.

 

Methionine (M) – Flexible side chain

• Methionine is generally compatible with α-helix formation.

• It has a relatively long and flexible side chain containing sulphur.

• The side chain has several rotatable bonds, allowing it to adopt different conformations.

• This flexibility means it does not strongly restrict the movement or geometry of the protein backbone.

• Methionine's side chain can extend away from the backbone, reducing steric interference with the α-helix.

• It is also hydrophobic, so it can contribute to hydrophobic interactions within the protein.

• Overall: Methionine is favourable for α-helices because its flexible side chain can accommodate the regular geometry of the α-helical backbone.

 

Lysine (K) – Long, flexible side chain with a positive charge

• Lysine is often compatible with α-helix formation.

• It has a long, flexible side chain ending in a positively charged amino group.

• The side chain extends away from the backbone, so the positive charge is relatively far from the peptide backbone.

• This reduces the likelihood of steric interference with the α-helical structure.

• The flexibility of the side chain allows it to move into a suitable position without strongly restricting the backbone.

• Lysine can also form electrostatic interactions with negatively charged amino acids, such as aspartate (D) and glutamate (E).

• These interactions can sometimes help stabilise an α-helix.

• Overall: Lysine is often favourable because its long, flexible side chain causes little steric interference and can form stabilising interactions with other charged residues.

 

Arginine (R) – Long side chain with a positive charge

• Arginine is often compatible with α-helix formation.

• It has a long, flexible side chain that ends in a positively charged guanidinium group.

• The long side chain allows the charged group to extend away from the protein backbone.

• This means there is relatively little steric interference with the α-helical backbone.

• Its flexible side chain allows arginine to adopt different conformations while the backbone maintains the regular α-helix structure.

• The positively charged guanidinium group can form electrostatic interactions with negatively charged residues.

• It can also form hydrogen bonds, which may contribute to protein stability.

• Overall: Arginine is often compatible with α-helices because its long, flexible side chain keeps the charged group away from the backbone while allowing favourable interactions with other residues.

Unfavourable amino acids in an alpha helix:

Glycine (G) – Helix destabiliser

• Glycine has a very small side chain: just H.

• This makes glycine very flexible.

• It can rotate into many different angles and shapes.

• An α-helix needs the backbone to stay in a specific, regular shape.

• Glycine's flexibility makes it harder to maintain this shape.

• This makes forming an α-helix less energetically favourable.

• Overall: Glycine destabilises α-helices because it is too flexible.

 

Proline (P) – Helix breaker

• Proline has a side chain that forms a ring with the backbone nitrogen.

• This makes proline very rigid.

• It restricts the rotation of the backbone, making it difficult to form the normal α-helix shape.

• Proline's backbone nitrogen also cannot form the usual hydrogen bond needed in an α-helix.

• This can cause a bend or kink in the helix.

• Overall: Proline breaks α-helices because it is too rigid and disrupts hydrogen bonding.

 

Proline at the ends of α-helices

• Proline can sometimes be found at the beginning or end of an α-helix.

• At the ends, its effects are less disruptive because there are fewer hydrogen bonds to interrupt.

• Its rigid structure can also help define the end of the helix.

• Key point: Proline is mainly a helix breaker when it is within the middle of an α-helix.

Beta sheet:

• Formed when 2 or more polypeptides line up side by side

• 2 types : parallel and anti-parallel

• The distance between amino acids in beta sheets is 0.7nm

Favourable amino acids in a beta sheet:

Beta-branched side chains – Threonine (T), Valine (V) and Isoleucine (I)

• Have a branch at the beta (β) carbon of the side chain.

• This structure makes them well suited to beta sheets.

• Their side chains fit well with the extended shape of a beta sheet.

• Examples: Threonine, Valine and Isoleucine.

• Beta-branched amino acids are favourable for beta sheets because their side chains fit well with the beta sheet structure.

 

Polar side chains – Serine (S), Aspartate (D) and Asparagine (N)

• Have polar or charged side chains.

• Their side chains can form hydrogen bonds.

• These hydrogen bonds can form with the backbone amino and carboxyl groups.

• This can help stabilise the beta sheet.

• Examples: Serine, Aspartate and Asparagine.

• Polar amino acids can favour beta sheets because they can form hydrogen bonds that help stabilise the structure.

 

Tertiary structure:

• Overall 3D structure of the entire polypeptide

• Tertiary structure involves interactions between amino acids side chains with another - many different set of noncovalent bonds

• 3D structure formed due to interactions between the R groups of the amino acids that make up the protein

• Three types of weak bonds: hydrogen bonds, electrostatic attractions and van der waals

• Other force involved is the hydrophobic clustering force - hydrophobic core forms

• The final folded structure of any polypeptide chain is one that minimises its free energy

• Most proteins it has a single stable conformation

• Conformation is very dynamic, experiencing constant fluctuations caused by thermal energy

• A proteins conformation can change when the protein interacts with other molecules in the cell

Properties of amino acids:

 

Amino acids have different properties depending on their R group (side chain). The R group determines how the amino acid behaves and how it interacts with other amino acids and water.

 

ALIPHATIC AMINO ACIDS

• Aliphatic side chains contain carbon and hydrogen and do not contain an aromatic ring.

• They are generally non-polar and hydrophobic.

• They tend to avoid water and are often found in the inside of proteins.

• Their side chains can vary in size and shape.
  Examples:

• Alanine (A) – small methyl group

• Valine (V) – branched side chain

• Leucine (L) – branched hydrophobic side chain

• Isoleucine (I) – branched hydrophobic side chain

• Glycine (G) – smallest amino acid; R group is H

 

AROMATIC AMINO ACIDS

 

• Have an aromatic ring in their R group.

• The ring contains a system of alternating bonds that gives it special chemical properties.

• They are generally hydrophobic.

• Aromatic amino acids can be involved in hydrophobic interactions within proteins.

• Their aromatic rings can also interact with other aromatic groups.
  Examples:

• Phenylalanine (F) – contains a benzene ring

• Tyrosine (Y) – contains a benzene ring with an -OH group

• Tryptophan (W) – contains a larger aromatic ring system

SULPHUR-CONTAINING AMINO ACIDS

• Contain a sulphur atom in their R group.

• The two sulphur-containing amino acids are:

  • Cysteine (C)

  • Methionine (M)

• Sulphur can give these amino acids important roles in protein structure and function.

• Cysteine is particularly important because it can form disulphide bonds.
  CYSTEINE (C) – R GROUP

• Cysteine has the R group: -CH₂-SH.

• The -SH group is called a thiol group.

• Two cysteine molecules can react with each other to form a disulphide bond.

• This forms a covalent bond between the two sulphur atoms.

• Disulphide bonds help stabilise the 3D structure of proteins.

• They are particularly important in proteins found outside cells.

• Cysteine is therefore important for maintaining protein structure.

METHIONINE (M) – R GROUP

• Methionine has a sulphur atom within its R group.

• Its R group is: -CH₂-CH₂-S-CH₃.

• It is generally non-polar and hydrophobic.

• Unlike cysteine, methionine does not normally form disulphide bonds.

• Its flexible side chain allows it to fit into different protein structures.

 

• Aliphatic → usually non-polar and hydrophobic.

• Aromatic → contain an aromatic ring and are generally hydrophobic.

• Sulphur-containing → cysteine and methionine.

• Cysteine → contains an -SH group and can form disulphide bonds.

• Methionine → contains sulphur but does not form disulphide bonds.

• The R group determines the properties and behaviour of each amino acid.

 

Disulphide bonds:

• Covalent disulphide bonds can form interchain (between two different polypeptides) or intrachain which is between two cysteines in the same chain

• These covalent bonds are the strongest type of bond and 300x stronger then the weak noncovalent bonds

• Much more energy required to break one covalent bond

• Can make a protein much more stable

 

Properties of amino acids:

• Different R groups are capable of hydrogen bonding :

• Amino acids with a hydroxyl (OH) are capable of hydrogen binding

• E.g.  Serine , threonine and tyrosine

• Amide containing amino acids are capable of hydrogen bonding

• E.g. asparagine and glutamine

• These are both polar and hydrophilic, however are not charged

 

Properties of amino acids:

• These R groups are capable of hydrogen bonding

• Due to being electrically charged they are capable of charge - charge interactions

• There are acidic and basic types.

Quaternary structure:

• Some proteins have a quaternary structure

• Spatial structure formed when two or more independent tertiary structures (polypeptide chains)

• Trimer - 3 polypeptide chains interacting

• Tetramer - 4 polypeptide chains interacting

• Pentamer - 5 polypeptide chains interacting

• When these form together, this is what forms the quaternary structure

• If all polypeptide bonds are the same it would be called a homotrimer

• If one or two are different it would be a hetrotimer

Functions of proteins: 

• Proteins three dimensional structure creates specific surfaces, pockets and binding sites 

• These allow proteins to interact with: 

• other proteins  

•  DNA 

• Small molecules  

• Lipids  

• Carbohydrates  

• Ions 

 

Functions of proteins:

1. Strength and support

• Proteins provide strength, support and structure to different parts of the body.

• Example: Collagen – provides strength and structure to the skin, bones and tendons.

 

2. Transport

• Some proteins transport substances around the body, such as oxygen and nutrients.

• Transport proteins can also move molecules or ions across cell membranes.

• Example: Haemoglobin – transports oxygen from the lungs to body tissues.

 

3. Communication and signalling

• Proteins allow cells to communicate with each other by sending and receiving chemical signals.

• This helps control important processes such as growth, metabolism, movement and reproduction.

• Example: Hormones – chemical messengers that carry signals around the body.

 

4. Defence and protection

• Proteins help protect the body against pathogens, such as bacteria and viruses.

• Example: Antibodies – proteins involved in the adaptive immune response that help recognise and defend against pathogens.

 

Protein homeostasis – proteostasis:  

• Proteins must retain conformational flexibility to function  

• They are only marginally thermodynamically stable in their physiological environment 

• As protein molecules are highly dynamic, constant chaperone surveillance is required ensuring protein homeostasis  

 

Protein denaturation:   

• Denaturation  occurs when a protein loses its normal structure and may lose its function  

• Long and disordered denatured protein

• Denaturation can be caused by: 

• High temperature  

• Extreme pH 

• Certain chemicals  

• Changes in ionic conditions  

• Denaturation does not mean that the peptide bonds have been broken , more to do with the weaker noncovalent bonds between higher structures

• Primary structure remains intact

• Some denaturation can be reversed, however some cannot be revered when a high temperature or pH has been used

What goes wrong when proteins go wrong?

Normal physiological role

Two important proteins are involved:

Amyloid-β (Aβ) monomers

A monomer is a single protein/peptide molecule.

Under normal conditions, Aβ has proposed physiological functions, including:

• Synaptic function – contributes to normal communication between neurons.

• BBB protection – may have a role in protecting the blood–brain barrier.

• Antimicrobial activity – Aβ may help defend against certain pathogens.

So, Aβ is not inherently a “bad” protein. It can have normal biological functions.

 

Tau monomers

Tau is a protein associated with microtubules, which are part of the neuronal cytoskeleton.

Its normal functions include:

• DNA protection

• Microtubule stabilisation – helps maintain the structure of neurons and facilitates intracellular transport.

• Dendritic development – contributes to the development and maintenance of neuronal structures.

2. Misfolding and oligomerisation

The key step in the diagram is oligomerisation.

Oligomerisation = individual protein molecules (monomers) joining together to form oligomers.

Under pathological conditions, Aβ and tau can adopt abnormal conformations and begin to aggregate.

The progression can be thought of as:

Monomer → misfolded protein → oligomer → larger aggregates

These abnormal protein assemblies can interfere with normal neuronal function.

 

3. Aβ oligomers → amyloid pathology

When Aβ molecules aggregate, they can form Aβ oligomers and eventually larger deposits known as amyloid plaques.

The diagram highlights several pathological effects of Aβ oligomers:

• Synaptic dysfunction → disrupts communication between neurons.

• Microglial activation → activates immune cells in the brain, contributing to neuroinflammation.

• Ca²⁺ dyshomeostasis → disrupts normal calcium ion regulation within neurons.

Why is this important?

Synapses are essential for neurons to communicate. If Aβ oligomers interfere with synaptic signalling, neuronal communication becomes impaired.

Abnormal calcium regulation can also damage neurons because excessive intracellular Ca²⁺ can activate damaging pathways and contribute to neuronal dysfunction and death.

4. Tau oligomers → neurofibrillary tangles

au can also misfold and aggregate.

Normally, tau helps stabilise microtubules. When tau becomes abnormally modified and misfolded, it can detach from microtubules and aggregate into tau oligomers.

These can eventually form neurofibrillary tangles (NFTs).

The diagram associates tau oligomers with:

• Disrupted neural circuits → impaired communication between groups of neurons.

• Microtubule degradation → loss of normal neuronal structure and intracellular transport.

• Synaptic loss → loss of functional connections between neurons.