Protein structures

What are proteins made up of?

Amino acids joined by amino acids linked by peptide bonds

What does the primary structure (sequence) of amino acids determine

The final 3D shape and function of a protein

What is a peptide bond

Covalent bond formed by condensation reactions (removal of water)

What are the functions of a protein

Catalysis, transport, structure and motion

Which proteins (enzymes) play a role in catalysis?

Enolase - envolved in glycolysis (the breakdown of sugar for energy)

DNA polymerase - helps replicate DNA

Which proteins play a role in transport?

Hemoglobin - carries oxygen in blood

Lactose permease - transport of lactose across cell membranes

Which proteins play a role in structural support?

Collagen - found in connective tissue

Keratin - found in hair, nails, feathers…

Which proteins play a role in movement?

Myosin - muscle contraction

Actin - muscle movement and cell motility

How are peptide bonds broken

By hydrolysis (water is added)

What are the ionizable groups of peptides

One free alpha-amino group

One free alpha-carboxyl group

Some R-groups (side chains)

Why are there non-amino acid components in proteins

Proteins → made up of polypeptides

They are not always JUST chains of amino acids

Some proteins require extra components to work correctly

What are the names of non-amino acid components in proteins

Cofactors, coenzymes and prosthetic groups

What are cofactors?

Non-protein molecules that assist protein function

Can be:

• Metal ions - help catalyse enzyme reactions

• Organic molecules - assist protein function

E.g. Hemoglobin uses iron (Fe2+) in heme group to bind and transport oxygen

What are coenzymes?

Organic molecules that assist the catalysation of molecules

Not permanently attached to protein

What are prosthetic groups?

Permanently bound to the protein

Play role in protein stability and function

E.g. Heme in myoglobin to help store and transport oxygen

What is the different between monomeric and multimeric proteins

Monomeric - one polypeptide chain. E.g. Myoglobin

Multimeric - two or more polypeptide chains. each chain is called a subunit and are non-covalently linked. E.g hemoglobin (4 subunits)

Difference between simple and conjugated proteins

Simple - only composed of amino acids, no additional chem group

Conjugated - contains amino acids + other chemical components (prosthetic group) which are critical for protein function

What are examples of weak, noncovalent interactions

Hydrophobic effect - non polar avoid water

Hydrogen bonding - forms between polar groups

Ionic interactions - attraction between charged side chains

Van der Waals forces - weak short range attractions

What is native conformation

Proteins fold into a specific 3D shape

What are chaperone proteins

Proteins that help proteins fold correctly

How does the hydrophobic effect cause protein folding

Hydrophobic amino acids cluster inside protein

Hydrophilic amino acids stay on the outside

This lowers entropy (low chaos of protein as water-loving molecules are outside and water-fearing molecules are inside) → folding is favourable

How do hydrogen bonds help stabilise folding?

Hydrogen bonds form between backbone atoms and the side chains of polar amino acids

They help maintain protein structure and overall protein stability

How do ionic interactions provide extra stability during folding?

Salt bridges occur between positively and negatively charged amino acid side chains

They increase stability, especially for proteins functioning at extreme pH

How do Van der Waals forces promote protein folding

Van der Waals forces - Short range interractions between nonpolar atoms

Individually are weak, but when combined they provide stability

Help protein maintain tight packing in folded state

What are the 4 levels of protein structure

Primary - sequence amino acids

Secondary - local structure like alpha helices and beta sheets

Tertiary - overall 3D folding of polypeptide

Quaternary - interaction of multiple polypeptide chains

What are the 4 types of proteins

Fibrous proteins - long strands

Globular proteins - spherical and water soluble

Membrane proteins - found in cell membranes

Intrinsically disordered proteins - lack of fixed shape

What is cellular proteostasis

Cellular system that ensures proteins fold correctly and prevents misfolding

What is denaturation

Loss of structure and function due to; heat, pH changes, organic solvents, chaotropic agents

Misfolded proteins can lead to:

Diseases such as (Alzeimers, Parkinsons, Huntingtons…)

What are amyloid fibers?

Insoluble protein aggregates when proteins misfold

Misfolded proteins stick together and form long, rigid fibrils

These fibers accumulate and cause cell damage in tissue