lecture 3 - proteins

What is a protien?

Large molecules (macromolecules) made from smaller units called amino acids

What is another word for amino acids?

Monomers

What are some functions of proteins?

• catalysing chemical reactions - enzymes

• Receiving cellular signals - receptors

• Transporting molecules - transporters

• Forming ion channels

• Providing structural support - cytoskeleton proteins

• Producing movement - motor proteins

• Regulating gene expression - transcription factors

How many types of protein structures are there?

4

What is the primary structure of a protein ?

It is the specific order of amino acids in a polypeptide chain

What is the secondary structure of a protein like?

• local folding of polypeptide backbone

• Beta pleated sheets or alpha helices

• Shape is due to hydrogen bonding between peptide bonding

What are some characteristics of beta pleated sheets?

• formed when 2+ polypeptides line up side-by-side

• Extended competition

• Parallel or anti-parallel

• Stabilised by h bonding

• 0.7 nm pitch

What are some characteristics of alpha helices?

• spiral structure

• Tightly packed , coiled polypeptide backbone core

• Side chain extend outwards

• 0.54 = pitch

• Found in globular proteins

How many types of amino acids are there in?

20

How are amino acids connected?

• they bond via peptide bonds during a condensation reaction

• They Jon together from the N-terminus of an amino group and C-terminus of a carboxylic group

What are the favourable amino acid side chains found on beta pleated sheets?

• threonine

• Valine

• Isoleucine

• Serine

• Aspartic acid

• Asparagine

What are the favourable amino acid side chains found on alpha helices?

• methionine

• Alanine

• Lysine

• Leucine

What are the unfavourable amino acid side chains found on alpha helices?

• glycine

• Proline

Why is alanine favourable in alpha helices ?

They fire small and structurally uncomplicated , therefore an excellent alpha helix former

• has a small methyl side chains

• Causes relatively Little steric interference

Why is leucine favourable in alpha helices?

They are a flexible hydrophobic side chains which are generally favourable for alpha helices

• have a larger branched hydrophobic side chain

• Flexible enough and does not strongly disrupt the backbone geometry

Why is methionine favourable in an alpha helix?

It is a flexible side chains which as it is generally compatible with alpha helix Formation

• it has a long flexible positively charged side chain

• It extends away from backbone so relatively little steric interference

Why is arginine favourable in an alpha helix?

It has a long side chain and postive charge therefore it is often comparatively with alpha helices

• it is a long side chain ending in a postive charged guanidinium group

• Relatively flexible and extended away from the backbone

Why is glycine unfavourable in an alpha helix?

• it is a helix destabiliser

• It’s side chains is simply H

• It has so many angles of rotation , it is conformationally flexible

• The amount of variability makes it energetically expensive to adopt the alpha helix structure

Why is proline unfavourable in an alpha helix?

• it is a helix breaker

• Side chains forms a ring with the backbone nitrogen so it cannot form another H-bond in usual helix structure

• It is unusually rigid and restricts the backbone’s ability to adopt the geometry required for a normal alpha helix

• It is however found at the beginning and end of helices , because of the rigitdity of its structure

Why is threonine, valine and isoleucine favourable in beta pleated sheets?

As they are beta-branched side chains there is a branch ay the beta carbon of the amino acid , which is the first carbon on its side chain , therefore they are favoured in beta sheets

Why are serine, aspartate and asparagine favourable in beta pleated sheets?

As they are polar side chains , they may form h bonds with backbone amino/carboxyl groups

What is the tertiary structure of a protein?

• The overall 3D structure of the entire polypeptide chain

• It is influenced by side chain amino acid interactions

What are the 4 type of weak bonds?

• LDF

• Electrostatic

• H bonds

• Hydrophobic clustering forces - central role in determine the shape of a protein

What is the importance of the final folded structure?

It is the one that minimises its free energy

What is a conformation?

• proteins must fold into a single stable conformation

• It is very dynamic and experiences constant fluctuations caused by thermal energy

• It can change when the protein interacts with other molecules in the cell

What is the quaternary structure of a protein?

• spatial structure formed by the interaction of 2 or more independent tertiary structures

• Trimer - 3

• Tetramer - 4

• Pentamer - 5

What are some examples of proteins providing strength and support?

• collagen - provides strength and structure to skin , bones , tendons and cartilage

• Keratin - provides strength and protection to hair , skin and nails

• Transport proteins - help carry substances such as oxygen, nutrients and hormones around the body

What are some examples of proteins moving molecules or ions?

• haemoglobin - transports O2 around the body

• Transport proteins/ membrane transport proteins

What are some examples of proteins allowing cells to communicate by sending , receiving and transmitting chemical signals ?

• hormones

• Receptors

• Signalling pathway proteins

What are some examples of proteins providing movement and mechanical processes within cell and tissues ?

• actin

• Myosin

• Motor proteins

What is proteostasis?

As proteins must retain conformational flexibility to function they are under constant chaperone surveillance to ensure protein homeostasis

What is protein denaturation?

This is when a protein loses its normal structure and consequently may lose its function

What can cause protein denaturation?

• high temperature

• Extreme pH

• Certain chemicals

• Changes in ionic conditions