Proteins - Calderglen High School – Just another …€¢Levels of protein structure 3) Quaternary structure •Association of two or more polypeptide chains that form a functional

Proteins

(b) Protein Structure and Conformational Change

Protein Structure and Conformational Change

• Proteins contain the elements carbon (C), hydrogen (H), oxygen (O2) and nitrogen (N2)

• Some may also contain sulfur (S)• Proteins are made from single units called amino

acids – there are approx 20 amino acids• Proteins are heteropolymers

– Molecules made up of different repeating units

• The number and sequence of amino acids makes one protein different from another in terms of their shape and function

(i) Amino Acid Sequence Determines Protein Structure

• All amino acids have the same basic structure

– Shown in the diagram below


• Attached to the central carbon there will be:

– An amino group (NH2)

– A carboxyl group (COOH)

– A side chain – also called an ‘R’ group

– A hydrogen atom (H)


• Only the side chain varies from one amino acid to another

• Amino acids are therefore grouped according to the properties of their side chain (R group)

• Amino acids can be grouped as being1) Acidic

2) Basic

3) Polar

4) Non-polar

https://www.youtube.com/watch?v=6OFJXw-Pghs

https://www.youtube.com/watch?v=6OFJXw-Pghs


• The R group may be as simple as a Hydrogen atom (such as in the amino acid glycine) or it may be a carbon skeleton with various groups attached (such as in glutamine).



• The physical and chemical properties of the side chain determine the characteristics of a particular amino acid– Amino acids with non-polar side chains (glycine)

are hydrophobic

– Amino acids with polar side chains are hydrophilic

– Amino acids with acidic side chains are negatively charged (due to the presence of carboxyl group)

– Basic amino acids have amino groups in their side chain that are positively charged


• Peptide bonds

– Amino acids are joined together via strong covalent bonds called peptide bonds

– A peptide bond forms between the amino group of one amino acid and the carboxyl group of the next

– This is a condensation (or dehydration synthesis) reaction


• Peptide bonds

– Note that a molecule of water is removed when these two amino acids join


• Peptide bonds– Although the peptide bond does not permit

rotation around the carbon and nitrogen atoms on either side of the bond, the single bonds on either side of the bond do allow the amino acids to rotate

– This means polypeptide chains are very flexible

– This is a very important property as it will determine how a polypeptide chain twists, folds and coils


• Peptide bonds

– A functional protein is made from one or more polypeptides twisted and folded and coiled into a molecule with a specific shape (conformation)

– It is the amino acid sequence of a polypeptide(s) that determine the final 3D shape of the protein molecule

– This also has an impact on the function of the protein

– E.g. Enzymes being specific to one substrate and antibodies being specific to an antigen


• Levels of protein structure

1) Primary structure

2) Secondary structure

3) Tertiary structure

4) Quaternary structure


• Levels of protein structure1) Primary structure

• Refers to the specific sequence of amino acids (linked by peptide bonds) in a polypeptide chain

• Amino acids do not link randomly – this is determined by the order of bases in DNA

• Even a slight change in the primary structure of a protein can affect its shape and therefore it will not be able to function correctly

• The main type of bonds in primary structure are peptide bonds



1) Primary structure


• Levels of protein structure2) Secondary structure

• Due to alpha helices and beta plated sheets

• Can be in the same polypeptide and both contribute to how the polypeptide chain folds and coils

• Folding and coiling is due to hydrogen bonds

• Hydrogen bonds are weak individually but as they are repeated many times over a relatively long region of the polypeptide chain, they are strong enough to support a particular shape for that part of the polypeptide



2) Secondary structure

• Due to alpha helices and beta plated sheets



2) Secondary structure – Alpha helices

• Held together by hydrogen bonds

• This causes the polypeptide chain to twist and fold and helps to stabilise it

• Several alpha helices can appear in the same polypeptide chain



2) Secondary structure – Beta pleated sheets

• Two beta-pleated sheets lie antiparallel to each other in the same polypeptide chain

• These antiparallel sheets are held together by hydrogen bonds between CO and NH of adjacent amino acids


• Levels of protein structure3) Tertiary structure

• The overall shape of a polypeptide due to its twisting and folding

• Due to the bonding that occurs between the side chains (R groups) of amino acids

• There are 4 types of bonding involved i. Hydrogen

ii. Ionic

iii. Disulphide

iv. Hydrophobic interactions




• Amino acids with hydrophobic (non-polar) R groups usually congregate in clusters at the centre of a protein where they will avoid contact with water

• Van der waals attractions (London dispersion forces) help to reinforce these hydrophobic interactions







• Association of two or more polypeptide chains that form a functional protein

• Polypeptide chain may be the same or could all be different

• Some proteins also have a prosthetic group (a non-protein part, usually metal) – Example: haem in haemoglobin which contains iron




http://www.youtube.com/watch?v=qBRFIMcxZNM

http://www.youtube.com/watch?v=qBRFIMcxZNM


• Effect of temperature and pH on interactions of R groups

– Any factor that changes the interactions of the R groups will change the shape of the protein

– If protein loses its shape it has been denatured

– Increasing temperature melts weaker bonds and finally the strong covalent bonds

– pH can change the acid/base characters of the R groups on particular amino acids


• Effect of temperature and pH on interactions of R groups– If pH or temperature are altered the protein may lose

its conformation and unravel

– This is called denaturation – the protein is biologically inactive

– Most proteins become denatured when they are transferred from an aqueous environment to an organic solvent• Protein turns inside out – its hydrophobic regions change

place with its hydrophilic portions


• Effect of temperature and pH on interactions of R groups

– Excessive heat an also disturb polypeptide chain and alter the weak interactions that stabilise the conformation

– Example: white of an egg becomes opaque during cooking because the denatured proteins are insoluble and solidify

(ii) Hydrophobic and hydrophilic interactions influence the location of cellular proteins

• Membrane composition and organisation

– Eukaryotic cells use membranes to divide the contents of the cell into specialised compartments called organelles

– The membrane is a living, selectively permeable structure consisting of phospholipids and protein molecules


• R groups at surface of protein determine its location within a cell

– Hydrophilic (water loving) R groups will mostly be found at the surface of a soluble protein found in the cytoplasm

– In these proteins, hydrophobic R groups may cluster at the centre to form a globular structure


• Membrane structure– The fluid mosaic structure is the accepted model of

the plasma membrane

– Protein molecules are dispersed throughout the phospholipid bilayer

– Phospholipids form a bi-layer because the hydrophobic tails are shielded from being in contact with water by the hydrophilic heads• Hydrophobic portions of both phospholipids and proteins

form a hydrophobic core

• These hydrophobic interactions hold the bi-layer together


• Membrane structure

https://www.youtube.com/watch?v=JBFvH2jyVvw

https://www.youtube.com/watch?v=JBFvH2jyVvw

Proteins - Calderglen High School – Just another …€¢Levels of protein structure 3) Quaternary structure •Association of two or more polypeptide chains that form a functional

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