Proteins CAQ

🥛 Proteins Describing and explaining how the different bonds and intermolecular interactions maintain the different levels of protein structures Explaining Hydrogen bonds can be formed between a hydrogen is attached to a highly electronegative atom such as nitrogen and atom making the hydrogen carry a partial positive charge, and a electronegative atom such as oxygen and nitrogen Ionic bonds are formed between oppositely charged R groups of amino acids Hydrophobic interactions is formed between hydrophobic non-polar R groups of amino acids Disulfide bond or bridges are formed only between two cytesine amino acids by oxidation of sulfydryl, SH groups which contains sulphur In collagen, covalent cross links form between lysine residues at C and N ends of adjacent parallel tropocollagen molecules Describing Primary structure: The single polypeptide chain contains a precise number, type and sequence of amino acids held together by peptide bonds within each chain, which determines the chemical interactions and bonds of R groups Secondary structure: The polypeptide chain coils and folds into the regular repeating secondary structures (a-helices/ beta pleated sheets) held together by hydrogen bonds between C0 and NH groups (of peptide linkages) of the amino acids in the main chain  R group not involved) Pr ot eins 1

Tertiary structure: The polypeptide chain further bends, coils and folds, to form a 3D shape / specific tertiary structure, maintained by intramolecular ionic bonds, hydrogen bonds, disulfide bonds and hydrophobic interactions between R groups of amino acids Questions regarding the amino acid residue cysteine Tips Note that only cysteine has a SH R group, making it the only one being able to form disulfide bridges with another cysteine molecule Disulfide bridges unaffected by temperature and PH For temperature, only hydrogen bonds and hydrophobic interactions are disrupted (aka weak intermolecular forces between covalent molecules) For pH, only hydrogen and ionic bonds affected Ionic as there is charge, can affect the charge Hydrogen bonds as there it can release H Pr ot eins 2

Compare hydrogen bonds in tropocollagen and alpha helix secondary structure Notes Do not write hydrogen bonds in tropocollagen formed between R groups (very vague) Tropocollagen also forms hydrogen bonds with CO and NH groups in its secondary structure Pr ot eins 3

Structure and properties of haemoglobin Common mistake: Consist of 2 alpha helices and 2 beta sheets Consist of 2 alpha globin and 2 beta globin Structure Properties It is a globular protein and has a quaternary structure compromising of 4 polypeptide subunits consisting of 2 alpha globin subunits and 2 beta globin subunits tightly packed into a tetrahedral conformation, making the structure compact, allowing many haemoglobin molecules to be packed Made up of 4 polypeptides packed in a tetrahedral conformation and held by weak hydrogen bonds which each carry a haem group The bonds result in the ability of the polypeptide chains to move with respect to each other. Hence, the binding of an oxygen molecule to one subunit induces a conformational change in the remaining subunits to increase the affinity for oxygen in these subunits, allowing cooperative binding and facilitate the effective loading and unloading of oxygen at the lungs and body tissues respectively, allows high capacity for carrying oxygen. At high CO2 concentration caused by lots of respiration, haemoglobin can bind to carbon dioxide which causes a conformational change in haemoglobin, decreasing affinity for oxygen and facilitating the release of oxygen (function) Each subunit is arranged so that most of the hydrophilic amino acid side chains are on external surface while hydrophobic amino making it soluble in aqueous environment and Can be transported and carry oxygen Pr ot eins 4

Structure Properties acidside chains are buried in interior from lungs to tissue and vice versa Each subunit is made of globin polypeptide and associated with haem prosthetic group held in the hydrophobic pocket of the polypeptide chains consisting of a porphyrin ring and an iron ion allowing haemoglobin to bind reversibly to oxygen.. Role of bonds in haemoglobin the two polypeptide chains in each dimer are held together by ionic bonds, hydrogen bonds and hydrophobic interactions between R groups so as to stabalise the alpha beta dimers The two diners held together weakly by hydrogen bonds between R groups results in the ability of the two dimers to move with respect to each other in order to increase the affinity of haemoglobin to oxygen, increasing efficiency of loading and unloading of oxygen Explain the significance of R groups of different amino acids to protein structure R groups of different amino acids have different properties such as non-polar, polar, acidic and basic Interactions between R groups of amino acids constituting the protein can form hydrogen bonds, ionic bonds,disulphide bonds and hydrophobic interactions These interactions between R groups are requiring to maintain specific three dimensional conformation of the tertiary and quaternary structures of proteins The hydrophobic interactions between the hydrophobic R groups of amino acids will cause the protein to fold in a way that keeps most hydrophobic R groups shielded from the aqueous environment Pr ot eins 5

Cytosine which has a sulfhydryl group allows formation of disulfide brudges contribute greatly to the stability of protein structure as it increases resistance to high temperatures extreme pH changes Acidic and basic R groups of amino acids can be attracted to each other, forming ionic bonds that play a part in determining the tertiary/quaternary protein structure Polar R groups such as amide groups and hydroxyl groups allow formation of hydrogen bonds that play a part in determining the tertiary/quaternary structure Structure and properties of collagen Structure Properties Mostly compromises of glycine in the alpha chains of the tropocollagen as every 3rd amino acid is glycine. Glycine has the smallest R group of all amino acids (importance of abundance of glycine in its function) This allows the alpha chains of tropocollagen to be able to wind tightly together and fit into the restricted space between alpha chains to allow formation of hydrogen bonds causing an increase in tensile strength of collagen making it suitable structural protein Each alpha chain of the tropocollagen molecules has a repetitive sequence has a repetitive sequence of Gly-XY where X mainly being proline and Y is often hydroxyproline 1. Proline and glycine have non-polar R groups and will not be able to form hydrogen bonds with water molecules, contributing to the insolubility of collagen. Hydroxyproline is a polar amino acid but the OH group is used to form hydrogen bonds with other polar amino acids in adjacent alpha chains of tropocollagen hence not able to form hydrogen bonds with water molecules making it insoluble 2. Hydroxylation of proline(hydroxyproline) allows for formation of hydrogen bonds with adjacent alpha chains of the tropocollagen molecules to further stabalise the tropocollagen structure and these tropocollagen molecules cam then form covalent bonds with adjacent tropocollagen molecules to form collagen fibrils in order to Pr ot eins 6

Structure Properties prevent tropocollagen molecules to slide against each other due to the unstability, increasing tensile strength (importance of hydroxylation of amino acids) It is a fibrous protein. has secondary and quaternary structure and compromises if 3 polypeptide chains coiled around each other, forming a loose triple left handed helix Gives rise to high tensile strength which means can stretch without breaking Triple helix allows greater surface area for cross linking/hydrogen bonds formation And also allows 3 polypeptide to wind around each other more tightly, needing more force to b