Biomolecules (PL1003) Notes on Proteins PDF

+-----------------------------------+-----------------------------------+ | **Amino acid structure** | Amino acids all have the same | | | basic structure. | | | | |...

+-----------------------------------+-----------------------------------+ | **Amino acid structure** | Amino acids all have the same | | | basic structure. | | | | | | They differ only in their side | | | chain. | +===================================+===================================+ | **Stereoisomerism** | Most naturally occurring amino | | | acids have L-configuration i.e. | | | the opposite from sugars. | +-----------------------------------+-----------------------------------+ | **Nature of R group** | **Side chain groups and therefore | | | amino acids can be characterised | | | into:** | | | | | | - **Hydrophobic - non polar | | | (**alkyl groups (alkane | | | branches) or aromatic | | | (benzene rings) | | | | | | - **Hydrophilic** - polar | | | (uncharged chains with polar | | | groups such as 'OH'; | | | negatively charged chains; | | | positively charged chains) | +-----------------------------------+-----------------------------------+ | **Effect of pH on amino acids.** | Two or more chargeable groups are | | | present. Overall charge depends | | | on which of these are charged and | | | therefore on pH. | | | | | | **Each** chargeable group has a | | | published pKa value. **General | | | rule**: if pH of a solution is | | | less than the pK~a~, the H^+^ is | | | on. If pH is higher than the | | | pK~a~ the H^+^ is off. | +-----------------------------------+-----------------------------------+ | **Peptides** | There are many examples of | | | natural peptides with important | | | functions eg. the **enkephalin** | | | (opioid)**, insulin (hormone) and | | | venoms.** | | | | | | **A good example of a synthetic | | | peptide is the sweetener | | | aspartame. This dipeptide | | | contains phenyl alanine and | | | aspartic acid. The phenylalanine | | | means it has to be avoided by | | | people with PKU (**people with | | | PKU cannot metabolise | | | phenylalanine (lack phenylalanine | | | hydroxylase) resulting in a | | | built-up of phenylalanine in the | | | body and possible organ damage as | | | a result. | +-----------------------------------+-----------------------------------+ | **Peptide bond** | Condensation reaction. | | | | | | The resulting bond has some | | | double bond characteristics which | | | restricts its rotation. This | | | limits the secondary level | | | structures that the peptide chain | | | can take. | | | | | |  | +-----------------------------------+-----------------------------------+ | **Protein structure** | Best described as levels of | | | structure. | +-----------------------------------+-----------------------------------+ | **Primary level of protein | Amino acid sequence and chain | | structure** | length. Involves covalent peptide | | | bonds linking the amino acids | | | together. 1^o^ structure | | | determines the physiological, | | | structural, and biological | | | properties and functions of a | | | protein. | +-----------------------------------+-----------------------------------+ | **Secondary level of protein | The secondary level of structure | | structure** | is the arrangement in space of | | | the atoms in the backbone of the | | | protein. The shape depends on the | | | geometry of the peptide bond | | | (restricted rotation) and local | | | hydrogen bonding between the | | | **H** on the **N** of one amide | | | in a peptide bond with the | | | carbonyl **O** of another amide | | | in a second peptide bond. | | | | | | The main types found are alpha | | | helix, beta pleated sheet "random | | | coil" or "irregular" structure. | | | | | | The secondary level of structure | | | adds properties such as strength, | | | flexibility etc. to the protein. | +-----------------------------------+-----------------------------------+ | **Secondary level of protein | Stabilised | | structure : alpha helix** | by hydrogen bonds formed between | | | the amide hydrogen of one peptide | | | bond and the carbonyl oxygen | | | above it which is located in the | | | next turn of the helix. | | | | | | Note that the bulky side-chain | | | (R) groups are directed outwards. | | | | | | Large amounts of α-helix results | | | in a strong, insoluble, fibrous, | | | flexible protein. | +-----------------------------------+-----------------------------------+ | **Secondary level of protein | Peptide chain adopt the | | structure : beta pleated sheet** | conformation of a sheet of paper | | | and the structure is stabilized | | | by hydrogen bonds between peptide | | | bonds. | +-----------------------------------+-----------------------------------+ | **Tertiary level of protein | Further | | structure** | folding of the secondary | | | structure gives overall 3 | | | dimensional shape - involves side | | | chain interactions. | | | | | | - **Disulphide crosslinks --** | | | covalent bonds between | | | cysteine residues | | | | | | - **Hydrophobic attractions** - | | | attractions between R groups | | | of non-polar amino acids | | | | | | - **Hydrogen bonding** - | | | interaction between polar | | | amino acid R groups | | | | | | - **Ionic bonding** - bonding | | | between oppositely charged | | | amino acid R groups. | | | | | | Protein function eg. enzyme | | | activity, is derived from the 3D | | | structure (conformation) | +-----------------------------------+-----------------------------------+ | **Quaternary level of protein | Proteins with more than a single | | structure** | peptide strand. May exist as | | | dimers, trimers, tetramers etc. | | | of often identical sub units eg. | | | haemoglobin. | +-----------------------------------+-----------------------------------+ | **Globular proteins** | Intricately folded so that | | | hydrophobic side chains are | | | tucked inside away from water. | | | They are water soluble and | | | roughly spherical in shape. | | | Examples include enzymes, | | | hormones, myoglobin etc. | +-----------------------------------+-----------------------------------+ | **Globular proteins: myoglobin** | Is the oxygen-holding protein in | | | muscle tissue and consists of one | | | polypeptide unit, of which 75% is | | | an a-helix, which is further | | | folded. Contains a non-protein | | | group (prosthetic group) called | | | haem which holds the oxygen | | | molecule. | +-----------------------------------+-----------------------------------+ | **Globular proteins: | Carries oxygen and carbon dioxide | | haemoglobin** | between the lungs and the muscle. | | | Has quaternary structure: 4 | | | polypeptide molecules (Globins). | | | The sub units are held together | | | by hydrophobic interactions, | | | electrostatic (ionic) attraction | | | and hydrogen bonds. | +-----------------------------------+-----------------------------------+ | **Fibrous proteins** | Water insoluble fibrous | | | structural materials in animals | | | eg. keratins, collagens | | | (cartilage & tendons). | | | | | | Typically have a repetitive 1^o^ | | | structure and lack | | | chemically-reactive side groups. | +-----------------------------------+-----------------------------------+ | **Fibrous proteins: alpha | Major component of hair, nails | | keratin** | and skin | | | | | | α keratin has a rope-like | | | structure - based on the alpha | | | helix, cross-linked into bundles. | | | In hair, for example, the | | | α-helices are held together by | | | disulphide crosslinks. | | | | | | **The degree of S-S bridging | | | determines the properties of the | | | keratin: Soft Keratins are low in | | | sulphur, making skin flexible, | | | extensible; Hard Keratins are | | | high in sulphur making horn | | | in-flexible and un-extensible.** | +-----------------------------------+-----------------------------------+ | **Fibrous proteins: collagen** | Major component of cartilage, | | | skin, blood vessels and bone. | | | | | | Collagen protein is in the form | | | of a **triple helix** (3 | | | **left-handed** helices) (known | | | as "Tropocollagen"). The triple | | | helix tightens under tension, | | | resisting stretching, making | | | collagen inextensible. | | | | | | Looking at its structure the | | | bulky proline and hydroxyproline | | | side chain rings point outwards | | | but are responsible for the | | | tendency to form left-handed | | | helices. Glycine at every third | | | position sits in the interior of | | | the helix, where there is little | | | space. Collagen fibres are | | | stabilised by extensive | | | inter-chain hydrogen bonding and | | | some covalent S-S cross-links. | +-----------------------------------+-----------------------------------+ | **Denaturation of proteins** | Beyond the | | | \'**normal**\' range of pH (high | | | and low) and at high temperatures | | | weak bonds (e.g. H. bonds) break, | | | dramatically altering the 3-D | | | shape of the protein (secondary | | | and tertiary level of structure ) | | | thus affecting their function. | | | However the strong peptide bonds | | | remain intact. In solution these | | | **denatured** proteins tend to | | | clump together and | | | coagulate/precipitate out of | | | solution. | +-----------------------------------+-----------------------------------+ | **Hydrolysis of proteins** | Heating in acid can result in the | | | protein being reduced to simpler | | | peptides and amino acids i.e. | | | breakage of peptide linkages. | +-----------------------------------+-----------------------------------+ | **pH and proteins** | Proteins have a large no. of | | | potentially charged groups and | | | demonstrate amphoteric properties | | | similar to those of amino acids. | | | Changing pH will alter the | | | overall charge on protein which | | | alters their solubility and | | | possibly their shape. | | | | | | The isoelectric point is the pH | | | at which the total charge on the | | | protein molecule is zero (no net | | | electric charge) and this varies | | | between proteins. At pH's below | | | the isoelectric point it has +ve | | | charge [overall] and | | | at pH's above it has --ve charge | | | [overall]. Charged | | | proteins repulse each other, | | | preventing aggregation. At the | | | isoelectric point proteins tend | | | to aggregate and are in their | | | least soluble undenatured form. | +-----------------------------------+-----------------------------------+ | **Separation by electrophoresis** | Proteins are loaded on a gel and | | | given a negative charge by using | | | a suitable buffer. A potential | | | difference is applied. Large | | | proteins move slowly, smaller | | | ones move more quickly. The gel | | | is stained eg. with Coomassie | | | blue. | +-----------------------------------+-----------------------------------+