Biomolecules 4 Proteins Notes PDF

Amino acids Essential Amino acids Peptides Proteins 1 Amino acids make up proteins and peptides. Some of them we can biosynthesize others are necessary components of our diet. The imp...

Amino acids Essential Amino acids Peptides Proteins 1 Amino acids make up proteins and peptides. Some of them we can biosynthesize others are necessary components of our diet. The importance of amino acids revolves around that of proteins, which are the machinery carrying out all the enzymatic reactions in a cell (among other things). 1  Amino acids Free amino acids R Carboxylic acid One of 20 natural side‐chains or residues Amine Zwitterion The R stereochemistry (L configuration) predominates in Nature R/L S/D 2 There are 20 naturally occurring amino acids, which form the basis of all proteins. All have the common NH2-CHR-COOH core structure and are distinguished by their different side-chains. In solution, all form zwitterions, by deprotonation of the acid group and protonation of the amine group. All the natural amino acids have the same configuration (L) which corresponds to R- stereochemistry. 2  Amino acids Natural amino acids Glycine Alanine Valine Leucine Isoleucine Proline Gly Ala Val Leu Ile Pro G A V L I P 1……….. Aliphatic side-chains …………6 Hydrophobic hydrocarbons 3 There are 6 aliphatic amino acid side chains. These are generally hydrophobic, but have different degrees of steric bulk. Note the unusual structure of proline. All amino acids have a 3 letter code and a single letter code for use in displaying protein sequences. 3  Amino acids Natural amino acids H2N NH NH2 HN O O HO NH2 HO NH2 Aspartate Glutamate Asparagine Glutamine Arginine Lysine Asp Glu Asn Gln Arg Lys D E N Q R K 7.. Acids Amides Bases …12 4 There are 2 carboxylic acids, 2 amide side chains, a guanidine and an amine (both strongly basic) 4  Amino acids Natural amino acids HO HO O O CH3 HO NH2 HO NH2 Histidine Tryptophan Phenylalanine Tyrosine Serine Threonine His Trp Phe Tyr Ser Thr H W F Y S T 13.. Aromatics Alcohols …18 5 There are 4 aromatic side chains. Histidine is weakly basic and tyrosine is weakly acidic. The other 2 are bulky and hydrophobic. Serine and threonine are simple alcohols. 5  Amino acids Natural amino acids Cysteine Methionine Selenocysteine Cys Met C M 19 Thiol / Thioether…. 21 6 There are 2 sulfur containing amino acids a thiol and a thioether. The 21st amino acid is selenocysteine – this is very rare, but has its own RNA codon specific to some organisms. 6  Amino acids Essential amino acids HN N HN O O O HO NH2 HO NH2 HO NH2 Valine Leucine Isoleucine Histidine Tryptophan Phenylalanine Val Leu Ile His Trp Phe V L I H W F H3C S HO Required by humans in their O O CH3 diet (protein) HO NH2 HO NH2 Cannot be synthesized Methionine Lysine Threonine quickly enough Met Lys Thr M K T 7 The essential amino acids are dietary requirements of humans. Consuming protein enables this requirement to be met. 7  Amino acids Peptide bonds Protein Synthesis (ribosome) + H2O Protease Linkage stable to non‐enzymatic degradation 8 A peptide bond forms an amide between 2 amino acids. Peptide bonds replace the ammonium and carboxylate ionic groups of amino acids. The resultant protein chain is not charged, but is capable of H-bonding. It is also very resistant to degradation (e.g. Keratin – hair, nails, claws). It can be hydrolysed by strong base or acid (see carbonyl chemistry) 8  Nucleic acids RNA Codons 9 Three RNA bases constitute a codon and specify the amino acid to be added to the protein chain. e.g. UUC = Phenylalanine. This takes place in ribosomes. 9  Nucleic acids Transcription 5’ end 3’ end A=T G≡C G≡C T=A C≡A T=A G≡C A=T A=T G≡C G≡C T=A DNA polymerase C≡A T=A RNA A G≡C A A=U Polymerase C T RNA strand 10 During transcription, the DNA must be unzipped. An RNA strand is generated on the template strand by RNA polymerase, which only adds bases to the 3’ end. 10  Nucleic acids Translation 8 Phe Amino acid carrier mRNA tRNA Helical region ribosome RNA anticodon 11 tRNA carries an amino acid to add to the chain during protein synthesis. It matches its anticodon to the mRNA encoding the protein within a ribosome. The ribosome moves along the mRNA to synthesize the protein. 11  Proteins Amino acids DNA CGATCACCAATAACACGA... Transcription RNA GCUAGUGGUUAUUGUGCU... Translation Protein A S G Y C A... Primary (1) structure: amino acid sequence N‐terminus 1 C‐terminus Chain Extension 12 DNA can be transcribed into mRNA, which is used as the template for the protein amino acid sequence (translation). This sequence is the protein primary structure. The N-terminous forms the start of the chain (denoted residue 1) and extension occurs at the C-terminous. 12  Secondary structure Amino acids ‐sheet 13 Secondary structure refers to how the linear protein sequence folds up to form “globules”. When protein strands align antiparallel to each other and the main chains H-bond, a b-sheet is formed. It doesn’t matter which residues are used, but some amino acids favour being in b-sheets more than others (predicting protein folding is extremely challenging). 13  Secondary structure Amino acids N C 2 Structure ‐sheet C N 14 This shows b-sheet representations – in cartoon form – just the main chain – with the sidechains included (looks messy). B-sheets are found in rigid structured proteins – e.g. the barrel of GFP. 14  GFP Amino acids 15 This shows b-sheet representations – in cartoon form – just the main chain – with the sidechains included (looks messy). B-sheets are found in rigid structured proteins – e.g. the barrel of GFP. 15  Secondary structure Amino acids ‐helix 16 Another element of secondary structure is the a-helix. This is stabilised by the main chain H-bonding along the direction of coiling. Shown in cartoon format – as just the main chain – with the sidechains. There are 4-5 amino acids in each turn of the helix. Example is keratin (hair, nails etc) a structural protein consisting of coiled a-helical coils. 16  Keratin Amino acids Another element of secondary structure is the a-helix. This is stabilised by the main chain H-bonding along the direction of coiling. Shown in cartoon format – as just the main chain – with the sidechains. There are 4-5 amino acids in each turn of the helix. Example is keratin (hair, nails etc) a structural protein consisting of coiled a-helical coils. 17  Tertiary structure Amino acids 3 Structure: “Domains” Domain B ‐sheets Domain A N Domain C C ‐helices 18 Different regions of protein can folded into distinct globules, depending on the sequence. This is known as the tertiary structure. Above shows a single protein chain folded into 3 domains. Each of which have b-sheet and a-helical secondary structural elements. 18  Tertiary structure Amino acids Domain B FAD Domain A FMN N Domain C NADP C 19 Often individual domains are shuffled and combined by evolution. The A, B, and C domains bind FMN, FAD and NADP cofactors respectively and bring the cofactors together to perform an enzymatic reaction. Rather like a machine built from 3 different components. 19  Quaternary structure Amino acids Subunit 2 Subunit 1 Hemoglobin tetramer C N N Subunit 4 C Subunit 3 20 Quaternary structure is the arrangement of different protein chains (subunits) to form a much larger globular protein. The chains can be either the same or different. Hemoglobin has 4 subunits, each binds one heme group. However, not all the protein chains are the same – this has an a2b2 arrangement. Interaction of the chains is very important for haemoglobin to bind oxygen cooperatively. 20  1 2 3 4 structure Amino acids 1 Primary sequence 2 Secondary ASGYCAHKA GWQGTFDCVN folding MGAPLIYNV CSAEDFHYIP HAGGARDEK NLIVVRLYFA 3 Tertiary domains 4 Quaternary subunits 21 The 4 categories of protein structure – sequence – folding – domains – subunits. 21  Amino acids Sidechain properties Ala Val Leu Ile Trp Phe Hydrophobic – found in the protein interior or spanning membranes Gly Pro Induces chain flexibility Induces rigid kinks in the chain ‐ found in mobile loops ‐ found in turns at the end of ‐sheets 22 The properties of sidechains affect how proteins fold and can provide chemical functionality. Hydrophobic sidechains are often found in the protein interior (this and H-bonding drives folding) and also enable proteins to span membranes, forming bridges or tunnels between different compartments of a cell. Gly and Pro have extreme structures that promote flexibility and rigidity. They are often found at the end of secondary structural features or within hinge/loop regions. 22  Amino acids Sidechain properties Asp Glu Asp Glu pH 7 H2N NH2 NH3 HN Arg Lys Arg Lys 23 In the normal cellular environment – the acidic groups deprotonate and become negatively charged. The basic groups protonate to become positively charged. 23  Amino acids Salt bridges + ‐ + ‐ O O H O O H N H H H N N H HN H ‐ + Arg Lys H‐bonding and Electrostatic attraction 24 The acidic and basic sidechains can therefore form electrostatic interactions (+/-), which help proteins/strands to attract each other. Often found in protein- protein recognition. 24  Amino acids Electrostatics Cytochrome c peroxidase Cytochrome c 25 Electrostatic interactions (+ blue/- red) help proteins to attract each other. Often found in protein-protein recognition. 25  Amino acids Disulfide bonds NH NH NH NH R R R R O O O O HN HN HN HN R R Oxidation O O SH O O S S NH NH HS NH NH R Reduction R O O O O HN HN HN HN R R R R O O O O 26 Thiol groups are known to form strong S-S bonds. Cys can do this in proteins to covalently attach strands together (e.g. in keratins – harder versions have more disulphide links). Disulfide bonds are formed on oxidation and can be broken by reduction. 26  Amino acids Disulfide bonds GIVEQCCTSICSLYQLENYCN FVNQHLCGSHLVEALYLVCGERGFFYTPKA Insulin: a dipeptide linked by S‐S bonds The hormone insulin consists of 2 peptides (short proteins) cross-linked together by disulphide bridges. 27  Amino acids Ligands M+ M+ Tyr M+ O- M+ CH3 O HO Thr H Ser Amino acid sidechains with lone-pair functionality can often bind to metal ions. The most common are His, Met, Asp, Glu and Cys. This enables the chemistry of metals to be exploited in enzyme active sites. 28  Amino acids Essential Amino acids Peptides Proteins 29 Amino acids make up proteins and peptides. Some of them we can biosynthesize others are necessary components of our diet. The importance of amino acids revolves around that of proteins, which are the machinery carrying out all the enzymatic reactions in a cell (among other things). 29