Biochemistry 1.2 Lectures PDF

Biochemistry 1.2 Dr. Oliver Joyce 25 September – 29 September Lectures by Dr. Oliver Joyce Dr. Oliver Joyce Stereochemistry of amino acids Chirality is an important consideration in various fields, especially in chemistry and biology, due to its impact on the prop...

Biochemistry 1.2 Dr. Oliver Joyce 25 September – 29 September Lectures by Dr. Oliver Joyce Dr. Oliver Joyce Stereochemistry of amino acids Chirality is an important consideration in various fields, especially in chemistry and biology, due to its impact on the properties and behaviour of molecules. Drug Effectiveness: – Many drugs are chiral, and often only one enantiomer is therapeutically active. The other enantiomer might be less effective or even harmful - thalidomide Stereochemistry of amino acids Enzyme Reactions: – Enzymes are chiral and usually only interact with one enantiomer of a substrate Pesticides and Herbicides: – The effectiveness and environmental impact of chiral pesticides and herbicides can vary between enantiomers. Stereochemistry of amino acids Flavour and Fragrance: – The taste and smell of chiral compounds can differ between enantiomers. – e.g. one enantiomer of carvone smells like spearmint, while the other smells like caraway. Optical Properties: – Chiral molecules can affect the optical properties of materials, such as their ability to rotate plane-polarized light, a property used in various applications, including liquid crystal displays (LCDs) Stereochemistry of amino acids For most considerations in this biochemistry module, the chirality of amino acids is not a critical point. – Therefore, we generally do not indicate chirality when drawing amino acids. – When synthesizing amino acids artificially in the lab, a racemic mixture is obtained Racemic – contains equal amounts of each enantiomer Stereochemistry of amino acids Biosynthetic processes almost always produce pure sterioisomers – That is Amino acids in proteins are always of the L configuration However, some bacterial peptides have D amino acids This makes them less susceptible to enzymatic attack.  Biochemistry Classification of Amino Acids Dr. Oliver Joyce. Lectures by Dr. Oliver Joyce Dr. Oliver Joyce Classification of Amino acids The R group, or side chain, determines the structural range and general physical characteristics of the amino acids The amino acids are generally grouped according to the various characteristics of their R groups – Non-polar amino acids (hydrophobic) – Polar (hydrophilic), uncharged amino acids – Polar (hydrophilic), charged either positive or negative  Biochemistry Spectroscopic Properties of Amino Acids Dr. Oliver Joyce. Lectures by Dr. Oliver Joyce Dr. Oliver Joyce Spectroscopic Properties All amino acids absorb light in the infrared region Only Tyrosine, Tryptophan and Phenylalanine absorb UV light Phenylalanine absorbs UV light to a lesser degree  Biochemistry The Origin of the Single Letter Code for Amino Acids Dr. Oliver Joyce. Lectures by Dr. Oliver Joyce Dr. Oliver Joyce Single letter code for amino acids Computers used in the early days of bioinformatics were very slow Dr. Margaret Dayhoff – a leader in the field, shortened the code from three letters to one letter to reduce the size of the files needed to document protein sequences. Single letter code for amino acids For six of the amino acids, the first letter of the name is unique and the code is therefore simple – Cysteine Cys C Histidine His H Isoleucine Ile I Methionine Met M Serine Ser S Valine Val V Single letter code for amino acids For the other amino acids, the first letter of the name is not unique. Dr Dayhoff assigned the letters as follows as these amino acids occur more frequently in proteins than the other amino acids having the same letters: Alanine Ala A Glycine Gly G Leucine Leu L Proline Pro P Threonine The T Single letter code for amino acids Some of the other amino acids are phonetically suggestive Arginine Arg R Phenylanine Phe F Tyrosine Tyr Y Tryptophan Trp W Threonine The T Aspartic acid Asp D Asparagine Asn N Glutamatic acid Glu E Glutamine Gln E Lysine Lys K  Biochemistry Modified Amino Acids Dr. Oliver Joyce. Lectures by Dr. Oliver Joyce Dr. Oliver Joyce Modified amino acids We have now considered all of the 20 amino acids that are coded for in DNA and are incorporated directly into proteins. Certain amino acids can however become chemically modified after they are assembled into proteins. Depictions of such modified amino acids are illustrated in the next slide with the modifying group shown in red. Cysteine The sulfhydryl group (–SH) of cysteine gives this amino acid the ability to make disulfide bonds  Biochemistry Ionizable Groups in Amino Acids Dr. Oliver Joyce. Lectures by Dr. Oliver Joyce Dr. Oliver Joyce Ionizable Groups in amino acids Amino Acids can ionize Put another way – the charge of an amino acid can change with a change in pH Amino Acids are Weak Acids – All amino acids have at least two acid – base groups – -carboxyl group – -amino group Ionizable Groups in amino acids Amino Acids are Weak Acids Some amino acids that have ionizable side chains (R groups) and so have three acid base groups – Lysine – Arginine – Histidine – Glutamic Acid – Aspartic Acid – Cysteine – Tyrosine Ionizable Groups in amino acids Consider the amino acid Alanine – Alanine does not have an ionizable side chain As a result, we are only considering the amino group & the carboxyl group – We discussed previously that at physiological pH (7.4), the zwitterionic form of the amino acid exists – Therefore if the pH changes, the charge of the amino acid changes Titration of Alanine