biochemistry
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what is the structure of an amino acid?
all contain an amine group and a carboxylic acid group a-amino acids have one amine group and one acid group separated by a C atom. there are 20 of these a-amino acids that occur naturally in proteins the R group varies between these amino acids
What about the amino acid structure makes it acidic?
carboxyl group- it can donate a proton COOH (reversible arrows) COO- + H+
what does amphoteric mean?
a molecule with both acidic and basic properties, this applies to amino acids
what about the structure of amino acids makes it basic?
the amino group as it can accept a proton NH2 + H+ (reversible arrows) NH3+
what happens if some amino acids have an extra carboxylic acid or amine group on the R group?
they are classed as acidic or basic (respectively)
how do we name an amino acid (IUPAC)?
find the longest carbon chain (including the carboxyl group) number the carbons starting with the carboxyl group find the position of any NH2 groups - call them ‘amino’ and state which carbon they are on write the name of any other functional group and state which carbon they are on
how are amino acids ‘zwitterions’ ?
zwitterions are species that have one part positive and one part negative the ‘no charge’ from an amino acid never occurs, instead the amino acid exists as a dipolar zwitterion there is ionic interactions between the positive part of one zwitterion and the negative part of another this explains why amino acids are solids at room temperature, opposed to the weaker hydrogen bodning that would form in the no charge form
how does amino acids being zwitterions effect their buffer strength?
they will act as weak buffers and will only gradually change pH if small amounts of acid or alkali are added to the amino acids
how is the optical activity of amino acids?
amino acids contain a chiral carbon (asymmetric) with 4 different groups attached (except for glycine) therefore they have 2 optical isomers in nature, only one of the two enantiomers is present
what are the 3 reactions of the NH2 group of amino acids?
• with acids; to protonate the amine group; acid-base reaction • with halogenoalkanes; to replace H atoms with alkyl groups; nucleophilic substitution • with acyl chlorides and acid anhydrides; to form amides; acylation (nucleophilic addition-elimination)
what are the 2 reactions of the COOH group of amino acids?
• with bases; to deprotonate the acid group; acid-base recaction • with alcohols (and conc acid catalyst); to form ester group in place of acid group; esterification
what are dipeptides?
simple combination molecules of two amino acids with one peptide bond for any two different amino acids there are two possible combinations of amino acids in dipeptide condensation reactions join amino acids together and form peptides
how do we hydrolyse di-peptides or proteins?
if they are heated with concentrated hydrochloric acid or concentrated strong alkalis, they can be hydrolysed and split back into their constituent amino acids. the composition of the protein molecule may then be deduced by using TLC chromatography
what are proteins?
polymers made from combinations of amino acids the amino acids are linked by peptide links
what is the primary structure of a protein?
the sequence of the amino acids in the polypeptide chain, joined together by peptide links
what is the secondary structure of a protein?
the chain of amino acids in the polypeptide chain folding into a particular 3D shape, beta pleated sheet or alpha helix The secondary structure if held together by hydrogen bonds, these are between the delta positive hydrogen of the NH group, and the lone pair on the oxygen of a CO group
what is the tertiary structure of a protein?
3D specific shape formed by further holding/ coiling of the secondary structure. it is held by interactions between the R-side groups in more distant amino acids these interactions could be disulphide bonds, ionic attractions, hydrogen bonds, Van der Waals forces
give an example of where ionic interactions could form between in tertiary structures of proteins?
between acidic and basic amino acids there is a transfer of hydrogen from the CCOH group to the NH2 group to form zwitterions
what is the quaternary structure of proteins?
combination of multiple polyppetide chains eg haemoglobin is made of 4 polypeptide chains
what kind of bonds are disulphide bonds and how can they be broken?
covalent disulphide bonds can be split by reducing agents
where are van der waals present in proteins?
weak forces of attraction between non-polar groups these can be split by a rise in temperature
what are enzymes?
globular proteins the active site of an enzyme is usually a hollow in the globular protein structure into which a substrate molecule molecule can bond to the amino acid side chains through a variety of interactions including: -hydrogen bonds -VDW -permanent dipole-dipole forces. -ionic interactions
how strong do interactions between the enzyme’s active site and the product need to be?
strong enough to hold the substrate for long enough for the enzyme catalysed reaction to occur, but weak enough for the product to be released
what is meant by the lock and key hypothesis for enzymes?
only substrate molecules with the right shape and correct positions of functional groups will fit and bind to the active site when the substrate binds to the active site this is called an enzyme-substrate complex