Lecture 4 - Building Blocks of Proteins: Amino Acids Flashcards
What do all amino acids contain:
An alpha carbon, Amino group, Carboxyl group, Side (R) Chain
An alpha carbon with 4 different groups is called what?
Chiral
What forms can amino acids exist in?
L or D (predominantly L form)
What are enantiomers?
Non-superimposable mirror images
What is the predominant form of amino acids in solution?
Zwitterion (COOH deprotonated and NH2 protonated)
What are common in the 20 amino acids?
The backbone
What are different in the 20 amino acids?
The side chains
What does each amino acid have (naming)
A full name, abbreviated 3 letter name, 1 letter name.
What do the amino acids have due to their different side chains?
Different chemical properties
What do amino acid side chains do in proteins?
Carry out the biochemical reactions for which proteins are known
How are amino acids classified?
Based on their chemical properties
What are most non-polar amino acids?
Hydrophobic
Where are hydrophobic amino acids found?
Typically on the inside of a protein stabilising the structure (forming the hydrophobic core)
What is glycine’s R group?
A hydrogen making it non-chiral, flexible because its R group is small meaning it is found in regions which need to get tight and close together
What is cysteine commonly found in?
Proteases
What do phenylalanine and tryptophan have?
Aromatic side chains (resonance structures)
What does the R group in proline do?
Bends back to the main chain N forming a 5 membered covalently closed ring. This makes it rigid.
What side chain do negatively charged polar (acidic) amino acids have?
One containing an acidic carboxyl group
What side chain do positively charged polar (basic) amino acids have?
One containing a basic amine group
What are common in non-polar side chains?
Have either C or H groups at end of side chain.
What are common in polar side chains?
Have either -OH, -NH2, or -O at the end of their side chains.
Non-polar amino acids are?
Hydrophobic
Polar amino acids are?
Hydrophilic
What are the three types of polar amino acids?
Uncharged, Positively charged, Negatively charged
What is the pKa value?
pH at which the ionisable group is 50% ionised.
What is the pI or Isoelectric point?
pH at which the net charge on an amino acid is zero
The smaller the pKa…
the stronger the acid
For non-ionisable amino acids the pKa is the ____ as the pI
Same
pH < pKa = ?
Protonation (extra H atom)
pH > pKa = ?
Deprotonation (is missing an H atom)
Where is the RNA translated into proteins
ribosomes
What is post translational modification?
Modification of amino acids after they are added to a protein.
Cysteine can sometimes form a covalent bond with another nearby cysteine via?
Disulfide bonds.
What are the main amino acid modification methods?
Phosphorylation,
Hydroxylation,
Carboxylation
Metal binding,
Iodination,
Glycosylation.
Peptide cleavage:
Shortening of a peptide to ensure correct folding
Cysteine - Cysteine disulfide bond formation allows?
Stability of protein structure
Phosphorylation is…
addition of a phosphate, often acts as a switch, turning a protein on or off.
Glycosylation is…
addition of glucose/sugars, increases stability and reduces flexibility of proteins
Hydroxylation is…
addition of a hydroxyl group, converts hydrophobic residues into hydrophilic residues
Carboxylation is…
addition of a carboxyl group, mostly occurs in blood clotting proteins
What is the name of the covalent bond in joining amino acids?
Peptide bond
What are the characteristic of the peptide bond
Planar, Trans, Dipole.
40% double bond character leads to planairty, rotational barrier of -80KJ/mol.
What are amino acid residues?
amino acids that are covalently bonded, leading to them being no longer complete, individual amino acids.
