Biological Molecules 4: Proteins Flashcards
What are amino acids?
Monomers that make up proteins and peptides
How many naturally occuring amino acids are there?
20
What are zwitterions?
Formed by amino acids in solution by deprotonation of the acid group and protonation of the amine group
(i.e. forms COO- and NH3+)
What is the configuration of all natural amino acids?
The L configuration
Corresponds to R-stereochemistsry
How many aliphatic amino side chains are there?
Six
Glycine (Gly)
Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Proline (Pro)
Generally hydrophobic but have different degrees of steric bulk
Proline has an unusual structure comparatively
How many carboxylic acid side chains are there?
Two
Aspartate (Asp)
Glutamate (Glu)
How many amide side chains are there?
Two
Asparagine (Asn)
Glutamine (Gln)
How many aromatic side chains are there?
Four
Histidine (His)
Tryptophan (Trp)
Phenylalanine (Phe)
Tyrosine (Tyr)
How many alcoholic side chains are there?
Two
Serine (Ser)
Threonine (Thr)
How many strongly basic side chains are there?
Two
Arginine (Arg)
Lysine (Lys)
How many sulfur-containing amino acids are there?
Two
Cysteine (Cys)
Methionine (Met)
What is the 21st amino acid?
Selenocysteine
Very rare
Has its own RNA codon specific to some organisms
How is a peptide bond formed?
Between 2 amino acids
Peptide bonds replace the ammonium and carboxylate ionic groups
Resultant chain is not charged but is capable of hydrogen bonding
Also very resistant to degradation (i.e. keratin)
Can be hydrolysed by strong bases or acids
Describe what occurs during transcription.
DNA can be transcribed into mRNA
mRNA used as template for protein amino acid sequence (translation)
Sequence is the protein primary structure
The N-terminous forms the start of the chain and extension occuts at the C-terminous
What is the primary protein structure?
Sequence of amino acids joined by peptide bonds
What is the secondary protein structure?
Initial folding of sequence of amino acids to form alpha helix or beta pleated sheets held by hydrogen bonds
Give an example of an alpha-helical protein.
Keratin (hair, nails, etc)
Give an example of a beta-pleated sheet in proteins.
The barrel of GFP (green fluorescent protein)
What is the tertiary protein structure?
Domains
Further folding of the protein due to hydrogen, ionic, and disulfide bonds
What is quaternary protein structure?
The arrangement of different protein chains to form a much larger globular protein
E.g. haemoglobin
Describe what chemical functionality is provided by hydrophobic side chains.
Found in the protein interior and enables proteins to span membranes by forming bridges or tunnels between different compartments of a cell
Which two amino acid side chains promote flexibility and rigidity?
Glycine and proline
Often found at the end of secondary structural features or within hinge/loop regions
What happens to acidic and basic groups in amino acids in normal cellular environments?
The acidic group deprotonates (COO-)
The basic group protonates (NH3+)
The acidic and basic sidechains can therefore form electrostatic interactions which helps protein strands to attract each other
What is the benefit of thiol groups?
Known to form strong S-S bonds
Cysteine can do this in proteins to covalently attach strands together
Disulfide bonds are formed on oxidation and can be broken by reduction
What is insulin?
Hormone consisting of two peptides cross-linked by disulfide bridges
What is the benefit of lone-pair functionality in amino acids?
Allows them to bind to metal ions
Most commonly His, Met, Asp, Glu, and Cys
Enables the chemistry of metals to be exploited in enzyme active sites
