Protein structure and function Flashcards
What elements do proteins provide?
Structural and functional
What do the functional products of the genome provide?
§ Carrier functions § Metabolic functions § Form parts such as ribosomes § Make up structural scaffolds such as microtubules § Sensing molecules like receptors
What is the polypeptide backbone?
a repeating sequence of atoms along the core of the polypeptide chain
What arrangement do amino acids have?
Tetrahedral
What do amino acids act as at a low pH?
A base and accepts H+
What do amino acids act as at a high pH?
An acid and donates H+
What do amino acids act as at a neutral pH?
Amino acid act as zwitterion
When an amino acid acts as an acid or base, what does this ensure??
Dynamic equilibrium
What do the side chains do??
confer the specific physiochemical properties
How do D and L isomers arise?
Due to the arrangement of atoms
What is the arrangement around the alpha carbon?
Chiral
What is exempted from D and L isomerism and why?
Glycine as it has 2 hydrogens attached to the alpha carbon therefore not a chiral centre
Where are D amino acid residues found and often used for?
Compromise cell walls in bacteria and often used in therapeutics
In what direction are D amino acids read?
Anticlockwise
In what direction are L amino acids read?
Clockwise
What is a peptide residue?
repeating unit of the polypeptide chain
In what arrangement are peptide residues usually organised in?
Trans conformation where R groups are in opposite direction
What percentage of peptide residues are in CIS conformation and why so less and what is the arrangement of there R groups?
• There are less than 0.1% with the Cis conformation because its less energetically favourable
○ where R groups are on the same side
How are Beta sheets formed and stabilized?
formed by continuous folding and there are intra molecular hydrogen bonds between beta strands
What is more stable, parallel or anti parallel beta sheets? Why?
- Anti parallel beta sheets are more stable than parallel beta sheets
- Loops connecting beta sheets, longer in parallel sheets compared to antiparallel
How are alpha helix formed and what is its structure?
- Stabilised by H-bonds between two amino acid 4 residues apart.
- Side chains give the proteins its structure
- Side chains in both alpha helix and beta sheet protrude outwards from the structure
How many residues per turn does an alpha helix have?
3.6
How many residues is a beta turn composed of and what shape does it give?
Composed of 4 residues and gives a U shape
Where are beta turns located and what does it do to the direction of the polypeptide?
• Located on surface of protein, reversing bends that reverse the direction of polypeptide backbone
What do beta turns do to large protein structures?
• Help large protein structures to bend into compact structures
What amino acids are commonly used in beta tuns and why?
• Glycine and proline commonly used in turns:
○ Glycine: lack in large side chain
Proline: built in bend
When folded into tertiary structures, what does formation depend on?
weak chemical bonds between side chains like disulfide bonds
What is the tertiary structure a combination of?
A combination of seondary structures
How is it folded into the quaternery structure?
- Two or more polypeptide chain combine to form the mature protein
- Eg, Haemoglobin have 2 alpha and beta polypeptide chains.
What structure is required for normal function?
• Water soluble proteins are globular in shape
• Hydrophilic residues are mostly on the external surface
• Hydrophobic residues are usually buried inside the protein
+• Membrane spamming regions like on receptors have externally located hydrophobic residues which interact with the membrane lipids
