protein structure function Flashcards
primary structure
linear sequence of amino acids linked together by peptide bonds
= non-covalent interactions
secondary structure
folding of the polypeptide chain into local alpha helices or beta sheets (&b turns)
tertiary structure
structure of a peptide composed of secondary structural elements & various loops & turns
- main form distinct, independently stable domains
quaternary structure
multiple polypeptides
exception amino acid in secondary structure
prolines can’t participate in hydrogen bonding & thus excluded from alpha helix
alpha helix bonds in secondary structure
= held together by hydrogen bonds b/w backbone aminde & carbonyl groups
beta strand bonds in secondary structure
= stabilised by hydrogen bonds b/w backbone oxygen & hydrogen atoms in amino acids on different strands
beta turn bonds in secondary structure
= composed of 4 residues
= reverses direction of polypeptide chain
= facilitate the folding of long polypeptides into compact structures
= glycine (smallest R group) & proline (built in bend) are commonly found
IDPs
= intrinsically disordered polypeptide regions
= have no particular structure
= change structure to adapt to function
- binding
- signalling
- tethering
- diffusion barrier
ways to visualise tertiary structure & what can see x5
- backbone trace = depicts how the polypeptide is tightly packed into a small volume
- ball and stick model = reveals locations of all the atoms
- ribbon diagram = highlights beta strands & alpha helices
- water-accessible surface = protein surface topology with positive charge & neg charge regions
- hybrid model
what is a structural motif & what protein level
= combination of different protein secondary structures with specific type function
- coiled-coil motif = transcription factors
- helix-loop-helix motif = calcium-binding & DNA- binding regulatory proteins
- zinc-finger motif = DNA binding proteins that help regulate transcription
define protein domains & what protein level
molecular units from which larger proteins are built
= repeated in a number of different proteins
example of protein domain types x2
- protein molecules that have elongated, fibrous shapes
- collagen found in extracellular space, tendons, ligaments, cartilage, skin
- crosslinks formed by hydroxylation of lysine = allow stretch & relax - globular proteins form long helical filaments example
- cytoskeleton protein F-actin formed from G-actin
what structure do multiple protein domains make
tertiary structure & multiple of them make quaternary
what are supramolecular complexes & example
- can contain hundreds of polypeptide chains & sometimes other biopolymers such as nucleic acid
e. g., transcription initiation complex = core RNA polymerase & general transcription factors containing about 20 subunits = transcribes DNA into mRNA
where are motifs found
secondary structure
where are domains found
tertiary structure
what can missfolded/denatured proteins form
well-organised amyloid fibril aggregates that can cause diseases e.g., alzheimer’s disease & parkinson’s disease
- structures accumulate inside, or outside of cells in various organs including joints, b/w bones, liver, brain = damage
how are tertiary structures stabilised
hydrophobic interactions between non-polar side chains & hydrogen bonds involving polar side chains & backbone amino & carboxyl groups
role of hydrophobic residues in tertiary structure folding
cluster together like drops of oil in folded protein core, driven away from the aqueous surroundings by the hydrophobic effect
charged & uncharged polar side chains role in tertiary structure folding
form stabilising interactions with surrounding water & ions on the protein surface
what interactions hold together tertiary structures
- hydrogen bonds (more interior)
- electrostatic attractions (more surface)
- van der waals attractions (more interior)
native state
= goal of folding = the most stable structure for prime functioning
usually the conformation with the lowest free energy
summary folding
- motif
- domains
- multiple domains = tertiary or could be one domain
- native state
