protein structure Flashcards
what types of forces are involved in forming the 3D shapes of a polypeptide
- mostly noncovalent
- hydrogen bonding
- ionic bonding
- hydrophobic interactions
- less of an interaction, more of an avoidance
- Van der Waal interactions
disulfide bridges
conformation vs configuration
- conformation is around a single bond and can rapidly interconvert
- configuration is how the molecule is arranged and would require bond breaking processes to change
disulfide bridges
- formed from the oxidation of the polar SH group of cysteine
- most intracellular proteins do not have disulfide bonds because the cell interior is a reducing environment
- seen in secreted or cell surface proteins
Why is protein folding thermodynamically favorable?
- folding decreases entropy, so it isn’t thermodynamically favorable
- the groups interacting with each other lowers delta G
- hydrophobic group have very constrained movement of water around it (low entropy of solvent)
- clustering of hydrophobic regions reduces this
define secondary structure of proteins
- local spatial arrangement of main chain (backbone) atoms
what type of bonding is involved in secondary structure?
- hydrogen bonding
- formation of secondary structures maximizes H-bonding
what are 3 common types of secondary structure
- alpha helix
- beta sheet
- beta turn
How are R groups oriented in alpha helices and beta strands
alpha helices:
- r groups protrude outward (perpendicular to helix)
beta strand:
- r groups protrude in opposite directions above and below the plane of the strand
loops
- when there are no regular secondar structures
- phi and psi angles aren’t constant for all residues in loops
- not random or disordered - conformation is stable
relative positions of H and O participating in alpha helix hydrogen bonding
- Carbonyl oxygens face towards the C-terminus
- amide H face toward N terminus
- bonds are about 3.6 residues apart (one turn around the helix)
How do dihedral angles in beta sheets compare to those in alpha helices
- ## angles are much wider in beta sheets
why do alpha helices have directional dipole?
- there is a dipole moment across the peptide bonds that align in an alpha helix to create a net dipole
- last few carbonyl oxygens don’t have an amide H to bond to
- last few amine Hs dont have carbonyl O to bond to
- C-terminus is negative
- N-terminus is positive
constraints that affect alpha helix stability
- amino acid makeup of the helix
- some more readily conform
- some are helix breakers
- bulkiness of R groups adjacent to each other in the polypeptide chain
- interactions between R groups near each other in the helix
- charge of amino acids found at helix termini
- neg residues at amino terminus is stabilizing
- pos residues at carboxy terminus is stabilizing
helix breakers
proline
- doesn’t have the flexibly in phi bond
- since the chain reattaches at the animo group, it doesn’t have the amide H to form hydrogen bonds
glycine
- too flexible (dihedral angles don’t hold well)
- makes a coiled structure very different from an alpha helix
which amino acids are interacting in an H bond in a beta turn?
- residues 1 and 4
why would a beta turn be near the surface of the protein structure rather than buried in the middle
- the turn’s internal 2 aa (proline most common) can form H bonds with water molecules
secondary vs tertiary structures
- secondary is interactions between aa’s near eachother on the chain
- tertiary is the overall 3D structure of the polypeptide
- secondary makes up tertiary
tertiary structure (and its properties)
- overall 3D structure of polypeptides
- includes interactions between R groups or R groups and backbone atoms
- held together by weak bonds (sometimes disulfide)
- amount of bending (like beta turns) dependent of number and location of residues that facilitate them (ex: proline, glycine)
- burial of hydrohpobic residues takes at least 2 layers of secondary structure
why does protein folding reduce entropy
even though there is less movement, the folded state is more stable and requires less energy for the polypeptide to sit in a folded conformation
two main groups of tertiary structure
- fibrous proteins
- globular proteins
fibrous proteins
- multiple polypeptide chains arranged in long strands or sheets
- mostly for structure, shape, and protection
- usually make of a singly type of repeating secondary structure
- keeps structure relatively simple
- insoluble in water - high concentration fo interior and surface hydrophobic residues
- ex: alpha keratin makes hair, nails, horns, hooves, outer layer of skin
globular proteins
- diverse structures and functions
- enzymes, regulatory proteins, chaperones, etc.
- often tightly packed
- percentages of helices and beta sheets depends on the protein
motif
- composed of two or more elements of secondary structure and the connections between them
- recognizable folding pattern seen in multiple proteins
- may or may not have independently stable folding or certain function
domain
- part of a polypeptide chain that is independently stable and/or move as a single entity relative to other parts of the protein
- seen in multiple proteins
- has a certain function
what does it mean for a protein to be intrinsically disordered
- lack ordered structure in solution
- don’t crystalize well if at all
- high density of charged amino acids
- proline common because they disrupt ordered structures
- fully disordered sequences lack sequestered hydrophobic aa
- may become ordered once bound to a substrate
quaternary structure
- two or more polypeptides come together
