protein structures Flashcards
how do you write amino acid sequence
written from amino or N terminus to carboxy or C terminus
what are 5 properties of peptide bonds
- very stable
- cleaved by proteolytic enzymes proteases or peptidases
- partial double bond
- flexibility around C atoms not involved in bond, allows multiple conformations
- usually one preferred native conformation, determined mainly by the type of side chains and their sequence in the polypeptide
what are the 2 types of ways to represent protein structure
backbone - a line following the peptide bonds
cartoon - a representation showing the fundamental secondary structures (helix/sheet)
how is the folded state of proteins stabilised
by interactions between amino acids which can be very far apart in the primary sequence
what are the 5 types of forces that hold proteins together
van der waals forces
hydrogen bonds
hydrophobic forces
ionic bonds
disulphide bonds
what are van der waals forces
weak attractive interactions between atoms due to fluctuating electrical charges
when are van der waals important
when 2 macromolecular surfaces fit closely in shape
can also be repulsive at very short distance
what are hydrogen bonds
interaction between dipoles
involving hydrogen and an oxygen/nitrogen
partial negative charges on negative atoms bound to H which has a partial positive charge
the partial charges allow weak attractive interactions between some amino acid side chains, main chain O and N and water
what are hydrophobic forces
uncharged and non polar side chains are repelled by water because they are poorly soluble
the side chains then form tightly packed cores in the interior of proteins, excluding water molecules
this attraction is the hydrophobic force
what are ionic bonds
bonds between fully or partially charged groups
they are weakened in aq systems by shielding by water molecules and other ions in solution
what are disulphide bonds
covalent bonding between side chains of cysteine residues
occurs in extracellular domains of proteins because conditions can be harsher so need extra stability
what is the primary structure of a protein
a linear sequence of amino acids linked by peptide bonds
what does the primary structure of a protein determine
it’s 3D conformation - the way in which the chain will fold to form its native structure
what are the 2 types of protein secondary structure
alpha helix
beta pleated sheet
what is the alpha helix protein structure
H bonds between each carbonyl group
H attached to the N which is 4 aa along the chain
side chains look outwards
proline breaks the helix (ring + no H)
what is the beta pleated sheet protein structure
H bonds between linear regions of polypeptide chains
chains from 2 proteins or same protein
parallel or antiparallel chains, pleated or not
if the chain is folding back, structure is usually a 4 aa turn, called hairpin loop or B-turn
what does the tertiary structure of protein mean
the overall 3D conformation of the protein
can be changed with pH and temperature
what forces are involved in protein tertiary structure
electrostatic
hydrophobicity
H bonds
covalent bonds
what are the types of conformational domains of tertiary structure (3)
barrel
bundle
saddle
what does the quarternary structure of a protein mean
3D structure of a protein composed of multiple sub units
same non covalent interactions as tertiary structures
how do we determine protein structure
X ray diffraction of protein crystals
what are enzymes
biological catalysts that bind the reactants (substrates) and convert them to products
then they release the products and return to their original form
what are benefits of enzymes (2)
speed up reactions
provide a way to regulate the rate of reactions
what occurs in mitochondria (3)
TCA cycle
fatty acid oxidation
decarboxylation of pyrvate
