exam 2 protein shape and structure Flashcards
what is protein structure determined by
the sequence of amino acids
what can proteins be divided into
functional and structural domains
what are function and structural domains
independently folding subregions within the protein sequence
what determines a protein’s function
the 3D structure of it
what is primary structure of proteins
linear sequence of amino acid residues determined by the mRNA code
what is primary structure held together by
peptide bonds between amino acids
what determines higher order structures
protein structure in combination with a protein’s environment
what is the sequence of proteins different from
the sequence that initiates folding process
what is the secondary structure of a protein
the folding and twisting of peptide backbone
what is the secondary structure held together by
weak H-bonds between C=O (carbonyl) and N-H (amine) groups in the backbone
what do the two bonds of every amino acid have
the two bonds have freedom of rotation
what is the purpose of side chains in the secondary structure
they make it more or less difficult for structure to form, but don’t hold secondary structure together
what are the two secondary structures
alpha helices and beta sheets
what is the structure of the alpha helix
rigid cylindrical structure
when does an alpha helix form
forms when H-bonding occurs between a carbonyl and amine group that are 4 amino acids apart on the polypeptide backbone
what makes one turn of the helix
four amino acids
what direction does coiling of the alpha helix happen in
a clockwise direction down the length of the chain
what is the beta sheet
a flat, folded, sheet-like structure
when does a beta sheet form
when H-bonding occurs between a carbonyl and amine group on adjacent polypeptide chains
what does it mean for an adjacent beta sheet chain to be parallel
adjacent chains run N-terminal to C-terminal
what does it mean for an adjacent beta sheet chain to be antiparallel
adjacent chains run in opposite directions
what do rigid proline residues do
insert a kink in a protein’s backbone and disrupt secondary structures
what is tertiary structure of proteins
3D arrangement of secondary structures to assume the lowest possible energy state
what is tertiary structure (detailed)
stretches of proteins that serve as links between secondary structures to allow them to fold up
what is tertiary structure held together by
non-covalent attractions between R-groups along with R-groups + the surrounding environment
what links secondary structures together to form tertiary structures
unstructured loops (aka random coils)
what can tertiary structure stabilized by
covalent interactions - most important are disulfide bonds
where can covalent disulfide bonds form to stabilize tertiary structures
between cysteine residues to cross-link parts of the polypeptide backbones
what does stabilizing tertiary structures do
makes it more difficult to unfold once it’s in the shape
what is the difference is the energy of unfolded and folded proteins
unfolded proteins have a higher free energy than when it’s folded due to entropy
what does protein stability depend on
the free energy change between the folded and unfolded states
what is delta G
G(folded) - G(unfolded) : products minus reactants
what charge creates the most stable folded protein
the most negative the change in free energy
what are molecular chaperones (chaperonins)
provide an isolated chemical environment in which they can fold, which proteins require to 3D fold
what is a prion
an infectious protein
what are prions evidence of
that some unusual contagious neurological diseases are caused by proteins alone
what happens when a prion protein interacts with a correctly folded protein
it recruits it to also fold incorrectly (ex: mad cow, kuru)
what is a protein domain
a region of the protein that folds essentially independently of other regions
how many protein domains can a protein have
single or multiple
what does a domain represent
a functional region of the protein - different domains have different function
what do catalytic protein domains do
inhibit host cell protein synthesis
what do hydrophobic protein domains do
inserts into the membrane
what do receptor binding protein domains do
attach to cell surface
what are motifs
similar domains that occur in many related proteins
what is quaternary protein structure
arrangement of multiple tertiary structures
what are quaternary structures held together by
weak bonds and some disulphide bonds
what are homomers of quaternary structures
identical subunit polypeptides
what are heteromers of quaternary structures
different subunit polypeptides
what is the final structure of a protein after quaternary structure
mature protein
what does a higher order structure increase
efficiency
