Protein Structure Flashcards
primary structure
sequence of amino acids
secondary structure
simple, repetitive motifs that are found in almost all proteins
tertiary structure
overall fold of a protein
quaternary structure
when several proteins fold together
Polypeptide chains
Peptide bond in the chain has a partial double bond character
C-N 1.49 angstroms
C=N 1.27 angstroms
Peptide bond 1.32 angstroms
rotation about bonds
structure adjusted by rotation about 2 pure single bonds
phi and psi
determine the path of polypeptide chain
Phi rotation
angle of rotation about bond
between N and alpha C
Psi rotation
angle of rotation about bond
between alpha C and carbonyl C
combinations of phi and psi
many combinations of the two rotations forbidden
due to steric collusions between atoms
values visualised on 2D plot called Ramachandran plot
folded structures
highly flexible polymers
large number of possible conformities
do not fold into unique structures
rigidity of phi and psi and peptide
limits the number of structures accessible to unfolded protein form
define the secondary structures
alpha helix
beta pleated sheet
turns and loops
Ramachandran Plot
LOOK AT GRAPH
Plot of angles phi and psi
red areas conly show where the combinations of the bonds can form the secondary structures
define: alpha helix
secondary structure
arises dur to H bonding capacity of N-H backbone and C-O groups
Properties of alpha helix
right handed
no residues (turns) = 3.6
pitch (distance helix rises) = 5.4 angstroms
H bonding
C=O bond points towards peptide N-H group
H bond at nearly optimal length
R groups point outwards
11 residues in globular proteins
Hydrogen bonding in alpha helices
LOOK AT DIAGRAM
CO group of residue n forms H bonds with amine group n+4
fold on top of each other every 4 residues
Helical wheel
amino acid residues facing out are in contact with water
hydrophilic are on outside
hydrophobic are on inside
what proteins are rich in alpha helices?
ranges widely
75% residues in ferritin are alpha helices
roughly 25% all soluble proteins are alpha helices connected by loops and turns
define: beta sheet
secondary structure composed of B strands
properties of data sheets:
at least two polypeptide chains
parallel or antiparallel
rippled or pleated
successive r groups
2 residue repeat of 7 angstroms
H bonding between C=O of one chain and N-H of another
15 residues long in globular proteins
4-5 (max 10) strands can come together in B pleated sheets
can be purely parallel or antiparallel or a mix
proteins rich in B sheet
usually depicted by arrows pointing in direction of carboxyl terminal end
B sheet: reverse turn
LOOK AT DIAGRAM
CO group of residue (i) is H bonded to NH of reside (i+3)
Stabilises abrupt changes of direction of polypeptide chain
It kind of turns back on itself to form a bond between i and i+3
forms
Define: loops
do not have regular periodic structure
often rigid and well defined
lie on the surfaces of proteins interact with other proteins/ molecules
define: super-secondary structure
elements on secondary structures that link together in different combinations
form mini domains that have own stability
formed in early process of making whole protein structure
many are symmetrical
define: tertiary structure
overall fold of the whole protein
can be made from any combination of alpha helices, beta sheets and loops
What is myoglobin?
an all alpha helix protein
single polypeptide chain of 153 amino acids
binds heme as a prosthetic group
70% of main chain folded into 8 alpha helices & rest is turns and loops
What is concanavalin A?
an all beta-sheet protein
a lectin (carbohydrate binding protein)
14 B strands in the molecules
define: structural motifs
most proteins has mix of alpha helices and beta sheets
common motif known as a beta barrel
define: domains
protein sections that could fold independently
each protein has at least one domain
some can have as many as 10
define: Quaternary structure
Many proteins form in groups of 2+ chains
define; homomultimers
quaternary structure with the same protein with 2+ copies
define; heteromultimers
quaternary structure with different proteins
What are fibrous proteins?
important components of elk cells
alpha helix e.g. hair
beta sheet e.g. insect silk
Alpha helix fibrous protein
all alpha helix
hair
very stable structure
have length of 1000 angstroms
cross linked by weak interactions
- van Der walls and ionic interactions
all beta sheet silk
structure made from repeating hexapeptide
collagen
main fibrous component of skin, bone, tendon, cartilage and teeth
three helical polypeptides, each roughly 1000 residues long
3 helices wound together making it rigid and string
crosslinks between all three chains
