Tertiary and quaternary structure Flashcards
What is a motif?
A recognizable folding pattern that includes 2 or more secondary structures and their connecting elements. Also called supersecondary structure
What secondary structures are found in a beta hairpin?
Two antiparallel beta strands and a turn
What secondary structures are found in an EF hand?
2 alpha helices, a beta strand, and a loop
Why is the loop in an EF hand significant?
It is a calcium binding site
What secondary structures are found in a beta-alpha-beta loop?
Two parallel beta strands connected by an alpha helix
What secondary structures are found in a coiled coil?
Two alpha helices
What is a greek key?
An extended beta hairpin
What structure can a really long greek key form?
Beta barrel
What secondary structures are found in an alpha/beta barrel?
Combination of a beta barrel formed by parallel beta sheets and the strands are connected by alpha helices
What type of proteins often have the alpha/beta barrel?
Enzymes. Also called a TIM barrel
What is a domain?
A globular part of the polypeptide chain that is independently stable and has a distinct function
What is a protein family?
Group of proteins with similar sequences, tertiary structure, and function
Why can protein structure and function be used to tell evolutionary relationships, but sequences can’t?
Sequences will diverge faster than structure or function
What is a protein superfamily?
2 or more protein families that have similar tertiary structure and function, but very little sequence similarity
What is an ancient fold?
A motif widely distributed and preserved throughout many distantly related groups
What is a new fold?
A motif that is limited to a small group of organisms
What is an oligomeric protein?
A protein with multiple subunits
What are the protein subunits called when they are identical?
Protomers. They can also be dimers and trimers
What are the advantages to having quaternary structure?
Allows for complex allosteric regulation, and more efficient protein synthesis
How does having quaternary structure allow for more efficient protein synthesis?
It is much easier and less wasteful to replace a subunit that has a mistake vs replace an entire protein. Having identical subunits also reduces the number of genes
What are the 3 types of rotational symmetry in quaternary structure?
Cyclic, dihedral, icosahedral
How many axises of rotation are there in a protein with cyclic rotational symmetry?
1
How are the subunits related to each other when they have C2 symmetry?
Twofold cyclic rotational symmetry. C2 has two subunits related by a 180° rotation
How are the subunits related to each other when they have C3 symmetry?
Threefold cyclic rotational symmetry. C3 has 3 subunits related by a 120° rotation
What is an example of a protein with cyclic rotational symmetry?
DNA sliding clamps. C2 in prokaryotes and C3 in eukaryotes
How many axises of rotation are there in a protein with dihedral rotational symmetry?
2, perpendicular to each other
How are the subunits related to each other when they have D2 symmetry?
Twofold dihedral rotation. 4 subunits. Vertical and horizontal axises have a twofold rotation 180°
How are the subunits related to each other when they have D4 symmetry?
Fourfold dihedral rotation. 8 subunits.
How many axises of rotation are there in a protein with icosahedral rotational symmetry?
3
Where are proteins with icosahedral symmetry found?
Viral capsids
How are the subunits related to each other when they have icosahedral symmetry?
5 fold rotation at each vertex, 3 fold rotation at each face, 2 fold rotation at each ridge
