Proteins II Flashcards
Levels of Protein Structures
Primary (1°) Secondary (2°) Tertiary (3°) Quaternary (4°)
“Supersecondary” structure between
2º and 3º
the linear sequence of amino acids, and the disulfide bonding pattern, in a polypeptide chain written from N-terminus to C-terminus going left to right. E.g. Met-Asn-Pro is a tripeptide.
1° structure:
Proteins can evolve via
genetic mutation
Nucleotide replacements can be ________ (e.g., leu to ile) or __________
conservative, non-conservative
forms when all the phi and psi dihedral angles of a contiguous stretch of polypeptide adopt the same set of values
2° structure
Regular local folding of a short stretch of polypeptide into one of several specific structural forms of secondary proteins:
- Various helices
- Various pleated sheets
- Reverse turns
- Loops (do not have regular, repeating structure)
Side chains radiate outward from helix axis Minimizes steric hindrance; allows for protein-protein and protein-ligand interactions (contains hydrogen bonds
The alpha-helix
The b-strands are not stable by themselves, but only when incorporated into
sheets
Strands can align in either a _____ or an ______manner; mixed sheets are also common
parallel, antiparallel
In alpha helix - n (# residues/turn) = ____ p (pitch) = _____ rise/residue = _____
3.6 5.4 Å 1.5 Å
In beta strands and beta sheets: n = _______ p = _____
n = 2 residues/unit p = 6.8 Å
Silk fibroin
400 kDa protein that has an extensive antiparallel beta sheet structure.
REVERSE TURNS
allow a long polypeptide chain to fold back on itself
Nearly ___of residues in globular proteins are involved in reverse turns.
1/3
What is the most common reverse turn?
the beta-turn
Number of residues required to complete a turn in a beta turn
four
1st residue hydrogen-bonds to _____ in a beta turn
the 4th
common in b-turns but tend to disrupt the a-helix
Gly & Pro
the folding of a continuous sequence of 2° elements into a specific and unique three-dimensional architecture.
Protein Tertiary Structure
Only about 30 residues long. Uses side chains of 2 His and 2 Cys (or 4 Cys) residues residues to coordinate Zn2+ ion
The Zinc-Finger DNA Binding Motif Occur via H-bonds, salt-bridges and hydrophobic interactions.
A feature of some transcription factors (eg., MyoD) that bind DNA and direct transcription, especially during development Forms dimers: 2nd helix involved in dimerization Some similarities to leucine zipper motif
The Helix-Loop-Helix Motif(a type of “supersecondary” structure)
How many Ig domains are present with the antibody (Ig) molecule with each domain containing an Ig fold?
12
Fold consists of a ___layer sandwich of _____ antiparallel beta-strands arranged in two beta-sheets with a ______ topology
2, 7-9, Greek key
largest protein structural family in human genome, with 765 members
Ig “superfamily”
proteins with Ig domains:
Titin; fibroblast growth factor receptor (FGFR), a tyrosine kinase; Cadherins, molecules that mediate ca2+ dependent cell-cell adhesion involved in cell polarisation and migration, have one or more Ig-like folds
Stores O2 in the muscle
Myoglobin
Transports O2 (and CO2, H+) in the blood.
Hemoglobin
An elaborate closed barrel structure that contains alternating segments of a-helices and b-strands
The alpha/beta or TIM barrel fold (an alpha/beta domain protein) TRIOSEPHOSPHATE ISOMERASE (TIM) and other glycolytic enzymes (aldolase,enolase, pyruvate kinase) have domains that fold into this structure
Topology of 8 antiparallel B-strands linked by Beta-turns
Beta-Barrel Structure: Retinol Binding Protein (a beta domain protein) ex. Retinol (vitamin A) a plasma carrier (RBP)
The particular arrangement of two or more polypeptides in association stabilized by non-covalent forces only Each component polypeptide is called a subunit of the oligomer.
Protein Quaternary Structure Each polypeptide has its own 3° fold; each folds into a specific arrangement that functions as a single unit.
Some Oligomeric Proteins
Some Oligomeric Proteins
- Mammalian enzyme: Allosterically inhibited by ATP, citrate;
- activated by AMP, Fru-2,6-BP
- KEY CONTROL POINT FOR GLYCOLYSIS
Phosphofructokinase-1
•Tetramer of four identical subunits
