Chapter 4: Protein 3D structure Flashcards
Which end of the polypeptide chain is the start?
START: amino terminal
END: carboxyl terminal
A dipeptide is formed when…..
2 a.a. bond together, accompanied by the loss of H2O
The backbone or main chain is……
a regular repeating part in the polypeptide chain + variable parts comprising of distinctive side chains.
The largest protein is ….. made up of ….. a.a.
Titin (muscle protein), 27000
Oligopeptides
made up of small number of a.a.
Important of a.a. sequence
- determines 3D structure
- sequence is essential to function
- reveal evolutionary history
+ alterations can produce abnormal function & disease
How are polypeptide chain restricted?
- Peptide bond is Planer
- double-bond character to resonance structure (prevents rotation, shortens bond length and constrains conformation of backbone)
- peptide bond is uncharged - polymers form tightly packed globular proteins
the 2 configurations possible for a planar peptide bond
Trans Config. –> 2 a-carbons are on opposite sides of the peptide bond (preferred configuration as prevents clashes between R-groups)
Cis Config. –> groups are pm the same side of peptide bond
peptide units can rotate because ….
single bonds link a-carbon to amino and carbonyl group
+ peptide units can therefore rotate, taking on various orientations
Ramachandran values
phi (φ) -> N – a-carbon
psi (ψ) -> Carbonyl carbon – a-carbon
Do R-groups play a role in secondary structure?
NO, interactions for protein structure occur due to H-bonding of backbone
Alpha Helix description
- single polypeptide coiled, H bonding on itself
- side chains projected outward
+ a.a. spaced 3-4 residues apart are spatially close in a helix.
+ helix can be clockwise or counterclockwise
+ clockwise helices are energetically more favorable (fewer clashes b/w side chains and backbone)
Which Helix formation is typically found in proteins?
Clockwise (right-handed)
Beta-pleated sheets description
- 2 or more polypeptide strands, not coiled (extended)
- 2 main H-bond patterns: parallel and anti-parallel
+important structural element -> fatty-acid binding
Most proteins have compact globular shapes. Reversals in the direction of protein chains are achieved by….
structural elements called reverse turns and loops
Turns and loops description
- exist on the surface of proteins
- role in interacting with the environment
+ loops are usually composed of a.a. with hydrophilic R-groups
a- Keratin
- fibrous protein with extensive 2ndary structure
- found in hair
- 2 right handed helices intertwined to form a left-handed superhelix called a coiled coil
Coiled-coil proteins
+superfamily of proteins
+2 or more helices can entwine to form stable structure
+humans have approx. 60 members of this family (including intermediate filaments and muscle proteins myosin and tropomyosin)
+ occurs by weak interaction such as van der Waals forces and Ionic interactions
+ helices may be linked by disulfide bonds formed by neighboring cysteine residues
Collagen description
- fibrous protein with extensive 2ndary structure
- skin, bone, tendons, cartilage, and teeth
- super helical cable of 3 intertwined polypeptide chains
- Unique with high Gly and Pro content in each strand (hydroxyproline)
+ most abundant mammalian protein
+ Gly appears every 3rd residue
+ Gly-Pro-Pro sequence recurs frequently
+ Each helix is stabilized by steric repulsion of the pyrrolidine rings of Pro residues.
+ 3 strands stabilized by H-bonds
Scurvy results in …..
lack of vitamin C (required for formation of hydroxyproline)
Tertiary structure refers to…
Spatial arrangement of a.a. residues that are far apart in the sequence - level of structure is result of interactions b/w R-groups
Interactions that can occur for tertiary structure are….
Disulfide bonds
H-bonds
Salt bridges
Hydrophobic interactions
Tertiary structure is often initiated by ….
Hydrophobic forces
+ folding so hydrophobic residues on interior and hydrophilic residues on exterior
+ especially for globular proteins
Globular Proteins
- form complicated 3D structures
- very compact with little to no empty space
- interior = hydrophobic a.a.
- exterior = charges and polar a.a.
Myoglobin description
+ extremely compact molecule
+ 153 a.a.
+ capacity of Oxygen binding depends on heme
+ asymmetric because of complex folding of main chain
+ only polar residues in interior are 2 His residues
Helix-turn-helix motifs
- super-secondary structure
+ a-helix separated from another helix by a turn
protein Domains
- regions on a polypeptide chain that have structural/functional roles
- usually found in protein that are involved multiple functions such as catalysis, binding
+ compact globular units
+ polypeptide chains fold into 2 or more compact regions that may be connected by a flexible segment of polypeptide chain (pearls on a chain)
+ different proteins may have domain in common even if overall tertiary structures are different.
Disulfide bonds
- formed by oxidation of thiols on 2 Cys
- reduction can break the bond
- increasing number of Cys usually associated with increased rigidity
- Covalent bond exists but not that stable due to red.
Quaternary structure
- distinct subunits brought together in one protein molecule
-may be multiple identical units or different units
+ the interactions among subunits are usually weak interactions (H-bonds, ionic bonds & van der Waals)
+ the simples quaternary structure is a dimer consisting of 2 identical subunits
Hemoglobin
- tetramer –> α2β2 subunits
