Lecture 3: Protein Structure Flashcards
Polypeptides
amino acids joined by peptide bonds. Aka proteins
Protein length
40 -> 30000 amino acids but average is ~300-400
Primary Secondary Tertiary and Quarternary Structure
1^ the amino acid sequence
2^ alpha helix and beta sheets
3^ intramolecular
4^ trimer and dimer for example
Hydrophobic effect
Water molecules surround hydrophobic molecules and form a cage like structure (low entropy)
coalition of multiple low entropy hydrophobic cages structure will lead to increased entropy so individual cage is preffered
Oil Drop
hydrophobic residues hide on the inside
a-helix and b-sheets
-Based on H bonding between peptide bond carbonyl O atoms on one amino acid and amino group hydrogens on different amino acid
-60% polypeptide chain is secondary structure
A-helix
-Amino acid H bonds with amino acid n+4 (C=O and N-H)
-3.6 residues per turn
B-sheets
-H bonds like adjacent beta strands
Structure-Driving interaction in amino acids
Non-Covalent bonds:
- H-bonds
- Ionic Bonds
- van der Waals
There is covalent:
- disulfide in s = cysteine
Cysteine Interactions
Intrachain causes tertiary
Interchain causes quarternary
Motifs
Secondary structure forming local distinct 3D structure
E.g.
- Coiled coil motif
HxxHxxxHxxHxxx…..
Motif vs Domain
If separated from the rest of the structure a domain will maintain its shape whereas a motif will denature
Protein Classes
Fibrous (long and thin)
Globular (blob)
Intergral membrane proteins
Intrinsically disordered (random coils under stable conditions that may adopt a more specific structure when bound to its well-structured partner protein
Structural Def of Domains
40 aa-long compactly folded region made of various motifs
(contains multiple protein structural class types)
Protein DOmains
Protein domains are often found to be closely conserved in very diverse proteins
