3. Protein Structure Flashcards
polypeptides
linear polymers of amino acids joined by peptide bonds
the hydrophobic effect
water molecules surrounding hydrophobic molecules adopt a constrained organisation that has low entropy
oil drop model of protein folding
protein conformation where hydrophobic amino acid side chains are embedded within the protein’s core while hydrophilic side chains are exposed in the surface
primary structure of proteins
amino acid sequence
secondary structure of proteins
alpha helix or B sheets: local conformations of peptide chain backbone
tertiary structure of proteins
interactions between secondary structures, overall polypeptide conformations
functions of a protein determined by
- its overall shape
- distribution of amino acid side chains
amino acid sequence is determined by
DNA
beta sheets properties
- can create large surfaces
- H-bonds link 2 adjacent B-strands
- sheets may be parallel or antiparallel
alpha helix properties
- straight rod
- amino acid (n) H-bonds with other amino acid at n+4
–> tilts axis of helix, driving periodicity of 3.6 residues/turn - surface properties exclusively dependent on side chains
quaternary structure of proteins
different tertiary structures come together
amino acid sequence determines
- protein structure
- protein function
secondary structure is based on
Hydrogen bonding between peptide bond between carbonyl oxygen and amino group hydrogen on a different amino acid residue
amino acid side chains protrude above and below B-sheet plane, determining…
interactions of B-sheets with other parts of the protein + its propensity to form
amino acid side chains mediate interactions between… (2)
- different parts of the protein
- the protein and its ligand GDP
most structure-driving interactions among amino acids are…
non-covalent bonds
disulfide bond
- type of covalent bond
- side chain of cysteine contains sulfhydryl group, forming S-S bonds with other cysteine side chains
- can be intrachain: contribute to tertiary structure
- can be interchain: contribute to quaternary structure
motifs of protein structure
combinations of secondary structures forming distinct local 3D structures
are motifs independent?
motifs are not structurally independent entities: too small, insufficient bonds
domains
40 amino acid long region, tertiary structures that are compactly folded
–> can be made of various motifs
are domains independent?
domains are structurally independent entities
motifs and domains are both…
local structures
motif examples
- coiled-coil motif: 2 long alpha helices joined together, involved in protein-protein interactions
- EFhand/helix-loop-helix motif: Ca2+ binding motif
- Zinc-finger motif: common in transcriptions factors -> binds to DNA/RNA
similar domains can be found in diverse proteins example
Epidermal Growth Factor (EGF) found in Neu oncogene protein and TPA tissue plasminogen activator
