Baker (Protein structure) Flashcards
How have protein structures been determined experimentally?
- NMR spec
- e- microscopy
- atomic force microscopy
- X-ray crystallography (discovered most)
What is an atomic orbital?
- particular regions of space w/in which e-s mostly reside
What is the Pauli exclusion principle?
- only 2e-s in each orbital and must have opp spins
What is Hund’s rule?
- if 2 or more orbitals of equal energy available, 1 e- must be placed in each until all half filled
What is an ionic bond?
- e- transferred from 1 atom to another
What is a covalent bond?
- 2 e-s shared in overlapping orbitals from 2 atoms w/ orbitals of similar energy
What 2 kinds of orbitals present in C?
- 2s and 2p
What is atomic orbital hybridisation?
- combining of atomic orbitals w/in atom to form new orbitals
- bonds involving hybrid orbitals more stable than those involving ‘pure’ atomic orbitals
What are the characteristics of a sp3 hybridised orbital?
- unsymmetrical about nucleus
- 1 lobe bigger, so overlaps better w/ orbital from another atom in covalent bond
- form stronger bond than unhybridised s/p orbitals
What is the arrangement of a sp3 hybrid orbital?
- tetrahedral
How is C-C bond formed in ethane?
- σ overlap of 2 C sp3 hybrid orbitals
What is a σ bond?
- overlap of 2 atomic orbitals is along line drawn between 2 nuclei
What is the arrangement of a sp2 hybrid orbital?
- planar trigonal
What is the bonding in ethene?
- σ bond between C + C = sp2-sp2 overlap
- σ bond between C + H = sp2-s overlap
- π bond between C + C = p-p overlap
What is a π bond?
- regions of e- density above and below internuclear axis, but not along axis
What is the arrangement of a sp hybrid orbital?
- linear
What is the bonding in ethyne?
- σ bond between C + C = sp-sp overlap
- σ bond between C + H = sp-s overlap
- 2 π bonds between C + C = py-py and p2-p2 overlap
What is the difference between polar and non-polar covalent bonds?
- non-polar = equal sharing of e-s
- polar = sharing of e-s between atoms of diff electronegativities
How does s character affect length, strength and angle of bond?
- the more s character, the shorter and stronger the bond, and the larger the bond angle
In what form do carboxylic acids exist under most biological conditions?
- carboxylate anions
What kind of AAs are all natural proteins made up of, and why?
- L-AAs
- to avoid changes in structure
Which AAs have are non polar?
- Gly
- Ala
- Pro
- Val
- Leu
- Ile
- Met
- Trp
- Phe
Which AAs are polar and uncharged?
- Ser
- Thr
- Tyr
- Asn
- Gln
- Cys
Which AAs are polar and +vely charged?
- Lys
- Arg
- His
Which AAs are polar and -vely charged?
- Asp
- Glu
In what direction are polypeptides written?
- from N to C terminus
What are the properties of peptide bonds?
- v stable
- partial double bond character
- planar
- cleaved by proteolytic enzymes
In which formation are most peptide bonds in proteins, and why?
- trans
- to avoid steric clashes
What does a Ramachandran plot show?
- possible combos of N-Cα and Cα-C angles which don’t cause steric clashes
What is the native conformation of proteins determined by?
- types of side chain
- seq in polypeptide
What does the function of a protein depend on?
- structure
- linear AA seq says little about function
What is protein folding driven by?
- non covalent forces of attraction
What are the 4 types of forces that hold proteins together?
- electrostatic interactions (ionic)
- VDW interactions (dipole-dipole)
- hydrogen bonds
- hydrophobic forces
Where in the protein are ionic interactions strongest and weakest?
- strong in interior
- weaker on surface
What are the 3 types of VDW interaction from strongest to weakest?
- interaction between permanent dipoles
- dipole-induced dipole interactions
- London dispersion forces
How does energy of VDW interaction change as 2 atoms approach each other?
- energy most favourable at VDW contact distance
- energy increases rapidly as atoms move closer, due to repulsion between e-s
What are the strongest hydrogen bonds?
- linear when donor H bond pointing along acceptors lone pair orbital
What are hydrophobic forces?
- influences that cause non-polar substances to mim contact w/ water and amphipathic molecules to form micelles in aq solutions
How does water act as a solvent?
- solubilises polar and ionic substances, and hydrophilic molecules
- form cages around non-polar hydrophobic parts of molecule
- bury these hydrophobic side chains, releasing caged water molecules, increasing solvent entropy
What is a disulphide bond?
- covalent bond between S atoms in 2 Cys residues
What does formation of a disulphide bond req?
- oxidative conditions
Where are disulphide bonds usually found, and why?
- extracellular domains
- give extra stability in harsh conditions
What is the role of chaperones?
- accessory proteins which help proteins follow correct folding pathway
What is the 1º structure of a protein?
- linear seq of AAs in polypeptide chain
What is the 2º structure of a protein?
- folding of polypeptide backbone into regular structures
- generally stabilised by H bonding between backbone atoms
What are the characteristics of α-helices?
- all main CO and NH H bonded –> C=O of residue i and NH of residue i + 4
- 3.6 residues per turn
- all side chains point away and down from axis
- tightly packed core due to VDW
- essentially all right handed
- dipoles of each peptide bond aligned and helix carries macro dipole –> NH end +ve and CO end -ve
- often amphiphilic
Where are amphiphilic α-helices often found?
- in globular proteins, hydrophobic face packs towards to interior and hydrophilic faces solvent
What kind of α-helices are found in transmembrane proteins?
- hydrophobic or amphiphilic
What are the characteristics of β-sheets?
- 2 or more polypeptide strands H bonded together, each in nearly extended formation
- can be made up of parallel, antiparallel or mixed strands
- side chains of consecutive residues on opp faces
- certain seq will gen amphipathic sheet
- can be relatively flat, but often twisted, due to steric clashes of backbone and side chains
- indiv strands can occur far apart in seq
What are β-turns and why are they req?
- reversal in direction of polypeptide chains
- req due to compact globular nature of proteins
How does proline affect 2º structure, and why?
- often causes kink in α-helix or β-sheet
- cyclic side chain binds to N of amide in main chain
What is the 3º structure of a protein?
- assembly of 2º structure elements into native protein structure
What is the 4º structure of a protein?
- assembly of 2 or more polypeptide chains into multisubunit structures
How are subunits usually assoc in 4º structure?
- non-covalently
What are allosteric interactions? (4º protein structure)
- binding of ligand to 1 subunit can alter affinity of ligand to another subunit
What are the types of supersecondary structure?
- β-α-β unit
- β hairpin turn
- α-α motif
What is a domain?
- assembly of part of polypeptide chain of protein into compact globular structure, often w/ specific function
What is the supersecondary structure?
- packing of 2º structure elements into local modules
What are some types of post translational mods of AAs?
- phosphorylation –> OH of Ser/Thr/Tyr can be reversibly phosphorylated, often acts as mol switch reg cellular processes
- glycosylation –> carb units added to specific Asn residues of proteins on surface of cells or secreted proteins, increases hydrophobicity and ability to interact w/ other molecules, carb can also link Ser and Thr
- hydroxyproline –> stabilises collagen fibres
- γ-carboxyglutamate –> carboxylation of certain glutamate residues
- many proteins cleaved and trimmed after synthesis
What can inhibit formation of hydroxyproline?
- lack of vitamin C
What are the similarities and differences between members of same protein family?
- closely related AA seq and 3D structure
- diff functions
When are σ bonds made?
- when anion and cation encounter each other
What is the role of a nucleophile and an electrophile?
- nucleophile supplies e-s
- electrophile accepts e-s
When does simultaneous making and breaking of σ bonds occur?
- when nucleophile approaches C atom w/ leaving group (L) in anti and rearward direction to its leaving group
