Baker (Protein structure) Flashcards
1
Q
How have protein structures been determined experimentally?
A
- NMR spec
- e- microscopy
- atomic force microscopy
- X-ray crystallography (discovered most)
2
Q
What is an atomic orbital?
A
- particular regions of space w/in which e-s mostly reside
3
Q
What is the Pauli exclusion principle?
A
- only 2e-s in each orbital and must have opp spins
4
Q
What is Hund’s rule?
A
- if 2 or more orbitals of equal energy available, 1 e- must be placed in each until all half filled
5
Q
What is an ionic bond?
A
- e- transferred from 1 atom to another
6
Q
What is a covalent bond?
A
- 2 e-s shared in overlapping orbitals from 2 atoms w/ orbitals of similar energy
7
Q
What 2 kinds of orbitals present in C?
A
- 2s and 2p
8
Q
What is atomic orbital hybridisation?
A
- combining of atomic orbitals w/in atom to form new orbitals
- bonds involving hybrid orbitals more stable than those involving ‘pure’ atomic orbitals
9
Q
What are the characteristics of a sp3 hybridised orbital?
A
- 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
10
Q
What is the arrangement of a sp3 hybrid orbital?
A
- tetrahedral
11
Q
How is C-C bond formed in ethane?
A
- σ overlap of 2 C sp3 hybrid orbitals
12
Q
What is a σ bond?
A
- overlap of 2 atomic orbitals is along line drawn between 2 nuclei
13
Q
What is the arrangement of a sp2 hybrid orbital?
A
- planar trigonal
14
Q
What is the bonding in ethene?
A
- σ bond between C + C = sp2-sp2 overlap
- σ bond between C + H = sp2-s overlap
- π bond between C + C = p-p overlap
15
Q
What is a π bond?
A
- regions of e- density above and below internuclear axis, but not along axis
16
Q
What is the arrangement of a sp hybrid orbital?
A
- linear
17
Q
What is the bonding in ethyne?
A
- 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
18
Q
What is the difference between polar and non-polar covalent bonds?
A
- non-polar = equal sharing of e-s
- polar = sharing of e-s between atoms of diff electronegativities
19
Q
How does s character affect length, strength and angle of bond?
A
- the more s character, the shorter and stronger the bond, and the larger the bond angle
20
Q
In what form do carboxylic acids exist under most biological conditions?
A
- carboxylate anions
21
Q
What kind of AAs are all natural proteins made up of, and why?
A
- L-AAs
- to avoid changes in structure
22
Q
Which AAs have are non polar?
A
- Gly
- Ala
- Pro
- Val
- Leu
- Ile
- Met
- Trp
- Phe
23
Q
Which AAs are polar and uncharged?
A
- Ser
- Thr
- Tyr
- Asn
- Gln
- Cys
24
Q
Which AAs are polar and +vely charged?
A
- Lys
- Arg
- His
25
Which AAs are polar and -vely charged?
- Asp
| - Glu
26
In what direction are polypeptides written?
- from N to C terminus
27
What are the properties of peptide bonds?
- v stable
- partial double bond character
- planar
- cleaved by proteolytic enzymes
28
In which formation are most peptide bonds in proteins, and why?
- trans
| - to avoid steric clashes
29
What does a Ramachandran plot show?
- possible combos of N-Cα and Cα-C angles which don't cause steric clashes
30
What is the native conformation of proteins determined by?
- types of side chain
| - seq in polypeptide
31
What does the function of a protein depend on?
- structure
| - linear AA seq says little about function
32
What is protein folding driven by?
- non covalent forces of attraction
33
What are the 4 types of forces that hold proteins together?
- electrostatic interactions (ionic)
- VDW interactions (dipole-dipole)
- hydrogen bonds
- hydrophobic forces
34
Where in the protein are ionic interactions strongest and weakest?
- strong in interior
| - weaker on surface
35
What are the 3 types of VDW interaction from strongest to weakest?
- interaction between permanent dipoles
- dipole-induced dipole interactions
- London dispersion forces
36
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
37
What are the strongest hydrogen bonds?
- linear when donor H bond pointing along acceptors lone pair orbital
38
What are hydrophobic forces?
- influences that cause non-polar substances to mim contact w/ water and amphipathic molecules to form micelles in aq solutions
39
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
40
What is a disulphide bond?
- covalent bond between S atoms in 2 Cys residues
41
What does formation of a disulphide bond req?
- oxidative conditions
42
Where are disulphide bonds usually found, and why?
- extracellular domains
| - give extra stability in harsh conditions
43
What is the role of chaperones?
- accessory proteins which help proteins follow correct folding pathway
44
What is the 1º structure of a protein?
- linear seq of AAs in polypeptide chain
45
What is the 2º structure of a protein?
- folding of polypeptide backbone into regular structures
| - generally stabilised by H bonding between backbone atoms
46
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
47
Where are amphiphilic α-helices often found?
- in globular proteins, hydrophobic face packs towards to interior and hydrophilic faces solvent
48
What kind of α-helices are found in transmembrane proteins?
- hydrophobic or amphiphilic
49
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
50
What are β-turns and why are they req?
- reversal in direction of polypeptide chains
| - req due to compact globular nature of proteins
51
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
52
What is the 3º structure of a protein?
- assembly of 2º structure elements into native protein structure
53
What is the 4º structure of a protein?
- assembly of 2 or more polypeptide chains into multisubunit structures
54
How are subunits usually assoc in 4º structure?
- non-covalently
55
What are allosteric interactions? (4º protein structure)
- binding of ligand to 1 subunit can alter affinity of ligand to another subunit
56
What are the types of supersecondary structure?
- β-α-β unit
- β hairpin turn
- α-α motif
57
What is a domain?
- assembly of part of polypeptide chain of protein into compact globular structure, often w/ specific function
58
What is the supersecondary structure?
- packing of 2º structure elements into local modules
59
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
60
What can inhibit formation of hydroxyproline?
- lack of vitamin C
61
What are the similarities and differences between members of same protein family?
- closely related AA seq and 3D structure
| - diff functions
62
When are σ bonds made?
- when anion and cation encounter each other
63
What is the role of a nucleophile and an electrophile?
- nucleophile supplies e-s
| - electrophile accepts e-s
64
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
