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MBB161 > Baker (Protein structure) > Flashcards

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)
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2
Q

What is an atomic orbital?

A
  • particular regions of space w/in which e-s mostly reside
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3
Q

What is the Pauli exclusion principle?

A
  • only 2e-s in each orbital and must have opp spins
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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
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5
Q

What is an ionic bond?

A
  • e- transferred from 1 atom to another
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6
Q

What is a covalent bond?

A
  • 2 e-s shared in overlapping orbitals from 2 atoms w/ orbitals of similar energy
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7
Q

What 2 kinds of orbitals present in C?

A
  • 2s and 2p
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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
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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
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10
Q

What is the arrangement of a sp3 hybrid orbital?

A
  • tetrahedral
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11
Q

How is C-C bond formed in ethane?

A
  • σ overlap of 2 C sp3 hybrid orbitals
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12
Q

What is a σ bond?

A
  • overlap of 2 atomic orbitals is along line drawn between 2 nuclei
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13
Q

What is the arrangement of a sp2 hybrid orbital?

A
  • planar trigonal
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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
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15
Q

What is a π bond?

A
  • regions of e- density above and below internuclear axis, but not along axis
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16
Q

What is the arrangement of a sp hybrid orbital?

A
  • linear
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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
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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

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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
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20
Q

In what form do carboxylic acids exist under most biological conditions?

A
  • carboxylate anions
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21
Q

What kind of AAs are all natural proteins made up of, and why?

A
  • L-AAs

- to avoid changes in structure

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22
Q

Which AAs have are non polar?

A
  • Gly
  • Ala
  • Pro
  • Val
  • Leu
  • Ile
  • Met
  • Trp
  • Phe
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23
Q

Which AAs are polar and uncharged?

A
  • Ser
  • Thr
  • Tyr
  • Asn
  • Gln
  • Cys
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24
Q

Which AAs are polar and +vely charged?

A
  • Lys
  • Arg
  • His
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25
Q

Which AAs are polar and -vely charged?

A
  • Asp

- Glu

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26
Q

In what direction are polypeptides written?

A
  • from N to C terminus
27
Q

What are the properties of peptide bonds?

A
  • v stable
  • partial double bond character
  • planar
  • cleaved by proteolytic enzymes
28
Q

In which formation are most peptide bonds in proteins, and why?

A
  • trans

- to avoid steric clashes

29
Q

What does a Ramachandran plot show?

A
  • possible combos of N-Cα and Cα-C angles which don’t cause steric clashes
30
Q

What is the native conformation of proteins determined by?

A
  • types of side chain

- seq in polypeptide

31
Q

What does the function of a protein depend on?

A
  • structure

- linear AA seq says little about function

32
Q

What is protein folding driven by?

A
  • non covalent forces of attraction
33
Q

What are the 4 types of forces that hold proteins together?

A
  • electrostatic interactions (ionic)
  • VDW interactions (dipole-dipole)
  • hydrogen bonds
  • hydrophobic forces
34
Q

Where in the protein are ionic interactions strongest and weakest?

A
  • strong in interior

- weaker on surface

35
Q

What are the 3 types of VDW interaction from strongest to weakest?

A
  • interaction between permanent dipoles
  • dipole-induced dipole interactions
  • London dispersion forces
36
Q

How does energy of VDW interaction change as 2 atoms approach each other?

A
  • energy most favourable at VDW contact distance

- energy increases rapidly as atoms move closer, due to repulsion between e-s

37
Q

What are the strongest hydrogen bonds?

A
  • linear when donor H bond pointing along acceptors lone pair orbital
38
Q

What are hydrophobic forces?

A
  • influences that cause non-polar substances to mim contact w/ water and amphipathic molecules to form micelles in aq solutions
39
Q

How does water act as a solvent?

A
  • 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
Q

What is a disulphide bond?

A
  • covalent bond between S atoms in 2 Cys residues
41
Q

What does formation of a disulphide bond req?

A
  • oxidative conditions
42
Q

Where are disulphide bonds usually found, and why?

A
  • extracellular domains

- give extra stability in harsh conditions

43
Q

What is the role of chaperones?

A
  • accessory proteins which help proteins follow correct folding pathway
44
Q

What is the 1º structure of a protein?

A
  • linear seq of AAs in polypeptide chain
45
Q

What is the 2º structure of a protein?

A
  • folding of polypeptide backbone into regular structures

- generally stabilised by H bonding between backbone atoms

46
Q

What are the characteristics of α-helices?

A
  • 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
Q

Where are amphiphilic α-helices often found?

A
  • in globular proteins, hydrophobic face packs towards to interior and hydrophilic faces solvent
48
Q

What kind of α-helices are found in transmembrane proteins?

A
  • hydrophobic or amphiphilic
49
Q

What are the characteristics of β-sheets?

A
  • 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
Q

What are β-turns and why are they req?

A
  • reversal in direction of polypeptide chains

- req due to compact globular nature of proteins

51
Q

How does proline affect 2º structure, and why?

A
  • often causes kink in α-helix or β-sheet

- cyclic side chain binds to N of amide in main chain

52
Q

What is the 3º structure of a protein?

A
  • assembly of 2º structure elements into native protein structure
53
Q

What is the 4º structure of a protein?

A
  • assembly of 2 or more polypeptide chains into multisubunit structures
54
Q

How are subunits usually assoc in 4º structure?

A
  • non-covalently
55
Q

What are allosteric interactions? (4º protein structure)

A
  • binding of ligand to 1 subunit can alter affinity of ligand to another subunit
56
Q

What are the types of supersecondary structure?

A
  • β-α-β unit
  • β hairpin turn
  • α-α motif
57
Q

What is a domain?

A
  • assembly of part of polypeptide chain of protein into compact globular structure, often w/ specific function
58
Q

What is the supersecondary structure?

A
  • packing of 2º structure elements into local modules
59
Q

What are some types of post translational mods of AAs?

A
  • 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
Q

What can inhibit formation of hydroxyproline?

A
  • lack of vitamin C
61
Q

What are the similarities and differences between members of same protein family?

A
  • closely related AA seq and 3D structure

- diff functions

62
Q

When are σ bonds made?

A
  • when anion and cation encounter each other
63
Q

What is the role of a nucleophile and an electrophile?

A
  • nucleophile supplies e-s

- electrophile accepts e-s

64
Q

When does simultaneous making and breaking of σ bonds occur?

A
  • when nucleophile approaches C atom w/ leaving group (L) in anti and rearward direction to its leaving group

MBB161 (6 decks)

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