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MBB161 > Rafferty (Enzymes and membranes) > Flashcards

Rafferty (Enzymes and membranes) Flashcards

1
Q

What is a strong acid/base?

A
  • ionise completely in solution
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2
Q

What is a weak acid/base?

A
  • don’t ionise completely
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3
Q

What is the charge of an AA at pIs below and above isoelectric point?

A
  • at pH below pI = net +ve

- at pH above pI = net -ve

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4
Q

When is the pI more complex to calculate?

A
  • if side chain also has titratable group
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5
Q

Through what effects do enzymes enhance reaction rates?

A
  • proximity and orientation
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6
Q

What types of reaction do enzymes convert between?

A
  • turns intermolecular reaction into further intramolecular one
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7
Q

How long do transition states last for?

A
  • exist on v short femtosecond timescales
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8
Q

Do enzymes prefer to bind to transition states, and why?

A
  • yes, so facilitate their formation

- more stable and can be isolated

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9
Q

Many of the best enzyme inhibitors are what?

A
  • transition state analogues
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10
Q

How tightly do enzymes bind substrates, and why?

A
  • not too tightly

- as activation barrier too large

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11
Q

What is the lock and key model?

A
  • substrate exact fit

- pockets have variety of features to make sure correct substrate binds

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12
Q

What is the induced fit model?

A
  • enzyme structure flexible and changes conformation to improve fit w/ substrates or transition states
  • substrate bound non-optimally and stressed when bound
  • strained when bound, strain energy lost when transition state reached
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13
Q

What are 3 types of catalytic mechanisms and how do they work?

A
  • general acid-base catalysis –> donation of H+ by group on enzyme acting as acid or abstraction of H+ by group on enzyme acting as base, both decrease free energy pathway to transition state
  • covalent catalysis –> form covalent bonds w/ substrates to gen transient reactive intermediates
  • metal ions in catalysis –> use of bound metal ions
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14
Q

What is a metalloenzyme? (catalytic mechanisms)

A
  • tightly bound metal ion
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15
Q

What is a metal activated enzyme? (catalytic mechanisms)

A
  • loosely assoc metal ion
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16
Q

How can metal ions participate in catalysis?

A
  • metals can gen nucleophilic species to participate in enzyme catalysed reactions
  • metal ions can stabilise transition state charge
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17
Q

What are co-factors?

A
  • metal ions or small molecules req by certain enzymes to function
  • used repeatedly and recycled in cell
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18
Q

What are coenzymes and the 2 types?

A
  • small organic molecules
  • can be loosely bound = cosubstrate
  • or tightly bound = prosthetic groups
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19
Q

What is an apoenzyme and holoenzyme?

A
  • apoenzyme = enzyme on own

- holoenzyme = enzyme + cofactor

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20
Q

What is a protein coenzyme?

A
  • not catalytically active

- generally involved in transport

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21
Q

What are the classifications of enzymes (by the type of reaction they catalyse)?

A
  • oxidoreductases (dehydrogenases) –> ox/red substrates, often use cofactor
  • transferases –> transfer of chemical groups between molecules
  • hydrolases –> cleavage reactions via addition of water
  • lyases (synthases) –> addition or removal of groups to form double bonds
  • isomerases –> interconversion of isomeric forms of compounds
  • ligases (synthetases) –> joining of 2 molecules req chemical energy source
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22
Q

What is the immunoglobulin fold?

A
  • pair of anti-parallel β- sheets

- β-sheets play supportive structural role

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23
Q

What size antigens make more contacts w/ antigens?

A
  • small antigens make fewer contacts than large antigens
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24
Q

Why so antibodies possess flexibility?

A
  • flexible positioning of antigen binding sites allows antibody to match distance between sites on antigen
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25
Q

What are the functions of membranes?

A
  • separation of cells from env
  • internal membranes from organelle boundaries
  • env from critical cellular process
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26
Q

What are membranes permeable too?

A
  • permeable to gases
  • permeable to small uncharged polar molecules
  • impermeable to large uncharged polar molecules
  • impermeable to ions
  • impermeable to charged polar molecules
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27
Q

What is the myelin sheath and how does it aid transmission of electrical impulse in neuronal axons?

A
  • stack of specialised plasma membrane sheets that wraps itself around axon
  • myelination increases velocity of electric signal conduction in neurons
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28
Q

What common features underlie diversity of biological membranes?

A
  • sheet like structures, only few molecules thick
  • lipids and proteins
  • non-covalent assemblies w/ fluid structures and asymmetric
  • most electrically polarised,
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29
Q

What are lipids soluble in?

A
  • water insoluble

- v soluble in organic solvents

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30
Q

What are the 3 main types of membrane lipids?

A
  • phospholipids
  • glycolipids
  • cholesterol
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31
Q

What is a plasmalogen?

A
  • alt form of glycerophospholipid
  • acyl group on C1 position of glycerol linked via vinyl ether
  • polar group typically ethanolamine or choline
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32
Q

What length fatty acids have the highest melting points?

A
  • longer chains
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33
Q

How do cis double bonds affect the melting point, and why?

A
  • lower melting point

- as prod bend in chain, so can’t pack as closely

34
Q

What is generally the central component of FAs and how is it attached?

A
  • glycerol

- via ester bonds

35
Q

What are sphingolipids?

A
  • sphingosine derivatives –> amino alcohol w/ long hydrocarbon chain containing trans double bonds between C4 and C5
  • various fatty acyl chains connected to sphingosine by amide bond at C2
  • group attached to C1 determines type
36
Q

What is cholesterol?

A
  • isoprenoid type of lipid
  • 4 ring structure
  • hydroxyl at C3 interacts w/ phospholipid heads and rest w/ FA chains
37
Q

Is cholesterol found in bacteria?

A
  • never
38
Q

What do ionised FAs readily form?

A
  • micelles
39
Q

What is each monolayer in phospholipid bilayer known as?

A
  • leaflet
40
Q

Is bilayer formation favourable?

A
  • yes, spontaneous process

- entropy of system increases through increased entropy of solvent

41
Q

How are lipid bilayers self sealing?

A
  • close in on themselves so no edges w/ exposed hydrocarbon chains, forming compartments
42
Q

How do lipids in the bilayer diffuse?

A
  • rapidly in plane of membrane (lateral)

- slowly between layer (transverse)

43
Q

How can transverse diffusion in bilayer be accelerated?

A
  • by flippases
44
Q

Where do glycolipids w/ big sugars generally stay?

A
  • on exterior
45
Q

Why are membrane lipids distributed asymmetrically?

A
  • consequence of mode of biosynthesis
46
Q

Where are membranes synthesised and made asymmetric?

A
  • euks –> synthesised asymmetrically in golgi/ER
  • bacteria –> add lipids to inner layer of cell membrane and create asymmetry by specific reg enrichment, as spontaneous flipping between layers v slow
47
Q

How is cholesterol distributed in euks?

A
  • relatively evenly
48
Q

What does membrane curvature depend on?

A
  • lipid segregation

- local curvature depends on relative size of polar heads and nonpolar tails

49
Q

What are the 2 shapes of phospholipids, and what types of bilayer do they dorm?

A
  • cylindrical –> large heads, form relatively flat bilayers

- cone-shaped –> small heads, form curved bilayers

50
Q

What is membrane fluidity determines by?

A
  • FA composition

- cholesterol content

51
Q

How does FA saturation affect membrane fluidity?

A
  • sat FAs favour rigid state
  • cis double bonds cause kink, lower Tm
  • longer chains have stronger attractions
52
Q

How do bacteria reg membrane fluidity?

A
  • varying no. double bonds and length of fatty acyl chains
53
Q

How do animals use cholesterol to influence membrane fluidity?

A
  • cholesterol diff shape and packs alongside fatty acyl chains, stiffens structure
  • cholesterol associates w/ sphingolipids formin lipid rafts
54
Q

How does lipid composition of bilayer influence thickness?

A
  • cholesterol has lipid-ordering effect on phosphoglyceride bilayers, makes them thicker
  • sphingomyelin assoc into more gel like state and makes thicker bilayer than other phospholipids
55
Q

What does thickness of membrane play role in?

A
  • localising proteins to particular membrane
56
Q

What transition do phospholipid bilayers undergo w/ heat, and what does this result in?

A
  • gel to fluid

- decreased thickness and order

57
Q

What type of phospholipids tend to assemble into highly ordered gel-like bilayers?

A
  • phospholipids w/ long sat fatty acyl chains

- little overlap of nonpolar tails in 2 leaflets

58
Q

How can liposomes be useful “experimental” tools?

A
  • delivery systems, can help cross cell barrier and evade IS
  • treatment of various diseases
  • commercial apps
59
Q

How much of the membrane is made up lipid, protein and carbs by mass?

A
  • 25-50% lipid
  • 50-75% protein
  • ~10% carb
60
Q

What is the most common drug target?

A
  • membrane proteins (70%)
61
Q

Why are membranes not rigid?

A
  • lipids and many proteins constantly in lateral movement
62
Q

What is FRAP and what is it used for?

A
  • fluorescence recovery after photobleaching
  • used to visualise rapid lateral movement of proteins
  • can quantify lateral movements of proteins and lipid w/in plasma membrane
63
Q

How does FRAP work?

A
  • fluorescent reagent binds uniformly to specific membrane lipid/proteins
  • laser focused over small area of surface, irreversibly bleaching bound reagent and decreasing fluorescence
  • fluorescence recovered as unbleached molecules diffuse in and bleached diffuse out
  • extent of fluorescence recovery proportional to fraction of labelled molecules mobile in membrane
64
Q

What important biological processes are the diff types of membrane proteins involved in?

A
  • ion pumps and channels –> reg ionic balance
  • carriers –> molecules in and out cell
  • cell surface receptors –> recognition of extracellular hormones and signalling molecules
  • conveyors of cell identity –> participate in immunological reactions
  • converters of energy stimuli
65
Q

What are the 3 classifications of membrane proteins?

A
  • intrinsic/integral
  • extrinsic/peripheral
  • lipid-anchored
66
Q

What are the characteristic of intrinsic membrane proteins?

A
  • all or partially embedded in membrane
  • often transmembrane
  • residues interact w/ hydrophobic membrane interior
  • often extra domains in aq phase
67
Q

What are the characteristic of extrinsic membrane proteins?

A
  • interact w/ membrane via lipid heads or integral proteins

- readily dissociate from membranes

68
Q

What are the characteristic of lipid-anchored membrane proteins?

A
  • protein polypeptide remains in aq phase
  • FA anchored –> covalently attached FA embedded in membrane
  • isoprenoid anchored –> attached via Cys sidechain
  • glycosylphosphatidyl-inositol anchored –> euks can use GP1 anchors linked to C-terminus of protein
69
Q

Do membrane proteins have unique orientation in membrane, and why?

A
  • yes, synthesised and inserted in asymmetric manner

- asymmetry preserved as don’t rotate from 1 side to other

70
Q

What do transmembrane proteins often use to span membrane?

A
  • α-helices
71
Q

What does a hydropathy plot show?

A
  • identifies poss transmembrane helices
72
Q

How can proteins utilise β strands to traverse lipid membranes, and where is this often found?

A
  • β-sheets of 8-22 strands can wrap around to form barrels
  • typically form pores or receptors
  • often found in bacteria and outer membranes of mito and chloro
73
Q

How can detergents be used to solubilise and purify integral proteins?

A
  • disrupts bilayer and brings protein into solution as protein-detergent complex
  • phospholipids also solubilised by detergent
74
Q

What are the classes of membrane transport proteins?

A
  • channels/pores
  • passive transporters
  • active transporters
75
Q

How do channel membrane transport proteins work?

A
  • central passage for ion or molecules (solutes)
  • diffusion both ways depending on grad
  • can be open permanently or regulated
  • can exhibit selectivity
76
Q

How do passive membrane transport proteins work?

A
  • specifically bind solutes
  • facilitate diffusion faster than normally
  • often gated
  • not open permanently
  • transport in direction of conc grad
77
Q

How do active membrane transport proteins work?

A
  • like passive but against conc grad

- req energy

78
Q

What does uniport mean?

A
  • transport of single solute type
79
Q

What does symport mean?

A
  • transport of 2 solute types in same direction
80
Q

What does antiport mean?

A
  • transport of 2 solute types in opp directions
81
Q

What does it mean for an energy source to be of 1º or 2ºorigin?

A
  • 1º = directly coupled to energy source

- 2º = coupled to ion conc grad

MBB161 (6 decks)

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