BIOC 222 - LECTURE 26

what are the main components of a membrane

• phospholipid bilayer

• integral proteins

• peripheral proteins

• cholesterol

what are the main membrane lipids

• glycerophospholipids

• glycolipids

• sterols

what is common between the main membrane lipids

• they have a hydrophobic and hydrophilic regions

describe the structure of a glycerophospholipid

• glycerol backbone

• 2 fatty acid tails (R groups)

• phosphate head group

• X group that is variable

describe the diversity of the x head group of the glycerophospholipid

• can be extremely variable depending on what proteins and enzymes it is exposed to and therefore what modifications it has

• head groups on either side of the membrane (inside facing vs outside facing) are extremely variable as well as they are exposed to completely different environments

what are the two ways in which the phospholipids in the membrane can move

• transverse

• lateral

describe transverse diffusion of the phospholipids

• transverse diffusion is describing the ability of a lipid to flip from the inside layer to the outside layer of the bilayer of vice versa

• this is an extremely slow and resisted process as the extremely hydrophillic head would have to move through the extremely hydrophobic region occupied by the tails

describe lateral diffusion of the phospholipids

• describing the ability of the lipids to move in 2 dimensions

• this is really fast because the hydryphobic regions are remaining in the hydrophobic regions and same with the hydrophillic regions

describe how the favourability of the types of movement of the phospholipid layer affects the composition of the layer

• transverse movement being unfavourable and slow means the inside and outside layers end up having super different compositions as they are constantly exposed to two very different environments

describe how membrane composition varies between cell types

• different cells have different organelles and therefore different environments that the inner membrane is exposed to

• as well as different cells in different regions of the body are going to have different external environments that the membrane is exposed to, and therefore different cells are going to have different membrane compositions

describe how intracellular membrane compositions vary (of organelles)

• the whole point of organelles is to provide different conditions to conduct different processes

• therefore different organelles with different internal conditions are going to have different membrane compositions

• membrane of a mitochondria and and a lysosome is going to signficantly vary

is it jsut the chemical nature of the membranes that vary

• no the protein to lipid ratio also varies

describe the difference in protein to lipid ratio of a membrane between an axon, mitochondria and the plasma membrane

• mitochodria has a 75-25 protein to lipid ratio - reflects its function as teh powerhouse of the cell

• axon has a 20-80 protein to lipid ratio

• plasma membrane has a 50-50 protein to lipid ratio

what are the two main classes of membrane proteins

• peripheral

• integral

basic description of peripheral proteins

• associate with the protein but do not transverse them

what must a protein do to transverse the membrane

• peptide bonds contain carbonyl and amide that are polar and can form hydrogen bonds

• to transverse the membrane HYDROPHOBIC region of the membrane - these must be shielded

how does a protein that is transversing the membrane shield its charges

• by forming secondary structures

• in alpha helices - the carbonyl and amide groups form hydrogen bonds within the helix

• in beta sheets - they form hydrogen bonds between neighbouring strands

• side chains must be hydrophobic as they are portruding outwards

what can be used to infer if a helices is potentially a transmembrane helices

• hydropathy plot

describe what a hydropathy plot is

• hydropathy scale ranks amino acids depending on how hydrophobic they are (+ for hydrophobic, - for hydrophillic)

• rolling averages of the amino acids through a protein is taken - if they amino acids has a larger proportion of hydrophobic side chains, this will be displayed as a positive deflection on the plot - which is an indiciation that it might be a transmembrane protein

• an protein with an even distribution of hydrophillic and hydrophobic chains will cancel out and show up as 0

why is hydropathy plots combined with secondary structure prediction

• provides stronger evidence

• eg 7 peaks for helcies and 7 hydrophobic peaks

• suggests 7 alpha helices transmembrane domains

why are hydropathy plots less useful for beta barrels

• beta barrels are beta strands arranged into a barrel

• with the outside having hydrophobic residues pointing out

• and the inside made up of polar residues facing in

• creates an alternating pattern of hydrophillic and phobic resiudes > will show up as nothing on a hydropathy plot

why are membrane proteins difficult to study

• labratory techniques work in aqueous solutions. but membrane proteins are adapted to contact hydrophobic tails > when taken out of the hydrophobic environment> they aggregate/unfold/lose activity

• expression system difficulties

• membrane proteins are super dynamic

what is a solution to studying membrane proteins

detergents

describe the structure of detergents

• hydrophobic region and hydrophillic region

• just like membrane proteins

describe how detergents are useful in studying membrane proteins

• when they reach a certain concentration, they from a micelle and replace the lipids that are coating the hydrophobic parts of the protein

• so we end up with a protein micelle complex

• hydrophobic regions facing the hydrophobic part of the proteins and the hydrophillic parts of the micelle (and the protein) facing the aqueous environment that we are studying in

what is a micelle

• assembly of detergent with hydrophobic regions gathered inward and hydrophilic regions exposed to water.

what is critical micelle concentration

• concentration above which micelles form appreciably.

are all detergents the same

• no there is lots of detergents with different CMC’s

• need to pick one suitable to the protein

describe how we can determine which detergent suits our protein

• size exclusion chromatography

• checks whether the detergent keeps the proteins evenly dispersed or lets them clump up

• One narrow peak: particles are mostly similar in size - a good sign.

• Broad or multiple peaks: a mixture of sizes, possibly including clumps of aggregated proteins due to improper shielding of micelle

what are nanodiscs

emerging way of studying membrane proteins

• provides a small patch of lipid bilayer surrounded by scaffold proteins that act like a belt around its edge.

• A membrane protein can sit within that lipid patch.

This offers:

• A more membrane-like environment around the protein.

• A particle that can still be handled in aqueous solution.