Biochemistry Exam 1

Membranes define the external boundaries of cells and

Control the molecular traffic across that boundary

In eukaryotic cells, membranes divide the internal space into

Discrete compartments to segregate processes and components

The biological membrane is a lipid bilayer with

Proteins of various functions (enzymes, transporters) embedded in or associated with the bilayer

Hydrophobic effect stabilizes structures (lipid bilayers + vesicles) in which lipids with

Some polar + some nonpolar regions can protect their nonpolar regions from interaction with water

Polar regions shield

Non-polar regions from water

How do polar regions shield non-polar regions from water?

Attain the lowest-energy configuration by reducing how much the hydrophobic surface is exposed to water

Membrane proteins are associated with

The lipid bilayer more-or-less tightly

Proteins and lipids are allowed

Limited lateral motion in the plane of the bilayer

The endomembrane system is

Dynamic + functionally specialized

The endomembrane system

Originated from the endoplasmic reticulum

Proteins and lipids synthesized in the ER

Move through the GA

Transmembrane proteins catalyze

Transmembrane transport of polar/charged molecules

Although the lipid bilayer is impermeable to charged or polar solutes, cells have

Membrane transporters + ion channels that catalyze the transmembrane movement of specific solutes

Passive transport 

Movement of molecules across the CM without the use of energy (ATP)

During passive transport

Molecules move from high → low concentration

Active transport 

Movement of molecules against the concentration gradient (low → high)

Active transport requires

Energy (ATP) or another energy source 

Protein composition (membrane composition) 

1. Transporters

2. Receptors 

3. Ion channels 

4. Adhesion molecules

At the cell surface, transporters move specific

Organic solutes and inorganic ions across the membrane

Receptors sense extracellular signals and

Trigger molecular changes in the cell

Ion channels

Mediate electrical signaling b/n cells

Adhesion molecules

Hold neighboring cells together

Membrane flexibility permits

Shape changes that accompany cell growth and movement

Membranes permit

Exocytosis, endocytosis, and cell division

Exocytosis

Fusion of an intracellular vesicle with the plasma membrane

W/n an intracellular vesicle fuses w/h the PM

The vesicle contents are released to the extracellular space

Endocytosis

Uptake of extracellular material by its inclusion in a vesicle (endosome) formed by invagination of the PM

The selective permeability of membranes allows them to

Serve as molecular gatekeepers 

The topology of an integral membrane protein can be

Predicted from its amino acid sequence

The presence of unbroken amino acid sequences of >20 hydrophobic residues in a membrane protein is evidence that

These sequences traverse the lipid bilayer, acting as hydrophobic anchors or forming transmembrane channels

What can we predict about the secondary structure of the membrane-spanning portions of integral proteins?

At 1.5 Å per amino acid residue, an α-helical sequence of 20 to 25 residues is just long enough to span the thickness (30 Å) of the lipid bilayer

Lipid bilayer at

 ~30 Å

α helices at

~1.5 Å per a.a

Hydropathy index

Free-energy change for an a.a. moved from a hydrophobic environment to water

The relative polarity of each amino acid has been determined by measuring the

Free-energy change accompanying the movement of that amino acid side chain from a hydrophobic environment into water

The hydropathy index is 

An average value from successive segments of a defined # of a.a.

The overall hydropathy index (hydrophobicity) of a sequence of amino acids is estimated by

Summing the free energies of transfer for the residues in the sequence

High hydropathy index —>

Highly endergonic —> high hydrophobicity

The hydropathy index is highly exergonic for

Charged or polar residues

The hydropathy index is highly endergonic for

Amino acids with aromatic or aliphatic hydrocarbon side chains

Hydropathy plot

Tells us how many transmembrane domains there are in a peptide

β-barrel

Structural motif common in bacterial + mitochondrial membrane proteins

1st component of β-barrel structure

Maximized intra-chain H-bonds

2nd component of β-barrel structure

Every second residue is hydrophobic

3rd component of β-barrel structure

Common in gram-negative bacteria

W/n no water molecules are available to H-bond with the carbonyl O and N of the peptide bond,

Maximal intrachain H bonding gives the most stable conformation

In β strands of membrane proteins, every second residue in the membrane-spanning segment is

Hydrophobic and interacts with the lipid bilayer

Lipidated microsomal proteins (MP) consist of

Covalently attached long-chain fatty acids, isoprenoids, + sterols

Some membrane proteins are covalently linked to one or more lipids, which may be

Long-chain FAs, isoprenoids, sterols, or glycosylated derivatives of phosphatidylinositol

The association of lipidated MPS is

Strengthened by positively charged a.a. stretches

Ionic attractions b/n positively charged Lys residues in the protein +

Negatively charged lipid head groups can add to the anchoring effect of a covalently bound lipid

The strength of the hydrophobic interaction between a bilayer + a single hydrocarbon chain linked to

A membrane protein is barely enough to anchor the protein securely

3 clusters of positively charged Lys and Arg residues (blue) interact with

The negatively charged head group of PIP2 on the cytoplasmic face of the PM

5 aromatic residues (yellow)

Insert into the lipid bilayer

Mitochondria + chloroplasts

Aren’t part of the endomembrane system

Most membrane lipids and proteins are

Synthesized in the ER

After membrane lipids + protein are synthesized in the ER,

They move to the GA, + then they move to their destination organelles or to the PM

Membrane trafficking includes

Changes in lipid composition and disposition across the bilayer

1st change due to membrane trafficking 

Decreasing phosphatidylcholine 

2nd change due to membrane trafficking 

Increasing sphingolipids + cholesterol

3rd change due to membrane trafficking 

Increasing bilayer asymmetry

Lipid (LTPs)

Non-vesicular lipid transport

A second route for redistributing lipids from their site of synthesis to

Their destination membrane is via lipid transfer proteins

LTPs are involved in

Inter-membrane lipid transfer

LTPs

Soluble in water

LTPs have a hydrophobic lipid-binding pocket in which

They carry a lipid from one membrane to another through the cytosol

Transfer using LTPs can occur

Against the concentration gradient 

W/n LTPs move molecules against the gradient,

They couple the process to ATP hydrolysis

ATP hydrolysis releases energy

Which is used to drive active transport

ATP-binding cassette transporters (ABC transporters) use ATP to

Transport lipids and other molecules across membranes

Transbilayer movement of lipids

Requires catalysis

“Flip-flop” occurs

Much slower compared to lateral diffusion

Lateral diffusion in the

Plane of the bilayer is very rapid

Transbilayer or "flip-flop"-movement requires that a polar or charged head group

Leave its aqueous environment and move into the hydrophobic interior of the bilayer

Flip-pose movement is a process with

A high, positive free-energy change

Flip-pose movement requires enzymes

Coupled with a negative free-energy change reaction

Flippases, floppases, and scramblases facilitate

The transbilayer movement (translocation) of individual lipid molecules

Flippases use ATP to “flip in” specific lipids from

The outer to inner side of the membrane

Flippases: phosphatidylserine exposure on the outer surface

Triggers apoptosis

Flippases catalyze translocation of phosphatidylethanolamine + phosphatidylserine

From the extracellular to the cytoplasmic leaflet of the PM

Flippases maintain 

Asymmetry of the membrane

Floppases use ATP to “flop out” lipids from

The inner to the outer side of the membrane

Floppases function in lipid export

Cholesterol, phosphatidylcholine, sphingomyelin, and phosphatidylserine

Floppases move PM phospholipids and sterols from

The cytoplasmic leaflet to the extracellular leaflet

Scramblases —> passive; equilibrate concentration

Move lipids passively in both directions (inner↔outer) to equalize lipid distribution b/n the two leaflets (toward equilibrium)

Scramblases move any membrane phospholipid across

The bilayer down its concentration gradient (from high to low concentration)

The liquid-ordered (Lo) state is a membrane phase that

Combines high lipid order (like a solid) with high fluidity

Lo state: polar head groups are uniformly arrayed at the surface, and

The acyl chains are nearly motionless and packed with regular geometry

The liquid-disordered (Ld) state is a fluid phase of a lipid bilayer in which

The lipid molecules move freely and randomly, giving the membrane high flexibility and low order

Ld state: acyl chains undergo

Thermal motion and have no regular organization

Lo state is favored by long-chain saturated fatty acids (>=C16)

Long-chain saturated fatty acids (16:0 + 18:0) tend to pack into a Lo gel phase

Ld state is favored by

Short-chain fatty acids (more mobile) + unsaturated fatty acids

1st biphasic effect of sterols

Compacting unsaturated fatty acids

2nd biphasic effect of sterols

Increase fluidity of regions with saturated acyl chains

Compacting unsaturated fatty acids → sterols interact w/h phospholipids containing unsaturated fatty acyl chains,

Compacting them + constraining their motion in bilayers

Increase fluidity of regions with saturated acyl chains → the association of sterols w/h sphingolipids + phospholipids

Having long, saturated fatty acyl chains makes a bilayer fluid

Fluorescence recovery after photobleaching (FRAP)

A measure of the rate of lateral diffusion of the lipids

Fluorescently tagged lipid → a small region of a cell surface w/h fluorescence-tagged lipids is

Bleached by intense laser radiation so that the irradiated patch no longer fluoresces when viewed with less-intense light

The cell region recovers its fluorescence as unbleached lipid molecules

Diffuse into the bleached patch + bleached lipid molecules diffuse away from it

FRAP measures fluorescent signal intensity over time —> after bleaching,

The fluorescence in that area drops sharply