Biochem Exam 2 (pt 3)

• A heterogeneous class of organic molecules with marginal solubility in water
• Hydrophobic
• Most functions relate to their hydrophobicity (directly or indirectly)

• Biological membranes
• Energy storage
• Hydro insulation/water repelling
• Electrical insulation
• Thermal insulation
• Signaling
• Hormone and vitamin precursors
• Digestion

Compartmentation and separation of "self" from "non-self"

Triglycerides

Waxes

• Impermeable for ions
• Ex: myelin sheath of nerves

Adipose tissue-- low in water and capillaries

Cholesterol, phosphatidylinositol, phosphoinositides

Steroids, Vitamins D,E,K,A

Example bile acids- emulsifiers that digest other lipids

• Open chain: polar head groups with long non-polar aliphatic tails 
• Fatty acids
• Triacylglycerols
• Phosphoacylglycerols
• Sphingolipids
• Eicosanoids
• Waxes

• Fused ring compounds
• Isoprenoids (isoprene is precursor)
• Steroids
• Lipid vitamins

Scaffold (glycerol, glycerolipids, or sphingolipids)

Polar groups (phospholipids or glycolipids)

Non-polar groups: (saturated or unsaturated fatty acids)

No double bonds

• Double bonds
• Mono-unsaturated and poly-unsaturated (2 or more)
• 

• Dodecanoate
• 0 double bond
• 12 C

• Tetradecanoate
• 0 double bonds
• 14 C

• Hexadecanoate
• 0 double bonds 
• 16 C

• Octadecanoate
• 0 double bonds
• 18 C

• Eicosanoate
• 20:0

• Cis-delta9-Octadecenoate
• 18:1

cis, cis-delta9,12-Octadecadienoate

• 20:4
• all cis-delta 5,8,11,14-Eicosateraenoate

LIL HOT

• Lyases
• Isomerases
• Ligases
• Hydrolases
• Oxidoreductases
• Transferases

Length: #double bonds (cys- or trans-delta ^{position of bonds})

Dodeca

Tetradeca

Hexadeca

Octadeca

Eicosa

-anoate/anoic acid

-enoate/enoic acid

-dienoate/dienoic acid

-trienoate/trienoic acid

-tetraenoate/tetraenoic acid

-pentaenoate/pentaenoic acid

Regardless of length of a fatty acid, the last carbon is always omega

Fatty acids with last double bond three carbons from the end are omega 3

Those with the last double bond six carbons from the end are omega 6

• Cause a bend in the hydrocarbon tail
• In the membrane context, cis-fatty acids make membranes more fluid

• Unnatural unsaturated fatty acids
• Found in hydrogenated vegetable oils, in which unsaturation is in trans form

• Stabilizes the hydrocarbon tail in the extended conformation
• Enables tight packing with other extended tails
• Makes the extended structures more rigid, less flexible
• Cis-Fatty acids do the opposite, break the extended state

• More carbons = higher melting temp (each C pair ~5-10 degrees)
• More hydrogen bonds decreases melting point more dramatically

Structure: three fatty acids are attached via ester bonds to OH groups of Glycerol

• Functions:
• energy (main and best way to store chemical energy long-term)
• thermo insulation
• major dietary lipid (Glycerol)

Low unsaturation in fats, high unsaturation in oils

• Energy is gained by oxidation of organic molecules
• Fatty acids are less oxidized and therefore can release more energy upon oxidation

White fat: nutrient storage, thermoinsulation (present in kids and adults)

Brown fat: produces heat=thermoregulation (abundant in newborns and hibernating mamals); scarce in adults-energy-burning adipose tissue rich in mitochondria-- which causes brown coloration

They live in colder areas

• Decrease risk of arrhythmias 
• Decrease triglyceride levels
• Slow the growth rate of atherosclerotic plaque
• Lower blood pressure
• Found in good sources of seafood i.e salmon or tuna, walnuts, canola, and soybeans

Essential since humans cannot synthesize

• Omega 6-derivatives promote inflammation
• Omega 3-anti inflammatory

Healthy ratio of w6:w3= 1:1=1:4

• Phosphoglycerides or glycerophospholipids
• 

• Water head group
• 

• Choline head group
• Major membrane constituent
• 

• Ethanolamine head group
• Major membrane constituents
• 
• 

• Serine head group
• Major constituent of the cytosolic (inner) side of cell membranes-- in apoptosis, this gets translocated to outer leaflet to trigger cell phagocytosis
• 
• 

• Glycerol head group
• 

• Diphosphatidyl glycerol (cardiolipin)
• Inner mitochondrial membrane
• Involved in regulation of proton transport

• Phosphatidyl inositol
• Signaling & membrane tracking
• Minor constituent of the cytosolic side of membrane
• Can be phosphorylated at multiple positions of inositol hydroxyls

• Sphingosine dialcohol instead of glycerol
• 

The foundation for other molecules (alcohol)

• Sphingosine+fatty acid
• 
• Only 1 fatty acid attached via an amide bond

• Ceramide+phosphate+choline or ethanolamine
• 
• Electral insolation of nerves

• Membranes of muscle and neural tissues
• Ceramide+glucose or galactose
• 

• Membranes rafts-- signaling
• Ceramide+oligosaccharide

• Built of multiple layers of schwann cell membrane rich in cerebroside and sphingomyelin
• Electrical insulation
• Increase the speed at which impulses propagate along the myelinated fiber

Loss of myelin sheaths as a result of neurodegenerative autoimmune diseases, e.g. multiple sclerosis

• Essential component of mammalian, but not prokaryotic, cell membranes (est. proper fluidity and permeability)
• Precursor of steroid hormones, bile acids, and vitamin D

Arteriosclerosis, thrombosis, heart attacks and strokes

• Control metabolism, inflammation, immune functions, mineral balance, sexual characteristic
• 

Testosterone: male sex hormone, anabolic steroid

• Progesterone
• Estradiol

Female sex hormones, menstrual cycle, pregnancy, embryogenesis

Cortisol

• Sugar-, fat-, protein-metabolism 
• Immune suppressor

Aldosterone

Water and salt homeostasis

Transport

Cholic acid & deoxycholic acid: emulsifiers/digestion

• Ursudeoxycholic acid (UDCA- bear bile): reduces cholesterol absorption, dissolves cholesterol gallstones
• Used in traditional medicine

Derivatives of arachidonate (20:4 all-cis delta^5,8,11,14)

• Arachidonic acid
• Prostaglandin E₂
• Thromboxane A₂
• Leukotriene D₄

Have powerful hormone-like, but local action

• Starting material
• 

• Blood vessel tonus, anti-microbe function, reproduction, inflammation
• Aspirin acts by reducing PGE2 synthesis

• Produced by platelets
• Blood clot formation and vasoconstriction

• Vaso- and bronchoconstriction
• Involved in anaphylactic response (immune reaction)

• Esters of fatty acids and long-chain alcohols
• Highly hydrophobic, high melting temp
• Waterproof coatings for plants and animals

• Bile acids are produced by the gall bladder
• Work as detergent, brake large fat/oil droplets to smaller particles accessible to enzymes

Triglyceride lipases (cleave triglycerides at positions 1&3)

• Phospholipases (produced by the pancreas)
• 

Venoms cause damage by breaking down membranes

• Lipoproteins of "extremely low density" produced in intestines to transport water-insoluble lipids by blood 
• Highest lipid content
• Fatty acids and monoacylglycerols get converted back into triglycerides and transported by these

Remnants consumed by liver

Protein component: apolipoprotein

Lipid component: triacylglycerols, phospholipids, cholesterol esters, lipid vitamins

• Very low density
• High lipid, lower protein than chylomicrons

• Intermediate density
• Lower lipid, higher protein

• Low density
• Lower lipid than VLDL but high lipid, low protein

• Produced by liver, consumed by liver
• Function: primary transporters of TAG & cholesterol to tissues

• VLDL
• IDL
• LDL

• Produced by liver, removed by liver
• High density and low lipid content

Function: scavengers of excessive cholesterol from tissues

HDL

• Lipids are highly hydrophobic
• In polar solutions they are under strong influence of hydrophobic effect and will self organize into noncovalent assemblies

Have 2 hydrophobic tails which means they are likely to be found in the membrane

• Large head and thin tails form this
• 

• This lipid forms fatty acids
• Unstable

• Lipids form glycerophospholipids
• Stable

• Triacyglycerols
• Unstable

Non-covalent assemblies of lipids and proteins that form boundaries of cells and organelles

Major consitiuents of all membranes: cytoplasmic, nuclear, ER, golgi, endosome

• Mitochondrion
• Autophagosome

• Can be done by sonication of phospholipids in water solutions of a desired drug
• As a result, the water soluble drug will be trapped in the lipid bilayer
• 

• Can carry different classes (hydrophobic and/or hydrophilic) of trapped molecules
• Can be targeted to a particular organ/region (i.e tumor) via targeting peptides
• Can be used for drug delivery

• Form spontaneously
• Seal-sealing
• Semi-permeable (nonpolar compounds)
• Asymmetric

The asymmetric distribution of FA between leaflets of the cytoplasmic membrane contributes to signaling, recognition of intruders (bacterial cells) and to apoptosis of cells destined to die

• Phosphatidylserine
• Phosphatidylinositol
• Phosphatidylinositol-4-phosphate
• Phosphatidylinositol 4,5-biphosphate

All negatively charged which allows the membrane to detect them

• Lipid can travel across ~1um of membrane in 2 second
• Avg size of human cell is ~30um

Hydrophobic bilayer is nearly impermeable to polar groups, including the polar or charged head groups of membrane lipids

• Fluorescent membrane marker (i.e lipid or protein)
• Defined membrane area is bleached with laser. Membrane remains undamaged
• Return of fluorescence to the photo-bleached area indicates lateral diffusion within the membrane
• Method can be used to evaluate the rate of diffusion and therefore, the size and association of diffusion molecules

Leaflet polarity are maintained by these enzymes; Flippase moves from outer to cytosolic leaflet and floppase is reverse

• Create and maintain asymmetry between the leaflets
• Break this difference when required (i.e initiate phagocytosis of apoptotic cells)

Membranes undergo a "phase transition" from a "solid-like" to "fluid" state at a transition temperature

• Chain length
• Degree of saturaturation

• Longer lipids w/ high saturation degree are required to maintain membrane integrity at higher temperatures
• Unsaturated lipids maintain membrane fluidity at low temperatures (in arctic animals or even in the peripheral organs (skin) of warm-blooded animals)

B) Eicosapentaenoate (EPA)

• Lipid tails are constantly in motion
• Viscosity is estimated to be that of light machine oil

• Mobility is high at the terminal methyl groups bc there is more variability in length
• Mobility is more limited near the head groups

• Rigid planar structure forces fatty acid tails into extended conformations= more rigid structure at high T degrees C
• Short length of rigid ring leads to increased mobility of neighboring fatty acid tails near terminal methyl groups

Consequently, cholesterol broadens the temp range of bilayer phase transition by supporting the "ordered liquid" state in between the solid and fluid membrane phases

• Organized patches of lipids which enrich cholesterol
• Also enriched by glycosphingolipids with large head groups

These rafts "float" in the membrane "sea" and diffuse as a group instead of as individual lipids; allows the membrane to be more fluid with melting temp

Endocytosis, exocytosis and signal transduction

Membrane proteins diffuse freely unless they are restricted by the cytoskeleton (inside) or extracellular matrix (outside)

Directly interact with membrane lipids via their hydrophobic domains (require detergents for isolation)

Non-covalently interact with lipid head groups or membrane proteins (only mild treatment (salts) to isolate)

• Covalently attached to lipid heads
• Can be extracted after phospholipase C or D treatment

• Have hydrophobic regions that span the membrane
• 

• 30A/5.4A per turn= 5.6 turns
• 5.6 turns, at 3.6 residues per turn: ~20 residues

So it takes 20 residues in an alpha-helix to span a 30A lipid bilayer

By clusters of hydrophobic residues in protein sequence

• Exterior residues interact with the membrane, and are hydrophobic
• Interior residues (lining the pore) are polar
• Minimum of 8 beta-strands are necessary to form a membrane spanning beta-barrel
• Large beta-barrel proteins may contain a hydrophillic pore (porins)

• Biological organisms are not at equilibrium with the environment
• Cells and organelles are not at equilibrium with other cells and organelles-- non-equilibrium= gradients of energy and compounds

• Membranes: most prominent and important barriers in our bodies
• Need to create and control gradients: membrane transport proteins
• Transfer information across: membrane signaling proteins= receptors

• Inversely proportional to polarity
• Diffustion depends on hydrophobicity/polarity and size of the molecule
• Predominately Hydrophobic molecules move freely (Hexanoic acid 10⁰)
• Water is able to diffuse but not as well (10^-2.5)
• Small ions have low permeability (transport must be facilitated)

• Oily compound produced by poison oak, Lacquer Tree, Poison ivy, poison sumac and mango tree
• Integrates into membrane and sticks to proteins, modifying their antigenic properties (gaptens)
• Antibody can be raised against "urushiol+proteins" and immune cells cann attack cell membranes containing urushiol

Urushiol

• Simple: unassisted
• Facilitated: assisted

• Polar molecules have to shed their water shells and overcome high energy barrier to cross a hydrophobic bilayer
• Limited to hydrophobic and small uncharged molecules, gases

Protein transporters can be considered as catalysts that lower the activation energy barrier for transport across a membrane

A substance moves through the membrane with the aid of a protein channel or carrier

• Substances move through the membrane down a concentration or charge gradient
• Proteins: pores, channels, (passive carriers)

Can be regulated by gates (open under certain circumstances)

Substances move through the membrane up a concentration gradient with an aid of protein pumps (active carriers)

Requires ATP hydrolysis or coupling to another energy source (another gradient)

• Pores in bacteria
• Simultaneously open to both sides of the membrane
• Always passive, but can be selective and regulated (weakly selective and follow linear kinetics)

• Open to only one side of the membrane at a time, involve conformational changes
• Can be passive or active
• Usually selective and regulated
• Follow hyperbolic (michaelis-menten) kinetics
• Saturated by a substrate

The high selectivity for K+ reflects the geometry of selectivity filter

K is bigger than Na, but it is selective bc carbonyl groups are arranged to coordinate and peel off a water shell from K, but not from smaller Na cations (Na w/water shell is bigger than K without it)

Electrostatic barrier and breaking hydrogen bonds between passing waters by forming bonds with Asn residues

• Energy of ATP hydrolysis (Na+/K+ pump)
• Energy of light (i.e. bacteriorhodopsin)
• Energy from red-ox reactions

• Utilizes gradients created by a primary active transport
• Uphill transport of one solute is coupled to downhill transport of another solute

• Transporters are classified by ligand and directionality:
• Uniport
• Symport
• Antiport

Moves one substance at a time

Transports two different substances in the same direction

Moves two different substances in opposite directions across the membrane

3Na out, 2K in, 1 ATP hydrolyzed