lipids

defined by insolubility in water

store energy (fatty acids/tryglycerides)

form core structure of biological membrane

other roles (signaling, protein anchors, cofactors, etc), involve smaller quantities

fatty acids

flexible due to ability to rotate around carbon-carbon bonds

extended conformation most stable due to steric constraints

oleic acid

most common fatty acid

18:1 cis-9

18 carbons, 1 cis double bond between 9 and 10

essential fatty acids

fatty acids needed by, but not synthesized in, the body

get from plants

used to synthesize arachidonic acid

arachidonic acid

precursor for eicosanoids

used to make prostaglandins (signal compounds)

physiological effects (ex; relaxation of smooth muscle)

partially hydrogenated fatty acids

generated from polyunsaturated fatty acids

chemically reduced

margarine

bad for you (increased LDLs)

triglycerides/triacylglycerols

high amount of fatty acids stored in these compounds

triglycerides/triacylglycerols

stored in adipose tissue

mono- and diacylglycerols less abundant

energy reserves

1 g fat yields 38 kJ energy

1 g protein/carb yields 17 kJ energy

why fatty acids?

fatty acid chains can be broken down and used for energy

two carbon fragments converted to acetyl-CoA

generate energy through oxidative phosphorylation

glycerophospholipids

glycerophospholipids

variety comes from various groups that are bound to phosphoric acid

glycerophospholipids

variety comes from differing fatty acids bound in positions 1 and 2

typically, position 1 is a saturated fatty acid, while position 2 is an unsaturated fatty acid

less frequent fatty acid containing structuressphingolipidsether glycerophospholipidswaxes

steroids

hormones

monolayers, micelles, bilayers

form spontaneously

critical micelle concentration (CMC)

eventually, bilayers will also spontaneously form from phospholipids

to prevent exposure of hydrophobic center, the bilayers fold in on themselves, forming closed vesicles

fluid mosaic model of biological membrane1972

membrane proteins

associated with the biological membrane

perform functions associated with the membrane

receptorstransporterschannelsother functions

peripheral membrane proteins

associate by weak forces

can be separated from this association by similar treatments to separate quaternary interactions

urea

carbonate (high pH)

integral membrane proteins

firmly anchored in membranesintermembrane portions nearly always -helix or -sheet

single transmembrane segment proteins

transmembrane spanning segment typically -helix

ex; glycophorin

amino acid stabilization energies

monoamine oxidase

important for neurotransmisson

MAO inhibitors

treat psychiatric disorders

bacteriorhodopsin

7 hydrophobic, membrane spanning domainsconnected by non-helical loops on either side of the membrane

outer AA residues interact with charged heads of phospholipids

bacteriorhodopsin

7 hydrophobic, membrane spanning domainslight-driven proton pump in bacteria

related to rhodopsin

model for membrane proteins

hydropathy plots

based on 1 structure

analysis of amino acid sequence to determine likely membrane spanning sequences

glycophorin A

bacteriorhodopsin

-barrel protein

different 1 structure pattern from transmembrane proteins with -helices

-strand alternates from one side of the barrel to the other

-helix more economical for membrane spanning, more prevalent in higher eukaryotes

facilitated diffusion

passive transport

can be specific for a molecule or allow non-specific molecules with particular characteristics

facilitated diffusion

passive transport

can be specific for a molecule or allow non-specific molecules of a particular characteristic

transporters

facilitated diffusion

ex; GLUT1

glucose transporter found in RBCs

allows for diffusion 50,000 times faster than uncatalyzed transmembrane diffusion

three classes of transport systems

GLUT1; uniport

chloride-bicarbonate exchanger

also found in RBCs

needed for CO2 transport from tissues to lungs

antiport

like GLUT1, believed to have 12 membrane spanning -helices

CO2 freely moves across membrane

picked up in tissues, converted to HCO3-, which goes back out into the blood

in lungs, HCO3- picked up again, converted back to CO2

increases rate of HCO3- transport across RBC membrane more than a millionfold

P-type ATPases

cation transporters

reversibly phosphorylated by ATP as part of the transport cycle

phosphorylation induces conformational change that triggers movement of cation across membrane

P-type ATPasesion binding

Na+/K+ pump

3 Na+ out for 2 K+ in

generates electrical potential along with concentration gradientscytosollumen

secondary active transport

ATP synthase

part of oxidative phosphorylation

fundamental conditions for life

self-replication

catalyze chemical reactions efficiently and selectively

generate energy!

enzymes

allow for harnessing of energy in a controlled way

thermodynamic potentiality

enzymatic pathways

enzymes sometimes require additional components for functionality

cofactor

one or more inorganic ions

ex; Fe2+, Mg2+, Mn2+, Zn2+

enzymes sometimes require additional components for functionality

coenzyme

more complex organic or metalloorganic molecules

can be derived from vitamins

ex; heme (cytochrome a3), vitamin C (prolyl-4-hydrolase, collagen)

enzymes sometimes require additional components for functionality

prosthetic group

tightly bound coenzyme

enzymes sometimes require additional components for functionality

holoenzyme; enzyme + cofactor/coenzyme

apoenzyme; enzyme cofactor/coenzyme

enzyme classification

based on reactions they catalyze

many enzymes are named by adding ase to substrate/activity

urease hydrolyzes urea

DNA polymerase generates DNA polymers

enzyme classification

oxidoreductasestransfer of electrons

transferasesgroup transfer reactions

hydrolaseshydrolysis reactions

enzyme classification

lyasesaddition of groups to double bonds or formation of double bonds by group removal

isomerasestransfer of groups within molecules to yield isomeric forms

ligasesformation of bonds by condensation reactions, usually coupled to cleavage of ATP

enzyme classification

ex;

ATP + D-glucose ADP + D-glucose-6-phosphate

ATP:glucose phosphotransferase

common name, hexokinase

catalysis

most reactions are slow in physiological conditions

many reactions require formation of unstable intermediates

enzymes provide specific environment that allows reaction to occur more rapidly

active site

specificityaffinity

catalyst

catalyst

enzymes lower activation energy (G) of reactionsG unchanged by enzymes

favorability of the reaction remains the same

for this reaction, forward Gbackward, +G

energy barriers

allow for stability of complex moleculeswithout barriers, compounds (such as sucrose) would break down spontaneously

enzymes lower barriers within cells to unlock energy from compounds or generate complex compounds

how do enzymes lower activation energy?

stabilization of transition state

side chains/cofactors/coenzymes associate with substrate in active site

can form temporary covalent bonds

bind with weak forces

how do enzymes lower activation energy?

form enzyme-substrate (ES) complex

releases small amount of free energy that stabilizes interaction

binding energy (GB)

GB is maximized with formation of transition state

transition state

Oxidative phosphorylation part of ATP*Phosphate causes it to be more ampipathic molecule. Major molecule in cellular membranes*Having some of each helps with membrane fluidity control and stability*Waxes are relatively uncharged, ear wax, peel on fruit, bearer on leaves*Important because structure can pass through cell membranes and effect function*Proteins are moving throughout membrane, fluid structure*Receptor=recognize signal molecule transporters=transport from one side of membrane to another (polar or charged can not cross quickly or well be themselves) channels=allow free diffusion of smaller molecule from one side to another can also have energy associated with them that promote crossing*Because of partial charge on alpha C and amino N would be more unstable if not into helix or sheet*Higher E means less stability****Big jump assumed to be segment*7 spanning membrane domain with exterior loops*Porin is a channel in outer mitcochondrial membrane, made of beta sheets folded into beta barrel. It allows just about anything to pass that is 10,00 Da or below. Mitochondria is made of two membranes, omm and imm. The cystosol is found outside omm. Intermembrane space is space between omm and imm. *Carrier binds to specific compound. Passive transporters recognize specific compound and it allow it to go down concentration gradient. Primary active recognize specific compound and can move it against the concentration gradient (require energy to transport). Secondary active use a gradient created by primary*Generated by photosynthesis, important for energy production. Needed in RBS especially because they do not undergo anerobic respiration*Uses diffusion rather than active transport*ATP causes Phospheraliton of membrane protein causes comformation change which ejects ions on onto other side of membrane. Partlcular binding site for certain ions*ATP synthase found in intermitochondrial membrane outside is intermembrane space of mitochondria*I, II, and IV are primary active transport, so the far left is secondary. It is using concentration gradient created by something else to generate energy (ATP)*Glucose has thermodynamic potentiality represented by bonds which hold a certain amount of energy. Energy harvested by breaking bonds*Glycolysis pathway. How glucose is broken down in cytosol to make pyruvate. 2 ATP is created in process. Each step is catalyzed by an enzyme. 100% efficient. 1 glucose makes 2 pyruvate*Typically coenzyme covalently bound to active sight.*Kinase genereally refers to phophorizationopposite of kinase is phospphatase (removes phosphate)

*Enzyme stabilizes the unstable transition site. They do this through the active site*Interact with weak forces to bind and stabilize*Catabolic reaction, generates energy. If needs energy is anabolic***