Biochem topic #2 Sorting+Membranes (Lectures #4-6)

Founder of chemical Synthesis

Bruce Merrifield

Downsides of chemical Synthesis

Low Yield (1.8%)

Single Codon Amino Acids

Met and Trp

Five Stages of Protein Synthesis Acronym

All intimate encounters terminate fast

Aminoacylated

Aminoacylation of tRNA

Igloos

Initiation of translation-mRNA and aminoacylated tRNA bind to ribosome 

Eskimos

Elongation-aminoacylated tRNA binding+peptide bond formation until STOP codon

Terminate

Termination of mRNA and protein, ribosome recycled

Frost

Folding and posttranslational stuff

SS for ER

N Term+(6-12hydrophbobics+1 basic) removed

SS for Mitochondria

Amphipathic helix (Arg and Lys on one side and hydrophobics on other) 20-50 residues

SS for Chloroplast

No pattern rich in Ser, Thr removed

SS for Peroxisome

PTS1 (Ser-Lys-Leu) at C Term

PTS2 at N Term not removed

SS for nucleus

Short segment rich in Lys and Arg not removed

Sec61a function

Translocon for peptides into or across ER lumen

Sec61a AA makeup

Pore of isoleucine

Collagen Structure

3.3 Residues per turn

Left handed super helix

Repeating (Gly-Pro-Pro/HyP)

4-Hydroxyproline function

Proline ring that increased hydrogen bonding between collagen strands

Lysyl Oxidase

Forms crosslinks of covalent bonds between hydroxyproline

Sterol (Like cholesterol) 

Four fused rings w/ hydroxyl group

Storage Lipids Neutral

Triacylglycerols 

Saturated fatty acids

Pack in more orderly way

Unsaturated fatty acids

Kinky (pack in less orderly way)

Unsaturated trans fatty acids

Highest melting point

Phosphatidylcholine

One of most abundant glycerophospholipid in cell membrane (not bacteria)

Sphingolipids vs glycerophospholipid

Sphingolipids contain backbone of sphingosine (Amide linkage vs ester stronger bond)

Sphingomyelin

in myelin sheath

Micelle forms

Amphipathic molecules that have larger head than tail

Liposome

Type of vesicle

Membranes are permeable to

small polar solutes and non-polar compounds

Gel phase

membrane molecules do not move

fluid phase

membrane molecules can move around

Flippase

P type ATPase moves PL from outer to internal

Floppase

ABC transporter moves PL from internal to external

Scramblase

Moves lipids in either direction

Lipid rafts (membrane subdomains)

Distinct membrane domains that contain sphingolipids, cholesterol and proteins move cholesterol through membrane

Membrane Protein Function (3)

Receptor(light-opsin), channels (aquaporin), enzymes (ATP synthase)

Peripheral membrane protein extraction

high salt or change in pH

Integral membrane protein extraction

detergents needed

Transmembrane domains

20-25 AA’s long reverse of globular protein AA arrangement (hydrophilic inside, phobic outside)

Tyr and Trp in integral proteins

Clustered near membrane surfaces can interact w/ both lipids and aqueous phases

Lys, His, Arg

In contact near cytosol due to neg charge of cytosol

High neg hydropathy index

Hydrophilic

Glycophorin

Single transmembrane protein (extracellular portion oligosaccharides- determiner for ABO and MN blood group)

Bacteriorhodopsin

composed of 7 transmembrane a-helices, generates proton gradient through light abs

Bacteriorhodopsin Central Retinal

Absorbs light and hydrocarbon chain changes from cis to trans pumps one H+ outside of cell

Insertion of proteins into membrane

Syrup Signals Stop Internal Signals

Syrup

SRP recognizes SS ( or SA)and delivers to translocon on ER membrane

Signals

Signal peptidase removes SS

Stop

Stop transfer anchor sequence interacts with translocon to be embedded into membrane

Internal Signals

Internal signal anchor sequence (SA)

SS

“Address only”, hydrophobic on N term cleaved by signal peptidase after translocation to lumen

SA

“Address and anchor” not cleaved more positive amino acids stay in cytosol

STA

“Stop Threading here” halts translocation through translocon

Type 1 integral membrane protein

SS+STA (N Term lumen C term cytosol)

Type 2 integral membrane protein

SA (N term cytosol C term lumen)

Type 3 integral membrane protein

SA (pos charges on c term)

Type 4 A/B

Multiple SA and STA Signals

B-Sheet Transmembrane proteins (porins) description

Hydropathy index cannot detect, every second residue in trans membrane region is hydrophobic, 9-11 AA per transmembrane strand

Beta barel integral proteins examples

FepA (iron) OmpLA Maltoporin (maltose transport)

Lipid Anchor Proteins Facts

Extracellular via GPI anchors Cytosolic via disulfide bonds w/ fatty acids

Farnesylation Sequence

CaaX (a aliphatic x-Met Ser Glu or Ala)

Farnesylation Enzyme

Farnesyl transferase

O linked Glycosylation

On alcohols (smaller)

N-Linked Glycosylation

Asparagine (bigger)

Membrane Curvature Protein

Caveola

Donnan Equilibrium

Electrochemical balance but not conc. balance across membrane