proteins (week 2 bio)

proteins

amino acids linked by peptide bonds through dehydration (polypeptide chain)

proteins become functional through

folding

primary structure

order of amino acids from n to c terminus (maintained by peptide/covalent bonds)

secondary structure

repeating 3d structure of peptide backbone (maintained by H bonds)

types of secondary structures

alpha helix, beta pleated sheet

tertiary structure

overall 3d structure of single polypeptide chain (maintained by interactions of side chains: covalent or noncovalent)

covalent interactions in tertiary structure

disulfide bonds between two sulfhydryl groups

what happens to non polar sidechains

hydrophobic forces force them to the center of the folded protein (shielded from water)

quaternary structure

overall 3d structure of multiple polypeptide chains interacting in a complex functional unit (maintained by same interactions as tertiary structure across multiple polypeptide chains)

what helps proteins fold into a shape that affects its function?

molecular chaperones

mutations effect on protein folding

AA sequence, non covalent interactions, change in size of side chain and charge (acidic/basic)

what would happen to a changed AA charge?

could turn hydrophilic to hydrophobic, shifting shape to hide and destablizing it, making it inefficient in job

infectious/misfolded prion protein

interact with normally folded prions and misfold them, leading to aggregation

aggregation

form hard plaque resistant to clean up by proteases

gel electrophoresis

separate proteins by size as they separate as they move towards positive electrode at bottom (denaturing and coating in negative charge)

denaturation

disrupt all noncovalent interactions and disulfide bonds

disruption of noncovalent interactions

boiling protein samples as increased energy leads to breaking of weak noncovalent bonds (covalent bonds stay)

disruption of disulfide interactions

using reducing agents that split the covalent crosslink apart by donating electrons and hydrogen atoms to the disulfide bridge and yielding two separate cysteine sulfhydryl groups per bond

coating proteins in negative charge

SDS detergent has a hydrophobic tail that binds to hydrophobic regions of proteins allowing it to be attracted to the positive electrode

location of bands vertically on gel

relative size of specific protein in sample

number of bands in lane

number of proteins

thickness/darkness of specific band

realtive amount of specific protein in sample