7 PROTEIN STRUCTURE AND FUNCTION

Primary structure 1

LINEAR AA seq

Secondary structure

Short regions of the peptide backbone fold into individual 3d structure

Tertiary structure

Fully folded 3d structure of protein

Quaternary structure

Multiple individual proteins combine into a large mega-structure

Multiple Sequence Alignment (MSA)

Compare primary sequences of different proteins

What does * represent in MSA

indicates all proteins have same AA residue at that position

Proteins fold first secondary structure and then tertiary (T/F)

F: formation of secondary and tertiary structures are simultaneous

______ bonds bw backbone atoms hold secondary structure together

hydrogen

two major second structures

alpha helix and beta sheet

alpha helix is a _____ stranded _____ hand helix

single, right

alpha helix is ___ nm per turn

0.54 nm

a helix bond pattern

which direction do side chain groups point from center of helix

otuwards

what represents placement of amino acids in alpha helix

helical wheel

amphipathic a-helix, are a-helices exclusively amphipathic

have both hydrophobic and hydrophilic surfaces

not all a-helices are amphipathic: some are completely polar and some are non polar, depends on function

Beta sheet

MULTIPLE polypeptide backbones aligning side by side to form paper like surface (appears pleated form the side hence the same)

How many nm/fold of beta-sheet

0.7 nm

In beta sheet how do side chains stick out

upwards/downwards

Beta-sheet bonding pattern

peptide backbones are held together by HBS that form bw different backbones (ALTERNATING FASHION)

Is B-sheet flat or twisted?

twisted

2 ways peptide backbones can e aligned in B-sheets

parallel and antiparralel

Protein domain

local region of the peptide backbone that folds somewhat independently from other regions of the backbone

• some can be SINGLE domain proteins, many proteins consist of MULTIPLE domains

• a lot of proteins in multiple domains can be physically separated and still retain folding form and function

Process of generating new proteins from domains using already existing ones → fasted than evolving from scratch

domain shuffling

name of mega structure that individual proteins combine to form

quaternary structure

name of individual proteins in quaternary structure

subunits

what bonds form bw matching surfaces (lock and key analogy) in quaternary structures of protein

non covalent bonds, disulfide bonds