BSCI 330 Exam II - protein shape and structure I

polypeptide chains

- highly ordered
- 3D structures
- multiple levels: 1, 2, 3, 4

primary structure

- linear sequence of AA residues held together by covalent peptide bonds
- determined by mRNA (gives linear seq of AA)
- primary structure (+ protein enviornment) determines secondary, tertiary, and quaternary structure

protein environment

- plays a factor in determining which order of protein structure

ex.
- in their normal environment = folded
- outside their normal environment = doesnt fold

Is the amino acid sequence of every protein identical to the genetically encoded primary sequence?

NO

- standard post translational modifications of AA's don't change the nature of amino acid

instead,
- we modify the protein after it has been folded
- modifying it before this event will make it so that it wont fold at all

secondary structure

- folding/twisting of peptide backbone

- once folded, we are at a lower E state and cannot be changed

- held together by weak hydrogen bonds between C=O and N-H groups in backbone

- R groups stick out from backbone

- 2 secondary structures: alpha helix and

beta sheet

alpha helix

- rigid cylindrical sheet (spirals)

- forms when H-bonding occurs between carbonyl and amine that are 4 amino acids apart on backbone

- it takes 4 AA to make 1 full turn of a hellix

- coding happens in clockwise direction down the length of the chain

beta sheet

- flat, sheet-like structure (pleated)
- forms when H-bonding occurs between carbonyl and mine on adjacent polypeptide chains
- more flexy than alpha

- parallel and antiparallel adjacent chains

parallel adjacent chains

- adjacent chains run N-term --> C-term
- loop around
- more difficult to form

antiparallel adjacent chains

- adjacent chains run in opposite directions
- u-turns

rigid proline residues

- inserts a kink in a protein's backbond and disrupts secondary structure
- creates rigid ring that doesn't fit into most secondary structures

1 proline residue

disrupt alpha helix

2+ proline residues

disrupts both alpha and beta struct

tertiary structure

- 3D arrangement of secondary structure (folds to interact with each other)

- mostly held together by noncovalent attractions between:

- R group (hydrogen bond between polar side chain)

- between R groups (hydrophobic side chains) and surrounding environment

- R group interactions lead folding of secondary structures into 3D structures (single polypeptide folding up

C-terminus

- carboxyl end
- arrow head of polypeptide

unstructured loops

- "random coils"
- links secondary structures together

disulfide bonds

- covalent disulfide bonds forms between cystine residues to cross link parts of polypeptide backbone
- locks tertiary structures in place
- these bonds dont occur until tertiary structure formation is complete

- seen in
- cell surface
- secreted proteins
- proteins of ljmens of organelles (golgi)
- NOT in cytosol

Gfolded - Gunfolded

= delta G

protein stability

- 3D folding of proteins results in structures that assume the lowest possible energy state
- increased protein stability when Gunfolded is greater than Gfolded

chaperonins

- 3D folding doesn't occur rapidly for all proteins
- proteins require molecular chaperones
- provides an isolated chemical environment (barell shape) in which they can fold

- facillitates folding into final
- takes partially folded P, unfolds, and refolds
OR
- takes partially folded protein, use ATP hydrolysis to unfold, and help it refold

- helps protein get it of local energy minimum; gets to true energy minimul

protein domains

- region of the protein that folds independent of other regions
- proteins can have single or multiple domains
- domains represent a functional region of the protein
- different domains have different functions

- proteins are modular
- they are built up form a tool box of domains

quaternary structure

- arrangement of multiple tertiary structures
- held together by weak bonds and some disulphide bonds
> same bonds used in tertiary structure
> can be locked in space with disulphide bonds

- function of protein requires every one of the subunits in it
- take away 1 subunit, function of protein goes away

homomers

identical subunit polypeptides

heteromers

different subunit polypeptides

simple quaternary structure

ex. hemoglobin; 2 copies of each of 2 subunits
- take away alpha helix, hemoglobin cannot carry oxygen in blood

complex quaternary structure

ex. RNA polymerase II: 17 subunits, 11 polypeptide chains