Bio Lec 4 - Protein Structures

Primary Structure

specific sequence of amino acids

how many amino acids are in a chain

20^n because there are 20 amino acids where n= the number of amino acids in the chain

typical protein is over 100 amino acids long (infinity number of possibilities)

which part of the amino acids give the amino acid its unique properties

the R group

protein structure can be described using what four commonly used representations

1. polypeptide back bone model

2. ribbon model

3. wire model (includes side chains)

4. space filling model

what drives protein folding

hydrophobic interactions (hydrophobic protein core)

how does protein folding happen

the nonopolar side chains will fold inward and the polar ones will fold outward (hydrophobic and hydrophyllic)

co translational

folding starts right away as the protein is being translated (will start with interactions from the translation process)

chaperones

proteins that assist other proteins to fold their functional shapes.

prevent inappropriate interactions with other cellular components

binds to the hydrophobic segments of protein to inhibit incorrect folding and will come off after

secondary structures

conformation of portions of the polypeptide chain arranged to maximize hydrogen bonds

what are the two commonly folding patterns of secondary structures

alpha helix and beta pleated sheets (also includes loops turns)

alpha helix

cylindrical twisting spiral R groups project outwards

when do alpha helices bond to amino acids on another alpha helix

carbon and amino bond at every 4 amino acids

what is the difference between left handed and right handed alpha helices

helices can be left-handed (counter-clockwise) or right-handed (clockwise).

Beta pleated sheets

hydrogen bonds extend from one part of the chain to another

lie side by side held tgr by hydrogen bonds

what are the two types of beta pleated sheets

antiparallel: opp directions parallel: same direction

what are loops and turns in a protein

pieces of a protein structure that join amino acids together

which side is the N group and C group of a beta protein

N at the beginning and C at the end

Coiled-Coil

Two α helices wrap around each other.

Tertiary structure (3o)

Conformation of the entire protein

• Interactions between R-groups in the protein

• Hydrophobic interactions

• Van der Waals interactions

• Disulfide bridges

what are the two major types of tertiary structures

fibrous (long) and globular (compact like a ball, irregular surface)

fibrous proteins

Elongated shape, form long strands or flattened sheets that resist shearing forces

• Usually have structural functions e.g. outside of cells e.g. keratin, collagen

Globular proteins

Polypeptide chain folds into complex compact shapes e.g., enzymes, hormones etc. → but can form long filamentous structures by joining multiple globular polypeptides

• Most proteins have a globular structure!

quaternary structure

Linking of multiple proteins to form large complexes with multiple “subunits” → Multi-protein complexes

• Intermolecular interactions of R groups

  • Disulfide bonds

  • Noncovalent interactions

protein subunit

A single, complete polypeptide chain that assembles with other polypeptide chains to form a functional protein complex.

types of quaternary structure 

protein subunits

homomers

heteromers

disulfide bonds 

can form within a polypeptide (3o) or between multiple polypeptides (4o)

oxidation forms disulfide bonds 

reduction can break that bond to create its subunits (comes apart)

a protein with just one binding site forms:

a dimer with another identical protein

a protein with two different binding sites often form:

a long helical filament

how does a protein subunit form a ring instead of a helix

If the two binding sites are oriented appropriately in relation to each other

protein family

A group of proteins that share evolutionary origin (related function or similar sequence/structure).

Protein superfamily

A larger group of protein families that share 3-D structure and mechanistic functions but very little sequence similarities → deep evolutionary relationship.

study this summary chart