Lecture 3

Protein Denaturation -Denaturation is _____ _______, usually with ____ of biological activity. Usually not reversible. Ex: hard-boiled egg, largely denatured lysosome, becomes insoluble.

-Denaturation is protein unfolding, usually with loss of biological activity. Usually not reversible. Ex: hard-boiled egg, largely denatured lysosome, becomes insoluble.

Protein Folding and Stability (2 of 2) 1. ______ ______- far from H2O as can 2. _____ ______- alpha and beta are stable 3. _______-______ _____ -van der Waals: optimum distance between atoms -electrostatic: interactions between + and - charged amino acids. 4. ______ ______: two cysteines come together to make cystine. Double bond--> strong. 5. _____ ____: protein may fold around ion. Ex: Zn, Mg, Ca. Different from functional ion.

-Forces stabalizing protein structure (determind largely by weak bonds) 1. Hydrophobic effect- far from H2O as can 2. Hydrogen bonding- alpha and beta are stable 3. charge-charge interactions -van der Waals: optimum distance between atoms -electrostatic: interactions between + and - charged amino acids. 4. Disulfide bonds: two cysteines come together to make cystine. Double bond--> strong. 5. Metal ions: protein may fold around ion. Ex: Zn, Mg, Ca. Different from functional ion.

Protein Folding and Stability (1 of 2)

-Primary structure determines the final tertiary and quaternary structure

Secondary Protein Structures

-The secondary structure of a polypeptide can consist of different types of elements at different locations in the primary structure. Ex: long stretch of amino acids. - Secondary structural elements can bring distant portions of primary structure close together in space. Ex: turn bringing two helicies or two beta-sheets together. Also random run can bring together. - Motifs- supersecondary structures, ex: helix-loop-helix. Motifs can come together to form domains Recognizable structures/patterns. -Domains- discrete, independently folded units of secondary structure and/or motifs. -Most proteins/polypeptides consist of several domains.

Four levels of protein structure -Name all four -What determines all other levels?

1. Primary structure- sequence of amino acids 2. secondary structure- regular folded structure of primary structure. alpha-helix, beta-sheet 3. tertiary structure- 3-dimensional shape of polypeptide. Secondary structures come together to form tertiary. -hemoglobin globule sphere and collagen- long fiber...opposite ends and then you have all structures in between. 4. Quaternary structure - 3 dimensional shape of multiple interacting polypeptides. -Each subunit has a tertiary that's made up of a secondary structure, which is determined by primary structure. *Primary strcuture determines all other levels! *Most polypeptides are a combination of different polypeptides.

Secondary Protein Structures

4 distinct domains in one polypeptide. If the polypeptide is cut in half it will still retain two domains. They don't refold bc they're already in the most stable formation! Can be isolated!

Protein Denaturation (chemicals)

Detergents and chaotropic agents allow H2O to enter hydrophobic areas and disrupt normal folding. Ex: clean clothes with detergent by denaturing proteins. Ex: SDS- sodium-dodesyl-sulfate Nonpolar Polar Look at Figure 432. Chaotropic- urea, two amino groups, polar molecule, can disrupt.

Protein Denaturation (heat) Heat- _____ temp disrupts weak bonds and secondary structures. _____ the protein DNA nucleic acid and RNA, one does not become reversible.

Heat- increasing temp disrupts weak bonds and secondary structures. Unfolds the protein DNA nucleic acid and RNA, one does not become reversible.

Protein Quaternary Structure -Hb tetramer -The two monomers each of Hb alpha and beta polypeptides are arranged _______ to form a functional tetramer. - ____ and _____ monomers are the product of different genes.

Hemoglobin tetramer -The two monomers each of Hb alpha and beta polypeptides are arranged symmetrically to form a functional tetramer. - Alpha and beta monomers are the product of different genes.

Protein Secondary Structure- The alpha-helix

Hydrogen bonding in a stretch of the alpha-helix...involves carbonyl oxygen and amine hydrogen 4 amino acid residues carboxyl. Look at slides.

Protein Secondary Structure- The beta-sheet Hydrogen bonding in sheets involves ______ _______ and _______ _______ in different layers of the sheet structure. a. _____-______ beta-sheet -two sheets run in opposite direction, hydrogen bonds allow pieces to come together. b. _______l b-sheet -backbones run in the same direction; can stack a lot of them together.

Hydrogen bonding in sheets involves carbonyl oxygen and amine hydrogen in different layers of the sheet structure. a. anti-parallel beta-sheet -two sheets run in opposite direction, hydrogen bonds allow pieces to come together. b. parallel b-sheet -backbones run in the same direction; can stack alot of them together.

Protein Quaternary Structure

In a protein quaternary structure, two separate polypeptides come together to form unit. -Most functional proteins consist of multiple polypeptides. -Polypeptides may be identical or different. -Usually the polypeptides interact in a symmetrical manner. Shown on slide is a dimer of identical subunits. Tetramer would usually have 4 symmetrical subunits.

Protein Secondary Structure- The beta-sheet -Loops and Turns

Loops and turns redirect the polypeptide backbone. If you see a turn, you'll see glycines, prolines. Glycines and prolines are very common amino acids in loops and turns. Turn is a "tight" change in backbone direction; Loop can be more meandering. Prolines- R group becomes a ring structure. Random run- sometimes find them that don't have any kind of feature, secondary structure.

Protein Tertiary Structure

Myoglobin as example... -heme group--> iron atom is 80% alpha-helix. The purpose of the alpha helix is to hold the structure so oxygen can bind.

Protein Secondary Structure- The beta-sheet Polypeptide chain is fully ________. Sheets are stabilized by ________ bonds. Sheets can be ______or ____-________.

Polypeptide chain is fully extended. Sheets are stabilized by hydrogen bonds. Sheets can be parallel or anti-parallel.

Secondary Protein Structures

Three distinct domain types in Pyruvate Kinase (single polypeptide). - likely that each domain has a different/independent function. Each domain is structural and can be functional. -Structures in the domain could be channels, could be ligand-binding domain.

Protein Denaturation (pH) changes ionization state of amino acid _ _____, disrupting secondary structures. Proteins have optimal __ and ____.

changes ionization state of amino acid R groups, disrupting secondary structures. Proteins have optimal pH and heat.

Protein Secondary Structure- The alpha-helix

hydrophobic inside of polypeptide and on the surface its polar. Amphipathic nature of some alpha-helicies (ADH_. Important in determining functional and structural properties. Helicies with net negative charge and net positive charge may come together.

Protein Tertiary Structure

look at slide 2 on p. 8. Distribution of polar and non-polar amino acids indicates most charged amino acids are on the exterior of the molecule (blue) and hydrophobic amino acids are in the interior (yellow). shows space-filling model and a slice through space-filling model to show interior.

Protein Secondary Structure- The alpha-helix

right-handed alpha-helix with 3.6 amino acids per turn. H-bond interactions bt amino acids stabilizes helix. Amino acid side chains point outward from helix center. Backbone consists of 11 atoms of a peptide bond that hold helix together.

Protein Secondary Structure- The beta-sheet -A mixed beta-sheet

sheet structures can come together to make cylinders. This is where one might find channels, pores.