lecture 5 protein structure

primary structure

the sequence of amino acid monomers in the polypeptide.

secondary structure

the local folding of the polypeptide into repeated patterns. There are two kinds of secondary structure: • α (alpha) helix and β (beta) pleated sheet.

alpha helix

right handed coil

β (beta) pleated sheet

two or more sequences are extended and aligned

hydrogen bonds

secondary structure held together by _______ between the amide H and the carbonyl O in the polypeptide backbone (the R groups are not involved).

peptide bonds (covalent bonds)

primary structure is held together by _____

Tertiary structure

the final folded structure of the polypeptide into a functional protein

a variety of bonds and forces

Tertiary structure held together by _______ between the R groups, but may include interactions between the R groups and the polypeptide backbone.

covalent bonds (disulfide bonds) • ionic bonds • hydrogen bonds • van der Waals interactions • hydrophobic interactions

a variety of bonds and forces for tertiary structure

quarternary structure

results from the ways in which two or more polypeptide chains (subunits) bind together and interact

same as tertiary

Quarternary structure help together by_____

denaturing

heat or chemicals disrupt weak interactions in a protein, destroying secondary and tertiary structure. may be able to return to normal when cooled or the chemicals are removed.

Protein functions

Determined by binding characteristics: Enzymes—catalytic molecules • Structural and motor proteins • Signal and regulatory proteins • Receptor proteins • Transport proteins • Defensive proteins • Storage proteins

ligand

molecule or ion that binds to another molecule. binding is specific and can involve multiple weak bonds, making a relatively strong interaction

binding affinity

strength of the interaction

shape of the portein

Ligand binding changes the ____. This causes the protein to become active (or inactive) depending on the specific protein).

R group modification

changes the protein’s shape or create or hide a ligand binding site. This causes the protein to become active (or inactive) depending on the specific protein)

Proteolysis

can also unmask a ligand binding site or create a binding site for other proteins. • This causes the protein to become active (or inactive) depending on the specific protein).

by proteolysis

some proteins are activated ____

addition of cofactor

Some proteins require a non-protein molecule or ion for function. These nonprotein molecules or inorganic ions (often a metal ion), are called _______ . Cofactors includes coenzymes and ATP

lower the activation energy

Enzymes _______ in almost all chemical reactions in cells. Enzymes do this through binding to their substrates • The formation of bonds releases free energy. • This free energy is used to change the shape of the enzyme and/or break bonds in the substrate.

subtrates ; active sites

Reactants are _____ : they bind to specific sites on the enzyme—the ______

change shape

Many enzymes _____ when the substrate binds

hydrogen bonding, ionic bonds, van der Waals interactions, or temporary covalent bonding

The enzyme–substrate complex (ES) is held together by

• inducing strain • substrate orientation • or by adding chemical groups

There are several mechanisms by which enzymes lower the activation energy. These include:

catabolic pathways

break down molecules into smaller molecules and release energy

anabolic pathways

synthesize complex molecules from simpler ones.

inhibitors

are molecules that bind to the active site, preventing the substrate from entering

rare ; reversible

Irreversible inhibition is ______, mostly occurs with certain drugs. Competitive inhibition is ______, inhibitor is similar to the substrate, but no reaction occurs.

allosteric regulation

nonsubstrate molecule binds to a site other than the active site

phosphorylation

a phosphate group is added by a protein kinase; in a hydrophobic region of the enzyme, the altered amino acid may induce a change to interact with hydrophilic regions.

protein phosphatase

remove phosphate groups from proteins.

glycosidic linkage

which interaction does NOT determine tertiary structure in proteins

secondary and tertiary

which levels of protein structure would be destroyed by the addition of denaturing reagent?