BIOL 213- chapter 4: protein structure and function

protein shape

based on the amino acid sequence, shape determine function, proteins fold into a conformation of lowest energy

amino acid components

amino group, carboxyl group, R group

hydrogen bonds and hydrophobic forces

help stabilize a protein molecule's folded shape

primary structure

the first level of protein structure; the specific sequence of amino acids making up a polypeptide chain, polypeptide bonds

secondary structure

the second level of protein structure; regions of repetitive coiling or folding of the polypeptide backbone of a protein due to hydrogen bonding between constituents of the backbone (not the side chains)

alpha helix

a spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure

beta sheet

folding pattern found in many proteins in which neighboring regions of the polypeptide chain associate side by side with each other through hydrogen bonds to give a rigid, flattened structure

helices

a generic term for the spiral structures that occur in proteins and nucleic acids, form readily in biological structures, many membrane-bound proteins cross the lipid bilayer as an α helix, intertwined α helices can form a stiff coiled-coil

β sheets

can form rigid structures at the core of many proteins, come in 2 varieties (antiparallel or parallel)

amyloid structures

misfolded proteins that can aggregate and cause disease, β sheets can stack to form an amyloid structure, prion diseases are caused by proteins whose misfolding is infectious

protein features

proteins also contain unstructured regions, few of the many possible polypeptide chains will be useful, proteins can be classified into families

large protein molecules

often contain more than one polypeptide chain, many protein molecules contain multiple copies of the same protein subunit

protein subunit assembly

can assemble into filaments, sheets, or spheres, many viral capsids are more or less spherical protein assemblies

fibrous proteins

proteins shaped like long fibers, collagen and elastin are abundant fibrous proteins

extracellular proteins

often stabilized by covalent cross-linkages, disulfide bonds help stabilize a favored protein conformation

proteins bind to other molecules

the binding of a protein to another molecule is highly selective, the binding sites allow a protein to form a set of noncovalent bonds only with certain ligands

antibodies

specialized proteins that aid in destroying infectious agents, an antibody is Y-shaped and has two identical antigen-binding sites, one on each arm of the Y, each has a different binding site

enzymes

proteins that speed up chemical reactions, an enzyme's performance depends on how rapidly it can process its substrate

competitive inhibitor

a substance that reduces the activity of an enzyme by entering the active site in place of the substrate whose structure it mimics

feedback inhibition

a method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway, catalytic activities of enzymes are often regulated by other molecules

allosteric enzymes

have both an active site for substrate binding and an allosteric site for binding of an allosteric effector (activator, inhibitor)

phosphorylation

the addition of a phosphate group to a molecule, can control protein activity by causing a conformational change, regulatory GTP-binding proteins are switched on and off by the gain/loss of a phosphate group