Ch 4: Protein Structure and Function Flashcards
Allosteric proteins
Most enzymes are allosteric proteins, which means they can exixt in two conformations that differ in catalytic activity. The enzyme activity can be turned on or off by ligands that bind to a distinct region to either stabilize the active or inactive conformation of the protein
What is feedback inhibition?
One of the most common ways to regulate enzyme activity where an enzyme early in a metabolic pathway is inhibited by the binding of one of the pathway’s end products
Phosphorylation and dephosphorylation
How many proteins are regulated in eukaryotic cells. Catalyzed by a protein kinase (phosphorylation), or a protein phosphatase (dephosphorylation)
Regulates the protein by altering the activity or properties of the target protein
Primary structure of a protein
The amino acid sequence
Secondary structure of a protein
Regular folding patterns in a polymer (aka a helixes and beta sheets)
Tertiary structure of a protein
Complete three dimensional structure of a fully folded protein
Quaternary structure of a protein
Complete structure formed by multiple interacting polypeptide chains that form a larger protein molecule
Antibody
protein produced by b lymphocytes in response to a foreign molecule or invading organism. Binds to that organism, inactivating it or marking it for destruction
Antigen
something that is recognized by an antibody
Binding site
region on the surface of a protein (usually a cavity or groove) that interacts with another molecule (a ligand) through the formation of multiple non covalent bonds
disulfide bond
covalent cross-link between two sulfhydryl groups on teh ocystein side chains that are often used to reinforce a proteins structure or join two proteins together
C terminus
the end of a polypeptide chain that carries a free carboxyl group (-COOH)
lysosyme
enzyme that severs the polysaccharide chains that form the cell walls of bacteria
Found in many secretions such as saliva and tears, so it acts as an antibiotic
N terminus
the end of a polypeptide chain that carries a free a-amino group
peptide bond
covalent chemical bond between the carbonyl group of one amino acid and the amino group of a second amino acid
Polypeptide backbone
repeating sequence of the atoms -N-C-C that forms the core of a protein molecule and to which the amino acid side chains are attached
protein domain
segment of a polypeptide chain that can fold into a compact, stable structure and that often carries out a specific function
protein kinase
Enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein
protein phosphatase
Enzyme that catalyzes the removal of a phosphate group from a protein, often with a high specificity for the phosphorylated site
transition state
transient structure that forms during the course of a chemical reaction, in this configuration the molecule has the highest free energy. It is no longer the substrate but not yet the product
Protein molecules that have a quaternary structure will always have two or more of which of the following?
Protein domains: they will contain multiple polypeptide chains or subunits, each of which will be formed from one or more protein domains
What does the primary structure of a protein refer to?
The linear amino acid sequence of a protein
Indicate whether the following is true or false and why:
Chaperone proteins provide the energy needed for a protein to fold into the correct conformation
False, because protein folding is an energetically favorable process and so does not require in input of outside energy. Chaperon proteins assist with folding, but not by providing energy.
Enzymes alter teh speed of a reaction without affecting the overall energy (thermodynamics) of its reactants or produces. Enzymes accomplish this by doing what?
Reducing the activation energy of a reaction.
What is true and what is false about enzymes?
True: they can bring reactants together in the proper orientation for chemistry to occur.
False: They usually require an input of energy from ATP for activation
True: They can form covalent bond with their substrates
True: They can change the shape of substrates to increase the rate of a particular reaction
What determines the specificity an antibody has for it antigen?
Polypeptide loops in its variable domains
How do most motor proteins ensure that their movements are unidirectional?
They couple a conformational change to the hydrolysis of an ATP molecule, which makes the reaction very difficult to reverse.
What correctly describes phosphorylation of a protein?
It can increase or decrease a protein’s activity, depending on the site of the phosphorylation and the structure of the protein.
How does phosphorylation control protein activity?
The phosphate group induces a change in the the proteins conformation. This is one way to regulate protein activity.
