Chapter 4 Flashcards
Describe the structure of antibodies
made of two identical light chains and two identical heavy chains (longer, attached to carbohydrates) and have two antigen-binding sites with hypervariable loops
What holds antibodies together?
disulfide bonds connect their beta sheets
Define polyclonal as it relates to antibodies
many similar antibodies
Define monoclonal as it relates to antibodies
many identical antibodies
What type of cell is responsible for producing antibodies?
immune B cells
Describe catalytic antibodies
bind to transition states, stabilizing them
Describe how polyclonal antibodies are created
injecting an animal with an antigen over a period of weeks will cause polyclonal antibodies to secreted into the bloodstream
Describe how monoclonal antibodies are created
fusing a B cell with a tumor cell will create hybrid cells that make monoclonal antibodies and divide forever
Define immunoprecipitation
antibodies are added to a mixture of molecules, then collected with their antigen by centrifugation
Define immunoaffinity column chromatography
This is a method for isolating proteins by filling a column with beads coated in antibodies. A mixture of molecules are poured in, then a wash to get rid of any stuck proteins, then the protein of interest is eluted.
Define Western Blotting
This is a type of gel electrophoresis in which proteins move downward a vertical gel, with their speed determined by size and net charge.
Describe the SDS Page gel
This is a type of gel electrophoresis in which proteins are first coated with SDS, then treated with Mercaptoethanol to break disulfide bonds and equalize the charge of each protein, so they move down the gel at a speed determined only by size.
Describe how proteins can be identified in gels via antibodies
After a gel, proteins can be transported to a membrane that is incubated with antibodies that will bind to the protein of interest, revealing its position. Frequently, two antibiotics are used, one to bind to the protein, and another to bind to the first antibiotic.
Describe how antibodies are used in microscopy
Fluorescent or gold-labeled antibodies can be combined with fluorescence or immunoelectron microscopy to detect proteins
How do enzymatic proteins bind to their ligands?
Proteins bind to their ligands (ligand=any molecule bound to a protein) by electrostatic and hydrogen bonds (and other noncovalent).
What are the three ways an enzyme can lower activation energy? What kind of reactions (delta G) do they catalyze?
binding two molecules together, rearranging electrons, or forcing substrates (substrates=ligands that bind to enzymes) into their transition states
do not always require ATP, as they also catalyze spontaneous reactions.
Describe the binding sites of enzymes
an active site, where their substrate binds, and an allosteric site, where regulators bind
Describe feedback inhibition
a type of negative regulation that occurs when a substrate binds to the allosteric site of an enzyme that was involved in its formation
Describe positive regulation
Positive regulation occurs when an enzyme is stimulated by a regulatory molecule. This can be used to activate another branch in a synthesis pathway. This can also occur with the addition of a nucleotide such as ADP.
Describe molecular switches
Molecular switches are intracellular signaling proteins that toggle between an active and inactive site in response to receiving a signal.
Describe the enzyme lysozyme. Include: ligand, bond, basic type, and details of the reaction
Lysozyme changes the shape of the oligosaccharide to a strained conformation state and brings the glycosidic bond close to two of its amino acids.
One forms a transient covalent bond with the substrate and other becomes charged by donating an H and polarizes the water.
This allows a hydrolysis reaction to take place, which binds an oxygen-hydrogen to the substrate. This reaction also lets the acimo acids return to their original state.
Describe competitive inhibitors and how they change Vmax or Km
Competitive inhibitors do not change Vmax, they just increase Km. The reaction needs more substrate to be as fast as it was before, but competitive inhibitors can be overcome with extra substrate.
Describe noncompetitive inhibitors and how they change Vmax or Km
Noncompetitive inhibitors do not affect Km, but they do lower Vmax. Noncompetitive inhibitors function by removing the number of active enzymes. They disable enzymes by causing a conformational change.
Define protein phosphorylation. Include purpose and catalysts.
Protein phosphorylation is the covalent addition of a phosphate group to a side chain of a protein. This can be done by removing a phosphate group from ATP.
Catalyzed by protein kinase and removed by protein phosphatases.
Phosphorylation can both stimulate or inhibit proteins, and be added or removed quickly.
Define protein family
a group of polypeptides that shares a similar amino acid sequence or 3D structure, reflecting a common evolutionary origin
Individual members often have related but distinct functions, such as kinases that phosphorylate different target proteins
Describe affinity chromatography and its use of isolating proteins that interact with the protein of interest
Affinity chromatography is used to separate polypeptides based on their ability to bind to a particular molecule. One example would be in immunoaffinity column chromatography. This can be used to isolate proteins that physically interact with the protein being studied by adding a mixture of proteins after the main protein has bound.
Define cell extract
Cell extracts (or homogenates) are the first step in protein purification, where cells are lysed
Define centrifugation
the most widely used procedure to separate a homogenate into different parts, or fractions
the homogenate is placed in test tubes and rotated at high speed in a centrifuge or ultracentrifuge
Define chromatography (general)
a technique used to separate the individual molecules in a complex mixture on the basis of their size, charge, or their ability to bind to a particular chemical group
In a common form of the technique, the mixture is run through a column filled with a material that either binds or lets through the desired molecule
Define electrophoresis (general)
a technique for separating a mixture of proteins or DNA fragments by placing them on a polymer gel and subjecting them to an electric field.
molecules migrate through the gel at different speeds depending on their size and charge
