chain of amino acids, usually 20-30 amino acids long
What is a polypeptide?
long chain of amino acids
What is a protein?
polypeptide having a 3-D structure
How is the mass of a protein or peptide expressed?
In terms of Daltons (Da)
1 Dalton is equal to...
A proteins shape is dictated by....
the amino acid sequence
What are the three types of noncovalent bonds that help proteins fold?
hydrogen bonds, van der Waals attraction, electrostatic attraction
What helps proteins fold into compact conformations?
Can denatured proteins recover their natural shape?
What is Urea?
A chemical that comes from the breakdown of proteins
What is an alpha helix?
a rodlike structure in which the peptide chain coils clockwise around a central axis
What is a beta sheet?
a secondary structure of a protein that is formed by a hydrogen bond of the atoms in a peptide bond that lie within linear regions of polypeptide, chain may run in same direction (parallel) or opposite direction (anti parallel), also can turn and fold back on itself
What is a coiled coil?
a structural motif in proteins in which 2-7 alpha-helices are coiled together like the strands of a rope
In what two varieties will you find beta sheets?
parallel and antiparallel
What are prion diseases?
Prion Diseases are diseases caused by native folded proteins becoming misfolded. This occurs when exogenous misfolded proteins infect an animal and convert native prion proteins into a misfolded form.
What is the primary structure of a protein?
sequence of amino acids
What is the secondary structure of a protein?
1) Twisting of the alpha helix
2) Beta sheets
3) Hydrogen bonding
What is the tertiary structure of a protein?
3D structure including bending
What is the quaternary structure of a protein?
interactions between different polypeptide chains in proteins composed of more than one polypeptide (subunit interaction) MULTIMERIC
T or F? Many proteins are composed of separate functional domains.
Identical protein subunits can
assemble into complex structures
An actin filament is composed of
identical protein subunits
A single type of protein subunit can pack together to form:
a filament, a hollow tube, or a spherical shell
Viral capsules are often
spherical protein assemblies
Disulfide bonds help....
stabilize a favored protein conformation
Is the binding of a protein to another molecule selective?
yes, it is highly selective
What is a ligand?
any molecule that binds specifically to a receptor site of another molecule
What is specificity?
ability of a protein to bind to one molecule or ion in preference to others
What is affinity?
degree of attraction—between the enzyme and substrate.
What is the ligand-binding site?
location on the receptor to which the ligand binds
how is affinity expressed?
The dissociation constant and affinity are ___________________ proportional.
What is an antibody?
A protein secreted by plasma cells, they are part of the immune response and bind to antigens and mark them for destruction.
An antibody takes on what shape?
An antibody is Y-shaped and has two identical antigen-binding sites, one on each arm of the Y
What provides stability for an antibody?
What are the two chains of an antibody?
light chain and heavy chain
Enzymes convert _______ to _________
What is a competitive inhibitor?
a molecule that competes with the substrate to bind in the active site of an enzyme.
What is a lysozyme?
enzyme that kills bacteria
What does a lysozyme cleave?
The cleft in an enzyme holds how many sugar residues?
Lysozymes have how many domains?
How does a lysozyme break a bond?
by adding H2O to the bond between sugars to break it
What are enzyme inhibitors?
Substances that interfere directly or indirectly with enzyme action
What does aspirin inhibit?
Methotrexate kills cancer cells by inhibiting
Statins inhibit HMG-CoA reductase and lower
What are prosthetic groups?
similar to cofactors, but they are bound to the enzyme, rather than being separate molecules or atoms
What is a cofactor?
a non-protein substance. Binds to active site on enzyme, allowing substrate to fit into active site.
What does the biological function of a protein depend on?
chemical properties of its surface and how it binds to other molecules
When a protein catalyzes the formation or breakage of a specific covalent bond in a ligand, the protein is called an _______________ and the ligand is called a ______________
At the active site of an enzyme,
the amino acid side chains of the folded protein are precisely positioned so that they favor the formation of the high-energy transition states that the substrates must pass through to be converted to product
What is feedback inhibition?
the end product of a metabolic pathway shuts down the pathway
What is an allosteric protein?
protein that undergoes a conformational change affecting its affinity for some ligand
**can exhibit cooperativity
What is an allosteric enzyme?
an enzyme whose activity is regulated by the binding of a small effector molecule
What is an allosteric site?
a different location that is not the active site of enzyme catalysis
Allosteric enzymes have
2 or more binding sites that influence one another
What is cooperativity?
a form of allosteric regulation that can amplify enzyme activity
a conformational change in a protein
GTP-binding proteins are switched on and off by
the gain or loss of a phosphate group
What causes a protein to walk along a cytoskeletal filament?
changes in their conformation
What are scaffold proteins?
help hold the coils together; concentrate interacting proteins in the cell
What are intracellular condensates?
form biochemical subcompartments in cells
Most enzymes are
allosteric proteins that can exist in two conformations
When GTP is bound to the alpha subunit, the G protein is _____.
When GDP is bound to the alpha subunit, the G protein is
Covalent modificiations added to a proteins amino acid side chains can control....
the location and function of the protein and can serve as docking sites for other proteins.
uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest
a technique that separates particles according to their mass
Most proteins belong to
What is a PDB file?
Protein Data Base File
What three analyses can be used to determine the function and structure of a protein?
NMR Spectroscopy, x-ray crystallography, and cryoelectron microscopy