Amino Acids, Proteins, and Enzymes (Lec. 3) Flashcards
Ch. 2 pg. 55-70
Summarize the properties of the different groups of amino acids.
There are 4 categories of amino acids according to side chain properties. One group is nonpolar (hydrophobic), one is polar neutral/hydrophilic, one is acidic, and one is basic.
Explain the roles of noncovalent bonds in protein folding
Noncovalent bonds create secondary, tertiary, and quaternary protein structure.
Explain why enzymes affect the kinetics of chemical reactions without changing the equilibrium between reactants and products
They increase the rate of chemical reactions without themselves being consumed or permanently altered. They don’t alter the chemical equilibrium because they accelerate both the forward and reverse reactions equally.
Summarize the mechanisms of enzymatic catalysis
Enzymes bring multiple substrates together, distort the conformation of substrates to approach the transition state, and forming bonds with reaction intermediates.
Distinguish between enzymes and coenzymes
Coenzymes work together with enzymes to enhance reaction rates by carrying chemical groups between substrates (ex: NADH carries electrons).
Explain why regulating the activity of enzymes is important to cell function.
By regulating enzyme activity, cells avoid wasting energy.
Explain the difference between integral and peripheral membrane proteins
Integral/transmembrane proteins are embedded directly within the lipid bilayer. Peripheral membrane proteins are associated with the membrane indirectly, generally by interactions with integral membrane proteins.
Can you draw the structure of an amino acid?
I sure hope so
Contrast the difference in location between hydrophobic and hydrophilic amino acids
Hydrophobic amino acids are typically located on the inside of proteins, away from the aqueous environment. Hydrophilic amino acids are typically located on the outside of proteins, facing the aqueous environment.
Where does a peptide bond form?
Between the amine group of one amino acid and the carboxyl group of another
Identify what shapes primary, secondary, tertiary, and quaternary protein structure.
Primary: amino acid sequence
Secondary: hydrogen bonds
Tertiary: noncovalent interactions
Quaternary: interactions between amino acids, water, and each other; largely spontaneous
How do the existence of prions relate to protein folding
Normal folding is an alpha helix, but misfolding can create beta pleated sheets, which can non-covalently interact with other proteins, triggering their misfolding. The beta-sheets can then line up to form insoluble structures, which can kill cells and form plaques.
What are IDPs and IDRs?
IDPs are intrinsically disordered proteins, which have entirely disorderly structures. IDRs are intrinsically disordered regions, which are proteins with proteins that are disorderly. Most proteins have stable final structures.
What are the two key properties of catalysts?
- Not consumed or permanently altered in the process.
- Do not alter the chemical equilibrium between reactants and products.
What does the +/- value of delta G mean?
Negative delta G: energy released
Positive delta G: energy absorbed
Delta G of zero: equilibrium
What are the two theories for how enzymes fit with substrates?
Lock-and-key model: fit perfectly together
Induced fit model: both distort a little bit to reach the transition state conformation
What are co-factors?
low-weight organic molecules that bind loosely to enzymes and are recycled during catalysis
What are the two different kinds of enzyme inhibition?
- Competitive inhibition: inhibitor binds to active site
- Noncompetitive inhibition: inhibitor binds to allosteric site (allosteric regulation)
What is allosteric regulation?
Small molecules non-covalently bind to sites other than the active site, which changes the shape of the enzyme (can be inhibitory or stimulatory)
What is feedback inhibition?
The product of a reaction inhibits an enzyme needed for its synthesis (negative feedback)
How does phosphorylation relate to enzyme regulation? Which enzymes phosphorylate and which dephosphorylate?
Phosphate is added; can activate or inhibit the activity. Kinases phosphorylate and phosphatases dephosphorylate.
