topic 4: Enzymes Flashcards
What are most enzymes?
Most enzymes are proteins, and proteins are polymers of amino acids.
What are amino acids?
Chemical compounds made up of amino (NH2-) group, carboxyl (COOH-) group and a differing R-group (different amino = different side chain). They use covalent bonds.
How are amino acids polymerized?
They are linked by peptide bonds through dehydration synthesis (forming through removal of H2O).
What are peptide bonds?
When the carboxyl group of one amino acid is linked to the amino group of the second amino acid (usually C-N).
Key differences in R-groups?
Some are polar (hydrophilic) and some are non-polar (hydrophobic). REMEMBER that amino acids can be non-polar despite having amino and carboxyl group.
Hydrophobic vs Hydrophilic R-groups?
Hydrophobic on inside of membrane bilayer (with tail) + have MOSTLY non-polar bonds in R-group (C-H mostly or S-S… . Hydrophilic have polar bonds (NH3, OH…) or can even have charges (+/- compound).
Peptide vs polypeptide vs protein
Peptide is 2-10 row of amino acids and a polypeptide is around 50 chain of amino acids. Protein differs by being a long polypeptide (>50) which has a FUNCTIONAL 3D SHAPE. Formation
What are the levels of protein structure?
Primary (sequence/raw polypeptide), Secondary (folds/helices), Tertiary (3d arrangement), and Quaternary (multiple tertiary, not all have).
What are the start and end of a polypeptide chain?
The N-terminus and C-terminus aren’t connected to anything.
Where are new Amino Acids added?
To the C-terminus from carboxyl group of last Amino Acid. ?
How is Helix (a-helix) shape created?
Through HB bond pattern- when O (carboxyl) and H (amino) from Aa1 and Aa4 (4 residues apart) repeatedly interact.
What is the b-strand?
The sheet part of the secondary protein structure, where stretched segments of polypeptide chain are arranged adjacently by hydrogen bonds. More likely to be anti-parallel.
When does a protein attain function?
At its 3rd structure where R-groups interact in 3d arrangement.
Same 4th?
Homo not hetero.
What is key thing in protein structure (besides raw sequence)?
The ARRANGEMENT of that sequence is just as important. Team does not equal Tame, even though same letters present.
Why do we need enzymes?
Biological reactions are extremely slow. When bonds of reactants are stable, external E must be inputed- or the reaction made easier. Enzymes are biological catalysts.
Energy required to set off reaction?
Activation Energy. This is what enzymes lower to increase rate of reaction.
State where old bonds breaking and new ones starting to form?
Transition State- highest potential E.
What remains the same even with enzymes?
deltaG- the (free) energy of the reactants/products is the same.
What are some ways to increase the rate of chemical reaction?
- Increase the temperature (more collisions + colliding with more E). 2. Add a catalyst to lower Ea. 3. Manipulate the concentration of reactants and products (more collisions + lechatelier (visualize)).
How do enzymes decrease activation energy?
They make it more likely for products to interact and collide at proper orientation. They have activation site, a region where Enzyme-subtrate complex is created and interaction lowers Ea.
Specific ways for enzymes to decrease activation energy?
The ES complex changes conformation of enzyme, creating an INDUCED FIT. The induced fit is shaped for the transition state where bonds of substrate rearranged- lowering Ea. The enzyme forces the subtrate into its transition state.
What happens after products are created in enzyme?
They are released and enzyme goes back to original conformation.
Different ways of forcing transition state?
Bringing reactants closer, polarizing, distort substrate molecules, ect.
Different ways of forcing transition state?
Bringing reactants closer, polarizing (making bonds unstable), distort substrate molecules, ect.
When are enzymes used as energy coupling devices?
When the free energy change (deltaG) is positive, enzymes need to catalyze multiple reactions at the same time.
How do enzymes work as E coupling devices?
They can transfer the energy released from one reaction to another reaction that requires E to complete it. They do this by becoming phosphorylated or being reduced. P to enzyme to Product
What does enzyme kinetics depend on and how do cells control?
Concentration of enzyme and substrate. Cells control this through enzyme activators/inhibitors.
What peaks?
Saturation leads to stagnation (max rate), but if enough substrate, additional enzyme will always increase speed.
What is denaturation?
Loss of protein structure = less functional (or completely). Reversible or permanent. Can also be due to heat (body conditions best). Different enzymes (in different body parts) have different preferences.
What is enzyme inactivity?
Lowering rate of reaction. Can be due to denaturation or inhibition. Reversable vs permanent
Reversible Competitive Inhibitor?
Similar structure to substrate- competes to fill active site and lower enzyme activity. Concentration of inhibitor vs substrate determines rate of reaction.
Reversible non-comptetitive inhibitor?
NOT chemically similar to subtrate. Binds to allosteric binding site and makes enzyme have low affinity for substrate. High concentrations of substrate DO NOT outcompete this.
What are regulatory (allosteric enzymes)?
All biochem pathways include regulatory enzymes that control rate of ENTIRE PATHWAY. Binds to enzyme to change shape to more active form= allosteric activator
Feedback inhibition?
When the final product of a biochem pathway is an allosteric inhibitor and it blocks an enzyme early in the pathway.
