Proteins Flashcards
What are two ways an enzyme can reduce the activation energy of a chemical reaction?
- Holding reacting substrates together in a precise alignment
- Rearranging distribution of charge in
(1) How does substrate concentration effect the rate of an enzymatic reaction? (2) Distinguish between the effects of competitive versus noncompetitive inhibitors.
• Rate of enzymatic reaction increases as the substrate concentration increases
• Low substrate concentration =
• High substrate concentration =
(2)
Competitive inhibitors - compete with substrate for binding to enzyme’s active site
• Do not change Vmax of a reaction
Noncompetitive inhibitors - bind to regulatory stirs elsewhere on enzyme surface
• Causes maximum reaction rate (Vmax) to decrease
• Affinity for substrate remains unchanged
What are chaperones? Compare how 2 different types of chaperones function in the cell.
Chaperon proteins - Proteins that assist in protein folding
- Chaperones that bind to partially folded proteins
- Chaperons with isolation chambers
How do small G-proteins regulate target protein function?
• Act as molecular switches (turn target proteins on and off)
• Active conformation when GTP is bound
• GTP hydrolyzed to GDP —> puts protein in inactive conformation
(1) Distinguish between kinases and phosphatases. (2) How do they regulate target proteins?
(1)
• Protein kinase - catalyzes addition of phosphate group to a protein
• Protein phosphatase - catalyzes removal of phosphate group from a protein
(2)
• Phosphate changes conformation/shape of protein
• —> Adds extra charges to negative areas (prevents or enhances access)
What is the difference between allosteric activation and inhibition in terms of feedback?
Allosteric activation:
• Bind to allosteric site and turn protein on
• Occurs when enzymes need a product to skyrocket
• Positive feedback
Allosteric inhibition:
• Bind to allosteric site and turn protein often
• Prevents making more of something
• Negative feedback
What is the compositional difference between fibrous and globular proteins in terms of secondary structure?
• Fibrous - can only have alpha helices OR beta sheets (not both)
• Globular - can have both alpha helices and beta sheets
What are amyloid fibrils? How do they lead to neurodegenerative disorders as a result of genetic mutation or infection?
Amyloid fibrils - B sheets stacked together in long rows
They lead to neurodegenerative disease when misfolded proteins form amyloid fibrils
(1) What are the roles of the hydrogen bonds, electrostatic and van der Waals interactions in protein folding? (2) What are the different levels of protein structure? (3) In which case(s) are backbone versus side chain interactions involved? (4) Under what circumstances are covalent interactions involved?
(1)
• Hydrogen bonds - attractive force between a hydrogen…
• Electrostatic attractions - ionic bonds between oppositely charged side groups
• van der Waals interactions - weak interactions between uncharged/nonpolar side chains
(2)
• Primary structure - amino acid sequence
• Secondary structure - alpha helices and beta sheets
(3) - backbone interaction
• Tertiary structure - final folded shape (final level of structure for proteins consisting of only a single polypeptide chain)
(3) - backbone to side chain or side chain to side chain interactions
• Quaternary structure - arrangement of individual chains (subunits) in a protein with 2 or more polypeptide chains
(4) Disulfide bonds
What is the difference between hydrolysis and dehydration reactions? What are the corresponding hydrolases that cleave nucleic acids, proteins, and carbohydrates?
Hydrolysis:
• Breaks down larger molecules into smaller subunits
• Water molecule is consumed/added
Dehydration reaction:
• Synthesizes smaller subunits into larger molecules
• Water molecules is expelled/released
Nuclease - nucleic acids
Proteases - proteins
N-terminus
End carrying amino group
C-terminus
End carrying carboxyl group
Describe the general structure of an amino acid.
A central carbon surrounded by:
• Hydrogen atom
• R group
• Amino group
• Carboxyl group
_______ determine the chemical properties of amino acids and ultimately proteins.
Side chains (R groups)
What are the main categories of side chains?
Polar
• Polar charged (positive/basic or negative/acidic)
• Polar uncharged
Nonpolar
Glycine is the simplest amino acid. What’s the R group?
Hydrogen
What are the noncovalent bonds that help proteins fold?
- Hydrogen bonds
- Electrostatic attractions
- Van der Waals interactions
Are there any sidechain (R group) interactions that involve covalent bonds?
Disulfide bonds
Compare nonpolar and polar side chains
Non polar side chains: tend to cluster in interior of folded protein
Polar side chains: tend to arrange themselves near outside of folded protein
Why do hydrophobic side chains tend to reside in interior of proteins?
To stay away from aqueous environment
Outside is interacting with water
Hydrogen bonds contribute to the stability of a protein via three distinct interactions?
- Backbone to backbone: hydrogen bond between atoms of two peptide bonds
- Backbone to side chain: hydrogen bond between atoms of a peptide bond and an amino acid side chain
- Side chain to side chain: hydrogen bond between atoms of two amino acid side chains
Urea can disrupt hydrogen bonding within proteins and protein-water interactions. How is this possible
T or F: amino acid sequence do not have the information for a protein to fold on its own. Therefore, it relies on chaperones to fold proteins.
F: amino acid sequence has all information for a protein to fold on its own. Chaperones make the process more efficient
Why would it be important for chaperones to have isolation chambers?
Without isolation chambers, proteins will start interacting/aggregating with each other
Prevents aggregation of proteins and prevents
Aggregation prevents proteins from forming into correct shape
