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
How are alpha helices formed?
Hydrogen bond is made between every fourth amino acid
Describe a coiled-coil. How is it formed? What are some examples?
• two or three Alpha helices coil around each other
• Hydrophobic regions are hidden away from aqueous environment
• Hydrophobic side chains are along one side
• Twist around each with hydrophobic regions facing i ward
Examples:
• a-keratin (intermediaye filament) found in hair and skin
• Collagen (found in ECM)
Compare parallel beta sheets and antiparallel beta sheets.
Parallel beta-sheet - neighboring segments run in same direction (loops are more expensive)
Antiparallel beta-sheet - neighboring segments run in opposite directions
What are prions?
• “Infectious” abnormally folded proteins
• Convert properly folded proteins into misfolded prion form
What are cofactors? Give a few examples.
Cofactors - nonprotein small molecules
Examples:
• Retinal: covalently attaches to Rhodopsin protein in photoreceptor (rod cells) in eye
• Heme group: oxygen carrying component of blood found in hemoglobin proteins
• Biotin (vitamin B7): found in carboxylases (enzymes that transfer a carboxyl group from one molecule to another)
What are substrates?
Molecules that enzyme work upon and chemically change
T or F: enzymes are altered and consumed by the end of a reaction (i.e., they are not recycled)
F: enzymes are not altered or consumed by the end of a reaction (i.e., they are recycled)
What are some characteristics of enzymes?
• Highly specific catalysts
• Facilitate a chemical reaction by speeding it up
• Highly specific to substrates
• Cannot be consumed in a reaction
The rate of a chemical reaction can be increased in two ways:
- Increasing energy of reacting molecules (heating)
- Lowering activation energy (what enzymes do)
Why is increasing energy of reacting molecules by heat bad for enzyme catalyzed reactions?
Heat denatures enzymes
What is the function of a lysozyme?
Cleave polysaccharides found in cell walls of bacteria
What happens when lysozyme disrupts cell wall of bacteria?
Bacteria burst (explode) under osmotic pressure
How many linked sugars of the polysaccharide can fit into the active site of the lysozyme?
6
Describe the reaction of lysozyme.
• Hydrolysis reaction
• Lysozyme is a hydrolytic glycosidase (cleaves glycosidic bonds)
• H2O is involved in cleavage reaction (hydrolysis) (water is added to a single glycosidic bond between two adjacent sugar groups)
• Lysozyme kills bacteria by lysing glycosaminoglycan chains in cell wall peptidoglycan
What is Vmax?
Maximum rate an enzyme can work (all active sites are full of substrate)
What is Km?
Substrate concentration at half maximum rate of reaction
Comparing substrates that bind tightly vs. weakly to the enzyme, how does this affect the relative Km value?
A more tightly bound substrate will results in a smaller Km (enzyme reaches maximum rate at a low concentration of substrate)
A weakly bound substrate will result in a larger Km, meaning a larger amount of substrate is needed
What is the active site?
Region on enzyme that binds to a substrate and catalyzes its chemical transformation
What part of the enzyme recognizes substrates?
Active sites
What is an allosteric site?
Recognize regulatory molecules
What is an example of how drugs inhibit enzymes?
Lipitor inhibits HMG-CoA reductase
HMG-CoA reductase: enzyme involved in synthesis of cholesterol by liver
Enzyme is inhibited from synthesizing cholesterol
What is a hydrolase?
General term for enzymes that catalyze a hydrolytic cleavage reaction
In what way are alpha helices and beta sheets similar?
Both are produced by hydrogen bonds between N-H and C=O groups in polypeptide backbone
T or F: Protein-protein interactions are highly specific.
True
What enzyme is described as having antibacterial properties and acts as a natural antibiotic found in egg white, saliva, and tears?
Lysozyme
What does allosteric mean in reference to proteins?
Describes a protein that can exist in multiple conformations depending on the binding of a molecule at a site other than the catalytic site
What is protein phosphorylation?
Covalent addition of a phosphate group to a side chain of a protein
Amino acid sequence
Unique order of amino acids present in a protein
Polypeptide backbone
Repeating sequence of atoms that form the core of a protein and to which the amino acid side chains are attached
What does conformation mean?
Final folded structure of a protein
What is a ligand?
Any substance that is bound by a protein (e.g., ion, small organic molecule, macromolecule)
Binding site
Region of a protein that associates with a ligand
Enzymes act as ________.
Catalysts
What aspect of enzyme-substrate interaction is important for dehydration?
Enzyme binds to two substrate molecules and orients them precisely to encourage a reaction to occur between them
What aspect of enzyme-substrate interaction is important for hydrolysis?
Enzyme strains the bound substrate molecule, forcing it toward a transition state that favors a reaction
