Quiz 4- Enzymes, Cell, Nucleic acids Flashcards
What are enzymes?
- Enzymes are proteins that increase the rate of chemical reactions
- They are each specific for one reaction
- They are not permanently changed in reactions
- They bind the reacting substances (substrates) and release the products once the reaction is complete
What are the three steps in an enzyme-catalyzed reaction?
- Binding of the substrate: E + S ↔ ES
- Conversion of substrate to product: ES ↔ EP
- Release of the product: EP ↔ E + P
What is the mechanism of action of an enzyme?
Enzymes lower the amount of energy required to go from reactants to products
- Do not change the reactants or products, but lower the activation energy so more molecules can enter the transition state and proceed to products
- Enzymes use different strategies to lower the activation energy so it speeds up the rate of reaction - this is accomplished by using functional groups, coenzymes and cofactors
How does zinc act as a cofactor?
- Zinc ion in carbonic anhydrase is another group that lines the active site
- Zinc is held in place by binding to 3 histidines in the active site
- The positive charge attracts electrons from water, making it easier for one of the Hs to be removed and the reaction to proceed
Which suffix denotes an enzyme?
-ase
Why do enzymes require a cofactor to bind for it to function?
The cofactor helps lower the energy required to cause the reaction
What are coenzymes?
- Coenzymes are organic molecules that are not proteins and are usually synthesized from vitamins
- They contribute functional groups that help catalyze the reaction, but are not very active on their own
What is the lock and key model?
- Focuses on an enzyme’s rigid lock and the substrate fits into this lock like a key
- This model explains the specificity of an enzyme but not the ability of the enzyme to stabilize the transition state
What is the induced fit model?
- Allows for flexibility of the enzyme in binding to the substrate and is thought to be the most accurate
- Binding of the substrate induces changes in the shape of the enzyme
- Allows for changes, such as closing of the acting fold of hexokinase once glucose is bound
What is pH dependence?
- Each enzyme has an optimal pH where they function most efficiently - typically physiological pH for many enzymes
- Some enzymes have evolved to work in acidic conditions
- I.e. Pepsin is a stomach enzyme that breaks down proteins at a pH of 1.5-2
- Above pH 5 it is denatured
How does temperature or concentration affect an enzyme?
- Rate of reaction of an enzyme increases until the temperature at which the protein (enzyme) is denatured
- Normal physiological temperature is 37℃, which is the optimal temperature for our enzymes to function
- Reaction rates increase as concentration increases
What is a competitive inhibitor?
- A molecule with a similar shape to a substrate that competes with the substrate to bind in the active site of an enzyme
- When an inhibitor binds instead of a substrate, the reaction cannot occur and the product is not produced
- Inhibitors can bind to enzymes reversibly or irreversibly
What are the two different types of competitive inhibitors?
- Reversible inhibitors: only inhibit when they are bound in the active site, many can be displaced by increasing the concentration of a substrate
- Irreversible inhibitors: do not detach and the enzyme action is permanently shut down (i.e. aspirin)
What is noncompetitive inhibition?
- Also known as allosteric
- Binds to a part of the enzyme away from the active site
- Binding of the inhibitor prevents the reaction from proceeding
- By changing the shape of the enzyme so that either the affinity of the enzyme for the substrates is reduced or the reaction can’t occur because of the change in shape
What are cytochrome P450 enzymes?
Large family of enzymes important in drug metabolism particularly in the liver
- Oxidize hydrophobic compounds making them more soluble, so they can be excreted (rather than building up in adipose tissue)
- Also intestinal cells, this is where grapefruit juice interferes, statins are not metabolized and can build up to toxic levels in the blood
What is a prokaryotic cell?
- Bacterial cell
- Does not contain a nucleus or other membrane bound organelles
- Do not have their DNA separated from the rest of the cell contents (no organelles)
What is a eukaryotic cell?
Found in humans, plants and animals
- Contain many compartments bounded by membranes
- Contain a nucleus and membrane bound organelles
- Have nuclei within their cells where DNA is found
What is the plasma membrane?
All cells are enclosed by a plasma membrane, which is a lipid bilayer
- Serves to restrict entry of substances into the cell
- There are proteins embedded in the membrane and anchored to it
- Different head groups appear more often on one side or the other of the cell membrane
- Phosphatidylserine (negative charge) makes up more of the inner membrane, along with phosphatidylethanolamine
What is the function of cholesterol in the cell?
Provides stability to the cell
What is a lipid bilayer?
Two layers with their polar groups facing the aqueous environment on either side
What are integral proteins?
- Proteins in the membrane that are embedded in the membrane and hydrophobic regions on either side
- Functions include channels or transporters, as well as receptors for hormones or neurotransmitter
What are peripheral proteins?
Attach to integral membrane proteins or to the edges of the lipid bilayer temporarily
What are the two components to an electrochemical gradient?
- The concentration gradient
2. The charge on the membrane
Describe cell transport
- The interior of the cell is more negatively charged so positive ions will be more likely to diffuse through
- Negative ions may require energy to transport them
- Usually only the concentration gradient is important for uncharged molecules
What are the modes of transport?
- Molecules can travel across the membrane by simple diffusion or facilitated diffusion, which require no energy expenditure
- Energy is required for active transport systems
- The membrane can also engulf molecules to bring them into the cell
- Cell membrane controls what comes in and goes out of the cell
What is facilitated diffusion?
- Form of passive transport
- Movement is from an area of high concentration to low concentration
- Molecule must bind to its transport but it is passive (no energy required)
- If there is a high concentration outside the cell and all transporters are occupied, transport is faster than it would be by simple diffusion
What is active transport?
Energy is required to transport substances against their electrochemical gradient
- This occurs with the Na+/K+ pump
- The maintenance of higher Na+ outside of the cell can be used to drive secondary active transport or to allow membrane depolarization in action potential
What is secondary active transport?
- Sodium is pumped out of intestinal cells so that it is low within the cell and can bind to a transporter that will then bind glucose (which is higher in the cell than lumen)
- Glucose can then go into the extracellular fluid, where its concentration is lower, by passive transport
- This mechanism moves sodium and glucose from the digestive tract into the body
- Requires Na+/K+ to work
What are lysosomes?
Break down proteins into amino acids
- Membrane bound digestive organelles
- Their pH is maintained at about 5.5 so that the enzyme enclosed in the organelle can function
- pH is maintained by enzymes that use energy to pump H+ into the lysosome
- The pH around them is lower than that inside the cell
- The recycling depot of the cell
What is the mitochondria?
Powerhouse of the cell in that they are the site of most of the energy generation
- Consist of an outer and inner membrane
- The inner membrane is the site of the enzymes involved in cellular respiration, while the citric acid cycle and other oxidative pathways occur in the matrix
- Contains a small amount of DNA
Which type of cell does not contain mitochondria?
Red blood cells
What is the nucleus?
The largest organelle and is where most of the cell’s DNA is located
- DNA replication occurs here along with transcription
- Once mRNA is transcribed and processed, it travels out of the nucleus through pores to be translated in the cytosol
What is nuclear transport?
- Proteins involved in processes in the nucleus, such as DNA replication and transcription are targeted to re-enter the nucleus after translation
- Proteins have a nuclear localization signal (NLS) attached that allows them to travel through the nuclear pores and re-enter the nucleus
