Unit 2 (Week 5) Enzymes, Temp, pH and Specificity Flashcards
Which compound comes from willow trees that now makes up aspirin?
Salicylic acid
Modern day aspirin is a derivative acetylsalicylic acid, which is gentler on the stomach.
What do the drugs, aspirin and ibuprofen, inhibit within the body to exert their effects of pain relief and fever reduction?
They inhibit enzymes.
The enzyme in this case is cyclooxygenase which has a role in synthesizing molecules called prostaglandins whose production is blocked and in turn relieving pain and fever.
What is a process in which one or more substances are changed into other substances? (4) ways
Chemical reaction
- Molecules attaching to each other to form larger molecules
- Molecules breaking apart to from two or smaller molecules
- Rearrangements of atoms within molecules
- The transfer of electrons from one atom to another
What are enzymes and what do they do?
They are proteins that act as catalysts to speed up thousands of different reactions in cells.
What is the sum of all bodily activities and chemical reactions that occur within an organism. Also, a specific set of chemical reactions occurring at the cellular level?
Metabolism
What two general factors determine the fate of a given chemical reaction in a living cell?
Direction and Rate.
aA + bB —->
What is the ability to promote change or do work?
Energy
What is kinetic energy?
Energy associated with movement. Swinging a Bat
What is potential energy?
Energy that a substance possesses due to its structure and location. Pulling back the draw string on a bow.
T/F Electrons have potential energy based on its positive relative to other electrons and a positively charged nucleus and its amount of energy is based on its energy level.
True.
Electrons also lose energy when it drops to a lower energy level or shell.
What is the potential energy contained within atoms and the bonds between atoms?
Chemical potential energy (or simply, chemical energy)
What molecule stores a great amount of energy that is used to make ATP, an energy intermediate?
Glucose
Name (5) different types of energy important in biology and their examples.
- Light - Photons captured by pigments in chloroplasts.
- Heat - Used to maintain constant body temperature and achieved by chemical reactions.
- Mechanical - Associated with movement and muscle contraction.
- Chemical potential - Covalent bonds in organic molecules, such as glucose and ATP store large amounts of energy. When bonds break in larger molecules to form smaller molecules, the energy that is released can drive cellular processes.
- Electrical/Ion gradient - During a stage of cellular respiration called oxidative phosphorylation, an H+ gradient provides the energy to drive ATP synthesis.
What is the study of energy interconversions?
Thermodynamics
What is the first law of thermodynamics (aka the law of conservation of energy)?
Energy cannot be created or destroyed.
It can only be transferred from one place to another and can be transformed from one type to another (as when, for example, chemical energy is transformed into heat)
What is the second law of thermodynamics?
Energy transfer or transformation from one form to another increases the degree of disorder of a system, called entropy.
What is entropy?
The degree of disorder of a system.
In other words, it is the measure of the randomness of molecules in a system.
Which do you think has more entropy, a NaCl crystal at the bottom of a beaker of water or the solution that would be formed after the Na+ and Cl– ions forming the crystal have dissolved in the water?
The solution
What makes energy “unsuable?”
Entropy (S)
What is the total energy of a system termed?
Enthalpy (H)
What is the amount of a system’s energy that is available and can be used to promote change or do work?
Free energy (G)
Fun Fact: The use of G is in recognition of American physicist J. Willard Gibbs, who proposed the concept of free energy in 1878.
What is the formula that relates the three components of energy proposed by Gibbs?
H = G + TS
T = absolute temperature in kelvins (K)
To rewrite the equation to focus on free energy,
G = H - TS
What is the difference of a spontaneous or non-spontaneous process in relation to biology?
A spontaneous process or reaction is one that occurs without being driven by an input of energy.
What is the key way to evaluate if a chemical reaction is spontaneous?
Determine the free-energy change that occurs as a result of the reaction
ΔG = ΔH - TΔS
The delta indicates change, such as before and after a chemical reaction.
When does a chemical reaction have a negative free-energy change?
The products of the reaction have less energy than the reactants, therefore free energy is released during product formation.
What refers to chemical reactions that release free energy and occur spontaneously?
Exergonic (favors the reactions from reactants to products)
What refers to chemical reactions that require an addition of free energy and do not proceed spontaneously?
Endergonic (favors the formation of reactants)
What is a molecule that is a common energy source for all cells?
Adenosine Triphosphate (ATP)
What is the hydrolysis of ATP?
When ATP is broken down into ADP (Adenosine diphosphate) and inorganic phosphate (HPO4 2-) or Pi
For the conversion of 1 mole of ATP to 1 mole of ADP and Pi, the deltaG equals -7.3 kcal/mol. Because this is negative value, the formation of the products is strongly favored making this process exergonic.
What is a state of a chemical reaction in which the rate of formation of products equals the rate of formation of reactants?
Chemical equilibrium
How does a endergonic reaction occur spontaneously?
By coupling with an exergonic reaction, whereas the net free-energy change for both processes combined is negative.
What is the attachment of a phosphate to a molecule which is salient to the process of using ATP as a method to input energy and make it exergonic?
Phosphorylation
T/F The breakdown of food molecules to smaller molecules is endergonic.
False. It is exergonic.
This process allows cells to make more ATP from the phosphorylation of ADP (endergonic reaction)
Fun Fact: How many pounds of ATP does the average human hydrolyze and how does it happen?
100 pounds of ATP/day. Each molecule undergoes about 10,000 cycles of hydrolysis and regeneration during an ordinary day.
If a large amount of ADP was broken down in a cell, how would this affect the ATP cycle?
If a large amount of ADP was broken down, the cell would not be able to synthesize as much ATP, which is made by the attaching a phosphate to ADP. The ATP cycle would be inhibited.
What has been analyzed to determine what proteins have ATP-binding sites and utilize ATP between those that do not?
Proteomes
What are a few examples of proteins using ATP for energy? (7)
Metabolic enzymes - ATP for endergonic reactions.
Transporters - Ion pumps with Na+/K-ATPase
Motor Proteins - Myosin, ATP to facilitate cellular movement
Chaperones - ATP in aiding the folding and unfolding of cellular proteins
DNA-modifying enzymes - Helicases and topoisomerases, use ATP to modify the conformation of DNA
Aminacyl-tRNA synthetases - enzymes that use ATP to attach to amino acids to tRNA
Protein Kinases - regulatory proteins that use ATP to attach a phosphate to a protein, there phosphorylating the protein and affecting its function.
[6.2 Start] T/F Agents that speeds up the rate of a chemical reaction, like a catalyst, are permanently changed or consumed during the reaction.
False. They are not permanently changed or consumed.
What are the most common catalysts in the human body?
Enzymes (proteins)
Some biological catalysts are RNA molecules known as ribozymes.
What is great example of a process that showcases the need for a catalyst?
If you put gasoline in a container with oxygen, nothing would happen. Wait a few million years, and the gasoline would be broken down. This reaction proceeds too low.
At the cellular level, enzyme-catalyzed reactions occur millions of times faster than the corresponding uncatalyzed reactions.
What is an example, within cells, where an enzyme is used to get rid of a molecule?
An organelle, peroxisomes, uses catalase to decompose hydrogen peroxide. This process is 10^15 faster than its uncatalyzed process.
What is the initial input of energy in a chemical reaction that allows the molecules to get close enough to cause a rearrangement of bonds?
Activation energy (E sub A)
What is the chemical reaction, a state in which the original bonds have stretched to their limit; once this state is reached, the reaction can proceed to the formation of products?
Transition state (after activation energy has been applied)
What are the two ways activation energy is lowered in a exergonic reaction?
The use of enzymes by straining the chemical bonds in the reactants.
The second way by binding the two reactants so they are close to each other in a favorable reaction.
How does lowering the activation energy affect the rate of a chemical reaction? How does it affect the direction?
Lowering EA speeds up the rate. When the activation energy is lower, it takes less time for reactants to reach the transition state, where a reaction can occur. Lowering EA does not affect the direction of a reaction.
What is the location in an enzyme where a chemical reaction takes place?
Active site
What is a substrate?
The reactant molecules that bind to an enzyme at the active site and participate in a chemical reaction.
Bonus: What are the substrates that bind to the active sites of the enzyme, hexokinase?
Glucose and ATP
What do you call the structure produced by binding an enzyme and its substrate(s)?
Enzyme-substrate complex
When an enzyme undergoes the conformational change after the binding of substrates, it puts torque on its substrates, a mechanical stress on the chemical bonds.
What about hexokinase allows it to create the products it does?
The high specificity of its products is largely determined by the structure of the active sites within it. This also prevents other sugars to bind to hexokinase because they are not recognized.
What is a phenomenon that occurs when a substrate(s) binds to an enzyme and the enzyme undergoes a conformational change that causes the substrate(s) to bind more tightly to the enzyme?
Induced fit (key component in reducing activation energy)
The enzyme, sucrase, on the microvilli within the small intestine hydrolyzes sucrose how?
One the single substrate, the disaccharide, attaches to the active site, the enzyme completes the conformational change which exposes the oxygen bridge allowing a water molecule to cleave it creating two monosaccharides.
What is the degree of attraction between an enzyme and its substrate(s)? How does substrate concentration affect relate to affinity?
Affinity
For enzymes with high affinities for their substrates, they readily recognize them at high or lower concentrations
For lower affinities, a higher concentration is needed for the enzyme to recognize its substrate.
Why does plateauing occur within the rate at which enzymes have substrates attached?
A high substrate concentrations, nearly all of the active sites of the enzyme are occupied with substrate, so further increasing the substrate concentration has negligible effect
When does a enzyme reach a point of its maximal rate of Vmax (maximal velocity, or rate, of an enzyme-catalyzed reaction)?
The enzyme is saturated with substrate.
Enzyme A has a KM of 0.1 mM, whereas enzyme B has a KM of 1.0 mM. The reactions the two enzymes catalyze both have the same Vmax. If the substrate concentration was 0.5 mM, which reaction—the one catalyzed by enzyme A or the one catalyzed by enzyme B—would have the higher velocity?
KM value of an enzyme is the substrate concentration at which velocity of the reaction is half the maximal velocity.
Enzyme A
KM is also called Michaelis constant.
A higher KM requires a higher substrate concentration to achieve a particular reaction velocity compared to an enzyme with a lower KM.
Enzymes with a high KM have a low affinity for their substrates—they bind them more weakly. By comparison, enzymes with a low KM have a high affinity for their substrates—they bind them more strongly.
How do cells modulate enzyme function?
Inhibitors
What is a molecule that binds noncovalently to the active site of an enzyme and inhibits the ability of the substrate to bind?
Competitive inhibitor (typically part of their structure mimics the structure of the substrate in which occupies the active site on the enzyme)
What happens when a competitive inhibitor is present?
The KM for the substrate increases and a higher concentration of the substrate is needed to achieve the same rate of the chemical reaction.
What is a molecule that binds noncovalently to an enzyme at a location that is outside the active site and inhibits the enzyme’s function?
Noncompetitive inhibitor
This lowers the Vmax for the reaction and not the KM of the enzyme.
What is the name of the site where a noncompetitive inhibitor attaches noncovalently and affects its function?
Allosteric site
What do you think a irreversible inhibitor does?
Irreversible inhibitors usually bind covalently to an enzyme to inhibit its function. Specifically, it binds to the amino acid within the active site, thereby preventing the enzyme to receive its substrate(s).
What is an example of a irreversible inhibitor on the
An example of an irreversible inhibitor is diisopropyl phosphorofluoridate (DIFP). DIFP is a type of nerve gas that was developed as a chemical weapon. This molecule covalently reacts with the enzyme acetylcholinesterase, which is important for the proper functioning of neurons.
Why would the body use a reversible inhibitor?
A reversible inhibitor allows the body to use the enzyme again, when the inhibitor concentration becomes lower. This is very energy efficient.
T/F Enzymes may sometimes require nonprotein molecules or ions to carry out their functions.
True
What is a small molecule that is permanently attached to the surface of an enzyme and aids in the enzyme’s function?
Prosthetic group
What are usually an inorganic ion that temporarily binds to the surface of an enzyme and promotes a chemical reaction?
Cofactor
What is an organic molecule that temporarily binds to an enzyme and participates in the chemical reaction that the enzyme catalyzes, but is left unchanged when the reaction is completed?
Coenzyme
What three conditions play an important role in the proper functioning of an enzyme?
Temperature, pH, and ionic conditions.
What is the significance of temperature on enzymes?
If the temperature is much higher or much lower than 37 degrees Celsius, the enzymes are inhibited. Extremely high may denature the protein causing it to unfold completing inhibiting the enzyme.
What is an example of pH affecting exnzymes?
They are sensitive to pH. In the stomach, pepsin is a protease (enzyme that digests proteins into peptides), that is released into the stomach and works optimally around pH 2.0.
Alternatively, cytosolic enzymes function optimally at a neutral pH, such as pH 7.2. Too high or below this would inhibit cytosolic enzymes.
What is a biological catalyst that is an RNA molecule?
Ribozyme
Briefly explain why it was necessary to purify the individual subunits of RNase P to show that it is a ribozyme.
RNase P has both a protein and an RNA subunit. To determine which subunit has catalytic function, it was necessary to purify them individually and then see which one was able to cleave ptRNA.
In living cells, what is a coordinated series of chemical reactions in which each step is catalyzed by a specific enzyme?
Metabolic Pathway
How are pathways in metabolism categorized?
Whether they build something or break something down.
What is a metabolic pathway in which a molecule is broken down into smaller components, usually releasing energy?
Catabolic reaction (often exergonic)
What is a metabolic pathway that involves the synthesis of larger molecules from smaller precursor molecules. Such reactions usually require an input of energy?
Anabolic reactions
What two uses does catabolic reactions serve?
- Recycling of organic building blocks, Proteases breakdown down proteins into amino acids for future use in other amino acids.
- Breakdown of organic molecules to obtain energy especially in endergonic processes in a cell.
T/F When cells break covalent bonds in organic molecules such as glucose, they directly use the energy released.
False.
This energy created, like an inorganic phosphate ion, is stored in an energy intermediate molecules such as ATP.
What is a method of synthesizing ATP that occurs when an enzyme directly transfers a phosphate from an organic molecule to ADP?
Substrate-level phosphorylation
What is a process for making ATP in which energy stored in an ion electrochemical gradient is used to make ATP from ADP and Pi?
Chemiosmosis
What is the removal of one or more electrons from an atom or molecule; occurs during the breakdown of small organic molecules?
Oxidation.
This process is called oxidation because oxygen is frequently involved in chemical reactions that remove electrons from other atoms or molecules.
What is the addition of one or more electrons to an atom or molecule?
Reduction
Named so because the addition of a negatively charged electron reduces the net positive charge or an atom or molecule.
What is a type of reaction in which an electron that is removed during the oxidation of an atom or molecule is transferred to another atom or molecule, which becomes reduced; short for a reduction-oxidation reaction?
Redox reaction
Ex formula:
Ae- + B —–> A (oxidized) + B- (reduced)
What happens to the energy level when an atom is oxidized and when one has been reduced?
The oxidized molecule or atom will have a loss of energy (less electrons) while the reduced atom or molecule will have its energy level increased (addition of a electron)
What is NAD+ stand for as an organic molecule that functions as an energy intermediate. It combines with two electrons and H+ to form NADH?
Nicotinamide adenine dinucleotide.
NADH is an energy intermediate
What are the two common ways NADH is used?
- Oxidation (reduction of energy) is highly exergonic reaction that can be used to make ATP.
- NADH can donate electrons to other organic molecules and thereby energize them. This helps other molecules create covalent bonds.
This process is SALIENT in the synthesis of larger molecules through the formation of covalent bonds between smaller molecules. NADH is also known as an electron carrier.
What organelle within a cell uses NADH?
The mitochondria which produces ATP. Remember: NADH has its own cycle just like ATP.
What is also called an anabolic reaction; a chemical reaction in which small molecules are used to synthesize larger molecules?
Biosynthesis reaction
What three was are metabolic pathways regulated?
The regulation of catabolic and anabolic pathways occurs at the genetic, cellular, and biochemical levels.
Since enzymes are proteins, what are they encoded by?
Genes
How do cells control metabolic pathways via gene regulation?
If a bacterial cell is not exposed to a specific sugar molecule in its environment, it will turn off the genes that encode the enzymes that are needed to break down sugar. Later, if the sugar is present, the cell will switch on the genes to produce the enzyme needed.
For cellular regulation, cell-signaling pathways often lead to the activation of protein kinases, that is, enzymes that covalently attach a phosphate group to a target group.
How does this relate to people who are frightened?
When frightened, people secrete a hormone called epinephrine into their bloodstream.
The hormone binds to the surface of muscle cells and stimulates the intercellular pathway that leads to the phosphorylation of specific enzymes involved in carbohydrate metabolism.
This leads to an increase of energy. After the flight-or-fight hormone dissipates, other enzymes called phosphatases remove the phosphate groups from the enzymes, thereby restoring original level of carbohydrate metabolism.
What previous topic was discussed that has an active role in biochemical regulation where the product of a metabolic pathway inhibits an enzyme that acts early in a pathway, thus preventing the overaccumulation of the product?
Competitive and noncompetitive inhibitors.
This specific example refers to the use of noncompetitive inhibitors and the use of a allosteric site in a process called Feedback Inhibition.
How does the Feedback Inhibition, a noncompetitive inhibitor process, and the use of a allosteric site actually prevent an enzyme from using its active sight with its respective substrate?
The enzyme undergoes a conformational change with changes the shape of the active site which no longer recognizes its substrate and absolves the catalytic function.
What is the slowest step in a reaction pathway?
Rate-limiting step. They have the greatest affect on rate when being inhibited or enhanced.
[6.4 Start] What large molecules exist for a low amount of time and may need to be recycled?
RNA, proteins, lipids, and polysaccharides.
What is the case in organic molecules in a cell, refers to the time it takes for 50% of the molecules to be broken down and recycled?
Half-life
mRNA has an average half-life of about 5 minutes in bacterial cells.
mRNA in eukaryotic cells tend to last for 30 minutes to 24 hours or maybe a few days.
Why is recycling important in biology?
To compete effectively in their native environments, all living organisms must efficiently use and recycle the organic molecules that are needed as building blocks to construct larger molecules and macromolecules. Otherwise, they would waste a great deal of energy making such building blocks from smaller molecules.
Since cells continually degrade proteins that are faulty or no longer needed, in order to degrade them, what are the proteins recognized by?
Proteases - enzymes that cleave the bonds between adjacent amino acids.
What is the primary pathway for protein degradation in archaea and eukaryotic cells?
Via a protein complex called a proteasome
What does a proteasome consist of?
4 stacked rings composed of 7 protein subunits.
In eukaryotic cells, these caps at each end control the entry of proteins into the proteasome.
What are advantages of protein degradation?
Protein degradation eliminates proteins that are worn out, misfolded, or no longer needed by the cell. Such proteins could interfere with normal cell function. In addition, the recycling of amino acids saves the cell energy.
What is a small protein in eukaryotic cells that is covalently attached to an unwanted protein, which directs the protein to a proteasome for degradation?
Ubiquitins
What are the three functions of ubiquitins?
- The enzymes that attach ubiquitins recognize improperly folded proteins.
- Changes in cellular conditions may warrant an increase in protein breakdown.
- The amino acids released from the proteasomes are used to make new proteins, saving the cell energy.
What is responsible for the digestion of substances that are taken up from outside the cell which is paramount in the process of endocytosis?’
Also, this unit is responsible for the degradation of whole organelles that are no longer needed and recycled back into the cytosol in a process known as autophagy.
Lysosomes
In autophagy, the double membrane that surrounds the organelle which eventually fuses with a lysosome is called a autophagosome.
