Module 6: Unit 2-3 Flashcards
With the lock and key analogy what is the key and what lock.
Enzymes have an active site that is complementary tot he substrate
Substrate - key
Active site - lock
How do enzymes function?
Enzymes = biocatalysts
- increase reaction rate (V0) by lowering the activation energy of a chemical reaction
What is the activation energy?
Is the energy that has to be overcome for a substrate to be converted to a product.
EX: breaking apart of surprise into fructose and glucose requires a huge amount of energy. Enzymes have the ability of lowering that activation energy and, thus INCREASE the probability of that action to occur
What happens when there is more enzyme present?
The faster the reaction occurs or the faster product is formed.
What factors impact enzyme velocity?
What is the driving factor for enzymes?
What is the common thread in changing reaction rates?
- pH
- Temperature
Driving factor is to get the body back to homeostasis
—> Common thread is conformation change
The relationship between substrate concentration and reaction rate is ________
Hyperbolic,
A hyperbolic equation is used to analyze enzyme kinetics, acid-base behavior, and absorption processes
Describe a hyperbola graph
Starts steep and plantos with higher concentrations
Name the four different types of schematic depiction of inhibitor action. *Picture on slide 16 from Module 6 unit 2-3
- Normal binding
- Competitive inhibition
- Noncompetitive inhibition (mixed)
- Uncompetitive inhibition
Name the inhibitor that binds at the active site instead of substrate, has unchanged Vmax, and Increased Km.
Competitive inhibitor
Name the inhibitor that bonds at a site other than the binding site, affects the conformation of the enzyme, including the shape of the active site; decreased Vmax, same Km
Mixed (noncompetitive) inhibitor
Name the inhibitor that binds at a site other than the binding site, but only is substrate is bound; once the inhibitor binds the reaction does not proceed; decreased Vmax, and decreased Km
Uncompetitive inhibitor
T or F
The product of one enzyme reaction can be the substrate of one or more other enzyme reactions.
T
T or F
All enzymes are regulated
F
Only certain enzymes are regulated (commonly first step in a pathway, or enzymes at or near ‘intersections’)
Reversible enzymes are rarely regulated
T or F
Enzymes in extracellular spaces are commonly catalyzed reactions independently of other enzymes.
T
T or F
Some enzymes are present in inactive form to be quickly activated when their activity is required
T
EX: enzymes in the digestive tract (break down nutrients to building blocks which then can be absorbed)
Explain the enzyme regulation overview of covalent reactions.
Reversible and nonreversible!!
Reversible - phosphorylation/dephophorylation… methylation/demethylation
Nonreversible - Removal of C-/N- terminal amino acids
Explain the enzyme regulation of non-covalent reactions.
Allosteric
- uncompetitive
- mixed
Competitive
- always reversible (equilibrium)
FITB
____-_______ and ________ are found in the intracellular realm
non-covalent, and reversible
T or F
The non-reversible modification is only found in the extrecellular realm.
T
T or F
Non-covalent is always reversible because it’s based on equilibrium situations, ligand binding interactions between the regulatory compound and the protein.
T
What is allosteric?
Inhibitor binds in ligand-binding fashion at a specific site that is not the active site
During Intracellular exhume regulation (non-covalent)
FITB
A positive modulator is _____________ (negative modulator is inhibiting)
Activating
The binding of the modulator affects the conformation (shape of both subunits and changes the affinity of the active site for S)
When a proteins conformation changes so does its _____ ______ ______
Change in function
What is an example of covalent, reversible regulation?
Phosphorylase phosphorylation/dephosphorylation
Give an example of intracellular enzyme regulation in a physiological situation.
Glycogen is broken down when the blood glucose levels drops due to use of glucose for energy production (NS, skeletal and heart muscle)
- dropping blood glucose levels —> hormone glucagon activated
- exercise —> hormone epinephrine released
What is the function of kinases?
Transfer phosphate from one molecule to another
What is the function of phosphatases?
Remove phosphate from molecules (releasing inorganic phosphate)
Explain Proteolytic Cleavage.
Involves enzymes that break peptide bonds. Hydrolysis of specific peptide bonds
Inactive precursors of enzymes normally have the prefix _______ and suffix _____
Prefix ‘pro’
Suffix ‘gen’
What do C- and/or N- terminal sequences of amino acids do?
Keep enzyme/protien inactive until they are removed by proteolytic cleavage (hydrolysis of specific peptide bonds); enzymes are proteases or peptidases
What are two examples within the Non-Reversible Enzyme Regulation (Proteolytic Cleavage) that we will be using in this unit?
- proteases in the digestive tract: ex; trypsin (enzyme), chymotrypsin (enzyme) (the trigger is the arrival of food)
- Blood clotting cascade (the natural tigger is injury in the BV; there are pathological triggers, ex; plaques in BV
In the example on slide 32 of proteases of the digestive tract chymotrypsinogen and trypsinogen are?
A. Active precursors
B. Median precursors
C. Regulatory precursors
D. Inactive precursors
D,
Because they end in the suffix ‘-gen’
Look at and explain the diagram on slide 32: proteases of the digestive tract. Understand the situation!!!!
We need a fast activation of an extracellular enzyme in the case of digestive proteases, which, it they were active all the time would actually target our own proteins in cell membranes and would start digesting our intensively tract. THATS WHY we can only have them active in the case of the presence of food.
*digestive proteases are inactive, when there is no food to digest (they would start breaking down our own proteins) —-> the arrival of food in the digestive tract triggers this series of events leading to the activation of digestive proteases.
What are digestive proteases?
Enzymes that break down proteins into smaller peptides and amino acids, facilitating digestion. Essential for various bodily functions, such as building and repairing tissues, producing enzymes and hormones, and supporting immune function.
Examples: pepsin, trypsin, chymotrypsin, carboxypeptidase, aminopeptidase
What is proteases?
Also known as proteinases or peptidases, are enzymes that catalyze the breakdown of proteins into smaller peptides or individual amino acids by cleaving the peptide bonds between the amino acids.
Trypsin and chymotrypsin are digestive proteases and are examples of ____-________ _________ ________ ________ through the removal of C an N-terminal sequences
Non-reversible covalent enzyme regulation
Blood clotting is an example of what enzyme regulation?
And is it intracellular or extracellular?
Non-reversible enzyme regulation
Extracellular
The blood clotting cascade is an example of what?
Non-reversible covalent enzyme regulation through the removal of C- and N- terminal sequences
In the Proteolytic cleavage in the blood clotting process, carboxylase is dependent on what?
Vitamin K-dependent
T or F
The gut microbiome is a major source of vitamin k
T
People who are on blood thinners have to be careful of what?
Not consuming to many green leafy vegetables, because it might mess with the concentration of their blood thinners,
Some blood thinners are vitamin K
A. Agonistic
B. Antagonists
C. Agonists
D. Precursors
B
They competitively bind to the vitamin K binding site on the glutamate carboxylase. Leads to inhibition —> less carboxylation —> less protease activity —> less fibrin formation —> less blood clotting
*antidote for this is more Vitamin K
Most enzymes are _____
Proteins
Tempurture, pH, certain ions, and regulatory measures affect the function of enzymes by
A. Blocking their active site
B. Altering the structure of the substrate
C. Affecting their conformation
D. Increasing or lowering the activation energy
C
*LOOK AT #3 on quiz 2 regarding Mechaelis-Menten kinetics equation and the parts of it
Which of the following types of regulations is non-reversible?
A. Feedback inhibition
B. Competitive inhibition
C.Phosphorylation.dephosphorylation
D. Proteolytic cleavage
D
In _________ inhibition, the structure of the inhibitor resembles the structure of the substrate of the affected enzyme
Competitive
Which of the following types of regulations is typical for extracellular space?
A. Phosphorylation
B. Competitive inhibition
C. Proteolytic cleavage
D. Feedback inhibition
C
Activation of the digestive proteases trypsin and chymotrypsin is an example of ______ regulation
A. Noncovalent, nonreversible
B. Covalent reversible
C. Covalent, nonreversible
D. Noncovalent, reversible
C
T or F
The higher the pH, the higher the enzyme catalyzed reaction rate
F
Warfarin, the active ingredient in the blood-thinning drug ‘coumadin’
A. Inactivates glutamate carboxylase by competitively binding instead of Vitamin K
B. Inhibits the activation of Ca2+ dependent proteases in blood-clotting cascade by chelating Ca2_ and thus making it unavailable as a cofactor
C. Inhibits fibrin molecules from cross-linking to form a blood clot
A
T or F
Enzyme activity is temperature dependent
T
Which portions of the Michaelis-Menten equation are constant?
Km and Vmax
In an inhibition experiment the effect of the inhibitor was to decrease Km and Vmax. This indicates that the mechanism of inhibition is ___________
A. Competitive
B. Mixed
C. Uncompetitive
C
Michaelis-Mentons enzyme kinetics graphs show what curves?
Hyperbolic
Phosphatases catalyze
A. Redox reactions
B. The removal of phosphate groups from organic molecules
C. The transfer of phosphate groups from one molecule to another
B
What is the first law of thermodynamics?
Energy cannot be created or destroyed
Conversion of one form of energy into another always leads to a loss of energy, typically, in the form of heat
What is the 2nd law of thermodynamics?
A highly organised system contains a lot of potential energy while a system that is disorganised (high chaos = entropy) contains a low amount of potential energy
Define metabolism, catabolism, and anabolism within bioenergetics
METABOLISM = CATABOLISM + ANABOLISM
Metabolism - the sum of all biochemical reactions in a cell or organism
BROKEN INTO:
—> Catabolism - the sum of all degradative reactions in a cell or organism
—> the sum of all biosynthetic reactions in a cell or organism
What do energy catabolic pathways do?
Generates energy (ATP, heat) and oxidize carbon (electrons to NAD+, NADP+, and FAD);
LARGE —> SMALL
What do energy anabolic pathways do?
Require energy (ATP) and reduce carbon (electrons from NADH, NADPH, and FADH2)
Small —> Large
Within the oxidation/reduction of carbon the OXIDATION of C would be:
Catabolism
Within the oxidation/reduction of carbon the REDUCTION of C would be:
Anabolism
An anabolic process required more or less energy?
More energy than catabolic
What are the three stages of cellular respiration?
From macronutrient to ATP
Stage 1 - Acetyl-CoA production (protein *amino acids, fats *fatty acids, carbs *glucose)
—> Oxidation of carbon, electrons come from stages 1 and 2
Stage 2 - Acetyl-CoA oxidation (citric acid cycle) *taking out e- to NADH and FADH2
—> Oxidation of carbon, electrons come from stages 1 and 2
Stage 3 - Electron transfer and oxidative phosphorylation into respiratory chain (ETC)
—> Reduction of oxygen
PURPOSE = FORMING ATP PRODUCTION
Give me an overview of glycolysis.
- Means the splitting of sugar
- involves partial oxidation of C
- Small amount of ATP
- Primary source of metabolic energy in some mammalian tissues and cell types (brain, RBC, anaerobic muscle, sperm, …)
-Two phase process - Many enzymes of glycolysis are Mg2+ dependent (magnesium)
During the preparatory phase of glycolysis what are key elements of this phase?
*Phosophorylation of glucose and its conversion to glyceraldehye 3-phosphate
- Staring point is glucose
- Ending point is Glyceraldehyde 3-P
- Glucose (very stable) has to be energetically activated
—> investment of 2 ATP
OVERALL - TWO MOLECULES of glyceraldehyde 3-phosphate are formed; both pass through the payoff phase
Glucose + 2 ATP —> 2 Glyceraldehyde 3-P +2 ADP
During the pay-off phase of glycolysis what are the key elements of this phase?
- Starting point: Glyceraldehyde 3-P
The potential energy of this metabolite can now be reaped:
—> 2 NADH/Glucose
—> 4 ATP/Glucose - End point: Pyruvate
OVERALL - Pyruvate is the end product of the second phase of glycolysis. For each glucose molecule, two ATP are consumed in the preparatory phase and four ATP are produced in the payoff phase, giving a net yield of two ATP and two NADH per molecule of glucose converted to pyruvate. Each of the two molecules of glyceraldehype 3-phosphate derived from glucose under goes oxidation at C-1; some of the energy of this oxidation reaction is conserved in the form of one NADH and two ATP per triode phosphate oxidised.
FORMULA: 2 Glyceraldehyde 3-P —> 2 Pyruvate + 2 ATP + 2 NADH
What is the overall final chemical formula of glycolysis?
Glucose +2 NAD+ + 2 ADP + 2 Pi ——————-> 2 Pyruvate + 2 NADH + 2 ATP
*Glucose gets converted to 2 Pyruvate and under the formation of 2 ATP and 2 NADH. The process requires 2 NAD+ (important to remember to understand fermentation)
T or F
Pyruvate comes from glycolysis (breaking down of glucose)
T
T or F
Acetyl-CoA gets transferred into the Cytric Acid Cycle
T
FITB
Coenzyme A bond in a metabolite makes it more _______
Reactive
FITB
Pantothenic acid is a ___ vitamin
B
Also called B5
What are the four enzymes within glycolysis?
And what are their functions
Kinase - Catalyze TRANSFER of a PHOSPHATE GROUP from one organic molecule to another, usually involving ADP or ATP (most of these are non-reversible)
Phosphatase - Remove a phosphate group, yielding inorganic phosphate
Isomerase - Catalyze the formation of an isomer of the substrate (requires the breaking of a bond, reversible reactions)
Dehydrogenase - Catalyze redox reactions (coenzyme NAD+/NADH, FAD?FADH2 or NADP+/NADPH)
In which stage of glyolysis is the citric acid cycle?
Stage 2, Acetyl-CoA oxidation
*MEMORIZE figure on slide 64. The Krebs Cycle process
Where is this cycle located? What makes up this cycle?
Located - matrix of mitochondria
Made up of:
- 8 intermediates (metabolites)
- 8 enzymes (4 dehydrogenases (2 catalyze an oxidative decarboxylation)
3 NAHD and 1 FADH2 are involved in which stage of glycolysis? And produce what?
Stage 3 and produce ATP
In which stages it carbon completely oxidised to CO2?
Stages 1 and 2
T or F
In stage 3 of oxidative phosphorylation we are going from low potential energy to high potential energy
F
We are going from high potential energy to low potential energy
Oxidative phosphorylation consists of what two processes?
ETC and ATP synthesis
T or F
Oxidative phosphorylation is an intercellular process
F
It takes place on the inner membrane of the mitochondria
What is ubiquinone (lipid)?
An intermembrane electron carrier. Can receive NADH or FADH
What are the four complexes of the ETC?
Membrane proteins that are redox enzymes. Use energy from redox reactions to move protons against the concentration gradient.
What micronutrients are in conjunction with the ETC?
Fe2+ (Iron)
Riboflavin = Vitamin B2
Experiments have determined that it takes ____ number of protons moving through the F0F1 complex for ____ ATP
4 protons
1 ATP
Fatty acids to ATP happen in how many stages? What happens in these stages?
3 stages
1 - B-oxidation: four recurring enzymatic reactions; can process saturated fatty acids
2- CAC (citric acid cycle)
3 - Oxidative phosphorylation
When we break down fat Triacylglycerol uses _______ to form 3 fatty acids + glycerol
Lipases
What breaks down proteins into amino acids?
Proteases
What is the overall yield of ATP per glucose?
ATP per fatty acid?
ATP per amino acid?
30-32 per glucose
Per FA - depends on size. larger FA the more ATP
Per AA- depends on which AA
What is involved in the fermentation reaction?
When does it occur?
- Pyruvate —> Lactate dehydrogenase —> Lactate
- When a cell becomes anaerobic condition (in skeletal muscle) *No mitochondria (RBC)
T or F
Fermentation occurs without oxygen, unlike aerobic respiration which requires oxygen
T
How many net ATP do we get from glycolysis?
2 ATP
What are the micronutrient requirements (vitamins)?
B1 = thiamin —> coenzyme TPP
B2 = riboflavin —> coenzyme FAD
B3 = niacin —> coenzymes NAD+ and NADP+
B5 = pantothenic acid —> coenzyme A
What are the micronutrient requirements (minerals)?
Mg2+ (magnesium)
Fe2+ (Iron) (ETC)
Cu2+ (copper)
What are the names for the Citric acid cycle?
CAC
TCA = tricarboxylic acid cycle
Krebs cycle
Which of the following metabolites is the point of convergence of carbohydrate fat, and protein catabolism for the purpose of ATP production?
A. Pyruvate
B. Acetyl-CoA
C. Citrate
D. Glyceraldehyde 2-phosphate
B
Which of the following coenzymes relies on riboflavin?
A. FAD
B. NADH
C. TPP
D. NAD+
A
Fermentation converts NADH to NAD+ so it can be used in ___________
Glycolysis
The sum of degradative reactions is called
A. Metabolism
B. Anabolism
C. Catabolism
D. Bioenergetics
C
Which of the following is carbon the most oxidized?
A. Alcohol
B. CO2
C. Carboxylic acid
B
Anabolic pathways
A. Require ATP and yield reduced electron carriers
B. Require ATP and reduced electron carriers
C. Yield ATP and reduced electron carriers
B
Citrate is a C_____ compound
6
FITB
_________ catalyze the transfer of phosphate groups from one organic molecule to another
Kinases
In the CAC cycle acetyl-CoA gets combined with __________ to form citrate
A. Succinct
B. A late
C. Oxaloavetate
C
Name processes in which oxidation of carbon occurs.
- Krebs cycle
- Glycolysis
- Beta-oxidation
- PDH (Pyruvate dehydrogenase) complex
Name the function of enzymes.
Lower activation energy (of chemical reactions)
—> catalysis
T or F
Reaction rate depends on substrate concentration
T
Enzyme Inhibitors:
What type of inhibition involves Km increase, and same Vmax?
Competitive
Enzyme Inhibitors:
What type of inhibition involves Km decrease, and decrease Vmax?
Uncompetitive
Enzyme Inhibitors:
What type of inhibition involves Km increase/same, and decrease Vmax?
Mixed (non-competitive)
T or F
Pure competitive inhibition has the same mechanism as mixed inhibitors but was given a separate name because of the two lines intersecting at or near the X-axis
T
Define enzyme inhibitors
Any compound that slows down or inhibits the catalytic activity of an enzyme. Used within a cell to control the activity of enzymes so that each of the thousands of reactions in a living cell proceeds at its appropriate velocity.
What factors can result in an enzyme being denatured?
Temperature and pH affect the secondary and tertiary structure of protiens and in extremes can denature an enzyme. A charge in the pH may cause subtle changes in the enzyme’s overall shape due to changes in hydrogen bonding.
Acetate can be used for…
Energy production (TCA cycle and oxidative phosphorylation)
As a building block for fatty acids, stored in the form of triacylglycerol (fat)
Acetate can be used for…
Energy production (TCA cycle and oxidative phosphorylation)
As a building block for fatty acids, stored in the form of triacylglycerol (fat)
Explain stage 1 of cellular respiration
Oxidation of fatty acids glucose and some amino acids yields acetyl-CoA.
Explain stage 2 of cellular respiration
Oxidation of acetyl groups in the citric acid cycle includes from steps in which electrons are abstracted
Explain stage 3 of cellular respiration
Electrons carried by NADH and FADH2 are funneled into a chain of mitochondrial (or, in bacterium plasma membrane — bound) electron carriers — the respiratory chain — ultimately reducing O2 to H2O. This electron low drives the production of ATP
Explain what elements come out of the process of glucose converting into pyruvate.
*look at metabolism sheet for reference
- Glycolysis!, is a near universal pathway by which a glucose molecule is oxidised, in two phases, to two molecules of pyruvate with energy conserved as ATP and NADH. Ten cytotoxic enzymes act sequentially in glycolysis. The overall reaction converts glucose to two molecules of pyruvate and energy is conserved in the synthesis of two molecules of ATP and two molecules of NADH.
T or F
Glycolysis requires NAD+; without fermentation, cells would run out of it and glycolysis and thus ATP formation would stop
T,
Fermentation serves to regenerate NAD+ which is a crucial coenzyme involved in redox reactions, allowing glycolysis to continue producing ATP in the absense of oxidative phosphorylation (which requires O2)
What is fermentation?
Refers to a metabolic process in which cells generate energy (ATP) through the partial breakdown of organic compounds, typically in the absence of O2.
Explain the three stages of fatty acids to ATP (B-oxidation)
1 - B- oxidation (a long-chain fatty acid is oxidised to yield adeptly residues in the form of acetyl-CoA. This is called B-oxidation)
2- Citric Acid Cycle (the acetyl groups are oxidized to CO2 via the citric acid cycle)
3- Oxidative phosphorylation (electrons derived from the oxidation’s of stages 1 and 2 pass to O2 via the mitochondrial respiratory chain, providing the energy for AATP synthesis by oxidative phosphorylation.
Amino acid catabolism involves what process?
Protein —> “Proteases” —> AA
Role of micronutrients in metabolism
Crucial roles by acting as cofactors or coenzymes in enzymatic reactions, supporting cellular function, and contributing to energy production
Explain dehydrogenase; lactate dehydrogenase; alcohol dehydrogenase
Dehydrogenase refers to a type of enzyme that catalyzes the removal of hydrogen atoms from a substrate molecule.
- Lactate dehydrogenase catalyzes the conversion of lactate to pyruvate, with the reduction of NAD+ to NADH
- Alcohol dehydrogenase facilitates the oxidation of ethanol to acetaldehyde, also reducing NAD+ to NADH in the process
Functioning in oxidation-reduction (redox) reactions
NAD+ and FAD reduce to what?
NADH and FADH2
Acetaldehyde is quickly converted to __________;
This can be used for….
Acetate
Energy production
As a building block for fatty acids, stored in the form of triacylglycerol
In Michaelis-Menten Equation (MM Equation) what does every part of the equation represent?
Example physiological enzyme regulation
- Glycogen is formed and stored when large amounts of carbohydrates are consumed to restore blood glucose homeostatsis
- Glycogen is broken down when the blood glucose levels drops due to use to glucose for energy production (nervous system, skeletal and heart muscle)
*dropping blood glucose levels —> hormone glucagon activated
*exercise —> hormone epinephrine released
Enzyme Regulation Overview:
Non-covalent vs covalent
- Non-covalent regulation involves the binding of molecules (such as substrates, inhibitors, or activators) at the enzyme without any covalent bonding. These are typically reversible. (TYPE: allosteric regulation; substrate binding; competitive inhibition; non-competitive inhibition)
- covalent regulation involves the attachment or removal of covalent bonds (through phosphorylation or other modifications) to the enzyme, leading to a change in its activity. These changes are usually irreversible. (TYPES: Phosphorylation; Dephosphorylation; Acetylation; Ubiquitination; Methylation)
Non-covalent enzyme regulation involves what?
- Allosteric
- Competitve inhibtion
- Feedback
- Mixed inhibition
- Uncompetitive inhibition
Non-reversible enzyme regulation involves?
Removal of C-/N- terminal sequences
Covalent enzyme regulation involves?
Phosphorylation/dephophorylation
Name two enzymes in the preparatory phase of glycolysis
Name the enzymes in the pay-off phase
Hexokinase, phosphfructose
Pyruvate kinase
