Bio 121 Unit 2 Energy, Enzymes and Metabolism

Energy
Ability to promote change or do work
Associated with movement;
Kinetic Energy
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Due to structure or location;
Potential Energy
Energy in molecular bonds, in form of potential energy;
Chemical Energy
Energy can neither be created nor destroyed. But it can be transferred from one type to another;
First Law of Themodynamics
Transfer of energy from one form to another increases entropy of a system;
Second Law of Themodynamics
Less energy is available for organisms to use to promote change.
What is the problem with increasing entropy?
Change in free energy
What determines the direction of chemical rxn?
Total Energy = Usable Energy + Unusable Energy
Total Energy = ?
Energy Transformations involve an increase in entropy (disorder that cannot be harnessed to do work)
Amount of Energy available to do work, G
Gibbs Free Energy
H = Enthalpy or Total Energy;
G = Free Energy or Amount of Energy for Work;
T = Absolute Temperature in K
S = Entropy or Unusable Energy;
H = G + TS Name the constituents?
Without input of additional energy;
Can be either fast or slow;
Ex: Breakdown of sucrose to CO2 and H2O is spontaneous, but will take a long time for sugar in a sugar bowl to break down;
How do spontaneous rxns occur?
Delta G is negative;
Rxn is exergonic;
Is delta G positive or negative in spontaneous rxns?
Spontaneous Rxn;
ΔG<0 (negative free energy change); Energy is released by reaction;
Exergonic Rxn
Not spontaneous Rxn;
ΔG>0 (positive free energy change);
Requires addition of energy to drive reaction;
Endergonic Rxn
ΔG = -7.3 kcal/mole;
Reaction favors formation of products;
The energy liberated is used to drive a variety of cellular processes;
Hydrolysis of ATP
To drive rxns;
An endergonic reaction can be coupled to an exergonic reaction;
The reactions will be spontaneous if the net free energy change for both processes is negative;
What do cell need Hydrolysis of ATP for?
Many Proteins Bind ATP and Use That ATP as a Source of Energy
Each ATP undergoes 10,000 cycles of hydrolysis and re-synthesis every day;
How many cycles of hydrolysis does 1 ATP undergo?
On average, 20% of all proteins bind ATP;
Likely an underestimate because there may be other types of ATP-binding sites;
This illustrates the enormous importance of ATP as an energy source;
What percentage of proteins bind ATP?
Particular amino acid sequences in proteins function as ATP-binding sites;
What part of protein function as ATP binding sites?
The energy to synthesize ATP comes from
chemical reactions that are exergonic.
ADP + P = ATP (energy needs to be put in to synthesize)
Where does the energy to synthesize ATP come from?
ATP hydrolysis provides the energy to drive
cellular processes that are endergonic.
ATP => hydrolysis = ADP + P
What provides energy to drive cellular processes?
an agent that speeds up the rate of a chemical reaction without being consumed during the reaction;
Catalyst
Protein catalysts in living cells;
Enzymes
RNA molecules with catalytic properties;
Ribozymes
Initial input of energy to start reaction;
Allows molecules to get close enough to cause bond rearrangement;
Activation energy
Can now achieve transition state where bonds are stretched;
What happens after Activation Energy is there?
Large amounts of heat;
Using enzymes to lower activation energy;
Common ways to overcome activation energy:
1. Straining bonds in reactants to make it easier to achieve transition state;
2. Positioning reactants together to facilitate bonding;
3. Changing local environment;
4. Direct participation through very temporary bonding;
How do enzymes lower activation energy?
Location where reaction takes place;
Active site
Reactants that bind to active site;
Substrates
Formed when enzyme and substrate bind;
Enzyme-substrate complex
Enzymes have a high specificity for their substrate;
Metaphor for substrate and enzyme binding – only the right key (substrate) will fit in the lock (enzyme);
“Lock and Key”
Interaction also involves conformational changes;
Induced fit phenomenon
Plateau where nearly all active sites are occupied by substrate;
Saturation
Velocity of reaction near maximal rate;
Y-Intercept;
Vmax
Substrate concentration where velocity is half maximal value;
Inversely related to affinity between enzyme and substrate;
Michaelis constant, KM
High KM enzyme needs higher substrate concentration;
X-Intercept
High Km Value
Molecule binds to active site
Inhibits ability of substrate to bind
Apparent KM increases – more substrate needed
Competitive inhibition
Lowers Vmax without affecting Km
Inhibitor binds to allosteric site, not active site;
Noncompetitive inhibition;
Small molecules permanently attached to the enzyme;
Prosthetic groups
Usually inorganic ion that temporarily binds to enzyme;
Cofactor
Organic molecule that participates in reaction but is left unchanged afterward;
Coenzyme
Most enzymes function maximally in a narrow range of temperature and pH;
Effect of pH and T on enzyme activity
Until 1980s, scientists thought all biological catalysts (enzymes) were proteins
Ribonuclease P (RNase P) is found in all living organisms, and involved in cleaving tRNA molecules;
Discovery of Ribozymes;
Ribonucleoprotein, with an RNA subunit and a protein subunit;
Experiments found the RNA subunit alone is able to cleave substrate;
The RNA is a true catalyst - it accelerates rate without being altered itself;
RNase P
Chemical reactions occur in metabolic pathways;
Each step is coordinated by a specific enzyme;
Metabolic Pathway
Breakdown cellular components;
Exergonic;
Catabolic pathways;
Synthesis cellular components;
Endergonic;
Must be coupled to exergonic reaction;
Anabolic pathways;
Breakdown of reactants;
Used for recycling building blocks;
Used for energy to drive endergonic reactions;
Energy stored in intermediates such as ATP, NADH;
Catabolic reactions
1. Substrate-level phosphorylation
2. Chemiosmosis
Two ways to make ATP
Enzyme directly transfers phosphate from one molecule to another molecule;
Substrate-level phosphorylation
Energy stored in an electrochemical gradient is used to make ATP from ADP and Pi;
Chemiosmosis
Electron removed from one molecule is added to another;
OIL RIG;
Redox reaction
A is oxidized, B is reduced
Ae- + B → A + Be-
Which is oxidized and which is reduced?
Electrons removed by oxidation of organic molecules are used to create energy intermediates like NADH;
NAD+ Nicotinamide adenine dinucleotide;
NADH – what is it?
1. Releases a lot of energy when oxidized that can be used to make ATP
2. Can donate electrons during synthesis reactions to energize them;
2 ways to use NADH
Biosynthetic reactions;
Make large macromolecules or smaller molecules not available from food;
Require energy inputs from intermediates (NADH or ATP) to drive reactions;
Anabolic reactions
Turn genes on or off;
Gene regulation
Cell-signaling pathways like hormones;
Cellular regulation
Product of pathway inhibits early steps to prevent over accumulation of product;

If the concentration of the final product becomes high,
it will bind to enzyme 1 and cause a conformational
change that inhibits the enzyme’s ability to convert the
initial substrate into intermediate 1.

Feedback inhibition
Most large molecules exist for a relatively short period of time;
All living organisms must efficiently use and recycle organic molecules;
Recycling of Organic Molecules
Time it takes for 50% of the molecules to be broken down and recycled;
Half-life
Conserve energy by degrading mRNAs for proteins no longer required;
Remove faulty copies of mRNA;
What is mRNA degradation important?
Enzymes cleave off nucleotides from end
Exonucleases in mRNA degradation
Multiprotein complex uses exonucleases;
Exosome in mRNA degradation
A large complex that breaks down proteins using protease enzymes;
Proteasome
Proteases cleave bonds between amino acids;
Proteases
Ubiquitin tags target proteins to the proteasome to be broken down and recycled;
Ubiquitin
1. Degrade improperly folded proteins;
2. Rapidly degrade proteins to respond to changing cell conditions;
Ubiquitin tagging allows the cell to….what?
1. Lysosomes contain hydrolases to break down proteins, carbohydrates, nucleic acids, and lipids;
2. Digest substances taken up by endocytosis;
Lysosomes
Recycling worn out organelles using an autophagosome;
Autophagy
1. Membrane tubule begins to enclose an organelle;
2. Double membrane completely encloses an organelle to form
an autophagosome.
3. Autophagosome fuses with a lysosome. Contents are degraded
and recycled back to the cytosol.
How does Lysosome work?
Potential energy
Q1: Water held behind a dam would best reflect ______.
heat energy
mechanical energy
chemical energy
potential energy
kinetic energy
Nitrogen.
Q2: All of the following are a form of potential energy that can be used by a cell EXCEPT:
concentration gradient.
an electrical/ion gradient.
NADH.
ATP.
nitrogen.
Energy cannot be created or destroyed.
Q3: An autotroph captures energy from other sources and does not actually produce energy because ____.
once energy is created it can be destroyed.
the transfer of energy increases the disorder of a system.
kinetic energy is based on location.
energy cannot be created or destroyed.
the transfer of energy increases entropy.
Free energy.
Q4: The amount of available energy that can be used to do work is called
The reaction will yield energy and is spontaneous. (Thx, Dr. Lee)
Q5: What would you predict about a reaction that has a ΔG Picture 0?
It has a change in free energy that is greater than 0.
Q6: What would your predict about the reaction: Pi + ADP –> ATP?
ΔG = +8 kCal
Q7: A reaction that has a _____ would require being coupled to the hydrolysis of at least two ATP molecules (ΔG = -14.6 kCal) in order to occur.
ΔG = -8 kCal
ΔG = -14.6 kCal
ΔG = +16 kCal
ΔG = +8 kCal
ΔG = -16 kCal
endergonic.
Endergonic – not spontaneous, G>0, requires an addition of free energy from environment;
Q8: A chemical reaction that has a positive ΔG is correctly described as
the reaction proceeds with a net release of free energy.
Q9: In ALL exergonic reactions, ___.
some reactants will be converted to products.
the products have more total energy than the reactants.
the reactions are nonspontaneous.
the reaction proceeds with a net release of free energy.
a net input of energy from the surroundings is required for the reactions to proceed.
Every chemical reaction must increase the total entropy of the universe.
Q10: A logical consequence of the second law of thermodynamics could be stated, ___.
A. if the entropy of a system increases, there must be a corresponding decrease in the entropy of the universe.
B. every chemical reaction must increase the total entropy of the universe.
C. if there is an increase in the energy of a system, there must be a corresponding decrease in the energy of the rest of the universe.
D. energy can be transferred or transformed, but it cannot be created or destroyed.
E. every energy transfer requires activation energy from the environment.
Once the enzyme binds A and B it goes through a conformational change.
Q11: If an enzyme catalyzes the reaction A + B –> C, then _____.
A. once the enzyme binds A and B it goes through a conformational change.
B. the enzyme energizes A and B to make them more reactive.
C. the active site of the enzyme binds C more tightly than A and B.
D. the enzyme will also catalyze the reaction C –> A + B
E. the enzyme could also convert A + B to another molecule D.
It lowers the activation energy of a reaction.
Q12: How does an enzyme work to catalyze a reaction?
A. It allows the reaction to proceed through different intermediates.
B. It supplies the energy to speed up a reaction.
C. It lowers the activation energy of a reaction.
D. It raises the temperature of a reaction.
E. It increases the concentration of the reactants in a reaction.
still -5 kcal/mole
Q13: If one were to double the amount of enzyme in a reaction with an initial ΔG of -5 kcal/mole, what would the ΔG be?
Prevent the substrate from binding the enzyme’s active site.
Q14: Altering the three-dimensional structure of an enzyme might
Reduce the energy of activation and increase the rate of a reaction.
Q15: The primary function of an enzyme or any biological catalyst is to
By using a catalyst.
Q16: How can a living cell increase the rate of a chemical reaction?
Enzymes in the cell catalyze the breakdown of glucose.
Q17: A bowl of sugar water is very stable. But if you feed it to cells it is rapidly broken down into carbon dioxide and water. What is the best explanation for this observation?
pH
Q18: The charge on amino acids in the active site of an enzyme would be affected by ___.
Anabolism;
Q19: In photosynthesis, carbon dioxide gas is reduced and combined to form glucose. This is an example of…
Endergonic;
Q20: Once ATP donates its phosphate to a coupled reaction it becomes ADP. The ADP can be converted back to ATP in a(an) ____ reaction.
removed by oxidation and stored in NADH
Q21: In a catabolic reaction, electrons from food are…
Is an exergonic reaction.
Q22: The reaction phosphoenolpyruvate + ADP ?? pyruvate + ATP (ÄG = -7.5 kcal/mole)
Molecule A is oxidized and molecule B is reduced.
Q23: In the reaction A- +B →A + B-, ____
Catabolism
Q24: The process of breaking glycogen down to glucose is an example of: ____.
Negative feedback
Q25: Your liver produces 90% of the cholesterol found in your body. When cholesterol levels get too high, the first enzyme in the pathway of cholesterol synthesis is inhibited. This is an example of:
Competitive inhibitor
Q26: You measure the amount of enzyme activity in the presence of compound X and note that as you add more substrate the amount of enzyme activity increases. This indicates that the compound X is a _____ .
Proteasome
Q27: Protein degradation in eukaryotes is performed by ____.
Recognizes improperly folded proteins and targets them for degradation.
Q28: Ubiquitin ____.
Unfolded proteins with ubiquitin attached
Q29: _____ will accumulate if a cell is treated with a proteasome inhibitor.
Ribosomes and proteasomes
Q30: The primary complexes for protein synthesis and degradation in eukaryotes are _____ and _____ respectively.
Glycogen must be broken down to glucose to be used in metabolism.
Q31: Patients with McArdle’s Disease lack an enzyme in their livers that catabolizes glycogen. These individuals tire easily during exercise. Which of the following would best explain this symptom?
Have lower blood glucose levels because they cannot break down glycogen.
Q32: Patients with McArdle’s Disease lack an enzyme in their livers that catabolizes glycogen. Compared to an unaffected individual you would predict that a patient with McArdle’s disease would ______.
Have an enlarged liver because they accumulate glycogen.
Q33: Patients with McArdle’s Disease lack an enzyme in their livers that catabolizes glycogen. Compared to an unaffected individual you would predict that a patient with McArle’s disease would ______.
An accumulation of old or damaged mitochondria
Q34: Patients with Parkinson’s Disease have been shown to have a block in the movement of autophagosomes towards lysosomes. Predict a condition that could result from this defect?
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