• Energy is the ability to do work. What does this mean?

It means energy provides the capacity to move matter against an opposing force, rearrange matter, or power cellular processes (like active transport and chemical synthesis).

• To sustain life, which must be higher? Energy in or Energy out. Explain.

Energy in must be higher. Living systems require a constant input of free energy to maintain order, grow, and reproduce; otherwise, they decay toward thermodynamic equilibrium (death).

• What is metabolism?

The totality of an organism's chemical reactions consisting of catabolic and anabolic pathways.

• What is meant by a metabolic pathway? Be sure to include the term sequential.

A metabolic pathway is a sequential series of chemical reactions where the product of one reaction becomes the substrate for the next, with each step catalyzed by a specific enzyme.

• Metabolic pathways can be catabolic or anabolic. Explain each. Be sure to include how energy is related.

Catabolic pathways break down complex molecules into simpler compounds, releasing energy (e.g., cellular respiration). Anabolic pathways consume energy to build complex molecules from simpler ones, storing energy (e.g., photosynthesis).

• How are Metabolic pathways used by cells as related to energy?

Cells couple catabolic pathways (energy

• When we study energy transformations in matter, what is that called?

Thermodynamics

• What is the first law of thermodynamics?

Energy cannot be created or destroyed, only transferred or transformed.

• Give another example of this law in living organisms besides the squirrel example already given.

A plant converting light energy from the sun into chemical energy stored in glucose during photosynthesis.

• What is the \(2^{nd}\) law of thermodynamics?

Every energy transfer or transformation increases the total entropy (disorder) of the universe.

• Given another example of this law in living organisms besides the squirrel. Be sure to describe heat.

As a human exercises, muscle cells convert chemical energy from ATP into mechanical motion, releasing a significant portion of that energy as unusable heat into the surroundings.

• How do living organisms not violate the \(2^{nd}\) law of thermodynamics?

Organisms are open systems. They decrease their internal entropy (maintaining complex order) by taking in external energy, while increasing the total entropy of their surroundings by releasing heat and metabolic waste.

• Entropy is often classified as "disorder" but what is it really?

A measure of thermal energy dispersal or randomness in a system at a specific temperature.

• Discuss how the phospholipid bilayer is related to entropy.

Hydrophobic tails aggregate together to minimize contact with water. This hydrophobic effect allows surrounding water molecules to remain free and disordered, maximizing the entropy of the water system.

• Discuss how protein folding is related to entropy.

When a protein folds, hydrophobic amino acid side chains are buried inside, releasing ordered water cages surrounding them, which overall increases the net entropy of the aqueous surroundings.

• Life requires order but that is the opposite of entropy. What do we constantly need to maintain homeostasis?

A constant input of energy

• What is meant by Endergonic and Exergonic?

Endergonic is a non

• What does ATP have to do with these concepts?

ATP acts as the energy currency of the cell. It drives endergonic cellular reactions by coupling them with its own highly exergonic hydrolysis.

• Reactions are normally so slow in most cases, they would never allow life to continue in the organism. So... we need ______________ to speed these reactions up.

Enzymes (or biological catalysts)

• Enzymes speed up reactions by lowering what?

Activation energy (\(E_{a}\))

• How do enzymes lower the activation energy?

By stretching or stressing chemical bonds, orienting substrates correctly, providing a favorable microenvironment, or directly participating in the brief covalent bonding of the reaction.

• How do you label a standard enzyme coordinate diagram?

Top curve peak = Activation energy without enzyme; Lower curve peak = Activation energy with enzyme; Left baseline = Energy of substrates; Right baseline = Energy of products; Difference between baseline levels = Change in free energy (\(\Delta G\)).

• What is meant by free energy?

Gibbs Free Energy (\(G\)) is the portion of a system's energy available to perform work when temperature and pressure are uniform.

• What do substrate, active site, and product mean as related to enzymes?

Substrate is the reactant an enzyme binds to; Active site is the specific pocket where the substrate binds; Product is the final molecule produced and released.

• What determines if the substrate is able to react?

The shape, chemical charge, and compatibility of the substrate matching perfectly with the active site of the enzyme, alongside overcoming the activation energy barrier.

• What is meant by induced fit of the substrate?

Upon binding, the enzyme undergoes a slight conformational change around the substrate to hug it more tightly and enhance catalysis.

• Enzymes have specificity and are reusable. Explain.

Specificity means an enzyme interacts only with a single type of substrate due to its unique shape. Reusable means enzymes are not consumed or permanently altered and can repeat the process immediately.

• What macromolecule is an enzyme?

Protein (except for ribozymes, which are RNA).

• How can I recognize something is an enzyme by the name?

It typically ends with the suffix "

• What does a catabolic enzyme reaction look like?

Enzyme + 1 single large substrate \(\rightarrow \) Enzyme

• What does an anabolic enzyme reaction look like?

Enzyme + 2 or more separate small substrates \(\rightarrow \) Enzyme

• What is a cofactor? What are they made of typically?

Non

• What is denaturation? How is enzyme affected?

The unfolding or disruption of a protein's structure where it loses its specific 3D shape, meaning the active site can no longer bind the substrate, making it nonfunctional.

• What does change in temperature (particularly heat) specifically do to the enzyme?

Excessive heat increases kinetic energy, causing the protein molecules to vibrate rapidly, which breaks fragile hydrogen and ionic bonds, denaturing the enzyme.

• What things can a change in the pH do specifically to the enzyme?

Altering pH adds or removes \(H^{+}\) ions, changing charges on amino acid side chains, which breaks ionic attractions and hydrogen bonds, disrupting the enzyme's shape.

• What are some examples of chemicals that also cause denaturation?

Strong acids, strong bases, heavy metal ions (such as lead or mercury), and organic solvents (like alcohol or urea).

• Is denaturation permanent in all cases? Explain.

No. If the denaturing agent is removed and the primary sequence is unharmed, some can undergo renaturation and refold; however, severe denaturation (like cooking an egg) is permanent.

• How does change in substrate concentration affect the rate of reaction? Explain.

Increasing substrate concentration increases the reaction rate because collisions between substrates and active sites happen more frequently, up until a maximum limit.

• What is substrate concentration saturation?

The point where every available enzyme's active site is continuously occupied by substrate; adding more substrate will not increase the rate of reaction anymore (\(V_{max}\)).

• Cells can regulate the activity of enzymes in what 2 ways?

1. Controlling the synthesis/production of the enzyme (gene expression). 2. Directly regulating the activity of existing enzymes (via inhibitors, activators, or allosteric modulators).

• What is meant by inhibitor?

A molecule that binds to an enzyme and decreases its catalytic activity.

• Which type of inhibitor binds directly in the active site? Can this be reversed?

Competitive inhibitor. Yes, it can be reversed by significantly increasing the concentration of the substrate.

• Which type of inhibitor binds to an alternative site "

not" the active site? Can this be reversed?

• What is an alternative site (not the active site) called?

Allosteric site

• How does an allosteric site work to prevent substrates from binding?

Binding to the allosteric site causes a global conformational change in the enzyme's structure, distorting the active site shape so it can no longer fit the substrate.

• What types of inhibitors are permanent?

Irreversible inhibitors, which form strong covalent bonds with functional groups inside the enzyme's structure (e.g., penicillin, cyanide, or nerve gases).

• Allosteric sites can also have activators (not inhibitors). What is meant by this?

An allosteric activator binds to a regulatory site and stabilizes the functional, open conformation of the enzyme's active sites, enhancing substrate affinity.

• What does an enzyme kinetics graph show regarding inhibitors?

A normal enzyme reaches \(V_{max}\) quickly; a competitive inhibitor delays it but reaches the same \(V_{max}\) with enough substrate; a noncompetitive inhibitor lowers \(V_{max}\) permanently.

• What is feedback inhibition?

A cellular regulatory mechanism where the final end

• What is the optimal pH and working range for Salivary amylase?

Optimal pH is around 7 (neutral); working range is approximately pH 4.5 to pH 8.5.

• What is the temperature range for Salivary amylase and what happens after 60°C?

It works from roughly 28°C to 65°C; after 60°C, the rate drops to zero because high heat breaks internal bonds, causing the enzyme to denature.

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