1. Chapter 6 - Metabolism
Energy and Enzymes

2. Living things need to acquire energy; this is a characteristic of life.
Energy is the ability to do work.
Cells use acquired energy to:
- Maintain their organization
- Carry out reactions that allow cells to develop, grow, and reproduce

3. Forms of Energy There are two basic forms of energy.
Kinetic energy is the energy of motion.
Potential energy is stored energy.
Food eaten has potential energy because it can be converted into kinetic energy.
Potential energy in foods is chemical energy.
Organisms can convert chemical energy into a form of kinetic energy called mechanical energy for motion.

4. Two Laws of Thermodynamics
The flow of energy in ecosystems occurs in one direction; energy does not cycle.
The two laws of thermodynamics explain this phenomenon.
First Law: Energy cannot be created or destroyed, but it can be changed from one form to another.
Second Law: Energy cannot be changed from one form to another without loss of usable energy.

5. Flow of energy
The plant uses solar energy to produce the organic nutrients taken in by the moose. All of the solar energy absorbed by the plant eventually dissipates as heat, and therefore energy does not cycle; rather it flows through living things and their cells.

6. When energy transformations occur, energy is neither created nor destroyed but there is always loss of usable energy, usually as heat.
For this reason, living things depend on an outside source of energy.
The ultimate source of energy for life is the sun, and this energy is passed from plants to animals.

7. Metabolic Reactions and Energy Transformations
Metabolism is the sum of all the chemical reactions that occur in a cell.
Reactants are substances that participate in a reaction; products are substances that form as a result of a reaction.
Biologists use the term “free energy” instead of entropy for cells.
Free energy, G, is the amount of energy to do work after a reaction has occurred.

8. ATP (adenosine triphosphate) is the energy currency of cells.
ATP is constantly regenerated from ADP (adenosine diphosphate) after energy is expended by the cell.
1) ATP is used in many types of reactions.
2) When ATP is converted to ADP + P, the energy released is sufficient for cellular needs and little energy is wasted.

9. The ATP cycle
In cells, the exergonic breakdown of glucose is coupled to the buildup of ATP, and then the exergonic breakdown of ATP is coupled to endergonic reactions in cells. When a phosphate group is removed by hydrolysis, ATP releases the appropriate amount of energy for most metabolic reactions. The high-energy content of ATP comes from the complex interaction of the atoms within the molecule.

10. Coupled Reactions
In coupled reactions, energy released by hydrolyzing ATP drives the conversion of substrates to products.

11. The breakdown of ATP is exergonic
The breakdown of ATP is exergonic. Muscle contraction is endergonic and therefore cannot occur without an input of energy. Muscle contraction is coupled to ATP breakdown, making the overall process exergonic. Now muscle contraction can occur.
Only 30% of the free energy of glucose is transformed to ATP; the rest is lost as heat.

12. Summary of ATP functions
ATP is used for:
Chemical work – ATP supplies energy to synthesize macromolecules, and in turn, build the organism
Transport work – ATP supplies energy needed to pump substances across the plasma membrane
Mechanical work – ATP supplies energy for cellular movements
Cellular movements include muscle contraction, movement of cilia and flagella, movement of chromosomes, and so forth.

13. Metabolic Pathways and Enzymes
Cellular reactions are usually part of a metabolic pathway, a series of linked reactions, illustrated as follows:
E E E E E5 E6
A → B → C → D → E → F → G
The letters A-G represent substrates and products
E1-E6 represent enzymes.
Metabolic pathways may be branched.

14. An enzyme is a protein molecule that functions as an organic catalyst to speed a chemical reaction.
An enzyme brings together particular molecules and causes them to react.
The addition of an enzyme does not change the free energy of the reaction, rather an enzyme lowers the energy of activation.
The reactants in an enzymatic reaction are called the substrates for that enzyme.

15. Every reaction in a cell requires a specific enzyme.
Enzymes are named for their substrates:
Substrate Enzyme
Lipid Lipase
Urea Urease
Maltose Maltase
Ribonucleic acid Ribonuclease
Enzymes can be synthetic (anabolic) and degradative (catabolic)

16. An enzyme has an active site, where substrates and enzyme fit together in such a way that the substrates are oriented to react. Following the reaction, the products are released and the enzyme is free to act again. Some enzymes carry out degradation; the substrate is broken down to smaller products.

17. Some enzymes carry out synthesis; the substrates are combined to produce a larger product.

18. An enzyme is a protein that catalyzes biochemical reactions.
Enzyme – Substrate Complex
An enzyme is a protein that catalyzes biochemical reactions.

19. Enzymes are very specific and catalyze only one type of reaction.
Enzymes work best over very specific pH and temperature ranges
Enzymes are very efficient at their task, which is reaction rate enhancement.
Nomenclature
Originally enzymes were named by adding –ase to the reactants.
A more systematic system has arisen, but we are not covering it in any detail. A full explanation is given in your text.

20. Enzymes are proteins and as such have a definite three-dimensional shape. This shape is the key to enzyme catalysis.
The reactant is called the substrate.
The active site is where the actual reaction will occur.
An oversimplified explanation is that the enzyme and substrate have certain shapes that must be complimentary. The specificity of an enzyme can be explained in this manner. This is referred to as the lock and key theory.
LOCK
KEY

21. Some enzymes can work with different substrates and will change its shape to accommodate the substrate. This is referred to as the induced-fit model.

22. Temperature and pH
As the temperature rises, enzyme activity increases because more collisions occur between enzyme and substrate.
If the temperature is too high, enzyme activity levels out and then declines rapidly because the enzyme is denatured.
Each enzyme has an optimal pH at which the rate of reaction is highest.
A denatured protein is one that has undergone a change in shape and can no longer function normally. A change in pH can alter the ionization of these side chains and disrupt normal interactions, and under extreme conditions of pH, denaturation eventually occurs.

23. Rate of an enzymatic reaction as a function of temperature and pH
At first, as with most chemical reactions, the rate of an enzymatic reaction doubles with every 10C rise in temperature. In the graph on the left, the rate of reaction is maximum at about 40C; then it decreases until the reaction stops altogether, because the enzyme has become denatured. In the right graph, pepsin, an enzyme found in the stomach, acts best at a pH of about 2, while trypsin, an enzyme found in the small intestine, performs optimally at pH of about 8. The shape enables these proteins to bind with their substrates is not properly maintained at other pHs.

24. pH Enzymes usually work in a narrow pH range.
pH optimum: pH at which each enzyme exhibits peak activity.
this reflects the pH of the body fluid in which the enzyme is found.

25. Other Factors Affecting Enzyme Action
Cofactors – (inorganic) can be a metal ion such as Cu, Zn, Fe
Coenzymes - organic plugin to an enzyme. The plugin is mostly made of vitamins
Substrate concentration – when all the enzymes are involved with substrates, the rate of reaction reaches a plateau.
Temperature can affect the reaction rate by providing too much or too little energy.
The pH must be stable in order to maintain the tertiary and quaternary structures.

26. Cofactors and Coenzymes
Needed for the activity of certain enzymes.
Cofactor:
Ions (Ca++, Mg++, etc.)
often transform and turn on the active site.
help bind the substrate
Coenzyme:
derived from vitamins
participate in the rxn
ALLOSTETIC SITE

27. Vitamin Deficiencies cause Diseases
Vitamin C - Scurvy
Niacin (B3)- Pellagra (Skin Disease)
Vitamin D - Rickets
Vitamin A - Night Blindness
Vitamin K - Blood clotting problems

28. Substrate Concentration
- Maximum rate occurs when enzyme is saturated.
- Additional substrate does not increase reaction rate.

29. Inhibiting Enzymes A) Competitive Inhibition
occurs when an active enzyme is prevented from combining with its substrate because a competitive substrate latches on. Some poisons work this way. Cyanide poisons human enzymes, Penicillin poisons bacterial enzymes. Antifreeze (wood alcohol) poisons enzymes of the liver, etc.

30. Inhibiting Enzymes B) Non-competitive Inhibition
inhibitor does not resemble the substrate
does not compete for active site binding but attaches to the enzyme and changes the shape of the active site
no competition with the substrate occurs
addition of more substrate cannot overcome this type of inhibitor
Ex ---> Lead Poisoning // Mercury Poisoning

31. Control of enzymes
A cell regulates which enzymes are present or active at any one time.
Genes must be turned on or off to regulate the quantity of enzyme present.
Another way to control enzyme activity is to activate or deactivate the enzyme.
- feedback regulation
- covalent modification
- phosphorylation

32. Oxidation-Reduction Reactions
Oxidation is the loss of electrons.
Reduction is the gain of electrons.
Because oxidation and reduction occur simultaneously in a reaction, such a reaction is called a redox reaction.
Oxidation also refers to the loss of hydrogen atoms, and reduction refers to the gain of hydrogen atoms in covalent reactions in cells.
A hydrogen atom contains one proton and one electron; therefore, when a molecule loses a hydrogen atom, it has lost an electron, and when a molecule gains a hydrogen atom, it has gained an electron.

33. Consider NaCl
Oxidized – loses electrons
Reduced – gains electrons

34. Oxidation-reduction reactions are exemplified by the overall reactions of photosynthesis and cellular respiration.
The pathways of photosynthesis and cellular respiration permit the flow of energy from the sun though all living things.

35. Photosynthesis (in Chloroplast)
6CO2 + 6H2O + energy → C6H12O6 + 6O2
During photosynthesis, hydrogen atoms are transferred from water to carbon dioxide, and glucose is formed.
water has been oxidized (ripped apart for electrons
carbon dioxide has been reduced. The electrons were used to put glucose together
Energy to form glucose comes from the sun.

36. Cellular respiration (Mitochondria)
C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy
It is opposite that of photosynthesis
In this case,
- glucose is oxidized (torn apart) (to CO2)
- oxygen is reduced (gets electrons to make) (to water).
The complete oxidation of a mol of glucose releases 686 kcal of energy that is used to synthesize ATP.
If the energy within glucose were released all at once, most of it would be dissipated as heat. Instead, cells oxidize glucose slowly, and gradually use the energy to synthesize ATP molecules.

37. For photosynthesis, chloroplasts capture solar energy and use it to convert water and carbon dioxide into carbohydrates that provide food for other living things.
Cellular respiration, the breakdown of glucose into carbon dioxide and water, occurs in mitochondria.
It is the cycling of molecules between chloroplasts and mitochondria that allows a flow of energy from the sun through all living things.

38. Relationship of chloroplasts to mitochondria
Chloroplasts produce energy-rich carbohydrates. These carbohydrates are broken down in mitochondria, and the energy release is used for the buildup of ATP. Usable energy is lost due to the energy conversions of photosynthesis and cellular respiration. Then, when ATP is used as an energy source, all usable energy is converted to heat.