BIO151 Concepts of Biology Study Guide Chapter 8 Metabolism

Dr. Elizabeth Rhoads

Preparation for Class

Instructions Before class, read Chapter 8 from page 142 to 159 Then complete the questions given below. Be prepared to share these answers in class. Question 1 What is metabolism and what are metabolic pathways? Question 2 What is potential energy and kinetic energy, in the context of a person about to jump into a lake (figure 8.2)? What is potential energy and kinetic energy, in the context of a molecule that becomes broken into smaller parts (figure 8.5c)? Question 3 What is the difference between the setup shown in Figure 8.7 part A and part B? Why is B said to be open? How does this relate to a living organism? Question 4 What are the three main types of work performed by cells? (see page 149) Is energy needed to make these processes happen? Question 5 What is ATP? Does it look like any of My answer

My answer Jumping into a lake: Molecule is broken up:

My answer

My answer

My answer

the monomers described in chapter 5? Question 6 Using as much of the biochemical terminology from chapter 5 as possible, describe what is an enzyme? Question 7 What is an active site? What function does it serve? Question 8 Using sucrase as an example of an enzyme (Figure 8.17), what are the six stages in the catalytic cycle of an enzyme? My answer

My answer

My answer 1. 2. 3. 4. 5. 6.

Question 9 Why would denaturing the polypeptide(s) used to build an enzyme cause the enzyme activity to change?

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Class Materials
Slide 2 Metabolism = Entire set of chemical reactions inside an organism or a cell. Best divided into metabolic pathways Catabolic Degrade macromolecules for energy. Anabolic Synthesize macromolecules using energy. Energy is also used to power My notes Metabolic pathways -catabolic- processes produce energy->breakdown sugar -anabolic- Require energy>synthesize polymers -movement or transportation Enzymes help to speed up process.

movement or transportation of molecules. Metabolism frequently involves transformation of energy: Potential energy D Kinetic energy For this course, its best to think of potential energy as the energy that is locked away in the electrons that make up covalent bonds of organic molecules like glucose. Kinetic energy can be thought of as something on the move such as rapidly moving molecules or electrons freed from a bond. Slide 3 Forms of Energy Kinetic Thermal Potential Chemical

Energy- capacity to cause change o Can be used to do work o Ability to re-arrange matter Kinetic Energy o Energy of motion o Thermal energy (heat) Potential Energy o Possessed by matter due to its location or structure o Chemical energyavailable for release in chemical reaction

Slide 4 Laws of Energy Transformation Transformation of energy from one form to another form happens a lot in biology. Such transformations obey the universal laws of thermodynamics: 1. First Law: We can transfer energy and transform it, but energy

My notes First Law= energy is always conserved. (energy cannot be created or destroyed!) Second Law= entropy (randomness) always increases. Energy is lost from biological system-cheetah eats to obtain energy but when running loses energy by heat-increases entropy.

cannot be created or destroyed. Energy is always conserved 2. Second Law: We can transfer energy and transform it, but as we do so, we increase the randomness of the universe. Entropy (degree of randomness) increases Slide 5 1. Does life violate the second law of thermodynamics? 2. Are living organisms made of matter that becomes increasingly random over time? 3. If life is made of highly-ordered molecular structures, how can we continue to survive without violating the second law of thermodynamics? Slide 6-7 Free Energy = Amount of available energy that can be used to do work. Also known as G. In this chapter we will see changes in the level of G from the start of a chemical reaction and the end. In other words we are interested in the change, or delta G ( G). Exergonic reactions release energy. e.g. Catabolism of glucose: G = -686 kcal/mol If the G is negative, it will occur spontaneously (on its own). Endergonic reactions take-in energy. e.g. Anabolism of glucose: My notes Glucose has a high G CO2 and H2O have a lower G Actual delta G is = -6.86 kcal/mol (amount of energy given off-amt. available for work. Exergonic reaction o Net releases of free energy o Spontaneous o Represents amount of work the reaction can perform Endergonic Reaction o Energy required for reaction o Non-spontaneous (must add energy to make happen-not on its own bec. Must have input of My notes 1. 2. 3.

 G = +686 kcal/mol If the G is positive, the reaction is non-spontaneous (it will not occur on its own). In any spontaneous chemical reaction, the free-energy decreases and G is negative. Slide 8 Adenosine Triphosphate (ATP) This is a nucleotide. Like other nucleotides this could be used to make a nucleic acid. However, this nucleotide has a very special function. Like any nucleotide, its made of three parts: A pentose sugar: Ribose A nitrogenous base: Adenine Phosphate groups: Three phosphates containing a lot of potential energy.

energy) o Free energy becomes stored in molecules Open Vs. Closed System Closed system: will reach equilibrium No more work can be done My notes Contains three phosphate groups that contain a lot of potential energy. When we add water (hydrolysis)we lose a phosphate 3 types of cellular work ATP is used for: o Chemical (endergonic reactions) o Active transport o Mechanical(muscles, cilia)

ATP is used to couple exergonic reactions to endergonic reactions. In other words it carries energy given out by exergonic reactions and it uses the energy to enable endergonic reactions to occur. A Slide 9 My notes Hydrolysis of ATP When we add water The breakdown of ATP (hydrolysis) (hydrolysis) we lose a phosphate releases a lot of energy. Hydrolysis of ATP yields adenosine diphosphate (ADP) and inorganic phosphate (Pi contains only phosphorus and oxygen; No carbon). Energy to add Pi back to ADP comes from catabolic pathways (e.g. glucose breakdown). ATP is quickly regenerated.

The addition of Pi to a molecule is called phosphorylation. The removal of Pi from a molecule is called dephosphorylation. Slide 10 Example of Energy Coupling From Figure 8.10: ATP hydrolysis is used to drive the conversion of glutamate to glutamine. Both of these substances are amino acids and we need both to survive. How can we make glutamine? Without ATP the creation of glutamine requires energy ( G = +3.4 kcal/mol) and is therefore non-spontaneous. This is not going to happen! By phosphorylating glutamate, to create a phosphorylated intermediate, the creation of glutamine with ATP becomes a spontaneous reaction ( G = -3.9 kcal/mol). This chemical reaction does happen, and it actually releases a small amount of energy (heat). Slide 11 Regeneration of ATP Fig 8.12 My notes If delta G of an endergonic reaction is less than amt of energy released by ATP hydrolysis, then the 2 reactions can be coupled Overall net delta G=exergonic When ATP helps for these chemical reactions to occur=coupling

ATP is a renewable resource Endergonic o Free-energy is required to phosphorylate ADP o Comes from exergonic reaction in cells

Slide 12 My notes Activation Energy Energy required to break bonds Spontaneous chemical reactions are at the beginning of reaction those that are very likely to occur, on Rate of reaction-is tied to the their own. activation energy

Sucrose + H2O Glucose + Fructose G = - 7 kcal/mol Although this is an exergonic, spontaneous reaction (the G is negative) - it can take a very long time to happen (years). Simply saying that a reaction is spontaneous does not tell us how fast the reaction is going to occur! In most cases, spontaneous reactions are going to need a little push to get going = Activation energy. To understand why there is an activation energy, we first need to know some more terminology: Reactants (substrates) = Chemicals at the start of reaction. Transition state = Short-lived transition. Products = The chemicals at the end of a reaction. During the transition state, bonds are under great stress. The substrates require the activation energy to overcome these stresses as they reach the transition state. Slide 13 Enzymes Enzymes are usually globular proteins. Their function is to speed up spontaneous chemical reactions. For example sucrase speeds up the hydrolysis of sucrose to glucose and fructose. Note that many enzyme names end in -ase, -in or -yme. Other facts about enzymes: They are substrate specific. They are catalysts (can be

Reaction proceeds rapidly after reaching transition state Heat(energy) could make breakdown sugar occur much faster- i.e. sugar in ice tea dissolves much faster when not cold

My notes Sucrase + water breaks it up into its two componentsfructose and glucose

reused). They are fast (~100,000 products per second).

Slide 14 My notes Enzymes Lower Activation Energy Enzymes lower activation of Enzymes speed up chemical energy reactions by lowering the activation energy of a reaction. This is a very important point enzymes do not change the G of a chemical reaction. In other words an enzyme cannot make a reaction any more or less likely to happen it only speeds up spontaneous exergonic reactions. How can enzymes lower the activation energy of a reaction? The active site is shaped so that the transition state is stabilized and is therefore easy to attain. Slide 15 Enzyme Structure Enzymes are usually globular proteins. (although some RNA molecules can act like enzymes) Active site = Cleft on side of protein where: Substrate (s) bind Transition state is formed Product is formed, and then released. Shape of active site closely matches shape of transition state. Polypeptide conformation determines shape and activity of active site. Slide 16 Enzyme Activity The rate of enzyme activity can be controlled or influenced by a number of factors. My notes

My notes

Proteins(enzymes) can become

1. Environmental conditions pH, temperature or salt can alter polypeptide conformation (denaturation). Each enzyme has an optimal set of conditions. Slide 17 2. Cofactors Some enzymes are catalytic only if another molecule (other than substrate) is present. Cofactors are ions (e.g. Mg2+, Ca2+). Coenzymes are organic molecules (e.g. vitamins).

denatured in unfavorable conditions

My notes Cofactors- non-protein helpers that bind to enzymes help some work more efficiently

Slide 18 My notes 3. Inhibitors Inhibitors- can put enzymes Inhibitors are substances that reduce in an inactive state2 types: (inhibit) enzyme activity. Competitive Inhibitors- block e.g. Penicillin. substrates from binding to the There are two types of inhibitors: enzymes active site Competitive inhibitors will sit Non-competitive inhibitorsin active site. These bind to another part of enzyme substances look very similar to and cause change in shape that the enzymes natural substrate. affects the active site Non-competitive inhibitors *Enzymes shape impacts will sit outside active site. function* They usually do not look anything like the substrate. Slides 19-22 Control of Metabolism How are metabolic pathways controlled? Remember: Enzyme are very fast sometimes too fast!! They need to be controlled. 1. Allosteric regulation---------- Many enzymes can be regulated by substances that can bind to My notes Cell controls when/where enzymes are active Enzymes are regulated

Activator molecules binds and stabilizes functional shape of enzyme

allosteric regulation sites located on the enzyme. This sounds like non-competitive inhibition, but is different in that the allosteric substance is a natural part of the metabolism of the organism, and not a poison. 2. Cooperativity In cases where enzymes are made of multiple polypeptides with their own catalytic activity, we say each is a subunit. In many cases when one subunit is active, it influences the other enzymes typically causing the other enzymes to increase their affinity for the substrate. 3. Feedback inhibition An entire metabolic pathway can be easily controlled by having the product at the end of the pathway binding to one of the first enzymes in the pathway usually by allosteric regulation. This type of negative feedback means that the pathway does not work too quickly. 4. Restriction of enzymes to specific organelles Although some enzymes can float free in the cytoplasm, many are kept inside organelles and therefore only participate in metabolic pathways found only in those organelles.

Inhibitor molecule binds and stabilizes inactive form Control of metabolism

Cooperativity- substate molecule binds to

Feedback Inhibition- metabolic pathway switched of when product binds and inhibits a step early in the pathway o Negative feedback Enzymes are restricted to specific parts of cell Enzyme location is NOT random-

Keyword List for Chapter 8

Metabolism Metabolic pathway Catabolic pathway

Anabolic pathway Molecular movement Molecular transportation Potential energy Kinetic energy Chemical energy Energy transformation Thermodynamics First law of thermodynamics Conservation of energy Second law of thermodynamics Entropy Energy Free-energy Spontaneous chemical reaction Exergonic reaction Endergonic reaction Adenosine triphosphate (ATP) Adenine Ribose Phosphate groups Inorganic phosphate (Pi) ATP hydrolysis Adenosine diphosphate (ADP) ATP regeneration Energy coupling Activation energy Reactants Substrates Transition state Products Enzyme Sucrase Substrate specificity Catalyst Active site Induced fit Environmental conditions Polypeptide conformation Denaturation Optimal pH Optimal temperature Cofactor Mg2+ Ca2+ Coenzyme

Vitamin Competitive inhibitor Non-competitive inhibitor Allosteric regulation Cooperativity Feedback inhibition