Biology Chapter 6

Couple reactions examples

1. Myosin assumes its resting shape when it combines with ATP 2. ATP splits into ADP and P, causing myosin to change its shape and allowing it to attach to actin Chemical to mechanical polypeptide is synthesized at a ribosome. There, an enzyme transfers a phosphate group from ATP to each amino acid in turn, and this transfer supplies the energy needed to overcome the energy cost associated with bonding one amino acid to another

the complete oxidation of a mole of glucose releases

686 kcal of energy, and to synthesis ATP molecules If the energy within glucose were released all at once, most of it would dissipate as heat instead of some of it being used to produce ATP

Organisms do not occur haphazardly in cells... they are usually part of a metabolic pathway

A series of linked reactions, beginning with a particular reactant and terminating with an end product They begin with a specific reactant and produce an end product Metabolic energy is captured and utilized more easily because it is released in increments Pathways may connect through common intermediates A to B to C to D

Functions of ATP

ATP can be used by cells for: Chemical work Energy to synthesize macromolecules (anabolism) Transport work Energy to pump substances across membranes Mechanical work Energy to make muscles contract, cilia and flagella beat, and so forth

There are many biological advantages to the use of ATP as an energy carrier in living systems

ATP is a common and universal energy currency because it can be used in many different types of reactions Also when ATP is converted to energy, ADP and P, the amount of energy released is sufficient for a particular biological function, and little energy is wasted ATP breakdown can be coupled in endergonic reactions in such a way it minimizes energy loss

A cell had 2 main ways to couple ATP hydrolysis to an energy-requiring reaction

ATP is used to energize a reactant, or ATP is used to change the shape of a reactant Both can be achieved by transferring a phosphate group to the reactant, so that the product is phosphorylated

The maximum rate

Active sites are always filled with substrate when the enzyme's active sites are filled almost continuously with substrate, the enzyme's rate of activity cannot increase anymore

ATP is a nucleotide composed of

Adenine (a nitrogen-containing sugar) Ribose (a 5-carbon sugar) Three phosphate groups Energy stored in these chemical bonds

How Enzymes Function

An enzyme binds with a substrate to form a complex The active site is a small part of the enzyme that complexes with the substrate The following equation indicated the sequence of steps in an enzyme-catalyzed reaction Binds with a substrate to form a complex Active site is a small part of the enzyme that complexes with the substrate

Forms of energy

Anytime you change energy you lose some of that energy as heat Always need to convert more energy than that will be used Solar Chemical: Animals are taking that heat and using it as energy Mechanical: Gasoline in your car Thermal (heat)

Products

Are substances that form as a result of a reaction C + D is the products

Enzymes

Are typically proteins that function as catalysts to speed a chemical reaction due to its particular shape Ribozymes are RNAs that can act as catalysts Catalysts participate in chemical reactions, but are not used by the reaction Do not cause reactions to go forward Free energy determines which reactions go forward

Organized to disorganized

As you are breaking down molecules you are increasing entropy Unequal distribution of hydrogen ions The 2nd law tells us that glucose fends to break apart into carbon dioxide and water because glucose is more organized and therefore less stable, than its breakdown products Also hydrogen ions on one side of a membrane tend to move to the other side unless they are presented from doing so because when they are distributed randomly, entropy has increased A neat room is more organized but less stable than a messy room, which is disorganized but more stable Allows you to do work Has potential energy Equal sharing of hydrogen ions Doesn't allow you to do work

Vitamin C

Commodore George Anson left England in 1740 with a fleet of six ships and more than 1000 men and returned with an enormous amount of treasure, but of his crew only 145 survived to reach home Many died of Scurvy Like loss of teeth Sunken eyes Pale skin Caused by the lack of vitamin C in their diet which is contained in fruit Came down to the position James Lind (1747) - "A Treatise of the Scurvy" Which says that every expedition should have lime on their ship

ATP

Common energy current for cells is a carrier of energy between exergonic and endergonic reactions ATP generated from ADP (adenosine diphosphate) + organic phosphate molecule P Glucose breakdown provides the energy to build up ATP When cells require energy, they "spend" ATP The more active the organism, the greater the demand for ATP

How do you know a neat room is less stable than a messy room?

Consider that a neat room always tends to become more messy

The second law of thermodynamics

Energy cannot be changed from one form to another without a loss of usable energy "Law of entropy" The second law of thermodynamics states that energy cannot be changed from one form to another without a loss of useable energy The heat released during photosynthesis (from the plant) and cellular respiration (from both the plant and moose) dissipates into the environment Heat that dissipates into the environment cannot be captured and converted to one of the other forms of energy Every energy transformation makes the universe less organized and more disordered

The first law of thermodynamics

Energy cannot be created or destroyed "Law of conservation of energy" The first law of thermodynamics explains the ability of organisms to convert chemical energy to mechanical energy During photosynthesis, plant cells use solar energy to convert energy-poor molecules, such as carbon dioxide and water to energy-rich molecules, such as carbohydrates The energy comes from the sun. The energy from the sun is not destroyed in the process because heat is also a form of energy Similarly, a moose uses the energy derived from carbohydrates to power its muscles and as the cells use this energy, none is destroyed, but some becomes heat, which dissipated into the environment

Two laws of Thermodynamics

Energy flows through an ecosystem. It does not recycle The flow of energy is an ecosystem can be explained by two laws of thermodynamics:

Energy of Activations

Energy that must be added to cause reactants to react with one another Enzymes 1. Lower the energy of activation 2. Do not change the end result of the reaction 3. Increase the reaction rate

Substrate concentration

Enzyme activity increases as substrate concentration increases because there are more collisions between substrate molecules and the enzyme More collisions between substrate and enzyme As more active sites are filled with substrate, more product results per unit time

Every enzyme reaction in a cell requires that its specific enzyme be present

Enzymes are often named for their substrate because they only comply with their substrate with the suffix -age Substrate: lipid , urea, maltose, ribonucleic acid, lacoste Enzyme: lipase, urease, maltase, ribonuclease, lactase

Note that the enzyme does not determine whether the reaction goes forward; that is determined by the free energy of the reaction

Enzymes simply increase the rate of the reaction

Cells and Entropy

Every process that occurs in cells increases the total entropy of the universe Cellular processes require an input of energy from an outside source For example, transport, biosynthesis Ultimately, living organisms depend on a constant supply of energy from the sun

chemical energy

Food is specially called chemical energy energy associated with the interaction of atoms in a molecule - because it contains energy in the chemical bonds of organic molecules

Some enzymes do more than simply complex with their substrate(s); they participate in the region

For example, trypsin digests protein by breaking peptide bonds The active site of trypsin contains 3 amino acids with R groups that actually interact with members of the peptide bond - first to break the bond and then to introduce the components of water this illustrates that the formation of the enzyme - substrate complex is very important in speeding up the reaction

Not all enzymes are reduced by the cell all the time

Genes can be turned on to increase the concentration of an enzyme in a cell or turned off to decrease the concentration But enzymes can also be present I the cell in an inactive form

Photosynthesis is a long reaction ... what is the product of photosynthesis?

Glucose

What would be a reactant of a hydrolysis reaction?

H2O

denatured

If the temp rises beyond a certain point, enzyme activity eventually levels out and then declines rapidly because the enzyme is denatured - loss of a protein's or enzyme's normal shape so that is no longer functions; usually caused by a less than optimal pH and temp high temperatures - loss of structure and function occurs

Reactants

In a chemical reaction, reactants are substances that participate in a reaction The stuff you start off with A + B is the reactants

Most metabolic pathways in cells are regulated by a more complicated type of feedback inhibition

In these instances, the end product of an active pathway binds to a site other than the active site of the first enzyme The binding changes the shape of the active site so that the substrate is unable to bind to the enzyme, and the pathway shuts down (inactive) Therefore, no more product is produced

The terms oxidation and reduction also apply to covalent reactions in cells

In this case, oxidation is the loss of hydrogen atoms, and reduction is the gain of hydrogen atoms Notice that when a molecule gains a hydrogen atom, it has gained an electron

Cellular metabolism

Is the sum of all the chemical reactions that occur in a cell Change in entropy Metabolism is the sum of all the chemical reactions that occur in a cell a significant part of cellular metabolism involves the breaking down and building up of molecules

The Sun is the ultimate source of energy for life

Most organisms cannot survive without the sun The major of organisms get their energy from organic nutrients produced by photosynthesizes ... therefore, life on Earth is ultimately depends on solar energy Some organisms are dependent directly on the sun Like organisms in the bottom of the ocean

Coenzymes

Organic non-protein cofactors are called non-protein organic molecule that aids the action of the enzyme to which it is loosely bound these cofactors assist the enzyme and may even accept or contribute atoms to the reactions examples of these are NAD + FAD, and NADP+, each of which plays a significant role in either cellular respiration or photosynthesis Vitamins are often components of coenzymes

Humans, like all eukaryotic organisms, are involved in the cycling of molecules between chloroplasts and mitochondria

Our food is derived from plants or we eat other animals that have eaten plants also, we take in oxygen released by plants nutrients from our food and oxygen enter our mitochondria, which produce ATP

How is solar energy captured?

Photosynthesis: Plants or photosynthetic bacteria was a requirement for life to keep existing on Earth Very first life was probably not photosynthetic, they used chemicals but chemicals were not plentiful Photosynthesis came about pretty early on in life Sunbathing: Like lizards use solar energy to warm up body which speeds up chemical reactions in body Two ultimate forms of energy: Kinetic energy Potential energy

Activation of enzymes occurs in many ways

Some enzymes are covalently modified by the addition or removal of phosphate groups In some proteins, adding phosphates activate them; in others, removing phosphates activates them Enzymes can also be activated by cleaning or removing part of the protein or by associating with another protein or cofactor

Catalase

Speeds up the breakdown of hydrogen peroxide by 600,000 times faster

ATP is constantly being generated from ADP (adenosine diphosphate)

The amount on hand at any moment is minimal because ATP is constantly being generated from ADP a nucleo tide with two phosphate groups that can accept another phosphate group and become ATP - and a molecule of inorganic phosphate

This form of oxidation-reduction is exemplified in the overall equations for photosynthesis and cellular respiration

The chloroplasts in plants capture solar energy and use it to convert water and carbon dioxide into a carbohydrate oxygen is a by-product that is released During photosynthesis, hydrogen atoms are transferred from water to carbon dioxide as glucose forms In this reaction, therefore, carbon dioxide has been reduced and water has been oxidized It takes energy to glucose, and this energy is supplied by solar energy

instead, cells oxidize glucose step by step

The energy is gradually stored and then converted to that of ATP molecules, which is used by organisms in a variety of ways

Eve though the reaction will proceed (free energy is negative)

The energy of activation must be overcome

Energy of activation

The energy that must be added to cause molecules to react with one another Even though the reaction will proceed, the energy of activation must be overcome The burning of firewood is a very exergonic reaction, but firewood in a pile does not spontaneously combust. The input of some energy, perhaps a lit match, is required to overcome the energy of activation Nevertheless, the addition of the enzyme does not change the end result of the reaction. Notice that the energy of the products is less than the energy of the reactants This results in a negative free energy, so the reaction will proceed But the reaction will not go at all unless the energy of activation is overcome Without the enzyme, the reaction rate will be very slow

Induced fit model

The enzyme is induced to undergo a slight alternation to achieve optimum fit Substrate and active site shapes do not fit together like a lock and key Change of shape to the active site facilitates the reaction that reaction that now occurs Needed for optimal reaction After reaction is completed, product(s) are released, and the active site returns to its original state, ready to bind to another substrate molecule

Each enzyme also has a preferred pH at which the rate of the reaction is highest

The globular structure of an enzyme is dependent on interactions, enzyme is dependent on interactions, such hydrogen bonding, between R groups A change in pH can alter the ionization of R groups and disrupt normal interactions and under extreme pH conditions, denaturation eventually occurs Measure of Free H+C Enzymes have optimal pH Enzyme structure depends Pepsin Trypsin

Cofactors

The inorganic ions are metals such as copper, zinc, or iron nonprotein assistant required by an enzyme in order to function; many cofactors are metal ions, others are coenzymes

Why do compost piles get so hot?

The loss of chemical reactions in forms of heat

The reactants in an enzymatic reaction are called the substrate for that enzyme

The presence or absence of an active enzyme determines which reaction takes place

Chaos will always win

The second law of thermodynamics can be stated another way: every energy transformation makes the universe less organized and more disordered Entropy refers to the relative amount of disorganization

Catabolism

The term is used to refer to the breaking down of molecules

In the pathway, one reaction leads to the next reaction, which leads to the next reaction, and so forth in an organized, highly structured manner

This arrangement makes it possible for one pathway to lead to several other because various pathways have several molecules in common Also, metabolic energy is captured and utilized more easily if it is released in small increments rather than all at once The products from the previous reaction become the reactants of the next reaction

Why we need energy

This energy allows living organisms to carry on the processes of life including growth, development, response to stimuli, metabolism, and reproduction Energy is the ability to do work or bring about change Cells and organisms need a constant supply Animals always have to have a source of energy (like when hibernating for the winter they use energy to stay warm)

Cholorplasts are able to capture solar energy and convert it to the chemical of ATP, which is used along with hydrogen atoms to reduce carbon dioxide

This reduction of carbon dioxide to form a mole of glucose stores 686 kcal in the chemical bonds of glucose This is the energy that living organisms utilize to support themselves only because carbohydrates (and other nutrients) can be oxidized in mitochondria

A lead cell photosynthesizes

Uses but does not create solar energy to form carbohydrates Some energy is lost as heat, none is destroyed

Reactions that involve the gain and loss of electrons are called oxidation-reduction reactions

a paired set of chemical reactions in which one molecule gives up electrons (oxidized) which another molecule accepts electrons (reduced); commonly called a redox reaction When discussing metabolic reactions, oxidation represents the loss of electrons, and reduction is the gain of electrons In the reaction Na + Cl to NaCl, sodium has been oxidized (loss of electron), and chlorine has been reduced (gain of electrons)

Using the concept of entropy, it is possible to state that

a reaction will occur if it increases the entropy of the universe but in cell biology, we do not consider the entire universe; we simply was to consider a particular reaction In such instances, cell biologists use the concept of free energy instead of entropy

mechanical energy

a type of kinetic energy associated with the position, or motion (such as walking or running) of an object When a moose walks, it has converted energy into a type of kinetic energy called mechanical energy

In an active pathway

a. the first reactant (A) is able to bind to the active site of enzyme E b. Feedback inhibition occurs when the end product (F) of the metabolic pathway binds to the enzyme of the pathway - at a site other than the active site. This binding causes the active site to change its shape Now reactant A is unable to bind to the enzymes active site, and the pathway shuts down

Exergonic reactions

are reactions that are spontaneous and release energy Products have less free energy than reactants Spontaneous

Vitamins

are relatively small organic molecules that are required in trace amounts in our diet and in the diets of other animals for synthesis of coenzymes that affect health and physical fitness The vitamin becomes a part of the coenzyme's molecular structure For example, the vitamin niacin is part of the coenzyme NAD, and riboflavin (B2) is part of the coenzyme FAD A deficiency of any one of these vitamins results in a last of the coenzyme and therefore a lack of certain enzymatic actions In humans, this eventually results in vitamin-deficiency symptoms for ex, niacin deficiency results in skin disease called pellagra, and riboflavin deficiency results in cracks at the corners of the mouth

Cellular processes, such as the synthesis of glucose and ion transport across a membrane, are possible because

cells have the ability to obtain an input of energy from an outside source This energy ultimately comes from the sun Life depends on a constant supply of energy from the sun because the ultimate fate of all solar energy in the biosphere is to become randomized in the universe as heat

A moose uses _____ for movement

cellular respiration

Through coupled reactions, ATP allows

chemical reactions that may not be favorable from an energy perspective for the cell

Enzymatic reactions proceed much more rapidly

consider the breakdown of hydrogen peroxide, it can occur 600,000 times a second when a catalase is present

cellular respiration therefore

consumes oxygen and produces carbon dioxide and water, the very molecule taken up by chloroplasts In this reaction, glucose has lost hydrogen atoms (been oxidized), and oxygen has gained hydrogen atoms (been reduced)

In addition to substrate concentration, the rate of an enzymatic reaction can be affected by

environmental factors (temp and pH) or by cellular mechanisms, such as enzyme activation, enzyme inhabitation, and cofactors

As temperature increases

enzyme activity increases... this occurs because higher temps cause more effective collisions between enzyme and substrate As temperature increases beyond a certain point, enzyme activity levels out Decrease of temperature decreases enzyme activity most enzymes are proteins, and the shape of the protein responds to temp temp often influences the protein's secondary and tertiary structure, preventing it from binding its substrate(s) efficiently Therefore, as the substrate of the enzyme changes, its activity decreases

A cell is assured of a supply of ATP because

glucose breakdown during cellular respiration provides the energy for the buildup of ATP in mitochondria Only 39% of the free energy of glucose is transformed to ATP; the rest is lost as heat

potential energy

is stored energy - its capacity to accomplish work is not being used at the moment The food we eat has potential energy because it can be converted into various types of kinetic energy

Energy

is the ability to do work or bring about a change

Free energy

is the amount of energy available - that is, energy that is still "free" to do work - after a chemical reaction has occurred The change in free energy after a reaction is calculated by subtracting the free energy of the reactants from that of the products A negative result means that the products have used free energy than the reactants and the reaction, if C and D have less free energy than A and B, the reaction will occur Reactions may have net free energies

Kinetic energy

is the energy of motion, as when a ball rolls down hill or a moose walks Is the energy of motion As when a ball rolls down a hill Like walking around is kinetic energy

Calories

is the unit given for the free energy

entropy

is to measure of disordered or randomness in a system Every energy transformation makes the universe less organized and more disordered because the processes that occur in cells are energy transformations, the second law means that every process that occurs in cells always does so in a way that increases the total entropy of the universe

when oxygen gains electrons

it becomes water

A living cell remains organized because

its functions to maintain a constant flow of energy

A living cells remains organized because

its functions to maintain a constant flow of energy

However, even though they are unfavorable, these processes must occur to create the high degree of order and structure essential for life

macromolecules must be made and organized to form cells and tissues; the internal composition of the cell and the organism must be maintained; and movement of cellular organelles and the organism must occur if life is to continue

Enzyme inhibition

means by which cells regulate enzyme activity; may be competitive or non-completive inhibition Enzyme inhibition occurs when the substrate is unable to bind to the active site of an enzyme The activity of almost every enzyme in a cell is regulated by feedback inhibition In the simplest case, when there is plenty of product, it binds to the enzyme's active site, and then substrate is unable to bind as the product is used up, inhibition is reduced, and more product can be produced In this way, the concentration of the product is always kept within a certain range

mitochondria presents in both plant and animals

oxidized carbohydrates and use the released energy to build ATP molecules

When oxygen (O) combines with a metal such as iron or magnesium (Mg)

oxygen receives electrons and becomes an ion that is negatively charged When magnesium oxide (MgO) forms, it is appropriate to say that magnesium has been oxidized On the other hand, oxygen has been reduced because it has gained negative charges

coupled reactions

reactions that occur simultaneously; one is an exergonic reaction that releases energy; and the other is an endergonic reaction that requires an input of energy in order to occur The energy released by an exergonic reaction is used to drive an endergonic reaction

Because oxidation and reduction go hand-in-hand, the entire reaction is called a

redox reaction

In most instances, only one small part of the enzyme, called the active site

region of an enzyme where the substrate binds and where the chemical reaction occurs - complexes with the substrate It is here that the enzyme and substrate fit together, seemingly like a key fits a lock However, cell biologists now know that the active site undergoes a slight change in shape in order to accommodate the substrate(s)

Endergonic reactions

require an input of energy Products have more free energy than reactants Require an input of energy to run In the body, many reaction such as protein synthesis, nerve impulses conduction, or muscle contraction, are endergonic, and they are driven by the energy released by exergonic reactions

ATP is a nucleotide composed of

the nitrogen-containing case adenine and the 5-carbon sugar ribose (together called adenosine) and three phosphate groups ATP is called a "high energy" compound because of the energy stored in the chemical bonds of the phosphates

Anabolism

the term is used to refer to the building up (synthesis) of molecules