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Chapter 4 cellular metabolism

Chapter 4

Emergent properties: is the process of complex pattern formation from simpler rules. those distinctive traits that cannot be predicted from the simple sum of the component parts.

A cellular proteome: is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organism's complete proteome, wich can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome. The term "proteome" has also been used to refer to the collection of proteins in certain sub-cellular biological systems. For example, all of the proteins in a virus can be called a viral proteome.

Protein: the most versatile biomolecule haave many shapes and diverse functions. Proteins become insoluble structural fibers of the cytoskeleton and extracellulara matrix, form passageways through cell membranes, or dissolve in the cytoplasm and EXF. one of the most important functions of soluble proteins is the role they play in the extraction, trancfer, and storage of biological energy, some of the chemical processes that are called metabolism.

Why people need energy?
1, growth 2, maintanance 3, building new buildings 4, repairing old ones.

metabolism: is the biochemical modification of chemical compounds in living organisms and cells. This includes the biosynthesis of complex organic molecules (anabolism) and their breakdown (catabolism). Metabolism usually consists of sequences of enzymatic steps, also called metabolic pathways. The total metabolism are all biochemical processes of an organism. The cell metabolism includes all chemical processes in a cell. Without metabolism we would not be able to survive.

The cycleing of energy in the environment and its use by living organisms is one of the fundamental concepts of biology:
All cells use energy to grow, make new parts and reproduce. 1, plants trap radiant energy from the sun and store it as chemical bond energy. (through photosynthesis) . They use carbone and oxygen from carbon dioxide, nitrogen from the soil and hydrogen and oxygen from water to make glucose and amino acids, and other biomolecules. Thus, energy from the sun trapped by photosynthesis is the ultimate energy source for all animals including humans. 2, animals cannot trap energy from the sun or use carbon and nitrogen from the air and soil to synthesize biomolecules. they must import enery and biomolecules synthesized by plants or obtained from plants by other animals. Animals extract energy from these biomolecules through respiration, consuming oxygen and producing carbon dioxide and water that recycle to be used again by plants. (not totally effiecnt, some turn into heat to environment). 3, If animals ingest more energy than they need for immediate use, the excess energy is stored in chemical bonds, as in plants. Glycogen (a glucose polymer) and lipid molecules are main energy store in animals.

What is energy?
Energy is the capacity to do work.

What is work?
three forms of work are : 1, chemical work: enables cells and organisms to grow, maintain a suitable internal envrionment, and store information needed for reproduction and normal activity. (protein synthesis for wound repair is an example of chemical work) 2, transport work: enables cells to move ions, molecules, and larger particles through the cell membrane and through membranes of organelles within the cell. It is particualrly used for creating concentration gradients. 3, mechanical work: used for movement. at the cellular level, this movement includes organelles that move around within the cell, and the beating of cillia and flagella. in whole animal, involves mucle contraction. most mechanical work whether in cells or entire animals , is mediated by the movement of intracellular fibers and filaments of the cytoskeleton.

What are two forms of energy?
1, Kinetic energy: the energy of motion. 2, Potential energy: is stored energy, may be stored in the position of a molecule with respect to its concentration gradient. In chemical bons, the potential energy is stored in the position of the electrons that form the bond.
A key feature of all forms of energy is the ability of potential energy to become kinetic energy and vice versa.

Works always involves movement and therefore always involves kinetic energy. Potential energy must be converted eto kinetic energy to perform work, and the conversion is never 100%. the amount of the energy lost in the transformation depends on the efficiency of hte process. In biological systems, potential energy is sotred in concentration gradients and chemical bonds.

What are the basic tules govern the transfer of energy in biology?
1, the first law of thermodynamics: the total amount of energy in the universe is constant. Energy can be converted from one form to another , but the ottal amount of energy in a closed system never changes. ( a human body is not a closed system) As an open system, it exchanges material and energy with its surroundings. human body doesn't create energy, it must import it from outside in the form of food.
2, the second law of thermodynamics: natural spontaneous processes move from a state of order (nonrandomness) to a condition of randomness or disorder, is entropy. is a measure of the amount of energy in a physical system that cannot be used to do work. Disorder occurs when open systems only lose energy to their surroundings.

Bioenergetics: living organism are characterized by their ability to extract energy from the environment and use it to support life processes. the study of energy flow throught biological systems is bioenergetics. in a biological system, chemical reactions are a critical means of transferring energy from one part of the system to another.

How does energy transfer?
Energy is transferred between molecules during reactions.
In chemical reaction: a substance becomes a differnet substance by breaking and / or making covalent bonds. A+B=C+D.

Reaction rate: the speed with which a reaction takes place, is the disappearance rate of the reactants (A and B), or the appearance rate of the products (C and D) . Reaction rate is measured as change in concentration during a certain time period and is often expressed as Molarity per second ( M/sec)

What is the purpose of chemical reactions? and how does it take place?
to transfer energy from one molecule to another or to use energy stored in the reactants to do work. The potential energy stored in the chemical bonds of a molecule is known as the free energy of the molecule. So complext molecules have hight free energies---thus theu can be used to store energy in cells.
1, the energy ( activation energy) is required to initiate a reaztion. 2, the difference in free energy between reactances and products is known as the net free energy change of the reaction.

activation energy: is the initial input of energy required to bring reactancts into a position that allows them to react with each other. the energy that must be overcome in order for a chemical reaction to occur.
1, a reaction with low activation energy will proceed spontaneously when the reactants are brought together. 2, reactions with high activation energies will not proceed spontaneously or will proceed too slowly to be useful.

Endergonic and exergonic reactions.
One characteristic property of any chemical reaction is its net free energy change. 1, if the free energy of the products is great than that of the reactants, some of the activation energy was trapped in the chemical bonds of the products. 2, if the gree energy of the products is lower than the free energy of the reactants, the reaction released energy.

Endergonic reaction: means to absorb energy. Its etymology stems from the suffix -ergonic as derived from the Greek root ergon meaning to work, combined with the prefix end- as derived from the Greek root en meaning put into. By thermodynamic standards, work, a form of energy, is defined normally to move from the system (the internal region) to the surroundings (the external region). Thus, an endergonic process, as contrasted with an exergonic process, is one where the system absorbs energy from the surroundings. Subsequently, during an endergonic process energy is put into the system. If the transformation occurs at constant pressure and temperature: ∆G > 0.An endergonic reaction is at first sight an exception to the Second Law of Thermodynamics. This type of reaction proceeds in an uphill (endergonic) direction. Endergonic reactions result in stability, decreased randomness, and increased order in a part of the observed system. The total entropy of the universe, however, is increased. These uphill reactions require an input of energy; that is, energy is consumed. As such, these reactions do not occur spontaneously. Examples of endergonic reactions in cells include protein synthesis, nerve conduction, and muscle contraction. some of the energy added to an endergonic reaction remains trapped in the chemical bonds of the products, which are often synthesis reactions in which complex molecules are made from small molecules.

Exergonic means to release energy. Its etymology stems from the suffix -ergonic, as derived from the Greek root ergon meaning to work, combined with the Greek prefix ex- meaning out of. By thermodynamic standards, work, a form of energy, is defined normally to move from the system (the internal region) to the surroundings (the external region). Thus, an exergonic process, as contrasted with an endergonic process, is one that releases energy from the system, of which it is a part, to the surroundings. As a result, during an exergonic process, energy is released out of the system. If the transformation occurs at constant pressure and temperature: ∆G < href="http://en.wikipedia.org/wiki/Thermodynamics#The_Laws_of_Thermodynamics" title="Thermodynamics">Second Law of Thermodynamics and proceed in a downhill (exergonic) direction. Thus, left to itself, any physical or chemical system will proceed in a direction of greater randomness, disorder, and instability. These reactions occur spontaneously. ATP +H2O--ADP +Pi +H+ energy.

Where does the activation energy for metabolic reactions come from?

The simplest cource of activation energy is to couple an exergonic reaction that produces energy to an endergonic reaction that requires energy.

Some coupled reactions are those that use the energy released by breaking the high energy bond of ATP to drive an endergonic reaction. in this, the two reactions take place simultaneously and in the same location, so that the energy from ATP can be used immesditately to drive the endergonic reaction of E and F.

Howeverm living cells have developed ways to trap and save energy released by exergonic reactions. the most common method for trapping energy is in the form of high-energy electrons carried on nucleotides. The nucleotide molecules NADH, FADH2, and NADPH a;; capture energy in the electrons of their hydrogen atoms. NADH and FADH2 usually transfer most of that energy to ATP, which can be used to drive endergonic reactions.

Reversible and irreversible reactions: a reversible reaction: a chemical reaction that can be proceed in both direction. ireversible reaction can only proceed in one direction. The net free energy change of a reaction determing whether a reaction can be reversed, because the net free energy change of the forward reaction contributed to the activation energy of the reverse reaction. one the main reasons that many biological reactions are reversible is that they aided by the proteins known as enzymes.

Enzymes: are biolocial catalyst, moles that speed up the rate of chemical reactions without themselves being changes. in enzymatically catalyzed reactions, the reactants are called substrates.

How does an enzyme increase the rate of a reaction?

In thermodynamic terms, it lowers the activation energy, making it more likely that the reaction will start. Enzymes accomplish this by binding to the reactant molecules and bring them together into the best position for reacting with each other. without it, it would depend on the random collision of the molecules to bring them into alignment. carbonic anhydrase, converts CO2 and water to cabonic aciss in 1 second, compared to 100 second without the enzyme.

How does an enzyme bring the substrates into the best position to react?

Most enzymes are larger protein molecules with complex 3-D shapes. On each enzyme molecule is a region as the binging site. part of the protein molecule that binds to the subtrates. When this binding takes place, the substrate molecules are brought close to each other and to the enzyme's active site, the region that promotes reaction of the substates with each other. (lock-and-key), however, the binding site and the substrates do not need to fit one another eaxctly.

The binding site needs only to atract the substrate to the region of the enzyme. then substrate interact, the binding site changes shape to fit more closely to the substrate. This is induced-fit model(reversibility).Then the binding site has an internediate shape that can change to fit either the substrate or the product molecules. This enable an enzyme to bind to either reactants or products and thus be able to catalyze a single reaction in bother directions.

Enzyme speicificity: most enzymes react with only one set of substrates or a groupd of similar substrate. the ability of an enzyme to catalyze a certain reaction of a groupd of related reactions is call specificity. Glucokinase to attach a phophate group onto glucose molecules when they enter a cell. Peptidase not very specific in action.

Name of enzyme: most with the suffix -ase.
The first part of the name usually refers to the type of reaction, the substrate upon which it acts, or both. Kinase adds a phophate group to the substrate. Addition of a phophate group is called phophorylation. Peptidase break up peptides into smaller peptides or amino acids by cleaving the peptide bond that links the amino acid. Pepsin and typsin: digestive enzymes.

Isozymes: are enzymes that catalyze the same reaction but under differnet conditions or in different tissues. their structures are slightly different , which causes the variability in their activity. Lactate dehydrogenase has several isozymes, one in heart and one in skeltal muscle and liver.

What is the advantage of having izozymes of one enzyme?can be used in medical diagosis of certain conditions.

What is proenzymes or zymogens?they are the enzymes not ready to catalyze reactions when they are first synthesized. the yare inactive molecules.

What is proteolytic activation? When the enzymes are needed, one or more portions of the molecule are shopped off and the inactive portein becomes an active enzymes. the enzymes involved in blood clotting and digestion are among those that are produced as proenzymes.

What if an enzyme has both an active and an inactive form? the inactive enzyme if often named by adding the suffix-ogen to the name of the active enzyme. Eg. pepsinogen is the inactive form of the digestive enzyme pepsin. Chymotrypsinogen is the inactive form of Chymotrypsin.

What is cofactor? Sometimes the activation of an enzyme required the presence of an additional molecule or ion called a cofactor. They may be either inorganic or nonprotein organic molecules.

What are the inorganic cofactors? they are ions such as Ca2+ or Mg2+, they must attach to the enzyme before the substrate can bind to the binding site.

What are the organic cofactors? The are called coenzymes. they do not alter the enzymes's binding site. Instead, they act as receptors and carriers for atoms or functional groupds that removed from the substrates during the reaction.Not required in large amount. Vitamins are the precursors of coenzymes, B vitamines, folicacid, biotin, are coenzyme. Vitamin C needed for adequate collagen syntheisis.

What is modulator? The ability of an enzyme to speed up a reaction can be altered by various factors, including temperature, pH, or molecules that interact with enzymes. A factor that influences enzyme activity is known as modulator. If a modulator activates an enzyme, the reaction rate will increase. If a modulator inactives the enymes, the reaction rate will decrease and may even stop the reaction.

What are two basic mchanisms by which modulator takes place? : 1, changes the ability of the substrate to bind to the binding site. 2, changes the ability of the enzyme to alter the activation energy of the reaction.

Different types of modulator:

1, Acidity and temperature: Changes in temperature and pH can disrupt the bonds that hold a protein in its tertiary donfiguration, causing the protein to lose its shape. Eg. fried egg,(temperature) raw fish marinated in lime juice result in meat becoming firm and opaque(pH aciditi)

Why enzyme is denatured? small changes in pH and temperature can increase or decrea the activity of enzymes. once the changes exceed critical point, the structure of the enzyme is altered so its activity is destroyed. in few cases, activity can be restored if the modulatore is removed. so this is one reason that these factors temperature and pH is closely regulated by the body.

2, Chemical modulators: molecules that bind to enzymes and alter their catalytic ability. three types of chemical modulator: 1, competitive inhibitors, 2, allosteric modulator 3, covalent modulators.

competitive inhibitors :the molecule binds to enzyme at its binding site, blocking the site and preventing the substrate from binding with the enzymes.Eg. antibiotic penicillin. inhabited bacterial growth. it is a competitive inhibitor that binds to a key baterial enzyme by mimicking the normal substrate. forming bonds that are unbreakable and inhibits the enzy,e. without the enzyme, the bacterium is unable to make a rigidcell wall, without the wall, the bacterium swells ruptures and dies.

Allosteric modulator: bind to the enzyme away from the binding site and change the shape of the binding site, this can either: 1, increase the probability of enzyme-substrate binding and enhance enzyme activity 2, decrease the affinity of the binding site for the substrate and inhibit enzyme activity. can also occurs in proteins other than enzymes.

Covalent modulators: are atoms or functional groupds that use covalent bons to bind to enzymes and alter the enzymes' properties. may increase or decrease the activity of the enzyme.Eg. phophate group. many enzymes in the cell can be wirther activated or inactivated when this groupd forms a covalent bond with them.

Enzyme and substrate concentration affect reaction rate:

Enzyme amount is a major dterminant of the rate of an enzyme reaction. no enzyme--reactions very slowly. enzyme is present, the rate will be proportional to the amount of enzyme. regulating enzyme concentration is an important strategy that cells use to control physiological processes. Cells alter the amount of an enzyme by influencing both its synthesis and its breakdown. if enzyme synthesis exceeds breakdown, enzyme accumulate and the reaction speeds up. it enzyme breakdown exceeds synthesis, the amount of enzyme decrease, as does the reaction rate. ?

The enzyme is catalyzing reactions as fast as it can, and the rate of reaction reaches a maximum value this condition is saturation.

Revesible reaction and the law of mass action and equilibrium

What are the four categories of catalyzed enzyme reaction?: 1, oxidation-reduction 2, hydrolysis-dehydration 3, exchange-addition-subtraction 4, ligation reactions.

Oxidation-reduction reaction: the most important reactions in energy extraction and transfer within the cell. reduction: gain electron or lose H+. oxidation: lose electron or gain H+.

Hydrolysis-dehydration reactions: dehydration: a water molecule is one of the products. in the process , one molecule loses a hydroxyle groupd and the other loses a hydrogen to create water. when a dehydration results in the synthesis of a new molecule, the process is known as dehydration synthesis. Hydrolysis reaction: a substrate changes into one or more products by adding water. The covalent bonds of the water molecule are broken so tha water react as a hydroxyl group and hydrogen. Eg. an amino acid can be removed from the end of a peptide with a hydrolysis reaction.

Enzyme names consists of the substrate name with the suffix -ase, causes a hydrolysis reaction. Lipase, breaks up large lipids into smaller lipids by hydrolysis. Peptidase removes an amino acid from a peptide.

Addition reaction: adds a functional groupd to one or more of the reactants.

Substraction reaction: removes a functional group from one or more of the reactants.

Exchange reactions: functional groups are exchanged between or among reactants.

Eg. Kinases: transfer a phophate group from a substrate to an ADP to create ATP, or from an ATP to a substrate. Creatine kinase transfer a phosphate groupd from creatine phophate to ADP, forming ATP and leaving behind creatine.

Deamination reaction: removal of an amino groupd from an amino acid or peptide.

amination: addition of an amino group.

Transamination: transfer of an amino group.

posted by C-T @ 5:26 AM