Ch8 The Metabolism of Microbes via Book

What are the 3 things that metabolism accomplished along way?

1. Anabolism: smaller to larger macromolecule 2. Catabolism: larger to smaller macromolecules 3. Releases and uses energy in the form of ATP or HEAT (P195)

The initial resistance can be overcome by what 3 things?

1. Increasing the heat or thermal energy 2. Increasing the concentration of reactants to increase molecular collisions 3. Adding a catalyst (most efficient and potent method)

This system classifies the enzyme in one of six classes, on the basis of its biochemical action: 1. _______ transfer electrons from one substrate to another, and _______ transfers a hydrogen from one compound to another

1. Oxidoreductases transfer electrons from one substrate to another, and dehydrogenases transfers a hydrogen from one compound to another

True of false? 1. Enzymes raise the activation energy required for a chemical reaction to proceed 2. Enzymes are used up or permanently changed by a reaction 3. Enzymes can be recycled, thus they function in extremely high concentration

1.False: Enzymes LOWER the activation energy required for a chemical reaction to proceed 2. FALSE: Enzymes are NOT used up or permanently changed by a reaction 3. False: Yes, Enzymes can be recycled, but they function in extremely LOW concentration

In general an enzyme name has two parts: (1) a prefix or stem word derived from a certain characteristic-usually the SUBSTRATES acted upon or the type of reaction catalyzed, or both-followed by (2) the ending "-ase"

>>

In general, metals activate enzymes, help help bring the active site and substrate close together, and participate directly in the chemical reactions with the enzymes substrate complex.

>>

Location of Enzyme Reaction: Enzymes perform their tasks either inside or outside of the cell in which they were produced.

>>

Naming Enzymes: Most metabolic reactions require separate and unique enzymes. A standardized system of nomenclature and classification was developed to keep things clear.

>>

Soon, we shall see that coenzymes carry and transfer hydrogen atoms, electrons, carbon dioxide and amino acid groups.

>>

The Sensitivity of Enzymes to Their Environment:

>>

The activity of an enzyme is highly influenced by the cell's environment. In general, enzymes operate only under the natural temperature, pH, and osmotic pressure of an organ- ism's habitat.

>>

Vitamin deficiencies prevent the complete holoenzyme from forming, making the chemical reaction and structure or function dependent upon that reaction do not work well.

>>

Enzyme-Substrate Interactions: For a reaction to take place, the substrate has to nestle into the active site. The fit is so specific that it is often described as a "lock and key" fit in which the substrate in which the substrate is inserted into the active site's pocket.

>>>

Like all proteins, an apoenzyme exhibits levels of molecular complexity called called the primary, secondary, and tertiary and in larger enzymes quaternary.

>>>

Metabolic Pathways Metabolic reactions rarely consist of a single action or step. More often, they occur in a MULTISTEP series or pathway, with each step catalyzed by an enzyme. An individual reac- tion is shown in various ways, depending on the purpose at hand (figure 8.7). #

>>>

Remember to go river LAG. LOG, stationary and death***that was on the quiz and you had no idea

>>>

View p198 Figure 8.3***

>>>

View p208 Figure 8.7 for different pathways

>>>

View Figure 8.9 on p209

>>>>

Direct Controls on the Action of Enzymes: The bacterial cell has many ways of directly influencing the activity of its enzymes. It can inhibit enzyme activity by supplying a molecule that resembles the enzyme's normal substrate.

>>>> (Cont)

The product of one reaction is often the reactant (substrate) for the next, forming a linear chain of reactions. Many pathways have branches that provide alternate methods for nutrient processing. #

>>>>>

As the level of the end product from a given enzymatic reaction has built to excess, the genetic apparatus responsible for replacing these enzymes is automatically suppressed (process figure 8.9). The response time is longer than for feedback inhibition, but its effects are more enduring.

>>>>>>

Controls on Enzyme Synthesis Controlling enzymes by controlling their synthesis is another effective mechanism, because enzymes do not last indefinitely. Some wear out, some are deliberately degraded, and others are diluted with each cell division.

>>>>>>

Others take a cyclic form, in which the starting molecule is regenerated to initiate another turn of the cycle. On top of that, pathways generally do not stand alone; they are interconnected and merge at many sites. #

>>>>>>

The "mimic" can then occupy the enzyme's active site, preventing the actual substrate from binding there. Because the mimic cannot actually be acted on by the enzyme or function in the way the product would have, the enzyme is effectively shut down.

>>>>>>

(Regulation of Enzymatic Activity and Metabolic Pathways): Metabolic reactions proceed in a systematic, highly regulated manner that maximizes the use of available nutrients and energy. The cell responds to environmental conditions by using those metabolic reactions that most favor growth and survival. Because enzymes are critical to these reactions, the regulation of metabolism is largely the regulation of enzymes by an elaborate system of checks and balances. Let us take a look at some general features of metabolic pathways.

>>>>>>>>>>>>>>>>>>>

A ______ or ______ bonds together many small molecules into large molecules.

A SYNTHETASE or POLYMERASE bonds together many small molecules into large molecules.

A classic model of enzyme induction occurs in the response of Escherichia coli to certain sugars. For example, if a particular strain of E. coli is inoculated into a medium whose principal carbon source is _____, it will produce the enzyme lactase to hydrolyze it into glucose and galactose.

A classic model of enzyme induction occurs in the response of Escherichia coli to certain sugars. For example, if a particular strain of E. coli is inoculated into a medium whose principal carbon source is lactose, it will produce the enzyme lactase to hydrolyze it into glucose and galactose.

A disease that causes throat and skin infections is called _______

A disease that causes throat and skin infections is called STREPTOCOCCUS PYOGENEs

Enzymes: Catalyzing the Chemical Reactions of Life: A microbial cell is not complete without ______, a protein catalyst that facilitates metabolic reactions. ______ are chemicals that increase the rate of a reaction becoming part of the products or being consumed in the reaction

A microbial cell is not complete without ENZYMES, a protein catalyst that facilitates metabolic reactions. CATALYSTS are chemicals that increase the rate of a reaction becoming part of the products or being consumed in the reaction

______ is the resistance to a reaction that must be overcome or amount of energy required to initiate a metabolic reaction.

Activation energy

After enzymes are made inside the cell, ___-enzymes are transported extracellularly, where they break down or ______ large food molecules or harmful chemicals.

After enzymes are made inside the cell, EXOenzymes are transported extracellularly, where they break down or HYDROLYZE large food molecules or harmful chemicals.

An enzyme that hydrolyzes peptide bonds of a protein is a ______, ______, ______ depending on the size of protein substrate, depending on the size of the protein substrate.

An enzyme that hydrolyzes peptide bonds of a protein is a PROTEINASE, PROTEASE, PEPTIDASE, depending on the size of protein substrate.

______, or _____ is the first type of metabolism; any process that results in the synthesis of cell molecules and structures; a building and bond making process that requires that input of energy; small molecules into larger ones

Anabolism or biosynthesis is the first type of metabolism; any process that results in the synthesis of cell molecules and structures; a building and bond making process that requires that input of energy; small molecules into larger ones

Another exoenzyme from this bacterium (S.pyogene) is called ______.

Another exoenzyme from this bacterium (S.pyogene) is called STREPTOLYSIN.

Another form of inhibition can occur with special types of enzymes that have two binding sites—the active site and another area called the ______ site (as shown in figure 8.8). These enzymes are regulated by the binding of molecules other than the substrate in their regulatory sites.

Another form of inhibition can occur with special types of enzymes that have two binding sites—the active site and another area called the REGULATORY site (as shown in figure 8.8). These enzymes are regulated by the binding of molecules other than the substrate in their regulatory sites.

APOENZYMES: Specificity and Active Site

Apoenzymes range in size from small polypeptides with about 100 amino acids and a 12,000 molecular weight of 12,000 to large polypeptide conglomerates with thousands of amino acids and a molecular weight of over a million.

At the molecular level, and enzyme promotes a reaction by serving as a physical site upon which the REACTANT molecules, called _______, can be positioned for different interactions.

At the molecular level, and enzyme promotes a reaction by serving as a physical site upon which the REACTANT molecules, called SUBSTRATES can be positioned for different interactions.

By contrast, ______ function inside of the cell. Endoenzymes remain in the cell and function there. Most enzymes of the ______ are Endoenzymes.

By contrast, ENDOENZYMES function inside of the cell. Endoenzymes remain in the cell and function there. Most enzymes of the METABOLIC PATHWAYS are Endoenzymes.

This form of inhibition is called ______ inhibition, because the MIMIC is competing with the substrate for the binding site (figure 8.8).

COMPETITIVE INHIBITION

______ is a an enzyme present in bacterial cells in constant amounts, regardless of he presence of a substrate. Enzymes of the ______ pathways are a prime example. (Dictionary)

CONSTITUTIVE is a an enzyme present in bacterial cells in constant amounts, regardless of he presence of a substrate. Enzymes of the CENTRAL CATABOLIC pathways are a prime example. (Dictionary)

Clostridium perfringens, an agent of GAS GANGRENE, synthesizes _______., a lipase that profoundly damages cell membranes and accounts for the tissue death associated with this disease.

Clostridium perfringens, an agent of GAS GANGRENE, synthesizes LECITHINASE C., a lipase that profoundly damages cell membranes and accounts for the tissue death associated with this disease.

________, an agent of GAS gangrene, synthesizes lecithinase C., a lipase that profoundly damages cell membranes and accounts for the tissue death associated with this disease.

Clostridium perfringens, an agent of GAS GANGRENE, synthesizes lecithinase C., a lipase that profoundly damages cell membranes and accounts for the tissue death associated with this disease.

Common Name: Lactate dehydrogenase Systemic name: Same as common name Enzyme Class: ______ Substrates: _______ Action: Catalyzes the conversion of ______ acid to _____ acid

Common Name: Lactate dehydrogenase Systemic name: Same as common name Enzyme Class: Oxidoreductase Substrates: Pyruvic acid Action: Catalyzes the conversion of PYRUVIC acid to LACTIC acid

Common Name: Oxidase Systemic name: ? Enzyme Class: ? Substrates: ? Action: ? (addition of electrons and hydrogens)

Common Name: Oxidase Systemic name: Cytochrome oxidase Enzyme Class: Oxidoreductase Substrates: Molecular oxygen Action: Catalyzes the reduction of O2 (addition of electrons and hydrogens)

Common: DNA polymerase Systemic Name: ? Enzyme Class: ? Substrates: ? Action: Synthesizes a strand of DNA using the complementary strand as a model

Common: DNA polymerase Systemic Name: DNA nucleotides-transferase Enzyme Class: Transferase Substrates: DNA nucleosides Action: Synthesizes a strand of DNA using the complementary strand as a model

Common: DNA polymerase Systemic Name: DNA nucleotides-transferase Enzyme Class: Transferase Substrates: DNA nucleosides Action: Synthesizes a strand of DNA using the complementary strand as a model

Common: DNA polymerase Systemic Name: DNA nucleotides-transferase Enzyme Class: Transferase Substrates: DNA nucleosides Action: Synthesizes a strand of DNA using the complementary strand as a model

Common: Lactase Systemic Name: ? Enzyme Class: ? Substrates: ? Action: Breaks down LACTOSE into _____ and _____

Common: Lactase Systemic Name: B-D-Galactosidase Enzyme Class: Hydrolase Substrates: Lactose Action: Breaks down LACTOSE into glucose and galactose

Common: Penicillinase Systemic Name: ? Enzyme Class: ? Substrates: Penicillin Action: Hydrolyzes _____ ring

Common: Penicillinase Systemic Name: Beta-Lactamase Enzyme Class: Hydrolase Substrates: Penicillin Action: Hydrolyzes beta-lactam ring

_____- is a process by which the weak bonds that collectively maintain the native shape of the apoenzyme are broken. This disruption causes extreme distortion of the enzyme's shape and prevents the substrate from attaching to the active site.

DENATURATION

DNA is hydrolyzed DEOXYRIBONUCLEASE, generally shortened to DNase

DNA is hydrolyzed ______, generally shortened to _____.

_____ are the molecules that are most important to the process of a metabolism. Linking anabolism and catabolism ensures the efficient completion of many processes.

ELECTRONS

Each enzyme is also assigned a common name that indicates the specific reaction it catalyses. With this system, an enzyme that digests a carbohydrate substrate is a ______;

Each enzyme is also assigned a common name that indicates the specific reaction it catalyses. With this system, an enzyme that digests a carbohydrate substrate is a CARBOHYDRASE.

Enzyme ______ is a means to stop further synthesis of an enzyme somewhere along its pathway.

Enzyme repression is a means to stop further synthesis of an enzyme somewhere along its pathway.

Enzymes are not all produced in equal amounts or at equal rates. Some enzymes, called ______ enzymes are always present and in relatively small amounts , regardless of the cellular environment.

Enzymes are not all produced in equal amounts or at equal rates. Some enzymes, called CONSTITUTIVE enzymes are always present and in relatively small amounts , regardless of the cellular environment.

The Role of Microbial Enzymes in Disease: Enzymes in bacteria that contribute to pathogenicity are referred to as _____ factors or ______ in some cases.

Enzymes in bacteria that contribute to pathogenicity are referred to as VIRULENCE factors or TOXINS in some cases.

Examples of EXOenzymes are _____, ______, and _____.

Examples of EXOenzymes are cellulose, amylase, and penicillinase.

For catalysis to continue, enzymes eventually must be replaced. This cycle works into the scheme of the cell, where replacement of enzymes can be regulated according to cell demand.

For catalysis to continue, enzymes eventually must be replaced. This cycle works into the scheme of the cell, where replacement of enzymes can be regulated according to cell demand.

For example, catalase, an enzyme that we learned in section 7.2 breaks down ______, and has _____ as a metallic cofactor

For example, CATALASE, an enzyme that we learned in section 7.2 breaks down HYDROGEN PEROXIDE, and has IRON as a metallic cofactor

For example, the enzymes involved in utilizing _____ are very important and thus are constitutive.

For example, the enzymes involved in utilizing glucose are very important and thus are constitutive.

The whole conjugated enzyme is referred to as the _____ enzyme

Holoenzyme

______ cleave bonds on molecules with the addition of water ______ add groups to or remove groups from double-bonded substrates.

Hydrolases cleave bonds on molecules with the addition of water Lyases add groups to or remove groups from double-bonded substrates

If the bacterium is subsequently inoculated into a medium containing only sucrose as a carbon source, it will cease synthesizing lactase and begin synthesizing _____.

If the bacterium is subsequently inoculated into a medium containing only sucrose as a carbon source, it will cease synthesizing LACTASE and begin synthesizing SUCRASE.

In ______ enzyme activity is inhibited by a molecule that resembles or mimics the enzyme's normal substrate. There are many drugs that are effective via the process of _____ such as aspirin (inhibits he synthesis of molecules that mediate swelling and pain).

In COMPETITIVE INHIBITION enzyme activity is inhibited by a molecule that resembles or mimics the enzyme's normal substrate. There are many drugs that are effective via the process of COMPETITIVE INHIBITION such as aspirin (inhibits he synthesis of molecules that mediate swelling and pain).

In connection to anabolism, _____ are abused by body builders. Normally they're taken for treating medical conditions such as delayed puberty and cachexia caused by AIDs. Use of this can result in damage to the ____ and ____ (organs), as well as cause ______, _____, and psychological effects (depression, aggression, irritability)

In connection to anabolism, ANABOLIC steroids are abused by body builders. Normally they're taken for treating medical conditions such as delayed puberty and cachexia caused by AIDs. Use of this can result in damage to the HEART and LIVER (organs), as well as cause INFERTILITY, BLOOD CLOTS, and psychological effects (depression, aggression, irritability)

In ______ hosts, streptolysin damages blood cells and tissues. It is also responsible for ______ red blood cells used in blood agar dishes, and this trait is used for identifying the bacteria growing in culture.

In mammalian hosts, streptolysin damages blood cells and tissues. It is also responsible for LYSING red blood cells used in blood agar dishes, and this trait is used for identifying the bacteria growing in culture.

In the early 1980s, a special class of enzymes was identified and found to be made of RNA called ______, which were RNA molecules that catalyze reactions on other RNA.

In the early 1980s, a special class of enzymes was identified and found to be made of RNA called RIBOENZYMES, which were RNA molecules that catalyze reactions on other RNA.

______ change a substrate into its isomeric form ______ catalyze the formation of bonds with the input of ATP and removal of water.

Isomerases change a substrate into its isomeric form Ligases catalyze the formation of bonds with the input of ATP and removal of water.

Patterns of metabolism. In general, metabolic pathways consist of a linked series of individual chemical reactions that produce intermediary metabolites and lead to a final product. These pathways occur in several patterns, including ____, _____, and ____.

LINEAR, CYCLIC, and BRANCHED

Many of the drugs developed to treat HIV/AIDS prevent maturation of the virus by the HIV _____. Certain antidepressants, diuretics, and antibiotics also act as competitive inhibitors

Many of the drugs developed to treat HIV/AIDS prevent maturation of the virus by the HIV PROTEASES. Certain antidepressants, diuretics, and antibiotics also act as competitive inhibitors

_______ is all the chemical reactions and physical workings of the cell, most of them fall into one of two categories.

Metabolism>>

Cofactors: Supporting the Work of Enzymes: The _____ cofactors, including iron, copper, magnesium, manganese, zinc, cobalt, selenium and many others help with precise functions between the enzyme and it's substrate.

Metallic cofactors

Enzyme Structure: Most enzymes are proteins and can be classified as two things: ____ enzymes consists of protein alone whereas _____ enzymes contain protein and some other nonprotein molecule or molecules.

Most enzymes are proteins and can be classified as two things: SIMPLE enzymes consists of protein alone whereas CONJUGATE enzymes contain protein and some other nonprotein molecule or molecules.

Not all microbial enzymes digest tissues; some, such as ______ INACTIVATE penicillin and thereby protect a microbe from its effects

Not all microbial enzymes digest tissues; some, such as PENICILLINASE INACTIVATE penicillin and thereby protect a microbe from its effects

______ is the loss of electrons and _______ is the gain of electrons

OXIDATION is the loss of electrons and REDUCTION is the gain of electrons

________ remove electrons from one substrate and add them to another

OXIDOREDUCTASES remove electrons from one substrate and add them to another

Often, the regulatory molecule is the product of the enzymatic reaction itself. This provides a _______ feedback mechanism that can slow down enzymatic activity once a certain concentration of product is produced.

Often, the regulatory molecule is the product of the enzymatic reaction itself. This provides a NEGATIVE feedback mechanism that can slow down enzymatic activity once a certain concentration of product is produced.

Other enzymes are _______ enzymes the production of which is either turned on or INDUCED "OR" turned off or REPRESSED in response to changes in concentration of the substrate.

Other enzymes are REGULATED enzymes the production of which is either turned on or INDUCED "OR" turned off or REPRESSED in response to changes in concentration of the substrate.

Other enzymes are regulated enzymes the production of which is either turned on or _____ OR turned off or ______ in response to changes in concentration of the substrate.

Other enzymes are regulated enzymes the production of which is either turned on or INDUCED "OR" turned off or REPRESSED in response to changes in concentration of the substrate.

Transfer Reactions by Enzymes: Other enzyme-driven processes that involve the simple addition or removal of functional group are important to overall workings of the cell. ______-reduction and other transfer activities are examples of these types of reactions.

Oxidation-reduction and other transfer activities are examples of these types of reactions.

______, a respiratory and skin pathogen, produces elastase and collagenase, which digests ELASTIC and collagen, 2 proteins found in connective tissue. These increase the severity of certain lung diseases and burn infections.

Pseudomonas aeruginosa, a respiratory and skin pathogen, produces elastase and collagenase, which digests elastic and collagen, 2 proteins found in connective tissue. These increase the severity of certain lung diseases and burn infections.

_____ are thought to be remnants of the earliest molecules on earth that could have served as both catalysts and genetic material. What does the RN hypothesis state?

RIBOZYMES are thought to be remnants of the earliest molecules on earth that could have served as both catalysts and genetic material. The RNA hypothesis states that RNA was the first genetic material within ancient cells. In natural systems. (p197)

A shorter word for oxidation-reduction reactions is

Redox reactions (very common in cells)

Some fats and other lipids are digested by ______.

Some fats and other lipids are digested by LIPASES.

Soon, we shall see that coenzymes ____ and _____ hydrogen atoms, electrons, carbon dioxide and amino acid groups.

Soon, we shall see that coenzymes carry and transfer hydrogen atoms, electrons, carbon dioxide and amino acid groups.

Soon, we shall see that coenzymes carry and transfer _____ atoms, ___, ______ and _____ groups.

Soon, we shall see that coenzymes carry and transfer hydrogen atoms, electrons, carbon dioxide and amino acid groups.

Streptococcus pyogenes is an exoenzyme produces a ______ that digests blood clots and apparently assists in invasion of wounds.

Streptococcus pyogenes is an exoenzyme produces a streptokinase that digests blood clots and apparently assists in invasion of wounds.

Such nonfunctional enzymes block metabolic reactions and thereby can lead to cell death. Low or high pH or certain chemicals like heavy ____ and _____ are also denaturing agents

Such nonfunctional enzymes block metabolic reactions and thereby can lead to cell death. Low or high pH or certain chemicals heavy metals and alcohol are also denaturing agents

The HOLOENZYME is a a combinations of proteins consisting of ___-enzymes and one or more _______, which are either organic molecules, called _____ or inorganic elements like _____

The HOLOENZYME is a a combinations of proteins consisting of APOENZYMES and one or more COFACTORS, which are either organic molecules, called COENZYMES or inorganic elements like METAL IONS

The coenzyme carriers are ______ and ______

The coenzyme carriers are NAD (nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide)

The compound that loses the electrons is _____ and the compound that receives the electrons is ______

The compound that loses the electrons is OXIDIZED and the compound that receives the electrons is REDUCED

The general function of a ______ is to remove a chemical group from one substrate molecule and add it to another substrate, thereby serving as a transient carrier of this group.

The general function of a coenzyme is to remove a chemical group from one substrate molecule and add it to another substrate, thereby serving as a transient carrier of this group.

The inverse of enzyme repression is enzyme ______. In this process, enzymes appear (are induced) only when suitable substrates are present—that is, the synthesis of an enzyme is induced by its substrate. Both mechanisms are important genetic control systems in bacteria.

The inverse of enzyme repression is enzyme induction. In this process, enzymes appear (are induced) only when suitable substrates are present—that is, the synthesis of an enzyme is induced by its substrate. Both mechanisms are important genetic control systems in bacteria.

The second type of metabolism is ______: the opposite of ______: a process where reactions break the bonds of larger molecules into smaller ones, and release energy.

The second type of metabolism is CATABOLISM: the opposite of ANABOLISM a process where reactions break the bonds of larger molecules into smaller ones, and release energy.

The site where the substrate binds is a crevice or groove called the ______ or _____ and there can be one or several such sites. The 3D shape of each site is formed by the way the amino acid chain or chains are folded. Each type of enzyme has a different primary structure, variations in folding, and very unique active sites.

The site where the substrate binds is a crevice or groove called the ACTIVE SITE or CATALYTIC SITE and there can be one or several such sites. The 3D shape of each site is formed by the way the amino acid chain or chains are folded. Each type of enzyme has a different primary structure, variations in folding, and very unique active sites.

This is _______ inhibition, because the regulator molecule does not bind in the same site as the substrate.

This is INCOMPETITIVE inhibition, because the regulator molecule does not bind in the same site as the substrate.

______ transfer functional groups from one substrate to another ______ cleave bonds on molecules with the addition of water

Transferases transfer functional groups from one substrate to another Hydrolases cleave bonds on molecules with the addition of water

One of the most important components of coenzymes is ______, which explains why they're important to nutrition and may be required as growth factors for living things.

VITAMINS

When enzymes are subjected to changes in these normal conditions, they tend to be chemically unsta- ble, or _____. ____ temperatures inhibit catalysis, and ____ temperatures denature the apoenzyme. (High/low)

When enzymes are subjected to changes in these normal conditions, they tend to be chemically unsta- ble, or LABILE. Low temperatures inhibit catalysis, and high temperatures denature the apoenzyme.

Coenzymes are one type of _____.

cofactor