EXAM 3 UCF Microbiology

Metabolism

is the total of all chemical reactions in the cell and is divided into two parts:

-Catabolism

-Anabolism

Catabolism

Metabolic pathways that break down molecules, releasing energy.

-fueling reactions

-energy-conserving reactions

-provide ready source or reducing power(electrons)

-generates precursors for biosynthesis

Anabolism

Metabolic pathways that construct molecules, requiring energy.

-the synthesis of complex organic molecules from simpler ones

-requires energy from fueling reactions

How many transformations does the nitrogen cycle have?

-It has 8 transformations

-4 are solely done by microbes. However, microbes are part of the other 4

Chemical Work

Synthesis of complex molecules

Transport Work

Take up nutrients, elimination of wastes, and maintenance of ion balances

Mechanical Work

cell motility and movement of structures within cells

What is thermodynamics?

-A science that analyzes energy changes in a collection of matter called a system, such as a cell

-All other matter in the universe is called the surroundings

first law of thermodynamics

Energy can neither be created NOR destroyed

-total energy in universe remains constant

-However, energy may be redistributed either within a system or between the system and its surroundings

Second Law of Thermodynamics

Physical and chemical processes proceed in such a way that the disorder of the universe increases to the maximum possible

-entropy=amount of disorder in a system

Entropy

Amount of disorder in a system

Calorie (cal)

amount of heat energy needed to raise 1 gram of water from 14.5 C to 15.5C

Joules (J)

Units of work capable of being done by a unit of energy

1 calorie=4.184J

Change in Free energy equation

ΔG = ΔH - TΔS

-Expresses the change in energy that can occur in chemical reactions and other processes

Note:

ΔG= free energy change, amount of energy available to do work

ΔH = change in enthalpy

T= Temp in Kelvin

ΔS= change in entropy

ΔG

free energy change, amount of energy available to do work

ΔH

Change in enthalpy

ΔS

Change in entropy

If ΔG is negative, then the reaction is___?

Spontaneous and exergonic

If ΔG is positive, then the reaction is___?

not spontaneous and Endergonic

When is a reaction at equilibrium?

When the rate of forward rxn=rate of reverse rxn

Standard Free Energy Change (ΔG^o')

(ΔG^o') is the free energy change defined at standard conditions of concentration, pressure, temperature, and pH

AMP

adenosine monophosphate (1 phosphate)

ADP

adenosine diphosphate(2 phosphates)

Exergonic break down of high energy ATP is coupled with _____ reactions to make them more favorable

endergonic

Exergonic Reactions

Chemical reactions that releases energy

Endergonic Reaction

Reaction that absorbs free energy from its surroundings.

GTP

Guanosine-5'-Triphosphate.

-Used for RNA transcription as the energy source. will become GDP when used.

CTP

cytosine 5'-triphosphate

UTP

Uridine 5'Ttriphosphate

ATP

(adenosine triphosphate) main energy source that cells use for most of their work

-Has a high phosphate transfer potential, which means that its readily able to send phosphates to other molecules. However, it doesn't have the highest phosphate transfer potential.

substrate-level phosphorylation (SLP)

The formation of ATP by directly transferring a phosphate group to ADP from an intermediate substrate in catabolism.

Oxidation-Reduction reaction

any chemical change in which one species is oxidized (loses electrons) and another species is reduced (gains electrons); also called redox reaction

NOTE:

LEO(Lose Electrons Oxidation)

GER(Gain Electrons Reduced)

or

OIL (Oxidation is Lose)

RIG (Reduction is Gain)

Electron Carries

are often used to transfer electrons from an electron donor to an electron acceptor, which can result in energy release, which can be conserved and used to form ATP

-The more electrons a molecule has, the more energy rich it is

-Glucose can donate up to 24 electrons

Oxidizing reaction

electron donating/losing

Reducing reaction

electron accepting/gaining

Conjugate Redox pair

acceptor and donor of a half reaction

Standard redox potential

Eo

-Equilibrium constant for an oxidation-reduction reaction

-Given in Volts

-A measure of the tendency of the reducing agent to lose electrons

A more negative Eo =_____?

Better electron donor (Reducing agent/reductant)

A more positive Eo=______?

Better electron acceptor (Oxidizing agent/Oxidant)

2 Rules of Redox pairs

1. When writing a redox couple, the reduced member of the pair that is more negative donates electrons to the oxidized member of the pair that is more positive

2. The greater the difference in redox potential (ΔE^o') between the redox pairs that serves the electron donor and the acceptor, the greater the amount of energy available (ΔG^o') in the oxidation-reduction reaction

Substances being oxidized, is the_____?

Electron donor/reducing agent/reductant

Substances being reduced, is the_____?

Electron acceptor/oxidizing agent/ oxidant

Oxidizing agents gets____?

reduced

Reducing agents gets___?

Oxidized

Nernst Equation

(ΔG^o') = -nF(ΔE^o')

Faraday's Constant (F):

23 kcal/volt

96.5kJ/volt

Faraday's Constant (F):

23 kcal/volt

96.5kJ/volt

(ΔE^o') equation

(ΔE^o') = (E of oxidizing agent)-(E of reducing agent)

or

(ΔE^o') = (E of more positive)-(E of more negative)

The first electron carrier has the most___(ΔE^o')?

negative

Electron Transport Chain (ETC)

The potential energy stored in the first redox couple is used to form ATP

-The first carrier is reduced and electrons are moved to the next carrier and so on

Its is found:

-Mitochondria or chloroplast of eukaryotes

-on the cell membranes of prokaryotes

Where is the ETC found in eukaryotes?

In the mitochondria or chloroplast

Where is the ETC found in prokaryotes?

Cell membrane

List the Main Electron Carriers

-NADH & NADPH

-FAD & FMN

-CoQ/ubiquinone

-Cytochromes

-Nonhemer iron-sulfur proteins

NADH and NADPH does what?

accepts two electrons and one proton

-both have a nicotinamide ring

FAD & FMN does what?

Carry two electrons and two protons

-Proteins with FAD and FMN are known as flavoproteins

Flavoproteins are proteins with___?

FAD and FMN

CoQ (ubiquinone)

transports two electrons and two protons

Cytochromes

use iron to transfer one electron at a time

-iron is part of a heme group

Nonheme iron-sulfur proteins

(Ferredoxin) use iron to transport one electron at a time

-iron is NOT part of a heme group

Biochemical Pathways

-enzymes can be linked together to form pathways

-pathways can be linear, cyclic, or branching

-Pathways often overlap/feed into each other which creates complex networks and dynamic pathways, which can be used to monitor changes in metabolite levels (Flux)

Enzymes

Carry outt reactions at physiological conditions so they proceed in a timely manner

-speeds up the rate at which a reaction proceeds toward its final equilibrium

-enzymes do NOT alter the equilibrium

-Lower activation energy by increasing concentrations of substrates at active site of enzyme

Protein Catalysts

have high specificity for the reaction catalyzed and the molecules acted on

-substances that increase the rate of a reaction without being permanently altered

Substrates

reacting molecules

Products (Enzyme)

substances formed by reaction

Apoenzyme

enzymes composed of one or more polypeptides

Cofactor

-Cofactors include metal ions or organic molecules

-nonprotein component

can be subdivided into:

-prosthetic group: firmly attached

-coenzyme: loosely attached, can act as carriers/shuttles

Prosthetic group

A cofactor or coenzyme that is covalently bonded(firmly attached) to a protein to permit its function

Coenzyme

an organic cofactor that is loosely attached and can act as carriers/shuttles

Holoenzyme

apoenzyme + cofactor

Transition-State complex

resembles both the substrates and the products

activation energy (Ea)

the energy required to form transition state complex

How do Enzymes lower activation energy?

-By increasing concentration of substrate at active site of enzyme

-By orienting the substrates properly with respect to each other in order to form the transition-state complex

-Induced fit model for the enzyme substrate interaction

What effects do Enzymes cause?

-Reaction increases as substrate increases. No further increase occurs after all enzyme molecules are saturated with substrate

-Enzyme activity is significantly impacted by substrate concentration (Km), pH, and temperature

Any of these kinds of impacts leads to denaturation

Denaturation

loss of biological activity

Competitive inhibitor

directly competes with binding of substrate to active site

-many drugs work like this, such as sulfa drugs inhibit the binding of PABA

Noncompetitive ihibitor

Binds to the enzyme at a site other than the active site

-changes the enzyme's shape so that it becomes less active

Thomas Cech and Sidney Altman

discovered that some RNA molecules can catalyze reactions, these molecules are known as Ribozymes

Ribozymes

-discovered by Thomas Cech and Sidney Altman

-Catalyze peptide bond formation, also known as translation

-Self splicing (Group I and II splicing)

-Involved in self-replication

List the three general approaches cells use to regulate metabolism

-Metabolic channeling (Compartmentation)

-Regulation of synthesis of a particular enzyme (Transcriptional and translational)

-Direct stimulation or inhibition of the activity of a critical enzyme (Post-translational):

*Irreversible - protein cleavage

*Reversible - allosteric regulation or covalent modification

List the three chemical groups commonly used to covalently modify an enzyme and its activity

Phosphate, methyl, and adenyl

Regulation of Metabolism

Important for conservation of energy and materials

maintenance of metabolic balance despite changes in the environment

3 Mechs:

-Metabolic channeling (Compartmentation)

-Regulation of synthesis of a particular enzyme (Transcriptional and translational)

-Direct stimulation or inhibition of the activity of a critical enzyme (Post-translational):

*Irreversible - protein cleavage

*Reversible - allosteric regulation or covalent modification

Allosteric Regulation

-reversible

-Most regulatory enzymes

-Activity altered by a small molecule known as allosteric effector

Allosteric Effector

binds non-covalently at regulatory site

-changes shape of enzyme and alters activity of catalytic site

-Positive effector increases enzyme activity

-Negative effector inhibits enzyme activity

covalent modification of enzymes

-Reversible on and off switch

-Addition or removal of a chemical group (Phosphate, methyl, adenyl)

-Advantages of this method is that it responds to more stimuli in varied/sophisticated ways, and regulation of enzymes that catalyze via covalent modification, adds second level of control

Pacemaker enzyme

Catalyzes the slowest or rate-limiting reaction in the pathway

Feedback Inhibition

-Also called end-product inhibition

-Inhibition of one or more critical enzymes in a pathways regulates entire pathway. This is done by pacemaker enzyme.

-Each end product regulates its own pathway, and the initial pacemaker enzyme

-Isoenzymes are different enzymes that catalyze the same reaction

Isoenzymes

Different enzymes that catalyze the same reaction

Carbon Source

-heterotrophs use organic molecules, which often also serve as energy source. Can use a variety of carbon sources

-Autotrophs use carbon dioxide. Must obtain energy from other sources.

Energy source

-Phototrophs use light

-Chemotrophs obtain energy from oxidation of chemical compounds

Electron Source

-Lithotrophs use reduced inorganic substances

-Organotrophs use organic compounds

Chemo-

chemical

Photo-

light

Organo-

Organic molecules

Litho-

Inorganic molecules

Hetero-

Organic molecules

Classes of Major Nutritional Types

-Photolithoautotrophs/photoautotrophs

-Chemolithoautotrophs

-Chemoorganoheterotrophs/Chemoheterotrophs/chemoorganotrophs

These are majority of the pathogens

auto-

inorganic molecules

Which classes of major nutritional types are the primary producers?

Chemolithoautotrophs & Photoautotrophs

Purple nonsulfur bacteria can be _____ without oxygen, or _____ in the presence of oxygen.

Photoorganoheterotroph/Chemoorganotroph

What are the fueling Reactions?

-ATP as an energy currency

-Reducing power to supply electrons for chemical reactions

-Precursor metabolites for biosynthesis

Chemoorganotrophic Fueling process

3 names: Chemoorganoheterotrophs/Chemoheterotrophs/chemoorganotrophs

-Energy source is oxidized

-releases energy(catabolism) and provides the carbon and electrons for anabolism.

-Processes include: Aerobic respiration, anaerobic respiration, and fermentation

-Oxidized organic energy source releases electrons->accepted by NADH/FADH2