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What is metabolism

The sum total of all chemical reactions that occur in a cell


What are metabolites

The small molecules involved in metabolism


What are catabolic reactions

Energy-releasing metabolic reactions (breakdown of food)


What are anabolic reactions

Energy-requiring metabolic reactions (building up)


What are nutrients

Supply of monomers (or precursors of) required by cells for growth


What nutrients do autotrophs require

They get their carbon from inorganic sources (CO2). They may require only inorganic molecules (water, CO2, salts, and trace metals) and can make everything they need from CO2


What nutrients do heterotrophs require

They get their carbon from organic sources. They require organic molecules and obtain them from autotrophs


What are macronutrients

Nutrients required in large amounts


What are micronutrients

Nutrients required in trace amount


What are the essential elements

Hydrogen, Carbon, Nitrogen, Oxygen, Phosphorus, Sulfur, and Selinium


Describe Carbon and the major classes of macromolecules that require carbon

It is required by ALL cells, a typical bacteria cell is 50% carbon, it is a major element in ALL classes of macromolecules (sugars, AA, lipids, and nucleotides). Heterotrophs use organic carbon and Autotrophs use inorganic carbon (CO2)


Describe Nitrogen

Typical bacteria cell is 12% nitrogen, it is a key element in proteins, nucleic acids, and other cell constituents. Nitrogen gas is very stable because of triple covalent bond


How is nitrogen used by organisms

Some prokaryotes can fix nitrogen from the air by converting N2 into NH4, a usable form of nitrogen. NH4 can also be converted to NO3, another usable form of nitrogen


Describe Phosphorus

It is used in nueclic acids and phospholipids


Describe Sulfur

Sulfur-containing amino acids (cysteine and methionine) and also in Vitamins and coenzyme A


Describe Sodium

Major monovalent cation (Na+)


Describe Potassium

Major monovalent cation (K+) and is required by some enzymes for activity


Describe Magnesium

Divalent cation (Mg 2+), stabilizes ribosomes, membranes, and nucleic acids, and also required for many enzymes


Describe Calcium

Divalent cation (Ca 2+), helps stabilize cell walls in microbes and plays a key role in heat stability of endospores. And very small amounts required as cofactors for certain enzymes


Describe Iron

Key component of cytochromes and FeS proteins involved in electron transport in respiration and photosynthesis.


What are siderophores

Iron is not very soluble and cells produce particular iron-binding organic molecules (siderophores) that bind iron in the environment and bring it into the cell


What are growth factors

Organic compounds required in small amounts by certain organisms. Vitamins, amino acids, purines, and pyrimidines. Function to allow for enzymatic activity of certain enzymes


Do autotrophs need growth factors

Many autotrophs that get CO2 from the environment typically require zero growth factors, they can make everything that they need.


What are vitamins

They are small, nonprotein, organic molcules commonly required growth factors, most function as coenzymes


What are coenzymes

Coenzymes are nonprotein organic, carbon-based molecules required for enzyme activity. Many enzymes are just the seqeunce of amino acid and its not enough to catalyze the reaction, so you need a specialized molecule to associate with the polypeptide chain of the enzyme and vitamins are one type of coenzyme.


What is culture media

Nutrient solutions used to grow microbes in the laboratory, must know or determine the nutritional requirements for each microbe


What are the classes of components of media

Defined and Complex media


What is defined media

The precise chemical composition is known


What is complex media

Composed of digests of chemically undefined substances. May know the exact composition of some chemicals but stuff like yeast, blood, and meat extracts, you won't know the exact compositions of.


What is selective media

Only allows the growth of certain strains, contains compounds that selectively inhibit growth of some microbes but not others. Nutrient present is one that only target organism can use, or toxic nutrient is present that will kill non-target organisms.


What is differential media

Certain strains can be identified because they show visible difference. Contains an indicator, usually a dye, that detects particular chemical reactions occurring during growth of certain microbes. Can differentiate between different organisms between shape or color, and target and non-target organisms will look different due to something like an indicator


What is a pure culture

Culture containing only a single kind of microbe, a clonal population. All genomes present in cells in a pure culture will be extremely similar, but there will be natural mutations


What are contaminants

Unwanted organisms in a culture


How can cells be grown

Cells can be grown in liquid or solid culture media.


How is solid media prepared

Solid media are prepared by addition of gelling agent (agar or gelatin)


What happens when cells are grown in solid media

When grown on solid media, cells form isolated masses called colonies


What is sterilization

Want to sterilize equipment before using it because microbes are everywhere and you do not want contamination.


What are two methods of sterilization

Heat (autocalve, a specialized pressure cooker) and Filtration


What is Aseptic (Sterile) Technique

Sterilization technique to prevent contamination. When you want to innoculate a broth:
1. Flame your loop
2. Unscrew cap from broth
3. Flame the tip of the tube
4. Innoculate the broth with loop
5. Flame the tip of the tube again
6. Screw cap back on tube


What are pure culture techniques for isolation of single colonies

Streak plate, pour plate, and spread plate


What do free-energy calculations not provide information on

Reaction rates


What is activation energy

The every required to bring all molecules in a chemical reaction into the reactive states.


What is a catalysis

It is usually required to breach activation energy barrier.


What is a catalyst

A substance that lowers the activation energy of a reaction, increases the reaction rate, and does NOT affect energetics or equilibrium of a reaction


What is a spontaneous reaction



What is a non-spontaneous reaction



What is the speed of a reaction with a high activation energy

The reaction is slow


What are enzymes and what kind of bonds do they form with substrates

They are biological catalysts, typically proteins (some RNAs), are highly specific for substrates and bonds made, and typically rely on weak bonds between enzymes and substrates: hydrogen bonds, van der Waals forces and hydrophobic interactions


What is the active site

The region of enzyme that binds substrate. The substrate is recognized by its shape of its bond at the active site


What are small nonprotein molecules that participate in catalysis but are not substrates

Prosthetic groups and coenzymes


What are prosthetic groups

Attached to enzymes. They bind tightly to enzymes and usually bind covalently or permenently (Heme group in cytochromes)


What are coenzymes

Diffusable. They are loosely bound to enzymes, derivatives of vitamins (NAD+/NADH). Coenzymes can be reversibly oxidized and reduced


How do cells get chemical energy to run their metabolism

Energy from redox reactions are used in synthesis of energy-rich compounds, redox occurs in pairs


What is an electron donor

The substance oxidized in a redox reaction


What is an electron accepter

The substance reduced in a redox reaction


What is reduction potential

E0, tendency to donate electrons, the more negative the number, the greater tendency to donate electrons, the more positive, the great tendency to accept electrons.


What are electron carriers

NAD+/NADH are both electron acceptors and donors. When electrons are transfered to NAD+ it is reduced, and when NADH donates the electron it is oxidized


What is the redox tower

Represents the range of possible reduction potentials. The reduced substances at the top (food) donate electrons and the oxidized substances at the bottom accept electrons. The farther the electrons "drop" the greater the amount of energy released. Most electronegative molecules at the bottom (NO3-, Fe3+, and O2)


What are the two classes of electron carriers

Prosthetic groups and Coenzymes


What is the evolutionary selection for carriers

Electron carriers can carry electrons to an electron acceptor on a different enzyme that's specialized for the second transfer. You just need one enzyme for each donor and one enzyme for each receptor


CHemical energy released in redox reactions is primarily stored in what phosphorylated compounds for a short period of time

ATP (prime currnecy), PEP, G6P, and Acetyl-CoA


What is needed for long-term storage of energy

Involved insoluble polymers that can be later oxidized to generate ATP


What are some examples of insoluble polymers used for energy storage in prokaryotes

Glycogen, PHB, and PHA


What are some examples of insoluble polymers used for energy storage in eukaryotes

Starch, Glycogen, and Lipids


What are the two reaction pathways used for energy conservation in chemoorganotrophs

Fermentation and Respiration


What is fermentation

Substrate-level phosphorylation; ATP directly synthesized from an energy-rich intermediate. (ATP made from glycolysis, no ATP actually made in fermentation itself) Pryruvate is converted to lactic acid or ethanol in order to recycle the NADH to NAD+


What is respiration

Oxidative phosphorylation; ATP produced from proton motive force across membrane which is generated by electron transport from reduced food molecules


What is Glycolysis

Pathway for catabolism of glucose, anaerobic process, and has 3 stages: glucose consumed, 2 ATPs made, and fermentation products generation.


What happens after Glycolysis

Glycolysis is the first process of breaking down sugar and will diverge depending on whether or not there is an external electron acceptor (oxygen, nitrate). If there is no acceptor then fermentation will take place, can't use electron carriers if you don't have an end "sink" to put all the electrons at the end


What are the substrates in Glycolysis

Glucose molecule, 2 ATPs, inorganic phosphate, and NAD+


What are the products in Glycolysis

Net gain of two ATP molecules (4 ATPs are made), 2 Pyruvates and 2 NADH


What is the work done in Glycolysis

A 6 carbon sugar is split into 2, 3 carbon molecules (pyruvate), and in this process we have made a net total of 2 ATPs. These chemical reactions require a reduction of NAD+ to NADH and if there is no external electron carriers then the reaction will stop because all the NAD+ available would have been converted to NADH


What is Aerobic Respiration

Oxidation using O2 as the terminal electron acceptor, it yields much more ATP than fermentation


What are electron transport systems

On the membrane, electron transport proteins (Fe and FeS cofactors associated) mediate transfer of electrons from reduced electron carriers (reduced by metabolism of food molecules) and the energy released during transfer is used to create PMF which is then used to synthesize ATP


Where does electron transport take place in bacteria

On the cytoplasmic membrane


What is exergonic

Energy releasing


What is endergonic

Energy absorbing


How are electron carriers arranged in the membrane

In order of their reduction potential, each transfer is exergonic. Organized in order of increasing oxidizing power.


What does the final electron carrier do

The final carrier in the chain donates the electrons and protons to the terminal electron acceptor, which for aerobes is oxygen


In the ETC what are the substrates

Oxygen and Electron Carriers


In the ETC what are the products



In the ETC what is the work done

The electron transfers work to produce a proton motive force by pumping protons to the outside of the cell. Results in generation of pH gradient and an electrochemical potential across the membrane (PMF)


Where do these pumped protons originate from

The NADH and the dissociation of water


Once the PMF is generated what are the conditions outside

Electrically positive and acidic


Once the PMF is generated what are the conditions inside

Electrically negative and alkaline


What is ATP Synthase (ATPase)

Protein complex that uses PMF to make ATP. It is a large enzyme composed of separate proteins and is anchored in the membrane. As the H+ lose their energy by diffusing down their electrochemical gradient, the energy is captured by the ATPase enzyme to combine ADP and P to make ATP. It has a turning mechanism


What are the substrates for ATP synthase

H+ protons, ADP, and phosphate


What are the products for ATP synthase



What is the citric acid cycle

Pathway through which pyruvate is completely oxidized to CO2, provides energy in the form of ATP, NADH, and FADH2


What are the substrates of the citric acid cycle

Pyruvate, phosphate and electron carriers: 4 NAD+, 1 FAD, 1 GDP, and Acetly-CoA


What are the products of the citric acid cycle

3 CO2, 4 NADH, 1 FADH2, and 1 GTP


What is the work done in the citric acid cycle

It is to make the electron carriers, 4 NADH, 1 FADH2, and GTP, they still have a lot of energy and can lose that energy when its transferred in the ETC


How many ATP's do you get from Glycolysis

Substrate Level: Net gain of 2 ATPs
Oxidative Level: 2 NADH -> 6 ATPs


How many ATP's do you get from Citric Acid Cycle

Substrate Level: 1 GTP -> 1 ATP
Oxidative Level: 4 NADH -> 12 ATPs and 1 FADHS -> 2 ATPs


How many ATP's total do you get from Aerobic Respiration

38 ATPs total (counting GTP as ATP) per glucose molecule. Glycolysis runs once but CAC runs twice


What compounds made in the CAC are available for biosynthetic purposes

a-Ketoglutarate, OAA, Succinyl-CoA, and Acetyl-CoA


What are the 5 mechanisms in which microorganism generate energy

Fermentation, Aerobic respiration, Anaerobic respiration, Chemolithotrophy, and Phototrophy


What is the energy generation process for chemoorganotrophs

Chemoorganotrophy means that you get energy from ORGANIC compounds, if there is no oxygen present you can do fermentation, in the presence of oxygen you can do aerobic respiration. You breakdown organic compounds to make CO2 to make ATP and NADPH


What is the energy generation process for chemolithotrophs

Means that you get energy from INORGANIC compounds, can be aerobic or anaerobic and proceed like chemoorganotrophs


What is the energy generation process for photoheterotrophs

Light energy is used in the ETC to generate ATP and NADH to be used with ORGANIC compounds in biosynthesis


What is the energy generation process for photoautrophs

Light is used in the ETC to generate ATP and NADH to be used with INORGANIC compounds (CO2) in biosynthesis


What is Anaerobic Respiration

The use of electron acceptors other than oxygen, Nitrate, Ferric Iron, Sulfate, Carbonate, and some organic compounds. There is generally less energy released compared to aerobic respiration. Still involved ETC, PMF, and ATPase


What is chemolithotrophy

Uses inorganic chemicals as electron donors (food). Begins with oxidation of inorganic electron donor, often autotrophic uses CO2 as carbon source


What is phototrophy

Uses light as an energy source


What is photophosphorylation

Light-mediated ATP synthesis


What are photoautotrophs

Uses redundant NADH and ATP for assimilation of CO2 for biosynthesis


What are photoheterotrophs

Uses ATP generated by photophosphorylation for assimilation of organic carbon from environment for biosynthesis


What are the 2 major modes of enzyme regulation

Amount and Activity


What is amount in enzyme regulation

Regulation at the gene level


What is activity in enzyme regulation

Temporary activation or inactivation of enzymes through changes in protein structure


What is feedback inhibition

Mechanism for turning off the reactions in a biosynthetic pathway. Usually the end product of the pathway binds to the first enzyme in the pathway, to inhibit activity


What is an allosteric enzyme

The enzyme that is inhibited in feedback inhibition.


What binding sites do enzymes have

An active site for substrate to bind to make product and an allosteric site for regulation


Why is feedback inhibition important

The cell doesn't want to waste energy making more end products than it needs, so when the cell has a certain number of end products it will shutdown the pathway


How does the end product regulate the enzyme

When the end product binds to the allosteric site, it changes the shape of the protein so the substrate can't bind to the active site and it can no longer carry out the catalytic reaction


What are covalent modifications

Method of regulating biosynthetic enzymes. Regulation involved a small molecule attached to or removed from the protein, which results in conformational change that inhibits or activates activation.


What are some covalent modifications

AMP, ADP, PO4 2-, and CH3


What regulates covalent modifications

Signal transduction pathway that causes a covalent modification of an enzyme, attaches a functional group or small molecule to the enzyme that results in a change in the shape, can turn the enzyme on or off


What is electronegativty

The tendency for a molecule to accept electrons. They are at the bottom at the redox tower. The more electronegative a molecule is, the more likely it is to accept electrons


In glycolysis what is the fermentated nutrient and its product(s)

The fermentated nutrient is the electron donor and the product is the electron acceptor


Where is oxygen in the redox tower.

Oxygen is at the very bottom of the tower, oxygen is the most electronegative molecule in the tower


What are a-ketoglutarate and OAA used for

Precursors for amino acids and OAA is also converted to phosphoenolyryruvate, a precursor of glucose


What is Succinyl-CoA used for

Required for synthesis of cytochromes, chlorophyl and other tetrapyrrole compounds


What is Acetly-Coa used for

Necessary for fatty acid biosynthesis