microbio week 3

substrate level phosphorylation

ATP molecules produced during the energy payoff phase of glycolysis are formed by substrate-level phosphorylation (Figure 8.11), one of two mechanisms for producing ATP. In substrate-level phosphorylation, a phosphate group is removed from an organic molecule and is directly transferred to an available ADP molecule, producing ATP. During glycolysis, high-energy phosphate groups from the intermediate molecules are added to ADP to make ATP.

nitrogen cycle

N is key component in nucleic acids/aas Without nitrogen, organisms could not make dna/rna or proteins Continuous series, nitro passes from air--> soil --> organisms, return to air or soil

noncyclic photophosphorylation

Both photosystems are excited by light energy simultaneously. If the cell requires both ATP and NADPH for biosynthesis, then it will carry out noncyclic photophosphorylation. Upon passing of the PSII reaction center electron to the ETS that connects PSII and PSI, the lost electron from the PSII reaction center is replaced by the splitting of water. The excited PSI reaction center electron is used to reduce NADP+ to NADPH and is replaced by the electron exiting the ETS.

Denitrification

Conversion of nitrates into nitrogen gas When nitrate is converted or reduced into nitrogen gas anaerobically by soil bacteria,

autotrophs

Organisms that make their own food

photosystems

Photosynthetic pigments within the photosynthetic membranes are organized into photosystems, each of which is composed of a light-harvesting (antennae) complex and a reaction center. The

two types of photosystems

Photosystem II and Photosystem I Cyanobacteria and plant chloroplasts have both photosystems, whereas anoxygenic photosynthetic bacteria use only one of the photosystems. Both photosystems are excited by light energy simultaneously.

nitrogen fixation

Process of converting nitrogen gas into ammonia

chemical reaction of lactic acid fermentation

Pyruvate + NADH ↔ lactic acid + NAD+Pyruvate + NADH ↔ lactic acid + NAD+

oxidation reactions

Reactions that remove electrons from donor molecules, leaving them oxidized,

reduction in LIR

Six molecules of both ATP and NADPH (from the light-dependent reactions) are used to convert 3-PGA into glyceraldehyde 3-phosphate (G3P). Some G3P is then used to build glucose.

fermentation

Some living systems use an organic molecule (commonly pyruvate) as a final electron acceptor through a process called fermentation. Fermentation does not involve an electron transport system and does not directly produce any additional ATP beyond that produced during glycolysis by substrate-level phosphorylation. Organisms carrying out fermentation, called fermenters, produce a maximum of two ATP molecules per glucose during glycolysis.

Embden-Meyerhof-Parnas (EMP) pathway

Embden-Meyerhof-Parnas (EMP) pathway two distinct phases (Figure 8.10). The first part of the pathway, called the energy investment phase, uses energy from two ATP molecules to modify a glucose molecule so that the six-carbon sugar molecule can be split evenly into two phosphorylated three-carbon molecules called glyceraldehyde 3-phosphate (G3P). The second part of the pathway, called the energy payoff phase, extracts energy by oxidizing G3P to pyruvate, producing four ATP molecules and reducing two molecules of NAD+ to two molecules of NADH, using electrons that originated from glucose.

activation energy

Energy needed to get a reaction started

nitrogen inputs and outputs

Enters ecosystem through nitrogen fixation Bacteria- convert atmospheric nitrogen (n2) to ammonia nh3- biologically available to plants Once in soil, other bacteria convert some of the ammonia to nitrate- also bio available to plants Nitrogen exists in the ecosystem when other bacteria convert nitrate back to molecular nitrogen (n2)

transition reaction/bridge reactoin

For pyruvate to enter the next oxidative pathway, it must first be decarboxylated by the enzyme complex pyruvate dehydrogenase to a two-carbon acetyl group in the transition reaction, also called the bridge reaction (see Appendix C and Figure 8.12). In the transition reaction, electrons are also transferred to NAD+ to form NADH. To proceed to the next phase of this metabolic process, the comparatively tiny two-carbon acetyl must be attached to a very large carrier compound called coenzyme A (CoA). The transition reaction occurs in the mitochondrial matrix of eukaryotes; in prokaryotes, it occurs in the cytoplasm because prokaryotes lack membrane-enclosed organelles.

oxygenic photosynthesis

H2O is split and supplies the electron to the reaction center. Because oxygen is generated as a byproduct and is released, this type of photosynthesis is referred to as oxygenic photosynthesis.

disruptions to nitrogen cycle

Human impact is disrupting the nitrogen cycle Fertilizers, vehicle emissions, doubling availability of nitrogen While nitrogen is no longer a limiting factor for plant growth, the additional nitrogen can disrupt the ecosystem

cyclic photophosphorylation

If a cell's need for ATP is significantly greater than its need for NADPH, it may bypass the production of reducing power through cyclic photophosphorylation. Only PSI is used during cyclic photophosphorylation; the high-energy electron of the PSI reaction center is passed to an ETS carrier and then ultimately returns to the oxidized PSI reaction center pigment, thereby reducing it.

input and outputs of carbon from ecosystem

Inputs- photosynthesis Use solar energy/co2. release o2 Producers- convert solar energy to chemical energy Outputs- cell resp, burning fossil fuels, forest fires, deforestation Cell resp Use o2, release co2. consumers Key concept: Nitrogen cycles through the environment in steps that depend on a wide variety of bacteria. Human impact is increasing the amount of usable nitrogen in the environment

atp synthase

Large protein that uses energy from H+ ions to bind ADP and a phosphate group together to produce ATP is a complex protein that acts as a tiny generator, turning by the force of the H+ diffusing through the enzyme, down their electrochemical gradient from where there are many mutually repelling H+ to where there are fewer H+. In prokaryotic cells, H+ flows from the outside of the cytoplasmic membrane into the cytoplasm, whereas in eukaryotic mitochondria, H+ flows from the intermembrane space to the mitochondrial matrix. The turning of the parts of this molecular machine regenerates ATP from ADP and inorganic phosphate (Pi) by oxidative phosphorylation, a second mechanism for making ATP that harvests the potential energy stored within an electrochemical gradient.

catabolism

Metabolic pathways that break down molecules, releasing energy. exergonic

anabolism

Metabolic pathways that construct molecules, requiring energy. endergonic

reduction reactions

; those that add electrons to acceptor molecules, leaving them reduced,

Entner-Doudoroff (ED) pathway

A glycolytic pathway in which glucose 6-phosphate is initially oxidized to 6-phosphogluconate, and ultimately yields 1 pyruvate, 1 ATP, 1 NADH and 1 NADPH.

atp

A living cell must be able to handle the energy released during catabolism in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the "energy currency" of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell.

redox potential

A measure of the tendency of a given redox pair to donate or accept electrons.

pentose phosphate pathway

A metabolic process that produces NADPH and ribose 5-phosphate for nucleotide synthesis.

photosynthetic pigment

A molecule such as chlorophyll that is responsible for capturing solar energy in photosynthesis embedded in the thylakoid membrane-- where light energy is converted into chemical energy

endergonic reaction

A non-spontaneous chemical reaction in which free energy is absorbed from the surroundings.

chemiosmosis

A process for synthesizing ATP using the energy of an electrochemical gradient and the ATP synthase enzyme. The potential energy of this electrochemical gradient generated by the ETS causes the H+ to diffuse across a membrane (the plasma membrane in prokaryotic cells and the inner membrane in mitochondria in eukaryotic cells). This flow of hydrogen ions across the membrane, called chemiosmosis, must occur through a channel in the membrane via a membrane-bound enzyme complex called ATP synthase

exergonic reaction

A spontaneous chemical reaction in which there is a net release of free energy.

B-oxidation

The breakdown of triglycerides into smaller subunits called free fatty acids (FFAs) to convert FFAs into acyl-CoA molecules, which then are available to enter the Krebs cycle and ultimately lead to the production of additional ATP. sequentially removes two-carbon acetyl groups from the ends of fatty acid chains, reducing NAD+ and FAD to produce NADH and FADH2, respectively, whose electrons can be used to make ATP by oxidative phosphorylation. The acetyl groups produced during β-oxidation are carried by coenzyme A to the Krebs cycle, and their movement through this cycle results in their degradation to CO2, producing ATP by substrate-level phosphorylation and additional NADH and FADH2 molecules

why are cells unable to carry out respiration

The cell lacks a sufficient amount of any appropriate, inorganic, final electron acceptor to carry out cellular respiration. The cell lacks genes to make appropriate complexes and electron carriers in the electron transport system. The cell lacks genes to make one or more enzymes in the Krebs cycle.

circumstances aerobic respiration is not possible

The cell lacks genes encoding an appropriate cytochrome oxidase for transferring electrons to oxygen at the end of the electron transport system. The cell lacks genes encoding enzymes to minimize the severely damaging effects of dangerous oxygen radicals produced during aerobic respiration, such as hydrogen peroxide (H2O2) or superoxide (O2-).(O2-). The cell lacks a sufficient amount of oxygen to carry out aerobic respiration.

fixation in LIR

The enzyme ribulose bisphosphate carboxylase (RuBisCO) catalyzes the addition of a CO2 to ribulose bisphosphate (RuBP). This results in the production of 3-phosphoglycerate (3-PGA).

oxidative phosphorylation

The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration.

regeneration in lir

The remaining G3P not used to synthesize glucose is used to regenerate RuBP, enabling the system to continue CO2 fixation. Three more molecules of ATP are used in these regeneration reactions.

proton motive force

This electrochemical gradient formed by the accumulation of H+ (also known as a proton) on one side of the membrane compared with the other Because the ions involved are H+, a pH gradient is also established, with the side of the membrane having the higher concentration of H+ being more acidic. Beyond the use of the PMF to make ATP, as discussed in this chapter, the PMF can also be used to drive other energetically unfavorable processes, including nutrient transport and flagella rotation for motility.

cytochrome oxidase

This electron carrier, cytochrome oxidase, differs between bacterial types and can be used to differentiate closely related bacteria for diagnoses. For

high energy phosphate bonds

Thus, the bonds between phosphate groups (one in ADP and two in ATP) are called high-energy phosphate bonds. When these high-energy bonds are broken to release one phosphate (called inorganic phosphate [Pi]) or two connected phosphate groups (called pyrophosphate [PPi]) from ATP through a process called dephosphorylation, energy is released to drive endergonic reactions

homolactic fermentation

When lactic acid is the only fermentation product,

nitrification

ammonia is converted to nitrate ions (NO3-).

holoenzyme

an enzyme with the necessary associated cofactor or coenzyme is called a holoenzyme and is active.

amp

at the heart of atp composed of an adenine molecule bonded to a ribose molecule and a single phosphate group. Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA.

allosteric activators

bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme's active site(s) for its substrate(s).

noncompetitive (allosteric) inhibitor

binds to the enzyme at an allosteric site, a location other than the active site, and still manages to block substrate binding to the active site by inducing a conformational change that reduces the affinity of the enzyme for its substrate (

Calvin-Benson cycle

biochemical pathway used for fixation of CO2, is located within the cytoplasm of photosynthetic bacteria and in the stroma of eukaryotic chloroplasts.

apoenzyme

cases, an enzyme lacking a necessary cofactor or coenzyme is called an apoenzyme and is inactive.

light independent reactions

chemical energy produced by the light-dependent reactions is used to drive the assembly of sugar molecules using CO2;

substrate

chemical reactants to which an enzyme binds are

phospholipases

cleave phospholipids

Xenobiotics

compounds synthesized by humans and introduced into the environment in much higher concentrations than would naturally occur. Such environmental contamination may involve adhesives, dyes, flame retardants, lubricants, oil and petroleum products, organic solvents, pesticides, and products of the combustion of gasoline and oil.

reaction center

contains a pigment molecule that can undergo oxidation upon excitation, actually giving up an electron. It is at this step in photosynthesis that light energy is converted into an excited electron.

where does glycolysis take place

cytoplasm

light dependent reactions

energy from sunlight is absorbed by pigment molecules in photosynthetic membranes and converted into stored chemical energy.

protease

enzyme that digests protein

lipases

enzymes that break down lipids reactions breaking down triglycerides are catalyzed by lipases and

phototrophs

get their energy for electron transfer from light are

where does the krebs cycle occur

in prokaryotes, this occurs in cytoplasm. in eukaryotes, this occurs in matrix of mitochondrian.

feedback inhibition

inhibition involves the use of a pathway product to regulate its own further production. The cell responds to the abundance of specific products by slowing production during anabolic or catabolic reactions

electron transport system

last component involved in the process of cellular respiration; it comprises a series of membrane-associated protein complexes and associated mobile accessory electron carriers (Figure 8.15). Electron transport is a series of chemical reactions that resembles a bucket brigade in that electrons from NADH and FADH2 are passed rapidly from one ETS electron carrier to the next. These carriers can pass electrons along in the ETS because of their redox potential. electrons move from electron carriers with more negative redox potential to those with more positive redox potential.

active site

location within the enzyme where the substrate binds

competitive inhibitor

molecule similar enough to a substrate that it can compete with the substrate for binding to the active site by simply blocking the substrate from binding. For a competitive inhibitor to be effective, the inhibitor concentration needs to be approximately equal to the substrate concentration.

electron carriers

molecules that bind to and shuttle high-energy electrons between compounds in pathways.

light-harvesting complex

multiple proteins and associated pigments that each may absorb light energy and, thus, become excited. This energy is transferred from one pigment molecule to another until eventually (after about a millionth of a second) it is delivered to the reaction center.

cofactors

nonprotein enzyme helpers inorganic ions such as iron (Fe2+) and magnesium (Mg2+) that help stabilize enzyme conformation and function. One

organotrophs

obtain electrons from organic compounds

chemotrophs

obtain energy for electron transfer by breaking chemical bonds.

chloroplasts

organelle that arose in eukaryotes by endosymbiosis of a photosynthetic bacterium (see Unique Characteristics of Eukaryotic Cells). These chloroplasts are enclosed by a double membrane with inner and outer layers. Within the chloroplast is a third membrane that forms stacked, disc-shaped photosynthetic structures called thylakoids (Figure 8.20). A stack of thylakoids is called a granum, and the space surrounding the granum within the chloroplast is called stroma.

coenzymes

organic helper molecules that are required for enzyme action. Like enzymes, they are not consumed and, hence, are reusable. The most common sources of coenzymes are dietary vitamins. Some vitamins are precursors to coenzymes and others act directly as coenzymes.

principal electron carriers

originate from the B vitamin group and are derivatives of nucleotides; they are nicotinamide adenine dinucleotide, nicotine adenine dinucleotide phosphate, and flavin adenine dinucleotide. Nicotinamide adenine dinucleotide (NAD+/NADH) is the most common mobile electron carrier used in catabolism. NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule. Nicotine adenine dinucleotide phosphate (NADP+), the oxidized form of an NAD+ variant that contains an extra phosphate group, is another important electron carrier; it forms NADPH when reduced. The oxidized form of flavin adenine dinucleotide is FAD, and its reduced form is FADH2. Both NAD+/NADH and FAD/FADH2 are extensively used in energy extraction from sugars during catabolism in chemoheterotrophs, whereas NADP+/NADPH plays an important role in anabolic reactions and photosynthesis. Collectively, FADH2, NADH, and NADPH are often referred to as having reducing power due to their ability to donate electrons to various chemical reactions.

carbon cycle

ost molecules in cell are made of c an h Some orgs can fix carbons or get abiotic carbon from env Most orgs get carbon from diets Movement of carbon through biotic and abiotic parts of ecosystem

redox reactions

pairs of reactions are called oxidation-reduction reactions,

Z scheme of photosynthesis

photosystem II transfers energy to photosystem I flow of electron

biogeochemical cycle

process in which elements, chemical compounds, and other forms of matter are passed from one organism to another and from one part of the biosphere to another

heterolactic fermentation

produces lactic acid and other compounds producing a mixture of lactic acid, ethanol and/or acetic acid, and CO2 as a result, because of their use of the branched pentose phosphate pathway instead of the EMP pathway for glycolysis. One

heterotrophs

rely on more complex organic carbon compounds as nutrients; these are provided to them initially by autotrophs. Many organisms, ranging from humans to many prokaryotes, including the well-studied Escherichia coli, are heterotrophic.

adp

second phosphate group to this core molecule results in the formation

enzymes

serve as catalysts for biochemical reactions inside cells. Enzymes thus play an important role in controlling cellular metabolism. lower activation energy of chemical reaction

3 stages of light independent reactions

stages: fixation, reduction, and regeneration

reactants and products to glycolysis

start- glucose end- 2 pyruvate

catalyst

substance that speeds up the rate of a chemical reaction

metabolism

term used to describe all of the chemical reactions inside a cell is

Photosynthesis

the biochemical process by which phototrophic organisms convert solar energy (sunlight) into chemical energy.

aerobic respiration

the final electron acceptor (i.e., the one having the most positive redox potential) at the end of the ETS is an oxygen molecule (O2) that becomes reduced to water (H2O) by the final ETS carrier.

glycolysis

the most common pathway for the catabolism of glucose; it produces energy, reduced electron carriers, and precursor molecules for cellular metabolism. Every living organism carries out some form of glycolysis, suggesting this mechanism is an ancient universal metabolic process. The process itself does not use oxygen; however, glycolysis can be coupled with additional metabolic processes that are either aerobic or anaerobic.

nitrogen mineralization

the release (often through urea or ammonium) of inorganic nitrogenous wastes Release of nh4+ (ammonium) during decomposition of litter and organic matter by soil microbes

biomediation

the use of bacteria and other microorganisms to change pollutants in soil and water into harmless chemicals leverages microbial metabolism to remove xenobiotics or other pollutants.

Krebs Cycle (Citric Acid Cycle)

transfers remaining electrons from the acetyl group produced during the transition reaction to electron carrier molecules, thus reducing them. because citric acid has three carboxyl groups in its structure. Unlike glycolysis, the Krebs cycle is a closed loop: The last part of the pathway regenerates the compound used in the first step Krebs cycle can be used in synthesizing a wide variety of important cellular molecules, including amino acids, chlorophylls, fatty acids, and nucleotides; therefore, the cycle is both anabolic and catabolic

net gain from single glucose in glycolysis

two ATP molecules two NADH molecule, and two pyruvate molecules.

lithotrophs

use inorganic molecules as a source of electrons hydrogen sulfide (H2S) and reduced iron. Lithotrophy is unique to the microbial world.

anaerobic respiration

using an inorganic molecule other than oxygen as a final electron acceptor. There are many types of anaerobic respiration found in bacteria and archaea. Denitrifiers are important soil bacteria that use nitrate (NO3-)(NO3-) and nitrite (NO2-)(NO2-) as

anoxygenic photosynthesis

when other reduced compounds serve as the electron donor, oxygen is not generated; these types of photosynthesis are called anoxygenic photosynthesis. Hydrogen sulfide (H2S) or thiosulfate (S2O2−3)(S2O32−) can serve as the electron donor, generating elemental sulfur and sulfate (SO2−4)(SO42−) ions, respectively, as a result.