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metabolism glycolisis, respiration, fermentation organism list and definitions

fermentation

ATP is generated by substrate level phosphorylation

RubisCO

enzyme that fixes carbon dioxide

atpase

driven by protons to phosphorylate ADP

carbon dioxide

molecule that pyruvate is fully oxidized to

oxygenic

photosynthetic electron transport the generates oxygen

chemoorganotroph

uses organic molecule as an electron source

anaerobic

nitrate or sulfate are possible electron acceptors (anything except oxygen)

gluconegenesis

glucose made from a noncarbohydrate carbon sorce

antenna

pigments such as carotenoids

heterotroph

organic molecule as its carbon source

chemiosmosis

use of ATPase to generate ATP

anoxygenic

photosynthetic electron transport that uses inorganic molecules as electron source

glycolysis

process that converts glucose to pyruvate

electron transport

generates a proton motive force

chemolithotroph

uses inorganic molecules as an electron source

autotroph

carbon dioxide is its carbon source

citric acid cycle

the cycle that oxidizes pyruvate

aerobic

oxygen is used as the terminal electron acceptor

chlorophyll

used by oxygenic phototrophs

bacteriochlorophyll

used by anoxygenic phototrophs

phototroph

uses light as an energy source

nucleotides

uridylate and inosinic acid are precursors for the biosynthesis of these

cytochrome

electon carriers with a single iron atom in the center of a large protein

quinone

non-protein electron carrier that also pushes protons outside the membrane

syntrophomonans

ferment butyrate to acetate for energy (syntroph - cooperative relationship with organism to degrade a compoud

streptococcus

homolactic fermentation

lactococcus

homolactic fermentation

leuconostoc

heterolactic fermentation

oscillatoria limnetica

oxygenic photosynthesis (but in presence of hydrogen sulfide will perform anoxygenic)

synechocysits and chlorella

used to study oxygenic photosynthesis (chloroplasts)

propionibacterium

propionic acid fermentation (propionibacterium acnes - causes acne)

trichomoans

anaerobic eukaryote flagellated protozoan with hydrogenosomes to oxidize pyruvate to generate ATP (substrate level)

panacoccus deritrificans

gram negative oxidize hydrogen

makinoella tosaesis

has lots of chloroplasts (green alga)

chlorobactulum tepidum

green sulfur bacteria chlorosome (use sulfur)

cholorflexus

green non-sulfur baacteria (chlorosomes)

chlamdomonas

green alga absorb high and low wavelengths

rhodopseudomonas

red alga absorbs different high and low wavelengths that green alga

chlorobium

used reduced sulfur compounds, deposit sulfur granules externally; contain chlorosomes

chromatium

purple sulfur bacteria
anoxygenic
bacteriochlorophyll
anaerobic

rhodobacter capsulatus

used to study anoxygenic photosynthesis

anabolic

A process in which large molecules are built from small molecules using energy

catabolic

breaking down molecules to gain energy

REDOX reaction

A chemical reaction involving the transfer of one or more electrons from one reactant to another; also called oxidation-reduction reaction.
Oil Rig.

oxidation

The loss of electrons from a substance involved in a redox reaction.

reduction

any process in which electrons are added to an atom or ion (as by removing oxygen or adding hydrogen) GAINING ELECTRONS

electron donor

reducing agent

electron acceptor

a substance that can accept electrons from an electron donor, becoming reduced in the process

NAD+/NADH

an organic molecule that serves as an electron carrier by being oxidized (losing electrons) to NAD+ and reduced (gaining electrons) to NADH

Adenosine Triphosphate

ATP, The molecule that stores energy that can be used by the cell

phosphoanhydride bond

A high energy bond between two phosphate groups.

Acetyl CoA

Acetyl coenzyme A; the entry compound for the citric acid cycle in cellular respiration, formed from a fragment of pyruvate attached to a coenzyme.

Thioester bond

are compounds with the functional group C-S-CO-C. They are the product of esterification between a carboxylic acid and a thiol. Thioesters are widespread in biochemistry, the best known derivative being acetyl-CoA.

Glycogen

An extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch.

Poly-B-hydroxybutyrate

(PHB) a common storage material of prokaryotic cells consisting of a polymer of b-hydroxybutyrate or another b-alkanoic acid or mixtures of b-alkanoic acids.

organic compound

A compound that contains carbon

inorganic compound

any compound that does not contain carbon

substrate-level phosphorylation

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

oxidative phosphorylation

an enzymatic process in cell metabolism that synthesizes ATP from ADP

glycolysis

a metabolic process that breaks down carbohydrates and sugars through a series of reactions to either pyruvic acid or lactic acid and release energy for the body in the form of ATP

glucose

a monosaccharide sugar that has several forms

pyruvate

Organic compound with a backbone of three carbon atoms. Two molecules form as end products of glycolysis

syntrophy

refers to the process in which two or more bacteria break down a substrate which, individually,the bacteria could not do alone.

homofermentative

Lactic acid bacteria that carry out simple fermentation; lactic acid is only product

lactic acid

Produced in muscle cells from the reduction of pyruvate (under anaerobic conditions) to regenerate NAD+ so that glycolysis can continue. A rise in lactic acid usually accompanies an increase in physical activity.

methanogen

archaebacteria found in anaerobic environments such as animal intestinal tracts or sediments or sewage and capable of producing methane

heterofermentative

Lactic acid bacteria that produce more than one product --> ethanol and carbon dioxide, as well as lactic acid.

mixed acid fermentation

E. coli, when bacteria ferment pyruvate to many different acids at the same time

butanediol fermentation

produces butanediol and carbon dioxide; involved in the Voges Proskauer test using the biproduct acetoin

hydrogenosomes

is a membrane-bound organelle of ciliates, trichomonads and fungi which produces molecular hydrogen and ATP. This organelle is thought to have most likely evolved from mitochondria.

respiration

the metabolic processes whereby certain organisms obtain energy from organic moelcules

citric acid cycle

in cellular respiration, series of chemical reactions that break down glucose and produce ATP; energizes electron carriers that pass the energized electrons on to the electron transport chain

electron transport system (chain)

A sequence of proteins (cytochromes) embedded in the inner membrane that surrounds a pigment complex.

electron carrier

A molecule that shuttles electrons (e-) within a cell EX: NADH and FADH2

NADH dehydrogenase

the first of the proteins in the electron transport chain to recieve the electrons; complex. membrane-embedded enzyme

Flavoprotein

Protein containing a flavin mononucleotide prosthetic group, is the first acceptor for NADH's electrons

Iron-sulfur protein

one of a family of proteins with both iron and sulfur tightly bound; passes the electrons to a compound called ubiquinone

cytochrome

an iron-containing protein, a component of electron transport chains in mitochondria and chloroplasts

quinone

Small, lipid-soluble, mobile electron carrier molecule found in the respiratory and photosynthetic electron transport chains.
expel protons to proton motive force

proton motive force

The potential energy stored in the form of an electrochemical gradient, generated by the pumping of hydrogen ions across biological membranes during chemiosmosis.
stored inbetween membranes

oxidative phosphorylation

an enzymatic process in cell metabolism that synthesizes ATP from ADP

photosynthesis

synthesis of compounds with the aid of radiant energy (especially in plants)

phototroph

an organism that gets its energy from sunlight

chlorosome

organelles found in green sulfur bacteria that act as light funnels that collect the relatively few photons in the water and store the light energy in food molecules

pigments

Colored chemical compounds that absorb light

reaction center

The chlorophyll a molecule and the primary electron acceptor in a photosystem; they trigger the light reactions of photosynthesis. The chlorophyll donates an electron, excited by light energy, to the primary electron acceptor, which passes an electron to an electron transport chain.

carotenoids

An accessory pigment, either yellow or orange, in the chloroplasts of plants. By absorbing wavelengths of light that chlorophyll cannot, carotenoids broaden the spectrum of colors that can drive photosynthesis.

phycobillins

a type of accessory pigment unique only to cyanobacteria and red algae

oxygenic

Chlorella (eukaryotic green alga)
Synechocystis (prokaryotic cyanobacteria)
Non-cyclic photophosphorylation
Cyclic photophosphorylation

anoxygenic

Rhodobacter capsulatis (purple nonsulfur Proteobacteria)
Cyclic photophosphorylation

autotroph

organism that can capture energy from sunlight or chemicals and use it to produce its own food from inorganic compounds; also called a producer

Calvin-Benson cycle

Light-independent reactions of photosynthesis cyclic pathway that forms glucose from CO2

Alternate pathways

Reverse citric acid pathway
Chlorobium (green sulfur Bacteria)
Aquifex (Bacteria hyperthermophile)
Hydroxypropionate pathway
Chloroflexus (green sulfur Bacteria, anoxygenic phototroph)
Sulfolobus (Archaea, Crenarcheaota)
Acetyl-CoA pathway
Acetogen
Treponema primitia (spirochete Bacteria)
Acetogenesis

heterotoph

organisms that obtains energy from the food it consumes (consumer)

mixotroph

An organism that is capable of both photosynthesis and heterotrophy.

hexose

a monosaccharide that contains six carbon atoms per molecule

gluconeogenesis

The formation of glycogen, a glucose storing compound, from fatty acids and proteins rather than carbohydrates.

pentose

any monosaccharide sugar containing five atoms of carbon per molecule

activated glucose

condensation of a sugar molecule like glucose with a nucleotide
uridine-5'-diphosphate (UDP) for activation of glucose

inosinic acid

the first nucleotide formed during the synthesis of purine

uridylate

product of biosynthesis pathway - converted to pyrimidine

acyl carrier protein

A small protein involved in fatty acid biosynthesis; it holds the growing fatty acid as it is being synthesized and releases it once it has reched its final length.

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