quiz 2

Comes from pre-formed compounds, includes sugars, proteins, fats and other complex molecules. Most OC molecules:
- contain C-H bonds
- usually contain at least 2 carbon atoms (bonded to eachother)

Ex: Methane, Glucose, Fatty Acids

Comes from much less complex, smaller molecules. Most IC molecules:
- Lack C-H bonds
- Lack C-C bonds

Ex: CO, CO2, CO3, cyanide

"Self-Feeding". Organisms whose principal carbon source is inorganic, usually CO2.

"Other/Outside-Feeding". Organisms whose principal carbon source is organic, such as sugars.

Get energy from sunlight (photosynthesis). Two types...
Photolithoautotroph: Inorganic carbon source (CO2), energy source is sunlight. Plants, Algae, Purple and green sulfur bacteria.
Photoorganoheterotroph: Organic carbon source, energy source is sunlight. Purple and green non-sulfur bacteria, Heliobacteria.

Get energy from chemical oxidations. Three types...
Chemolithoautotroph: Inorganic carbon source (CO2), energy source is inorganic chemicals. Bacteria in nutrient cycling, Nitrifying bacteria.
Chemolithoheterotroph: Organic carbon source, energy source is inorganic chemicals
Chemoorganoheterotroph: Organic carbon source, energy source is organic chemicals (often same as carbon source). Animals, Fungi, many prokaryotes.

A bacteria that changes it's energy and carbon sources depending on what's available. Energy source:
- if there's light: phototrophic
- if no light and organic matter: chemoorganotrophic
- if no light and no organic matter: chemolithotrophic

Carbon source:
- if there's organic matter: heterotrophic
- if no organic matter: autotrophic

Organisms that need O2 to survive, i.e. are able to use O2 as terminal electron acceptor in cellular respiration.
Obligate Aerobe: Must have O2 to survive.
Microaerophilic: Requires O2 but must be below atmospheric concentration.

Organisms that don't need O2 to survive, i.e. does not use O2 as terminal electron acceptor to generate energy.
Obligate Anaerobe: Harmed or killed by exposure to O2.
Facultative Anaerobe: Will use O2 if avaible but still grow in absence of O2.
Aerotolerant Aneaerobe: Doesn't use O2 but not harmed if O2 present.

Complete oxidation of glucose to H2O and CO2.

Incomplete oxidation of glucose to an intermediate compound of repiration, i.e. lactic acid or ethanol.

Atoms or molecules with one or more unpaired electrons. These are chemically incomplete, unstable atoms or molecules that tend to steal electrons from other molecules in order to stabilize themselves. Normal aerobic metabolism produces free radicals.

Free radicals comprised of O2, also called Toxic Oxygen Species. ROS can leak away from their area of production in any sort of aerobic organism and wreak havoc. Three types produced from normal aerobic cellular respiration, in following order:
- Superoxide (O2-)
- Hydrogen Peroxide (H2O2), produced when O2- reduced
- Hydroxyl Radical (OH*), very short lived but extremely reactive and damaging

Another type produced due to absorption of light energy or transformation by some enzymes:
- Singlet Oxygen (1O2), Molecular O2 that has been raised to a higher energy level

ROS type. Molecular O2 that is partially reduced by a single electron. Formed as an intermediate during normal aerobic respiration where O2 is ultimately reduced to H2O, hence O2- constantly being produced. So toxic it is used in our immune systems by white blood cells to kill pathogenic microorganisms.

Molecular O2 that has been raised to a higher energy level, produced by absorption of light energy or transformation by enzyme. Has no additional or unpaired electrons, but spin direction of it's native electrons' changes. The outer 2 valence electrons in a "normal" ground state O2 spin in the same direction. In singlet oxygen (1O2), valence electrons spin in opposite directions. Spin shift forms a much more reactive O2 molecule.

They initiate a destructive chain reaction in fatty acid molecules of lipids called lipid peroxidation, which is the oxidative destruction of the C=C bonds in the fatty acids that comprise lipids. This causes irreparable damage to cell membrane lipids, leading to loss of membrane fluidity and semi-permeability. i.e. cells leak uncontrollably and die. Free radicals can cause:
- Membrane destruction
- DNA oxidation, particularly mitochondrial DNA in eukaryotes and chlorplast DNA in photosynthesizers. These DNA are particularly susceptible because they are the sites of electron transport activy and hence the generation of free radicals (i.e. ROS)
- Oxidation of biomolecules (enzymes, proteins, etc.), deactivating or destroying biomolecules by causing lipid-lipid, lipid-protein and protein-protein crosslinking.

Causes the formation of oxidatively modified guanine bases.

Numerous mechanisms to neutralize ROS have evolved, including:
- Detoxifying Enzymes
- Antioxidants

- Superoxide Dismutase (SOD), catalyzes O2- + O2- => O2 + H2O, dismutation refers to the simultaneous oxidation + reduction of a molecule to produce 2 different products
- Catalase, catalyzes H2O2 + H2O2 => O2 + H2O
- Peroxidase, catalyse H2O2 + NADH + H+ => H2O + H2O + NAD+

Molecules capable of slowing or preventing the oxidation of other molecules. Usually have several C=C bonds that mimic important biomolecules that would normally be damaged by ROS (namely fatty acids).
- Carotenoids, organic pigment molecules with many C=C bonds. Ex: Beta Carotene, C=C bonds react with 1O2, absorbs high E wavelengths of light to reduce the formation of 1O2, scavanges free radicals (mimics lipid peroxidation).
- Ascorbic Acid (Vitamin C), reacts with O2- and H2O2 to form dehydroascorbate.
- Tocopherol (Vitamin E), donates H atoms to "quench" ROS.
- Gluthathione (GSH), antioxidant function facilitated by the sulfhydryl group (SH) of cysteine. In the presence of an oxidant (ROS), the SH of one GSH reacts with the SH of another GSH forming a disulphide bond (S-S), thereby "quenching" ROS.