Exam 2 Flashcards

Question

Examples of complex molecules?

Answer 1

Complex Molecules: Carbohydrates, Lipids, DNA, RNA, Proteins

Answer 2

- Many metabolic processes involve oxidation-reduction reactions (electron transfers) - electron carriers are often used to transfer electrons from an electron donor to an electron acceptor - Transfer of electrons from a donor to an acceptor - 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 •One is electron donating (oxidizing reaction) •One is electron accepting reaction (reducing reaction) •Acceptor and donor are conjugate redox pair •Acceptor + e− donor

Answer 3

- Electron carriers organized into ETC - first electron carrier having the most negative E′0 - potential energy stored in first redox couple is released and used to form ATP - First carrier is reduced and electrons moved to the next carrier and so on

Answer 4

- Located in plasma membranes and intracytoplasmic membranes of bacterial and archaeal cells - Located in internal membranes of mitochondria and chloroplasts in eukaryotic cells - Examples of electron carriers include NAD, NADP, FADH2 and ATP

Answer 5

-Nicotinamide adenine dinucleotide carries 2-3x as much energy as ATP. - NADH is the reduced form. - NAD+ is the oxidized form Overall, reduction of NAD+ accepts two hydrogen atoms and two electron to make NADH.

Answer 6

-FAD: Flavin adenine dinucleotide; is another coenzyme that can transfer electrons. - FADH2 (reduced form) versus FAD (oxidized form) - Unlike NAD+, FAD is reduced by two electrons and two protons. •FMN: flavin mononucleotide; riboflavin phosphate •Coenzyme Q (CoQ): A quinone; Also called ubiquinone -Cytochromes: Use iron to transfer electrons (iron is part of a heme group) •Nonheme iron-sulfur proteins: For example, ferredoxin; Use iron to transport electrons (iron is not part of a heme group

Answer 7

•Pathways can be varied: - Linear; Cyclic; Branching - Pathways often overlap/ feed into each other - complex networks - Dynamic pathways can be used to monitor changes in metabolite levels (flux)

Answer 8

- Protein catalysts: High specificity for the reaction catalyzed and the molecules acted on; substance that increases the rate of a reaction without being permanently altered - Substrates = reacting molecules - Products = substances formed by reaction - Some enzymes are composed solely of one or more proteins - Some enzymes are composed of two parts: one protein component and a nonprotein component

Answer 9

- Apoenzyme: protein component of an enzyme - Cofactor: nonprotein component of an enzyme - Prosthetic group—firmly attached - Coenzyme—loosely attached, can act as carriers/shuttles - Holoenzyme = apoenzyme + cofactor

Answer 10

•Enzymes may be placed in one of six general classes and usually are named based on the substrate they act on and the reaction they catalyze - look at table!

Answer 11

Substrate concentration, pH, Temperature

Answer 12

Competitive inhibitor: Directly competes with binding of substrate to active site - Noncompetitive inhibitor: Binds enzyme at site other than active site, changes enzyme's shape so that it becomes less active

Answer 13

- Differential localization of enzymes and metabolites - Compartmentation: Differential distribution of enzymes and metabolites among separate cell structures or organelles; Can generate marked variations in metabolite concentrations

Answer 14

* Most regulatory enzymes * Activity altered by small molecule known as an allosteric effector * Binds noncovalently at regulatory site * Changes shape of enzyme and alters activity of catalytic site * Positive effector increases enzyme activity * Negative effector inhibits the enzyme

Answer 15

* Reversible on and off switch * Addition or removal of a chemical group (phosphoryl, methyl, adenylyl) * Advantages of this method * Respond to more stimuli in varied/sophisticated ways * Regulation of enzymes that catalyze covalent modification adds second level of control

Answer 16

* Also called end product inhibition * Inhibition of one or more critical enzymes in a pathway regulates entire pathway * Pacemaker enzyme: catalyzes the slowest or rate-limiting reaction in the pathway * Each end product regulates its own branch of the pathway * Each end product regulates the initial pacemaker enzyme Isoenzymes * Different enzymes that catalyze same reaction

Answer 17

NADH, NADPH, and FADH2

Answer 18

Many microorganisms can grow in the presence of molecular oxygen (O2) - Some even use oxygen as a terminal electron acceptor (TEA) in the electron transport chain - This process is called aerobic respiration

Answer 19

Many of the cell's energy transfer reactions involve energy carriers. - Molecules that gain or release small amounts of energy in reversible reactions - Examples: NADH, FADH2 and ATP§ Energy carriers can also transfer electrons. - NADH: Electron donor - NAD+: Electron acceptor

Answer 20

``` Adenosine triphosphate (ATP) contains a base, sugar, and three phosphates. - ADP plus inorganic phosphate makes ATP. ```

Answer 21

ATP contains three phosphate molecules that yield energy upon hydrolysis. - ATP transfer energy in three different ways: 1. Hydrolysis-releasing phosphate (Pi) 2. Hydrolysis-releasing pyrophosphate (PPi) 3. Phosphorylation of an organic molecule

Answer 22

- transfer of phosphate from high- energy molecule to ADP | - Require a kinase enzyme

Answer 23

- Microbes catalyze many different kinds of substrates - Polysaccharides are broken down to pyruvate - glycolysis. - Pyruvate are fermented or further catabolized to CO2 and H2O via the TCA cycle. - Lipids and amino acids are catabolized to glycerol and acetate, as well as other metabolic intermediates.

Answer 24

Often satisfied together: Carbon source often provides H, O, and electrons - Heterotrophs: Use organic molecules as carbon sources which often also serve as energy source; Can use a variety of carbon sources - Autotrophs: Use carbon dioxide as their sole or principal carbon source; Must obtain energy from other sources

Answer 25

- Based on energy source: - Phototrophs use light - Chemotrophs obtain energy from oxidation of chemical compounds - Based on electron source: - Lithotrophs use reduced inorganic substances - Organotrophs obtain electrons from organic compounds

Answer 26

- also called chemoheterotrophs - Processes used to catabolize energy source: - Aerobic respiration; Anaerobic respiration; fermentation

Answer 27

- Aerobic respiration—final electron acceptor is oxygen - Anaerobic respiration—final electron acceptor is different oxidized molecule such as NO3−, SO42−, CO2, Fe3+, or SeO42− - As electrons pass through the electron transport chain to the final electron acceptor, a proton motive force (PMF) is generated and used to synthesize ATP

Answer 28

- Uses an endogenous electron acceptor - Usually an intermediate of the pathway used to oxidize the organic energy source (for example, pyruvate) - Does not involve the use of an electron transport chain nor the generation of a proton motive force - ATP synthesized only by substrate-level phosphorylation

Answer 29

- Many different energy sources are funneled into common degradative pathways - Most pathways generate glucose or intermediates of the pathways used in glucose metabolism - Few pathways that each break down many nutrients greatly increase metabolic efficiency

Answer 30

- Despite diversity of energy, electron, and carbon sources used by organisms, they all have the same basic needs: - ATP as an energy currency - Reducing power to supply electrons for chemical reactions - Precursor metabolites for biosynthesis

Answer 31

- Include enzymes that function both catabolically and anabolically - For example, many enzymes of the Embden-Meyerhof pathway function catabolically during glycolysis but anabolically during gluconeogenesis

Answer 32

- Embden-Meyerhof pathway - Entner-Doudoroff pathway - Pentose phosphate pathway

Answer 33

- Occurs in cytoplasmic matrix of most microorganisms, plants, and animals - The most common pathway for glucose degradation to pyruvate in stage two of aerobic respiration - Function in presence or absence of O2 - Two phases: Six-carbon phase Three-carbon phase

Answer 34

Essential Catabolism of Glucose - Plants animals and microbes - It occurs in the cytoplasm of the cell - It functions in the presence or absence of O2 - It involves ten distinct reactions that are divided into two stages

Answer 35

Glucose is "activated" by 2 phosphorylations - Two ATPs are expended - Investment: 2 ATP - Fructose-1,6-bisphosphate is cleaved into two 3-carbon- isomers: - Dihydroxyacetone phosphate (DHAP) - Glyceraldehyde-3-phosphate (G3P)

Answer 36

- Each glyceraldehyde-3-phosphate molecule is ultimately converted to pyruvate. - 2 Pyruvate - Redox reactions produce two molecules of nicotinamide adenine dinucleotide (NADH) - 2NADH - Four ATP molecules are produced by substrate-level phosphorylation - Net ATP = (total - invested) = 2 ATP

Answer 37

- Addition of phosphates "primes the pump" | - Oxidation step—generates NADH, high-energy molecules used to synthesize ATP by substrate-level phosphorylation

Answer 38

Primary pathway to convert ONE glucose to TWO pyruvate - pathway generates: - Net gain of 2 ATP, 2 pyruvate - 2 ATP expended to break glucose - 4 ATP harvested - 2 NADH ----------- will generate more ATP later

Answer 39

- Microbes reduce pyruvate to different end products Glycolysis/ Embden-Meyerhof Pathway • 2 ATP and 2NADH Entner-Dourdoroff (ED) Pathway • 1 ATP, 1 NADH, 1 NADPH Pentose Phosphate Pathway (PPP) • Sugars (3-7 Cs), 2 NADPH

Answer 40

- Used by some Gram-negative bacteria, especially those found in soil - Replaces the 6-carbon phase of the Embden-Meyerhof pathway - Yield per glucose molecule: - 1ATP - 1 NADPH - 1NADH

Answer 41

- Also called hexose monophosphate pathway - Can operate at same time as Embden-Meyerhof pathway or Entner-Doudoroff pathway - Can operate aerobically or anaerobically An amphibolic pathway: - Glucose-6-P + 12NADP+ + 7H2O --- 6CO2 + 12NADPH + 12H+ Pi

Answer 42

1. Fermentation - Recycling of NADH to NAD+ - Produce acid and/or alcohol 2. TCA cycle for additional metabolites and more NADH and FADH2

Answer 43

2 ATP and 2 NADH

Answer 44

1 ATP, 1 NADH, and 1 NADPH

Answer 45

- Fermentation - Respiration - Photoheterotrophy

Answer 46

1. Fermentation: recycling of NADH to NAD+ Produce acid and/or alcohol 2. TCA cycle to create additional precursor (biosynthesis) metabolites and more NADH and FADH2

Answer 47

In prokaryotes, it occurs in the cytoplasm - In eukaryotes, in the mitochondria - Glucose catabolism connects with the TCA cycle through pyruvate breakdown to acetyl-CoA and CO2 - Acetyl-CoA enters the TCA cycle by condensing with the 4-C oxaloacetate to form citrate

Answer 48

Conversion of pyruvate to acetyl-CoA is catalyzed by a very large multisubunit enzyme called the Pyruvate Dehydrogenase Complex (PDC)

Answer 49

- Key player in directing glucose catabolism into respiration - Defects in PDC in human mitochondria can cause issues in organs with high metabolic rates - Myocardial infarction - Heart Failure - Neurodegeneration - Inhibited by increased Acetyl-CoA • Converted to Acetate

Answer 50

For each Pyruvate oxidized: - Pyruvate Dehydrogenase Complex (PDC) - 1 CO2, 1 NADH - Kreb's Cycle/TCA Cycle - 2 CO2 are produced by decarboxylation - 3 NADH and 1 FADH2 are produced - 1 ATP is produced by substrate-level phosphorylation. - Some cells make GTP instead of ATP (it still is only 1 molecule produced!) - However, GTP and ATP are equivalent in stored energy.

Answer 51

- Originally evolved to aid in Amino Acid Production - 2-oxoglutarate to Glutamate to Glutamine - Oxaloacetate to Aspartate to Nucleotides - Amphibolic Pathway - Treponema pallidum (Syphillis) abandoned TCA through reductive evolution and rely on host amino acids for survival

Answer 52

``` NADH= 3 ATP X 2 Glycolysis+8 TCA= 30ATP FADH2 = 2 ATP X 2 TCA= 4ATP 2 ATP Glycolysis + 2 ATP TCA Electron Carriers Theoretical Yield = 38 ATP E. coli produces 20 ATP per glucose; extreme variation of the number of ATP produced by bacteria .... **Oxygen and Carbon source availability ```

Answer 53

- When glucose is absent, cells can catabolize acetate or fatty acids using a a process called Glyoxylate Shunt/ Glyoxylate Bypass - Includes two enzymes that divert Isocitrate to Glyoxylate - Incorporate a second Acetyl-CoA to form Malate - The Glyoxylate Bypass cuts loss of CO2 - Produces 2 NADH , 1 FADH2

Answer 54

- In 1998 - 6.7 million cases with 2.4 deaths Most lethal infection in the world Latent TB in over 2 million people • Grow within macrophages; can persist for long periods Provide lipids via Glyoxylate Bypass -Diverts Carbon to build sugars/amino acids Glyoxylate Bypass essential to the pathogenicity of M. tuberculosis

Answer 55

Mitochondria, plasma membrane

Answer 56

Microbes transfer energy

Answer 57

- Each Glucose consumed: (10 NADH + 2 FADH2) - Glycolysis: 2 NADH - Transition step (Pyruvate to Acetyl-CoA): 2 NADH - TCA: 6 NADH; 2 FADH2

Answer 58

The mitochondrial electron transport chain (ETC) = a series of e- carriers, operating together to transfer e- from NADH and FADH2 to a terminal e- acceptor, O2 e- flow from carriers with more negative reduction potentials (E0) to carriers with more positive E0

Answer 59

- Each carrier is reduced and then reoxidized - Carriers are constantly recycled - the difference in reduction potentials electron carriers, NADH and O2 is large, resulting in release of great deal of energy

Answer 60

- Located in plasma membrane - Some resemble mitochondrial ETC, but many are different: - Different electron carriers - Different terminal oxidases - May be branched - May be shorter—fewer protons and therefore less energy

Answer 61

- Microbes transfer energy by moving electrons - Electrons move from reduced molecules to energy carriers - From energy carriers to membrane protein carriers, and then - Finally to oxygen or oxidized minerals - ETS generate "proton motive force (PMF)" - The PMF will be used to make ATP

Answer 62

- Organotrophy (organic electron donors) - Lithotrophy (inorganic electron donors) - Phototrophy (light excites electrons) - Many prokaryotes use more than one type of metabolism. - Rhodopseudomonas palustris, use all three e- sources

Answer 63

- ETS occurs in the bacterial cell membrane - Microbes use many electron acceptors. - Aerobic: Oxygen (O2) - Anaerobic: metals, oxidized ions of nitrogen or sulfur. - Salmonella Typhimurium infecting the gut epithelium - Use toxic compound tetrathionate (S4O62-) as a terminal electron acceptor.

Answer 64

- NADH delivers - e- transfers across to systems - protons pumped out of the membrane

Answer 65

- Different array of cytochromes used than in mitochondrial chain - Branched pathway - Upper branch— stationary phase and low aeration - Lower branch— log phase and high aeration; more O2; more ATP

Answer 66

Process by which ATP is synthesized as the result of electron transport driven by the oxidation of a chemical energy source

Answer 67

A respiratory electron transport system includes at least three functional components: 1. Oxidoreductase (or dehydrogenase) 2. A mobile electron carrier 3. A terminal oxidase

Answer 68

1. The substrate dehydrogenase receives a pair of electrons, such as from NADH 2. It donates the electrons ultimately to a mobile electron carrier, such as quinone (Q) - Quinone picks up 2 H+ from solution and is thus reduced to quinol (QH2) 3. The oxidation of NADH and reduction of Q is coupled to pumping 4H+ across the membrane 4. A terminal oxidase complex, typically includes a cytochrome, receives the two electrons from quinol (QH2) - 2H+ are translocated outside the membrane - In addition, 2H+ are pumped across the membrane, when the electrons are passed through the terminal oxidase complex. 5. The terminal oxidase complex transfers the electrons to a terminal electron acceptor such as O2 - E. coli ETS can pump up to ~ 8-10 H+ for each NADH molecule, and ~ 6 H+ for each FADH2 molecule - Generates an electrochemical gradient of protons, called a proton motive force

Answer 69

- The most widely accepted hypothesis to explain oxidative phosphorylation - Protons move outward from the mitochondrial matrix as e- are transported down the chain - Proton expulsion during e- transport results in the formation of a concentration gradient of protons and a charge gradient - The combined chemical and electrical potential difference make up the proton motive force (PMF)

Answer 70

Mitochondrial ETS differ from that of E. coli in these respects: 1. Possess an intermediate cytochrome oxidase complex for transfer of electrons. 2. Mitochondrial ETS pumps 12 H+ per NADH, 2 more than E. coli

Answer 71

The transfer of H+ through a proton pump generates a proton motive force. - It drives the conversion of ADP to ATP through ATP synthase. - This process is known as the chemiosmotic theory. - 1978 - Peter Mitchell wins Nobel Prize

Answer 72

- The F1Fo ATP synthase is a highly conserved protein complex, made of two parts: - Fo: embedded in the membrane - Pumps protons - F1: protrudes in the cytoplasm- Generates ATP

Answer 73

- Harvest energy from proton motive force to synthesize ATP - 10 protons pumped out per NADH - 1 NADH produces 3 molecules of ATP - 6 protons pumped out per FADH - 1 FADH2 produces 2 molecules of ATP - look at pictures on slide

Answer 74

- Maximum ATP yield can be calculated - includes phosphorus to oxygen (P/O) ratios of NADH and FADH2 - ATP produced by substrate-level phosphorylation - The maximum total yield of ATP during aerobic respiration by eukaryotes is 32

Answer 75

- Amount of ATP produced during aerobic respiration varies depending on growth conditions and nature of ETC - Under anaerobic conditions, glycolysis only yields 2 ATP molecules - Factors affecting ATP yield:: - Bacterial ETCs are shorter and have lower P/O ratios - ATP production may vary with environmental conditions - PMF in bacteria and archaea is used for other purposes than ATP production (flagella rotation) - Precursor metabolite may be used for biosynthesis

Answer 76

Substrate phosphorylation: 4 ATP generated; Net 2 from glycolysis; 2 ATP from TCA - Oxidative phosphorylation: 34 ATP generated; 6 ATP from glycolysis; re-oxidation of 2 NADH § 6 from transition step; re-oxidation of 2 NADH § 22 from TCA cycle; re-oxidation of NADH and FADH2 - Total yield from 1 Glucose: 4 + 34 = 38 (theoretical maximum) - Eukaryotic cells have theoretical maximum of 36; 2 ATP spent crossing mitochondrial membrane

Answer 77

T: Substrate dehydrogenase, mobile electron carrier, and terminal oxidase

Answer 78

- Since it is unique to prokaryotes, they use alternative electron acceptors - Some bacteria use nitrate - Nitrate reduced to nitrite (NO3-→NO2-) - Some use Sulfur compounds - Sulfate reduced to sulfite (SO42-→SO32-)

Answer 79

- test for nitrate breakdown - inoculate with material - add reagent - clear- red- reduced! - stays clear- add Zn2+- red change here it - now

Answer 80

- H2S byproduct | - pumped out fewer H+, so less ATP

Answer 81

- Uses electron carriers other than O2 - Generally yields less energy because E0 of electron acceptor is less positive than E0 of O2 - Dissimilatory nitrate reduction: - Use of nitrate as terminal electron acceptor, making it unavailable to cell for assimilation or uptake - Denitrification - Reduction of nitrate to nitrogen gas - In soil, causes loss of soil fertility

Answer 82

- complex - branched chain - different e- carriers - nitrate reduced - nitrite-- nitric oxide - NO-- nitric oxide--- N2

Answer 83

Turns Produces ATP

Answer 84

- No ATP because of no ETC - most fermenters produces acids - e- from NADH/NADPH donated to pyruvate - energy stored in ATP - during glycolysis- substrate level - O2-- not needed! - NADH-- NAD+ - Still need PMF- reverse ATP synthase to pump H+ out of cell - Recycle NADH-- NAD+ needed to get rid of e- Completion of Glucose Catabolism - Electrons from NADH (NADPH) are donated to pyruvate - Byproducts including alcohols, carboxylates as well as Hydrogen and CO2 - Energy Stored in ATP -Most fermentations do not generate ATP beyond that produced by glycolysis - Microbes compensate by consuming large quantities of substrate and - Excreting large quantities of byproducts.

Answer 85

- Homolactic fermentation: Produces 2 molecules of lactic acid - Ethanolic fermentation: Produces two molecules of ethanol and two CO2 - Heterolactic fermentation: Produces 1 molecule of lactic acid, 1 ethanol, and 1 CO2 - Mixed-acid fermentation: Produces acetate, formate, lactate, and succinate, as well as ethanol, H2, and CO2

Answer 86

- used to identify the microbe causing a disease and prescribe an effective antibiotic, hospitals use rapid and inexpensive biochemical tests - Starts red--- yellow if acid produced/more acidic - Agar: White colonies fail to ferment sorbitol, unlike red colonies; can cause illness

Answer 87

- It is a simple broth that contains peptone, buffers, and glucose - Methyl red differs from Phenol red in that it is yellow at pH 6.2 and above and red at pH 4.4 and below - Positive Result will be RED - MR: turn RED if the organism uses the mixed acid fermentation pathway to make acids - VP: tests for organisms that use butylene glycol pathway and produce acetoin - Positive - Deep red - Negative - copper color

Answer 88

- Oxidation of NADH produced by glycolysis - Pyruvate or derivative used as endogenous electron acceptor - Substrate only partially catabolized - Oxygen not needed - Oxidative phosphorylation does not occur - The only ATP created is formed by substrate-level phosphorylation

Answer 89

- Many different carbohydrates can serve as energy source | - Carbohydrates can be supplied externally or internally (from internal reserves)

Answer 90

- Monosaccharides: Converted to other sugars that enter glycolytic pathway - Disaccharides and polysaccharides: Cleaved by hydrolases or phosphorylases

Answer 91

- Triglycerides are common energy sources - Hydrolyzed to glycerol and fatty acids by lipases - Glycerol degradedvia glycolytic pathway - Fatty acids often oxidized via β- oxidation pathway

Answer 92

- created of e- carriers: more energy | - FA broken down

Answer 93

- protease: hydrolyzes protein to amino acids - Deamination: removal of amino group from amino acid - Resulting organic acids converted to pyruvate, acetyl-CoA, or TCA cycle intermediate - Can occur through transamination

Answer 94

- Carried out by certain bacteria and archaea- released from inorganic molecule energy source - Transferred to terminal e- acceptor by ETC - ATP synthesized by ETC and oxidative phosphorylation

Answer 95

- Bacterial and archaeal species have specific electron donor/acceptor preferences - Much less energy is available from oxidation of inorganic molecules than glucose due to more positive redox potentials

Answer 96

- Have significant ecological impact - Several bacteria and archaea oxidize hydrogen - Nitrifying bacteria oxidize ammonia to nitrate - Sulfur-oxidizing microbes - Hydrogen sulfide (H2S), sulfur (S0), thiosulfate (S2O32−) - ATP can be synthesized by both oxidative phosphorylation and substrate-level phosphorylation

Answer 97

- Calvin cycle requires NAD(P)H as e- source for fixing CO2 - Many energy sources used by chemolithotrophs have E0 more positive than NAD+(P)/NAD(P)H - Use reverse electron flow to generate NAD(P)H - F1: Knob outward, proton potential (-)

Answer 98

- Energy from light trapped and converted to chemical energy - A two-part process - Light reactions: light energy is trapped and converted to chemical energy - Dark reactions: energy produced in the light reactions is used to reduce CO2 and synthesize cell constituents

Answer 99

- Photosynthetic eukaryotes and cyanobacteria - Oxygen is generated and released into the environment - Most important pigments are chlorophylls

Answer 100

- Major light-absorbing pigments | - Different chlorophylls have different absorption peaks

Answer 101

- Accessory pigments (for example, carotenoids and phycobiliproteins) - Transfer light energy to chlorophylls - Absorb different wavelengths of light than chlorophylls

Answer 102

- Photoreceptors absorb light - Excites an e- to a higher orbital level and subsequent return to ground state - High # of photoreceptors found in membrane - Photoexcited electrons used to power cell growth - e- are transferred through ETS to pump protons - The absorption and relaxation of the light absorbing molecule is coupled to energy storage - Proton Gradient

Answer 103

- Reaction Center delivers e- through carriers to ETS e- produces NADH and NADPH - Electrochemical gradient created across photosynthetic membrane - ATP created through photophosphorylation

Answer 104

- Purple bacteria and Cyanobacteria's membranes are folded in oval pockets (thylakoids) to increase the opportunity to trap photons of energy - The F1 knob of ATP synthase appears to face "outward" in photo synthetic organelles - proton potential is more negative in the cytoplasm, thus drawing protons through the ATP synthase to generate ATP.

Answer 105

- Antenna system - Complex of chlorophylls that capture photons and transfer the energy among photopigments - Light harvesting pigments: Bacteriochlorophyll (G, P, R), carotenoids (O, R, Y), chlorophylls (G) phycocyanins (B), phycoerythrins (R) • Capable of trapping light outside of the visible spectrum of light - Transfer energy to Reaction Center - Reaction Center Complex: - Photosystem I and II - Light harvesting complexes absorb light energy - Photon energy separates an electron from chlorophyll (e- is replaced by H2S (PSI) or from ETS (PSII))

Answer 106

- Oxygen producing bacteria that appear green due to presence of chlorophyll - Phototrophic Autotroph - Variety of sizes - "Light Reactions" of Photosynthesis - Photoexcitation leads to splitting of H2O and release of e- - e- are transferred to ETS which creates a proton potential that will power ATP Synthase to create ATP * *Purple Sulfur Bacteria split H2S to acquire e-**

Answer 107

- Chromophore: Light absorbing e- carrier - Chlorophyll absorbs red/blue and reflects green - Cyanobacteria - Rhodobacter aka Purple-Sulfur bacteria• Absorbs far red to UV range due to Bacteriochlorophyll - Absorbs light "missed" by cyanobacteria and algae - Photolysis of H2S

Answer 108

- Anaerobic Photosystem I: Receives e- with H+ from H2S, HS-, H2 or reduced iron, Chlorobia sp - Anaerobic Photosystem II: Returns e- from ETS to bacteriochlorophyll - Oxygenic Z pathway: Two pairs of e- received from water to generate O2, Cyanobacteria and Chloroplasts • Electron Transport System - Each photoexcited e- enters ETS; PSI: e- transferred to NADP+, PSII from ETS - H2O photolysis- e- flow from PSII to PSI releasing O2 from H2O - Oxygenic Photosynthesis **H2S and thiosulfate serve as e- donors during Anoxygenic photosynthesis - Oxygen byproduct is not made • Energy Carriers PSI e- make NADPH, PSII e- activate H+ pumps to drive ATP Synthesis - Oxygenic Z pathway- makes both NADPH and ATP Both are used to FIX Carbon

Answer 109

Classic demonstration of the metabolic diversity of prokaryotes. - All life on earth can be categorized in terms of the organism's carbon and energy source: - Energy can be obtained from: light reactions (phototrophs) or from chemical oxidations of organic or inorganic substances (chemotrophs); the carbon for cellular synthesis can be obtained from CO2 (autotrophs) or from preformed organic compounds (heterotrophs). - Only in the domain bacteria - and among the bacteria within a single Winogradsky column - do we find all four basic life strategies. - Classic demonstration of how microorganisms occupy highly specific microsites according to their environmental tolerances and their carbon and energy requirements. - And, finally, the column enables us to see how mineral elements are cycled in natural environments - Cyanobacteria on top of column

Answer 110

- Energy from catabolism is used for biosynthetic pathways - Using a carbon source and inorganic molecules, organisms synthesize new organelles and cells - Antibiotics inhibit anabolic pathways - A great deal of energy is needed for anabolism

Answer 111

Macromolecules are synthesized from limited number of simple structural units (monomers) - Saves genetic storage capacity, biosynthetic raw material, and energy - Many enzymes do double duty - Many enzymes used for both catabolic and anabolic processes; saves materials and energy - Catabolic and anabolic pathways are not identical as some enzymes function in only one direction - Anabolism consumes energy - Anabolic and catabolic reactions are physically separated - Located in separate compartments - Allows pathways to operate simultaneously but independently - Catabolic and anabolic pathways use different cofactors - Catabolism produces NADH - NADPH used as electron donor for anabolism - Large assemblies (for example, ribosomes) form spontaneously from macromolecules by self-assembly

Answer 112

Generation of precursor metabolites is critical step in anabolism - Carbon skeletons are used as starting substrates for biosynthetic pathways - Examples are intermediates of the central metabolic pathways - Most are used for the biosynthesis of amino acids and nucleotides

Answer 113

- Calvin-Benson (Calvin) cycle - Reductive TCA cycle - Reductive acetyl-CoA pathway - 3-hydroxypropionate/4-hydroxybutyrate pathway - Dicarboxylate/4-hydroxybutyrate cycle

Answer 114

- Used by most autotrophs to fix CO2 - Also called the reductive pentose phosphate cycle - in eukaryotes, occurs in stroma of chloroplasts - In cyanobacteria, some nitrifying bacteria, and thiobacilli, may occur in carboxysomes - Inclusion bodies that may be the site of CO2 fixation - Consists of 3 phases: - The Carbon Fixation phase - The Reduction phase - The Regeneration phase - Three ATPs and two NADPHs are used during the incorporation of one CO2

Answer 115

- Catalyzed by the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) - Rubisco is thought to be the most plentiful enzyme on earth - Rubisco catalyzes addition of CO2 to ribulose 1,5-bisphosphate (RuBP), forming 2 molecules of 3-phosphoglycerate (PGA)

Answer 116

- 3-phosphoglycerate reduced to glyceraldehyde 3-phosphate (G3P) - RuBP reformed - Carbohydrates (for example, fructose and glucose) are produced

Answer 117

- Used by some chemolithoautotrophs | - Runs in reverse direction of the oxidative TCA cycle

Answer 118

- Synthesis of Glucose from noncarbohydrate precursors - Shares 6 enzymes with the Embden-Meyerhof pathway - Four reactions catalyzed by enzymes specific for gluconeogenesis: - Two enzymes are involved in converting pyruvate to phosphoenolpyruvate - One enzyme is involved in formation of fructose 6-phosphate from fructose 1,6-bisphosphate - One enzyme removes the phosphate from glucose 6-phosphate to generate glucose

Answer 119

- several sugars are synthesized while attached to a nucleoside diphosphate such as uridine diphosphate glucose (UDPG) - Synthesis of starch and glycogen also involves nucleoside diphosphate sugars

Answer 120

- Complex process involving Uridine Diphosphate (UDP) derivatives (NAM and NAG - Bactoprenol phosphate used to transport NAG-NAM-pentapeptide units across the cell membrane - Cross links are formed by transpeptidation -NAM/NAG synthesized in cytosol and carried by UDP derivatives to membrane - NAM/Nag joined together - attached to bactoprenol to carry across to membrane - once across, join NAM and HAG to growing polypeptide chain - bactoprenol- lose p to transfer back across read slides!

Answer 121

Bactoprenol is connected to N-acetylmuramic acid (NAM) by pyrophosphate

Answer 122

Vancomycin: inhibits peptidoglycan synthesis and prevents linking of molecules; Blocks transpeptidation Bacitracin: stops p from leaving

Answer 123

- Used by bacteria to reduce nitrate to ammonia and then incorporate it into an organic form - Nitrate reduction to nitrite catalyzed by nitrate reductase - Reduction of nitrite to ammonia catalyzed by nitrite reductase

Answer 124

- Reduction of atmospheric nitrogen to ammonia - Catalyzed by nitrogenase - Found only in a few bacteria and archaea

Answer 125

- Occurs in 3 steps to reduce N2 to 2 molecules of NH3 - Requires large ATP expenditure!! - Once reduced, NH3 can be incorporated into organic compounds

Answer 126

- Sulfur needed for: - Synthesis of amino acids cysteine and methionine - Synthesis of several coenzymes (for example, coenzyme A and biotin) - Sulfur obtained from: - Cysteine and methionine—obtained from either external sources or intracellular amino acid reserves - Sulfate

Answer 127

- Sulfate = inorganic sulfur source - used by fungi - Assimilatory sulfate reduction - sulfate reduced to SO32− and then to H2S, then used to synthesize cysteine - Cysteine can then be used to form sulfur- containing organic compounds - different than dissimilatory sulfate reduction, where sulfate acts as electron acceptor for anaerobic respiration

Answer 128

- Used in the synthesis of multiple amino acids | - A single precursor metabolite can give rise to several amino acids

Answer 129

- TCA cycle intermediates are used in many amino acid biosynthetic pathways - Replenishment of these intermediates is provided by anaplerotic reactions - Allow TCA cycle to function during periods of active biosynthesis • For example, anaplerotic CO2 fixation - For example, glyoxylate cycle

Answer 130

Phosphoenolpyruvate (PEP) carboxylase • Phosphoenolpyruvate + CO2 ® oxaloacetate + Pi • Pyruvate carboxylase • Pyruvate + CO2 + ATP + H2O-- oxaloacetate + ADP + Pi

Answer 131

- Other anaplerotic reactions are part of the glyoxalate cycle, a modified TCA cycle - isocitrate lygase--glycoxlate - malate synthesis - fill in the blank

Answer 132

- Most microbes can synthesize their own purines and pyrimidines - Purines - Cyclic nitrogenous bases consisting of 2 joined rings - Adenine and guanine - Pyrimidines - Cyclic nitrogenous bases consisting of single ring - Uracil, cytosine, and thymine- - Nucleoside = nitrogenase base-pentose sugar - Nucleotide = nucleoside-phosphate

Answer 133

- Phosphorus found in nucleic acids as well as proteins, phospholipids, ATP, and some coenzymes - Most common phosphorus sources are inorganic phosphate and organic molecules containing a phosphoryl group - Inorganic phosphate (Pi) incorporated through the formation of ATP by: - Photophosphorylation - Oxidative phosphorylation - Substrate-level phosphorylation

Answer 134

- Major required component in cell membranes - Most bacterial and eukaryal lipids contain fatty acids or their derivatives - Fatty acids - Synthesized then added to other molecules to form other lipids such as triacylglycerols and phospholipids

Answer 135

Synthesized from acetyl-CoA, malonyl-CoA, and NADPH by fatty acid synthase complex • During synthesis, the intermediates are attached to the acyl carrier protein • Double bonds can be added in two different ways

Answer 136

- Major components of eukaryotic and bacterial cell membranes • Synthesized from phosphatidic acid by forming CDP- diacylglycerol, then adding an amino acid - DHAP transformed into G3P to triglycerol - precursor molecules for phopholipids

Answer 137

``` Lipid A: endotoxin O Antigen: immune response LPS molecules are an important component of the Gram-negative bacterial cell wall structure • Combines lipid and carbohydrate anabolic pathways • Lipid A-core branch • Oligosaccharide core • O-antigen branch - Fatty acid synthesis + UDP ---- LPS ```

Answer 138

Current model suggests multiple proteins, called Lpt proteins, “walk” newly-made LPS across the cell wall - LPS outer membrane - periplasmic space- between inner/outer membrane

Answer 139

light as energy!

Answer 140

energy! from chemicals

Answer 141

electrons from inorganic matter

Answer 142

electrons from organic matter

Answer 143

reduced organic molecules

Answer 144

CO2 as source of energy

Answer 145

Precursor metabolites

Answer 146

Reducing power through electrons

Exam 2 Flashcards

(179 cards)