Microbiology Exam 2

End of Catabolism

Have pyruvate and build up of NADH - If inorganic electron acceptor is present -> respiration - If no inorganic acceptor -> fermentation to regenerate NAD+

nitrogen cycle

the series of processes by which nitrogen and its compounds are interconverted in the environment and in living organisms, including nitrogen fixation and decomposition.

TCA cycle (Krebs cycle)

- A cycle of aerobic chemical reactions in the mitochondria that oxidize glucose, amino acids, and fatty acids, producing hydrogen ions to be used in the electron transport chain, some ATP, and by-products carbon dioxide and water. - (TCA) cycle, also known as the Krebs or citric acid cycle, is the main source of energy for cells and an important part of aerobic respiration. The cycle harnesses the available chemical energy of acetyl CoA into NADH - Generates: 6 NADH, 2 FADH2, 2 ATP and Produces CO2 - Occurs when there is an electron receptor present - Pyruvate is transformed into acetyl CoA via pyruvate process and acetyl CoA enters TCA - Makes intermediates for biosynthesis - Regenerate oxaloacetate

Calvin cycle regulation

- Expression of CO2 fixing enzymes varies w/temp, light and CO2 concentration - Because CO2 can diffuse through membranes, different mechanisms needed to have high concentrations of CO2 for Rubisco function: -Convert CO2 to bicarbonate (HCO3 - ) which is trapped in the cytoplasm - Carboxysomes are packed with rubisco, can take up bicarbonate and turn it into CO2, then do step 1 of calvin cycle and release PGA into cytoplasm - Low CO2 concentration triggers expression of bicarbonate and CO2 transport proteins - Use alternative CO2 fixation system that can deal with different CO2 levels

Glycolysis

- first step in releasing the energy of glucose, in which a molecule of glucose is broken into two molecules of pyruvic acid Start by spending 2 ATP Split to 3C molecule 2 G3P Add some Pi End: 2 ATP, 2 NADH, 2 pyruvate Regulated by feedback inhibition and other ways Most efficient

Pentose Phosphate Shunt Pathway

- less efficient, loses energy as heat, evolutionary shunt pathway precursor to glycolysis 1. Starts like ED 2. Then oxidation to NADPH End: 1 ATP, 2 NADPH, 2 pyruvate - Uses sugars that are used in biosynthetic pathways (amino acids) - Can generate biosynthetic precursors or reenter glycolysis

Photoheterotrophy

- use of organic compounds as a carbon source during bacterial photosynthesis - gain energy from light while using organic carbon substrates for catabolism

Fermentation

A catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces a characteristic end product, such as ethyl alcohol or lactic acid. All electrons from organic substrates are put back on organic products, final electron acceptor is pyruvate derivative - A partial breakdown of organic molecules and use of organic compound as electron donor and acceptor - Regenerate NAD+ which can be used in glycolysis to get ATP - High yield of waste products and not efficient - Essential for anaerobes

Thylakoids

A flattened membrane sac inside the chloroplast, used to convert light energy to chemical energy.

Oxygenic Z Pathway

An ATP-producing photosynthetic pathway consisting of photosystems I and II. Water serves as the initial electron donor (generating O2) and NADP+ is the final electron acceptor, generating NADPH. - Homologs of photosynthesis I and II, split H2O to O2 - Generate 3 ATP & 2 NADPH - Done by cyanobacteria and green plant chloroplasts

Entner-Doudoroff Pathway

An alternate pathway for the oxidation of glucose to pyruvic acid - can start with glucose but mainly catabolizes sugar acids 1. Start by spending 1 ATP 2. Split to 3C molecule 3. 1 G3P + 1 pyruvate End: 1 ATP, 1 NADH, 1 NADPH, 2 pyruvate - Essential for enteric bacteria to colonize the intestinal epithelium

Catabolism

Breakdown of large, complex molecules into several smaller, simpler molecules → yields energy

Catabolism Substrates

Carbohydrate: - Ultimately get glucose for entry into glycolysis - Easiest to digest - starch, pectins - Cellulose - animals can only digest with the help of microbes Lipids: - Hydrolyzed to glycerol and fatty acids Amino Acid: - Usually amino acids make protein, but when there is too much protein they can be catabolized to yield energy - Decarboxylation removing carboxyl group (low pH) - Deamination removing amino group (high pH) Aromatics: - Highly stable benzene ring, hard to digest

Enzymes

Catalysts for chemical reactions in living things. They lower the activation energy of the transition state.

Photolysis

In the thylakoid membranes of a chloroplast during light-dependant reactions, two molecules of water are split to form oxygen, hydrogen ions, and electrons. - Photoexcitation of light absorbing pigment (chlorophyll) causes light-driven separation of an electron from a molecule coupled to an ETS (photolysis) which ultimately produces energy carriers - To maximize light collection - orient and increase amount of chlorophyll

Bacteriorhodopsin

Light driven proton pump Used by halophilic archaea and marine bacteria Single protein light driven proton pump Mechanism: photon causes photoexcitation of retinal Return to ground state causes retinal trans->cis, changing protein shape and picking up proton from inside

Anabolism

Metabolic pathways that construct molecules, requiring energy. - Use simple molecules to build complex molecules → requires energy - Use substrates from metabolic pathways to make complex molecules (i.e. vitamins, antibiotics, building blocks...) - Involve reduction reactions - Tightly regulated How to get energy: Organotrophy: organic molecules Lithotrophy: inorganic molecules Phototrophy: light

Carbon Fixers

Oxygenic phototrophs (cyanobacteria) - Coupled to oxygenic Z pathway to produce O2 Chloroplasts - Coupled to oxygenic Z pathway to produce O2 Facultative anaerobic purple bacteria (R. rubrum) - Anaerobic Photosystem II: separate electrons from bacteriochlorophyll to produce oxidized byproduct Lithotrophs - Oxidation of inorganic molecule coupled to CO2 fixation

Antenna complex

Part of a photosystem, containing an array of chlorophyll molecules and accessory pigments, that receives energy from light and directs the energy to a central reaction center during photosynthesis.

Phototrophy

Phototrophy: light absorption provides electron Harness photoexcited electrons to power cell growth Performed by phototrophic bacteria Photoautotrophs: light absorption drive CO2 fixation Photoheterotrophs: catabolism with light absorption

Nitrogen Fixation

Process of converting nitrogen gas into ammonia - N2 is very stable because of its triple bond - N2 requires a lot of energy to fix - All life depends on N2 fixing bacteria and archaea

Calvin Cycle

Reactions of photosynthesis in which energy from ATP and NADPH is used to build high-energy compounds such as sugars. - CO2 is fixed to ultimately form glucose other molecules and regenerate starting material, the reducing agent is NADPH, and it Spends 9 ATP and 6 NADPH - CO2 reduced into 5C sugar to make 6C sugar that is subsequently broken down into 2 PGA (3C) - PGA is phosphorylated, hydrolyzed and reduced into G3P Some G3P used to make glucose & some G3P ultimately becomes starting 5C molecule

Anaerobic Respiration

Respiration in the absence of oxygen. This produces lactic acid. - This type of respiration through which cells can break down sugars to generate energy in the absence of oxygen - Use molecules other than O2 as final electron acceptor in electron transport chain - Different substrate (alternative oxidoreductases) oxidation, metals, and multiple redox states

Electron Transport Chain

Series of electron carrier proteins that shuttle high-energy electrons during ATP-generating reactions - Couple reactions to pumping protons across a membrane - Transfer electrons from electron donors to electron acceptors via redox reactions and couples this electron transfer with the transfer of protons across a membrane.

Anaerobic photosystem I

Takes electrons from H2 or H2S; uses the electrons to make NADPH; doesn't pump H+ but does make an H+ gradient by releasing protons (from H2 or H2S) outside the membrane. - separating electron associated with hydrogen - electrons ultimately transferred to form NADH/NADPH

Anaerobic photosystem II

Takes electrons from chlorophyll itself; too weak to make NADPH; pumps a few H+ to make ATP and returns the electrons to chlorophyll. separate electrons from bacteriochlorophyll - separate electrons from bacteriochlorophyll - produces S or oxidized organic byproduct, but not O2, - Pumps H+ to generate ATP - Done by purple nonsulfur bacteria

Lithotrophy

The acquisition of energy by oxidation of inorganic electron donors. -Inorganic compounds donate electrons -Derives energy from the breakdown of inorganic molecules Very inefficient - most inorganic substrates are poor electron donors, so they need a strong terminal electron acceptor Ex. Nitrogen Oxidation Nitrifiers convert NH4 into NO3 as part of the nitrogen cycle Ex. Sulfur oxidation Suffolobus converts H2S into H2SO4 Ex. Methanogenesis CO2 + 4H2 into CH4 +H2O is does by methanogens

Rubisco

The most abundant protein on earth. Performs Carbon Fixation in the Calvin Cycle. - It is a large multi-subunit complex - High affinity for CO2, requires high concentrations (5%) of CO2 to function - Carbon fixation efficiency decreases in the presence of O2 oxygen - Because it is energy intensive, the calvin cycle is highly regulated (often through affecting CO2 concentration)

Glucose Catabolism

The degenerative oxidation of glucose occurs in two stages, Glycolysis and cellular respiration. - Provides energy and substrates for biosynthesis Splits 6-C sugar into 2 3-C sugars - Generates ATP - Generates NAD(P)H

Electron Transport System

The final sequence of reactions in the aerobic production of ATP - Reactions that transfer electrons are coupled to a membrane - Series of carrier molecules harvest the reduction potential of electrons in small steps

Carbon Fixation

The incorporation of carbon from carbon dioxide into an organic compound by an autotrophic organism. - Reduction, requires energy, multiple pathways and is done by different organisms that couple it to processes to gain energy - One of the most common mechanisms is the Calvin cycle which fixes CO2 into glucose or other molecules

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. Chemiosmotic gradient powers: ATP synthase -> ATP Flagella rotation Nutrient uptake Efflux of toxic drugs

Respiration

The process by which cells break down simple food molecules to release the energy they contain. Uses electron transport chain to donate electrons to O2 (aerobic) or other inorganic electron acceptor (anaerobic)

Carbon fixation in anaerobes

They can use the calvin cycle or Reverse TCA - CO2 reduction to make acetyl CoA -> sugars - Regenerates RCA intermediates - Uses many of the same enzymes as TCA plus some new ones - Original mechanism of CO2 fixation on Earth - Used by hydrothermal vent symbionts

Redox Reactions

When there is a transfer of one or more electrons from one reactant to another. - Much of metabolism involves redox reactions - Couple energy yielding reaction to energy spending reaction - Energy carriers help prevent loss of energy as heat by capturing energy for use in other reactions - A chemical reaction that takes place between an oxidizing substance and a reducing substance. - The oxidizing substance loses electrons in the reaction, and the reducing substance gains electrons

Gibbs Free Energy Change

ΔG = ΔH - TΔS The change in Gibbs free energy observed when reactants are converted to products. Change in free energy tells us the amount of energy available to do work Predicts the direction of a reaction Tells us how favorable a reaction is ΔG = exergonic, spontaneous ΔH = change in enthalpy, heat energy absorbed/released ΔS = change in entropy, # states of a system ΔG Summary: Intrinsic properties of the reaction (stability of reactants/products, entropy change) determine the standard value of ΔGo Concentrations of reactants and products affect ΔG In living cells, energy-spending reactions are coupled with yielding reactions A concentration gradient stores energy