Microbiology Exam 1 (Lectures 3-4)

Chapters 8

microbial metabolism

all of the chemical reactions in a microorganism

exergonic reaction

chemical reaction that does not require energy beyond activation energy to proceed; RELEASES ENERGY WHEN REACTION OCCURS

endergonic reaction

REQUIRES ENERGY BEYOND ACTIVATION ENERGY TO OCCUR

anabolism

chemical reactions that convert simpler molecules into more complex ones; endergonic reaction

catabolism

chemical reactions that break down complex molecules into simpler ones; endergonic reaction

autotrophs

organism that converts inorganic carbon dioxide into organic carbon

ex: plants and cyanobacteria

heterotrophs

organism that uses fixed organic carbon compounds as its carbon source

ex: humans and e coli

photoautotroph

autotrophs that obtain organic carbon energy from light

get energy from light and can fix carbon dioxide to organic carbon

all plants, algae, cyanobacteria, and green/purple sulfur bacteria

photoheterotroph

heterotrophs that obtain inorganic carbon energy from light

use light to produce ATP but use organic carbon to build biomass

green/purple nonsulfur bacteria and heliobacteria

Ex: Halobacterium salinarum use a protein called photorhodopsin to generate ATP, but dont use it to fix CO2

chemoautotroph

obtain inorganic energy by breaking chemical bonds

convert non-organic carbon into organic matter using energy from inorganic compounds (chemosynthesis)

H, S, Fe, N, and C monoxide-oxidizing bacteria

lithoautotroph

chemoautotrophs that get energy from inorganic compounds, including hydrogen sulfide and reduced iron; unique to microbial world

chemoheterotroph

obtain organic energy by breaking chemical bonds

get energy, electrons, and carbon from chemicals

all animals, most fungi, protozoa, and bacteria

organotrophs

chemotrophs that obtain energy from organic compounds

rules of cellular metabolism

1. enzymes catalyze metabolic reactions by lowering activation energy
2. energy is transferred by passing electrons from one molecule to another (ex: cellular respiration transfers electrons from glucose to oxygen)
3. electrons can be stored in intermediate compounds until the cell needs it (ex: NADH in electron transport chain and Krebs cycle)
4. cells prefer to transfer electrons between molecules in incremental steps to reduce the amount of energy lost as heat (ex: electron transport chain passes electrons down a series of membrane bound proteins

enzyme

catalyst for biochemical reactions inside cells

\-lower activation energy required for chemical reaction to take place (makes it faster)

enzyme’s bind at the _________ site

active

\-convert it to a product

\-when substrate binds to the enzyme, the enzyme’s shape changes slightly called induced fit

enzyme binding steps

1. substrate enters active site of enzyme
2. enzyme/substrate complex forms using induced fit
3. substrate is converted to products
4. products leave the active site of the enzyme

___________,____________,and__ _________ interactions between the substrate and enzyme are key to enzyme function

electrostatic, hydrophobic/hydrophilic, and covalent

what actually catalyzes the reaction?

change of enzyme shape

enzymes lower activation energy in three ways

1. positioning substrates in close proximity and in the correct orientation
2. putting stress on bonds
3. providing a favorable microenvironment (can be different conditions than the rest of the cell)

steps of lowering activation energy by positioning substrates in close proximity and in correct orientation

1. enzyme binds the substrates at binding sites within the active sites
2. binding brings the substrates into close proximity with one another to form the enzyme-substrate complex

Ex: DNA polymerase introducing nucleotides to replicating DNA strand

steps of lowering activation energy by putting stress on bonds

ex: sucrase breaking down sucrose by stressing glycosidic bond


1. substrate sucrose consists of glucose and fructose bonded together
2. substrate binds to enzyme forming enzyme-substrate complex
3. binding of the substrate and enzyme places stress on glucose-fructose bond and the bond breaks
4. products are released and enzyme is free to bind to other substrates

catalyst

molecule that increases the rate of a chemical reaction but is not used or changed during the chemical reaction and is reusable

activation energy

energy needed to form or break chemical bonds and convert a reactant or reactants to a product or products

substrate

chemical reactants of an enzymatic reaction

active site

location within an enzyme where substrates bind

cofactor

inorganic ion that helps stabilize enzyme conformation and function

\-mostly metal ions

coenzyme

organic molecule required for proper enzyme function that is not consumed and is reusable

\-non-protein molecules

steps of enzyme reaction with a cofactor

1. substrates bound at the active site in proximity to the cofactor
2. substrate A transfers the group to the cofactor
3. cofactor transfers the group to substrate B
4. both substrates are released as products

apoenzyme

enzyme WITHOUT its cofactor or coenzyme

holoenzyme

enzyme with a bound cofactor or coenzyme

competitive inhibitors

molecules that bind to an enzyme’s active site preventing substrate binding

\-physically compete with substrate

noncompetitive inhibitors

AKA allosteric inhibitors

molecules that bind to allosteric sites inducing a conformational change in the enzyme’s structure that prevents it from functioning

allosteric site

location within an enzyme, other than the active site, to which molecules can bind, regulating enzyme activity

feedback inhibition

when the product of a metabolic pathway binds to an enzyme early in the pathway, preventing the synthesis of that product

allosteric activation

molecule binds to an enzyme’s allosteric site, INCREASING the affinity of the enzyme’s active site for the substrates

carbohydrate catabolism

breakdown of carbohydrates to yield ATP

glycolysis

breakdown of glucose; ancient universal process; occurs in cytoplasm; most common

\-independent of oxygen

\-stage one of cellular respiration

\-embden-meyerhof-parnas (EMP) pathway

Yields: 2 pyruvates, 2 ATP, 2 NADH

Embden-Meyerhof-Parnas (EMP) pathway

1. energy investment phase: uses energy from 2 ATP molecules to modify a glucose molecule in order for it to be split evenly into two phosphorylated 3 carbon molecules (G3P)
2. energy payoff phase: extracts energy by oxidizing G3P to pyruvate, producing 4 ATP molecules and reducing 2 NADs to 2 NADH

\-found in animals and most common in microbes

substrate-level phosphorylation

direct method of ATP production in which a high-energy phosphate group is removed from an organic molecule and added to and ADP molecule

\-ATP molecules produced during energy payoff phase pf glycolysis are formed by this

Entner-Doudoroff (ED) pathway

alternative glycolysis pathway

\-ex bacteria that use this pathway: Pseudomonas aeruginosa

\-E coli can use either this pathway or EMP pathway

pentose phosphate pathway (PPP)

AKA phosphogluconate pathway or hexose monophosphate shunt

\-alternative glycolysis pathway that produces intermediates used for biosynthesis of nucleic acids and amino acids

\-potentially most ancient universal glycolytic pathway

transition reaction

conversion of pyruvate to acetyl coenzymeA which goes into the Krebs cycle. AKA bridge reaction

\-each pyruvate is decarboxylated and oxidized, forming NADH, and the two resulting 2-carbon acetyl group is attached to a large carrier called coenzyme A, resulting in acetyl-CoA and CO.

\-gains another 2 NADH in the process

Krebs Cycle (citric acid cycle/tricarboxylic acid cycle)

oxidizes acetyl CoA to CO2

\-occurs in cytoplasm of prokaryotes and in mitochondrial matric of eukaryotes

\-independent of oxygen

\-intermediate compounds used in synthesis of amino acids, fatty acids, nucleotides, and chlorophylls

YIELDS: 2CO2, 3NADH, 1 ATP, 1 FADH2, and 4H+

oxidative phosphorylation

mechanism for making ATP that uses the potential energy stored within an electrochemical gradient to add Pi to ADP creating ATP.

\-potential energy created through beginning of cellular respiration from electron transfers is harvested to generate an electrochemical gradient across the membrane, making ATP

electron transport system

last component involved in cellular respiration

\-uses products from glycolysis, transition reaction, and Krebs cycle to transfer electrons through a series of steps to a final INORGANIC electron acceptor to produce ATP

\-oxygen is most efficient terminal electron acceptor, but only done in aerobic respiration

\-anaerobic respiration use other inorganic terminal electron acceptors including S, N, or Fe.

\-inner part of cell membrane for prokaryotes and inner membrane of mitochondria in eukaryotes

obligate aerobes

require oxygen as final electron acceptor

ex: Bacillus anthracis

facultative anaerobes

can switch from using oxygen to another electron acceptor

Ex: E coli

obligate anaerobes

require an element other than oxygen as final electron acceptor; oxygen can be toxic to these organisms

redox potential

tendency for a molecule to acquire electrons and become reduced; electrons flow from molecules with LOW redox potentials to those with HIGH redox potentials

high redox potential

tendency to gain electrons and become reduced

low redox potential

tendency to lose electrons and become oxidized

cytochrome oxidase

final ETS complex used in aerobic respiration that transfers energy-depleted electrons to oxygen to form H2O

anaerobic ETS carriers

can uses other types of cytochrome oxidase or altered ETS carriers when aerobic respiration is not possible

reasons cells go through anaerobic respiration instead of aerobic cellular respiration are because the cell:

\-lack genes that encode the appropriate cytochrome oxidase for transferring electrons to oxygen

\-lack genes encoding enzymes that deal with dangerous oxygen radicals such as H202 and O2

\-lack sufficient amounts of oxygen

chemiosmosis

flow of hydrogen ions across the membrane through ATP synthase

\-takes electrons from NADH and FADH2 and uses them to pump protons across the membrane

\-creates a high concentration of protons outside of the cell

\-the proton wants to naturally diffuse back into the cell and the cell facilitates this with ATP synthase

ATP synthase

integral membrane protein that harnesses the energy of the proton motive force by allowing hydrogen ions to diffuse down their electrochemical gradient, causing components of this protein to spin, making ATP from ADP and Pi

\-facilitates diffusion of H from coming back into the cell

\-uses mechanical energy of protons rushing back into the cell to reduce ADP and Pi into ATP

the higher the redox potential (ability to pull electrons from another molecule) the ________________

more energy is gained

not all cells can carry out respiration due to the following circumstances

1. lack appropriate inorganic final electron acceptor
2. lack genes to make complexes and electron carriers in ETS
3. lack genes to make enzymes for the Krebs cycle

fermentation

energy production using an ORGANIC molecule as final electron acceptor

\-YIELDS ONLY 2 ATP

\-recycles NADH to NAD+ for glycolysis by donating the electron to pyruvate to form acids, alcohols, and gases

homolactic fermentation

only produces lactic acid

\-microbes that do this use EMP glycolysis pathway

Ex: Lactobacillus delbreuckii and Streptococcus thermophilus in yogurt production

heterolactic fermentation

produces lactic acid, ethanol/acetic acid, and CO2

\-microbes that do this use PPP pathway in glycolysis which is why they generate multiple fermentation products

Ex: Leuconostoc mesenteroides used in pickling

total ATP outputs

aerobic respiration: 38 ATPs

anaerobic respiration: 5-36 ATPs

fermentation: 2 ATPs

catabolism of lipids and proteins

B oxidation for lipids

protease enzymes for proteins

B oxidation

process of faty acid degradation that sequentially removes two carbon acetyl groups, producing NADH and FADH2, on entry into the Krebs cycle

\-cleaves terminal carbon-carbon bonds

\-cycles until only 2 carbons left

YIELDS: 1 NADH2, 1 FADH2, 1 acetyl-CoA

proteases

enzyme involved in protein catabolism that removes individual amino acids from the ends of peptide chains

\-breakdown proteins into smaller peptide subunits and further to amino acids.

\-ex: gelatinase and caseinase (degrading primary protein in milk)

photosynthesis

biochemical process by which phototrophic organisms convert solar energy into chemical energy

\-uses energy from light to drive fixation of CO2 into organic carbon

\-in eukaryotic cells, occurs inside plant cells in chloroplasts which contain thylakoids stacked into grana.

\-in bacteria, occurs along infolded regions of the plasma membrane also called thylakoids

2 stages: Light-dependent Reactions and Light-independent Reactions

light dependent reactions

process by which energy from sunlight is absorbed by pigment molecules in photosynthetic membranes and converted into stored chemical energy in the forms of ATP and NADPH

\-produces ATP, and releases O2

light-independent reactions

process by which chemical energy, in the form of ATP and NADPH produced by light-dependent reactions, is used to fix inorganic CO2 into organic sugar; referred to as the Calvin cycle

\-occurs in cytoplasm of photosynthetic bacteria; stroma of eukaryotic chloroplasts

\-fixes CO2 to organic sugar

photosynthetic pigments

pigment molecules used by a cell to absorb solar energy; each one appears the color of light that it transmits or reflects

\-chlorophyll

photosystems

organized unit of pigments found within a photosynthetic membrane, containing both a light-harvesting complex and a reaction center

light-harvesting complex

group of multiple proteins and associated pigments that each may absorb light energy to become excites, and then transfer this energy from one pigment molecule to another until the energy is delivered to a reaction center pigment

\-absorb energy from photons to excite electrons which are then passed to reaction center

reaction center

protein complex in a photosystem, containing a pigment molecule that can undergo oxidation upon excitation by a light-harvesting pigment, actually giving up an electron

\-electron is now actually excited

\-moves electron to an electron transport system

once the light harvesting complex transfers the energy to the reaction center, the reaction center delivers its high energy electrons to

an electron carrier (ETC) in an ETS and electron transfer is initiated

\-ETC uses energy to produce a proton motive force to generate ATP (similar to respiration)

\-the electron lost by reaction center must be replenished, so a reduced molecule such as water supplies that missing electron

\-wide range of electron donors

Calvin-Benson cycle

fixation pathway of CO2 in light-independent reaction

3 stages:


1. Fixation-ribulose biphosphate carboxylase (RuBisCO) catalyzes addition of CO2 to ribulose biphosphate (RuBP), resulting in 3 phosphoglycerate (3-PGA)
2. Reduction-6 ATP and 6 NADPH (from light-dependent reaction) convert 3-PGA to glyceraldehyde 3-phosphate (G3P), used to build glucose
3. Regeneration-some G3P is used o generate RuBP

oxygenic photosynthesis

type of photosynthesis found in plants, algae, and cyanobacteria in which WATER is used as the electron donor to replace electron lost by reaction center pigment, resulting in OXYGEN AS BYPRODUCT

anoxygenic photosynthesis

type of photosynthesis found in many photosynthetic bacteria, including the purple and green bacteria, where an electron donor OTHER THAN WATER is used to replace elctron lost by reaction center, resulting NO OXYGEN PRODUCTION

elements must be ______ or they will run out

RECYCLED

\-the 6 macronutrients need to be recycled!

biogeochemical cycling 3 main components

1. elements are contained in reservoirs (terrestrial, lithosphere, aquatic and atmosphere)
2. flux is the movement of elements between reservoirs
3. microorganisms are ultimately responsible for all biogeochemical cycling on earth

natural biogeochemical cycling include

cellular respiration, fermentation, photosynthesis, and methanogenesis

\-ALL PART OF CARBON CYCLE, REGENERATING CARBON

\-constant exchange of CO2 between heterotrophs and autotrophs

\-atmospheric CO2→phototrophs (plants and photosynthetic organisms)→aquatic bacteria and dissolved organic carbon→sediments→fossil fuels and cement production bring carbon back into atmosphere

biogeochemical cycle

recycling inorganic matter between living organisms and their nonliving environment

nitrogen fixation

bacterial biochemical pathways that incorporate inorganic nitrogen gas into organic forms more easily used by other organisms

\-takes atmospheric N2 and fixes it into ammonia NH3

N2+8H+ +8e-→ 2NH3 +H2

\-only bacteria fix nitrogen

\-microorganisms participate in nitrogen cycle through denitrification, nitrification, and nitrogen fixation

nitrogenase

use 16 moles of ATP to make 2 moles of ammoniums

\-triple bond in N2 so needs lots of energy to break the bond

___________ will denature nitrogenase

OXYGEN

\-nitrogen-fixing bacteria must do do in ANAEROBIC ENVIRONMENTS

\-some Anabaena will specialize into a structure called a HETEROCYST which protect from oxygen and fix nitrogen for the rest of the population, which in turn supplies carbon and energy to the heterocyst via oxygenic photosynthesis

organic nitrogen turns back into nitrogen gas by 3 steps

1. ammonification: bacteria and fungi convert nitrogenous waste from living/dead animals into NH3; some bacteria and archaea use ammonia as an energy souce
2. nitrification: formation of nitrate; soild bacteria oxidize NH3 to nitrite (NO2-) then to nitrate (NO3-) the terminal electron acceptor
3. denitrification: NO3 used by some soil bacteria as a terminal electron acceptor forming N2

phosphorous cycle

microorganisms participate by decomposing dead biomass

\-phosphorus is not found in the air

\-rock cycle participates by recycling sediments into new rock

sulfur cycle

microorganisms participate through various oxidation and reduction reactions

\-used as electron donor to contribute sulfate (SO4 2-)

decomposition of dead organisms by fungi and bacteria REMOVE sulfur groups, returning inorganic sulfur to the environment

oxygen cycle

microorganisms participate through photosynthesis and cellular respiration

population

all members of the same species which libe in the same area

microbial populations are ______

clonal (identical copies) since they mostly reproduce asexually

niche

functional role of an organism within an ecosystem

\-different populations occupy specific niches

\-can be based on available carbon/energy sources

community

interacting groups of various species in a particular environment

\-microbial communities can be incredibly diverse

guilds

functional groups within a community

ecosystems

include interactions and exchanges of materials between organisms and the environment

\-between macro and microbial worlds

\-between living and nonliving things

4 main ecosystems

1. marine
2. freshwater
3. terrestrial
4. deep subsurface (below ground)

marine ecosystems

structured around phytoplankton


1. top of the ocean/SURFACE ZONE: less than 200 m deep, photosynthetic phytoplankton
2. dark mid-water zone: 200-1000 m deep; zooplankton feast on corpses of phytoplankton (death by viruses)
3. deep-sea zone: greater than 1000 m deep; pressure is 1000x that at sea level; low energy, productivity, and diversity. “slow, steady pace of life”; bacteria along hydrothermal vents oxidize H2S to fix carbon

\-chemoautotrophs are primary producers at hydrothermal vents. reduced inorganic molecules serve as electron donor to fix CO2 into biomass

freshwater ecosystems

stratified by temperature and oxygen (seasonal or permanent)

\-Shelford’s Law of tolerance and Liebig’s Law of minimum determine which populations can survive

shelford’s law

any environmental factor has a range of tolerance which determine if an organism can survive that tolerance

ex: temperature

liebig’s law

nutrients in least abundant supply drive which organisms can survive in the environment

____________ from terrestrial systems can have massive impacts on aquatic systems.

nutrient flux

\-by dramatically increasing the available N and P

\-seasonal and man-made fluctuations in nutrients can cause algal/cyanobacterial blooms