breaking down molecules for energy

ex: food is broken down so you can use it for energy

Breakdown large molecules in a series of steps and cause reactions that store energy in small carriers such as

ATP and NADH

the balance between catabolism and anabolism

breaking and building up things

what is used for catabolism and anabolism?

Whats is the TCA cycle

(Citric Acid or Krebs cycle)?

glycoliysis, pentose phosphate shunt

chemical reactions used by all aerobic organisms to generate energy through

oxidization of acetate

derived from carbohydrates, fats and proteins

into carbon dioxide.

catalytic proteins

speed up biochemical reaction rates

lower activation energy by bringing substrates into proximity of each other and correctly orienting them

portion of an enzyme to which substrate binds

very specific for their substrate

(starch vs cellulose)

they can have small non proteins that help in catlysis but arent part of the enxyme  or substrate

Types of enzymes:

Prostethic group-

coenzymes-

prostethic group- bound tightly to their enzyme, usually covalently and permanently

EX:(heme group (non protein) in cytochromes(protein)

Coenzyme- loosely bound to their enzyme, may associate with different enzymes usually derivatives of vitamins

Ex: NAD+ derivative of niacin, can move from one enzyme to another

named after either the substrate they bind to, or the chemical reaction they catalyze with addition of suffix- ase.

ex: cellulase breaks down cellulose into glucose

lithotrophy- inorganic molecules

organotrophy- organic molecules

phototrophy- uses light energy to reduce compounds then use these as an electron donor

electron acceptors:

respiration- inorganic molecules

fermentation- organic molecules

in Redox reaction:

OILRIG

substance oxidized is the electron donor

substance reduced in the electron acceptor

*are membrane bound, prostethic groups like cytochrome c.

*freely diffusible coenzymes like NAD+ or NADP+

energy released through a redox reaction that is stored in the formaiton of compounds with energy rich bonds

main carrier energy of the cell

phosphate added to ADP via dehydration to make ATP

hydrolysis of ATP to ADP yields energy

how does ATP transfer energy to cell processes?

• hydrolysis, releasing 1-2 phosphates
• phosphorylation of an organic molecule in the phophotransferase system
• derivatives of coenzyme A have thioester bonds that release free energy upon hydrolysis
• long term storage of energy involves glycogen and poly-B-hydrocybutyrate which can be consumed to yeild ATP
  

 light absorption by chlorophyll drives photolysis of an organic molecule

no exogenous (outside) electron acceptors

electron acceptor must be derived from the electron donor

(redox)- breakdown of organic molecule with electron transfer to inorganic molecule such as Oxygen or Nitrogen (yeilds more enrgy than fermentation)

molecular oxygen or some other terminal electron acceptor is present

ATP is produced by both substrate level phosphorylation & oxidative phosphorylation

 (redox)- partial breaksdown of organic matter without transfer of electrons to an inorganic terminal electron acceptor

ATP is produced by substrate level phosphorylation during catabolism of an organic compound

substrate level phosphorylation- a phosphate group is added to an intermediate in a biochemical pathway and is eventually transferred from ADP to form ATP

ATP is synthesized by a proton motive force generated by redox reactions

requires enzyme ATP synthase which uses proton motive force to produce ATP from ADP.

method of producing ATP in photosynthetic organisms

light instead of a chemical compound drives the reox reaction that generates the proton motive force

Bacteria and Archaea

3-Main routes to convert glucose to pyruvate

glycolysis/Embden-Meyerhof (EMP)

generates 2 ATP and 2 NADH

major pathway of glucose metabolism

series of reaction in which each molecule of glucose is oxidized to 2 molecules of pyruvate with a small amount of energy (ATP being generated

many carbon molecules are broken down into glucose and then enter glycolysis

Bacteria and Archaea

3-Main routes to convertglucose to pyruvate

Entner-Doudoroff (ED) pathway

glucose or sugar acids are converted to pyruvate generating 1 ATP, 1 NADH and 1 NADH

common in enterics

(intestinal bacteria)

Bacteria and Archaea

3-Main routes to convert glucose to pyruvate

phentose phosphate shunt (PPS)

glucose is converted to sugars with 3 to 7 carbons which are precursors for biosynthesis

or to pyruvate generating 1 ATP and 2 NADPH

precursor metabolites

(compounds used to make all the macromolecules in the cell)

made in glycolysis

• glucose is oxidized to 2 molecules of pyruvate
• net gain of 2 ATP
• 6 precursor metabolites are made
• NADH is formed which will be converted back to NAD in the electron transport system or in the fermentation reaction (NADH -> NAD)

Entner-Dudouroff Pathway

• studied for its role in production of cactus beer by Zymomonas fermentation of the blue agave plant
• ED pathway allows E. Coli and other enterics to feed on mucus secreted by intestinal epithelium
  
• Glucose -> pyruvate (different enzymes than glyco.)
  
• Net gain 1 ATP/ glucose and precursor metabolites
• used by enterics and enterococcus faecalis
  

Pentose Phosphate Pathway

phosphorylations pentose (5 carbon sugars)

formed from G6P

-ribulose
-xylulose
-ribose

used for production of precursor metabolite s in anabolic reactions

Net gain 1 ATP/glucose

 respiration-(TCA cycle) to be fully oxidized to carbon dioxide; this makes more ATP, so if an organism has a choice it will choose respiration

Ribulose 1,5-biphosphate ( used in Calvin Cycle) is made by phosphorylating a precursor from this pathway

-pyruate can either be used in fermentaion (to make alcohols acids gases)

  respiration-(TCA cycle) to be fully oxidized to carbon dioxide; this makes more ATP, so if an organism has a choice it will choose respiration 

What pathway forms this pyruvate?

can occur in the presence of O2

1 glucose molecule -> 2 ATP

partial oxidation of glucose

reduction of pyruvate

fermentation products

NAD+

1 glucose molecule -> up to 38 ATP

complete oxidation of glucose to CO2

oxidation of pyruvate by TCA cycle

uses electron transport chain (ETC) and ATP synthesis

glycolysis occurs followed by fermentation reactions (NO TCA, NO ETC)

1. electrons from glucose are passed to 2 NAD+ creating NADH
2. electrons are then passed from NADH to pyruvate, regenerating NAD+ so glycolysis can continue

homolactic fermentation

alcoholic fermentation

homolactic fermentation

once electrons from NADH are passed to pyruvate, pyruvate is reduced to lactic acid

ex: lactobacillus- ferments lactose sugar in milk to produce lactic acid, this gives us yogurt

once electrons are passed from NADH to pyruvate, pyruvate is reduced to alcohol adn CO2

ex: Yeast, ferment the sugars in malted graisn to produce alcohol and CO2 (beer, wine, bread)

electron donor- glucose

electron acceptor- pyruvate (which is made from glucose)

uses oxygen or other compounds from the environment to accept the electrons from NADH

uses other compounds from the environment other than oxygen

may be inorganic compound such as Nitrate, ferric iron, sulfate or carbonate

Tricarboxylic Acid Cycle

TCA cycle

krebs cycle

citric acid cycle

cyclic pathway to fully oxidize organic materials

into a small amount of ATP

-NADH and FADH2 (also used in ETC)

-CO2 is a waste product

-Precursor metabolites

occurs during respiration

oxidized pyruvate completely to CO2

only possible with an inorganic electron acceptor

produces more energy than fermentation

pyruvate dehydrogenase complex (PDC)

converts pyruvate to acetyl-CoA

removes CO2 (changes 3 carbons into 2 carbosn) (decarboxylation)

alpha-ketoglutarate & oxaloacetate

(used to make amino acids and nucleotides)

Acetyl CoA + oxaloacetate (4C)= citrate (6C)

acetyl CoA is oxidized to CO2

original oxaloacetate is regenerated

CO2 is released

NADH & FADH are generated

precursor metabolites are made to be used for biosynthesis

aromatic compounds (benzene rings) converted to pyruvate which enters the TCA cycle

allows for growth in wide range of environments

used for bioremediation

(cleaning oil spills, industrial sites, degrading toxic compounds)

pair of electrons from NADH is passed through  series of intermediates to oxygen

NADH is oxidized back to NAD+, oxygen is reduced to water

Oxygen is the terminal electron acceptor

flavoproteins

cytochromes

quinones

iron-sulfur proteins

ETC

(electron transport chain)

ETC is made up of intermediates

(such as flavoproteins)

prokaryotes: ETC is the cytoplasmic membrane

eukaryotes: ETC is the mitochondria

(powerhouse of cell)

ETC, series of membrane associated electron carriers that carry electrons from the primary electron donor to the terminal electron acceptor

 known as oxireducatases-

because they oxidize one substrate and thenr educe another

different organisms have different ETC

some have more than one due to different growth conditions

at each step: some electrons are used to push hydogen ion across the cytoplasmic membrane into the periplasm or to the outside of the CM

hydrogen ion gradient

proton motive force

chemiosmosis

creates a hydrogen ion gradient across the CM

The outside of the CM becomes more acidic &

more + charged that the cytoplasm

(halophiles use sodium motive forces (Na+ ion gradient)

gradient is a source for potential energy

ATPase enzyme

ADP -> ATP

 adds a phosphate group to ADP to make ATP

allows protons to cross back into the cytoplasm

energy is released by reducing the hydrogen ion gradient

this energy is used to make the high energy bond of ATP

oxidative phosphorylation- process of using the hydrogen ion gradient to make ATP

glucose -> pyruvate -> pyruvate is oxidized-> CO2(TCAcycle)

electrons from NADH are transferred to oxygen through ETC

same as aerobic respiration

energy is used to move protons across cytoplasmic membrane to periplasm

ATPase uses energy from hydrogen ion gradient to produce ATP

difference is that the final electron acceptor is some compound other than oxygen

11 precursor metabolites in E. Coli

6 from glycolysis 3 from TCA 2 from Pentose phosphate

convert precursors into building blocks (monomers) such as amino acids and nucleotides

Monomers are polymerized to form macromolecules (proteins and nucleic acids) & structures (LPS)

Monomer->

Sugar->

Nucleotide->

Amino Acid->

Fatty Acid->

Polymer

Polysaccharide

Nucleic Acid

Protein

Lipid

anabolism-

use light to form a proton motive force and make ATP

cyanobacteria= photoautotrophs

anoxygenic- no oxygen is produced

(most photosynthetic bacteria are anoxygenic phototrophs)

oxygenic- water is split to produce oxygen

cyanobacteria- (only bacterial group) and photosyntheric eukaryotes (plants) are oxygenic autotrophs

chlorophylls in oxygenic phototrophs

bacteriochlorophylls in anoxygenic phototrophs

do not have chloroplasts

the photosynthetic membranes are:

cytoplasmic membrane in many bacteria

chlorosomes in green bacteria

thylakoid in cyanobacteria

anoxygenic phototrophs

(use photosynthesis in the light, respiration in the dark and grow in the presence or absence of oxygen)

proteobacteria (purple sulfur and non purple sulfur)

Chloroflexus (green non sulfur)

chlorobium (green sulfur)

heliobacteria (ONLY Gram +)

Rhodobacter species- are used for stufying anoxygenic

photosynthesis

algae & cyanobacteria use electrons from H2O to reduce NADP for CO2 fixation producing O2 as a byproduct

2 seperate reactions :

photosystem I- resembles anoxygenic rxn

photosystem II- splits H2O to yield O2

Autotrophic Fixation

autotrophs use CO2 as sole carbon source

convert CO2 into organic carbon compounds (CO2 fixation)

The Calvin Cycle

RubisCO enzyme catalyzes condensation of CO2 + ribulose,

1-5 biphosphate ->  3- phosphoglycerate -> glyceraldehyde-3-phosphate ->

fructose-6-phosphate

requires large amount of ATP

F-6-P goes into glycolysis

reverse TCA cycle for CO2 fixation

uses the hydrooxypropionate pathway

energy from the oxidation of inorganic electron donors

oxidize inroganic chemicals as their sole source of energy

autotrophs-> fix CO2 as their carbon source

hydrogen oxidation

oxidation of reduced sulfur compounds-(H2S, S)

iron oxidation- oxidizes ferroud iron (fe+2)-> ferric iron (fe+3)- most are obligately acidophilic

nitrification- convert ammonia to nitrate (NH2->NO3)

nitrate reduction and denitrification

nitrate (NO3-) ->

nitrite (NO2-) ->

(g)Nitric oxide (NO) ->

(g)nitrous oxide (N2O) ->

(g)dinitrogen (N2)

all used reductase enzymes

reduce nitrate  to gases such as nitrogen, nitrous oxide, nitric oxide

nitrate is the electron acceptor

ETC process is the same as aerobic respiration

only difference is that electrons are used to reduce nitrate instead of oxygen

reduction of atmospheric N2 to ammonia NH3

energy expensive (40 ATP consumed for fixation of 1 N2)

requires nitrogenase which is inhibited by oxygen

most organisms only fix N when growing anaerobically

 protective proteins to stabilize

removal of O2 by respiration

O2 retarding slime layers

compartmentalization of nitrogenase in special cells  

(cyanobacteria have heterocysts where N fixation occurs)

some are symbiotic with plants and provide plants the necessary N in exchange for protection (plants grow fuller)

bacteria

archaea

eukarya

Domain

Phylum

Class

Order

Family

Genus

Species

optimum growth temperatures 80C found near hydrothermal vents and hot springs

fastest growing cells known

grouped with thermophiles due to ribosome similarities

highly resistent to radiation due to DNA repair mechanisms

Gram + thick peptidoglycan layer but has outer membrane like G-

thermophile

DNA polymerase used in PCR

large group of oxygenic phototrophs

fix CO2 (calvin cycle)

fix N2 (heterocysts)

can cause nuisance blooms (takeover water and keep growing)

 have thylakoids- site of photosynthesis

(like chloroplasts)

can grow as:

filaments (many cells growing in a line)

colonies

have gas vesicles for buoyancy

secrete neurotoxins and can kill animals that have ingested the water

form akinetes (specialized spore cells) to survive long periods of dessication and germinate when conditions improve

prochlorococcus

possibly the most abundant oxygenic phototroph on earth

divided into two groups based on % of guanine and cytosine in DNA

low GC- firmicutes

high GC-actinobacteria 

rods and cocci

pathogens

staphylococcus

gram +

endospores are extremely heat resistent for millenia

toxin-formers

clostridium (tetanus, botox, gangrene)

bacillus (anthrax, Bt)

molicutes-

ex: mycoplasma

without a cell wall

small genomes

pleomorphic (no distinct shape)

classifed as Gram + due to phylogenetic relatedness

pathogenic

Gram + Actinobacteria

ex: streptomyces (earthy odor of soil)

branching filaments called mycelia

(like filamentous fungi)

reproductive spores called conidia

sporulation triggered by nutrient depletion

mycobacteria-

ex: tuberculosis leprosy

mycobacterium

acid fast due to mycolic acids

some human pathogens

many are slow growers

largest group and most metabolically diverse group of bacteria

5 major phylogenetic subdivisions

alpha proteobacteria-

ex:

rhizobium, argobacterium in plants root nodules plant tumors

rickettsias in animals- rocky mountain spotted fever

some endosymbionts

get matbolites from host

transmitted between animal arthropods

reproduce by budding

appendages used for attachment

aquatic environments

lithotrophs- nitrate sulfur iron oxidizers

pathogens- nisseria gonnorrhea Gram - cocci

gamma proteobacteria

ex: vibrio and photobacterium

purple sulfur and non sulfur bacteria

(found in mud and water)

lithotrophs

can use iron or H2S as an electron donor

some are anoxygenic phototrophs

some bioluminescent

enterics

ex: e. coli

colonize human colon

motile- different arrangement of flagella

some in biofilms, some pathogenic

delta proteobacteria

myxococcus

attacks other bacteria in packs, (Social movement)

aggregates into fruiting bodies

disperses myxospores

delta proteobacteria-

bdellovibrio

parasitizes other bacteria

grows in periplasms

lyse host

epsilon proteobacteria

heliobacter pylori

smallest group of proteobacteria

causes stomach ulcers

burrows below protective mucous layers

1st identified by rRNA sequencing (little known about them)

spiral shaped

nitrite oxidizers; obligate aerobes

some found in microbial mats near hot springs

obligate anaerobes

bacteroides

predominant microbe in lower digestive tract of humans and other animals can be pathogenic

in digestive tract, undigested food is fermented by bacteroides

fermentation products are used by animal as carbon and energy source

chlorobium 

green sulfur bacterium

anoxygenic photolithotroph (dont produce oxygen)

contain chlorosomes- bacteriochlorophyll containing structure that are attached to the cytoplasmic membrane

found at greatest depths of water in any phototrophic organism

use H2S as electron donor and oxidize it to sulfur

sulfur granules are deposited outside of the cell

autotrophs- no calvin cycle ; reverse citric acid cycle 

motile

endoflagella located in the periplasm of the cell

ex:

teronema pallidum causes syphillis

(cant be grown in lab culture)

borrelia burgdorferi causes lyme disease, has a linear chromosome

obligate intracellular parasites of animals

little metabolic capacity

no peptidoglycan

causes human disease (VD, Psittacosis(epidemic in birds causes pneumonia in humans), conjunctivitis (leads to blindness)

larger reticulate body (grows within cells doesnt survive outside of host)

small elementary bodies (survive outside host, similar in function to endospores)

planctomycetes

Gemmata- membrane bound nuclear material (unique in prokaryotes)

s layer protein cell wall

reproduce by budding

some have stalks for attachment

multiple internal membranes

verrucomicrobia-

wrinkled microbes

irregular shape

contains tubulin

Phylum Eukaryarchaeota

Phylum Crenarchaeota

Phylum Nanoarchaeota

Phylum Korararchaeota

4 groups-extreme halophiles, methanogens, thermoplasmatales, hyperthermophiles

extreme halophiles

halobacterium salinarium

at least 9% NaCl for growth

common in salt lakes and salterns

give red color to water

to prevent water loss in hypertonic environment- 

1) pump inorganic ions (k+) into cell

2) make or concentrate an organic solute in cell

release 100 millions tons of methane into atmosphere each year

found in anaerobic environments (strict anaerobes)

freshwater sediments

gastrointestinal tract of animals

rumen

landfills

termite gut

thermoplasmatales

thermoplasma

lack cell walls

thermophilic and acidophilic

most strains have been isolated from self heating coal refuse piles

hyperhtermophiles

pyrococcus "fireball"

Phylum Crenarchaeota

sulfolobus

irregular in shape

may have no cell wall

always have unique liquid

most are hyperthermophiles (hot springs)

some are psychophiles (sea ice)

often very acidic or anaerobic

most use sulfur as electron acceptor

nanoarchaeum cells are symbionts or parasites of Ignicoccus (creoarchaeote)

small genome

lack genes for most metabolic functions; depend on the host

hydrothermal vents and hot springs

Phylum Korararchaeota

(Ancient Archael Group)

found in obsidian pool at yellowstone

hyperthermophiles 85*C

no pure culture exists

fungi

algae

protozoa

fungi

rhizopus- bread mold

cell walls contain chitin

non-motile

most grow hyphae

mycelium-branched mass of hyphae

absorptive heterotrophs

 motile flagella reproductive zoospores

(symbiont in bovine rumen, frog pathogen)

nonmotile sporangiospores spread through air or water fuse to form a zygospore

arbuscal mycorrhizae-assoc. w plant roots, increase absorption

ascomycetes

candida- yeast that causes thrush and yeast infections

fruiting bodies form asci containing acsospores

morels and truffles grow low to the grown, very expensive

produces spores called basidiospores

true mushrooms

phytoplankton

all have chloroplasts

many have paired flagella

cell wall made of glycoprotein or cellulose

contractile vacuole removes excess water

stores energy as starch

algae- chlorophyta

green algae

chlorophyll

grow near top of water

multiple life forms

unicellular forms have flagella

filaments- spirogyra

individual cells- chlamydomonas

sheets- ulva

colonies- volvox

algae- rhodophyta

red algae

phycoerythrin gives red color

sulfated sugar polymers- agar, agarose carrageenan

unicellular, filaments, or sheets

porphya- nori (used for sushi wraps)

Protists- Amoebozoa

entamoeba histolytica

amorphous shape

move using pseupods

actin pushes cytoplasmic streams ahead

cell rolls over membrane

engulf with pseudopods

slime molds

aggregate to form a fruiting body

spores are released from the fruiting body

live in marine habitats

radiolarians- needle-life pseudopods, shells made of silica, stabilized with microtubules

foraminiferans- shells mad eof calcium carbonate, indicators of petroleum deposits

alveola- flattened vacuoles at outer cortex

extrusomes- secrete enzymes, toxins

microtubules- stabilize the structure

multiple cilia or flagella

many cilia for motility, also for feeding

contractile vacuole to maintain osmotic balance

stalked ciliate attach to surface

phytoplankton 

cartenoids in some-red color

two long flagella (one wrapped around cell groove)

extrusome secretes toxins(neurotoxins)

endosymbionts- essential for coral survival

coral bleaching- when dinoflagellates leave the presence of the coral, they will lose their color

alveolates- apicomplexans

plasmodium- malaria

apical complex invades host cell

no cilia

obligate parasite

trypanosomes

lesihmania major- carried by sand-fly skin and organ infections

trypanosoma brucei- carried by tsetse fly(african sleeping sickness)

T. cruzi-carried by kissing bug (Chaga's Disease)

excavates

Giardia lamblia- passed around in daycares or water (stomach illness)

lack mitochondria (cant produce energy)

obligate parasites

anaerobes