Bios313 11/22/2011

• Mollicutes
• clostridia
• bacilli

• 3 classes:
• Mollicutes
• Clostridia
• Bacilli

• The mycoplasmas
• lack cell walls and are pleomorphic
• canno synthesize peptidoglycan precursors
• penicillin resitant
• lysozyme resistant
• smallest bacteria capable of self-reproduction

• pathogens
• Mycoplasma mycoides: bovine respiratory disease in cattle
• Mycoplasma hypnuemoniae: pneumonia in swine and primary atypical pneumonia in humans
• genomes: less than 1000 genes and one of the smalles prok.

• genus: Clostridium
• fermentative metabolism
• ferment amino acids using stickland rxn
• oxidation of one amino acid using another ass an electron acceptor
• the fermentations produces responsible for unpleasant odors associated with putrefaction

• C. botulinum: food spoilage (canned foods) botulism
• C. tetani: tetanus
• C. perfringens: gas gangrene
• C. acetobutylicum: manufacture of butanol

• gram positive
• 2 orders: Bacillales and Lactobacillales

• model organism for cellular differentiation, divison and other processes
• varies species produce antibiotics

• B. anthracis: anthrax
• B. thuringiensis and B. sphaericus: parasporal body and have solid protein crystals that contains toxin

• facultatively anaerobic
• nonmotile
• gram-positive cocci
• usually form irregular clusters
• normally assoicated with warm blooded animals in skin, skin glands, and mucous membranes

• produces virulence factor: coagulase which cause blood plasma to clot
• produces alpha hemolysin which is a toxin which lyses cells
• Major cause of food posioning
• found in nasal membranes and sking and GI and urinary tracts

• largest genus
• lactic acid bacteria
• grow optimally in slightly acidic conditions pH= 4.5- 6.4
• lactic fermentation
• ferment sugars for energy

• widely distributed in natures
• on plants surfaces
• in dairy products, meat, water, sewage, beer, fruits
• normal flora of mouth , intestinal tract and vagina

• non motile
• facultative and strict anaerobes
• homolactic fermentation
• alpha hemolysis: incomplete lysis of RBC seen as greenish zone around colony in blood agar
• beta hemolysis: complete lysis of RBC seen as clear zone around the colony in blood agar

• Actinomycetes
• Corynbacterium

• source of most currently used antibiotics
• also produce metabolites that are anticancer, antihelminthic and immunosupressive ex Steptomyces
• complex life cycle

• involves developments of filamentous cells (hyphae) and spores
• hyphae can form brancing network
• can grow on the surface of substrate or into it to produce substrate mycelium
• some hyphae differeniate and form aerial mycelium which extends above the substatum and form exospores which are called sporangiospores
• at this stage forms seconadry metabolites

• in soil
• important role in mineralization of organic matter
• most free living and few are pathogens

• Family: Corynebacteriacae
• harmless soil and water saprophytes
• many are animal and human pathogens
• C. diphtheria: diptheria

• Family: Mycobateriaceae
• M. bovis: tuberculosis in catter and other ruminants
• M tuberculosis: tuberculosis in humans
• M. leprae: leprosy

• nonsporing rods
• founds in mouth and intenstinal tract of warm blooded animals in sewege and in insects

• largest phylogenetically cohereant baterical group
• over 2000 species assinged to more than 500 genera

• metabolically flexible
• normall grow anaerobically as anoxygenix photo-ogranoheterotrophs
• posses bateriaochlorohphylls a or b
• if there is no light some carry out fermentations and can grow anaerobically
• found in mud and water of lakes and ponds with abundant organic matter and low sulfide levels
• some marine species

• resting cells: resitant to desiccation but less tolerant of heat and UV than bacterial endospores
• made is response to nutrient limitation
• have thick outer coat and store polyhydroxybutyrate

• class : Alphaproteobacteria
• order: Rickettsiales
• family: Rickettsiaceae

• similar to rickettsia
• Class: Gammaproteobacteria
• order; Legionellales
• family: Coxiellacae

• gram-neg cell walls
• no flagella
• very small
• parasite or mutualistic
• parasite species grow in vertebrate erthrocytes, macrophages, and vascular endotheial cells
• also live in blood-sucking arthropods which serve as vectors or primary hosts.

causitive agent of Rocky Mtn Spotten Fever

typhus fever

Q fever

• have at 1 of 3 distinguishing features
• 1. prostheca: extension of cell. including plasma mem, that is narrower than a mature cell
• 2. stalk: nonliving appendage produced by the cell and extending from it
• 3. reproduction by budding, the progeny cell is a bud that first appears as a small protrusion on a parent cell and enlarges to form a mature cell

• Class: Hyphomicrobiaceae
• prosthecate, budding bateria
• aerobic chmoheterotrophs
• grow in ethanol, acetat, and one-carbon molecules ( faculative methyltroph)
• frequently attached to solid objects in aquatic and terrestrial env.

• 1. hypha forms
• 2. new nucleoid moving into hypha
• 3. young bud
• 4. Hypha lengthens more and produces another bud
• 5. swarmer cell with subpolar to lateral flagellum (1 to 3)

• gram neg motile rods
• contain poly-beta-hydroxybutrate granules
• grow symbiotically as nitrogen-fixing bacteroids within root nodule cells of legumes
• bacteria induce formation of and live in nodules on the roots of legumes

• do not stimulate nodule formation or fix nitrogen
• invade crown, roots, and stems of many plants
• transform infected plants cells into autonomously proliferating tumors

causes crown fall disease by means of tumor-inducing (Ti) plasmid

• ammonia to nitrite to nitrate
• happens by action 2 genera
• 1. Nitrosomonas (beta)- ammonia to nitrite
• 2.Nitrobacter (alpha): nitrite to nitrate
• nitrate is easliy used by plants

• nonmotile
• gram neg cocci
• have capsules and fimbrae
• some human pathogens:
• Neisseria gonorrhoeae: gonorrhea
• Neisseria menigitidis: meningitis

• nitrogen fixiation
• both genera form symbiotic associations with legumes silimlar to rhizobia

• mammalian parasites that multiply in respiratory epithelial cells
• Bordetella pertussis: non motile encapsulated species
• causes whooping caugh

• family: Pseudomonadaceae: has 15 genera
• psuedomonas most important genus
• gram neg straight or slightly curved rods
• motile by one or several polar flagella

• metabolically versatile
• degrade alot of organic molecules
• mineralization
• microbial breakdown of organic materials to inorganic substrates
• important in experiemtns
• major animal and plant pathogens
• some cause spoilage of refrig. food
• can grow at 4 c

• one family: Vibrionaceae that has 8 genera
• most are aquatic
• most free-living
• important pathogens
• symbiotic in luminous organs of fish and other aniamsl
• closley related to 2 other orders Enterobacteriales and Pasteurellales

• causes cholera
• 2 circular chromosomes
• copies of some genes present on both chromosomes

• capable of bioluminescence
• emession of ligth catalyzed by luciferase
• 2 species
• free-living

Escherichia coli

• inhabits most intenstinal tracts of animals
• idicators organisms for testing water for fecal contamination
• some strains are pathogenic
• gastroenteritis
• UTI

• Salmonella: typhoid fever and gastroenteritis
• Shigella: bacillary dysentery
• Klebsiella: pneumonia
• Yersinia: Plague (black dead)
• Erwinia: blights, wilts, crop plants

• important pathogens
• Pasteurella multiocida: fowl cholera
• Pasteurella haemolytica: pneumonia in cattle sheep and goats
• Haemophilus: meningitis in children

• family: Bdellovidbrionaceae
• which has 4 familys Bdellovibrio:
• predatory bacteria

• Desulfuromondales
• Myxococcales
• Desulfomonile
• Syntrophobacteraceae
• Desulfobactereae
• Desulfobubbasceae
• Desulfovibrionales

• smallest proteobacteria class
• one order: Campylobacteriales with 3 families

pathogenic and nonpathogenic

• reproductive disease and abortions in cattle and sheep
• septicemia (pathogens or their toxins in blood)and enteritis in (inflammation of intestinal tract) humans

• abortions in sheep
• enteritis diarrhea in humans

• Helicobacter pylori
• cuases gastritis and peptic ulcer disease
• produce large quantaties or urease
• urea hydrolysis apears to be associated with birulence

• all thermophillic prok
• optimum growth at temps above 85 C Arachea
• Bacteria: Aquificae and Thermotogae

• deepest and oldest branch of bacteria
• 1 clas, 1 order and 5 genera
• Aquifex and Hydrogenobacter

• second deepest branch of Bacteria
• 1 class, 1 order, and 6 genera
• Thermotoga

• gram neg rods
• optimum growth at 80 C maz at 90 C
• grow in active geothermal areas
• marine hydrothermal vents and terrestrial solfataric springs

• class: Deinococci
• order: Deincoccales and Thermales

• spherical or rod-shaped
• pars or tetrads
• mesophilic
• aerobic
• catalas pos
• produce acid from only a few sugars
• genome: 2 ciruclar chromosomes, a megaplasmid, and small plasmid
• radiation resistant due to the ability to repair the genome which is damaged
• DNA system repair
• resistant to desiccation and radiaiton
• isolated from gound meat, feces, air, fresh water,

• 3 groups of gram neg photo. bact
• purple bacteria
• green bacteria
• cyanobactiria

• carry out oxygenic photosynthesis
• have 2 photosystems
• use water as electrom donor and geneate oxygen during photosyntheis
• obligate photolithoautotrophs
• can grow slowly in the dark as chemoheterotorpsh

small motile fragments of filamentous cyanobactiera

• specialized, dormant, thick-walled resistant cells that are resistnat to desiccation
• oftner germentate to from new filaments

• produced by multiple fission
• small, spherical cells, escape when the outer wall ruptures
• some motules by gliding motiltiy

• specialized cells used for nitrogen fixiation
• produced by an organism is nitrogen deprived
• differentiate from individual cells in fimalent
• reorganization of photosynthetic mem
• thick heterocyst wall prevents oxygens diffusion into heterocyst which would inactivate nitrogenase which is the enzyme responsible for nitrogen fixiation

• tolerant env. extreme
• grow up to 75 C
• often primary colonizater
• caused bloo,s in nutreint rich ponds and lakes produce toxin

• phototrophic partner to most lichens
• symbionts with protozoa and fungi
• nitrogen-fixing species for associations with plants

• gram neg
• obligate intracellular parasites
• cause diease
• can grow within hosts , protist and vertebrate and invertebrate cell with out adverse effects

• nonmotile coccoid gram neg bacteria
• cell walls lack muramic acid and peptidoglycan
• small genomes
• obligate intracellular parasites
• forms elementatry body and reticulate body

• infects humans and mice
• causes trachoman, nongonococcal urethritis, and other disease in humans

• infects humans and many other animals
• causes psittacosis in hums

cause human pneumonia

• gram neg bacter
• slender long flexible helical shape
• creeping and crawl;ing molitlity due to axial fialment
• chemoheterotrophs

axial fibrils rotate and cause a corck-screw shape outer sheath to roated and move throughout the liquid

• gram neg rods
• anaerobic chemoheterotropsh
• fermentatives
• oral cavity and intestinal tract

• Beneficial: provide vitamins, decompose, and
• produce antibiotics
• Harmful: responsible for infections

• Disprove spontaneous generation with swan flask
• experiment.
• Would be full of organisms if spontaneous
• generation was true. No organisms
• Organisms grow from dust contacting sterile
• liquid

• Arachea
• bacteria

• Plant (macro)
• Animals (macro)
• Algae
• Fungi
• Protozoa

• Agriculture: N2 fixation, nutrient
• cycling, and animal husbandry
• Food: food preservation, fermented
• foods, food additives
• Disease: indentifying new diseases,
• treatment and cure, and disease prevention
• Plant disease:
• great potato blight of Ireland caused by oomycetes bacteria another example
• anthrax, Bacillus anthracis. Bacteria
• Energy/environment: biofuels (methane
• and ethanol), bioremediation, and microbial mining
• Biotechnology: genetically modified organisms, production of
• pharmaceuticals, gene therapy for certain disease

circular

• elongated
• or rod shaped

spiral

chains of rod shape and produce antibiotics.

• Step 1: isolate blood samples from and
• healthy animal and diseased animal
• Step 2: grown suspected organism in a
• pure culture
• Step 3: give organism to healthy
• animal, should cause disease
• Step 4: reisolate organism from second
• animal and compare it to the first pure culture. Should be the same.

creates biofuels (ethanol) by fermenting sugar with the activities for specific microorganisms

• Involved in
• carbon, nitrogen, and sulfur cycles

• Oxidation of
• iron, sulfur, and ammonia obtain energy

• uptake
• chemicals from the environment and eliminate waste into the environment. Open
• system

• chemicals from
• the environment are turned into new cells under the direction of pre-existing
• cells

• forming a new cell structure is
• part of the life cycle (example: producing a spore)

• cells communicate and interact through chemicals that are
• released or absorbed

• evolve to display new biological properties. Short, rapid
• generation time leads to evolution

200 µm

• micrometer
• = 10^-6 m

10^-9 m

Å= 10^-10 m

refracted (bent) when passed through a medium

a measure of the amount a substance slows the velocity of light

strength related to focal length. the short the focal length= greater magnification

where the light rays focus

• distance between the center of the
• lens and the focal point

• distance
• between the objective and the slide with the specimen

• ability of the lens to separate or
• distinguish small objects that are close together.

Shorter wavelength = greater resolution

• bright-field microscope,
• dark-field microscope, phase-contrast microscope, fluorescence micro scope, and
• confocal microscope. Compound
• microscopes (2 lenses).

• produces dark image against a
• bright background

Many objective lenses.

Living organisms

• remain in focus when the
• objectives are changed.

• Total magnification: product of
• the magnifications of the ocular lenses and the objective lenses.

• Too see objects really small,
• replace water with immersion oil. The different medium caused the light rays to
• refract and reflect different. Oil = 100x

• image is formed by light reflected
• or refracted by the specimen and produces a bright image of the object against
• a dark background

• see living, unstained
• preparations

• observe internal structures in
• eukaryotic cells

identify bacteria

gives more contrast

• converts slight differences in
• refractive index and cell density into easily detected variations in light
• intensity

• light rays from the hallow cone
• of light passes through the unstained cell and dark compared to background

living cells

motility

internal structures

detect endospores

• DIC. Creates image by detecting
• differences in refractive index and thickness of different parts of the
• specimen

Living cells, unstained

Appear brightly- colored and 3-D

• Cell walls, endospores, granules,
• vacuoles, nuclei are clearly visible

• exposes specimen to ultraviolet,
• violet, or blue light

• Specimens usually stained by
• fluorochromes (make fluorescent).

• Shows bright image of the object
• that results from the fluorescent light that is emitted by the specimen

Light generated by laser

• Used to indentify unknown
• pathogens (fluorochrome-labeled probes: antibodies or tags.

• Can localized specific proteins
• in cells

• confocal scanning laser microscopy
• (CLSM) creates a sharp, composite 3-D image by using laser beams, an aperture
• to eliminate stray light and computer interface

study of biofilms

rotate in space on computer

can also use for florescence

increase visibility of specimen

• accentuates specific morphological
• features

preserve specimen

increase contrast

• make internal and external
• structures of the cell more visible by increasing the contrast with the
• background 2 common features

• chemical
• groups with conjugated double bounds. Gives the dye its color

have charged groups

basic dyes: positive charges

acid dyes: negative charges

single stained used

• determines size, shape and
• arrangement of bacteria

• divides microorganisms into groups
• based on their staining properties

• two groups, color based on
• difference in the structure of the cell wall.

gram positive: purple

gram negative: pink/red

• used to detect the presence or
• absence of structures (endospores, flagella, capsules)

• heated, and double staining technique. The endospore turns one
• color while the vegetative cell is a different color.

• used
• to visualize capsules around bacteria. Negative
• staining makes the capsules colorless against the background

• mordant
• applied to increase the thickness of the flagella

• preserves internal and external
• structures

• usually killed and firmly attached
• to slide

• used with bacteria and archaea.
• Preserves the overall morphology but not internal structures

• larger
• more delicate organisms. Protects fine cellular substructure and morphology

• Electrons replace light with a
• illuminating beam

• Wavelength is shorter than light
• and results in a higher resolution

Morphology in great detail

1000x

• High
• lipid content in the cell walls helps stain

• electrons scatter as they pass
• through the sections of the specimen

Under vacuum

• Denser regions in a specimen
• scatter more electrons and appear darker.

1000x

Black and white

• must be cut very thin, After cut, they are chemically
• fixed and stained with electron dense materials (heavy metals) that will
• scatter electrons

Negative stain: heavy metals create a dark background

• Shadowing: coating specimen with a thin film of heavy metal on one
• side only (morphology, flagella, and DNA). 3-D image

• Freeze etching: freeze the specimen and fracture it along the lines
• of greatest weakness. Allows 3-D observation of shapes of intracellular
• structures and reduces artifacts

• use electrons reflected from the
• surface of the specimen to create a detailed image. 3-D image of the specimen’s
• surface. Black and white. Replace water with carbon dioxide

• freezing
• technique 3-D. extremely high resolution. Can see cytoskeletal elements,
• magnetosomes, inclusion bodies, flagellar motors, and viral structures.

• Scanning tunneling microscope: 100 millionX. Atoms on the surface
• of a solid. Use of a steady current through a tunnel that is maintaining
• between the microscope probe and the specimen. The up and down movement of the
• probe and it maintains current produces an image of the surface of the
• specimen. DNA

• Atomic force microscope: no current. Sharp probe moves over the
• surface of a specimen at a constant distance and the up and down probe detects
• the distance and creates an image

• Complex cell walls/ membranes
• Simpler interior
• Much smaller than Eukaryotes
• Range from 7,000 nm to 27 nm

• allow
• components/ molecules to go in and out.

• one
• component transported in one direction

• 2
• components transported at the same time in the same direction

• 2
• components transported at the same time if opposite directions

• interchange
• or nutrient exchange

• proteins
• are sensors of the environment source of nutrients or toxic compound, PH, temp
• and react to adapt and survive

• react
• depending on environment

• Cholesterol (steroid) gives stability in PM to
• Eukaryotic cells and bateriohopantetrol (hopanoid) gives stability plasma
• membrane to Prokaryotic cells

goes all the way through the PM

only stick to one side

• phospholipid bilayer with glycolipids, sugars,
• and proteins.

Inner membrane differ depending on amino acids

• in
• cyanobacteria the membrane system is involved in photosynthesis and contain
• inclusions

• false
• results, artifacts

• Hydrophobic: fatty acid tail,
• H-C bonds with –COOH (carboxylic acid)

Hydrophilic: glycerol head

Dynamic structure

• Proteins can move through
• membrane help with nutrient and waste transport through PM

purple

• Thick
• peptidoglycan layer in cell wall

Plasma membrane

Teichoic Acid anchors PM to peptidoglycan

Negative charge

pink/red

Cell wall has a thin peptidoglycan layer and outer membrane

Plasma membrane

Outer membrane contains porin (transport proteins)

• causes negative charge
• Outer lipid layer is LPS and the inner
• lipid layer is a phospholipid layer (not phospholipid bilayer)

which is a toxic component

has O side of the chain which is an antigen

• differences in O chains determine what kind of
• antibodies or how to fight the infection

• Lipid A (glucosamine and fatty acid, P) + core
• polysaccharide + O side chain (antigen)

• anchors
• the outer membrane to the peptidoglycan layer

• hallow
• and form complex that allows the pass of molecules.

• space in cell wall between the peptidoglycan and
• the plasma membrane

• Differences in colors due to structure of cell
• wall

• : formed
• by simple monimers and becomes repeated molecules in a long chain that are
• parallel to each other and linked together by peptides to form a thick layer.
• (Gly-Peptide interbridge)
• .
• Peptidoglycan is not stained put is permeable to the crystal violet and it goes
• into the periplasmic space

• The cell wall protects the cell from the
• environment and osmotic stress.

• inhibits
• call wall synthesis (formation) and forms protoplast.

• cell without a cell wall and needs same osmotic
• pressure on the outside of the cell as on the inside of the cell in order to
• survive.

• When a protoplast is
• transferred into a dilute medium (water into cell) the cell swells due to water
• influx and causes it to lysis (break)

• in pathogenic cells
• resistant to phagocytosis
• ex: Streptococcus
• pneumoniae causes strep throat
• have 3 layers
• slime layer
• Glycocalyx
• S-layer: contributes to fool the immune system.
• Sticks to the surface to produce biofilm.

• hard to treat, more resistant to chemicals.
• Water contamination.
• Functions:
• Adhesion to surfaces
• Protection against environmental conditions (PH,
• temperature)
• Protected against the immune system because
• cells will a capsule cannot be detected by the immune system
• Produced when the cell experiences environmental
• stresses.

• thinner
• than flagella and are not involved in motility

• less abundant than Fimbriae and Larger and are
• required for bacterial mating. They interchange DNA by horizontal transfer.

• Monotrichous: one
• flagellum

• Amphitrichous: two
• flagellum, one at each pole

• Lophotrichous: two
• flagellum clusters, one at each pole

Peritrichous: flagellum evenly spread over the surface

• Gram-Positive: less
• complex than negative.
• M ring in PM about 22 nm
• S ring in Periplasmic Space
• Rod goes connected to the S
• ring and goes through periplasmic space and peptidoglycan layer
• Hook inside of rod
• Filament inside of the hook

• Gram-Negative:
• More complex than positive
• All positive components plus
• the following
• P ring in peptidoglycan layer
• L ring in outer membrane

pushed through hallow base.

One globular protein

• Ribosome to mRNA flagellin
• (filament) synthesized through hook

• Once formed they are rigid like
• a propeller

• Movement depends on how many
• flagellum and where they are located
• Mechanical portions are
• proteins
• Rotation driven by proteins or
• sodium gradients and force direction in one direction or another
• Motor proteins near PM and is
• connected to a sensing mechanism that responds to the gradient of sodium ions
• and caused it to move
• Mot B and Mot A integral
• proteins in PM
• Fli G, M , N compose the C ring

• movement towards or away from
• chemicals.

Have chemoreceptors

Positive: towards

Negative: away

• Inclusion bodies
• organic or inorganic and are
• used for storage of glycogen and glucose
• With or without a single
• membrane
• Organic example: poly-β-hydroxybutric
• acid (PHB) which is used for bacteria to store polymers of glycogen (glucose =
• monomer)
• Inorganic example:
• polyphosphate, sulfur, iron (magnetosomes)

• makes
• bacteria float close to the surface in aquatic environments

• protein synthesis
• in the cytoplasmic matrix and are smaller than Eukaryotic ribosomes

• where DNA is located and used
• to classify organisms. Has NO nuclear membrane

• resistant structure that is
• produced when the organism experiences a harmful environment.

Gram-positive bacteria: Bacillus

a lot of layers

position of endospore varies

• axial filament formation: the PM invaginates and starts
• to separate the DNA (cell wall around PM remains unchanged)
• septum formation:of the PM to completelyseparate into 2 sections inside the cell wall each surrounded by PM, Smallsection is the endospore
• Engulfment of the endospore by other part of the cell
• DNA not located inside of the endospore starts to degrade because of the harmful environment
• Cortex formation around the endospore by adding a lot of layers around it
• Coat synthesis begins and a exosporium surrounds the spore coat which surrounds the cortex which surround the endospore and protects the DNA
• After the completion of coat synthesis there is an increase in refractility and heat resistance
• Lysis of sporangium causes the spore to be released and is then a free spore

Membrane-delimited nuclei

Nucleus has double membrane

• Membrane-bound organelles that
• perform specific functions

• More structurally complex
• (internal) than Prok.

All fungi have cell walls

• Fluidmosaic model: fluid and flexible
• Allows proteins to move
• Majormembrane Lipids: phospholipids
• Phosphoglyceride
• Sphingolipids: greater in number in PM because they are related to sensing and signaling
• Cholesterol (no cholesterol in
• Prok.)
• Lipid rafts: micro-domains that are enriched for certain lipids (sphingolipid)

• cell movement- shape and
• direction

• transduction- signaling that
• causes a cascade to a genetic response

cytoplasmic matrix: (CM) internal network where many organelles are located

• cytoskeleton: formed
• from filaments and plays a role in cell shape and cell movement

one type of protein: actin

4 to 7 nm in diameter

• Scattered within the CM or
• organized into networks and parallel arrays

• Involved in cell motion and
• shape changes

• more than 1 type of protein:
• tubuline (2 types: α-subunit and β-subunit) and is constantly being synthesized
• and desynthesized

• shaped like thin cylinders
• about 25 nm in diameter

helps maintain cell shape

• involved with microfilaments in
• cell movement

• participate in intracellular
• transport processes because it creates “high ways” for motor proteins to move
• along that transport molecules and requires energy

only in cytoskeleton

10 nm in diameter

Role unclear

• Helps cells connect together to
• form tissues

• Irregular network of branching
• and fusing membranous tubules (cisternae, cistern) and flattened sacs
• Group of cisternae creates ER

• Functions
• Transport:proteins, lipids, and other materials in cell
• Cellsynthesis
• Proteins (rough ER)
• Lipids (smooth ER)
• Lysosomes.

Ribosomes attached

• Synthesis of secreted proteins associated
• with ribosomes in vesicles

No ribosomes

• Synthesis of lipids of
• associated enzymes

• Membranous organelle made of dictyosomes: cisternae stacked on each
• other

• Involved in modification,
• packaging, and secretion of materials

• Receives vesicles from the ER
• and they fuse with the Golgi and then modification takes place

• Peripheral
• tubules

• Cis/forming
• face: associated with ER and receive secretary vesicles

• Trans/maturing
• face: where molecules exit

Single Membrane-bound vesicle

• Involved in intracellular
• digestion

Contains hydrolases, enzymes which hydrolyze molecules

• Enzymes process nutrients or
• help degrade damaged or unused cells

• Function best under slightly
• acidic environment which is maintained
• by pumping protons into their interior

Formed in ER

• Proteins synthesized by
• ribosomes on the rough ER and a released small vesicles cis face of Golgi trans
• faces of Golgi and released
• After vesicles released from trans they
• deliver their contents to lysosomes or cell membrane
• Membrane of vesicle because part of the
• cytoplasm after it exits the Golgi

• Ubiquitin
• polypeptides: target unfolded or misfolded proteins that are
• secreted by the cystol to destroy

• Proteasomes:
• destroy target proteins that are damaged and need to be destroyed

Requires activation by enzyme

Requires ATP

• Ubiquitin
• protein ligation: needs
• ATP and 3 enzymes: Ubiquitin-activating, Ubiquitin-conjugating, and Ubiquitin-ligase.
• Protein attached to polyubiquitin chain

• Recognition
• of Ubiquitin-conjugated protein: labeling. recogniczed by
• proteasome

• Degradation
• of Ubiquitin-conjugate protein: by proteasome into degraded
• peptides (was damaged protein). Need ATP

• Release
• and recycling of Ubiquitin: regeneration

• Endocytosis: bring
• materials inside of cell

• Solutes or particles are taken
• up by extensions of the cytoplasm and are enclosed in vesicles that are pinched
• from the PM, the PM fuses and the vesicle is engulfed

• Most cases delivered to
• lysosomes and destroyed

• Endocytosis.
• Uses the cell surface protrusions to surround and engulf a particle when a
• substrate is detected by receptors in the membrane

• resulting vesicles which are
• formed by subunits and once inside of the cell it will disassemble

• involves membrane regions
• called coated pits (coated by clathrin protein on the cytoplasmic side)

• Coated pits have external
• receptors that specifically bind to macromolecules

• The coated pits are pinched of
• to form coated vesicles

• Molecules enriched in
• cholesterol and the membrane protein Caveolae

• Do not deliver their contents
• to lysosomes

• Play a role in signal
• transduction

• Transport of small molecules
• and macromolecules

digestion without Endocytosis

• Digestion and recycling of
• cytoplasmic components (internal parts: damage cell part, organelles, or
• mitochondria)

• Autophagosome: double
• membrane the surround the cell component

Double membrane is possibly from ER

• Autophagosome fuses with late
• endosome which forms a lysosomes

80S in size

• Maybe attached to ER or free in
• cytoplasmic matrix

• Proteins made on ribosomes of
• RER are often secreted or inserted into the ER membrane to create integral
• proteins. Attached ribosomes synthesize secretory or membrane proteins

• Free ribosomes synthesize
• nonsecretory and non membrane proteins and some are inserted into organelles

• site of tricarboxylic acid
• cycle activity (TCA cycle)

where ATP is generated

• electron transport and
• oxidative phosphorylation

double membrane

• a lot of folding structures and
• are attached to ATP-ase which is present on the membrane and is a
• enzyme/protein

• cristae: crista
• folded structures inside of IM increase surface area and production of ATP

• location of enzymes and
• electron carriers for electron transport and oxidative phosphorylation

• contains
• porin

inside space of inner membrane

• contains ribosomes,
• mitochondrial DNA, and large phosphate granules

• contains enzymes of the TCA
• cycle and enzymes involved in catabolism of fatty acids

carboxylic acid

• pigment-containing organelles
• in plants and algae

• site of photosynthetic
• reactions

double membrane

• matrix in the Inner Membrane of
• the chloroplast

contains DNA

ribosomes

lipid droplets

starch granules

• flattened,
• membrane-delimited sacs and is the site of light reactions. Traps light energy
• to generate ATP, NADPH, and Oxygen\
• grana:
• granum, stacks of thylakoids
• pigment necessary for
• photosynthesis
• site of dark reactions: formation for carbohydrates from water and carbon
• dioxide

• membrane-bound structure that
• houses genetic material or Euk. Cell has

double membrane

• dense fibrous material in
• nucleus

gives stability

contains DNA

• condenses to form chromosomes
• during cell division

double membrane with pores

• transfer to cytoplasm through
• meditative transport

• double membrane structure that
• delimits the nucleus

• nuclear pores that allow
• materials to be transported into or out of the nucleus that are regulated by
• proteins

not membrane enclosed

important ribosome synthesis

• directs synthesis and
• processing of rRNA

• directs assembly of rRNA and
• ribosomal proteins to form ribosomes

one component of cell cycle

distributes DNA to 2 nuclei

• ploidy: number
• of chromosomes

• ploidy of parent and progeny
• cells are the same

• diploid organism remains
• diploid

• two stage process of nuclear
• division

• hapliod
• ploidy

haploid gametes

rigid

Algae: cellulose and protein

Diatoms: silica

• Fungi: chitin, cellulose,
• glucan

• Oomycytes (not true fungi):
• cellulose

• rigid
• layer of components just beneath plasma membrane

• Not as strong or rigid as cell
• wall

Provides shape and protection

Rich in proteins

Helps with Endocytosis

• 50
• to 200 micrometers long

• 100-200
• micrometers long

Axoneme: set of microtubules (9+2) arrangement

• Basal body: at
• base of flagellum or cilia and directs synthesis of flagella and cilia and
• anchors
• membrane bound

• Basic chemical composition:
• same molecules and polymers

Genetic code

Basic metabolic processes

• the
• total of all chemical reactions in the cell

the energy-conserving rxns

• the synthesis of complex organic molecules
• from simpler ones

Requires energy. ATP

• Requires a source of electrons that are stored
• in the form of reducing power

• energy
• from organic molecules

• energy
• from inorganic molecules

• energy from
• light

CO2

• organic
• molecules

organic molecules

• organic
• molecules

• = monomers/building blocks to make macromolecules
• The processes organisms use to obtain energy
• and do chemical work are the basis of functioning ecosystems

• capacity
• to do work or cause a particular change

• synthesis
• of complex molecules

• take up of
• nutrients, elimination of wastes, and maintenance of ion balances

• cell motility
• and movement of structures with in cells

• a science that analyzes energy changes in a
• collection of matter called a system. ( all other matter in universe besides
• the system is call its surroundings)

• Calorie
• (cal): amount of heat energy needed to raise 1 gram of water from 14.5 to 15.5 °C

Joules (J): units of work capable of being done by a unit of energy

1 cal = 4.184 J

energy cannot be created or destroyed

• The total energy in the universe remains
• constant

• physicl and
• chemical processes lean towards the most possible disorder/chaos

• the
• amount of disorder in a system

• the change in energy that can occur in
• chemical reactions and other processes

• used to decide if rxn will spontaneously
• occur

• ∆G = change in
• free energy and is the amount of energy available to do work.

• ∆H= the change
• in enthalpy (heat)

• T= temperature
• in Kelvin

• ∆S= change in
• entropy

• Free energy is always defined at standard
• conditions

• K_eq=
• equilibrium constant: the equilibrium concentrations
• of products and reactants (products/reactants)

• When the forward and reverse reaction rates
• are equal

Exothermic

K_eq> 1

∆ is G negative

Thermodynamically favorable, spontaneous rxn

Products favored

• K_{eq =} 1
• ∆G is positive
• non spontaneous

• adenosine
• 5-triphosphate and is the energy currency of the cell

• in Exergonic rxns the breakdown of ATP is
• couple with and Endergonic rxn to make the Endergonic rxns more favorable

aerobic respiration

anaerobic respiration

fermentation

photosynthesis

chemical work

transport work

mechanical work

• electron
• transfers

• used to transfer electrons from an electron
• donor to an electron acceptor.

• When electrons are transferred, it can result
• in a release of energy which can be conserved or used as ATP.

• Electron Carriers
• NAD:nicotinamide adenine dinucleotide
• NADP: nicotinamide adenine dinucleotide phosphate
• FAD: flavin adenine dinucleotide
• FMN: flavin mononucleotide
• CoQ: coenzyme Q
• Quinone
• Ubiquinone
• Cyctochromes: use iron to transfer electrons Iron is part of heme group
• Nonheme: iron proteins
• Ferrodoxin :Use iron to transport electrons and iron is
• not part of the heme group

equilibrium constant for redox rxn

• The measure of the tendency of the reducing
• agent to lose electrons

• More negative E0 : better
• electron donor

• More positive E0 better
• electron acceptor

• The more negative ∆G, the greater difference
• between the of the acceptor and the of the donor. (Exergonic rxns)

• Electron carriers organized so that the first
• electron carrier has the most negative E₀

• This causes the potential energy stored in the
• first redox couple is released and used to form ATP

• have
• great specificity for the rxn catalyzed and the molecules acted on

• substance that increases the rate of the rxn
• without being permanently altered

• reacting
• molecules

• substances
• formed by the rxn

• Some
• composed only of polypeptides

• Some have 1 or more than one polypeptide with
• a non-protein component

• protein
• component of an enzyme

non-protein component of an enzyme

• Prosthetic
• group:
• firmly attached

• Coenzyme: loosely
• attached

• apoenzyme
• + cofactor

• act as carriers and transport substances
• around the cell

• Small organic non-protein molecules that
• carry chemical groups

Also known as co-substrates

• An enzyme with a coenzyme position to react with
• 2 substrates

• Coenzyme picks up the chemical group from
• substrate 1

• Coenzyme readies the chemical group for
• transfer to substrate 2

• Final action is when group is bound to
• substrate 2 and altered substrates are released from the enzyme

• redox
• rxn

• rxns involving
• transfer of groups between molecules

hydrolysis of molecules

• removal of groups to form a double bond or
• addition of groups to a double bond

• rxn
• involving isomeraztions

• joining
• of 2 molecules using ATP energy

resembles both the substrate and the products

• the
• energy required to form a transition- state complex Enzyme speeds up rxn by lowering the Ea

• Increasing the concentrations of the
• substrate at the active site of the enzyme

• By orienting substrates close to each other
• in the right orientation to form the transition-state complex

• Rate increase as the substrate concentration
• increases

• Not further increase if rate after all the
• enzyme molecules are saturated (all active sites filled) with the substrate

• Vmax: the rate
• of product formation when the enzyme is saturated with the substrate and is
• acting as fast as possible

• Km= the
• substrate concentration required by the enzyme to operate at half its max
• velocity

• loss of enzyme’s structure and activation
• when the temp and pH rise too much above optima
• pH and
• temperature
• each enzyme
• has a specific temp and pH optima

• directly competes with binding of substrate
• to an active site

• : binds
• enzyme at allosteric site (site other than the active site)

• Changes the enzyme’s shape so it becomes less
• active

Conservation of energy and materials

• Maintenance of metabolic balance even when
• there are changes in the environment

• Metabolic channeling: can generate marked variation in metabolite concentrations
• different localizations of enzymes and
• metabolites

• compartmentation:
• differential distribution of enzymes and metabolites among separate cell
• structures and organelles

• regulation of amount of synthesis of a
• particular enzyme

• reversible
• control

• allosteric regulation: effector binds and alters
• the shape of the active site and the enzyme is inactive because it cannot bind
• to the enzyme that catalyzed the rxn

• covalent
• modification: regulation of glutamine synthetase requires ATP which creates 12
• adenyl groups covalently bound

• feedback
• inhibition: post-transcriptional regulation and is also called end product
• inhibition

• inhibition of one or more critical enzyme in
• a pathway regulates the entire pathway

• pacemaker
• enzyme:
• catalyzes the slowest or rate-limiting rxn in the pathway

transcriptional regulation

• chemotaxis: regulated
• by enzyme activity

• system involves a number of enzymes and other
• proteins that a regulated by covalent modification

• phosphorelay system which has a sensor kinase
• and a response regulator

• modulation of the activity of the
• phosphorelay system determines the rotational direction of the flagella and
• where the cell will run or tumble

oxygen is the final electron acceptor

• final
• electron acceptor is exogenous

• NO 3-, SO4
• 2-, CO2, Fe3+, SeO4 2-

• Organic
• acceptors may also be used

• is generated
• as the electrons move through the ETC to the final electron acceptor

• used to make
• ATP

• carbon atoms
• can also be used as a electron/energy source

• substrate
• level P

requires ADP

• makes ATP
• and CO2

uses an endogenous electron acceptor

• usually and
• intermediate of a pathway that is used to oxidize organic energy

pyruvate

acetaldehyde

does NOT use ETC or PMF

• only way ATP
• is synthesize in fermentation

• How ATP is
• made in glycolysis (ADP +P = ATP)

3 stage process

• ATP primary
• made by oxidative P

Stage 1

• Polymers
• (large molecules) are degraded to monomers (small molecules)

• Polysaccharides
• to monosaccharides

• Sucrose to
• fructose +glucose

• Proteins to
• amino acids

• Lipids to
• glycerol and FA

Stage 2

• Initial
• oxidation and degradation of pyruvate

Glycolysis

• monosaccharide
• to pyruvate

• pyruvate to
• Acetyl CoA

• glucose to
• pyruvate produces NADH and ATP

• pyruvate to
• acetyl CoA produces NADH

• Amino acids
• to NH2 and other intermediates that can then go through glycolysis

• Glycerol +
• FA convert to acetyl CoA and produce NADH and FADH2

Stage 3

• Oxidation
• and degradation of pyruvate by TCA cycle

• Produces
• ATP, NADH, FADH2, and CO2

• Acetyl CoA
• from pyruvate

• Intermediates
• from amino acids go through the TCA cycle

• NADH and
• FADH2 transferred to CoQ

• NADH AND
• FADH2 are produced from glycolysis, glycerol +FA, and the TCA cycle

• CoQ
• transfers to Cyctochromes

• Cyctochromes
• to oxygen

Produces ATP

• Function as
• both catabolic and anabolic pathways

Examples

• Occurs in
• the cytoplasm (P and E)

• Most common
• pathway for glucose to pyruvate

• Stage 2 of
• aerobic respiration

• Broken into
• 3 carbon and 6 carbon phases

One 6C molecule (glucose to F1,6-BP)

• Only G6-P to
• F6-P is reversible

Two 3C molecules ( rest of cycle) 2x all rxn

• All rxn
• except pyruvate to PEP is reversible

Pathway: ( enzyme and produced or consumed)

• Glucose + P
• +ATP +hexokinase Glucose 6-P
• +ADP

• G6-P is the
• precursor metabolite and starting molecule for the pentose phosphate pathway

• ATP in, ADP
• out

• G6-P + phosphoglucose
• isomerase Fructose 6-P

• G 6-P is an
• aldehyde

• F 6-P is a
• ketone an precursor metabolite

• F6-P + phosphofructokinase + ATP Fructose
• 1,6-biphosphate + ADP

• ATP in ADP
• out

• F1,6-BP + aldose dihydroxyacetone phosphate and glyceraldehye
• 3-P

• Produces two
• 3 carbon molecules

• Only G3-P is
• a precursor

DHP + Triphosphate isomerase G3-P

• Now both 3
• carbon molecules are precursor metabolites

(2x) G3-P + gylceraldehyde 3-P dehydrogenase + NAD+ (2x) 1,3-bisphosphate + NADH

• Phosphorylation
• oxidizes G3-P

• The
• electrons released reduce NAD+ to NADH

(2x) 1,3BP + phosphogylcerate kinase + ADP 3-phosphogylcerate +ATP

• (2x) ADP in
• ATP out

• ATP produced
• by substrate level P

(2x) 3-PG + phosphogylcerate mutase 2-phosphogylcerate

(2x) 2-PG + enolase phosphoenolpyruvate

• loss of
• water

(2x) PEP + pyruvate kinase + ADP pyruvate + ATP

• Pyruvate is
• one the most important precursor metabolite

• (2x) ADP in
• ATP out

• important
• info for pathway

• adding P
• primes the pump

• oxidation
• step (dehydrogenase) generates NADH

• NADH are
• high energy molecules used to synthesize ATP by substrate level P

• Also called
• hexose monophosphate pathway

• Operates at
• the same time as Glycolytic pathway

• Can operate
• both aerobically and anaerobically

Amphibolic

• Produces
• NADPH which is needed for biosynthesis

• G6-P to
• 6-phosphogluconate

• G6-P is
• oxidized that reduces NADP+ to NADPH

• 3 H2O and 3
• NADP + in

3 NADPH and 3 H+ out

6-PG to 3 ribulose 5-P

• 6-PG is
• oxidized and decarboxylated

3 NADP+ in

• 3 CO2, 3
• NADPH, and 3 H+ out

• Sugar
• transformation rxns

• Catakyzed by
• transalsolase and transketolase

• Some further
• degraded and catabolized into pyruvate

• Some
• regenerate more G6-P

• The sugars
• necessary for biosynthesis are produced

• Two 5-carbon
• molecules react ( 10 c total)

• Produce one
• 7-carbon molecule and a 3-c molecule

• A 5- carbon
• molecule and a 4-c molecule (9 carbons total)

• Produce a
• 6-carbon mole and a 3-carbon molecule

• a 7-C and a
• 3-C react (10 C total)

• Produce a 6C
• and 4C

• Glucose goes
• through the rxns of the pentose P pathway and then goes through the rxns of the
• Glycolytic pathway

Yeiled per glucose

1 ATP

1 NADPH

1 NADH

• Also called
• the citric acid or Kreb’s cycle

• Common in
• aerobic bacteria, free living protozoa, most algae and funi

• Major roles
• is the source of carbon skeletons that are used from biosynthesis

• For each
• acetyl-CoA that is oxidized, the TCA cycle procuces:

2 CO2

3 NADH

1 FADH2

1 GTP

• In plasma
• membrane

• Moves H+
• into the periplasmic space

• Different
• electron carries

• May be
• branched

• May be
• shorter

• May have a
• lower P:O ratio: the number of
• molecules of ATP generated per atom of oxygen consumed in the ETC

• Branched
• pathway

Upper branch: stationary phase and low aeration

Lower branch: log phase and high aeration

• How ATP is
• made from the ETC that is driven by the oxidation of a chemical energy source

• Diffusion of
• H+ back across the membrane (down the gradient) drives formation of ATP

• : enzyme that
• uses the H+ down gradient to catalyze ATP synthesis

• is located
• in the Matrix and has a tail attached to the IM in Euk.

from glycolysis

2 NADH

8 ATP total

• 6 ATP from
• OP

• 2 ATP from
• SLP

• Pyruvate
• oxidation

• 6 ATP from
• OP

TCA cycle

5 NADH

2 FADH2

24 ATP total

• 18 ATP from
• OP of NADH

• 4 ATP from
• OP of FADH2

• 2 GTP from
• SLP

Total aerobic yield = 36-38 ATP

• NADH
• produces 3 ATP

• FADH2
• produces 2 ATP

• Pyruvate or
• derivative used as an endogenous electron acceptor

• Substrate
• only partially oxidized

• Oxygen is
• not needed

• Pyruvate
• fermentation produces lactate and recycled molecules

• Uses NADH
• and NAD+ is recycled

• Ethanol:
• alcohol fermentation

• Lactate:
• homolactic fermenters and heterolactic fermentors

• Used for
• food spoilage

• Stickland rxn: the
• oxidation of one amino acid with the use of a second amino acid as an electron
• acceptor

• Carried out
• by some Clostridium

• Alanine to
• pyruvate to acetyl CoA to acetyl P to acetate

• 2 glycine to
• acetate

• Carbohydrates
• = energy source

• Can be
• supplied externally or internally (internal reserves)

Monosaccharides

• Converted to
• other sugars that enter the glycoltic pathway

Disaccharides and polysaccharides:

• Cleaved by
• hydrolases or phosphorylases

• Maltose: 2
• glucose (maltase)

• Sucrose:
• glucose + fructose (sucrase)

• Lactose:
• galactose + glucose

• Cellobiose:
• 2 glucose

Reserved polymers

• Used as
• energy sources in the absence of external nutrients

• Glycogen and
• starch

• Cleaved by
• phosphorylases

• Glucose 1-P
• goes to Glycolytic pathway

PHB

Poly-hydroxybutyrate

• PHB to
• acetyl CoA

• Acetyl CoA
• enters the TCA cycle

• Trigylcerides
• are common energy sources

• Hydrolyzed
• glycerol and FA by lipases

• The glycerol
• is degraded via gly. Pathway

• FA oxidized
• via β oxidation pathway

• FA chain is
• shortened by 2 C atoms

• Produces
• FADH2 and NADH

• hydrolyzes
• protein to amino acids

removal of an amino group from an amino acid

• Results in
• organic acids that are converted to pyruvate, acetyl-CoA, or other TCA cycle
• intermediates

• Occurs
• through transamination: transfer
• amino group

• Alanine + α-ketoglutarate
• which is made into pyruvate and glutamate

• Electrons
• released from an energy source (inorganic molecule)

• Transferred
• to the terminal electron (O2) in the ETC

• ATP
• synthesized by OP

• Calvin cycle
• requires NADH as the electron source for fixing CO2

• Use reverse
• electron flow to generate NADH

• Can switch
• from chemolithotrophic metabolism to chemoorganotrophic metabolism

• Can switch
• from autotropich metabolism (calvic cycle) to heterotrophic metabolism

• Nitrifying bacteria: Oxidizes
• ammonia to nitrate

ATP by OP and SLP

• energy from
• light is trapped and converted to chemical energy

• 2 part
• process

• Light rxn: light
• energy is trapped and converted to chemical energy

• Dark rxn: uses the light energy produces to reduce CO2
• and synthesize cell constituents

• euk. And
• cyanobacteria

• In the light
• rxn

• chlorophylls are major
• absorbing pigment

• accessory pigments:
• transfer energy to the chlorophylls through carotenoids and phycobiliproteins

• absorb
• different wavelengths of light than chlorophylls

• different
• chlorophylls have different absorption peaks

• all other
• bacteria

• H20 not used
• as electron source and o2 is NOT produced

• Only 1
• phosphostem involved

• Uses different
• pigments and mechanism to generate reducing power

• Carried out
• by phototrophic green and purple bacteria, and heliobacteria

• From carbon source and inorganic molecules,
• microbes can synthesize new organelles and cells

A lot of energy require for biosynthesis

• continual degradation and resynthesis of
• cellular constituents by non-growing cells

• Rate of turnover is balanced by the rate of
• biosynthesis

Metabolism carefully regulated

• stores
• genetic info

• Info is
• duplicated by replication and passed on
• to the next generation

• Process
• called gene expression

• Expression
• of DNA determines structure and function of the cell

• DNA divided
• into genes

Transcription: yields RNA

• RNA: ribonucleic acid, copy of
• specific gene

• Translation: use mRNA to
• synthesize polypeptide

• DNA and RNA
• are nucleic acids

• Polymers of
• nucleotides that linked by phosphodiester bonds

n base and sugar

• n base,
• sugar, phosphate group

• Two
• complimentary strands

• Adenine and
• thyamine A:T = 2 H bonds

• Guanine and
• cystine G:C = 3 H bonds

• Purine
• paired with a pyrimindine A:T

combination of DNA and proteins

• 2 strands
• separate and each serve as a template for a synthesis of a complimentary strand

• : each
• daughter cell has one ole and one new strand

• iniation of replication and binds origin of
• replication

• helicase 5
• to 3 breaks the h bonds of the double helix

promotes DNA primase activity

• Involved in
• primosome assembly