Chapter 1
1) Microbiology is the study of microbes (microorganisms and viruses)
2) Chemical Makeup- Proteins(polypeptides with a function, amino acids, structure, catalysis(enzymes)
flagella, FtsZ), Lipids(Diverse, structure, Fats, Wax), Carbohydrates(Polysaccharides, sugar for energy
and structure),Nucleic acids (Genetic info, dNTP, DNA, rNTP, RNA)
Polypeptides- Transport of molecules across cell membrane
Ribonucleotides- produce Polypeptides
3)Phylogenetic tree- 50 years ago we used to divide into Eukarya and Prokaryotes but now Prokaryotes
is no longer an acceptable classification. (Used to be based of clear organelle structures and nucleus),
phylogeny based off 16S ribosomal RNA gene sequencing (Evolutionary Distance)
Three Domains of Life- Bacteria, Archaea, and Eukarya
Bacteria(least related to the others)
No Nucleus
Histone- like proteins
Archaea
Eukarya
Plasma Membrane diff than the Histones
other 2
Nucleus
No nucleus
4)The importance of Microbes: Easy to study, small genome, effect all of life, reproduce quickly
5)Evolution of life on Earth-timeline: Anoxic (no O2). Molten chemical surface (Pre-biotic 4.5-3.8
BYA)Semiorganized chemical structures to true cellular life, Microbial life abundant by 3.5 BYA)
6)Miller- Urey experiment – replicated early earth environment (Need H2O and light to convert
inorganic materials to organic) (Inorganic molecules combined in presence of light and water to form
organic molecules)
Ammonia(NH3), Electricity, Methane (CH4), Hydrogen(H2)
NH2NH3 Nitrogen FIXATION
Organic compounds formed spontaneously in early earth conditions
Early Earth Environment- contained iron which allowed for formation of macromolecules(stuck the
molecules together), hot, wet, primordial soup(formed micelle)
7)Endosymbiotic Theory- (Eukaryotes came from prokaryotes) Eukaryotes came from endosymbiosis of
1.Mitochondria (Turn O2 to energy) and 2.Chloroplasts (Co2 to organic material)
8)DNA vs RNA- RNA was used in the first life, Can be used as an enzyme to catalyze biochemical
reactions as well as store (and translate) genetic information
Ribozymes- Catalyze chemical reactions (RNA and Enzymes)
DNA- used in life now because it is 100xs more stable than RNA, double stranded so it has a backup copy
of genetic information
RNA- self-replicating and catalytic qualities
9)Robert Hook and Van LeeuwenhoekVan Leeuwenhoek- (Van Leeuwenhoek took a look w/ his 300x single lens microscope) Father of
microbiology, viewed bio ultra-structures
Cell Theory- Robert Hook “All living things made of “boxes” (cells)
10) Louis Pasteur – Pasteurization of milk, NOT STERILIZATION (bc it doesn’t kill spores) used “s”-shaped
flask, finally disproved spontaneous generation hypotheses (life form inorganic material), proved
biogenesis theory – “S”uckin’ tiddies
Spontaneous Generation- Hypothesis that life can spontaneously arrive from nonorganic material
Biogenesis Hypothesis- Only Preexisting life can give rise to new cells
Robert Koch (Bacillus anthracis and Mycobacterium tuberculosis)-Physician and microbiologist,
discovered microorganisms were causative agents.
Germ Theory-Specific Organisms give rise to specific diseases
11) Control of infectious Disease- Microorganisms are the leading cause of human death, death
decreased the last 100 years w prevention (personal hygiene, vaccines, pasteurization, antiseptics) and
treatment(antibiotics/antimicrobials)
**Remembering Names
Van Leeuwenhoek took a look in his microscope 300 times, he’s father time and so the story goes.
Robert Hook checked some boxes and discovered cells, for target practice Paul Ehrlich just might ring a
bell and while Pasteur was “s”uckin’ tiddies, he proved biogenesis, Robert Koch would blame disease,
(TB, anthrax) on microorganisms. Now John Needham believed in spontaneity, he contaminated his
broth, that’s so foolish, inorganic life tom foolery
Robert Koch? Robert Crotch-disease/germs
Lazzaro Spallanzani- like spaghetti, he came up w/ biogenesis(closed lid first)
Chapter 1 outline
A) Describe the key features of living organisms
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Cells- Smallest unit of life
6 characteristics of life-Metabolism(energybio molecules), Growth(increase mass), Reproduction(replicate),
Genetic Variation(Evolution), Response/adapt(Effect of environment),
Homeostasis(control internal environment)
Lecture Definition-** “A set of characteristics that resolve and reenforce its existence
in the environment”**
Describe subunit and functions of 4 macromolecules necessary for life? Examples
B) Classify the Three domains of living organisms with examples
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Original 2 categories- Aristotle(plants vs animals) Prokaryote(no nucleus), Eukaryote (nucleus
and organelles-mitochondria) . (Prokaryote is no longer a valid in Phylogenetics, it’s not
monophyletic
Carl Woese -New view of phylogenetic tree. Focus on RNA sequencing (rather than protein bc
rRNA is universally present in all cells), small subunit (SSU rRNA), “molecular chronometer”shows evolutionary time
(Bacteria-16s rRNA,Eukarya-18s rRNA)
Phylogenetic Tree-Shows “relative divergence”, natural taxonomic system. Linear distance =Diff
in 16s rRNA sequence
Viruses- Not considered to be living , they use the host’s machinery to replicate, acellular
C) State the Importance of Microorganisms in research


Advantages-Small genetic code, easy to manipulate, reproduce quickly
Bacteria- Most studied Microorganisms
D) Discuss the relationship b/w microbial genetics and evolution of life on earth

E) ???
Chapter 2 Bacteria
12)
Morphology of bacterial cell-(5) types
Coccus(Spherical)
Bacillus(Rod)
Vibrio(Curved Rod)
Spirillum - Spiral
Pleiomorphic(Varied Shape, typically tinier than average sized bacteria)
Organization “multicellular”
Hyphae- branching filaments
Mycelium- tufts of hyphae
Trichomes-smooth unbranched chains (Cyanobacteria-adhere through cell wall, photosynthesis and
myxobacteria-in soil, large genomes, feed on insoluble organic substances)
13)Cytoplasm – gel like appearance(80% water), macromolecules float here (RNA , proteins), outside
nucleus , inside plasma membrane
Protein Filaments Present?= rod or spherical shape
Plasmid (Not found in all DNA)– Replicate independently, small circular double stranded DNA molecule
(NOT CHROMOSOMAL), genes offer advantages like antibiotic resistance
Ribosomes- Make proteins, made of RNA and proteins
Nucleoid region- replication machinery, genetic material (DNA)
Inclusion bodies(Elementary bodies) cytoplasmic aggregates of stable substances (i.e.. Proteins),sites of
viral multiplication, consists of viral capsid proteins
Gas Vesicles (Gas Vacuoles)- Buoyancy control, hollow, made of proteins, regulate position in response
to stimuli (typically restricted to planktonic organisms)
Chromosomes- Usually singular circular DNA, can be linear or have multiple
Bacterial Organelles:
Carboxysomes- polyhedral protein shells, filled w/ Rubisco (rate limiting enzyme in carbon fixation), at
carbon fixation rxn sites
Magnetosomes- store magnetic material, gram negative, lipid membrane and crystalline magnetic
material, direct bacteria to low-oxygen environments
Extra:
Carboxysomes-polyhedral like a hexagon, whore rub one out rubisco
Gas vesicles- buoyancy control, plankton like in the ocean, hollow bc no heart, yummy made of protein
Mr. Mageneto- too cool for oxygen but has a negative attitude
Plasmid- like blood plasma, has DNA and resistance to things
Nucleoid- replication DNA
14)Cytoskeleton – organization of the cell
MreB (actin homologue) – Found in non-spherical bacteria, form actin-like helical bands next to plasma
membrane
TfsZ(tubulin homologue) - facilitates cell division, filamentous and temp sensitive, form ring at septum
of cell division
ParMRC system( Facilitate segregation of plasmids)-ParM (Directs plasmid movement), ParR (DNAbinding adaptor protein, binds to ParC), ParC DNA site
Extra:
MreB- Men be actin, membrane, Men have a harder time getting around
TzfZ- tube, temp, facilitate division
ParMRC – Part plasmids, M-movement, R-DNA+C, C-DNA site
15)Fluid Mosaic PM-(separates inside form outside) Integral proteins span hydrophobic and hydrophilic
regions of membrane, Hopanoids-Influence membrane permeability(analog of cholesterol)Stability
across temp ranges
Can capture energy, hold sensory systems, and participate in protein synthesis and secretion
16)Bacterial Cell Wall-( in 90% of bacteria), provide structure and protection, made of cross-linked
peptidoglycan strands (NAG-b-1,4-glycosidic bond-NAM-Pentapeptide)
NAM-Peptidoglycan crosslinks can form b/w these but contain unusual D-Amino acids, (differ b/w
species)
Formation of cell wall(2 stages)- Bactoprenol lipid transports peptidoglycan subunits across PM
1.Cytoplasm stage-(made form glutamine and fructose-6-p )Bactoprenol-NAM + NAG
2.Periplasm stage- Bactoprenol flips NAG+ NAM into periplasm, adding it to the glycan chain,
Transglycolase binds NAG-NAM (transglycosylation)
Extra: Cholesterol I hop,influencer
Flipped by bactoprenol
17)Gram positive vs Gram negative- based on cell structure, effects staining, **diff in antibacterial
susceptibility**
Staining Process(4 steps)
1. Crystal Violet (purple)
2. Iodine
3,Organic Solvent wash
4. Safranin stain (pink)
Gram (+)-Purple, Large pores (nutrient enters),Thick layers of bacterial glycan, (90%), narrow
periplasmic space (Teichoic acids-are glycopolymers)
Teichoic Acid (negative charge(Mg and Na), give rigidity to cell wall)
Lipoteichoic Acid-(anchored to membrane w/ glycolipid)
Wall teichoic Acid- (covalently attatched to peptidoglycan)
Gram (-)- Pink, Thin cell walls (10% peptidoglycan), surrounded by second lipid membrane w/
lipopolysaccharides and lipoproteins, Wide periplasmic space,(nutrient enters) Porin and TonB proteins
transfer nutrients into periplasmic spaceActive transport into cytoplasm
LPS-Lipopolysaccharide in outer layer (3 parts)
LipidA(endotoxin, inflammatory response, hydrophobic, anchors to outer membrane), coPolysaccharide, O side chain (Varies greatly, changed by microbes to avoid host immune
response)
Extra:
Periplasmic space- area b/w plasma membrane and cell wall
Positive ass- Gram positive has teichoic acid, positive, purple,pores,tight (periplasmic space),ass asid
Gram- are por like Toby, need to transfer nutrients to periplsmic__>active in cytoplasm
18)Bacterial Cell surface (S-layer) – Part of cell envelope, diverse function (protect from
bacteriophages),monomolecular layer (identical glycoproteins),
Flagella(types + structure)- Hair like appendages, characterized by function(NOT BY STRUCTURE),
motility and sensory function (Parts: Filament, hook, basal body)
External Flagella- Polar (ends of cells), Monotrichous (only one).Amphitrichous (both
sides),Lophtrichous(1+),Petrichous(multiple)
Internal Flagella- Axial (in periplasmic space, cork-screw rotation of cell body)
Energy to move – Generated by e transport chain (proton pump)
Adherence(sex pilus and fimbriae) – Hair like appendages on surface, thinner, shorter than flagella,
pathogenesis, binding to target cells
Sex pili – Conjugation, transfer DNA from one plasmid to another
Fimbriae – (1st step of bacterial pathogenesis) attach to other cells
Capsules (k antigen)- layers of polysaccharides surrounding some bacteria, defend against host
immunity and drying out, facilitate bacterial biofilms (protect from harsh environment)
Extra:
Sex pili- sex DNA, transfer from one to another , conjugation
Fimbriae – like fibroids, attach and pathogenic
Cork-screw like turning an axis
19)Bacterial Taxonomy (classification + nomenclature)- Binomial System (ex. Staph-aureus- follows
genus, species)
Genus- Closely related species
Species- group of strains w/ common features (diff from other strains)
Chapter 2 Outline
Primary active transport=NaK (3,2) pump 1 atp hydrolyzed
Antiporter NaCa(3,1) entropic energy(opp directions)
Syn(NaGlucose) intestines same direction
Secondary active – na agco transport against e gradient
Primary K, antiport A,syn salt and sugar, secondary just salt
Chapter 4
20) Introduction to Archear:
One of the 3 domains of life which can survive in environments with extreme chemical/ or physical
proterties
Group of single cell prokaryotic organisms
1/5 of microbes in the ocean
Extremophiles- first discovered archaea
21) Evolution of Archea:
Phylogenetic tree based on 16s rRNA seq: (LUCA)bacteriaArchaea (histones for temp stability) and
Eukarya
Histones: Notable growth requirement for selected archea
22) Morphology of archaeal cells:
Structure: Cell wall, PM bilayer, fatty acids-ester- glycerol-3P, isoprenoids (phytanyl) attatched to
glycerol-1P
Same size as bacteria (Ignicoccus and Nanoarchaeium grow together), round or rod, thin, flat, square
Sulfolobus-irregular
Thermoproteum- rectangular
23)Archaeal cytoplasm:
Cytoplasm- nucleoid, singular circular chromosome, DNA and RNA polymerase, gas vesicles, plasmids
Histones- suggest they evolved early in history (increase genomic size of DNA in Eukaryotic cells)
24)Cytoskeleton:
Ta0583- Actin homolog (Thermoplasma species-similar to Eukaryal actin)
Cytoskeleton proteins-(M. Thermoplasma acidophilum and M. Kandleri- similar to bacteria)
25)Archaeal Plasma membrane:
Ignicoccus- Have outer membrane (+ transport out,+ flow in you get ATP) and large periplasm (similar to
gram negative bacterial cells)
ATP synthase- embedded in the outer membrane (In bacteria they’re found on the PM)
26)Cell wall: Provides strength and osmotic protection
Thermoplasma acidophilum – no cell wall, non-spherical
Bacterial glycan (in archaea) -structure of pseudomurein(NAG Beta 1-3 linkage NAT- L stereoisomers)
(In actual Bacterial glycan- NAG Beta 1-4 linkage NAM- D-amino acid)
Lysozyme and Penicillin- ineffective in archaea (due to pseudopeptidoglycan 1-3 cell walls)
27)Cell surface:
Cannulae- hollow glycoprotein tubes connecting individual cells
Archaeal flagella – Provides movement (Archaeal compared to bacteria are… thinner ,many more diff
compositions, rotate together as a group, powered by ATP, growth subunits added to base)
Archaeonics- Antibiotic like chemicals
PCR (Thermus aquaticus )- Taq DNA polymerase enzyme
Pfu (Pyrococcs furiosus) - to clone DNA, more thermal stability than Taq, 3’ to 5’ exonuclease proof
reading (can remove messed up DNA) will have fewer errors than Taq
Infections- species of methanogens may be involved in mouth infections
28) Major Phyla of archaeons:
Euryarchaeota (methanogens-Strict anaerobes and halophiles salt,sulfate >1.5Mol)
Methanogen- Methanobrevibacter smithi in human gut(M. smithii), recycle H2 (turn to CO2 and
Methane)
Halophiles- great salt lake (5-25% sat), Dead Sea (34%)
Halobacterium salinarum – high intracellular concentration of K+
Isotonic- no net change
Hypotonic (low salt) -Net gain
Hypertonic(High salt)- Net loss
Crenarchaeota(thermophiles >55⁰C, acidophiles low pH, barophiles)- most abundant archaea in marine
environment (sulfolobus solfataricus 80⁰C, pH3) Tetra ether lipids or lipid monolayer, more alpha, salt,
arg/tyr, less cyst/ser, strong chaperones(extra stability at high temp) Reverse DNA gyrase enzyme(
increase super coiling of DNA, harder to denature) also includes mesophiles and psychrophiles- cycle
carbon and nitrogen in oceans (low temps <15⁰C)
Chaperones- proteins that help fold + refold denatured proteins (closely resemble eukaryal chaperones)
Know the adaptations
29) Other phyla of archaea: Based on 16s Ribosomal RNA sequencing
Thaumarchaeota (mesophiles and psychrophiles)
Korarchaeota- Unusual thermophilic species, closely related to Crenarchaeota
Nanoarchaeota – symbiotic, Nanoarchaeum equitans, only 1 member
Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN)- Microarchaeota and Parvarchaeota
(one of the smallest known organisms)
30)Extremophiles and Biotechnology: Pfu DNA polymerase
Stopped on slide 33-36
Chapter 14
31) Microbes in the environment:
ecosystems,
Niche- specific functional role of organism w/ their surroundings
Biofilms- Usually on surfaces, held together by exopolysaccharides (bacteria, fungi, protists),protects
bacteria, ↑antibacterial resistance
E. coli – secrete Colanic acid
Pseudomonas aeruginosa - secrete alginate
Steps:
1. Primary layer – binding + forming layer (Appendaged bacteria Colanic acid-produced by
ecolik12 for biofilm formation)
2. Microcolonies secrete exopolysaccharides (EPS) (provide protection, water channels for
nutrients/waste)- through cell signaling/ population density the cells know when to do this
32) Cell number and biomass in diff environments on earth:
Subsurface
Surface
Diversity
unknown
Soil (most), Aquatic(least)
Cells x10^28
Terrestrial (most)
Aquatic(least)
Bacteria + Archean= 10^30 cells on earth
Carbon associated w/ microorganisms = Amount associated with plants
33) Cultivation -Dependent technique: Organisms that can be cultured
Enrichment cultures: Nitrogen fixing bacteria (Azotobacter)
Aerobic, free living soil microbes
Atmospheric N NH3 (Ammonia) into soil
Use medium w/o Nitrogen (it will fix atmospheric nitrogen)
34)Cultivation-Independent techniques: Organisms that can’t be cultured
Direct seq of Ribosomal RNA genes: DNA from environment, SSU genes amplified by PCR, compare to
known species
Metagenomics(eco, community, environmental)-Study of genetic material recovered directly from
environmental samples
1. DNA extracted
2. Isolated + digested w/ restriction enzymes (DNA fragmented)
3. Transform plasmids into bacterial cells
4. study unknowns w/ sequencing or functional analysis
other technique names:
- Denaturing gradient gel electrophoresis (DGGE) - Terminal restriction fragment length polymorphism
(TRFLP) - Fluorescent in situ hybridization (FISH) - Flow cytometry
35)Aquatic ecosystems:
Marine ecosystems (3 ocean zones) – Cover 2/3 of earth, 98% biomass = bacteria, archaea, eukaryal
microbes, 3.5% salt(Na and Cl ions)
1. Surface Zone(0-200m)- Light penetrates, phytoplankton(Photosynthetic primary producers,
oxygenate water, like cyanobacteria) heterotrophs
2. Dark Mid Water Zone(200-4000m)- 2-3 ⁰C, Phytoplankton lysis releases nutrients for
heterotrophic microbes
3. Deep Sea Zone(3500m-11000m) – High pressure (1k x sea lvl), Barophiles (some obligate,↑
unsaturated fatty acids for PM fluidity) and piezophiles
4. Sea floor- Very cold, No O2, less biodegradation, sediment forms (oil + gas), increased
archaeon proportions (more than bacteria in oceans)
Dead zones(~400, Baltic Sea)- active microbial communities, no eukaryotes( not enough O2)
Creation- ↑Nutrients=↑Microbes=↓O2 Dead zone
*Direct connection to agriculture*
Zones- Characterized by light, depth, temp, and pressure
Heterotroph- all animals + most bacteria, can’t make their own food
Oligotroph- live in low nutrient, low ion environment, slow growth, low metabolism rates
Phytoplankton- production drifts down, feeds lower lvl zooplankton, photosynthetic (produce ½ of all
photosynthetic activity on earth)
Natural ocean – Low N and P = Low phytoplankton activity
Synthetic Fertilizer added- High N and P = High phytoplankton activity (produce more energy
and organic Carbon)Increased microbesHypoxia(O2 consumed)
Viruses – 10^30 present( 10x > microbes) supply nutrients (lyse cyanobacteria in top zone PM,DNA
and protein fragment released as nutrient)
36)Cultivation of oligotrophic microbes from sea water:
Difficulties in Lab: heterogeneity of seawater can’t be replicated, too high in nutrition
Metabolic properties- Use metagenomics
Physiological properties – Use pure culture
Oligotroph- prefer low nutrient environment, small quantities in sea water (won’t naturally form large
colonies)
Dilution to extinction method: How to culture obligate oligotrophs
1.Collect Sea water (count microbes)
2. Dilute (A few cells per aliquot) Place into autoclaved water
3. Incubate ( All samples w/ growth mixed into large bottle)
4. Centrifuge and analyze
37)
Terrestrial ecosystems:(Soil layers)
Biomes- Ecosystems with diff vegetation characteristics (abiotic factors- Temp + Precipitation)
Soil- From microbial decomposition of organic matter + abiotic minerals
Zones based on depth:
O Horizon- Organic matter present on surface of soil
A Horizon(Topsoil) – Has the most organic material, Most microbes present
B Horizon(Subsoil) -some organic material
C Horizon- Deepest, mostly inorganic
Rhizosphere- Soil immediately surrounding plant roots, Organic Carbon from plant exudate
Symbiosis- More plants (Carbon)= More Microbes (Fix N,P, control plant pathogens)
Plant (Primary producers) Exudate- Sugars, sugar alcohols, organic acids (support microbial growth)
38) Bioremediation- clean up contaminants with microbes
Xenobiotics- derived from petroleum, polycyclic aromatic hydrocarbons(PH) and polychlorinated
biphenyls (PCB)
Biodegradation- slow, limited by O2
Biostimulation- ↑O2↓N↓P =↑ Microbial activity
Bioaugmentation- Add bacteria to an environment to degrade contaminants
Oligo? More like oligno nutrients
Chapter 10 Outline
(Cyanobacteria-adhere through cell wall, photosynthesis and myxobacteria-in soil, large genomes, feed
on insoluble organic substances)
Assignment Qs -Need 150 words for each , Due 8pm
Medford one large and 2 medium pizzas- order in 10 minutes
9-10:10 (10-1:300) 3.5 hrs
1:40-2pm (academic advising)
2-7 (finish miro-assignment) 5hrs
3. In thinking about the origin of life, many envision a fundamental “chicken and egg” type problem. Since
DNA and proteins play vital roles in the storage of information and in catalysis in the modern world, we
would seem to have a problem. DNA needs protein to be replicated and maintained, while proteins
cannot be synthesized without the information encoded in DNA. Which came first, the protein or the
DNA? Hint: The answer may be “neither.” What may have come first, and how would this make sense?
While animal cells now may use DNA and protein, organisms before that may not have used DNA.
Before the use of DNA and proteins it is theorized that early life utilized RNA for the storage of
information. Since RNA is self-replicating, it can store and translate genetic information, and can be used
to catalyze biochemical reactions, this would have made it a very useful tool for early organisms.
According to Carl Woese RNA world theory those traits would have made RNA the first genetic
molecule. He postulated that the use of DNA probably came along later on in evolution, being favored
over RNA because of its increased stability. Since DNA is double stranded it has a built in back up copy
for genetic information, making it less likely for mistakes to occur in its replication, it is also significantly
more stable than RNA. The presence of histones, allowed DNA to be tightly packed, while also providing
some protection in environments where temperature is high, which would also be an advantage to have
in modern cells.
Work on 5 and 9
-neither, RNA as used as a form of storage for genetic information prior to DNA being used. DNA was
later used bc it was more fvorable for its stability
4. Describe the polypeptide secretion pathway in bacteria. Be sure to include: all Sec proteins, SecYEG,
etc.
The secretion pathway in bacteria is the movement of proteins from the cytoplasm, through the
plasma membrane into the extracellular space. To facilitate the movement of the proper proteins a
polypeptide secretion pathway is used. The pathway begins with SecB protein binding to newly
established polypeptide, this prevents the polypeptide from folding while it is still in the cytoplasm. The
prtoein is able to recognize that this is the correct polypeptide to bind to because there are hydrophobic
amino acids present on the N-terminus of the polypeptide.The polypeptide is then passed on to SecA
protein, which will associate itself with SecYEG. SecA protien is able to push the polypeptide through the
SecYEG channel and out of the plasma membrane, using energy form the hydrolysis of ATP. After the
polpypeptide is outside of the cell the signal peptide is removed and the protein is able to fold and can
now perform its function.
5. Explain the role of the cell membrane in the process of cellular respiration. How are cells able to exploit
the differences in chemical gradients between the intracellular and extracellular space to capture energy?
The plasma membrane of the cell is where a protein gradient is generated, capturing energy for cellular
use. During cellular respiration oxidation occurs and the energy generated by this is then used to form
ATP. To move nutrients across the plasma membrane cells can utilize facilitated diffusion, or they can
use active transport, where either ATP can be utilized, or an electric chemical gradient can be used.
Active transport requires the use of energy, ATP to drive particles from low to high concentrations, going
against their concentration gradient, moving protons from the cytoplasm to outside the extracellular
space. This then creates a force promoting protons to flow down their electric chemical gradient and
across the plasma membrane, due to the uneven distribution of protons, this leads to the creation of
energy which the cell then use.
Completed Questions
2. Describe the “RNA world” theory of evolution. What is a progenote? Explain how primitive cells were
able to form in the primordial soup present in the sterile earth. What structures are necessary for cellular
life?
The “RNA world” theory began with Carl Woese, he proposed that in life, RNA was the initial form
of storage for genetic information. Since RNA can be used as a way to store genetic information, translate
it and can also catalyze biochemical reactions, these features may have been useful in early life.
According to Woese ,the first living organism was a progenote, it would have been able to reproduce and
likely had progeny with genetic variations which would allow it to evolve over time, before prokaryotes
had evolved. The Miller-Urey experiment was performed in an attempt to understand how early life may
have formed in sterile earth which is thought to have contained ammonia, methane and hydrogen. This
experiment supported the idea that water and light were necessary for inorganic molecules to combine
and form organic molecules. The presence of iron in the early earth environment may have also aided in
the formation of macromolecules by allowing molecules to stick together. According to endosymbiotic
theory mitochondria, which were able to convert oxygen to energy, and chloroplasts which could turn
carbon dioxide into organic molecule, may have been endocytosed into early Eukaryotic cells in order to
support life.
6. Explain osmotic balance in cells. What happens to a cell that is placed in a hypotonic solution,
hypertonic solution, or isotonic solution? What is special about the maintenance of osmotic balance in
halophiles that would allow them to survive in high salt concentrations? What is the natural habitat of
archaea species halobacterium salinarum?
Osmosis occurs when water flows into or out of a cell, across the plasma membrane. Water flows
from high solvent levels to low solvent levels across the plasma membrane, in order to avoid major efflux
or influx of water cells must maintain an osmotic balance. If a cell is exposed to a hypotonic solution, a
solution where the ion concentration is lower than the concentration within the cell, the cell will become
enlarged due to an influx of water into it. If the cell is exposed to a hypertonic solution, it will shrink due to
a loss of water, since the outside environment is higher in ion concentration compared to inside the cell. If
the cell is placed in an isotonic solution the net zero exchange of water in/out of the cell, meaning water
flows in at the same rate it exits. Halophiles manage their osmotic balance by keeping potassium levels
inside of the cell high, in order to balance out the high salt concentration of the surrounding environment.
Through this method halophiles can prevent major water loss. One such halophile is Halobacterium
salinarum, which exists in salted foods as well as in the deep sea.
7. What are different examples of Crenarchaeota? Where are they often found? How do they maintain
stability? How do molecular chaperones contribute to stability?
Crenarchaeota typically exist in high temperature environments as thermophiles or
hyperthermophiles, they can also be acidophiles or barophiles. Some of the locations they occupy are
thermal springs, geysers, areas of high sulfur concentration, and locations with low pH levels. Some
Crenarchaeota may possess tetraether lipids lipid monolayers in their plasma membranes which helps
with stability. Damage to the plasma membrane can be detrimental to cells since they are sources of
protection and transport of materials, so it is important that Crenarchaeota maintain their stability. Protein
denaturation is also an event that could have devastating effects since they are needed to carry out vital
processes within organisms. It is believed that Crenarchaeota having increased α-helical regions, arginine
and tyrosine help to strengthen interactions amount amino acids making it harder for their proteins to be
denatured. They also contain molecular chaperones which help to make sure proteins are folded into their
proper structures, further maintaining the stability of the organism. Two examples of Crenarchaeota are
Sulfolobus solfataricus and Pyrolobus fumarii.
8. What are piezophiles (also known as barophiles), and in which ocean zone are they located? What
does it mean to be an obligate piezophile? What is one challenge of living in a high pressure
environment, and how have piezophiles adapted to overcome this challenge?
Piezophiles are microorganisms that exist in extremely high atmospheric pressures, they are
typically located in the deep sea where the pressure Is much greater. Obligate piezophiles are
microorganisms that require these high levels of pressure in order to survive, without the pressure they
would not be able to exist at all. One challenge within these environments is that the pressure may
make the plasma membrane less fluid. Since the plasma membrane is important for the flow of
materials in and out of the cell this can challenge the microorganism ability to survive. The plasma
membrane not only separates the inside of the cell from the outside world, but it also be used to detect
changes in the environment as well as capturing energy, which are important functions in many cells. In
order to overcome this loss of fluidity, some piezophiles have high levels of polyunsaturated fatty acids
in their plasma membranes.
9. Describe the different sources primary producers can utilize to acquire energy. Include 2 different
examples in your response.
Primary producers can be organisms that use photosynthesis to capture energy, or they can be
non-photosynthetic organisms existing in environments where photons are unavailable. They can exist
in many different environments which differ greatly in what materials are available as an energy source.
We can categorize primary producers into different groups called guilds. Within guilds organisms in an
ecosystem, which may or may not be genetically related, carry out similar activities. In terrestrial
ecosystems plants make up the majority of primary producers, utilizing photons for photosynthesis. In
deep sea hydrothermal vents, where photosynthesis is not possible due to a lack of photons, bacteria
are the primary producers. One such bacteria is called Thiobacillus sp., a sulfur oxidizer which performs
chemosynthesis, using H2S as an electron source for carbon fixation.
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Application Questions