Good luck to any pre-nursing students reading this. I just got accepted into CSULB’s Nursing program for the Spring ’14! It will happen.


Tuesday WK 6

Catabolism of other organic food molecules include: Proteins & Lipids.

Anabolic Pathways: Photosynthesis

Photosynthesis – synthesis of food molecules such as glucose, using light energy

Photosynthesis in Plants, Algae & Cyanobacteria:

6CO2 + 12H2O + light → C6H12O6 + 6O2 + 6H2O
Main Stages:
  1. Light Reactions – light energy is converted to chemical energy (ATP, NADPH)
  2. Calvin-Benson Cycle – Carbon incorporated into the organic molecules of plants from CO2 in the atmosphere & used to make food such as glucose. (Carbon Fixation)

Photosystem – Collection of pigments such as chlorophyll A, chlorophyll B and others that absorb light energy. 

1. Relationship  between 2 photosystems involved in light RXNs (Light RXN)

  • Light energy is absorbed & transferred from one pigment to another and finally to the reaction center. (Chlorophyll A)
  • Electrons jump from to primary acceptor and go through electron transport chain, extra electrons are added from (H+) water. 
  • NADP is final electron acceptor becoming NADPH
Note: these light reactions take place in photosystems that are embedded in Thylakoid Membrane.
Cyclic Photophosphorlation – in some cases, electrons circle back from photosystem 1 into the ETC again to generate more ATP
Non Cyclic – Electrons do not circle back through electron transport chain from photosystem 1. 

2. Calvin-Benson Cycle

This cycle occurs in Stroma in Eukarya

This cycle occurs in cytosol for Prokarya

  • ATP that is used to conduct this cycle is from first ETC of the light RXN
  • Main product of this cycle is glucose
  • H+ being used comes from the light dependent RXNs of photosynthesis catabolic pathways. (NADPH in, NADP+ out)
  • RuBP – most abundant molecule on earth (Ribulose triphosphate)

Photosynthesis by Purple Sulfur Bacteria & Green Sulfur Bacteria

  • H2S is electron donor (not H2o)
  • Nonoxygenic (does not produce 02)


Microbial Genetics: Terminology

Nucleic Acid – Molecules that store genetic information and are made of nucleotides

Genome – All of an organisms DNA

Chromosome – DNA + protein (protein generally structural)

Gene – sequence of nucleotides that contains instructions for making a specific product such as a protein

Genotype – genetic makeup or instructions

Phenotype – physical outcome (product) of the genetic intructions (genotype) 

Hologenome – all of an organisms DNA + DNA from symbionts (microbes on our bodies) 


Monday WK 6

Aerobic Cellular Respiration

2nd Stage: Formation of Acetyl Coenzyme A (COA)


  • 2 Pyruvic acid
  • 2 coenzyme A


  • 2 CO2
  • 2 NADH
  • 2 Acetyl COA

3rd Stage: Krebs Cycle


  • 2 Acetyl COA


(Goes through Krebs cycle twice)

  • 3 NADH    x2 = 6 NADH
  • 2 CO2        x2 = 4 CO2
  • 1 ATP         x2 = 2 ATP
  • 1 FADH2   x2 = 2 FADH2

ATP is made by substrate-level phosphorylation during Krebs cycle.

NAD+ (oxidized) can take on H+ and carry them becoming NADH (reduced)

4th Stage: Electron Transport Chain & Chemiosmosis


  • 10 NADH
  • 2 FADH2
  • 6O2


  • 34 ATP
  • 6 H2O
  • 10 NAD+
  • 2 FAD

Chemiosmosis – Chemical osmosis. Flow of electrons back down their gradient through ATP synthase. 

(ETC) – Electron Transport Chain – Series of molecules (embedded in cell membranes) that transport/carry electrons through redox RXNs, releasing energy for making ATP. Final electron acceptor is Oxygen. (O, not O2)

Process: the electron transport chain is embedded in the cytoplasmic membrane of bacterial cells or the inner membrane of mitochandria in eukaryotes. The electrons are passes through molecules in Redox RXNs, being pulled towards the oxygen that has the highest electronegativity, where is will finally be accepted. During this process H+ (which are taken from the FADH2 & NADH) are pushed through the membrane and began to buildup against their gradient, the H+ are filtered out through ATP synthase “portals” through the membrane creating ATP (this process is the Chemiosmosis)  in this RXN:          


3 Types of Electron Carriers in ETC:

  1. Flavoproteins – ex. flavin mononucleotides (FMN)
  2. Cytochromes (contain iron) – ex. Cytochrome C
  3. Ubiquinones – Coenzyme Q (COQ)

Summary table:

Glycolysis:                    4 ATP – 2 ATP used = 2 ATP          2 NADH

COA & KREBS:           2 ATP – 2 ATP used for eukaryotes only = 0 ATP             8 NADH            2 FADH

ETC:                              34 ATP

Net For Prokaryotes = 38 ATP

Net For Eukaryotes = 36 ATP. Note: Eukaryotes glycolysis process (stage 1) takes place in the cytosol, 2 ATP are expended to move the RXN through the membrane.


Alternate Pathways for Glycolysis

Pentose Phosphate Pathway

  • produces pentose sugars (for nucleotide synthesis)

Entner-Dourodoff Pathway

  • Glucose catabolized to pyruvate but w/ different enzymes
  • Occurs in a few prokaryotes (but not eukaryotes)
  • ex. Pseudomonas aeruginosa & Enterococcus faecalis

Carbohydrate Catabolism: Fermentation

  • Uses an organic molecule as final electron acceptor (NAD+ → NADH)
  • Does not require O2
  • Produces 2 ATP per glucose molecule
  • Other Products: Various acids such as lactic acid; gases such as CO2; alcohols

Thursday WK 5 Notes

Carbohydrate Catabolism

2 Major Process:

  1. Cellular Respiration – breakdown (oxidation) of glucose or other molecules to generate ATP (INORGANIC)
  • Anaerobic Respiration – uses inorganic molecule other than oxygen as final electron acceptor.
  • Aerobic Respiration – uses oxygen as the final electron acceptor

2. Fermentation – uses ORGANIC molecule as final electron acceptor.

4 Stages of Aerobic Cellular Respiration

  1. Glycolysis – Glucose is oxidized, producing 2 molecules of pyruvic acid (Does not require Oxygen)
  2. Acetyl COA Production – Pyruvic acid gets further oxidized, producing 2 acetyl coenzyme A (COA) molecules
  3. Krebs Cycle or Citric Acid Cycle – 2 molecules of Acetyl COA get completely oxidized
  4. Electron Transport Chain & Chemiosmosis – Hydrogens (electrons & protons) go through a series of Redox RXNs, releasing energy for making 34 ATP.

Carbohydrate Catabolism: Gycolysis

Glucose is broken down into 2 molecules of pyruvate, producing 2 ATP (net) per glucose molecules.

3 Stages:

  1. Energy Investment Stage
  2. Lysis Stage
  3. Energy-Conserving Stage

ATP is made by substrate-level phosphorylation during glycolysis.

Monday WK 5 Notes

Enzymes, ATP & Bioenergetics

Living organisms require an outside energy source (Photo/chemo) & a means for transferring energy. (Metabolism)

Bioenergetics – energy transfer mechanisms associated with living organisms.

Bioenergetics is tied to metabolism. Metabolism is the sum of all chemical RXNs occuring within living organisms.

Oxidation: Looses electrons

Reduction: Gains electrons (ADP + P → ATP )

2 Types of Metabolism:

  • Catabolism: Breakdown RXNs (breakdown into smaller molecules)→ exergonic (release energy)
  • Anabolism: Building or synthesis (build larger molecules) → endergonic (require energy)


Chemical RXNs in living organisms are catalyzed (sped up) by: Enzymes & Ribozymes (specific in action)

  • Enzymes – Organic catalyst; proteins, usually globular sometimes quaternary (complex). These catalyze or speed up chemical RXNs by millions of times.
  • Ribozymes – (Ribo enzymes) RNA molecules with catalytic ability.

ATP – Adenosine Triphosphate; high energy compound (energy currency) 

Cells can make ATP, but not store it in any quantity (requires energy from light or chemicals)

◊ Oxidative, Substrate Level & Photophosphorylation RXNs

ATP is not the only high energy compound there is also GTP, CTP, UTP etc.

Enzymes can be used over & over again, they are not degraded by the RXNs they catalyze. Enzymes can lower the amount of activation energy required to initiate reactions.

Enzymes can increase interactions between molecules.

Substrate: Molecule that is undergoing reaction catalyzed by enzyme

Enzyme Catergories:

1. Endoenzymes vs. Exoenzymes

Active inside the cell vs. Active outside the cell

2. Simple vs. Conjugated

Protein active alone vs. Protein requires some type of helper to be active

Terms for Conjugated enzymes:

Apoenzyme: protein alone = inactive

Holoenzyme: protein + helper = active


  1. coenzymes – organic cofactor; non-protein (ex. NAD, FAD); less specific than enzymes 
  2. Cofactor – Inorganic, non-protein “helper” molecule 
  3. Prosthetic groups – inorganic, and permanently bound (iron, copper and some other metals) 

Note: NAD & FAD – important electron carrier molecules, which are derived from vitamins. Cells use each of theses molecules in specific metabolic pathways to carry pairs of electrons.

Enzymes with Iron Prosthetic groups: Cytochromes

Cytochromes (cell colors): pigmented and involved in electron transport chains; these move H+ across membranes (cell membranes, cristae [mitochandria], or thylakoids [ribosomes])

3. Constitutive vs. Repressible vs. Inducible

Constitutive – always present because they are essential to cell function. Always being made (not inducible or repressible)


Factors Influencing Enzyme Activity:

  1. Temperature
  2. pH
  3. Concentration – of enzymes or substrate
  4. Light
  5. Inhibitors & Enhancers

Inhibitors: Enzyme inhibition can be categorized as competitive or allosteric

Competitive Inhibitor : binds to active site of enzyme, blocking substrate

Allosteric Inhibitor: bind to alternate (allosteric) location on enzyme, causing a change in shape in enzyme so substrate cannot bind to active site.

Active site – site on enzyme that binds to substrate

NOTE : Enzyme names often end in -ase. 

Ex. Luciferase – enzyme used for bioluminescence.

ATP Synthase – Catalyzes formation of ATP.

AMP – Stimulates energy creation

Phosphofructokinase – used to breakdown glucose & makes ATP.





Thursday Notes

Taxonomy & Phylogeny

Taxonomy – the classification & naming of organisms

Phylogeny – evolutionary history of a group of organisms

5 – Kingdom Classification System

Developed by Robert Whittaker in 1969

  1. Monenra (bacteria) (No longer used)
  2. Protista (algae, protozoa, etc.) (No longer used)
  3. Fungi
  4. Plantae
  5. Animalia

Domain System – Developed by Carl Woes in 1978, based on similarities in rRNA

◊Note – There are no Kingdoms in Bacteria & Archaea (Prokaryotes)

Bacterial Species – population of cells w/ similar characteristics

Strains – sub-species ex. 0157-H7

Domain Archaea


  • Extreme halophiles (Halobacterium): Salt environments
  • Hyperthermophiles (pyrodictium): Hot environments
  • Acidophiles (sulfolobus): Acidic environments

Methanogens (Methanobacterium) → Methane generating archaea CH4

Domain Bacteria

Phylum Proteobacteria Characteristics:

  • Gram-Negative
  • Largest, most diverse group of bacteria
  • Proteo- meaning “many forms”


  • Alphaproteobacteria
  • Betaproteobacteria
  • Gammaproteobacteria
  • Deltaproteobacteria
  • Epsilonproteobacteria

Class: Alphaproteobacteria:

Rickettsia rickettsiiRocky Mountain Spotted Fever:

  • Obligate intracellular parasite
  • Transmitted by vector – tick (Dermacenter)
  • Infects endothelial cells, including those of capillaries & lyces cells which creates the red spots.
  • Symptoms: Fever, headache, chills, nausea & spotted non-itchy rash.

Orientia tsutsugamushi – Scrub typhys

  • Vector is chiggers (mites)
  • endemic to Eastern Asia, Australia, Western Pacific Islands
  • Symptoms – Muscle pain

Class: Betaproteobacteria

Neisseria gonorrhoeae – Gonorrhea”the clap” (term came from french word for brothel – Clapoir)

  • STD
  • Humans are only host/reservoir
  • Virulence Factors – fimbriae & capsules that cause the bacteria to adhere to mucous membranes of host.

Bordetella pertusis – Whooping Cough

  • Virulence factors – bacteria attached to lipids in cytoplasmic membranes of tracheal cells via adhesions such as pertussis toxin & hemagglutinin. This causes increased mucus production while paralyzing the cilia of tracheal cells. 
  • Survives in phagocytes & can travel to other parts of body.

Class: Gammaproteobacteria

Vibrio Cholerae – Cholera

  • Humans become infected by ingesting contaminated food or water
  • Virulence factor – causes secretion of water & electrolytes in host
  • Environment of human body causes toxins in genes to be expressed → toxins cause intestinal cells to secrete water & electrolytes.

Legionella pneumophila – Legionaire’s Disease

  • Got name from outbreak at American legion meeting in Philly in 1970
  • Common in water, including condensation in air conditioning units & water towers. Live inside protozoa in fresh water such as rivers.
  • Exposure route – Inhalation.

Haemophilus influenzae  – Meningitis, pneumoniae

  • Obligate intracellular parasite
  • colonizes mucus membranes
  • Capsules that evade phagocytes
  • Type B causes most problems in humans.

pseudomonas auruginosa –

  • Opportunistic pathogen, common in soil
  • green pigment

Francisella tularensis – tularemia

  • Capsules
  • intracellular parasite
  • reservoirs – rabbits, ticks
  • symptoms include buboes, dry cough

Yersina pestis – Plague

  • buboes (swollen lymph nodes)
  • vector – flea; reservoir – rodents
  • 2 types: Bubonic plague & pneumonic plague
  • 14th century it killed 1/3 of Europeans & mid 500s AD – late 1700s AD killed 40 million people.

Extra Notes

Virulence Factor Definition – characteristics of a pathogenic organism that causes harm to the host

Note – Archaea & Eukarya have histones (proteins associated w/ DNA) Bacteria do not.

Ex Credit:  Lichen – fungus & algae &/or cyanobacteria, crusty material found on branches or rocks.

3 Types of Symbiotic Relationships:

  1. Parasitic – one organism is harmed
  2. Commensalistic – one organism is neutral
  3. Mutualistic – both organisms benefit