Biology

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Gibbs Free Energy Equation:

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∆G = ∆H - T∆S

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Enthalpy Equation:

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∆H = ∆E - P∆V

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Oxidation:

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Increase number of bonds to oxygen
Remove Hydrogen
Remove Electrons

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Reduction:

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Decrease number of bonds to oxygen
Add Hydrogen
Add Electrons

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Glycolysis:

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9 Step Process (occurs in the cytoplasm):

1 Glucose + (4 ADP + 4 P[i]) + 2 NAD+ ----->
2 Pyruvate + 4 ATP + (2 NADH + 2 H+) + 2 H2O

NET ENERGY PRODUCTION: 1 Glucose ---> 2 ATP + 2 NADH

**1st Step catalyzed by Hexokinase
****3rd Step catalyzed by Phosphofructokinase (PFK) -- This is the Committed Step, and PFK is inhibited by ATP
******5th Step converts Aldehyde to COOH (ate), and in doing so generates the only NADH produced in the reaction

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Pyruvate Dehydrogenase Complex (PDC):

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Occurs between Glycolysis and the Kreb's Cycle (in the mitochondrial matrix) to convert Pyruvate (3C) into Acetyl-CoA (2C) via decarboxylation, and thus reduce NAD+ to NADH + H+

Pyruvate + Coenzyme A + NAD+ -----> Acetyl-CoA + CO2 + (NADH + H+)

NET ENERGY PRODUCTION: 1 Glucose (2 Pyruvate) ---> 2 NADH

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Kreb's Cycle (Citric Acid Cycle, or Tricarboxylic Acid Cycle [TCA cycle]):

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Acetyl-CoA (2C) + Oxaloacetate (4C) ---> Citrate (6C)
---> (5C) + CO2 + NADH ---> (4C) + CO2 + NADH ---> Oxaloacetate + GTP + NADH + FADH2

NET ENERGY PRODUCTION: 1 Glucose (2 Pyruvate) ---> 2 GTP + 6 NADH + 2 FADH2

**(2 ATP + 2 NADH)/glucose in Glycolysis;
(2 GTP + 8 NADH + 2 FADH2)/glucose in PDC &TCA cycle

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Electron Transport Chain (ETC):

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Takes place across the inner mitochondrial membrane.

1) NADH Dehydrogenase (Coenzyme Q Reductase) oxidizes NADH ---> NAD+
2) NADH Dehydrogenase passes the 2 e- (harvested from the oxidation of NADH) to Ubiquinone (Coenzyme Q), which allows 4 protons to be pumped into the intermembrane space from the matrix.
3) Ubiquinone (Coenzyme Q) then passes the 2 e- to Cytochrome C Reductase. (NOTE: This is where FADH2 enters the ETC and is oxidized to FAD)
4) Cytochrome C Reductase then passes the 2 e- to Cytochrome C (reducing it, duh), and allowing 4 additional protons to be pumped into the intermembrane space.
5) Cytochrome C Oxidase then passes the 2 original e- as well as the 2 additional e- from step 4 to oxygen, thus pumping 2 protons into the intermembrane space and producing 2 molecules of water.

**A total of 10 protons are pumped into the intermembrane space from the matrix for every one molecule of NADH oxidized.
****A total of 6 protons are pumped into the intermembrane space for every molecule of FADH2 oxidized (which enters the cycle AFTER complex 1/NADH dehydrogenase).

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Oxidative Phosphorylation:

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Oxidative Phosphorylation is the coupled process of the electron transport chain as well as resulting ATP production.

The Electron Transport Chain is coupled to the function of the ATP Synthase, which utilizes the proton gradient generated by the ETC to convert ADP + P(i) ---> ATP; (one molecule of ATP is generated for every 4 protons allowed to flow down it's gradient into the matrix).

**1 NADH ---> 2.5 ATP
1 FADH2 ---> 1.5 ATP
1 GTP ---> 1 ATP

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Net Energy Production of Cellular Respiratory Processes:

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Glycolysis:
-2 ATP ---> 4 ATP + 2 NADH
=
-2 ATP + 4 ATP + 3 ATP (eukaryotes*) OR + 5 ATP (prokaryotes)
-----------------------------------------------------------------------------
Pyruvate Dehydrogenase Complex (PDC):
+2 NADH
=
5 ATP
-----------------------------------------------------------------------------
Krebs Cycle:
+ 2 GTP + 6 NADH + 2 FADH2
=
2 ATP + 15 ATP + 3 ATP

TOTAL:
30 ATP (eukaryotes)
32 ATP (prokaryotes)

*The 2 NADH molecules produced during glycolysis require transport into the mitochondrial matrix for eukaryotic electron transport. Upon delivery, they're delivered directly to Ubiquinone (Coenzyme Q), and thus only yield 1.5 ATP per molecule, as opposed to the normal 2.5 ATP.

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Glycogenolysis:

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Refers to the breakdown of the glucose polymer Glycogen, found in muscle and liver cells, and used as the main form of carbohydrate storage in animals.

Occurs in response to the hormone Glucagon, when blood sugar levels are low, and results in the release of glucose into the blood.

*Glycogenesis is the synthesis of glycogen, and is an opposing process

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Gluconeogenesis:

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Refers to the conversion of non-carbohydrate precursor molecules (e.g. lactate, pyruvate, Krebs cycle intermediates, and the carbon skeletons of most amino acids) into Oxaloacetate, and subsequently Glucose.

Occurs when dietary sources of glucose are unavailable and the liver has depleted stores of glucose. Primarily takes place in the liver.

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Aromatic Bases:

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Pyrimidine Bases:
Cytosine
Uracil (RNA only)
Thymine (DNA only)

Purine Bases:
Adenine
Guanine

**Mnemonic: Pyramids have sharp edges that CUT.

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Structure of DNA in the Nucleus:

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Deoxyribose ---(+ aromatic base)--> Nucleoside ---(+ 3 phosphates)--> Nucleotide ---(Polymerize w/ loss of 2 phosphates)--> Oligonucleotide ---(Continue polymerization)--> ss Polynucleotide ---(2 complete chains form H-bonds [anti-parallel orientation])--> ds DNA chain ---(coiling)--> ds DNA Helix ---(wrapping around histones)--> Nucleosomes ---(complete packaging)--> Chromatin

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Prokaryotic DNA Replication:

FIX ME WITH CLASS NOTES

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Single origin of DNA replication; Proceeds via Theta replication

DNA Pol I: Same as DNA Pol III, but slower. Also has 5' to 3' exonuclease activity in order to remove RNA primers.
DNA Pol II: Unknown
DNA Pol III: 5' to 3' polymerase activity and 3' to 5' exonuclease activity (Fastest of the polymerases).

Helicase unwinds the double helix and separates the strands

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Eukaryotic DNA Replication:

FIX ME WITH CLASS NOTES

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--

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Prokaryotic Transcription:

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Eukaryotic Transcription:

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Prokaryotic Translation:

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Eukaryotic Translation:

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Lytic Cycle of Phages:

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1) Attachment (or Adsorption) to the exterior of a bacterial cell
2) Injection of the viral genome into the host cell (penetration/eclipse)
3) Early gene production, namely Hydrolase (which degrades the host genome)
4) Multiple copies of the phage genome are assembled using the dNTP's from the degraded host genome
5) Automatic capsid assembly around the new copies of the phage genome
6) Late gene production, namely Lysozyme (which destroys the bacterial cell wall and causes the host bacterium to burst under osmotic pressure).
7) Subsequent release of progeny phages

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Lysogenic Cycle of Phages:

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1) Attachment (or Adsorption) to the exterior of a bacterial cell
2) Injection of the viral genome into the host cell (penetration/eclipse)
3) Conversion of the phage genome into a prophage via incorporation into the bacterial genome (host is now referred to as a Lysogen)
4) Normal bacterial replication occurs (thus also replicating the prophage genome with it)
5) Eventually, the prophage activates and removes itself from the host genome (a process called excision), and then enters the lytic cycle.

**The Lysogenic cycle (unlike the lytic) allows the opportunity for Transduction, or the incorporation of some of the host's DNA into the viral genome during excision.

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Productive Cycle of Animal Viruses:

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1) Binding of virus to surface receptors on the animal cell
2) Endocytosis of virus by the animal cell
3) Viral genome replication and capsid assembly
4) Enveloped viruses exit membrane via budding (note: this means that the host cell does not necessarily lyse during this process)

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Lysogenic Cycle of Animal Viruses:

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1) Binding of virus to surface receptors on the animal cell
2) Endocytosis of virus by the animal cell
3) Conversion of the viral genome into a provirus via incorporation into the animal host genome
4) Normal cell replication occurs (thus also replicating the provirus genome with it)
5) Eventually, the provirus activates and removes itself from the host genome (excision), and then enters the lytic cycle.

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Viral Genomes:

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+ ss RNA: must encode RNA-dependant RNA pol (does NOT need to carry it)

- ss RNA: must BOTH carry and encode RNA-dependant RNA pol

Retroviruses: must encode Reverse Transcriptase

ss DNA: small genomes

ds DNA: largest viruses, carry almost all of their proteins, including genes for enzymes involved in the deoxyribonucleotide synthesis

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Bacterial Shape Classification:

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Round: Coccus/Cocci
Rod: Bacillus/Bacilli
Spiral: Spirochete or Spirillum/Spirochetes or Spirilla

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General Bacterial Structures:

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Peptidoglycan cell wall

Capsule/glycocalyx (some bacteria) - sticky layer covering the entire bacterium; aids in adhesion

Flagella (some bacteria) - long whip-like filaments involved in motility.
**monotrichous: one flagellum located at only one end
amphitrichous: two flagellum located one at either end
peritrichous: multiple flagella

Pili: Long projections on the bacterial surface involved in attaching to different surfaces
**sex pilus: special pilus attaching F+ (male) and F- (female) bacteria which facilitates the formation of conjugation bridges.

Fimbrae: smaller structures not involved in locomotion or conjugation, however are involved in adhering to surfaces.

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Endotoxins vs Exotoxins:

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Endotoxins: normal components of the outer membrane of Gram-negative bacteria that aren't inherently poisonous. When enough Gram-negative bacteria die and their disintegrated outer membranes are released into the circulation, cells of the host immune system release so many chemicals that the patient goes into septic shock (much of the aqueous portion of the blood is leaked into the tissues).

Exotoxins: Highly toxic substances secreted by both Gram-negative and Gram-positive bacteria. Exotoxins aid in competition between different bacterial species (such as the normal inhabitants of the mammalian gut).

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Gram-positive vs Gram-negative Bacteria:

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Gram Positive: Thick peptidoglycan exterior cell wall and one interior membrane
Gram Negative: Thin peptidoglycan cell wall in the Periplasmic Space (between the inner membrane and outer membrane [outer membrane contains lipopolysaccharide and endotoxins].

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Bacterial Climate Classifications:

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Hot: Thermophiles
Moderate: Mesophiles
Cold: Psychrophiles

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Bacterial Energy Source Classifications:

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Chemotroph: Uses Chemicals for nutrients

Phototroph: Uses Sunlight for nutrients

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Bacterial Carbon Source:

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Heterotroph: Uses Organic compounds

Autotroph: Uses CO2

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Endospore Formation:

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Generation of a tough, thick external shell comprised of peptidoglycan to allow bacterial survival in unfavorable conditions.

Germination is the metabolic reactivation of an endospore.

**Can only be done by Gram-positive bacteria.

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Fungi Structures:

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Nonmotile, multicellular eukaryotes (except for unicellular yeast).

All contain a rigid cell wall composed of chitin, and are chemoheterotrophs.

Hyphae (Septate/Aseptate): Long filaments of cells connected end to end - separated by walls called septa (septate hyphae) or joined together in a long tube in which the cytoplasmic contents and the nuclei are shared (aseptate).

Haustoria: hyphae specialized to digest and absorb nutrients in a parasitic fashion.

Mycelium: meshwork of hyphae.

Thallus: large fungal structure visible to the naked eye.
**vegetative portion of the thallus is involved in obtaining nutrients
fruiting body portion of the thallus is involved in reproduction (by making spores)

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Fungal Life Cycles:

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Asexual reproduction: can occur via budding, fragmentation or spore production.

Budding: a new smaller hypha (or single cell) grows outward from an existing one.

Fragmentation: mycelium is broken into small pieces, each of which develops into a separate mycelium.

Asexual spore formation: occurs through mitosis to generate many spores from one cell.

Adults are haploid, sexual reproduction occurs when haploid adult cells fuse, and form a diploid zygote. This diploid zygote quickly enters meiosis to produce haploid cells (again).

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Alterations to Bacterial Genome:

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Conjugation:
Transfer of genetic material unidirectionally from an F+ to an F- bacterium.

Transduction:
Incorporation of a viral genome into the bacterial genome.

Transformation:
Incorporation of naked, Prokaryotic DNA into the bacterial genome

Transfection:
Incorporation of naked, Eukaryotic DNA into the bacterial genome

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Taxonomic Categories (in order):

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Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

"Dumb King Phil Came Over For Great Sex"

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Ectoderm Formations:

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Entire nervous system

Pituitary gland (both lobes), adrenal medulla

Cornea and lens

Epidermis of skin and derivatives (hair, nails, sweat glands, sensory receptors)

Nasal, oral, anal epithelium

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Mesoderm Formations:

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All muscle, bone, and connective tissue

Entire cardiovascular and lymphatic system, including blood

Urogenital organs (kidneys, ureters, gonads, reproductive ducts)

Dermis of skin

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Endoderm Formations:

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GI tract epithelium (except mouth and anus)

GI glands (liver, pancreas, etc.)

Respiratory epithelium

Epithelial lining of urogenital organs and ducts

Urinary bladder