Recitation 10 : Topics for Exam III
TRANSCRIPTION,
TRANSLATION
Structural difference between RNA and DNA ( RNA: ribonucleotides, U, A, G, C )
Transcription: cellular location of transcription.
Mechanism of transcription: Attachment of RNA polymerase to promoter site, termination of
transcription through hairpin formation.
Post transcriptional modification : poly A tail, 5' cap, exon, intron.
t-RNA : empty t-RNA ( unusual bases, anticodon region ) , amino-acyl tRNA (requires specific
aminoacyl transferases), wobble base
Genetic code : degeneracy, 3 stop codes, AUG code for Met
Translation (Protein synthesis): Initiation (small subunit / mRNA / met-t-RNA - complex);
elongation (P-site, A-site, peptide bond formation, empty t-RNA); termination (stop codon)
Mutations : silent, point (missense, nonsense), frame shift
VIRUSSES
Morphology : enveloped or non-enveloped, DNA or RNA embedded in protein coat ( capsid ),
envelop contains peripheral proteins, glycoproteins
Lytic, lysogenic cycle (events that trigger the lytic cycle),
RNA viruses : (-) RNA, (+)RNA (=mRNA), dsRNA
Flu-virus: (-)RNA, Hemaglutinin (H) and Neuraminidase (N); Viral hepatitis: DNA or RNA virus; Rhinovirus (response to nasal receptors)
Retroviruses: HIV (via a surface glycoprotein) attached to MHC II proteins on T-cells : reverse
transcriptase, cDNA, lysogenic cycle, protease inhibitor, AZT
GENE EXPRESSION
Protein DNA Interactions : helix - turn -helix motif, Zinc Finger motif, Leucine Zipper
Trp operon: Promoter, operator, structural genes (feedback mechanism)
Lac-Operon : Promoter, operator, enhancer, structural genes, inhibitor protein gene. Low glucose,
high cAMP, cAMP/cap protein associate with enhancer site, lactose forms complex with repressor
protein, removing repressor from operator
Transcription in eukaryotes: TATA box, transcription factors, activators, distant enhancer sites
Telomerases: truncated 5'-3' replicated strand, cancer cells
Transposon: cut and paste ( transposon codes for enzymes that can excise transposon and integrate
in an other location on chromosome); reverse transcriptase: cDNA copy inserted at an other
location on chromosome; alu transposons (sensitive to hormone activation)
GENETIC EGINEERING
gel-electrophoresis (short fragments migrate faster). Restriction enzymes (sticky ends fragments)
Bacterial DNA (ds circular), plasmid DNA, genes coding for antibiotic resistance
Recombinant plasmid DNA : plasmid has genes for Amp and Tc resistance, Tc gene has restriction
enzyme site, foreign DNA inserted at restriction enzyme site. Screening: Amp containing media:
only bacteria with plasmids, Tc media: bacteria with DNA insert will not grow.
Alternative method: Amp gene and lac gene that has restriction enzyme site. Media contains Amp
and gal-dye (colorless), in presence of organisms with intact lac gene, the enzyme galactosidase
cleaves gal-dye to gal and dye (blue). Bacteria with DNA insert appear as colorless colonies.
Active genes( mRNA, rev. transcriptase, labeled cDNA, microarray)
Application of genetic engineering (e.g. insulin, somatotropin), agrobacterium, cloning protocol
PCR : temperature dependent reactions (denaturing, annealing of primer, DNA synthesis)
VTRS in forensic analysis (judge form electrophoretogram if two individuals are related)
CELL SIGNALING
Three forms of signaling (endocrine, paracrine, neurotransmitters)
Action of histamine. What are hormones
RTK receptors: activation by signaling molecule (hormone) , ras activation, MAP kinase activation,
cellular responses
G-protein receptor: activation by signaling molecule, G-protein activation, either cAMP, PKA activation
or IP3, Ca++, PKC activation.
Deactivation of signaling pathway : hormone degradation and deactivation of ras and G-protein.
Glucagon, Epinephrine : g-protein , PKA , cellular response;
Insulin : ras, MAP, cellular response
Neurotransmitters: release of acetylcholine by motor nerve cells, receptors (Na-channel) on muscle
cells, Ca++ release and enzyme activation , muscle contraction.
Inhibitory (GABA) and excitatory (Asp, Glu) brain neurons. Agonists, Antagonists
Proto-Oncogenes ( code for ras , G-protein).
IMMUNE SYSTEM
None specific response : tears, mucus, secretions
White blood cells acting through phagocytosis: Phagocytes Macrophages, Eosinophils
MHC I, MHC II (on Macrophages, T and B-cells), Antibodies: (immunoglobulins , 5 classes) variable
and conserved regions.
Cellular immune response: Action of cytotoxic T-cells (injection of perforin, lysis)
White blood cells involved in humoral immune response (Lymphocites) : B-cells (develop into antibody
producing plasma cells and in memory cells), T helper cells
Autoimmune diseases
HISTORY OF EARTH
Principle of C-14 Dating, Potassium-Argon Dating and Rubidium-Strontium Dating
Geological Eras : Cenozoic Era (65 mya to today)
Mesozoic Era (245 to 65 mya): Cretaceous ( Cretaceous/
tertiary major extinction,
meteoroid), Jurassic (Archaeopteryx), Triassic (Dinosaurs appear)
Paleozoic Era (544 to 245 mya), Cambrian (543 mya) : major diversification of animal phyla (trilobites,
horseshoe crab, brachiopods). Devonian (400 mya) tetrapods (Coelacanth),
fern-trees
Precambrian Era (4,500 to 544 mya) primitive algae (3.6 bya), stromatolites , Vendian strata:
Ediacaran fauna,
Plate tectonics:
Convergent plates: Nazca/
Indian plate /
Eurasian plate :
Divergent : Mid-Atlantic Ridge
Hot spot :
Cambrian (Gondwanaland,
Major extinctions : meteoroid impact, super volcanoes, plate
movements,
mitochondrial DNA evidence
Major ice ages: cause (plate movement, atmospheric CO2 content, Earth axis tilt, eccentricity)
Temperature history: hot during much of Mesozoic , cold during carboniferous to Triassic
Sea levels: depend on temperature (ice ages: low sea levels) and land mass (high during
Gondwanaland)
Oxygen in the Earth atmosphere: Steadily rising. Major increases during Cambrian (fast growth
through respiration) and Devonian / Carboniferous (forest formation)
Leakage of carbon into geocycle increases oxygen levels