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What is cell theory?
- All organisms are composed of one or more cells
- The cell is the structural unit of life
- Cells arise from pre-existing cells by division (aren't spontaneously created)
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What are the basic properties of cells?
- Life
- Highly complex and organized
- Posses a genetic program and the means to use it
- Capable of producing more of themselves
- Aquire and utilize energy
- Carry out a variety of chemical reactions
- Engage in mechanical activities
- Able to respond to stimuli
- Capable of self regulation
- Evolve over time
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Examples of Domain Bacteria
- Mycoplasma: smallest known cells
- Cyanobacteria: photosynthetic, gave rise to green plants and O2 rich atmosphere
- Some capable of N2 fixation
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Examples of Domain Archaea
- Methanogens
- Halophiles
- Acidophiles
- Thermophiles
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6 Model Organisms
- E. Coli (bacterium)
- Saccharmyces (yeast)
- Arabidopsis (mustard plant)
- C. elegans (nematode)
- Drosophila (fruit fly)
- M. musculus (mouse)
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Various aspects of cell replacement therapy
- Embryonic stem cells have more potential for differentiation than adult stem cells (pluripotent). Must be differentiated in vitro.
- Cell repl therapy: somatic cell + denucleated egg = cells that won't be rejected by host
- Induced pluripotent cells: reprogramming of fully differentiated cel into pluripotent stem cell
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Limiting aspects of cell size
- Volume of cytoplasm that can be effectively controlled by the genes in the nucleus
- Volume of cytoplasm that can be supported by exchange of nutrients
- Distance over which substances can efficiently diffuse
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Virus outside hose cell?
Virion
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Viral infections
- Lytic: virus redirects host into making more particles then lyses to release viruses
- Integration (lysogenic): virus integrates its DNA into host's chromosomes. May give rise to progeny via budding, may become cancerous, may cause lysis after triggered event
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Viroids?
Pathogens that consist ONLY of a single naked RNA molecule that binds to single stranded mRNA making them unreadable by ribosomes
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Evidence to support endosymbiont theory
- Absence of intermediate stage of evolution
- Symbiotic relationships seen amongst other organisms
- Organelles contain their own DNA, arrange prokyaryotically
- rRNA sequencing reveals similar structure of eu organelles and pro
- Organelles duplicate independently of nucleus
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What is hydrolysis?
Water + energy = cleaving of polymers
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Carbohydrate formula? Two types? Enantiomers? Bonds between sugars? Various polymers?
- (CH2O)n
- Ketose sugars: Carbonyl (c=o) on terminal carbon
- Aldose sugars: Carbonyl on terminal carbon
- Enantiomers: D or L. D is found in nature.
- Glycosidic bonds (H-O-H)
- Glycogen, Starch, Cellulose, Chitin, Glycosaminoglycans (cell/cell communication).
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Amino Acid structure? Natural Amino acid? Links between AA?
- C attached to amine, carboxyl, H, and R group
- L stereoisomer (opposite of sugar)
- Peptide bonds
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Protein levels of structure
- Primary: sequence of amino acids
- secondary: conformation of adjacent amino acids in a-helix or b-sheet
- tertiary: conformation of entire polymer
- quaternary: protein subunits interacting
- multiprotein complex
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Protein misfolding diseases/description
Creutzfeld-Jakob Disease, Mad dow, kuru, scrapie. Prion (misfolded protein) causes other proteins to fold abnormally.
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Describe proteomics
- Study of the proteome (entire inventory of organism's proteins)
- Current technology can create artificial genese to code for specific AA sequences
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Nucelotide parts
- Pentose (5-cardbon) sugar [ribose or deoxyribose]
- Phosphate group
- Nitrogenous base
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Purines vs pyrimidines
- Purines: Adenine, Guanine
- Pyrimidines: Cytosine, Thymine, Uracil
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Laws of thermodynamics
- 1) Law of conservation of energy: Energy can neither be created nor destroyed, it is tranduced between states
- Change in internal E = heat - work (deltaE = Q - W), dE neg is exothermic, dE pos is endothermic
- 2) Events in universe tend to proceed from higher E to lower E. Loss of available E during the process is result of tendency for entropy of universe to increase. (TdeltaS)
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Gibbs free energy
- dH = dG + TdS (aka dG = dH - TdS). dG neg means rxn is spontaneous (exergonic), dG pos means rxn is endergonic
- At equilibrium dG = 0 (no free energy)
- Correction for standard conditions dG = dGstandard + RT lnK
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Cofactor vs coenzymes
- Cofactor: inorganic enzyme conjugates (metals)
- Coenzymes: organic enzyme conjugates (vitamins)
- Typically located within the active site of an enzyme
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Mechanisms of enzyme catalysis
- Substrate orientation
- Changes in substrate reactivity
- Inducing strain in substrate
- Conformational changes
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Enzyme kinetics information
- Vmax = velocity at saturation
- Turnover # = number of substrate -> product per minute per enzyme molecule at Vmax
- Km (Michaelis constant) = substrate concentration at half Vmax (reflects affinity of enzyme for substand. Lower Km indicates higher affinity for enzyme)
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Enzyme inhibitors
- Irreversible inhibitors: bind tightly to the enzyme
- Reversible inhibitors: bind loosely to the enzyme
- -competitive inhibitors: compete w/ enzyme for active sites (can be overcome w/ increased substrate)
- -noncompetitive inhibitors: bind to alternate sites, change shape of enzyme (Vmax cannot be reached, inhibition cannot be overcome)
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What is fermentation?
NAHD is oxidized to NAD+ by reducing pyruvate (lactate or ethanol)
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NAD+ vs NADP+
Phosphate transfered to NAD+ from ATP when cell has much excess energy. NADPH is used for forming biomolecules, NADH allows the cell to create additional ATP.
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Overview of membrane functions
- Compartmentalization
- Scaffold for biochemical activites
- Selectively permeable barrier
- Transporting solutes
- Responding to external signals
- Intercellular interaction
- Energy transduction
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Main types of membrane lipids
- Phosphoglycerides (diacylglycerides w/ small functional head groups)
- Sphingolipids (sphingosine to fatty acids)
- Cholesterol (smaller, less amphipathic, only animals)
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What is a liposome
spontaneous lipid bilayer that occurs in aqeuous environments
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Membrane carbohydrates
- Glycoproteins are for interactions with other cells/outside cell
- Glycolipids may be cell-to-cell recognition sites
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Membrane proteins
- Integral: aphipathic, anchored in in the bilayer and hydrophilic regions. Anchored to one side (eg channel proteins)
- Peripheral: easy to removed, attached by weak bonds
- Lipid-anchored: Glycophophatidylinsoitol (GPI)-linked found on outer leaflet, weak bonds
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4 basic mechanisms by which molecules cross membranes
- Simple diffusion: small, nonpolar
- Open channels: (ion channels, v-gated channels) ions
- Facilitated Diffusion: large, hydrophilic. Use of cotransport
- Active transport (pumps): 3Na out, 2K in
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