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257 Cards in this Set
- Front
- Back
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Cellular Level
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Atoms, Molecules, Organelle, Cell
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Organismal Level
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tissue, organ, organ system, organism
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Population
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species, community, ecosystem, biosphere
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Hypothesis
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Possible explanation for an observation that is tested in many ways to allow predictions
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Theory
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Interconnected concepts supported by experimental evidence to express ideas to which we are almost certain about
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Reductionism
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break into simpler parts
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systems biology
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Focus on larger parts that can't be understood by simpler parts
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Deductive reasoning
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uses general principles to make specific predictions "V"
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Inductive reasoning
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specific to general conclusions "^"
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Founder Effect
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alleles lost or changed drastically
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Bottleneck Effect
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Population size reduced results in loss of genetic variation
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Natural Selection
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change occurs. Population adapts and favors phenotype with greater fitness
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Artificial Selection
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Favors phenotype traits
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5 agents of evolutionary change
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mutation, gene flow, non-random mating, small pop. size, selection.
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components of fitness
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survival, # of offspring, sexual selection, traits favored for one component may be disadvantage for others
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7 objections of evolution
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Evolution not demonstrated, no fossil intermediates, intelligent design, violates thermodynamics, proteins too improbable, doesn't imply evolution, irreducible complexity
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Counter to objections
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not enough evidence, some proposed have been found, natural selection not random, not closed system, can't argue backwards, artificial selection, evolution from simple changes
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elements found in living organisms
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Carbon, Hydrogen, Oxygen, Nitrogen
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Hydrogen bond properties of water
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High specific heat, high heat of vaporization, solid water less dense than liquid water, good solvent, organizes nonpolar, forms ions, pH=7
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Covalent bond
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Atoms share 2 or more valence electrons. No net charge
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Ionic bond
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oppositely charged ions
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Hydrogen bond
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Polarity of water allows it to attract to one another
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Polar
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unequal sharing of electrons
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Non-polar
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equal sharing of electrons
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Reduction
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gain of electron
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Oxidation
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loss of electron
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Hydrophilic
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water-loving
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Hydrophobic
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water-fearing
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Acid
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dissociates in water to increase [H+] and lower pH
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Base
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combines with H+ in water to lower [H+] and increase pH
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Buffer
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keeps [H+] relatively constant. Absorbs H+ ions when acid is added and releases them when base is added
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Carbohydrate
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(1:2:1) (CH2O)n
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monomer of a Carbohydrate
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sugar monomers-> glucose, fructose, galactose
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4 types of polysaccharides
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starches, glycogen, cellulose, chitin
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starches
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O bonds, alpha linkage
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glycogen
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animal energy forms
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cellulose
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Beta-linkage. Forms tough fibers
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Chitin
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anthropods, polymer of glucose and proteins
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Protein functions
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enzymes, defense, transport, support, motion, regulation, storage
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Amino Acid Structure
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central carbon atom attached to an Amino Group, Carboxyl group, a single hydrogen, and an "R" group. Monomer of proteins
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"R" group in an amino acid
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determines function and structure of proteins
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Four levels of protein structure
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Primary:sequence of amino acids
Secondary: group in peptide bonds tertiary: final folded shape of protein Quaeternary: multimetric folding |
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Peptide bond formation
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covalent bond that holds amino acids together formed in ribosomes through dehydration synthesis. OH is removed from carboxyl, H from amino, and covalent bond forms between the two giving off water as excess
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Chaperone proteins
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helps proteins fold correctly (heat shocked proteins)
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Structure of a nucleotide
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in DNA: sugar (deoxyribose), a Base (ATCG) and a phosphate
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DNA
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deoxyribose. Double helix connected by H-bonds, ATCG, with a sugar phosphate backbone
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RNA
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Ribonucleic acid. U instead of T. Single polynucleotide strand used from DNA to specify sequence
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Cell theory
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all organisms are made from cells, cells are the smallest living things and arise from existing cells only
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Prokaryotic Cells
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Cell wall, plasma membrane, nucleoid, flagella, capsule, pili. Lack membrane
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Eukaryotic Cells
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membrane, cytoskeleton bound organelles and endomembrane system
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Animal Cell:
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endomembrane system, vesicles, chromosomes, cytoskeleton, nucleus, nucleolus, nuclear envelope, nuclear pores, chromatin, ribosome, RER, SER, golgi apparatus, mitochondrion
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Plant Cell:
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cell wall, cell membrane, endoplasmic reticulum, vesicles, ribosomes, microtubules, golgi apparatus, nucleus, mitochondria, chloroplast, chromosomes, lysosomes
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Cytoskeleton
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Contains actin filaments, microtubules, intermediate filaments
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Actin filaments
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protein chains that have + and - ends that designate growth of filaments. Responsible for cellular movements such as pinching and crawling during division
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Microtubules
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alpha and beta tubulin. Tube Shaped. Organize cytoplasm and move material within cell itself
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Intermediate filaments
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Fibrous protein that gives mechanical strength
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Cell membrane components
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phospholipid bilay, transmembrane proteins, interior protein network, cell surface markers
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Phospholipid bilayer
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flexible matrix barrier to permeability
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transmembrane proteins
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transport and communicate across membrane
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Interior protein network
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reinforce membrane shape
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cell surface marker
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identity markers
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Phospholipid structure
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hydrophobic tail (non-polar) with a hydrophilic head
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Membrane transport
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small molecules (water) move eaily across but large molecules must use vesicles
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Osmosis
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Net diffusion of water across membrane toward higher solute. Force needed to stop & creates pressure. Reach equilibrium inside and out.
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Passive Transport : Diffusion
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high to low [ ] no energy required
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Passive transport: Facilitated
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requires channel protein to move through channel when open OR carrier protein that attaches then changes shape
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Hypertonic
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higher solute [ ] than water. Causes cells to shrivel
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Hypotonic
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lower solute [ ] than water. Causes cells to burst.
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Isotonic
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same osmotic [ ]
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Active Transport proteins
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Uniporters, symporters, antiporters
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Uniporters
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one molecule moved at a time
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Symporters
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two molecules in same direction
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Antiporters
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two molecules in opposite directions
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Coupled transport
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Na+ uses diffusion of Na+ to move glucose against [ ] gradient. Molecules move in same direction
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Active Transport steps
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1. uses ATP directly. antiporter moves 3Na+ out and 2K+ in against gradient. changes shape of carrier protein and binds, ATP,"", shape change, Release 3Na+ to pick up 2K+ and releases shape change.
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Exocytosis
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movement of substances out of a cell
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phagocytosis
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cell takes in solid matter
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Pinocytosis
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cell takes in fluid matter
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Receptor-mediated endocytosis
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specific molecules are taken in after binding to receptor
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Energy
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Capacity to do work
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Entropy "S"
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measure of a system's disorder
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Forms of energy
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mechanical, light, radioactive, heat, sound, and electric are all types
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Enthalpy "H"
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internal energy of a system plus the product of pressure and volume (H=E+PV). The amount of energy released or used in a system at constant pressure
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Role of ATP in cell
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"currency" all cells use. Drives endergonic reactions
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Exergonic
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- delta G (cellular respiration)
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Endergonic
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+ delta G (photosynthesis)
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Free energy
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energy that can be taken in or extracted at standard conditions.
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+ delta G
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products > reactants. Non spontaneous, endergonic
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- delta G
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products < reactants. spontaneous, exergonic
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Delta G
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change in free energy
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ATP and structure
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Adenosine Triphosphate: ribose, adenine, 3 phosphates
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Protein enzymes
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enzyme to substrate and convert to product at active site. forms enzyme to substrate complex and applies stress to distort a bond and lower the activation energy
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Coupling
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sharing of intermediates to drive an equation
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metabolism
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total of all chemical reactions carried out by an organism
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catabolism
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harvest energy by breaking down molecules
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Anabolism
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expand energy to build up molecules
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Feedback inhibition
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end product of pathway binds to an alleosteric site on enzyme that catalyzes first rxn in pathway
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Structure of Chloroplast
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Thylakoid membrane, Grana, Stroma lamella, Stroma
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Thylakoid Membrane
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chlorophyll and pigments clustered into photosystems
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Grana
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Stacks of thylakoid membrane sacs
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Stroma lamella
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surround grana
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Stroma
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semiliquid around thylakoid membranes
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Pigments involved in photosynthesis
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1. chlorophylls 2. carotenoids. Capture visible light ~400-740 nm
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Photosynthesis Equation
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6CO2 + 12H2O --> C6H12O6 + 6H2O + 6O2
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Light independent reaction
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Catalyze RuBP to PGA (RuBP + CO2 --> PGA)
PGA to G3P (reduction) PGA regenerates RuBP 3 turns for carbon to produce 1 G3P 6 turns for 1 Glucose |
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Light dependent reaction
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energy from sunlight to make ATP and reduce NADP+ to NADPH.
1. Photon is captured by pigment 2. charge separation- energy is transfered to rxn center and an excited e- is transported to acceptor 3. e- transport. e- move through carriers to reduce NADP+ 4. Chemiosmosis- produces ATP |
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Chemiosmosis in photosynthesis
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Electrochemical gradient to synthesize ATP.
Move down gradient to allow ADP + Pi to make ATP Choroplast has ATP synthase enzymes in Thylakoid membrane to allow protons in stroma. Stroma has enzymes that catalyze rxn of carbon-fixation/calvin cycle rxns |
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Carbon Fixation / Calvin Cycle
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1. Attaches CO2 to RuBP to get PGA. Uses enzymes called RUBISCO
2. RuBP + CO2 --> PGA 3. PGA reduce to G3P 4. Regeneration PGA to RuBP 3 turns of carbon for 1 G3P 6 turns of carbon for 1 Glucose |
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Heterotroph
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live on organic compounds produced by others
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Rubisco
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most prodominant enzyme in animal kingdom
- lowers activation energy of reactions |
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Autotroph
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produce their own organic molecules through photosynthesis
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Fermentation
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After glyolysis
Pyruvate + NADH + H to lactic acid and/ or ethanol + NAD+ |
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Cellular Respiration Equation
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C6H12O6 + 6O2 --> 6H2O + 6CO2
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Aerobic respiration
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final e- receptor is O2
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Anaerobic respiration
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final e- receptor is an inorganic molecule (not O2)
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ATP in the cell
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ADP + Pi = ATP; substrate- level phosphorylation and oxidative phosphorylation
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Substrate level phosphorylation
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transfer phosphate directly to ATP during glycolysis
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Oxidative phosphorylation
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ATP synthesis uses energy from a proton gradient
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Stages for complete oxidation of glucose
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1. glycolysis
2. pyruvate oxidation 3. krebs cycle 4. electron transport chain |
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glycolysis
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occurs in cytoplasm
1. priming: phosphates from 2 ATP break down glucose 2. Clevage: glucose to 2 pyruvate 3. oxidation: produces ATP; 3 carbon release phosphate to make ATP |
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Products of glycolysis
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1. 4 ATP (2 net)
2. 2 NADH |
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Pyruvate oxidation
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in mitochondria. Plama membrane of Pro,
1. pyruvate oxidized to acetyl-CoA to enter Kreb's cycle (aerobic) 2. Pyruvate reduced to oxidize NADH back to NAD+ for fermentation (anaerobic |
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Pyruvate oxidation + Glycolysis Products
(per glucose) |
1. 4 ATP
2. 2 CO2 3. 2 NADH 4. 2 Acetyl- CoA |
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Kreb's Cycle
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in matrix of mitochondria. Oxidizes acetyl group from pyruvate
1. Acetyl-CoA + oxaloacetate --> citrate 2. citrate rearrangement and decarboxylation 3. Regeneration of oxaloacetate 4. e- to carriers (NADH and FADH2) citrate to oxaloacetate |
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Krebs cycle Products
(per glucose) |
4 CO2
2 FADH 2 ATP 6 NADH |
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Krebs + Pyruvate + Glycolysis Products
(per glucose) |
6 CO2
4 ATP 10 NADH 2 FADH2 |
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Electron Transport chain
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1. e- from NADH and FADH2 to complexes of ETC
2. create proton motive force 3. powers synthase: pump produces gradient for chemiosmosis) 4. produces high amounts of ATP - occurs in innermembrane mitochondria |
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Theoretical yield
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~36 ATP
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Actual Yield
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~30 ATP
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Reason for difference in ATP yields
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leaky membrane
use of proton gradient for other purposes |
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Binary Fission
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colonal cyle.
single chromosome is replicated (circular) origin to termination |
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Septation
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separate cell components. begins formation of ring of FtsZ protein. Pinch cell into 2 cells
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Chromosomes
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specific to species. Humans have 46 or 23 pairs
made of chromatin, |
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chromatid
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half of a chromosome
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Chromatin
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complex of DNA and protein
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homologus
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maternal + paternal chromosome
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Heterochromatin
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Not expressed
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Euchromatin
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expressed
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Solenoid
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nucleosome coiled further
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histones
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+ charged proteins attracted to phosphate groups of DNA
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nucleosome
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DNA + Histones that guide coiling
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centromere
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hold sister chromatids together
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kinetochore
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attach to microtubules. Connected to chromosomes
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Haploid
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one set of chromosomes
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Diploid
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total number of chromosomes in a cell (2x haploid) or (2n)
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cell cycle
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1. G1
2. S 3. G2 4. Mitosis 5. Cytokinesis |
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Interphase
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includes G1, S, and G2
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G1
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cell growth
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S
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DNA replicates
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G2
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chromosomes coil tightly using motor proteins; centrioles replicate tubulin synthesis
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Checkpoints
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G1/S
G2/M Late Metaphase |
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G1/S Checkpoint
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cell decides to divide
-primary point for external influence Checks DNA |
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G2/M
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makes commitment to mitosis
assesses success of DNA replication |
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Late metaphase
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Checks to make sure all chromosomes are attached to spindle
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M phase in mitosis
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Prophase
Prometaphase Metaphase Anaphase Telophase |
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Prophase
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chromosomes condense, held together at centromere, spindle forms, envelope breaks down
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Prometaphase
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chromosomes attach to microtubules, each X connected at different poles, and move to center
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Metaphase
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X aligned, attach to opposite poles and under tension
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Anaphase
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centromeres split, cohesion proteins removed. sisters pulled to opposite poles. X to outside poles to outside
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telophase
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spindle disassembles, nuclear envelope forms around X's, X's uncoil, nucleolus appears
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Cytokinesis
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clevage of the cell into 2. Animals : constriction of actin filaments
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Cell regulation
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1. cell cycle has 2 reversible points
-replication of genetic material -separation of sister chromatids 2. can be put on hold at specific points -checked for accuracy and halted -respond to signals |
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Cyclin-dependent Kinases (Cdks)
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enzymes that phosphorylate proteins. levels go up when in a phase and down when not
primary mechanism for cell controll |
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Tumor-suppressor genes
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prevent development of mutated cells. Key role in G2 checkpoint that monitors integrity of DNA
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Proto-oncogenes
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Encode receptors for growth factors. If damaged, result in uncontrollable cell division
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Apoptosis
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self-destruction of a cell
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sexual life cycle
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made of meiosis and fertilization
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diploid cells are
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somatic cells of adults 2 sets of X's
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haploid cells are
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gametes 1 set of X's (germ cell)
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sexual life cycle is an alternation of...
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haploid and diploid stages
humans: diploid dominates mitosis to diploid meiosis to haploid |
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Nondisjunction
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failure of x's to move to opposite poles during either division
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meiosis vs mitosis: 4 features
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synapsis and crossing over
sister chromatids remain joined at centromeres throughout meiosis 1 dna replication suppressed b/w meiosis 1 and 2 |
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Meiosis
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includes meiosis 1 and 2.
Each has PMAT |
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Crossing over
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swapping of genetic materials b/w non-sister chromatids
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Meiosis Prophase 1
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x coil tightly become visible envelope disappears, spindle forms. Synapsis and crossing over
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Meiosis Metaphase 1
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chiasmata holds x's together. microtubules from opp poles align x
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Meiosis Anaphase 1
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microtubules shorten; chiasmata break, pairs separate. each pole has haploid set x. Independent assortment of maternal and paternal x
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Meiosis Telophase 1
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envelope reforms; sisters no longer same
2 cells into meiosis 2 |
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meiosis 2 prophase 2
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new spindle, envelope break down (like mitosis)
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meiosis 2 metaphase 2
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x align, microtubules attach to kinetochores (like mitosis)
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meiosis 2 anaphase 2
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microtubules shorten. sister chromatids to opposite side (mitosis)
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meiosis 2 telophase 2
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membrane forms, cytokinesis into 4 haploid cells with none alike
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DNA primase
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RNA polymerase that makes RNA primer
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Primer
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made by primase.
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DNA ligase
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seals backbone and fragments
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DNA polymerase 3
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proofreads in the 3'-5' direction
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3 Models of DNA replication
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conservative
semi-conservative (correct) dispersive |
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DNA replication steps
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1. initiation
2. Elongation 3. Termination requires parent DNA |
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DNA replication
1. initiation |
replication begins
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DNA replication
2. Elongation |
new DNA strands formed by DNA polymerase
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DNA replication
3. Termination |
replication is terminated of DNA
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Helicases
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use energy from ATP to unwind DNA
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Single-stranded-binding proteins
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coat strands of DNA to keep apart
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Topoisomerase
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prevent tangling of DNA during DNA replication
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DNA gyrase
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relax super- coils of DNA
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Semidiscontinuous
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DNA synthesize 1 way (5'-3')
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leading strand
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3'-5' strand. continuous from primer
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lagging
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requires multiple primers 5'-3' strand
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okazaki fragment
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multiple fragments for lagging strand
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DNA polymerase
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matches existing bases with complimentary nucleotides then links them
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Prokaryotic DNA replication
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single circle dna begins at origin to both directions around x
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DNA polymerase 1
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remove primers and replace with dna on lagging strand
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DNA polymerase 2
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DNA repair polymerase
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DNA polymerase 3
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replication enzyme that also has proofreading capability for DNA
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Replisome components
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1. enzyme involved in DNA replication form a macromolecular assembly
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Primosome in the Replisome
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Primase, helicase, proteins
complex of 2 DNA pol 3 |
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Telomeres
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protect end of x's and are turned off as we age
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mutagens
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any agent that increases the # of mutations
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photorepair: non-specific
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that uses single mechanism to repair multiple lesions of DNA
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photorepair: specific
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one mechanism for one lesion of dna
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Early ideas about genes came from....
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studying drosophilia and human diseases
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one gene/one-enzyme hypothesis
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each gene codes for the production of a specific polypeptide
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Central dogma
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information flows from DNA->RNA->Protein
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________ violate the order of the central dogma using reverse transcriptase to convert _____ genome into _____
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Retroviruses, RNA, DNA
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Transcription is...
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DNA to RNA
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Translation is....
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RNA to Protein
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Genetic code
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order of nucleotides in DNA encoded amino acid order
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codon
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block of 3 DNA nucleotides that correspond to an amino acid
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degenerate coding
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some amino acids are specified by more than one codon
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Prokaryotic Transcription
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doesn't require a primer. does require promoter, start site, termination site
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Prokaryotic transcription promoter
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forms recognition and binding site for RNA polymerase. is upstream of start site and not transcribed
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Prokaryotic transcription elongation
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5'-3' direction. forms bubble: RNA polymerase, DNA template and growing RNA transcript. After it passes DNA is rewound as it the leaves the bubble
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Prokaryotic transcription termination
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sequence signals stop to polymerase.
causes formation of phosphodiester bonds to stop RNA-DNA hybrid within transcription bubble dissociates RNA polymerase releases DNA and it rewinds |
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Prokaryotic translation
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coupled to transcription. mRNA begins to translate before transcription is finished
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Eukaryotic Transcription
RNA polymerases |
polymerase 2 transcribes mRNA and each recognizes its own promoter
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Modified Primary Transport in Eukaryotic Transcription
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adds 3' poly-A tail created by poly-A polymerase for protection
adds 5' cap to protect and for initiation |
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splicing
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in eukaryotic transcription to cut out introns
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Introns
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non-coding regions
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exons
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coding regions
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splicesome
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remove introns specifically
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Transportation for Eukaryotic Transcription
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mature mRNA are taken to cytoplasm for translation
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Binding Site
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multiple sites for tRNA translation
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P-site
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binds tRNA attached to growing peptide chain
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A-site
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binds tRNA carrying the next amino acid
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E-site
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Binds tRNA that carried the last amino acid
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Ribosome functions in transcription/translation
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decode mRNA and forms peptide bonds
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peptidyl transferase
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forms peptide bonds b/w amino acids
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Eukaryotic Translation
initiation |
complex forms on mRNA with large and small ribosomal units. initiator tRNA with first amino acid on p-site (a-site empty)
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Eukaryotic Translation
Elongation |
adds amino acids. 2nd charged tRNA can bind to a-site. Peptide bond forms. Addition of successive amino acid occurs as a cycle
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Euk. Translation
tRNA & codons |
fewer tRNA's than codons
wobble pairing allows less stringent pairing b/w 3' base of codon & 5' base of anticodon Allows fewer tRNA to accomodate all codons |
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Euk. Translation
Termination |
elongation continues until ribosome encounters a "stop" codon that is recognized by release factors that release the polypeptide from the ribosome
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Prokaryotic regulation
Activators |
control of transcription initiation. + control increases frequency of initiation of transcription
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positive control effectors
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enhance binding of RNA polymerase to promoter
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positive control repressors
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can enhance or decrease
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Negative control
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decrease frequency
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negative control effectors
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bind to operators in DNA, allosteric
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Negative control repressors
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respond to effector molecule and enhance or abolish binding to DNA
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Eukaryotic vs. Prokaryotic regulation
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control of transcription, more complex.
Eu. have DNA into chromatin protein-DNA interaction can alter transcription eu. occurs in nucleus amount of DNA differs |
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regulatory proteins
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control gene expression by binding to specific DNA sequences
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motifs
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gain access to bases of DNA at major groove and sit there
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Zinc-Finger
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pattern of secondary structure that possess DNA-binding motifs. Every protein that binds to DNA has one
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Induction
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enzymes for a certain pathway that are produced in response to a substrate
+ control. Nothing blocked |
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Repression
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capable of making an enzyme but doesn't. Environment doesn't need it to
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lac operon
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group of genes that code for proteins that work together in a pathway. Use of lactose as energy source gene for lacl is linked to rest of it.
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lacZ
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B-galactosidase
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lacY
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permease
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lacA
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transacetylase
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