80 Cards in this Set
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covalent bond
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strong bonding through the sharing of electrons
nonpolar: equal sharing (C-H or H-H)
polar: non equal sharing due to differences in electronegativity (O-H)
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ionic bond
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complete electron transfer between cations and anions
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Solvents/Solute/Solution
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Solvents dissolve the solute
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Why water is efficient solvent?
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1. O-H bonds polar due to differences in electronegativity so O has partial negative charge (bond to cations) and H have partial positive charge (can bond to anions); this causes hydrogen bonding
2. bent structure keeps positive H's away from negative O, making the overall molecule po…
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Cohesion
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attractions between like polar molecules (hydrogen bonding)
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Adhesion
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attractions between liquid and surfaces with polar components
-ex. meniscus: adherence to glass pulls up and cohesion to other water molecules pulls down
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Surface Tension
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water molecules at surface can only bond to molecules below; stronger attractive forces resist changes to water's surface area
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Why water is denser as a liquid than a solid
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Crystal lattice forms in ice due to repeating structure of hydrogen bonds and there is space in between; for liquid bonds always form and break so no space in between
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equilibrium
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dynamic but stable state in which forward and reverse reactions occur at same rate
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Energy
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capacity to do work or supply heat
potential energy: stored (chemical); greater in outer shells than inner shell; polar bonds = less PE
kinetic energy: energy of motion (thermal)
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Laws of Thermodynamics
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1. Energy neither created or destroyed
2. Entropy increases in spontaneous reactions (∆S > 0)
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Spontaneous Reactions
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reactions that happen on their own
1. entropy (randomness) increases
2. products have lower PE
3. Gibbs Free Energy decreases
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Amino Acid
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20 different kinds of these monomers make up polymer (protein)
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Amino Acid Structure
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1. H+ atom
2. Amino
3. Carboxylic Acid
4. R group (determines charge/polarity)
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Nonpolar Side Chains
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no charge; lack charged or electronegative molecules (have C-H) bonds; make amino acid hydrophobic; do not dissolve
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Polar Side Chains
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hydrophilic; have charged or electronegative molecules (O atom will cause polar covalent bond)
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Charged Side chains
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negative charge: acidic (lost proton)
positive charge: basic (gained proton)
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Polymerization
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monomers link together to form polymers
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Condensation (Dehydration) Reactions
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Polymerization when newly formed bonds results in the loss of a water (H₂O) molecule
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Hydrolysis
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Reverse of condensation reaction; adds a water to break up polymers; favors because increases entropy and spontaneous (no energy needed)
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Peptide Bond
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How amino acids polymerize into proteins
*C-N bonds; N of amino from one amino acid bonds to a C of another amino acid and water lost;
electron sharing makes similar to double bond
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3 characteristics of Peptide Bonded Backbone
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1. R groups stick out, allowing interactions to occur
2. N to C terminus
3. Flexibility; single bonds on each side of peptide bond can rotate
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Peptide/Oligopeptide
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<50 amino acids bonded together
Polypeptide: 50 or more amino acids bonded
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Primary Structure of Protein
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sequence of amino acids
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Secondary Structure of Protein
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hydrogen bonding WITHIN same peptide backbone
Bond between O (from C = O) on one amino acid with H (from N-H) of another; only when parts of backbone close together
-α helix: coiled
-β pleated sheet: segments bend 180° then fold
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Tertiary Structure
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R groups bond w/ SAME backbone or other R groups
1. Hydrogen Bonding
2. Hydrophobic Interactions
3. Van der Waals Interactions
4. Covalent Bonds (S-S bonds)
5. Ionic Bonds
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Quaternary Structure
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Similar to Tertiary Structure but multiple polypeptides
(ex. hemoglobin, macromolecular machines)
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Denaturing
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Unfolding of a protein that causes a loss of function
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Folding
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Spontaneous due to the energy supplied by the bonds, hydrophobic interactions, van der waals; crucial to function of proteins --> flexibility
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molecular chaperones
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facilitate folding; heat shock proteins bind to hydrophobic patches in denatured proteins to cause refolding
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prions
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proteinaceous infectious particles; when proteins fold into infectious, disease causing agents
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Protein Functions
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1. Catalysis (enzyme)
2. Defense (antibodies)
3. Movement (actin/myosin)
4. Signalling
5. Structure
6. Transport
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Substrates
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Reactant molecules
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Active Site
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Where substrates bind and react; catalysis occurs
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Carbohydrate (Sugar)
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monomers: monosaccharides
polymers: oligosaccharides (small) polysaccharides (large)
-consist of carbonyl (C=O), several hydroxyls (OH) and hydrocarbons (C-H); reactivity and hydrophillics
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Distinguishing Carbohydrates
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1. Carbonyl group: at either end of molecule: aldose
in middle: ketose
2. # of carbons (triose, pentose, hexose)
3. Spatial arrangement of hydroxyl group
4. Form α/β rings (C-O bond; C1 carbon bond with C5 oxygen; C5 gives H to C1 turning carbonyl to hydroxyl)
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Disaccharides
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2 sugars linked together
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Glycosidic Linkages
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Monosaccharides polymerize to polysaccharides; condensation reaction between 2 hydroxyls
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Monosaccharides polymerize to polysaccharides; condensation reaction between 2 hydroxyls
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1. Starch
2. Glycogen
3. Cellulose
4. Chitin
5. Peptidoglycan
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Starch
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-α glucose monomers; in plants stored energy
-α 1-4 glycosidic linkages coil into helix
-2 polysaccharides
i. amylose (unbranched α 1-4 glycosidic linkages)
ii. amylopectin: (branch α 1-6 glycosidic linkages one out of every 30 monomers
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Glycogen
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-energy storage in animal cells (liver)
-α 1-4 glycosidic linkages
-branched form of starch
-1-6 glycosidic linkages one out of every 10 monomers
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Cellulose
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-in plants/algae, structure for cell wall
-β glucoses; β1-4 glycosidic linkages
-Each monomer flips, which causes linear structure with hydrogen bonds connecting strands
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Chitin
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-cell walls of fungi, in protists and other animals
-β NAG; β 1-4 glycosidic linkages
-every other flipped; h bonds between strands
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Peptidoglycan
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-structural support in bacteria cell wall
-two types of monosaccharides linked β 1-4
-amino acids attached; peptide bonds between strands
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Carbohydrate Function
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-provide structure (β 1-4 linkages insoluble and have strong interactions; hydrolysis hard)
-indicate cell identity (identification badge)
-store chemical energy (in C-H bonds)
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Glycoprotein
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protein with oligosaccharides covalently bonded to it that act as identification
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Phosphorylase
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catalyzes hydrolysis of α 1-4 glycosidic linkages
ex. break glycogen to glucose to be used for energy
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Amylase
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enzyme breaks down α 1-4 glycosidic linkages in starch (ex. salivary glands/pancreas)
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Fatty Acid
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hydrocarbon chain bonded to carboxyl
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Saturated
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single bonds between carbons; solid @ room temp
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Unsaturated
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double bonds between carbons; liquid room temp
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3 types of lipids (all insoluble)
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1. fats
2. steroids
3. phospholipids
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Fats
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-3 fatty acids linked to glycerol (3 carbon molecule)
-oils when polyunsaturated
-purpose is storage (store 2x amount of carbs)
-dehydration reaction form ester linkages between glycerol and fatty acid
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Steroids
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-bulky 4 ring structure
-ex. cholesterol: OH at top ring; isoprenoid tail
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Phospholipids
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-polar/hydrophillic head (polar/charged group, phosphate, glycerol)
-nonpolar/hydrophobic tail (fatty acids or isoprenoid)
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Lipid Bilayer
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-2 sheets of lipids align; form spontaneously
-polar heads outside, nonpolar tails inside
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Permeability
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-tendency to allow certain molecules to pass through
-selective permeability: certain molecules pass through easier (small, nonpolar, non charged)
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What Affects Membrane Permeability
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1. saturated vs unsaturated: unsaturated double bonds = more space = more permeable
2. hydrocarbon tail length: longer tails, more packed membrane = less permeable
3. Cholesterol: cholesterol fills in spaces, less permeable
4. temperature: molecules have more energy = move faster = mor…
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Diffusion Equation
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Diffusion Rate = D(Area/Thickness) x conc gradient
D = diffusion constant
A inc, Diffusion inc; Thickness inc Diffusion Decrease
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DIffusion
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Movement of molecules and ions due to kinetic energy
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Concentration Gradient
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net movement from high concentration to low concentration; spontaneous
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Osmosis
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diffusion of only water when selectively permeable membrane holds back solutes
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Hypotonic
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Inside has LOWER concentration than outside, cell is hypotonic (hypertonic solution outside); cell shrinks
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Hypertonic
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Inside has HIGHER concentration than outside, cell is hypertonic (hypotonic solution outside; cell swells
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Isotonic
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Concentration inside and outside cell are equal; cell stays same size
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Freeze Fracture Electron Microscopy
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-Use scanning electron microscope
-freeze cell, fracture it, split to view inside
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Integral Membrane (Transmembrane) Proteins
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Proteins that go through both inside and outside cell
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Peripheral Membrane Proteins
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Bind to membrane without passing through it
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Detergent
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Amphipathic molecule that helps isolate proteins
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3 Ways Proteins Affect Permeability
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ion channels, carrier proteins, pumps
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ion channels
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openings in membrane allow ions to flow along concentration gradient (high to low concentration)
-Inside: net negative -Outside: net positive
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Electrochemical Gradient
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combined concentration and electrical gradient that determines ion movement
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Channel Proteins
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selective; only particular ions can pass through (ex. aquaporins)
-gated channels: open and close in response to signal
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Passive Transport
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powered by diffusion along electrochemical gradient
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Facilitated Diffusion
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passive transport of substances that would not cross a membrane readily
-through channel proteins or carrier proteins
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Carrier Proteins
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specialized membrane proteins change shape during transport process
ex. GLUT 1: changes shape of glucose to get it through hydrophobic membrane
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Active Transport
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transport against electrochemical gradient, requires energy usually in form of ATP (ATP transfers phosphate group to pump, active transport protein)
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Sodium Potassium Pump (Na/K ATP-ase)
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3 sodium out, 2 potassium in
-phosphate from ATP changes shape to release Na
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Gibbs Free Energy
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∆G = ∆H - T∆S
∆G < 0: exergonic, spontaneous, no energy needed; release energy instead
∆G > 0: endergonic, nonspontaneous, need energy
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Effects on Reaction Rates
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1. Temperature: higher temp, faster reaction
2. Concentration: higher conc, faster reaction
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BIO 112: BIOLOGY 112