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BIO 112: EXAM 1
covalent bond |
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)
|
ionic bond |
complete electron transfer between cations and anions |
Solvents/Solute/Solution |
Solvents dissolve the solute |
Why water is efficient solvent? |
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 polar
|
Cohesion |
attractions between like polar molecules (hydrogen bonding) |
Adhesion |
attractions between liquid and surfaces with polar components
-ex. meniscus: adherence to glass pulls up and cohesion to other water molecules pulls down |
Surface Tension |
water molecules at surface can only bond to molecules below; stronger attractive forces resist changes to water's surface area
|
Why water is denser as a liquid than a solid |
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 |
equilibrium |
dynamic but stable state in which forward and reverse reactions occur at same rate |
Energy |
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) |
Laws of Thermodynamics |
1. Energy neither created or destroyed
2. Entropy increases in spontaneous reactions (∆S > 0)
|
Spontaneous Reactions |
reactions that happen on their own
1. entropy (randomness) increases
2. products have lower PE
3. Gibbs Free Energy decreases
|
Amino Acid |
20 different kinds of these monomers make up polymer (protein)
|
Amino Acid Structure |
1. H+ atom
2. Amino
3. Carboxylic Acid
4. R group (determines charge/polarity) |
Nonpolar Side Chains |
no charge; lack charged or electronegative molecules (have C-H) bonds; make amino acid hydrophobic; do not dissolve |
Polar Side Chains |
hydrophilic; have charged or electronegative molecules (O atom will cause polar covalent bond)
|
Charged Side chains |
negative charge: acidic (lost proton)
positive charge: basic (gained proton) |
Polymerization |
monomers link together to form polymers |
Condensation (Dehydration) Reactions |
Polymerization when newly formed bonds results in the loss of a water (H₂O) molecule
|
Hydrolysis |
Reverse of condensation reaction; adds a water to break up polymers; favors because increases entropy and spontaneous (no energy needed) |
Peptide Bond |
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
|
3 characteristics of Peptide Bonded Backbone |
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 |
Peptide/Oligopeptide |
<50 amino acids bonded together
Polypeptide: 50 or more amino acids bonded |
Primary Structure of Protein |
sequence of amino acids
|
Secondary Structure of Protein |
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 |
Tertiary Structure |
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
|
Quaternary Structure |
Similar to Tertiary Structure but multiple polypeptides
(ex. hemoglobin, macromolecular machines) |
Denaturing |
Unfolding of a protein that causes a loss of function
|
Folding |
Spontaneous due to the energy supplied by the bonds, hydrophobic interactions, van der waals; crucial to function of proteins --> flexibility
|
molecular chaperones |
facilitate folding; heat shock proteins bind to hydrophobic patches in denatured proteins to cause refolding
|
prions |
proteinaceous infectious particles; when proteins fold into infectious, disease causing agents |
Protein Functions |
1. Catalysis (enzyme)
2. Defense (antibodies)
3. Movement (actin/myosin)
4. Signalling
5. Structure
6. Transport |
Substrates |
Reactant molecules |
Active Site |
Where substrates bind and react; catalysis occurs |
Carbohydrate (Sugar) |
monomers: monosaccharides
polymers: oligosaccharides (small) polysaccharides (large)
-consist of carbonyl (C=O), several hydroxyls (OH) and hydrocarbons (C-H); reactivity and hydrophillics |
Distinguishing Carbohydrates |
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) |
Disaccharides |
2 sugars linked together |
Glycosidic Linkages |
Monosaccharides polymerize to polysaccharides; condensation reaction between 2 hydroxyls
|
Monosaccharides polymerize to polysaccharides; condensation reaction between 2 hydroxyls
|
1. Starch
2. Glycogen
3. Cellulose
4. Chitin
5. Peptidoglycan |
Starch |
-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
|
Glycogen |
-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 |
Cellulose |
-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 |
Chitin |
-cell walls of fungi, in protists and other animals
-β NAG; β 1-4 glycosidic linkages
-every other flipped; h bonds between strands |
Peptidoglycan |
-structural support in bacteria cell wall
-two types of monosaccharides linked β 1-4
-amino acids attached; peptide bonds between strands |
Carbohydrate Function |
-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)
|
Glycoprotein |
protein with oligosaccharides covalently bonded to it that act as identification |
Phosphorylase |
catalyzes hydrolysis of α 1-4 glycosidic linkages
ex. break glycogen to glucose to be used for energy |
Amylase |
enzyme breaks down α 1-4 glycosidic linkages in starch (ex. salivary glands/pancreas) |
Fatty Acid |
hydrocarbon chain bonded to carboxyl
|
Saturated |
single bonds between carbons; solid @ room temp |
Unsaturated |
double bonds between carbons; liquid room temp |
3 types of lipids (all insoluble) |
1. fats
2. steroids
3. phospholipids |
Fats |
-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
|
Steroids |
-bulky 4 ring structure
-ex. cholesterol: OH at top ring; isoprenoid tail |
Phospholipids |
-polar/hydrophillic head (polar/charged group, phosphate, glycerol)
-nonpolar/hydrophobic tail (fatty acids or isoprenoid) |
Lipid Bilayer |
-2 sheets of lipids align; form spontaneously
-polar heads outside, nonpolar tails inside |
Permeability |
-tendency to allow certain molecules to pass through
-selective permeability: certain molecules pass through easier (small, nonpolar, non charged)
|
What Affects Membrane Permeability |
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 = more permeable |
Diffusion Equation |
Diffusion Rate = D(Area/Thickness) x conc gradient
D = diffusion constant
A inc, Diffusion inc; Thickness inc Diffusion Decrease |
DIffusion |
Movement of molecules and ions due to kinetic energy |
Concentration Gradient |
net movement from high concentration to low concentration; spontaneous
|
Osmosis |
diffusion of only water when selectively permeable membrane holds back solutes
|
Hypotonic |
Inside has LOWER concentration than outside, cell is hypotonic (hypertonic solution outside); cell shrinks
|
Hypertonic |
Inside has HIGHER concentration than outside, cell is hypertonic (hypotonic solution outside; cell swells |
Isotonic |
Concentration inside and outside cell are equal; cell stays same size
|
Freeze Fracture Electron Microscopy |
-Use scanning electron microscope
-freeze cell, fracture it, split to view inside |
Integral Membrane (Transmembrane) Proteins |
Proteins that go through both inside and outside cell |
Peripheral Membrane Proteins |
Bind to membrane without passing through it |
Detergent |
Amphipathic molecule that helps isolate proteins |
3 Ways Proteins Affect Permeability |
ion channels, carrier proteins, pumps
|
ion channels |
openings in membrane allow ions to flow along concentration gradient (high to low concentration)
-Inside: net negative -Outside: net positive |
Electrochemical Gradient |
combined concentration and electrical gradient that determines ion movement
|
Channel Proteins |
selective; only particular ions can pass through (ex. aquaporins)
-gated channels: open and close in response to signal
|
Passive Transport |
powered by diffusion along electrochemical gradient |
Facilitated Diffusion |
passive transport of substances that would not cross a membrane readily
-through channel proteins or carrier proteins |
Carrier Proteins |
specialized membrane proteins change shape during transport process
ex. GLUT 1: changes shape of glucose to get it through hydrophobic membrane
|
Active Transport |
transport against electrochemical gradient, requires energy usually in form of ATP (ATP transfers phosphate group to pump, active transport protein) |
Sodium Potassium Pump (Na/K ATP-ase) |
3 sodium out, 2 potassium in
-phosphate from ATP changes shape to release Na |
Gibbs Free Energy |
∆G = ∆H - T∆S
∆G < 0: exergonic, spontaneous, no energy needed; release energy instead
∆G > 0: endergonic, nonspontaneous, need energy |
Effects on Reaction Rates |
1. Temperature: higher temp, faster reaction
2. Concentration: higher conc, faster reaction |