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Animate matter -Is organized (structure/function specialization) -Consumes energy to build order (grow and reproduce) -Senses and responds to environment -Evolves (biological diversity)
Common structural features of bacteria -Ribosomes for protein synthesis -Nucleoid containing single circular DNA -Pili for adhesion -Flagella for locomotion -CEll envelope: either gram (+) or (-)
Component of an Animal Cell -Ribosomes -Peroxisome -Lysosomes -Transport vessicles -cytoskeleton -Golgi -Nucleous & Nucleolous -Smooth & Rough ER -Plasma Membrane -Nuclear Envelope
What percentage of a cell is dry weight? 25-30%
What percentage of the dry weight in a cell is made up of proteins? 50%
In a cell, what level of organization contains the strongest bonds? Primary (Sugars, AA, nucleotides) linked by covalent bonds at ~400 kJ/mol
Centrifugation Fc = mea = meω2r S = m(1 – vρ)/6πηrs
Universal features of living cells All cells have a nucleus or nucleoid, a plasma membrane, and cytoplasm
What is the difference between cytoplasm and cytosol? cytosol is defined as that portion of the cytoplasm that remains in the supernatant after gentle breakage of the plasma membrane and centrifugation of the resulting extract at 150,000 g for 1 hour.
What is the supernatant? concentrated solution of enzymes, RNA, monomeric subunits, metabolites & inorganic ions
How many bulk elements are essential for life? What are they? 10; H C N O P S Cl Na Ca K
What is a trace element and how any are there? element required of life only in trace amounts; 12
What is a Svedburg? The unit in which a protein (especially a ribosome) is measured
Define van der Waals interaction. A momentarily induced dipole due to weak attraction and interaction between molecules
Greatest potential energy occurs at what formation around the C-C bond in ethane? Eclipsed
Methyl R-CH3
Ethyl R-CH2CH3
PHENYL R-C6H6 (Aromatic)
Achiral molecule Rotated molecule CAN be superimposed on its mirror image
Chiral molecule Rotated molecule CANNOT be superimposed on its mirror image because all four substituents are different
Enantiomer mirror image of a molecule
Diastereomer pairs of stereoisomers that are not mirrow images
Biological complexity n!/r!(n – r)!
Define Open, Isolated & Closed Systems -Open: System and Surroundings exchange both energy and matter -Closed: only energey is exchanged -Isolated: neither energy nor matter is exchanged
Define terms for the equation EInternal = EKinetic + EPotential -System has internal energy, EInternal -EKinetic is translational, rotational, vibrational -EPotential is electronic, bonds
What is the equation of the conservation of energy? ΔEInternal = q – w where q is heat absorbed and w is work done
How are volume and pressure related? at constant pressure volume can change, allowing work of expansion: w = PΔV
What is the equation of the change in enthalpy? ΔH ≡ ΔEInternal + PΔV = q
What is enthalpy? heat content of a system
If ΔH < 0 & q < 0 is the system exothermic or endothermic? exothermic
If ΔH > 0 & q > 0 is the system exothermic or endothermic? endothermic
State the equation for change in Gibbs free energy & indicate what values signify spontaneous reactions ΔG = ΔHSystem – TΔSSystem ΔG < 0 is spontaneous
Define endergonic. A chemical reaction that consumes energy (ΔG is positive)
Define exergonic A chemical reaction that releases energy (ΔG is negative)
A strong Hydrogen [H] bond will always be what shape? Linear
How many [H] bonds does one molecule of H2O form in ice? 4 bonds; 2 giving and 2 accepting e-
How many [H] bonds does one molecule of H2O have in liquid, on average? 3.4 bonds
Define flickering cluster Liquid water molecules held together by [H] bonds that are constantly being broken and reformed every 1-20 ps
Define the hydrophobic effect forces, but not true bonds, holding nonpolar regions together; help form micelles & bilayers
List noncovalent interactions from weakest to strongest. van der Waals < hydrophobic < [H] bonds < ionic
Osmosis water movement across a semipermeable membrane driven by differences in osmotic pressure
Isotonic solutions of equal osmolarity on both sides of the membrane
Hypertonic a higher osmolarity (solute concentration) is outside the cytosol & the cell shrinks as water flows out
hypotonic lower osmolarity (solute concentration) outside the cytosol & swells as water enters in
What is the equation for pH? -log[H+]
What is the pH for 1.0 x 10-8 M HCL? What is the pOH? pH = 8 pOH = 6
What is more acidic, gastric juice or red wine? Gastric Juice (pH = 1.5) Red wine (pH = 3.7)
What is more acidic, saliva or tears? Saliva pH = 6.5 (same as milk) Tears pH = 7.2 (same as blood)
Define the Henderson-Hasselbach equation pH = pKa + log [A-]/[HA]
Define buffer region. The area = pKa (+/-)1 that is "resistant" to a change in pH from the addition of OH
What is the alpha-carbon in an amino acid? the C-2 chiral center
How can you easily recognize an L or D amino acid? Holding your hands palms up: -thumbs will be facing outward, representing amino group (given that COO- is oriented above alpha C & R is below) -if the amino group is on the left, L -if the amino group is on the right, D
Do intracellular environments promote oxidation or reduction? Reduction
Do extracellular environments promote oxidation or reduction? Oxidation
Name the only two amino acids suitable for buffering at pH = 7.0 Cys & Hist
What is the average molecular weight of Amino Acid residue corrected for occurance? 110 g/mol
Zwitterion a dipolar ion with spacially separated positive and negative charges
define isoelectric pH. pH at which the net electric charge is zero. pI = (pk1 + pK2)/2
What type of bonds hold proteins together? peptide bonds
How are peptide bonds formed? dehydration synthesis
How are peptide bonds broken? hydrolysis
How do peptide bonds compare to covalent bonds? -shorter, stronger -double bond character -resonance -no rotation -planar -trans
How are amino acids written and read? Amino to carboxyl, left to right (conventionally)
What is the pKa of an amino acid that is 6 residue groups apart? pKa ~8.0 *For all residue groups >= 4 apart, pKa will remain approximately the same (around 8.0) since the two ends are so far apart inductive effect is basically zero
when are proteins least soluble? at their pI -molecules are not attracting or repelling one another
What is the omega loop? defined structure within the tertiary structure of a PPT chain without a recurring pattern -no two are alike -not a motif
What are the important bonds of a primary struture? Peptide & disulfide bonds
What are the important bonds of a secondary struture? [H] bonds
What are the important bonds of a tertiary struture? Ionic, [H] bonds, van der Waals & hydrophobic effect
What are the important bonds of a quaternary struture? Ionic, [H] bonds, van der Waals & hydrophobic effect
What affects pKa more: the inductive effect or the electrostatic effect? electrostatic effect: stronger & operates over longer distances