BIOCHEM ExamI
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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)
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| 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 (-)
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| Component of an Animal Cell | -Ribosomes -Peroxisome -Lysosomes -Transport vessicles -cytoskeleton -Golgi -Nucleous & Nucleolous -Smooth & Rough ER -Plasma Membrane -Nuclear Envelope
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| What percentage of a cell is dry weight? | 25-30%
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| What percentage of the dry weight in a cell is made up of proteins? | 50%
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| In a cell, what level of organization contains the strongest bonds? | Primary (Sugars, AA, nucleotides) linked by covalent bonds at ~400 kJ/mol
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| Centrifugation | Fc = mea = meω2r S = m(1 – vρ)/6πηrs
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| Universal features of living cells | All cells have a nucleus or nucleoid, a plasma membrane, and cytoplasm
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| 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.
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| What is the supernatant? | concentrated solution of enzymes, RNA, monomeric subunits, metabolites & inorganic ions
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| How many bulk elements are essential for life? What are they? | 10; H C N O P S Cl Na Ca K
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| What is a trace element and how any are there? | element required of life only in trace amounts; 12
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| What is a Svedburg? | The unit in which a protein (especially a ribosome) is measured
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| Define van der Waals interaction. | A momentarily induced dipole due to weak attraction and interaction between molecules
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| Greatest potential energy occurs at what formation around the C-C bond in ethane? | Eclipsed
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| Methyl | R-CH3
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| Ethyl | R-CH2CH3
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| PHENYL | R-C6H6 (Aromatic)
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| CARBONYL ALDEHYDE | R-CO-H
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| CARBONYL KETONE | R-CO-R'
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| HYDROXYL | R-OH
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| ETHER | R-O-R'
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| ESTER | R-COO-R'
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| ANHYDRIDE | R-COOCO-R'
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| AMINO | R-NH2
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| AMIDO | R-CO-NH2
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| SULFHYDRYL | R-SH
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| DISULFIDE | R-SS-R'
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| THISESTER | R-COS-R'
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| PHOSPHORYL | R-OPOO-OH
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| Achiral molecule | Rotated molecule CAN be superimposed on its mirror image
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| Chiral molecule | Rotated molecule CANNOT be superimposed on its mirror image because all four substituents are different
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| Enantiomer | mirror image of a molecule
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| Diastereomer | pairs of stereoisomers that are not mirrow images
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| Biological complexity | n!/r!(n – r)!
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| 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
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| Define terms for the equation EInternal = EKinetic + EPotential | -System has internal energy, EInternal -EKinetic is translational, rotational, vibrational -EPotential is electronic, bonds
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| What is the equation of the conservation of energy? | ΔEInternal = q – w where q is heat absorbed and w is work done
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| How are volume and pressure related? | at constant pressure volume can change, allowing work of expansion: w = PΔV
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| What is the equation of the change in enthalpy? | ΔH ≡ ΔEInternal + PΔV = q
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| What is enthalpy? | heat content of a system
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| If ΔH < 0 & q < 0 is the system exothermic or endothermic? | exothermic
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| If ΔH > 0 & q > 0 is the system exothermic or endothermic? | endothermic
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| State the equation for change in Gibbs free energy & indicate what values signify spontaneous reactions | ΔG = ΔHSystem – TΔSSystem ΔG < 0 is spontaneous
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| Define endergonic. | A chemical reaction that consumes energy (ΔG is positive)
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| Define exergonic | A chemical reaction that releases energy (ΔG is negative)
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| A strong Hydrogen [H] bond will always be what shape? | Linear
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| How many [H] bonds does one molecule of H2O form in ice? | 4 bonds; 2 giving and 2 accepting e-
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| How many [H] bonds does one molecule of H2O have in liquid, on average? | 3.4 bonds
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| Define flickering cluster | Liquid water molecules held together by [H] bonds that are constantly being broken and reformed every 1-20 ps
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| Define the hydrophobic effect | forces, but not true bonds, holding nonpolar regions together; help form micelles & bilayers
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| List noncovalent interactions from weakest to strongest. | van der Waals < hydrophobic < [H] bonds < ionic
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| Osmosis | water movement across a semipermeable membrane driven by differences in osmotic pressure
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| Isotonic | solutions of equal osmolarity on both sides of the membrane
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| Hypertonic | a higher osmolarity (solute concentration) is outside the cytosol & the cell shrinks as water flows out
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| hypotonic | lower osmolarity (solute concentration) outside the cytosol & swells as water enters in
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| What is the equation for pH? | -log[H+]
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| What is the pH for 1.0 x 10-8 M HCL? What is the pOH? | pH = 8 pOH = 6
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| What is more acidic, gastric juice or red wine? | Gastric Juice (pH = 1.5) Red wine (pH = 3.7)
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| What is more acidic, saliva or tears? | Saliva pH = 6.5 (same as milk) Tears pH = 7.2 (same as blood)
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| Define the Henderson-Hasselbach equation | pH = pKa + log [A-]/[HA]
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| Define buffer region. | The area = pKa (+/-)1 that is "resistant" to a change in pH from the addition of OH
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| What is the alpha-carbon in an amino acid? | the C-2 chiral center
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| 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
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| Do intracellular environments promote oxidation or reduction? | Reduction
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| Do extracellular environments promote oxidation or reduction? | Oxidation
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| Name the only two amino acids suitable for buffering at pH = 7.0 | Cys & Hist
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| What is the average molecular weight of Amino Acid residue corrected for occurance? | 110 g/mol
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| Zwitterion | a dipolar ion with spacially separated positive and negative charges
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| define isoelectric pH. | pH at which the net electric charge is zero. pI = (pk1 + pK2)/2
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| What type of bonds hold proteins together? | peptide bonds
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| How are peptide bonds formed? | dehydration synthesis
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| How are peptide bonds broken? | hydrolysis
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| How do peptide bonds compare to covalent bonds? | -shorter, stronger -double bond character -resonance -no rotation -planar -trans
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| How are amino acids written and read? | Amino to carboxyl, left to right (conventionally)
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| 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
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| when are proteins least soluble? | at their pI -molecules are not attracting or repelling one another
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| 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
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| What are the important bonds of a primary struture? | Peptide & disulfide bonds
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| What are the important bonds of a secondary struture? | [H] bonds
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| What are the important bonds of a tertiary struture? | Ionic, [H] bonds, van der Waals & hydrophobic effect
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| What are the important bonds of a quaternary struture? | Ionic, [H] bonds, van der Waals & hydrophobic effect
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| What affects pKa more: the inductive effect or the electrostatic effect? | electrostatic effect: stronger & operates over longer distances
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