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71 Cards in this Set

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  • Back
What is the molecular hierarchy of the cell
cells
organelles
supramolecular complexes
macromolecules= biopolymers
monomers
metabolites
inorganic precursors
What is compartmentalization?
What does it do?
Protects from adverse conditions. Prevents diffusion (loss of cell compounds). Can maintain or change to a specific pH.
Standard features of a prokaryote.
Nucleoid (contains DNA), plasma membrane (inhibits diffusion), peptidoglycan cell wall (strong mechanical strenth).
Optional features of a prokaryote.
Outer membrane/periplasmic space (gram negative, large pores), flagellum (simple filament, spins around like a motor), mesosome (invagination of pm which an serve as a site for DNA replication, metabolic pathways).
Standard features of eukaryote.
Nucleaus (DNA storage):
*double membrane
*nuclear pores: decisions for passage in and out
*nucleolus: ribosomal RNA synthesis/processing
Plasma Membrane
Endoplasmic reticulum
*RER: ribosomes, protein synthesis
*SER: phospholipid synthesis
Golgi Apparatus: packaging center
Mitochondria: *power plant of cell (ATP production)
*Oxidation center: breakdown CHO, Lipids, proteins
Peroxisomes: uses O2 to oxidize problem molecules
Cytoskeleton: give structure, provide roadways
Optional features of eukaryote.
Chloroplasts: production of Oxygen, fixing CO2 to sugars
Cilia/Flagella: bending machine, sensory organ
K eq (equilibrium constant)
[H+][OH-]/[H2O]
[H+][OH-]= 1.O X 10 -14
what is pH
convenient way to designate [H+]. pH= log 1/[H+] or
-log [H+].
Logarithmic measure of [H+].
What do strong acids and bases do? Weak acids and bases?
Strong completely dissociates in water.
Weak only partially dissociates in water.
What is a buffer and what does it do.
It is a weak acid and its conjugate base. It permits solution to resist change in pH when H+ ions or OH- ions are added to the system.
Dissociation constant Ka

pKa
[H+][A-]/[HA]

-log Ka
What is the Henderson-Hasselbalch equation?
pH=pKa-log [HA]/[A-]
What is the H-H equation used for?
It is used to understand and prepare buffers.
What are the restrictions on buffers?
Buffers stabilize the pH of a solution when and only when the pH of the solution is fairly close to pKa of that buffer (+/- 1 unit from pH)
Why does the cell care about pH?
Cellular machinery requires a specific range of pH to carry out funtions.
Typical bonding behavior of
Hydrogen, Carbon, Nitrogen, Oxygen, Phosphorus, and Sulfur.
H: loses only electron to form a proton (H+), shares 1 e- for covalent bonds, participates in hydrogen bonding
C: Tends to share 4 e-'s with combinations of elements listed here
N: Tends to share 3 e-'s with combos of H and C, sometimes bonds an additional C or H+ (carries positive charge)
O: electron loving, strong electronegativity, tends to share 2 e-'s, often forms poar or charged funct. groups
P: bonds primarily with O2
S: Bonds primarily w/ C, H, O
Covalent bonds are
formed by the sharing of e- between 2 atoms
very strong
Electrostatic bonds occur
between oppositely charged atoms
Hydrogen bonds:
two electronegative atoms share a hydrogen
Most common, N and O, Carbon never H-bonds
hydrogen donor

Hydrogen acceptor
atom to which H is most closely associated
Atom to which H is less closely associate
Van der Waals attractions occur
when two atoms are w/in 3-4 A there will be a weak bonding which dissipates quickly if the two atoms move apart
also produce very high repulsive forces if two atoms get too close
Though H-bonds and Van der Waals attractions are weak they
help and play critical roles in stabilizing and defining 3-d structures of protiens, nucleic acids, lipids
Bond strenth
covalent > ionic, hydrogen > Van der Waals
Energy conversions
1 J (KJ)= .239 cal (Kcal)
1 cal (Kcal)= 4.184 J (KJ)
What does it mean that water is polar
The hydrogen carries a partial positive charge and the Oxygen carries a partial negative charge (wants the e-'s more)
Why is the H2O molecule linear. The geometry is tetrahedral like.
Oxygen has 2 pairs of unshared e-'s that approximate a tetrahedron
Why is H2O highly cohesive?
Each molecule is polar
Bond geometry is tetrahedral
Extensive H-bonding in solid or liquid
Each hydrogen atom in ice is h-bonded to

each hydrogen atom in water is h-bonded to
4.0 H2O molecules


3.4 H2O molecules
Why isn't H20 a thick viscous syrup?
The half life of h-bonds change rapidly (10 -9 seconds)
Why are the melting points of other molecules so much lower that H2O?
They do not have h-bonding.
How does water drive hydrophobic interactions?

These interactions are the driving force behind:
H2O tends to exclude nonpolar, noncharged molecules.
* the folding of proteins, DNA, RNA, lipid bilayers
*the formation of membranes
*the solubilization of grease/oil/lipids by soaps.
Describe hydrophobic interaction
H2O forms a stable cage around the hydrophobic tail which decreases entropy (more order). The caged water stays in place longer than 10 -9 seconds. Lipid molecules become clustered so only lipid portions at the edge of the cluster force the ordering of water. Entropy is increased. Micelles, all hydrophobic groups are sequestered from water, ordered shell of h2o molecules is minimized, entropy increases.
How does a soap bubble work?
The liquid is a two phase system where a layer of H2O solvates the polar head of the soap
molecules while the hydrophobic tails of the soap molecules stick out into the air layer.
Who discovered that urea could be synthesized from heating ammonium cyanate?
Freidreick Wolher in 1828.
Marked the end of the vital force theory (organic compounds could only be synthesized within a living organism or w/ organism extract.
Tetrahedral geometry
four single bonds
free rotation
trigonlal planar
two single bonds and one double bond
no rotation
linear
onle triple bond and one single bond
no rotation
Hydrocarbons
only carbon and hydrogen
-saturated: all C atoms are single bonded
-unsaturated: at least one double (or triple) bond
-polyunsaturated: two or more double (triple) bonds
Describe nucleophilic acyl substition
the carbon atome of the carbonyl group has a net partial positive charge while the oxygen has a net partial negative charg. the partially positive carbonyl carbon is very susceptible to nucleophilic attack by bases (unshared electron pairs)
What are proteins?
Biological macromolecules; linear arrays of amino acids
Amino acids contain
at least one of the following
-amine/amino group
-acid
What is a zwitterion?
When groups each carry a charge but balance each out to make a neutral molecule
(ex. glycine)
How do the amino acids behave?
The amino group is charged/protonated at neutral and acidic pH, the carboxylate group is deprtonated at neutral and basic pH.
What are the pKa's of the carboxylate and amino groups?
Carboxylate: 2-3
Amino: 9-10
pH < 2

3 < pH < 9

pH > 10
NH3+, COOH

NH3+, COO-

NH2, COO-
For every chiral carbon (4 different groups bound to a single carbon) what can there be?
Two different mirror image isoforms, L&D isomers. Only the L form of amino acids occur in proteins.
What are peptide bonds and how are they formed?
What is it an example of?
a specific class of amide bonds which are formed when the alpha carboxyl group of one aa condenses with the alpha amine of a second aa. It is and example of nucleophilic acyl substitution and results in the loss of H2O.
The forward direction of peptide bond formation is...
thermodynamically unfavorable and requires energy input.
What is the reverse reaction of peptide bond formation?
Hydrolysis, occurs when H2O is consumed while breaking a single bond; it is energy releasing.
What did Linus Pauling and Robert Corey discover in the late 1930's?
The peptide unit is rigid and planar, it did no freely roate as one would expect from single bond.
Why does the C-N bond have partial double bond character?
Resonance, the bond is 1.32 A away which is halfway between typical C-N bonds (1.49) and C=N double bonds (1.27).
What is amino acid analysis?
Complete hydrolysisof polypeptides/proteins. The individual aa are derivatized with phenylisothiocyanate so each aa can be identified.
Reveals what aa and in what ratio. Does not reveal size or primary aa sequence.
mass spectrometry
measures mass precisely and accurately to < 1.0 da
fast and sensitive, but can require fairly pure protein and equipment and technical expertise.
Electrophoresis
separates proteins and measures apporximate size.
fast, cheap, easy, show purity, but not precise for Molecular weight
Edman degradation:
uses phenylisothiocyanate to remove one aa from NH2 terminus and form a PTH-aa. sequences entire aa, once amino terminal identified, the next one can be and so on.
CNBr:
cleaves specifically on the C-terminal side of Methionine (Met M).
Trypsin:
cleaves specifically on the C-terminal side of most basic amino acids, Lysine (Lys K)and arginine (Arg R)
Chymotrypsin:
cleaves specifically on the C-terminal side of aromatic amino acids; phenylalanine (Phe, F), Tyrosin (Tyr T), Tryptophan (Trp W)
Elastase:
cleaves specifically on the C-terminal side of smallest amino acids.
Brief: Alanine (Ala A), Glycine (Gly G)
Long term: Serine (Ser S), Cysteine (Cys C)
What does electrophoresis do?
Separate molecules based on size and charge. charge particles feel a force when placed in electric field.
What is PAGE and why is it most commonly used?
polyacrylamide gel elctrophoresis. the gel impedes the movement of larger molecules, producing better separation between polypeptids of varying size.
Native PAGE
no reductants or denaturants, not common or trivial, proteins retain 3-d structure, multimeric protein complexes stay together
Non-reducing gels
protein is denatured (unfolded) with either 8-10 M urea or 6 M guanidine HCl. protein is not reduced
what happens to protein with SDS PAGE
protein is reduced and denatured. most common for routine and analytical analysis of polypeptide composition.
What is the full name of SDS?
sodium dodecyl sulfate
Why do we use SDS
It is an anionic (-) detergent and binds to the polypeptide 1 SDS/2 aminon acid. it unfolds the protein and generates consistant charge to mass ratio for all proteisn so separation is based on size.
What does beta-mercaptoethanol do?
Reduces (cleaves) disulfide bonds.
What are the two most common stains to visualize the separated amino acids.
Coomassie blue
silver stain
Isoelectric focusing:
occurs when a protein is electrophoresed in a gel that contains a pH gradient (generated by a fairly complex mixture of buffer molecules call ampholytes). It moves through the field until it reaches its isolectric point. at that point the net charge on the portein is 0.00.
Isoelectric point (pI)
the pH at which the net charge of the protein is zero.
2 dimensional gel electrophoreses comebines...
isoelectric focusing and SDS PAGE. separates by pH gradient and size.