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BICH 410: EXAM 1
A peptide bond is a |
covalent bond |
Non-Polar Amino Acids |
Alanine
Valine
Leucine
Isoleucine
Proline
Phenylalanine
Methionine
Tryptophan |
Polar, Uncharged Amino Acids |
Asparagine
Glutamine
Tyrosine
Threonine
Serine
Cysteine
Glycine (except doesn't form H-bond with water) |
Acidic Amino Acids |
Aspartic Acid
Glutamic Acid
Both have a net negative charge at neutral pH. |
Basic Amino Acids |
Histidine
Arginine
Lysine
Net positive charge at neutral pH |
Hydrophobic Amino Acids |
GAVLIPF |
Hydrophilic Amino Acids |
RNDCEQHST |
Amphiphatic |
LMYW |
Order of Deprotonation |
Carboxyl Group
Side Chain Carboxyl group
Amine Group
Side Chain amine group |
At low pH, all ionizable groups are |
protonated (H+ on), cationic form |
At mid pH what form dominates? |
Zwitterion (no net charge) |
At high pH, ionizable groups are
|
deprotonated (H+off), anionic form |
When pH<pKa |
H+ on |
When pH>pKa |
H+ off |
Isoelectric point |
pH at which molecule carries no net charge |
C,H,O,N constitute __% of atoms in the human body |
99% |
Organic molecules contain |
carbon |
Thermodynamics |
Study of heat and energy and its effect on matter |
1st Law of Thermodynamics |
Energy is neither created nor destroyed |
2nd Law of Thermodynamics |
Total entropy of the universe is always increasing |
Enthalpy |
(H) - Reflects the number and kinds of chemical bonds or non-covalent interactions made or broken
Energy of system and its surrounding are constant E=q+w |
Entropy
|
(S) - Randomness or disorder. |
Endothermic |
ΔH>0
Heat is absorbed, new bonds formed are less stable, non-favorable |
Exothermic |
ΔH<0
Heat is evolved by system, new bonds are more stable, favorable |
Living organisms are _______ systems |
open |
Open systems take up nutrients and release waste products are never at _______ |
Equilibrium |
Steady State |
Existing with a constant flow so that the system does not change with time. Formation and degradation of individual components are balanced. |
Enzymes |
Molecules that catalyze or promote certain chemical processes by physically interacting with substrates to provide a more favorable pathway |
Endergonic |
ΔG>0
non-spontaneous |
Exergonic |
ΔG<0
Spontaneous |
Entropy (S) |
... |
When ΔS<0 the final state is ____ ordered than initial state |
More. Products are more complex and ordered. |
When ΔS>0, the final state is ____ ordered than the initial state |
Less. Products are less complex and more disordered. |
Isolated System |
No exchange of matter or energy |
Isolated System |
No exchange of matter or energy |
Close System |
Energy change may occur |
Open System |
Energy and/or matter exchange can occur |
Keq>>1 |
Favors product formation so ΔGº is large and negative |
Keq<<1 |
Favors reactant formation so ΔGº is large and positive |
When ΔGº=0 ________ occurs |
equilibrium |
The relationship between Keq and ΔGº is ______ dependent |
Temperature |
How to drive unfavorable reaction forward |
Compartmentation: increased concentrations of reactants
Coupling of reactions: favorable + unfavorable |
Hydrophilic |
Polar, ionic
interact (dissolve) in water |
Hydrophobic |
non-polar
do no interact with water |
Polar |
Unequal sharing of electrons |
Polarity is determined by the ________ of the atom |
Electronegativity. Atoms within polar molecules can carry a partial negative charge or partial positive charge. |
Electrostatic interactions between the ______ of the water molecules allow for formation of _______ bonds.
|
Dipoles;hydrogen |
Hydrogen Bond |
electrostatic interaction between a weakly acidic donor group (O-H or N-H) and a weakly basic acceptor group (O or N). Strongest H-bonds have the donor atom and the acceptor atom 180º apart. Non-linear h-bonds are weaker.
|
Entropy ______ as salt dissolves in water. |
Increases. Spontaneous reaction that is entropically driven. |
Aggregation |
Dispersion of lipids in water: entropy is decreased
Clusters of lipid molecules: entropy is increased.
Aggregation of non-polar molecules allows for greater disorder of the water molecules. |
Hydrophobic Effect |
Tendency of water to minimize its contacts with hydrophobic molecules |
Hydrophobic interactions |
Apparent affinity of non-polar substances for each other in the presence of water. Entropically driven process. Weakly temperature dependent. |
At low temperatures, mobility of water molecules are ________ |
lessened, Change in entropy is less favorable at low temp. change in free energy increases, becoming more unfavorable. |
Amphiphatic |
Contain both polar and non-polar groups. |
Aggregates are stabilized by _________ effects |
Hydrophobic |
Non-covalent interactions |
Weaker than covalent in bond strength but numerous non-covalent interactions occur making them important in overall structure and thus function. |
___________ Bonds determine the complexity of molecular interactions within and between biomolecules. |
Non-covalent |
Non-Covalent bonds are ______ and ______ |
Reversible;specific.
Size, shape, and type of interaction all must be correct for binding and/or proper folding. |
Proton Jumping |
Accounts for increased mobilities of H+ and OH- |
Keq is the ratio of |
Products to reactants |
Ionization Constant of Water (Kw)
|
Water only weakly ionizes. Kw=[H+][OH-]= 1 x 10-14 M |
pH = -log[H+] |
Concentrations of [H+] over 14 orders of magnitude, though this change is small because [H+] is very low relative to [H2O]
Soren Sorenson |
Acid is proton ______ |
donor |
Base is proton _______ |
Acceptor |
The strength of an acid is based on its _______ ______ or its ability to transfer a _____ to water |
dissociation constant; proton |
In a biological system, we classify molecules on the basis of their _______, their interaction with water |
Polarity |
At physiological pH, amino groups are _______. |
Protonated |
At physiological pH, carboxylic acid groups are in their conjugate base form or _________. |
Deprotonated. |
Charge of free carboxyl and free amino group |
pka = 3.5 (carboxyl)
pka = 8.5 (amino) |
Two amino acids condense to form a dipeptide through a __________ reaction. |
Condensation. |
Avg. Weight of an amino acid is _____ Da |
110 Da/
1 residue |
Beer-Lambert Law |
A=∈lc
absorb = extinction coeff x path length x concentration |
Protein Purification |
1) Isolate protein
2) Detection of protein
3) Assay protein activity
4) Separation Techniques
5) Quantitation |
Salting Out |
Different proteins precipitate at different salt concentrations. Use low concentration to precipitate unwanted proteins (removes protein with lower solubility). Use higher salt concentration to precipitate target protein. |
Ion exchange Chromatography |
charge |
Hydrophobic Interaction Chromatography |
Purifies non-polar molecules. Based on interactions between non-polar protein and phenyl group. As salt concentration is decreased, hydrophobic proteins elute. |
Gel Filtration Chromatography |
Separate by size or molecular weight |
Affinity Chromatography |
binding affinity |
UV Detection |
Aromatic amino acids |
Purification Assessment |
Desired protein/amount of protein = purity. If desired protein is an enzyme then amount is quantitated as "activity" and purity is know as "specific activity" |
Gel Electrophoresis |
estimate weight and polarity. SDS - detergent used to denature protein and disrupt subunit interactions.
All proteins coated with SDS have negative charge thus separate by size rather than charge. |
Isoelectric focusing |
Determine pH. |
Protease |
An enzyme that hydrolyzes peptide bonds |
Endopeptidases |
hydrolyze internal peptide bond |
Exopeptidases |
hydrolyze N-Term or C-Term |
Edman Degradation |
1) Subunit interactions depend on weak force
2) Cleavage of disulfide bonds
3) Determine AA sequence
4) End group determination
- N-Term: Dansyl Chloride, FDNB
- C-Term: Corboxypeptidases A/B
5) Cleave each chain into smaller fragments
6) Repeat Step 5
7) Sequence all peptides produced
8) Reconstruct sequence.
|
Trypsin |
Cleaves c-term side of Arg,Lys |
Chymotrypsin |
Cleaves c-term side of Phe, Trp, Tyr |
CNBr |
Cleaves c-term side of Met |
Mass Spectrometry |
Measure mass-to-charge (m/z) ratio for ions in the gas phase. <25 residues. |
Electrospray Ionization (ESI) |
used to regenerate gas-phased macromolecular ions |
Primary Structure determined by ________ bonds |
covalent |
Secondary structure determined predominately by backbone ______ |
H-bonds |
Tertiary Structure determined by ________ interactions, __ bonds, ionic interactions, van der waals, hydrophobic interactions |
side-chain; H-bonds |
Peptide Bond |
40% double bond character. Two resonance structures. uncharged, but polar. Planar because of peptide bond. |
α-helix |
3.6 residues/turn
5.4 A/ 1 turn |