Biochem exam 1

Aliphatic, nonpolar amino acids

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine

Aromatic amino acids

phenylalanine, tyrosine, tryptophan

Polar, uncharged amino acids

serine, threonine, cysteine, asparagine, glutamine

Positivly charged amino acids

Lysine, Histidine, Arginine

Negatively charged amino acids

aspartate, glutamate

Sulfur containing amino acids

cysteine and methionine

Side chains with alcohols amino acids

Serine and Threonine

Glycine

Gly, G

Alanine

Ala, A

Proline

Pro, P

Valine

Val, V

Leucine

Leu, L

Isoleucine

Ile, I

Methionine

Met, M

Phenylalanine

Phe, F

Tyrosine

Tyr, Y

Tryptophan

Trp, W

Threonine

Thr, T

Serine

Ser, S

Cysteine

Cys, C

Asparagine

Asn, N

Glutamine

Gln, Q

Lysine

Lys, K

Histidine

His, H

Arginine

Arg, R

Aspartate

Asp, D

Glutamate

Glu, E

Glycine

Alanine

Proline

Valine

Leucine

Isoleucine

Methionine

Phenylalanine

Tyrosine

Tryptophan

Threonine

Serine

Cysteine

Asparagine

Glutamine

Lysine

Histidine

Arginine

Aspartate

Glutamate

Amino acids with pkR

Tyrosine, Cysteine, Lysine, Histidine, Arginine, Asparate, Glutamate, sometimes Serine

Oxygen atoms are more \_____ than hydrogen atoms because an oxygen nucleus attracts electrons more strongly

Electronegative

The angled arrangement of the polar bonds of water creates a permanent \____

Dipole

A hydrogen bond is most \____when the hydrogen atom and the two electronegative atoms associated with

Stable

The ability of water molecules in ice to form four hydrogen bonds and the strength of these hydrogen bonds give ice an unusually \___ melting point because a large amount of energy, in the form of heat, is required to disrupt the hydrogen-bonded lattice of ice.

High

Water molecules in ice form an open \__ lattice in which every water molecule is hydrogen-bonded to four others.

Hexagonal

Why is water a good solvent?

1. Polar

2. Low intrinsic viscosity

3. Small compared to other solvents

The ions of crystalline sodium chloride are held together by \____ forces. Water \___ the interactions between the positive and negative ions and the crystal dissolves.

Electrostatic, weakens

The shell of water molecules that surrounds each ion is called a \____ \_____ and it usually contains several layers of solvent molecules.

Solvation Sphere

Other groups that confer water solubility include \___ \_____ and \______ groups. Molecules containing such groups disperse among water molecules with their polar groups forming hydrogen bonds with water.

Amino, Hydroxyl, Carbonyl

An \_____ in the number of polar groups in an organic molecule increases its solubility in water.

increase

Hydrocarbons and other nonpolar substances have very low \____ in water because water molecules tend to interact with other water molecules rather than with nonpolar molecules.

Solubility

Nonpolar molecules are said to be \___

Hydrophobic

Detergents, sometimes called \_____, are molecules that are both hydrophilic and hydrophobic.

Surfactants

Chaotropes \___ the solubility of nonpolar compounds in water by disordering the water molecules

Enhance

Charge-charge interactions, hydrogen bonds, and van der Waals forces are variations of a more general type of force called \______ \_______.

Electrostatic interactions

pH < pKa

environment is considered acidic and the compound will exist predominately in its protonated form.

pH \> pKa

considered basic and the compound will exist predominately in its deprotonated form

pH \= pKa

\[HA] \= [A-]

Henderson-Hasselbalch equation

pH \= pKa + log [A-]/[HA]

Hydrolysis is \_____ favored but \_____ slow,

thermodynamically, kinetically

Properties of water

• High boiling point, melting point, heat of vaporization and surfacetension
• Maximum density is in the liquid state
• Negative volume of melting (ice occupies more space than liquidwater)
• High dielectric constant,e
• High conductivity (only when salts are dissolved)

Liquid water is more \___ than ice

packed

Entropy \___ as NaCl dissolves in

increases

Water molecules are \__ around thenonpolar solute (unfavorableprocess)

Ordered

Amphipathic molecules form \___ inwater

Micelles

Bicarbonate (H 2 CO 3 ) is the most importantbuffer in human \___

Blood

Gaseous CO2 is in \___ with dissolved CO2 in the lungs

equilibrium

Proteins are the \__ most abundant material in cells

second

Amino acids are \___ (except 1)

Chiral

L and D configuration amino acids

Hydropathy defines hydrophobicity or hydrophilicity

Measures the free-energy associated with transfer of amino acid from the interior of a lipid bilayer to water

Amino acids are \__ acids

weak polyprotic

Isoelectric point

Point at which a compound is electrically neutral.

Methods for determining PI

• Identify all the ionizable protons
• Write down the pKa s from smallest to largest
• Determine the charge of each corresponding species
• Average the pKa s on either sideof the 0 charge molecule

• Protonate everything that can be protonated; write down the charge
• Start removing protons until charge \= -1
• Take the average of the last two pKa

Protein sequences specified by genes, \____ from N- to C-terminus

synthesized

phi and psi angles

only bond angles that can rotate
-not all torsion angles are possible due to sterics

Proteins Belonging to the Same Class Have \___ Amino Acid Compositions

Similar

Orthologs

proteins from different species with similar sequence(derived from a common ancestral gene during evolution)

Paralogs

proteins within a single species with similar sequence(arose through gene duplication)

Family

proteins with similar sequence and function (ex: globins)

Homologs

general term for members of a protein family

Determination of the Primary Structure of Proteins

Determine the N-Terminal Residue(s)
-Chromatography is used to separate sample;Known elution profiles ofthe DNP derivatives allow for ID of amino acid conjugated to ring

Edman Degradation
-N-terminal residue labeled and cleaved from peptide without disrupting other peptide bonds

Protein Mass and Sequence Can Be Determined by Mass Spectrometry

• Mass spectrometry separates particles by mass-to-charge ratio (m/z)
• Fragments of proteins can be generated invarious ways
• MS separates these fragments
• Mass determined with high precision

Electrospray Mass Spectrometry (ESI)

Uses electrical energy to transferions from solution to gas phase

Matrix-Assisted Laser Desorption Ionization (MALDI)

• Protein mixed with a chemical matrix; solvent evaporated

• Laser energy à matrixà protein à desorption

• Proteins sent to detector

Tryptic Fingerprint To Determine Sequence

• Cut protein band from gel, elute in water/buffer

• Digest with protease, such as trypsin

• Take mass spec (above)

• Each peak is further fragmented to determine its sequence ("tandem MS" or MS/MS)

Separation and Purification of Proteins

• Chromatography

• Dialysis

• Electrophoresis

Ion Exchange Chromatography:

Separation Based on Charge

Gel Filtration (Size Exclusion)

Chromatography: Separation Based on Size

Affinity Chromatography:

Separation Based on Specific Ligand Interactions

Dialysis is used to remove small \___ molecules

Macro

PAGE

1. Non-reducing(native)

2. Reducing(SDS-PAGE)