BIOCHEM (USE THIS EXAM 1)

Why is water a good solvent for ions?

Water forms ion-dipole interactions and has a high dielectric constant that shields attractions between ions.

What causes water’s high boiling point and heat of vaporization?

Many short-lived hydrogen bonds between water molecules.

Hydrogen-bond donor

A group with H attached to an electronegative atom, usually O-H or N-H.

Hydrogen-bond acceptor

An atom with an available lone pair, commonly O or N.

What geometry makes a hydrogen bond stronger?

A nearly linear donor-H-acceptor arrangement.

Amphipathic molecule

A molecule with both polar and nonpolar regions.

Hydrophobic effect driving force

Release of ordered cage-like water around nonpolar groups, which increases entropy.

Why do long-chain fatty acids form micelles?

The hydrophobic effect releases ordered water by sequestering nonpolar tails; tail-to-tail bonding is not the main driving force.

O2 and CO2 polarity and water solubility

Both are nonpolar overall and poorly soluble in water; CO2 has polar bonds but no net molecular dipole.

Quiz molecule classifications

Glucose is polar; fats and waxes are nonpolar; free phenylalanine is amphipathic.

Colligative properties depend on what?

The number of dissolved particles, not their chemical identity.

Examples of colligative properties

Vapor-pressure lowering, boiling-point elevation, freezing-point depression, and osmotic pressure.

Osmotic-pressure equation

Pi = RT times the sum of i times c; i is particles per formula unit and c is concentration.

Which ideal 1 M solution has the greatest osmotic pressure: NaCl, CaCl2, glucose, or sucrose?

CaCl2, because it dissociates into about three particles per formula unit.

What form does H+ take in water?

Hydronium, H3O+.

Kw at ordinary biochemical conditions

[H+][OH-] = 1 x 10^-14.

pH equation

pH = -log[H+].

Proton concentration from pH

[H+] = 10^(-pH).

Relationship between pH and pOH

pH + pOH = 14.

What does a one-unit pH change mean?

A tenfold change in proton concentration.

If pH is below pKa, which form dominates?

The protonated acid form.

If pH is above pKa, which form dominates?

The deprotonated base form.

What happens when pH equals pKa?

Acid and conjugate base concentrations are equal.

Buffering range

Approximately pKa plus or minus 1 pH unit.

Henderson-Hasselbalch equation

pH = pKa + log([base]/[acid]).

What does added OH- do to an acetate buffer?

It reacts mainly with acetic acid and converts it to acetate.

Common biological buffer systems

Phosphate, bicarbonate, and amine/ammonium systems; fluoride is not a common biological buffer.

At equal concentration, how does pKa predict acid pH?

The lower-pKa acid is stronger and generally produces the lower pH; formic acid is stronger than acetic acid.

TI-30XA: enter 6.3 x 10^-7

Press 6.3, EE, 7, then +/-.

TI-30XA: find pH after entering [H+]

Press LOG, then +/- to apply the negative sign.

TI-30XA: calculate 10^-6.2

Press 6.2, +/-, 2nd, LOG.

pH 6.2 corresponds to what [H+]?

6.31 x 10^-7 M, which is 0.631 micromolar.

[OH-] = 4.3 x 10^-10 M corresponds to what pH?

pOH = 9.37, so pH = 4.63.

General alpha-amino-acid structure

The alpha carbon is attached to NH3+, COO-, H, and an R group.

Where is the R group attached?

The alpha carbon.

Why is glycine achiral?

Its R group is H, so the alpha carbon has two hydrogens.

What does L mean for protein amino acids?

The alpha-carbon configuration is compared with L-glyceraldehyde.

Zwitterion

A molecule with positive and negative charges but no net charge.

Isoelectric point pI

The pH at which a molecule has no net charge.

Charge below pI

More positive.

Charge above pI

More negative.

How is pI calculated?

Average the two pKa values surrounding the neutral charge state.

Aspartate pI using 1.88 and 3.65

(1.88 + 3.65)/2 = 2.77.

A pKa near 9.5 in an amino acid usually describes what?

Deprotonation of the positively charged amino group NH3+ to NH2.

Aromatic amino acids

Phenylalanine F, tyrosine Y, and tryptophan W.

Main amino acids responsible for protein UV absorbance

Tryptophan and tyrosine, with a smaller contribution from phenylalanine.

Cystine

Two cysteine residues linked by an oxidized disulfide bond.

Five amino-acid groups used in lecture

Nonpolar, aromatic, polar, negative, and positive.

Nonpolar amino acids

Gly G, Ala A, Val V, Leu L, Ile I, Met M, and Pro P.

Polar uncharged amino acids

Ser S, Thr T, Cys C, Asn N, and Gln Q.

Negatively charged amino acids

Asp D and Glu E.

Positively charged amino acids

Lys K, Arg R, and His H.

Glycine codes and side chain

Gly, G; side chain H.

Alanine codes and side chain

Ala, A; side chain CH3.

Valine codes and side chain

Val, V; side chain CH(CH3)2.

Leucine codes and side chain

Leu, L; side chain CH2-CH(CH3)2.

Isoleucine codes and side chain

Ile, I; side chain CH(CH3)-CH2-CH3.

Methionine codes and side chain

Met, M; side chain CH2-CH2-S-CH3.

Proline codes and key feature

Pro, P; its side chain forms a ring with the backbone nitrogen.

Phenylalanine codes and key feature

Phe, F; hydrophobic aromatic phenyl side chain.

Tyrosine codes and key feature

Tyr, Y; aromatic phenol side chain.

Tryptophan codes and key feature

Trp, W; aromatic indole side chain.

Serine codes and side chain

Ser, S; CH2-OH.

Threonine codes and side chain

Thr, T; CH(OH)-CH3.

Cysteine codes and side chain

Cys, C; CH2-SH.

Asparagine codes and side chain

Asn, N; CH2-CONH2.

Glutamine codes and side chain

Gln, Q; CH2-CH2-CONH2.

Aspartate codes and side chain

Asp, D; CH2-COO-.

Glutamate codes and side chain

Glu, E; CH2-CH2-COO-.

Lysine codes and side chain

Lys, K; (CH2)4-NH3+.

Arginine codes and side chain

Arg, R; guanidinium side chain.

Histidine codes and side chain

His, H; imidazole side chain.

Peptide-bond formation

A condensation reaction joins a carboxyl group to an amino group and releases water.

Peptide-bond counting rule

A linear peptide with n residues has n - 1 peptide bonds; AEGAI has 5 residues and 4 peptide bonds.

Peptide sequence direction

N-terminus to C-terminus.

Why is the peptide bond rigid?

Resonance gives the C-N bond partial double-bond character and planar geometry.

Simplest way to obtain protein sequence

Deduce it from the gene sequence when genomic information is available.

Edman degradation

Sequentially identifies residues from the N-terminus.

FDNB identifies what?

The N-terminal amino acid.

MS/MS peptide analysis

Fragments a selected peptide and uses mass differences to determine sequence.

Trypsin cleavage rule

Cuts after Lys K or Arg R.

Chymotrypsin cleavage rule

Cuts after Phe F, Trp W, or Tyr Y.

V8 protease cleavage rule

Cuts after Asp D or Glu E.

Cyanogen bromide cleavage rule

Cuts after Met M.

Anion-exchange chromatography binds what?

Negatively charged peptides or proteins.

When should an anion exchanger be used relative to pI?

At a pH above the peptide or protein pI.

Size-exclusion chromatography elution order

Largest proteins elute first because they enter fewer pores; smaller proteins elute later.

Which elutes second: IgG 145 kDa, albumin 68.5 kDa, ribonuclease A 13.7 kDa, or cytochrome c 13 kDa?

Serum albumin; IgG elutes first and albumin is the second largest.

Four levels of protein structure

Primary, secondary, tertiary, and quaternary.

Primary protein structure

Amino-acid sequence.

Secondary protein structure

Stable local backbone arrangements such as alpha helices, beta strands, and beta turns.

Tertiary protein structure

The complete three-dimensional shape of one polypeptide.

Quaternary protein structure

The arrangement of multiple polypeptide subunits.

Phi rotation

Rotation around the N-C-alpha bond.

Psi rotation

Rotation around the C-alpha-carbonyl C bond.

Alpha helix dimensions

3.6 residues per turn and 5.4 angstroms per turn, or 1.5 angstroms per residue.

How many residues make a 27 angstrom alpha helix?

27/1.5 = 18 residues.

Beta strand dimensions

2 residues per turn; about 7 angstroms per turn antiparallel and 6.5 angstroms parallel.

Length of a 36-residue antiparallel beta strand

18 turns x 7 angstroms = 126 angstroms.

Beta-turn structure

A 180-degree turn in four residues with an H bond from residue 1 carbonyl to residue 4 amide.