BIOCHEM chapter 1-4

Stereochemistry of chiral α-carbon in amino acids

L-configuration

All chiral amino acids have which configuration?

S-configuration — except cysteine, which is R

Aspartic acid

Polar amino acid. Negatively charged. Acidic. [Asp, D]

Lysine

Polar amino acid. Positively charged. Basic. [Lys, K

Arginine

Polar amino acid. Positively charged. Basic. [Arg, R]

Glutamic acid

Polar amino acid. Negatively charged. Acidic. [Glu, E]

Cysteine

Polar amino acid. Uncharged. [Cys, C]

Threonine

Polar amino acid. Uncharged. [Thr, T]

Tyrosine

Polar amino acid. Uncharged. [Tyr, Y]

Asparagine

Polar amino acid. Uncharged. [Asn, N]

Glutamine

Polar amino acid. Uncharged. [Gln, Q]

Serine

Polar amino acid. Uncharged. [Ser, S]

Glycine

Nonpolar amino acid. [Gly, G]

Tryptophan

Nonpolar amino acid. [Trp, W]

Proline

Nonpolar amino acid. [Pro, P]

Methionine

Nonpolar amino acid. [Met, M]

Alanine

Nonpolar amino acid. [Ala, A]

Phenylalanine

Nonpolar amino acid. [Phe, F]

Isoleucine

Nonpolar amino acid. [Ile, I]

Leucine

Nonpolar amino acid. [Leu, L]

Valine

Nonpolar amino acid. [Val, V]

Histidine

Polar amino acid. Positively charged. Basic. [His, H]

Which amino acid is NOT chiral?

Glycine (no chiral center)

Non-polar amino acids

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

Amino acids with aromatic side chains

Tryptophan, Phenylalanine, Tyrosine

Polar (uncharged) amino acids

Serine, Threonine, Asparagine, Glutamine, Cysteine

Negatively charged amino acids

Aspartic acid, Glutamic acid

Positively charged amino acids

Arginine, Lysine, Histidine

pKa

The pH at which [HA] = [A⁻]; exactly half the molecule is deprotonated

Isoelectric point (pI)

The pH at which an amino acid has no net charge; average of two flanking pKa values

pI formula for neutral amino acids

(pKa1 + pKa2) / 2 — using COOH and NH₂

pI formula for basic amino acids

(pKa2 + pKa3) / 2 — using NH₂ and R group

pI formula for acidic amino acids

(pKa1 + pKa3) / 2 — using COOH and R group

How are peptide bonds formed?

Dehydration synthesis — releases H₂O

How are peptide bonds broken?

Hydrolysis — addition of H₂O

Primary protein structure

Linear sequence of amino acids

Secondary protein structure

α-helix and β-pleated sheets; proline disrupts these structures

Tertiary protein structure

3D shape; stabilized by hydrophobic interactions and disulfide bonds

Disulfide bond

Bond between two cysteine residues; the resulting molecule is called cystine

Quaternary protein structure

Assembly of multiple subunits

Conjugated protein

Protein with a covalently attached non-protein molecule (prosthetic group — e.g., vitamin, ion, lipid)

Denaturation

Loss of 3D protein structure caused by heat or high solute concentration

What do enzymes do?

Biological catalysts — increase reaction rate without changing ΔG or ΔH

Oxidoreductase

Catalyzes oxidation-reduction reactions (e.g., dehydrogenase, reductase)

Transferase

Transfers functional groups between molecules (e.g., kinase transfers phosphate from ATP)

Hydrolase

Cleaves bonds using water

Lyase

Cleaves bonds without water

Isomerase

Catalyzes rearrangement of bonds to form isomers

Ligase

Catalyzes joining of two molecules

Lock and Key model

Enzyme and substrate are a perfect, rigid match

Induced fit model

Enzyme changes shape to match the substrate upon binding

Cofactor vs. coenzyme

Cofactor = metal cation; Coenzyme = organic molecule

Enzyme saturation

As [S] increases, reaction rate increases until Vmax is reached, then plateaus

Michaelis-Menten equation

Vo = Vmax[S] / (Km + [S])

Cooperative coefficient > 1

Positive cooperative binding

Cooperative coefficient < 1

Negative cooperative binding

Cooperative coefficient = 1

No cooperative binding

Effect of temperature on enzyme activity (in vivo)

Activity increases with temperature; doubles every 10°C; optimal temp is 37°C

Effect of salinity on enzyme activity (in vitro)

Changes in salinity can alter enzyme action

Structural proteins (examples)

Collagen (strength & flexibility), Elastin (strength & recoil), Keratin (cell integrity), Actin (polar)

Motor proteins

Use ATPase activity for movement; examples: Myosin, Kinesin, Dynein

Kinesin direction

Moves vesicles toward the positive end (e.g., delivering neurotransmitters)

Dynein direction

Moves vesicles toward the negative end (e.g., waste/recycling)

Cell adhesion molecules

Cadherins (calcium-dependent), Integrins (link to extracellular matrix), Selectins (bind carbohydrates on immune cells)

Antibody functions

Neutralize antigens; mark pathogens for destruction; agglutinate pathogens for phagocytosis

Ungated ion channels

Always open

Voltage-gated ion channels

Open in response to changes in membrane potential

Ligand-gated ion channels

Open when a hormone or neurotransmitter binds

G protein-coupled receptor mechanism

Ligand binds → GDP replaced by GTP on Gα → Gα dissociates and activates adenylate cyclase or phospholipase C → GTP hydrolyzed back to GDP → Gα rejoins Gβγ

Homogenization

Crushing/blending tissue into a uniform mixture

Centrifugation

Uses speed to isolate proteins from smaller particles

Native PAGE

Separates proteins by mass-to-charge ratio; hard to compare across proteins

SDS-PAGE

Denatures proteins and masks native charge; separates by size only for accurate comparison

Isoelectric focusing

Separates proteins by pI; protein migrates until pH equals its pI

Column chromatography

Polar stationary phase + nonpolar mobile phase separates by polarity

Ion-exchange chromatography

Charged column + salt gradient separates proteins by charge

Size-exclusion chromatography

Porous beads — large proteins pass around beads (fast); small proteins enter beads (slow)

Affinity chromatography

Beads coated with a specific receptor or antibody that binds the target protein

Bradford protein assay

Most common protein concentration assay; dye shifts from brown-green to blue

Edman degradation

Sequential method for determining amino acid sequence

X-ray crystallography

Used to determine 3D protein structure

Aldose

A sugar whose most oxidized group is an aldehyde

Ketose

A sugar whose most oxidized group is a ketone

D-sugar

The highest-numbered chiral carbon has its -OH group on the right

L-sugar

The highest-numbered chiral carbon has its -OH group on the left

Enantiomers (in sugars)

D- and L- forms of the same sugar — mirror images of each other

Diastereomers

Sugars that differ at one or more — but not all — chiral carbons

Epimers

Diastereomers that differ at exactly ONE chiral carbon

Anomers

Epimers that differ specifically at the anomeric carbon (α vs β forms)

Anomeric carbon

The new chiral center created when a sugar undergoes ring closure

α anomer

OH group at the anomeric carbon is axial (pointing down); trans configuration

β anomer

OH group at the anomeric carbon is equatorial (pointing up); cis configuration

Mutarotation

The interconversion of a cyclic sugar between its α and β anomeric forms

Which anomer is favored?

β anomer is favored (equatorial position is more stable)

Monosaccharide

A single carbohydrate unit; can undergo oxidation/reduction, esterification, and glycoside formation

Oxidation of aldoses

Aldoses can be oxidized to aldonic acids

Reduction of aldoses

Aldoses can be reduced to alditols

Benedict's reagent

Tests for a free aldehyde group in aldoses; a positive result is a red precipitate

Tollens' reagent

Reduced by aldehydes to produce a silvery mirror — indicates aldehyde presence