Biochemistry Key Concepts: Carbohydrates, Lipids, Nucleic Acids, and Enzyme Regulation

Carbohydrate functions

Fuel source, structural material, and cell surface properties

Aldose vs Ketose

Aldose has an aldehyde group; Ketose has a ketone group

Sugar classification by carbon number

Triose (3C), Tetrose (4C), Pentose (5C), Hexose (6C), Heptose (7C)

Common glycosidic linkage in glycogen/amylose

α(1→4) glycosidic linkage

Anomer definition

Sugars differing at the anomeric carbon (C1)

α vs β anomers

α = OH below (axial); β = OH above (equatorial)

L vs D configuration (Fischer projection)

OH on right = D; OH on left = L

Epimers definition

Sugars that differ at one chiral center (e.g., glucose vs galactose)

Reducing vs Nonreducing sugar

Free OH on anomeric carbon = reducing; no free OH (e.g., OCH₃) = nonreducing

Pyranose vs Furanose

Pyranose = 6-membered ring; Furanose = 5-membered ring

Unsaturated fatty acids

Contain one or more double bonds (usually cis)

Arachidonic acid

20:4(Δ5,8,11,14)

Saturated fatty acids to know

Myristic (14:0), Palmitic (16:0), Stearic (18:0)

Synthetic fatty acid configuration

Trans at double bonds

Triacylglycerol structure

Glycerol + 3 fatty acids

Phospholipid vs Sphingolipid

Phospholipid: glycerol + 2 FA + phosphate; Sphingolipid: sphingosine backbone + 1 FA

Most common phospholipid & sphingolipid

Phosphatidylcholine and Sphingomyelin

3 lipids linked to proteins

Palmitic acid, Myristic acid, Cholesterol

Cholesterol and membrane fluidity

Broadens Tm and stabilizes fluidity

Glycosphingolipid composition

Ceramide + sugar residues

Cerebroside vs Ganglioside

Cerebroside = 1 sugar; Ganglioside = 3+ sugars

Terpene rule

# of carbons ÷ 5 = # of isoprene units

Purines vs Pyrimidines

Purines: A, G; Pyrimidines: C, U, T ("CUT the PY")

Nucleoside vs Nucleotide

Nucleoside = base + sugar; Nucleotide = base + sugar + phosphate

RNA vs DNA sugar

RNA = ribose; DNA = deoxyribose

Nucleic acid backbone

5′ → 3′ phosphodiester linkage

Left-handed DNA form

Z-DNA

Bases per turn (DNA forms)

A = 11, B = 10, Z = 12

Negative ∆G

Exergonic, spontaneous, Keq > 1

Positive ∆G

Endergonic, nonspontaneous, Keq < 1

Spontaneous meaning

Thermodynamically favorable but not necessarily fast

∆G° and Keq relationship

∆G° = -RT ln(Keq)

Standard state conditions

1 M, 1 atm, 25°C

Michaelis-Menten equation

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

Km definition

[S] at ½ Vmax, measure of enzyme affinity

Low Km means

High substrate affinity

Competitive inhibitor

Binds E only (active site); ↑Km, Vmax unchanged

Noncompetitive inhibitor

Binds E & ES (different site); Km unchanged, ↓Vmax

Uncompetitive inhibitor

Binds ES only; ↓Km, ↓Vmax

Mixed inhibitor

Binds E and ES with different affinities; ↓Vmax, Km ↑ or ↓

Overcoming competitive inhibition

Increase [S] to outcompete inhibitor

Cofactor definition

Non-protein molecule/ion required for enzyme activity

Metal ion cofactors

Mg²⁺, Mn²⁺, Fe²⁺

Coenzymes examples

NAD⁺, FAD, CoA

Holoenzyme vs Apoenzyme

Holoenzyme = enzyme + cofactor (active); Apoenzyme = enzyme alone (inactive)

Allosteric regulation model

Monod-Wyman-Changeux model

Protomer definition

Single subunit of an allosteric protein with one ligand-binding site

Glycogen phosphorylase function

Releases glucose from glycogen by cleaving α-1,4 linkages

Glycogen phosphorylase regulation

Regulated by phosphorylation / dephosphorylation

Where glycogen phosphorylase acts

At the nonreducing ends (C4 side) of glycogen