Exam #2 Study Guide: Carbohydrates, Lipids, Membranes, and Nucleic Acids

Vocabulary practice flashcards covering monosaccharide stereochemistry, carbohydrate derivatives, storage and structural polysaccharides, lipid classes and self-assembly, biological membrane dynamics and transport thermodynamics, and nucleic acid structure, replication, and stability.

Monosaccharide

A carbohydrate that cannot be hydrolyzed into a simpler carbohydrate; chemically classified as a polyhydroxy aldehyde or ketone, frequently represented by the empirical formula $(CH_2O)_n$.

Aldose

A monosaccharide whose open-chain form contains an aldehyde carbonyl group (e.g., glucose).

Ketose

A monosaccharide whose open-chain form contains a ketone carbonyl group (e.g., fructose).

D versus L Monosaccharide

A stereochemical classification determined by the orientation of the hydroxyl group at the highest-numbered chiral center in a standard Fischer projection: $-OH$ on the right designates a D-sugar, while $-OH$ on the left designates an L-sugar.

Enantiomers

Nonsuperimposable mirror-image stereoisomers in which all corresponding stereocenters are inverted (e.g., D-glucose and L-glucose).

Diastereomers

Stereoisomers that are not nonsuperimposable mirror images of each other (e.g., D-mannose and D-galactose).

Epimers

Diastereomers that differ in stereochemical configuration at only one chiral center other than the anomeric carbon (e.g., D-glucose and D-mannose at C2; D-glucose and D-galactose at C4).

Anomers

Stereoisomers of a cyclic carbohydrate that differ in configuration specifically at the anomeric carbon created during ring closure (e.g., $\alpha\text{-D-glucopyranose}$ and $\beta\text{-D-glucopyranose}$).

Conformers

Molecules that differ through bond rotation or ring puckering without any change in covalent stereochemical configuration (e.g., two chair conformations of the same pyranose sugar).

Anomeric carbon

The carbon atom that was the carbonyl carbon in the open-chain form (C1 in aldoses, C2 in ketoses) and becomes a new chiral center upon intramolecular cyclic hemiacetal or hemiketal formation.

Mutarotation

The spontaneous interconversion between $\alpha$ and $\beta$ anomeric forms in aqueous solution via reversible ring opening and reclosing through the open-chain intermediate.

Glucose Cyclization to β-D-Glucopyranose

The intramolecular nucleophilic addition of the C5 hydroxyl oxygen to the C1 aldehyde carbonyl carbon of linear D-glucose, generating a six-membered pyranose ring with an equatorial C1 anomeric hydroxyl pointing upward.

Sugar acid

An oxidized carbohydrate derivative; oxidation at C1 forms an aldonic acid (e.g., gluconic acid), oxidation at C6 yields a uronic acid (e.g., glucuronic acid), and oxidation at both C1 and C6 produces an aldaric acid (e.g., glucaric acid).

Sugar alcohol (Polyol)

A carbohydrate derivative formed by reduction of a carbonyl group to an alcohol group, converting $C=O$ to $C-OH$ (e.g., glucose to sorbitol/glucitol, mannitol, and xylitol).

Glycoside

A carbohydrate derivative in which the anomeric $-OH$ group of a hemiacetal or hemiketal is replaced by an $-OR$ group via condensation with an alcohol, forming an acetal or ketal and locking the anomeric configuration.

Reducing sugar

A sugar possessing a free hemiacetal or hemiketal at its anomeric carbon that can equilibrate into an open-chain carbonyl form to reduce oxidizing agents such as $\text{Cu}^{2+}$ in Benedict's test or $\text{Ag}^+$ in Tollens' test.

Maltose

A reducing disaccharide formed by two D-glucose units linked by an $\alpha(1\rightarrow 4)$ glycosidic bond, leaving one C1 anomeric carbon free.

Cellobiose

A reducing disaccharide composed of two D-glucose units connected by a $\beta(1\rightarrow 4)$ glycosidic bond, leaving one C1 anomeric carbon free.

Lactose

A reducing disaccharide composed of D-galactose and D-glucose linked by a $\beta(1\rightarrow 4)$ glycosidic bond, wherein the glucose anomeric carbon remains free.

Sucrose

A nonreducing disaccharide composed of D-glucose and D-fructose joined by an $\alpha(1\leftrightarrow 2)\beta$ glycosidic linkage that involves the anomeric carbons of both monosaccharides.

Amylose

The unbranched structural component of plant starch, consisting of D-glucose residues connected exclusively by $\alpha(1\rightarrow 4)$ glycosidic bonds in a helical conformation that stains blue with iodine.

Amylopectin

The branched component of plant starch consisting of D-glucose chains linked by $\alpha(1\rightarrow 4)$ glycosidic bonds with $\alpha(1\rightarrow 6)$ branch points.

Glycogen

A highly branched animal storage homopolysaccharide composed of D-glucose units linked by $\alpha(1\rightarrow 4)$ bonds with frequent $\alpha(1\rightarrow 6)$ branches, abundant in liver and muscle to provide numerous nonreducing ends for rapid mobilization.

Cellulose

An unbranched structural homopolysaccharide in plant cell walls composed of D-glucose monomers joined by $\beta(1\rightarrow 4)$ glycosidic linkages, forming extended linear chains stabilized by intra- and interchain hydrogen bonds.

Glycogen phosphorylase

An enzyme that mobilizes stored glucose by using inorganic phosphate ($\text{P}_i$) to cleave terminal $\alpha(1\rightarrow 4)$ bonds at nonreducing ends, releasing $\text{glucose-1-phosphate}$ while leaving $\alpha(1\rightarrow 6)$ branch points intact.

Peptidoglycan

A bacterial cell wall heteropolymer consisting of an alternating carbohydrate backbone of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) joined by $\beta(1\rightarrow 4)$ linkages, cross-linked by short peptide stems attached to NAM.

Lipopolysaccharide (LPS)

A structural glycoconjugate anchored in the outer membrane of Gram-negative bacteria, consisting of a lipid anchor (Lipid A), a core oligosaccharide, and an outward-extending O-antigen repeating carbohydrate chain.

N-linked glycan

An oligosaccharide chain covalently attached to the side-chain amide nitrogen of an asparagine (Asn) residue within a glycoprotein.

O-linked glycan

An oligosaccharide chain covalently attached to the side-chain hydroxyl oxygen of a serine (Ser) or threonine (Thr) residue within a glycoprotein.

Fatty acid notation (Δ versus ω)

Methods of specifying double bond positions in fatty acids: $\Delta$ notation designates positions counting from the C1 carboxyl carbon, while $\omega$ notation designates the first double bond position counting from the terminal methyl carbon ($\omega = \text{total carbons} - \Delta_{\text{highest}}$).

α-Linolenic acid (ALA)

An essential $\omega\text{-3}$ polyunsaturated fatty acid with shorthand all-cis-$18:3\,(\Delta 9,12,15)$ and systematic name all-cis-$9,12,15$-octadecatrienoic acid.

Lipid peroxidation

A free-radical oxidation process that degrades polyunsaturated fatty acids by abstracting hydrogens from weak bis-allylic methylene carbons ($-CH=CH-CH_2-CH=CH-$) through initiation, propagation, and termination stages.

Triacylglycerol (TAG)

A neutral, hydrophobic energy-storage lipid composed of a glycerol backbone esterified to three fatty-acyl chains, lacking a phosphate head group and yielding approximately $38\,kJ/g$ upon oxidation.

Glycerophospholipid

An amphipathic membrane lipid consisting of a glycerol backbone attached to two fatty-acyl chains via ester linkages and a polar phosphate-containing head group at the third carbon.

Sphingosine

An 18-carbon amino alcohol that serves as the fundamental structural backbone for all sphingolipids.

Ceramide

The parent structural unit of sphingolipids, formed by attaching a fatty acid to the amino group of sphingosine via an amide bond.

Sphingomyelin

A sphingophospholipid composed of a ceramide unit linked to a phosphocholine polar head group, abundant in nervous-system membranes.

Cerebroside

A neutral glycosphingolipid consisting of a ceramide unit linked to a single glucose or galactose residue via a $\beta$-glycosidic bond.

Ganglioside

A complex glycosphingolipid consisting of a ceramide backbone attached to an oligosaccharide head group that contains at least one sialic acid residue.

Lipid packing parameter (P)

A dimensionless geometric ratio defined as $P = \frac{V}{A \times l_c}$, where $V$ is hydrophobic chain volume, $A$ is polar head-group area, and $l_c$ is chain length, used to predict self-assembly into micelles ($P < 1/3$), cylindrical micelles ($1/3 < P < 1/2$), vesicles ($1/2 < P < 1$), planar bilayers ($P \approx 1$), or inverted phases ($P > 1$).

Integral membrane protein

A membrane protein permanently embedded within the lipid bilayer, typically spanning it via nonpolar transmembrane $\alpha$-helices or $\beta$-barrels that interact directly with the hydrophobic fatty-acyl core.

Peripheral membrane protein

A membrane protein associated noncovalently with the polar membrane surface or with integral proteins through electrostatic interactions, hydrogen bonds, or amphipathic segments.

Lipid-anchored protein

A membrane protein located on a bilayer surface that is anchored through covalent attachment to a lipid molecule embedded in the membrane.

Translocon

A membrane protein complex that mediates the cotranslational insertion of nascent hydrophobic transmembrane segments into the endoplasmic reticulum bilayer via a lateral gate.

Fluorescence Recovery After Photobleaching (FRAP)

An experimental technique measuring the lateral diffusion of membrane lipids and proteins by photobleaching a localized fluorophore patch with a laser and recording the rate of fluorescence recovery as unbleached molecules move in.

Transverse diffusion (Flip-flop)

The spontaneous transfer of a phospholipid from one leaflet of a bilayer to the opposite leaflet, an extremely slow event due to the large thermodynamic barrier of moving a hydrated polar head group across the hydrophobic core.

Flippase / Translocase

A membrane-bound transport enzyme that catalyzes the transbilayer movement (flip-flop) of specific phospholipids between leaflets to maintain or establish membrane asymmetry.

Facilitated diffusion (Channel versus Carrier)

Passive transport down an electrochemical gradient across a biological membrane, operating either through a selective hydrophilic pore (channel, e.g., aquaporin) or via specific solute binding accompanied by alternating conformational changes (carrier, e.g., GLUT).

Primary active transport

The uphill movement of a solute against its electrochemical gradient directly driven by an exergonic chemical reaction, such as ATP hydrolysis (e.g., $\text{Na}^+/\text{K}^+\text{-ATPase}$).

Secondary active transport

The uphill movement of a solute coupled to the downhill flow of an ion whose electrochemical gradient was previously established by a primary active transport pump (e.g., $\text{Na}^+\text{-coupled}$ glucose uptake).

Na+/K+-ATPase

An electrogenic primary active transport pump that couples the hydrolysis of one ATP molecule to the outward export of $3\,\text{Na}^+$ ions and the inward import of $2\,\text{K}^+$ ions against their respective electrochemical gradients.

Electrochemical transport free energy (ΔG)

The thermodynamic equation describing the free-energy change for transporting a solute from compartment 1 to compartment 2: $\Delta G_{1\rightarrow 2} = RT \ln\left(\frac{[A]_2}{[A]_1}\right) + zF\Delta\psi$, combining chemical concentration and electrical potential contributions.

Nucleoside versus Nucleotide

A nucleoside consists of a nitrogenous purine or pyrimidine base covalently linked to a pentose sugar (ribose or 2-deoxyribose); a nucleotide is a nucleoside esterified to one or more phosphate groups.

Phosphodiester linkage

The covalent bond joining successive nucleotides along a nucleic acid strand, formed between the $3'\text{-OH}$ group of one pentose sugar and the $5'\text{-phosphate}$ group of the adjacent sugar.

Base tautomerization

The reversible migration of a proton accompanied by a rearrangement of conjugated double bonds within a nitrogenous base (e.g., keto-enol or amino-imino forms), which changes hydrogen-bonding patterns and can induce replication mispairing.

Syn versus Anti conformation

The torsional orientation of a nitrogenous base relative to its pentose sugar around the N-glycosidic bond; anti points the base away from the sugar (standard in B-DNA), whereas syn rotates the base over the sugar ring (e.g., guanine in Z-DNA).

Beer–Lambert law

The linear physical relationship between light absorbance and solute concentration: $A = \varepsilon l c$, where $A$ is absorbance, $\varepsilon$ is molar absorptivity, $l$ is optical path length, and $c$ is concentration.

B-DNA

The canonical right-handed antiparallel double-helical conformation of DNA under physiological conditions, exhibiting approximately $10.4$ base pairs and $3.4\,\text{nm}$ per helical turn.

DNA linking number (Lk)

The topological invariant of a covalently closed circular double-stranded DNA molecule, defined by the formula $Lk = Tw + Wr$, where $Tw$ (twist) represents the helical winding of strands around each other and $Wr$ (writhe) represents the superhelical coiling of the duplex axis.

Semiconservative replication

The mechanism of DNA synthesis confirmed by Meselson and Stahl in which each replicated daughter duplex contains one original parental strand and one newly synthesized strand.

DNA polymerase III

The primary replicative enzyme in E. coli that synthesizes new DNA strands in the $5'\rightarrow 3'$ direction and contains a $3'\rightarrow 5'$ exonuclease proofreading domain.

DNA ligase

An enzyme that seals single-strand nicks in the phosphodiester backbone by catalyzing covalent bond formation between an adjacent $3'\text{-OH}$ and $5'\text{-phosphate}$, such as during Okazaki fragment maturation.

Alkaline RNA hydrolysis

The degradation of RNA in alkaline solution facilitated by the ribose $2'\text{-OH}$ group, which undergoes base deprotonation and attacks the adjacent phosphodiester bond to form a $2',3'\text{-cyclic}$ phosphate intermediate that cleaves the chain.

DNA Melting Curve and GC Content

Thermal denaturation curves demonstrating that relative UV absorbance ($A_{260}$) increases as DNA strands separate, with duplexes of higher G-C percentage exhibiting higher melting temperatures ($T_m$) due to enhanced base stacking and three Watson-Crick hydrogen bonds.

G-quadruplex

A higher-order four-stranded nucleic acid architecture stabilized by the stacking of square-planar guanine quartets (G-quartets) held together by Hoogsteen-like hydrogen bonds, commonly found in telomeric DNA sequences.