Biochemistry: Carbohydrates and Lipids

Comprehensive vocabulary flashcards covering the biochemical classification, nomenclature, chemical properties, structures, and physiological roles of carbohydrates and lipids.

D-Glyceraldehyde Structure

• Classification: Aldotriose (3 carbons)

• Fischer Projection Configuration:

  • $C1$: Aldehyde ($-CHO$)

  • $C2$: $-OH$ on the right

  • $C3$: Primary alcohol ($-CH_2OH$)

• Significance: The simplest aldose and reference standard for designating D and L stereoisomers.

D-Erythrose Structure

• Classification: Aldotetrose (4 carbons)

• Fischer Projection Configuration:

  • $C2$: Right

  • $C3$: Right

• Relationship: Epimeric to D-threose at $C2$.

D-Ribose Structure

• Classification: Aldopentose (5 carbons)

• Fischer Projection Configuration:

  • $C2$: Right

  • $C3$: Right

  • $C4$: Right (all $-OH$ groups on the right)

• Significance: Essential structural component of ribonucleic acid (RNA), ATP, and nucleotide coenzymes.

D-Xylose Structure

• Classification: Aldopentose (5 carbons)

• Fischer Projection Configuration:

  • $C2$: Right

  • $C3$: Left

  • $C4$: Right

• Relationship: The $C3$ epimer of D-ribose.

D-Glucose Structure

• Classification: Aldohexose (6 carbons)

• Fischer Projection Configuration:

  • $C2$: Right

  • $C3$: Left

  • $C4$: Right

  • $C5$: Right (pattern: Right-Left-Right-Right)

• Significance: The primary circulating metabolic monosaccharide in animals.

D-Mannose Structure

• Classification: Aldohexose (6 carbons)

• Fischer Projection Configuration:

  • $C2$: Left

  • $C3$: Left

  • $C4$: Right

  • $C5$: Right (pattern: Left-Left-Right-Right)

• Relationship: The $C2$ epimer of D-glucose.

D-Galactose Structure

• Classification: Aldohexose (6 carbons)

• Fischer Projection Configuration:

  • $C2$: Right

  • $C3$: Left

  • $C4$: Left

  • $C5$: Right (pattern: Right-Left-Left-Right)

• Relationship & Role: The $C4$ epimer of D-glucose; constituent monomer of milk sugar (lactose).

Dihydroxyacetone Structure

• Classification: Ketotriose (3 carbons)

• Formula & Structure:

  • $$CH_2OH-C(=O)-CH_2OH$$

• Significance: The only simple monosaccharide that lacks a chiral center; interconverted with glyceraldehyde-3-phosphate in glycolysis by triose phosphate isomerase.

D-Erythrulose Structure

• Classification: Ketotetrose (4 carbons)

• Fischer Projection Configuration:

  • $C1$: $-CH_2OH$

  • $C2$: Ketone carbonyl ($C=O$)

  • $C3$: $-OH$ on the right

  • $C4$: $-CH_2OH$

D-Ribulose Structure

• Classification: Ketopentose (5 carbons)

• Fischer Projection Configuration:

  • $C2$: Ketone carbonyl ($C=O$)

  • $C3$: Right

  • $C4$: Right

• Significance: Keto-isomer of D-ribose; key metabolic intermediate in the pentose phosphate pathway.

D-Xyulose Structure

• Classification: Aldopentose (5 carbons)

• Fischer Projection Configuration:

  • $C1$: $-CH\text{ }_2OH$

  • $C2$: $-OH$ on the right

  • $C3$: $-OH$ on the left

  • $C4$: $-OH$ on the right

  • $C5$: $-CH\text{ }_2OH$

• Significance: Important sugar in plant metabolism; variant of D-ribulose.

D-Fructose Structure

• Classification: Ketohexose (6 carbons)

• Fischer Projection Configuration:

  • $C2$: Ketone carbonyl ($C=O$)

  • $C3$: Left

  • $C4$: Right

  • $C5$: Right

• Significance: Fruit sugar; keto-isomer of D-glucose; preferentially cyclizes into a 5-membered furanose ring.

Chair Conformations of $\beta$-D-Glucopyranose

• Structure: Six-membered pyranose ring in the chair conformation.

• Stability Feature: $\beta$-D-glucopyranose is the most stable aldohexose because all bulky substituents (the four $-OH$ groups and the $-CH_2OH$ group) are in equatorial positions.

• $\alpha$ vs. $\beta$ Anomer: In $\alpha$-D-glucopyranose, the anomeric $C1$ $-OH$ is axial (downward), whereas in $\beta$-D-glucopyranose it is equatorial (upward).

Triose Phosphate Isomerase (TPI) Mechanism

• Reaction: Catalyzes the interconversion of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GAP).

• Mechanism: General acid-base catalysis via an enediol/enediolate intermediate.

• Enzyme Kinetic Property: A catalytically perfect enzyme operating at a diffusion-controlled rate.

Lactose Structure and Linkage

• Components: $\beta$-D-galactose + $\beta$-D-glucose

• Glycosidic Linkage: $\beta(1 \rightarrow 4)$ glycosidic bond

• Chemical Nature: Reducing sugar (glucose unit contains a free anomeric hemiacetal)

• Enzyme: Cleaved by lactase; deficiency causes lactose intolerance.

Sucrose Structure and Linkage

• Components: $\alpha$-D-glucose + $\beta$-D-fructose

• Glycosidic Linkage: $\alpha(1 \rightarrow 2)$ linkage joining both anomeric carbons ($C1$ of glucose and $C2$ of fructose)

• Chemical Nature: Non-reducing sugar (no free hemiacetal/hemiketal).

Cellulose Structure and Linkage

• Polymer: Linear, unbranched homopolysaccharide of up to 15,000 D-glucose units

• Glycosidic Linkage: $\beta(1 \rightarrow 4)$

• Conformation: Extended linear ribbons that pack side-by-side into parallel hydrogen-bonded sheets of immense tensile strength; water-insoluble plant structural polymer.

Chitin Structure and Linkage

• Repeating Monomer: N-Acetylglucosamine (GlcNAc)

• Glycosidic Linkage: $\beta(1 \rightarrow 4)$

• Function & Occurrence: Structural homopolymer forming the exoskeleton of arthropods and cell walls of fungi.

$\alpha$-Amylose Structure and Conformation

• Monomer Unit: D-Glucose

• Glycosidic Linkage: Unbranched $\alpha(1 \rightarrow 4)$

• Conformation: Left-handed helical coil; isomer of cellulose and linear component of plant starch.

Amylopectin vs. Glycogen Branching Architecture

• Linear Chains: $\alpha(1 \rightarrow 4)$ D-glucose linkages

• Branch Points: $\alpha(1 \rightarrow 6)$ glycosidic bonds

• Branching Frequency:

  • Amylopectin: Branch every 24 to 30 residues (plant storage)

  • Glycogen: Branch every 8 to 12 residues (animal storage; highly branched for rapid mobilization).

Fatty Acids

• carboxylic acids with long-chain hydrocarbon side group

• Saturated fatty acids pack tightly and form more rigid, organized aggregates

  • fully reduced and have no double bonds

• Unsaturated chains bend and pack in a less ordered way, with greater potential for motion

  • have double bonds

FA Nomenclature and observations

• cis configuration

• db are never conjugated

• first db occurs between C9 and C10

• positions of db are indicated by delta

  • example: • C18:2(Δ9,12)- Describes the

    structure of linoleic acid

Palmitic Acid Structure (16:0)

• Formula: $CH_3(CH_2)_{14}COOH$

• Notation: $16:0$

• Features: Saturated 16-carbon fatty acid with no double bonds; fully reduced hydrocarbon chain that packs tightly into crystalline aggregates.

• mp: 63.1

Stearic Acid Structure (18:0)

• Formula: $CH_3(CH_2)_{16}COOH$

• Notation: $18:0$

• Features: Saturated 18-carbon fatty acid; high melting point ($69.6^\circ\text{C}$) due to extensive van der Waals contacts.

• mp:69.6

Oleic Acid Structure ($18:1\Delta^9$)

• Notation: $18:1(\Delta^9)$

• Structure: 18-carbon monounsaturated fatty acid with a single cis double bond between $C9$ and $C10$.

• Effect of Double Bond: Causes a $30^\circ$ bend/kink in the hydrocarbon chain, disrupting packing and lowering melting point to 12 degrees C

Linoleic Acid Structure ($18:2\Delta^{9,12}$)

• Notation: $18:2(\Delta^{9,12})$

• Structure: 18-carbon polyunsaturated fatty acid with two cis double bonds separated by a methylene bridge ($-CH_2-$).

• Classification: Essential $\omega$-6 fatty acid.

• mp: -5

$\alpha$-Linolenic Acid Structure ($18:3\Delta^{9,12,15}$)

Notation: $18:3(\Delta^{9,12,15})$

• Structure: 18-carbon polyunsaturated fatty acid with three cis double bonds separated by methylene groups.

• Classification: Essential $\omega$-3 fatty acid.

• mp: -11

Omega Fatty Acids

• Numbering Rule: Numbering begins at the methyl-terminal carbon ($\omega$ carbon), opposite to the carboxylic acid carbonyl ($C1$).

• $\omega$-3 Fatty Acid: The first double bond is situated at carbon 3 from the terminal methyl end.

• $\omega$-6 Fatty Acid: The first double bond is situated at carbon 6 from the terminal methyl end.

Determinants of Fatty Acid Melting Temperature ($T\_m$)

• Chain Length: Melting temperature increases with increasing number of carbons due to greater surface contact and extensive additive van der Waals interactions.

• Unsaturation: Introducing cis double bonds causes a rigid bend in the acyl chain, preventing compact crystalline packing and markedly decreasing melting temperature.

• Hierarchy Rule: The degree of unsaturation (number of double bonds) takes precedence over chain length in determining melting temperature (e.g., stearic acid $18:0$ melts at $69.6^\circ\text{C}$, while oleic acid $18:1\Delta^9$ melts at $13.4^\circ\text{C}$).

Myristic acid

14:0, saturated, mp=53.9

palmitoleic acid

16:1n-7, unsaturated, mp=-0.5

FA Composition of Three Fat Foods

• oil is mostly unsaturated, low mp

• butter is saturated and unsaturated, high mp

• beef is mostly saturated, highest mp

Triacylglycerol Generic Structure

• Backbone: Glycerol ($CH_2OH-CHOH-CH_2OH$)

• Linkages: Three fatty acid chains ($R_1, R_2, R_3$) esterified to $C1$, $C2$, and $C3$ of glycerol.

• Properties: Nonpolar, hydrophobic energy reservoir stored in adipocytes.

Biological role of triacylglycerols

• energy reservoirs which are found in adipocytes

  • provide long-term energy storage, which is why humans can survive starvation for up to 3 months

  • provides 6x more metabolic energy than the same amt of glycogen (carbs), which can only supply the energy the body needs for up to a day (short term storage)

Glycerophospholipid Generic Structure

• $C1$: Typically esterified to a saturated $C_{16}$ or $C_{18}$ fatty acid chain.

• $C2$: Typically esterified to an unsaturated $C_{16}$ or $C_{18}$ fatty acid chain.

• $C3$: Esterified to a phosphate group linked to a variable polar alcohol head group ($X$).

• Function: Major structural amphiphilic building block of lipid bilayers.

Glycerophospholipid Head Groups ($X$-Groups) to Memorize

• $-H$: Phosphatidic acid

• $-CH_2CH_2NH_3^+$: Phosphatidylethanolamine (PE)

• $-CH_2CH_2N(CH_3)_3^+$: Phosphatidylcholine (PC / lecithin)

• $-CH_2CH(NH_3^+)COO^-$ : Phosphatidylserine (PS)

• $-CH_2CH\left(OH\right)CH_2OH$ : Phosphatidylglycerol

Sphingosine and Ceramide Structures

• Sphingosine: 18-carbon amino alcohol containing a trans double bond between $C4$ and $C5$, an amino group at $C2$, and hydroxyl groups at $C1$ and $C3$.

• Ceramide: Parent unit formed by attaching a fatty acid via an amide bond to the $C2$ amine of sphingosine.

Sphingolipid Subclasses: Sphingomyelins

• Sphingomyelin: Ceramide + phosphocholine or phosphoethanolamine head group at $C1$ (abundant in myelin sheaths).

Sphingolipid Subclasses: Cerebrosides

• Cerebroside: Ceramide + single neutral monosaccharide (glucocerebroside or galactocerebroside).

Sphingolipid Subclasses: Gangliosides

• Ganglioside: Ceramide + complex oligosaccharide containing 3 or more sugars, at least one being sialic acid.

• receptors for certian pituitary glycoprotein hormones and bacterial protein toxins

• specific determinants in cell-cell recognition

  • play a role in carcinogenesis in cancer

  • interact with glycan recognition molecules involved in cell adhesion and immune regulation

• 6% of brain lipids are gangliosides

Tay-Sachs disease

• deficiency in GM2 Ganglioside (neurological disorder)

• fatal

Steroids

• signaling lipids

  • phosphatidylinositol function regulates cell structure and metabolism

  • eicosanoids mediate inflammatio, fever, and pain response

• pigments/antioxidants

• cofactors

• derivatives of cyclopentanoperhydrophenanthrene

Cyclopentanoperhydrophenanthrene

• Cyclopentanoperhydrophenanthrene: Fused four-ring steroid core (three 6-membered rings A, B, C and one 5-membered ring D) which is part of cholesterol

Cholesterol

• three 6-membered rings and one 5-membered ring all fused together

  • sterol: C3-OH group, important for storage and transport of cholesterol and can condense with a FA to form a sterol ester

• found in plasma membrane lipids

• increases rigidity due to ring system

Cholesteryl Stearate

• Composition: Formed by esterification of cholesterol's $C3$ hydroxyl group with the 18-carbon saturated stearic acid.

• Properties: Highly hydrophobic sterol storage ester associated with lipid transport and atherosclerosis plaque accumulation —> heart attack or stroke

Steroid Hormones: Glucocorticoids

• affect carb, protein, and lipid metabolism

• all steroid hormones are water insoluble and thus bind proteins for transport

• made in adrenal gland

Steroid Hormones: Mineralocorticoids

• regulate excretion of salt and water by the kidneys

• made in adrenal gland

Steroid Hormones: Androgens and Estrogens

• affect sexual development and function

• made in the ovaries(estrogen)/testes(androgens)

Addison’s disease

• hypoglycemia (low blood glucose)

• muscle weakness

• sodium/potassium loss

• impaired cardiac function

• increased stress susceptibility

• treatment with glucocorticoids and mineralcorticoids

• Shamu has addison’s disease

Cushing’s syndrome

• characterized by fatigue, hyperglycemia (high blood sugar), edema(water retention), redistribution of body fat

• typically caused by a tumor of the adrenal cortex

Vitamin D

• Sterol derivative formed by UV ring disruption between $C9$ and $C10$; regulates calcium metabolism.

• increases intestinal absorption of dietary calcium

  • too little —> deformed bones and stunted growth (rickets)

  • too much —> kidney stones and failure

Vitamin A (retinol)

• derived from B-carotene in plant products

• oxidized to form retinal which functions as the eye’s photoreceptor

  • deficiency leads to blindness

Vitamin K

• about half of a human’s daily req is supplied by intestinal bacteria

• participates in caarboxylation of Glu residues involved in blood clotting

Vitamin E

• present as a-tocopherol

• hydrophobic molecule in cell membranes that functions as an antioxidant to protect membrane proteins and lipids from oxidative damage

  • in anti aging and wound healing products

Fat-Soluble Vitamins (D, A, K, E)

• 
  

• Vitamin A (Retinol): Isoprenoid derived from $\beta$-carotene that oxidizes to retinal for vision photoreception.

• Vitamin K: Essential cofactor for the carboxylation of glutamate in blood clotting proteins.

• Vitamin E ($\alpha$-tocopherol): Lipophilic, membrane-bound antioxidant protecting lipids from oxidative free-radical damage.

Isoprenoids

• found in membranes that are soluble in the lipid bilayer

• composed from 5C unit with same skeleton as isoprene

• Ubiquinone (coenzyme Q) —> 10 isoprenoid units

Phospholipase Cleavage Specificity ($A_1$, $A_2$, C, D)

• Phospholipase $A_1$: Cleaves the ester bond at glycerol $C1$.

• Phospholipase $A_2$: Cleaves the ester bond at glycerol $C2$ (releases arachidonic acid).

• Phospholipase C: Cleaves before the phosphate on $C3$, producing diacylglycerol (DAG) and phosphorylated head group.

• Phospholipase D: Cleaves after the phosphate group, releasing head group alcohol ($X$) and phosphatidic acid.

Enantiomers Definition and Characteristics

• Definition: Chiral stereoisomers that are non-superimposable complete mirror images of one another.

• Example: D-Glucose and L-Glucose (every single asymmetric chiral center is inverted).

• Physical Properties: Share identical chemical properties, melting points, and solubility in achiral environments, but rotate plane-polarized light in equal and opposite directions.

Epimers Definition and Key Distinctions

• Definition: Diastereomers that differ in stereochemical configuration at only ONE asymmetric carbon atom.

• Key Hexose Examples:

  • D-Mannose is the $C2$ epimer of D-glucose.

  • D-Galactose is the $C4$ epimer of D-glucose.

    

• Non-Epimer Comparison: D-Mannose and D-Galactose are NOT epimers of each other because they differ at two chiral centers ($C2$ and $C4$), making them general diastereomers.

D- and L-Monosaccharide Configuration Convention

• Standard: Determined by the orientation of the hydroxyl ($-OH$) group on the highest-numbered asymmetric chiral carbon (the carbon furthest from the carbonyl) in a Fischer projection.

• D-Monosaccharide: The $-OH$ on the reference chiral carbon is oriented to the right.

• L-Monosaccharide: The $-OH$ on the reference chiral carbon is oriented to the left.

• Total Isomers Formula: A monosaccharide containing $n$ chiral centers has $2^n$ potential stereoisomers.

Anomeric Carbon and Anomers Definition

• Anomeric Carbon: The carbonyl carbon ($C1$ in aldoses, $C2$ in ketoses) that becomes a new chiral stereocenter during ring cyclization (forming a hemiacetal or hemiketal).

• Anomers: Cyclic stereoisomers that differ in configuration exclusively at the anomeric carbon.

• Stereochemical Designation:

  • $\alpha$ Anomer: The anomeric $-OH$ points downward (trans to $C6$ $-CH\_2OH$ in D-pyranoses).

  • $\beta$ Anomer: The anomeric $-OH$ points upward (cis to $C6$ $-CH\_2OH$ in D-pyranoses).

    

Reducing vs. Non-Reducing Sugars

• Reducing Sugar: A sugar retaining a free, unlinked anomeric carbon (hemiacetal/hemiketal) capable of ring-opening into a linear chain with a free reactive carbonyl to reduce mild oxidizing agents (e.g., glucose, maltose, lactose).

• Non-Reducing Sugar: A sugar in which the anomeric carbons are locked in an acetal/ketal glycosidic bond and cannot undergo ring opening (e.g., sucrose, where both anomeric carbons are joined in an $\alpha(1 \rightarrow 2)$ bond).

Aldonic Acids

• Aldonic Acid: Produced by the selective oxidation of the carbonyl aldehyde group at $C1$ to a carboxylic acid ($-COOH$) (e.g., D-glucose converted to D-gluconic acid).

Uronic Acids

• Uronic Acid: Produced by the selective oxidation of the terminal primary alcohol group ($C6$ in hexoses) to a carboxylic acid ($-COOH$), preserving the $C1$ aldehyde carbonyl (e.g., D-glucose converted to D-glucuronic acid).

Aldehydes are reduced to form?

alcohols

Sugar alcohols

ribitol, xylitol, glycerol

Homopolysaccharides vs. Heteropolysaccharides

• Homopolysaccharide: A complex carbohydrate polymer composed of only a single recurring type of monosaccharide unit (e.g., cellulose, glycogen, amylose, and chitin).

• Heteropolysaccharide: A complex carbohydrate polymer assembled from two or more distinct types of monosaccharide building blocks (e.g., peptidoglycan, glycosaminoglycans, and cell-surface ABO antigens).

Biosynthetic Precursors of Glycogen vs. Amylopectin

• Amylopectin Synthesis: Plants synthesize amylopectin utilizing ADP-glucose as the activated glucosyl donor substrate.

• Glycogen Synthesis: Animals and fungi synthesize glycogen utilizing UDP-glucose as the activated glucosyl donor substrate.

• Significance: Tagging glucose with distinct nucleotide diphosphates regulates carbohydrate storage pathways across biological kingdoms.

Enzymes of Starch Breakdown

• $\alpha$-Amylase: Salivary and pancreatic enzyme that cleaves internal $\alpha(1 \rightarrow 4)$ glycosidic bonds.

• $\alpha$-Glucosidase: Exoglycosidase that sequentially hydrolyzes one terminal glucose residue at a time.

• Debranching Enzyme: Hydrolyzes both residual $\alpha(1 \rightarrow 4)$ bonds and branch point $\alpha(1 \rightarrow 6)$ bonds to enable complete starch degradation.

Enzymes of Glycogen Breakdown

• Glycogen Phosphorylase: Phosphorolytically cleaves $\alpha(1 \rightarrow 4)$ glycosidic bonds sequentially inward from the non-reducing ends, releasing glucose-1-phosphate without expending ATP.

• Glycogen Debranching Enzyme: Hydrolyzes $\alpha(1 \rightarrow 6)$ branch connections to release free glucose and expose remaining linear chains for continued breakdown.

Metabolic Consequences of Carbohydrate-Deficient Diets

• Brain Fuel Requirement: The brain cannot utilize unesterified fatty acids directly and relies primarily on circulating glucose for normal metabolic function.

• Kidney Stones: Carbohydrate restriction elevates uric acid production, leading to decreased urine solubility and uric acid calculus formation.

• Gout: Elevated systemic uric acid crystallizes within joint spaces, precipitating acute inflammatory arthritis.

• Caloric Guideline: Carbohydrates should account for approximately $20\%$ of total daily caloric intake in a balanced diet.

Glycosaminoglycans (GAGs) Structure and Function

• Structure: Long, unbranched heteropolysaccharides consisting of repeating disaccharide units composed of an amino sugar and an uronic acid.

• Physiological Role: Major structural components of connective tissues, extracellular matrix, and synovial fluid providing mechanical joint lubrication.

• Hyaluronic Acid: Essential high-molecular-weight GAG that prevents intracranial hemorrhage in premature infants and maintains tissue hydration.

Cartilage Glycan Components: Glucosamine and Chondroitin Sulfate

• Constituents: Glucosamine (an amino monosaccharide) and chondroitin sulfate (a sulfated glycosaminoglycan) serve as primary structural building blocks of articular cartilage.

• Biological Role: Provide mechanical shock absorption and cushioning between articulating bones in synovial joints.

• Therapeutic Synergy: Combined administration (e.g., Dasuquin) stimulates cartilage extracellular matrix synthesis and reduces joint degradation in osteoarthritis.

Proteoglycans and Glycoprotein Linkages (O-Linked vs. N-Linked)

• Proteoglycans: Hybrid macromolecules consisting of a core protein covalently bound to one or more glycosaminoglycan chains.

• O-Glycosidic Bonds: Oligosaccharides attached via the hydroxyl oxygen of Serine (Ser) or Threonine (Thr) residues.

• N-Glycosidic Bonds: Oligosaccharides attached via the amide nitrogen of Asparagine (Asn) or Glutamine (Gln) residues.

ABO Blood Group Antigen Structures

• O Antigen (Core): Foundational oligosaccharide chain terminating in an $\alpha(1 \rightarrow 2)$-linked fucose (Fuc) on galactose.

• A Antigen: Core modified by addition of an N-acetylgalactosamine (GalNAc) residue via an $\alpha(1 \rightarrow 3)$ glycosidic bond.

• B Antigen: Core modified by addition of an extra D-galactose (Gal) residue via an $\alpha(1 \rightarrow 3)$ glycosidic bond.

ABO Blood Group Transfusion Compatibility

• Type O: Expresses only H (O) antigen core; contains anti-A and anti-B antibodies; universal erythrocyte donor, can receive only Type O red cells.

• Type A: Expresses A antigen; contains anti-B antibodies; can safely donate to A and AB, and receive from O and A.

• Type B: Expresses B antigen; contains anti-A antibodies; can safely donate to B and AB, and receive from O and B.

• Type AB: Expresses both A and B antigens; contains neither anti-A nor anti-B antibodies; universal recipient, can donate red cells only to Type AB.