CHEMISTRY OF CARBOHYDRATES

- at least 3 carbon (C) atoms and multiple hydroxyl (-OH) groups; carbonyl group (C=O) either aldehyde or ketone
- most abundant bio compound, energy, cell membrane component
- suffix: -ose; di- on same C, bis- on diff C
- Classified by their ability to be hydrolyzed into smaller compounds
o Mono- - 1, cannot be hydrolyzed, single polyhydroxyl aldehyde or ketone
o Bi- - 2
o Oligo- - 3-12, same or different monosaccharides
o Poly- - >12, linear or branched
- Classified by the number of C atoms: triose, tetrose, pentose, hexose, heptose, etc.
- Classified by f(x)al group: aldose (aldehyde @ C1), ketose (ketone @ C2), or derived

ISOMERISM
- isomers same chem formula, diff spatial configuration
- asymmetrical / chiral C 4 diff groups attached
- 2^n # of possible isomers, n is # of asC
- D and L OH group of penultimate C (asC farthest from carbonyl group) is right (dextro, D) or left (levo, L); D and L are
enantiomers or mirror-images of each other, non-super-imposable
- Diastereomers isomers that differ in one (epimers) or more non-penultimate C
- Anomers for 5 C cyclization = ring structure; aldehyde or ketone group reacts with penultimate OH group O ring:
hemiacetal or hemiketal ring
o C1 (aldoses) or C2 (ketoses) becomes anomeric C; anC is bound to O and has OH group
o OH of anomeric C is same side as O ring = anomer, if opposite = anomer;
o and anomers are in equilibrium, mutarotation = spontaneous interconversion using open-chain structure
- Stable ring structures: pyranose = 5C, 1O; furanose = 4C, 1O
- if OH is below, if OH is above
- for cyclic ketopentoses / furanoses = C2 has OH group
- Nonplanar configuration stable chair, less favored boat; OH groups are in axial (vertical) or equatorial (non-vertical)
- Optical activity d- if rotates to right, l- if left

DERIVATIVES OF MONOSACCHARIDES
- Sugar acids oxidation of terminal group to COOH; aldonic acid aldehyde oxidation, uronic acid ketone oxidation, or
aldaric / saccharic acid - aldehyde and terminal carbon oxidation
- Amino sugars OH to NH on sugar ring; acetylated or sulfated
- Deoxysugars OH to H on sugar ring, 2-deoxy-D-ribofuranose
- Phosphoric Acid Esters sugar phosphates sugar + phosphate group from high-energy compound (ATP)
- Sugar alcohols / Polyols reduction of carbonyl group to OH
- Glycosides asymmetric mixed acetals, anC of hemiacetal / pyranose + OH of another monosacch = disaccharide
- Glycoproteins sugar + protein via covalent combination; N linked or O linked

OLIGOSACCHARIDES
- specific sugar monomers and stereoconfigs, C positions in linkages, order of monomers, anomeric config of OH on C1
- Reducing sugars = free anomeric C on last monomer; non-reducing = no free anC on either sugar
- Homo-oligosaccharides one kind of sugar upon hydrolysis
- Hetero-oligosaccharides different sugars upon hydrolysis

Name Monomers Glycosidic Bond Reducing / Non-reducing

Maltose D-glucose 14 R
Isomaltose D-glucose 16 R
Cellobiose D-glucose 14 R
Lactose (in milk) D-galactopyrosyl, D-glucopyranose 14 R
Sucrose (in cane/table sugar) D-glucopyranosyl, D-fructofuranose 12 NR

POLYSACCHARIDES
- Homoglycans polysaccharides with 1 type of repeating monosaccharide unit
o Amylose linear -D-glucose in 14, repeating maltoses
o Amylopectin amylose with 16 branching linkages,
o Starch amylase + amylopectin
o Glycogen more branching amylopectin
o Cellulose linear -D-glucose in 14, repeating -cellubiose
- Heteroglycans 2 or more different monosaccharide residues
o Pectin D-galacturonic acid in 14, some carboxyls as methyl esters
o Mucopolysaccharides / GAGs more than 1 type of monosaccharides that are aminated, sulfated, or N-acetylated;
hyaluronic acid, heparin and chondroitin sulfate

STORAGE POLYSACCHARIDES
- for plants and animals; molecule must be sufficiently insoluble to for granules that have a loose 3 structure for enzyme access
- plants: amylase (10-30%) + amylopectin (70-90%) = starch; animals: glycogen; polymers of -D-glucopyranose
- Starch = amylose + pectin, plants
o Amylose 20% of sta5rch, linear, 100-1000 glucose residues, helical left-handedly, darkblue with iodine
o Amylopectin branches every 25-30 glucose residues, 5000 glucose residues, dull reddish brown with iodine
- Glycogen similar to amylopectin, branches every 8-10 residues, red-violet with iodine, animals
- Inulin 21 polyfructose in plants
- Dextrans 16 glucose polymers in yeasts and bacteria
- Fructans homopolymer of D-fructose in plants
- Mannans polymannose in bacteria, yeasts, molds, higher plants
STRUCTURAL POLYSACCHARIDES
- structural elements, for protection, support, shape, elasticity, rigidity, usually in longer polymer chains, does not allow OH-H2O
interaction
- Cellulose most abundant, 50% of plants, very long 14 parallel glucose (cellubiose) chains (300-15,000), chains H bond
with each other, cemented with hemicellulose, pectin and lignin, extensin - collagenlike
- Chitin linear homopolymer of N-acteyl-glucosamine in 14, insect wings, exoshells, exoskeletons
- Bacterial Cell Wall very long N-acetyl-glucosamine 14 N-acteyl-muramic acid chain, peptide bond crosslinks =
peptidoglycan
o Gram Positive (G+) multiplayered peptidoglycan outside lipid cell membrane, stains bright violet
o Gram Negative (G-) single / few peptidoglycan sandwiched between lipid bilayer, stains red
o Penicillin interferes peptidoglycan wall synthesis, lysozymes attack peptidoglycan
- Glycosaminosglycans (GAGs) formerly mucopolysaccharides, long, unbranched, repeating disaccharide of uronic acid
(except keratin sulfate) and hexosamine, many negative groups (carboxylates, sulfates), for connective tissue and lubrication

GAG Hexosamine Disacch Uronic Acid Bond Uniqueness, f(x)

Bond bet
Disacch
Hyaluronic D-glucuronic acid N-acetyl-D-glucosamine Non-sulfated, lubricant, shock
13 14
acid absorber
D-glucuronic acid N-acetyl-galactosamine- Cell coats, cartilage, bone,
4-sulfate cornea, skin, arteries
Chondroitin L-iduronic acid N-acetyl-galactosamine-
13 14
sulfate 4-sulfate
D-glucouronic acid N-acetyl-galactosamine-
6-sulfate
Dermatan D-glucouronic acid N-acetyl-galactosamine- Non-major, skin, cornea, bone,
13 14
Sulfate or L-iduronic acid 4-sulfate blood vessles, heart, valves
D-galactose N-acetyl-glucosamine-6- Non-uronic acid, adult
sulfate mammalian cartilage; Type I
Keratan Sulfate 14 13
protein, Type II serine /
theronine OH
L-iduronic acid (70- N-acetyl-glucosamine Natural anticoagulant, cofactor
Heparin 90%) or glucuronic 14 14 for lipoprotein lipase, basophils,
acid mast cells
Glucuronic acid or N-acetyl-glucosamine More uronic acid groups, lungs,
Heparan
L-iduronic acid 14 14 arteries, basal lamina, cell
Sulfate
surfaces

SYNTHESIS OF PROTEOGLYCANS
- polysaccharides assembled in ER (protein) and Golgi (others)
1) Synthesis of core protein
2) Assembly of polysacch chains into core
3) Covalent modification of sugar polymer
4) Packaging
5) Secretion into ECM

MUCOPOLYSACCHARIDOSES
- human genetic disorders, excessive accumulation and exretion of oligosacchs of proteoglycans, deficiency of one or more
lysosomal enzymes responsible for the degradation of dermatan / heparin sulfate

CHEMISTRY OF AMINO ACIDS AND PROTEINS

- most abundant cellular component, enzymes, antibodies, hormones, transporters, most diverse and dynamic molecule

AMINO ACIDS
- protein molecule = 20 AAs
- carbon (chiral) with carboxylic acid, amino, hydrogen and R (side chain)
- amino group optically active: L- or D- forms
- zwitterions in solution double charged (carboxylate , amino +)
- 20 AAs

Type Side Chain AAs

Aliphatic CH glycine, alanine, valine, leucine, isoleucine
Hydroxyl OH serine, threonine
Sulfur S cysteine, methionine
Aromatic Benzene ring phenylalanine, tyrosine, tryptophan
Acidic / Amide Carboxyl / N and C=0 aspartic acid / asparagine, glutamic acid / glutamine
Basic Amine arginine, histidine, lysine
Imino connected to amino group proline

- Neutral/Basic/Acidic R group does not ionize / R group accepts H / R group donates H

o Basic lysine, arginine, histidine (weak)
o Acidic glutamic acid, aspartic acid, cysteine (weak), tyrosine (weak)
- Polar/Non-Polar hydrophilic, readily solvated by water / hydrophobic, not readily solvated by water
o Charged at ph=7 strong acids and all bases
o Uncharged ph=7 asparagine, glutamine, serine, threonine, cysteine, tyrosine
- Essential/Non-essential cannot produce endogenously in body / synthesizable in body
o Essentials PVT TIM HALL: phenylalanine, valine, threonine, tryptophan, isoleucine, methionine, histidine*,
arginine*, leucine, lysine
 o * infancy and illness only

AA 3-letter 1-letter AA 3-letter 1-letter

Alanine Ala A Leucine Leu L
Arginine Arg R Lysine Lys K
Asparagine Asn N Methionine Met M
Aspartic Acid Asp D Phenylalanine Phe F
Cysteine Cys C Proline Pro P
Glycine Gly G Serine Ser S
Glutamine Gln Q Threonine Thr T
Glutamic Acid Glu E Tryptophan Try W
Histidine His H Tyrosine Tyr Y
Isoleucine Ile I Valine Val V

- Peptides AA chain
o Oligopeptide - 10 residues
o Polypeptide - >10 residues
o Protein - >50 residues
- Peptide Bond covalent, -carboxyl + -amino + removal of H2O; partial double bond
- Polypeptide chain regularly repeating C C N C C N chain and variable R group; 2 ends: amino and
carboxyl terminals

PROTEINS
- Four levels of architectural organization:
- Primary (1) Structure amino acid sequence
- AA Dogma: Sequence Structure Function
- Secondary (2) Structure 3D folding, steric relationships of AA residues close to one another in a line, stabilized by H
bond of C and N of main chain
o Partial double bond of peptide bond prevents rotation of carboxyl C and N; atoms directly connected C and N lie in a
plane
o Rotational flexibility allows folding into regularly repeating structures; rotatable at:
Psi bond () -C and carbonyl C
Phi bond () -C and N
o -Helical rod-like, side chains outside, stabilized by H bond @ CO and HN, 3.6 AA per turn, axial distance 1.5
o -pleated sheet H bond to parallel or antiparallel strand
o Collagen helix repating praline/hydroxyproline prevent -helical or pleated sheet
- Tertiary (3) Structure geometric relationship between distant segments of 1 structure and side chains in 3D
o Stabilized by non-covalent (hydrophobic, electrostatic, H bond, and Van der Waals forces) and covalent (disulfide)
bonds
Fibrous long, rod-shaped, structural, water insoluble
Globular compact, spherical, dynamic, water soluble
- Quaternary (4) Structure multiple polypeptide chains (subunits or domain), non-covalent,
- Protein Denaturation loss of protein structure,2-4 structures only, 1 needs proteolytic enzymes

IONIC PROPERTIES
- -carboxyl and -amino does not contribute to charges since they are in a peptide bond
- ionic character depends on acidic and basic R group
- Bronsted acid donates H, base receives H
- Acid conjugate base, Base conjugate acid
- acids dissociate first, then bases
- groups dissociate first, then distally
- pKa value at which 50:50 of protonated and dissociated group
- Henderson Hasselbach Equation
pH = pKa + log [A]
[HA]

- When molar concentration of acid and conjugate base are equal: pH = pKa
- pI (isoelectric point) pH at which AA is in isoelectric form (net charge of zero)
- near pKa greatest buffering
- near pI least buffering
- Conclusions based on Titration Curve
1) Net charge of AA depends on pH, charge will change with pH
o pH > pI = () pH <pI = (+)
2) Since no 2 AA have exactly the same ionization tendency, no 2 AA will have the same net charge at the same pH (basis of
electrophoresis)

Type # of ionizations / pKas Species Location of pI (average)

Neutral 2 +1, 0, -1 pKa1 pKa2
Acidic 3 +1, 0, -1, -2 pKa1 pKa2
Basic 3 +2, +1, 0 , -1 pKa2 pKa3