chem 352 - exam four

carbohydrates

polyhydroxy aldehydes and ketones or compounds that can be hydrolyzed to them; storehouses of chemical energy

in RNA, DNA, pharmaceuticals, plant structure, etc.

monosaccharides

3-7 carbons with a carbonyl group at C1 or C2 and most carbon atoms have a hydroxyl group

aldoses

monosaccharides with aldehyde carbonyl at C1

ketoses

monosaccharide with ketone carbonyl at C2

fischer projection formulas

carbon at each intersection, horizontal bonds come forward on wedges, vertical bonds go back on dashes, ketone or aldehydes carbonyl is put on or near the top; nonstereogenics not drawn in

All carbohydrates except dihydroxyacetone contain at least one stereogenic center

NOT how molecules form shape, drawn in eclipsing conformation

R and S designations

assign priorities to four groups; when lowest priority occupies a vertical bond and projects behind plane, tracing a circle in clockwise direction in order of priority gives R configuration and counterclockwise gives S; if horizontal, reverse answer obtained above

D and L monosaccharides

D: R at stereocenter furthest away, OH always to the right

L: S at stereocenter furthest away, OH always to the left

epimers

two diastereomers that differ in the configuration of only one stereocenter

physical properties of monosaccharides

sweet tasting; polar with high melting points; polar functional groups induce H bonding and water solubility; insoluble in organic solvents like diethyl ether, usually form rings

haworth projections

Place O atom in upper right corner of hexagon and add CH2OH group on first carbon counterclockwise, up for d sugars and down for l sugars; place anomeric carbon first carbon clockwise from O, OH down in D sugar for a anomer and OH up in D sugar for beta Anomer; add substituents on the right side of Fischer projection drawn down and substituents on left up

beta anamer

OH group up; cis to CH2OH group at C5

alpha anomer

OH group down, trans to CH2OH at C5

chair forms

draw pyranose ring with O as “up” atom, “up” substituents on Haworth became “up” bonds, either axial or equatorial, and “down” substituents become “down” bonds

furanose rings

Aldopentoses and ketohexoses; cyclization forms new stereocenter where for D sugars OH is drawn down in a anomer and up in beta; use same drawing conventions, with D sugars CH OH is drawn up

ribose

primarily forms pyranose but furanose is biologically significant

glycoside formation

monosaccharides with alcohol and HCl converts hemiacetal to acetal; proceeds by planar carbocation to form two glycosides; only hemiacetal OH reacts because of resonance stabilized carbocations; acetal product does NOT undergo mutarotation

glycoside hydrolysis

hydrolyzed with acid and water to cyclic hemiacetals and alcohol; reverse of glycoside formation

reactions of monosaccharides at OH groups

OH converted to esters with acetic anhydride or acetyl chloride with and ethers with treatment of base and alkyl halides; only acetyl ether is hydrolyzed with acid, creating new stereocenter

Monosaccharides are insoluble in common organic solvents, but monosaccharide derivatives that have five ether or ester groups are readily soluble

monosaccharide + base

NOT USEFUL, forms too many products

forms epimers, enediols, and constitutional isomers with carbonyl at C2

reduction of carbonyl

carbonyl on aldose is reduced to a primary alcohol using NaBH4 and CH3OH, forming an alditol

oxidation of aldehyde to carboxylic acid

Carbonyl is the most easily oxidized functional group in aldose, forms aldonic acid; does not give high yield; hemiacetal is in equilibrium with acyclic aldehyde and will be oxidized, while acetals will NOT

Br2, H2O: best yield

Cu compounds: color change, analytical purpose

Ag2O, NH4OH: low yield

reducing sugar

carbonyl carbon may be reduced with Ag2OH, benedict and feblings (Cu based compounds), and Br2, H2O

oxidation of aldehyde AND primary alcohol

oxidized to carboxylic acid groups by treatment of warm nitric acid, forms aldaric acid

may or may not have plane of symmetry (may change chirality)

wohl degradation

shortens length of aldose by cleaving C1-C2 bond

aldose → NH2OH → oxime → Ac2O → CN → NaOAc → cyanohydrin → base → lose HCN and form aldehyde with one less C

epimers at C2 yield same aldose in Wohl degradation

kiliani fischer synthesis

lengthens carbohydrate chain by adding one carbon to aldehyde end of aldose, forms two epimers

NaCN + HCl → H2, Pd-BaSO4 → H3O+

disaccharides

two monosaccharides joined by glycosidic linkage, connected by O that is a part of the acetyl; glycoside formed from anomeric carbon of one and the OH of another; one acetal plus another acetal/hemiacetal

numbered beginning with anomeric carbon

maltose

mutarotation, reacts with oxidizing reagents; reducing sugar

1→4 alpha glycosidic linkage of D alpha and beta glucose

lactose

beta galactose + beta glucose; mutarotation, reducing sugar; digested with lactase

beta glycosidic linkage

sucrose

one glucose + one fructose

six membered glucose bonded to C2 of fructofuranose by alpha glycosidic bond

NOT reducing sugar

cellulose

repeating glucose joined by 1→4 beta glycosidic linkage

H bonds BETWEEN sheets, H2O insoluble, fibrous

amylose (starch)

repeating glucose joined by alpha glycosidase

accessible OH, H2O soluble

hydrolyzed by alpha glycosidase

can form branches at 1→6 alpha glycosidic linkages; more efficient at storing energy

glycogen

polysaccharide storage in animals → extensive branching with alpha glycosidic bonds

human milk oligosaccharides

3-4 monosaccharides, helps give bacteria and antibodies to infant

amino sugars

NH2 instead of OH at non-anomeric carbon

N-glycosides

monosaccharides reacted with amine in mild acid

forms amine at anomeric carbon

hydrolyzable lipids

cleaved by water and contain ester unit

waxes, triacylglycerols, and phospholipids

nonhydrolyzable lipids

cannot be cleaved by water; varied in structure

fat soluble vitamins, eicosanoids, terpenes, and steroids

waxes

esters formed from high molecular weight alcohol and fatty acid

long hydrocarbons → hydrophobic

triacylglycerols

principal function of energy storage; yields CO2, H2O, and energy

essential fatty acids

cannot synthesize in body and must be acquired through diet

linoleic and linolenic acids

unbranched by may be saturated or unsaturated, even number of carbons; naturally have Z configurations; melting point dependent on degree of unsaturation

melting points and saturation

as number of double bonds increases, melting points decrease

fats are saturated and have high melting points

oils are unsaturated and have low melting points

allylic C-H bonds

weaker than other C-H bonds and are more susceptible to oxidation

may be hydrolyzed, hydrogenated or oxidized

phosphoacylglycerols

second most abundant lipid; principle lipid component of cell membrane; middle carbon is a stereocenter and is usually R

polar head with two nonpolar tails, ionic heads oriented outside with tails inside

sphingomyelin

derivative of amino alcohol sphingosine, has a phosphodiester at C1 and an amide formed with a fatty acid at C2; C3 has C-OH-E alkene

also part of lipid bilayer in membranes

vitamin A

fish oils and dairy

synthesized from beta carotene (orange pigment in carrots)

vitamin A is converted to II cis retinal, the light sensitive compound in vision

needed for healthy mucous membranes

vitamin A deficienty = night blindness, dry eyes, and skin

vitamin D3

most abundant D vitamin (not vitamin because synthesized from cholesterol)

regulates calcium and phosphorus metabolism

deficiency: rickets (bone disease characterized by knock-knees), spinal curvature, and deformaties

vitamin E

class of structurally similar compounds

antioxidant, protects unsaturated chains in fatty acids from oxidation

deficiency: neurologic problems

vitamin k

regulates prothombin synthesis and blood clotting proteins

deficiency: excessive and fatal bleeding

eicosanoids

biologically active compounds with 20 carbon atoms derived from arachidonic acid

local mediators which perform function in environment in which they are synthesized while hormones are syntehsized and transported in bloodstream to site of action

prostaglandins

lower blood pressure, inhibit blood platelet aggregation, control inflammation, lower gastric secretions, stimulate uterine contractions, and relax smooth muscles of uterus

unstable in body

thromboxanes

constrict blood vessels, trigger blood platelet aggregation

prostacyclins

dilate blood vessels and inhibit blood platelet aggregation

leukotrienes

constrict smooth muscle, especially in lungs

NSAIDS

inactivate COX enzymes and block prostaglandin synthesis

increase in gastric secretions, increasing susceptibility of ulcers

terpenes

repeating five carbon units with four carbon chain with a one carbon branch

may be sigma or pi bonds, always connected by at least one C-C bond, each carbon part of one isoprene unit

heteroatoms may be present but are ignored when identifying isoprenes

steroids

three 6-membered rings and one 5-membered ring; two angular methyl groups at ring junctions; substituents at ring fusion might be cis or trans with trans conformation being more stable

cholesterol

starting material for steroid synthesis (both sex hormones and adrenal cortical steroids)

increases rigidity of cell membranes

out of 256 stereoisomers only one is formed via tetracyclization

estradiol and estrone

estrogens synthesized in ovaries

develop female secondary sex characteristics

regulate menstrual cycle

progesterone

prepares uterus for implantation of fertilized egg

testosterone and androsterone

androgens synthesized in testes

control male secondary sex characteristics

cortisone and cortisol

anti-inflammatory, regulate carbohydrate metabolism

aldosterone

regulate blood pressure and volume via Na+ and K+ concentrations

nucleic acids

unbranded polymers composed of repeating nucleotides

3’ OH → 5’ phosphate via phosphodiester bonds, alternating sugar-phosphate backbone

RNA

ribonucleic acid, translate DNA to proteins

D ribose; uracil as a base; single stranded

DNA

deoxyribonucleic acid, stores genetic information and transmits information from one generation to another

purines

adenosine and guanine

pyrimidine

cytosine, thymine, and uracil

nucleoside

N glycoside; joins CI with NI of pyrimidine or N9 of purine in beta glycosidic linkage

ribonucleoside

D ribose + base

deoxyribonucleoside

2’-deoxy-D-ribose + base

DNA double helix

two polynucleotide strands that wind into a right handed double helix; phosphate backbone on outside and bases inside, perpendicular to the helix axis; both strands are anti parallel and bases are stabilized by hydrogen bonds between complementary base pairs; major and minor grooves; 10.6 base pairs per turn

base pairs

A-T: adenine pairs with thymine using two hydrogen bonds

G-C: guanine pairs with cytosine using three hydrogen bonds

replication

process by which DNA makes a copy of itself during cell division

transcription

ordered synthesis of RNA from DNA, stored information passed

translation

synthesis of proteins from RNA, determines specific amino acid sequence of a protein; one to two percent of DNA encodes proteins

semiconservative replication

strands of DNA separate and each serves as a template for a new strand; sequences of daughter DNA exactly matches sequence of parent DNA

replication steps

unwind to expose bases and creates “bubbles” where replication can occur by breaking H bonds; DNA polymerase catalyzes replication process using the four nucleotide triphosphates; new phosphodiester bond formed between 3‘ phosphate and 5‘ OH of new DNA; replication only proceeds three prime to five prime

leading strand

grows continuously from five prime to three prime by adding complementary bases

lagging strand

synthesized in Okazaki fragments which are sealed by ligase

ribosomal RNA

most abundant, found in ribosomes in cytoplasm; where polypeptides are assembled during protein synthesis

messenger RNA

carrier of information from DNA in nucleus to ribosomes; each gene corresponds to specific mRNA and sequence determines protein

exact copy of coding strand but U replaces T in RNA

transfer RNA

interprets information in mRNA and brings specific amino acids to site of protein synthesis; forms anticodons complementary to three bases in mRNA and identifies amino acid next in polypeptide chain

RNA synthesis

DNA unwinds and mRNA synthesized from template strand; RNA polymerase uses complementary base pairing to synthesize 3’ → 5’ and completes when particular sequence of bases on DNA is reached. DNA reformed

genetic code

set of three nucleotide units called codons that correspond to amino acids; series of codons determines amino acid sequence

stop codon

UAA, UAG, UGA

anticodon

three nucleotides complementary to codon in mRNA that is brought by a tRNA; new peptide bond formed by nucleophilic acyl substitution of amino group to one tRNA bonded amino acid with ester carbonyl of another

DNA sequencing

cut and sequence smaller DNA using restriction enzymes, which recognize a particular sequence of bases and cut both DNA strands; can be blunt or sticky ends

PCR

synthesize copies of any gene using a polymerase chain reaction; needs the segment of DNA to be copied, two primers complementary to strand ends, DNA polymerase to catalyze synthesis; nucleoside triphosphates

Taq: heat tolerant, can be reused across cycles

viruses

infections agent consisting of DNA or RNA molecule contained within protein coating; incapable of replicating until host organism is invaded

NAD+/NADH

NAD+: biological oxidizing agent; pyridinium ring accepts hydride

NADH: biological reducing agent; transfers H- to organic substrate to form NAD+

used for carbonyls/alcohols

FAD/FADH2

FAD: biological oxidizing agent, adds two H to cyclic sp2 nitrogen

FADH2: biological reductant

from vitamin B2 (greens, soy, almonds, liver); is yellow

functional groups that are not carbonyls/alcohols

reducing agents

electron reduced coenzymes are transferred via electron transport chain

1 NADH = 2.5 equiv ATP

1 FADH2 = 1.5 equiv ATP

beta oxidation

oxidation → conjugate addition → oxidation → reverse claisen

glycolysis

anaerobic, 10 step pathway to convert glucose into two pyruvates, two NADH and 2 net ATP

acetyl CoA

formed from pyruvate

O2 not directly needed by supply of NAD+ is oxygen dependent

aerobic

lactate

pyruvate reduced to lactate under anaerobic conditions, solely to oxidize NADH → NAD+ to maintain glycolysis

causes muscle soreness and oxygen debt

ethanol

fermentation

glucose metabolized to ethanol under anaerobic conditions due to generation of NAD+

citric acid cycle

breakdown of acetyl CoA into 2CO2, 3 NADH, 1 FADH2, 1 GTP, and 10 total ATPs (32 total, 3 acetyl CoA per glucose + 2 ATP from glycolysis)

polymers

large organic molecule composed of monomers; chain growth are prepared by chain reactions and step growth involve monomers with two functional groups joining and the loss of a small molecule

chain growth polymers

converts ethylene or derivative to a polymer via a radical, cation, or anion; may have substituent; involves initiation, propagation, and termination