MOLECULAR MODELING PRACTICUM - FUNCTIONAL GROUPS, FATS, PROTEINS, AND CARBS

hai gl guys

Alcohol or Hydroxyl
-OH (an oxygen bonded to a hydrogen attached to a carbon)
Polar. Found highly in carbohydrates.

Amine
-NH2 (a nitrogen bonded to two hydrogens attached to a carbon)
Polar & basic & in amino acids

Alkane
Carbon chain with only single C-C bonds the rest of the bonds have hydrogens (C-C and C-H)
Nonpolar

Alkene
Carbon chain with at least one C=C double bond
Nonpolar

Alkyne
Carbon chain with at least one C≡C triple bond
Nonpolar

Aldehyde (elbow lookin double bond o)
-CHO (a carbon double bonded to an oxygen and single bonded to a hydrogen at the end of a carbon chain)
Polar

Ester (oo)
-COO- (a carbon double bonded to one oxygen and single bonded to another oxygen which connects to a second carbon chain)
Polar, however minimally, when in triglycerides, fats and oil molecules

Ether (cute spider one)
C-O-C (an oxygen single bonded between two carbon chains)
Polar

Ketone
C=O in the middle of a carbon chain (a carbon double bonded to an oxygen with carbon chains on both sides)
Polar

Carboxyl (ooh)
-COOH (a carbon double bonded to one oxygen and single bonded to a hydroxyl group attached to an R group)
Acidic, found in amino acids and all organic acids

Phenyl or Aromatic Ring
A six-carbon ring with alternating double bonds (benzene ring) attached to an R group
Nonpolar

Phosphate
-PO4 (a phosphorus atom bonded to four oxygens, one O has a hydrogen)
Polar, can be acidic or basic. Found in all nucleic acids

Sulfhydryl or Thiol
-SH (a sulfur bonded to a hydrogen attached to a carbon)
Polar, stabilizes tertiary polypeptide structure

Amide
-CONH2 (a carbon double bonded to an oxygen and single bonded to a nitrogen attached to an R group)
Polar, in peptide bonds

Thioether (cute spider thing with an S this time)
C-S-C (a sulfur single bonded between two carbon chains)
Polar (moderately). Note: Found in methionine

Phosphoester (phosphate group in a bigger molecule)
R-O-P (a phosphate group bonded to an R group through an oxygen)
Acidic and present in all DNA/RNA polymers, when in "phosphodiester" bonds.

CPK COLORS

carbon = black

hydrogen = white

oxygen = red

nitrogen = blue

phosphorus = orange

sulfur = yellow

What makes a functional group polar?

PONS

PENTANE
Fats

• C5H12, five carbons in a chain with only C-C and C-H single bonds

• Nonpolar throughout, neutral

• 1 alkane (the whole molecule), no other listed groups

• 3 isomers: n-pentane, isopentane, neopentane

• Hydrophobic, LDF only (guys i put this in gpt it has some random info)

• More branching means a lower boiling point

BUTANOL
Fats

• C4H10O, four-carbon chain with one -OH

• -OH end is polar, carbon chain is nonpolar, overall neutral

• 1 alcohol/hydroxyl, 1 alkane (the carbon chain)

• 4 alcohol isomers: 1-butanol, 2-butanol, isobutanol, tert-butanol

• 7 total isomers if you count the 3 ethers

• 2-butanol is chiral (2 mirror-image forms)

• Only partly water soluble, and less so as the chain gets longer

• Classified as primary, secondary, or tertiary by the -OH carbon

BUTYRIC ACID
Fats

• CH3CH2CH2COOH, C4H8O2

• Propane chain plus a carboxyl group (the carboxyl carbon is the 4th carbon)

• Carboxyl head is polar and acidic, propyl tail is nonpolar

• Loses H+ to become butyrate (COO-)

• 1 carboxyl, 1 alkane (the propyl tail), no separate ketone or alcohol

• 2 acid isomers: butanoic acid and isobutyric acid

• Esters like ethyl acetate share the formula but have a different functional group

• Much more water soluble than long-chain fatty acids

Geometric isomers

Molecules that have the same chemical formula and bond connectivity, but a different 3d arrangement (ie. cis and trans double bonds in fatty acids)

Structural isomers

Aka constitutional isomers, share the same molecular formula but different bond connectivity or arrangement of atoms (ie. glucose / fructose / galactose)

CIS VS. TRANS DOUBLE BONDS

Fats

• Same formula either way

• Carboxyl head is polar and acidic, hydrocarbon tail is nonpolar

• Cis vs. trans does not change polarity

• 1 alkene per C=C, 1 carboxyl, alkane in the saturated stretches of the tail

• Cis and trans are geometric isomers (2 forms per double bond)

• Double bond position can also vary

• Cis: H's on the same side, tail kinks, loose packing, low melting point, liquid (oils)

• Trans: H's on opposite sides, tail stays straight, tight packing, higher melting point

• Trans fats come from partial hydrogenation (adding h2)

TRIGLYCERIDE

Fats

• 1 glycerol (C3H8O3) plus 3 fatty acids, joined by dehydration synthesis (3 H2O released)

• Overall nonpolar and hydrophobic, neutral

• Tails are strongly nonpolar, ester bonds and glycerol core are slightly polar

• No free carboxyls or hydroxyls remain, so no acidic or basic parts

• 3 esters, 3 alkane tails

• Alkenes only if a tail is unsaturated (1 or more per unsaturated tail)

• 0 carboxyl, 0 alcohol

• 1 form if all 3 fatty acids match

• If all 3 differ: 3 arrangements, 6 counting mirror images

• Cis/trans tails add more

• Stores energy (about 9 kcal/g), insulates, cushions

• Fats are mostly saturated and solid, oils mostly unsaturated and liquid

• Broken down by hydrolysis

• Not a phospholipid, which swaps one fatty acid for a phosphate group

Dehydration synthesis

delete dat hoh the water will flow the polymer grows when you delete dat hoh

one gives up h one gives up oh

What does chiral mean?

A molecule has a mirror image

Isomers

Molecules that share the exact same chemical formula but have different arrangements or connections of their atoms

Enantiomers

A specific pair of isomers (stereoisomers???) that are non-superimposable mirror images of each other. Every chiral center in one molecule is inverted in its enantiomer

Chiral center

Carbon atom bonded to 4 diff groups

Chiral centers for each macromolecule

• A chiral center is a carbon bonded to 4 different groups

• A carbon with a double bond can never be chiral, triple bond, ch3 or ch2, or any carbon with 2 identical grps attached

• The “candidates” or wtv have 4 single bonds at one H AT MOST

• If all 4 attached grps are diff, it’s a chiral center

• Chiral molecules come as enantiomers

FATTY ACIDS (IN GENERAL)

• Long unbranched hydrocarbon tail (usually 12-24 carbons, most often 16 or 18) with a carboxyl group on one end

• Saturated fatty acids follow CnH2nO2

• Each C=C removes 2 hydrogens

• Amphipathic: carboxyl head is polar and acidic, hydrocarbon tail is nonpolar

• Acidic

• Overall hydrophobic, since the long tail

• 1 carboxyl

• Alkane in the saturated parts of the tail

• 0 alkene if saturated, 1 or more if unsaturated (1 per C=C)

• Isomers vary by tail length, double bond position, and cis vs. trans at each C=C

• Saturated: no C=C, straight tail, packs tightly, higher melting point, usually solid (fats)

• Unsaturated: 1 or more C=C, cis bonds kink the tail, packs loosely, lower melting point, usually liquid (oils)

• Monounsaturated = 1 C=C, polyunsaturated = 2 or more

• Longer tail raises melting point, more double bonds lower it

• Building block of triglycerides (via ester bonds with glycerol) and phospholipids

ALKANE NAMES

meth/eth/prop, but, pent, hex, hept, oct (don toliver), non, dec

Proteins

• Made mostly of C, H, O, and N (sulfur in cysteine and methionine)

• Nitrogen is what sets them apart from carbs and fats

• Monomer: amino acid (20 types)

• Each has an amine, carboxyl, H, and R group on a central carbon

• Joined by peptide bonds or amide links via dehydration synthesis

• R group decides polarity and acid/base behavior

• Functions: enzymes, structure, transport, defense, signaling

ok sum random helpful stuff

Backbone: amine is basic, carboxyl is acidic, peptide bond is polar

• R groups vary: nonpolar, polar, acidic (negative), or basic (positive)

Fats/lipids

• Made mostly of C, H, and O, with far more H than carbs have

• Little oxygen compared to the amount of carbon, which makes them nonpolar

• Phospholipids add phosphorus (and sometimes nitrogen)

• Not true polymers, so there is no repeating monomer

• Building blocks: glycerol and fatty acids

• Triglyceride = 1 glycerol + 3 fatty acids, joined by ester bonds via dehydration synthesis

• Nonpolar and hydrophobic, so they do not dissolve in water

• energy storage, insulation, membranes, hormones

Carbs

• Made of C, H, and O, usually in a 1:2:1 ratio (CH2O)n

• Monomer: monosaccharide (glucose, fructose, galactose)

• Joined by glycosidic bonds via dehydration synthesis

• Disaccharides: sucrose, lactose, maltose

• Polysaccharides: starch, glycogen, cellulose, chitin

• Polar and hydrophilic, because of all the hydroxyl groups

• Functions: quick energy, energy storage, structure (cellulose, chitin)

Donates H+ ions

ACID ph < 7

Receives H+ ions

BASE ph > 7

Proteins: Functional Grps

functional grps
Amine (-NH2): in every amino acid, basic

• Carboxyl (-COOH): in every amino acid, acidic

• Amide: the peptide bond between amino acids

• Alkane: nonpolar R groups (alanine, valine, leucine, isoleucine)

• Alcohol/hydroxyl (-OH): serine, threonine, tyrosine, polar

• Sulfhydryl/thiol (-SH): cysteine, forms disulfide bonds

• Thioether (C-S-C): methionine

• Phenyl/aromatic ring: phenylalanine, tyrosine, tryptophan, nonpolar

• Extra carboxyl: aspartate, glutamate (acidic R groups)

• Extra amine: lysine, arginine, histidine (basic R groups)

• Extra amide: asparagine, glutamine (polar R groups)

• Phosphate/phosphoester: not built in, but added to serine, threonine, and tyrosine

Not found in proteins: aldehyde, ketone, ester, ether, alkene, alkyne

Fats: Functional grps

• Alkane: the hydrocarbon tails

• Alkene: C=C in unsaturated tails

• Carboxyl: head of a free fatty acid, acidic

• Alcohol/hydroxyl: glycerol (3 of them), also on cholesterol

• Ester: links fatty acids to glycerol in triglycerides

• Phosphate: head of phospholipids, negative charge

• Phosphoester: links phosphate to glycerol in phospholipids

• Amine: in some phospholipid heads (phosphatidylethanolamine, phosphatidylserine)
  
  Not typically found in fats: aldehyde, ketone, amide, ether, sulfhydryl, thioether, alkyne

Carbs: Functional grps

• Alcohol/hydroxyl: on nearly every carbon, makes sugars polar

• Aldehyde: in aldose sugars like glucose (open chain)

• Ketone: in ketose sugars like fructose (open chain)

• Ether: the ring oxygen in cyclic sugars

• Amine and amide: in modified sugars like chitin (N-acetylglucosamine)

• Phosphate/phosphoester: in sugar phosphates like glucose-6-phosphate and in ribose of nucleotides

Not typically found in carbs: alkene, alkyne, carboxyl, ester, phenyl, sulfhydryl, thioether

Alkane Alkene Alkyne equations

alkane = Cn H2(n+2)
alkene = Cn H2n
alkyne = Cn H2(n-2)

hydrogen bonds

weak bond between hydrogen and another atom

• Glycerol

• C3H8O3, three-carbon chain with one -OH on each carbon

• Polar and hydrophilic, neutral (the -OH groups do not donate H+ in water)

• 3 alcohol/hydroxyl, 1 alkane backbone (3 sp3 carbons)

• 0 chiral centers (C2 has two identical CH2OH groups)

• No stereoisomers

• Backbone of triglycerides and phospholipids

• dissolves fully in water

• GLYCERALDEHYDE

• C3H6O3, HOCH2-CHOH-CHO

• Polar, neutral

• 1 aldehyde, 2 alcohol/hydroxyl

• Simplest aldose (an aldotriose)

• 1 chiral center (C2), so 2 enantiomers: D-glyceraldehyde and L-glyceraldehyde

• look at what side the OH group is on: IF OH IS IN LINE WITH UPPER O, then its D-, if OH is in line with upper H, then its L

• D-glyceraldehyde is the reference that defines D and L for all sugars

• Structural isomer: dihydroxyacetone (a ketone, 0 chiral centers)

this is the d-enantiomer

• RIBOSE

• C5H10O5, five-carbon sugar (pentose)

• Ring form is a furanose (5-membered ring: 4 carbons + 1 oxygen) (what is this who knows)

• Polar, neutral

• 4 alcohol/hydroxyl (C1, C2, C3, and the CH2OH on C5), 1 ether (the ring oxygen)

• 4 chiral centers in the ring (C1, C2, C3, C4), 3 in the open chain

• Open-chain isomers: 8 aldopentose stereoisomers (ribose, arabinose, xylose, lyxose, each with D and L) (lowkey no clue what this means ok ignore it)

• Found in RNA (backbone), ATP, NADH, FAD