BBE 4001 MASTER LIST

Proteins in plant materials

natural polymer, contains carbon, nitrogen, and sulfur for growth and development. They serve as structural components, enzymes, and play a role in metabolic processes.

amino acids

the building blocks of proteins, consisting of a central carbon atom, an amino group, a carboxyl group, and a unique side chain. They link together via peptide bonds to form proteins.

what does the “L” mean in l-amino acid?

Indicates that the amino group is on the left side of the fischer projection.

what does the “alpha” mean in alpha-L-amino acid?

indicates that the amino acid is on the alpha carbon.

amphoteric/zwitterion

a molecule that can donate a positive and/or a negative charge (amino acids are these)

Different R groups in amino acids

• Contains Sulfur

• Contains a Carboxyl group

• Contains a basic amino group

• Neutral

• Contains an -OH group

polypeptides

amino acids linked by polypeptide bonds. Point of bond rotation limited due to resonance structure containing a double bond

peptide bond

covalent bond between amino acids, connects amino group to the carboxyl group

primary structure

amino acid sequence

secondary structure

arrangement of primary structure; alpha-helix or beta folded sheet

tertiary structure

arrangement of secondary structure in space, ex. coiled up helix

quaternary structure

arrangements of several proteins in one structure

how do protein structures stay together?

• hydrogen bonds

• ionic bonds

• hydrophobic/philic interactions

• electrostatic forces

• covalent bonds (eg. sulfur bonds)

• side group (R) size

denatured protein

happens after a protein is exposed to high heat (65-90C) or low pH; non-reversable unfolding of their structure, loss of functionality

what is corn protein/zein used for?

coating and plastics

isoelectric point

where the concentration of the dipolar ion is at maximum

enzyme

a catalyst that changes the rate of reaction without being consumed in the process by lowering the activation energy— reaction rate 10^6 to 10^12 higher

how are enzymes effective?

structure provides active site

substrate specific and based on active site

will only react with their substrate—one reaction with one substrate but done very efficiently

how do enzymes catalyze reactions

• active site provides a template for two or more reactants to come together in the right orientation

• can stretch or distort the substrate molecule to make bonds that need to be broken weaker

• active sites with amino acids that contain acid groups can provide a pocket of low pH

enzymatic reaction rate depends on…

• substrate concentratiom

• increase in temperature, optimal temperatures between 30 and 50C

• increase in pH, optimal pH between 6-8

• binding affinity; how fast the substrate could get to the active site and how fast the product can leave

cofactors

• often inorganics like metal

• assists enzyme by binding to the enzyme

• metals often found in redox reactions

platform chemical

starting material that can be converted to useful materials for other applications

what is used for cellulose/hemicellulose hydrolysis to produce sugars?

acids or enzymes

is hemicellulose or cellulose easier to convert?

hemicellulose is easier to convert than cellulose since it can dissolve

why are stronger acids needed for cellulose?

to ensure crystalline areas are attacked

problems with hemicellulose/cellulose hydrolysis

• hard to isolate the cellulose

• acid and enzymes are hindered by lignin

• biomass needs pretreatment to open up cells

pretreatment methods need to…

• reduce size of particles

• reduce crystalline areas, potentially with ball milling

• produce a homogeneous mixture

mechanical method

• milling/grinding

  • creates a higher surface area

  • homogeneous mixture

  • breaks up some crystalline areas

  • considered a necessity

steam explosion (hydrothermal)

• steam in pressurized vessels (180-280C)

• short retention time, quick release of pressure

  • explodes cells

  • natural acids (acetic acid) start to break down polysaccharides

  • breaks some LCCs

hot water treatment

• presteaming/hot water extraction

• 20 minute retention time

  • natural acids released

  • large part of hemicelluloses removed

  • little lignin removed

  • cells open

thermochemical treatment, Acid

• uses sulfuric, HCl, SO2, or nitric acid (diluted)

• causes random chain cleavage

thermochemical treatment, alkaline

• Uses NaOH or Ca(OH)2

• causes peeling reactions + dissolving

• takes out hemicellulose and lets enzymes react with cellulose

thermochemical treatment, AFEX

Ammonia Fiber Expansion

• water/conc. ammonia, 60-140C, 5-45 min

• explosive release

• ammonia can be recovered and used as N source, like fertilizer

• Removes acetyl groups and LCC bonds to open cell wall, may dissolve some lignin

chemical treatment

most often used for removing lignin

• oxygen

• ozone

• peracetic acid, etc.

biological treatment, fungi

uses white rot which can eat lignin (with a bit of carbs), but can take a long time

how does lignin hinder enzymes?

Lignin can get in the way physically, and cellulase enzymes sometimes attaches to lignin instead and inhibit themselves

biological treatment, esterases

breaks ester bonds in LCC, takes a day or two

biological treatment, laccases

oxidative and can remove lignin, takes a day or two

furfural reaction

strong acids and high temperatures applied to pentoses

glucose to hydromethylfurfural

(under acid conditions)

1. acid conditions cause OH group on C3 to leave as water, H on C2 moves down to form double bond

2. OH group on C4 gets protonated, double bonds shift

3. H on C5 forms double bond, C3-C4 double bond moves up, C2 double bond moves electrons back to O

4. C2 OH electrons go to C2, forming a ring. double bonds shift accordingly

5. OH on C1 becomes double bond, bonds shift accordingly

HMF to levulinic acid

succinic acid

biomass → pretreatment → fermentable sugars (enzyme/acid) → microorganisms + CO2 → product

• Reaction consumes CO2

• platform chemical

lactic acid monomer reaction

lactic acid dimer reaction

Bio-isobutanol to paraxylene reaction

Paraxylene to tereptalic acid

why is the lactic acid dimer reaction preferred over the monomer reaction?

• since the monomer reaction is reversible, the acid would get taken apart as you are making it

• the dimer reaction creates a cyclic structure that allows for a more efficient and stable polymerization process

enzymatic hydrolysis

uses a mixture of cellulase to break down cellulose including:

• endocellulase

• exocellulase

• beta-glycosidase

endocellulase

breaks down crystalline areas

exocellulase

breaks down glucose into small subunits

beta-glucosidase

breaks down 2-4 subunits to glucose

ABE process

process that produces acetone, butanol, and ethanol using solventogenic clostridia and fermentation

• can use easily digestible sugars, cannot directly digest cellulose (needs to be pretreate)

paraxylene

feedstock for terephthalic acid (PTA), can be made from bio-isobutanol

terephthalic acid (PTA)

monomer used in the production of polythylene terephthalic (PET)

polylactic acid (PLA)

made from plant starch, compostable; needs heat and water to break down

polyhydroxyalkanoate (PHA)

biodegradable polymers (polyester) produced by bacteria— can be degraded by other organisms right away

similar to petroleum based polymers

PHB

produced by genetically engineered soil bacteria as energy storage, biodegradeable

plant bottle

30% renewable material and 100% recyclable—made with ethylene glycol and terephtalic acid

• only 30% because terephtalic acid does not have viable pathways for renewable production

xylitol

also called wood/birch sugar, sugar alcohol from hydrogenating (reacting with H2) xylose. used as a low calorie sugar substitute

sorbitol

also called glucitol, sugar alcohol of glucose. low calorie sweetener

maltitol

sugar alcohol of maltose

sucralose

600 times sweeter than table sugar but contains chlorine in its chemical structure

turpentine

solvent for varnishes and paints, produced using polymerization to polyterpenes (pressure sensitive or hot melt adhesives)— used in fragrances and insecticides as well

plasticizer

material mixed with polymers to make more flexible (ex. PVC)

used to be made with phtalates but creates health issues

soft and safe

plasticizer — acetylated monoglyceride of castor oil, replaces fatty acid in triglyceride with acetyl group

most common use of lignin

burning for energy

lignin based products

• vanillin

• DMS and DMSO

• phenol formaldehyde resins

• dispersant, emulsifier

• tanning agent

where would you get lignin from?

pulping liquors, organosolve (needs high temperatures and pressure, also hard to recycle solvent)

vanillin

flavoring agent, produced from softwood lignin (G-lignin) and fermentation

• 2-12 hours at 100-165C with NaOH

• typical yield ~10% due to the production of other compounds (which get burned)

DMS and DMSO

produced from demethylation reactions with craft liquor and the addition of sulfur—used as a solvent

dissolving pulp

cellulose extraction, removal of hemicellulose, acid pre-hydrolysis, or alkaline pulping (low yield due to peeling)

alkali cellulose

also known as ripening; swelling of cellulose to different degress depending on metal

• if exposed to oxygen, can decrease degree of polymerization, but in this process you want shorter chains

• disassociates OH groups

cellulose reaction with acid

(esters)

NO2 reactive species, produces cellulose nitrate/guncotton

cellulose reaction with acid mechanism

degree of subsitution

number of free OH in cellulose that can be reacted with. Determines properties. (higher number means more explosive)

C3, has 2 more H-bonds and is more hindered

in DS, which carbon reacts the slowest and why?

cellulose sulfate

used as a viscosity modifier and has been trialed a a microbicide

cellulose acetate

bioplastic with many uses (plastic, films, fibers, coatings for glasses, etc)

cellulose acetate reaction

cellulose ethers

methyl and ethyl cellulose, used in thickening and dispersion agents (pseudoplastic)

cellulose ether reaction

carboxylmethylcellulose

most common water soluble cellulose, prepared from alkali cellulose and chloroacetate

used in detergents, food, and paper coatings for its water binding capability

cellulose xanthate

also known as rayon.

• xanthate dissolved in caustic → viscose

• spun into acid → rayon → regenerated cellulose

cellulose xanthate reaction

lyocell

newer process developed to address environmental concerns with rayon—cellulose directly dissolved in N-methylmorpholine N-oxide

spun into water bath with dilute amine oxide to regenerate cellulose

cellulose grafting

co-polymer system comprised of a backbone material (cellulose) where a second polymer is attached at intervals along the chain—done to improve compatibility/composite materials

viscose

xanthate + NaOH

rayon

also known as artificial silk…

regenerated cellulose

viscose + acid

water soluble

if a material has a low DS, it means…

What groups are included in the term "phenolic extractives"

-Lignans
-Tannins
-Flavonoids

Structure of Rubber vs guts percha

Rubber: 1-4-cis polymer
Guta Percha: 1-4 trans polymer

What do heartwood and bark often contain large varieties of?

Aromatic extractives

Phenolic extractives can be a problem in acid processes because they result in...

-burned chips
-condensation reactions

Does extractive content of wood increase or decrease during storage?

Decrease

What extractive group is lost first during storage?

Terpenes

What do all natural fatty acids have?

Even number of carbons

What is the immediate precursor of fatty acids?

Acetyl-CoA

What does the biosynthesis of fatty acids start with?

Glucose