Biochem Exam 3

What are the function of polysaccharides?

Storage, structure, and recognition

What is a homopolysaccharide and a heteropolysaccharide?

Homo: the polysaccharide contains only one type of monosaccharide

Hetero: the polysaccharide contains more than one type of polysaccharide

What polysaccharides are storage molecules?

Starch (energy reserve in plants)

Glycogen (storage molecule in animals)

Dextran (bacteria - dental plaque)

What polysaccharides are structural molecules?

Cellulose (plant cell wall)

Chitin (fungi and exoskeleton cell wall)

Alginates (marine brown algae)

Agarose (marine red algae)

Glycosaminoglycans (extracellular)

Discuss starch.

Starch is a plant storage polysaccharide. It has two forms: amylose and amylopectin. It is 10-30% amylose and 70-90% amylopectin.

Discuss the differences between amylose and amylopectin.

Amylose:

• alpha (1-4) linkage on the main chain

• one reducing end

• no branches

• a-amylose has a helical structure

Amylopectin:

• alpha (1-4) linkage on the main chain

• alpha (1-6) linkage for the branches

• branches every 12-30 residues

Why does branching occur in starch?

Phosphorylase releases glucose-1-P products from amylose or amylopectin. It is cleaved from the terminal, non-reducing end. The more branches, the more site for phosphorylase attack and the release of more glucose for energy. The branches in amylopectin provide a mechanism for the quicker and easier release of glucose, but it doesn’t mean that it necessarily has more energy.

Discuss glycogen.

It is an animal storage polysaccharide. It makes up 10% of liver mass and 1-2% of muscle mass. It is stored energy for the organism. The only different between it and amylopectin is that glycogen is even more highly branched. There are alpha (1,6) branches every 8-12 residues. The main molecule has alpha (1,4) linkage. It has a red-violet color with iodine like amylopectin.

Discuss dextrans.

Dextrans are formed by bacteria and are components of dental plaque. The main chain linkage is alpha (1,4). Branches can be (1,2), (1,3), or (1,4). Cross-linked dextrans are used in Sephadex columns.

How does the composition of structural polysaccharides differ from storage ones?

Structural polysaccharides have beta (1,4) linkage. Small structural differences greatly influence properties.

Discuss cellulose.

It is a plant cell wall structural polysaccharide and is the most abundant polymer in the world. Cotton, wood, and bark contain cellulose. It has beta (1,4) linkage of glucose molecules that allows it to adopt a fully extended conformation, compared to the helical conformation of amylose. Interchain and intrachain hydrogen bonds strengthen the parallel sheets of cellulose.

Discuss chitin.

It is a structural polysaccharide that is in the exoskeleton of insects, spiders, crustaceans, and the cell walls of fungi. It is the second most abundant polymer. It is similar to cellulose but has N-acetyl C2s. The strands can be parallel or antiparallel. It has beta (1,4) linkage of N-acetylglucoseamine.

Discuss agarose and agaropectin.

They are galactose polymers. Agarose is a comment of agar from marine red algae with a chain of alternating D-galactose and 3,6-anhydro-L-galactose. In water, agarose favors a double helix conformation with a threefold screw axis. Agarose gels are used in labs to separate based on size.

Discuss glycosaminoglycans.

They are linear chains of repeating disaccharides with one being an amino sugars and one or both having negative charges.

Examples:

• heparin has a high negative charge and is a natural anticoagulant

• dermatan sulfate is a component of the extracellular matrix of skin

• glycosaminoglycans are constituents of proteoglycans

Discuss bacterial cell walls.

They are made of one or two bilayers and a peptidoglycan shell.

Gram-positive bacteria have a thick peptidoglycan outer shell surrounding the cell membrane. The pentaglycine bridge connects tetrapeptides.

Gram-negative have a thin peptidoglycan shell between the outer and inner cell membrane. There is a direct amide bond between tetrapeptides.

Discuss the structure of peptidoglycan.

It is a chain of linked tetrapeptides.

D-Ala linked to L-Lys linked to isoglutamate linked to L-ALA linked to a sugar

L-Lys links to the peptidoglycans.

Discuss the structure of gram-positive peptidoglycan.

There is a pentaglycine crosslink between the amino acids and the next chain of amino acids. It is a pentaglycine bridge that forms a crosslink between tetrapeptides. The cell wall has a single bilayer membrane with a peptidoglycan coat that reacts with the gram stain.

Discuss the structure of gram-negative peptidoglycan.

The linkage between tetra peptide segments involves a direct amide bond between L-Lys and D-Ala. There is no pentaglycine crosslink. They are considered hairy. The cell wall has two bilayers with peptidoglycan in between and lipopolysaccharides coming off the top layer. The grams stain cannot react with the peptidoglycan.

Discuss the structure of lipopolysaccharides.

They consist of a lipid group that is anchored in the outer membrane that is connected to a polysaccharide made of long chains with various repeating structures.

What is the role of the glycoproteins and proteoglycans on the surface of animal cells?

They regulate cell-cell recognition and interaction. Their uniqueness is determined by the enzymes that synthesize the polysaccharides.

What are glycoproteins?

It is a protein with one or more carbohydrates attached to the polypeptide backbone. They can be N-linked or O-linked. N-linked saccharides are attached via the amide nitrogens of asparagine resides. O-linked saccharides are attached to hydroxyl group of serine, threonine, or hydroxylysine.

What are the types of N-linked glycoproteins?

High mannose: branches contain mannose only

Complex: branches contain different sugars

Hybrid: one branch has mannose and the other contains different ones

Discuss O-linked saccharides in glycoproteins.

They adopt an extended conformation that resembles bristle brushes that can extend the functional domains above the glycocalyx.

How do polar fish depend on antifreeze glycoproteins?

The glycoproteins have repeats of AAT and the thr residues are glycosylated with disaccharides. Chains of the glycoproteins form flexible rods with regions of threefold left-handed helices. These surround one crystals and inhibit further growth.

Discuss N-linked saccharides in glycoproteins.

The oligosaccharides can alter the chemical and physical properties of the protein. They can stabilize protein conformations and/or protect against proteolysis.

The cleavage of monosaccharide units from N-linked glycoproteins in blood targets them for degradation in the liver and can serve as a timing device for protein degradation.

What are proteoglycans?

They are glycoproteins whose carbohydrates are mostly glycosaminoglycans O-linked to serine residues. They are components of the cell membrane and the glycocalyx. They typically consist of proteins with one or two types of glycosaminoglycan. They can include soluble and membrane proteins.

Ex: transmembrane protein syndecan

What is the glycome?

It is the complete set of glycine and glycoconjugates that are made by a cell/organism.

Are all biological lipids amphipathic?

Yes

What are the different classes of lipids?

• fatty acids

• triacylglycerols

• glycerophospholipids

• sphingolipids

• wxes

• isoprene-based lipids (steroids)

Discuss fatty acids.

A carboxylic acid with a long-chain hydrocarbon side group, typically joined to a glycerol backbone in ester linkage. They are made of a long hydrocarbon tail and a terminal carboxyl head. The carboxyl group is typically deprotonated at physiological pH. They are usually esterified to glycerol/other backbones and are rarely in a free, uncomplexed state. They usually have an even number of carbons and the most common length is 16.

What is the difference between saturated and unsaturated fatty acids?

Saturated: no double bonds, linear, chains pack closer and tighter and are more rigid/organized

Unsaturated: double bond(s) in cis confirmation, kink/bend in the structure, chains pack in a less ordered way with greater potential for motion, more dynamic, not as hard to separate

• monounsaturated if only one double bond

• polyunstaurated if multiple double bonds

What is the name of the fatty acid with 16 carbons?

Palmitic acid

Why are longer fatty acids more stable?

They have more hydrophobic and van der Waals interactions.

What is a lipid?

It is a biological molecule that is largely or wholly hydrophobic and insoluble in water but soluble on organic solvents.

Discuss triacylglycerols/triglycerides.

They are a major energy source for many organisms because they are the most reduced form of carbon in nature with efficient packing and no solvation needed. They a lipid in which three fatty acids are esterfied to a glycerol backbone. Found primarily in adipose tissue/body fat. They can pack closely. Simple ones have the same three fatty acids and mixed ones have two or three different fatty acids.

Discuss glycerophospholipids.

Amphiphilic lipid with two fatty acyl groups attached to a glycerol-3-phosphate with the phosphate group linked to a polar group. It is a 1,2-diacylglycerol that has a phosphate group esterified at C3 of the glycerol backbone. If a phospholipid has an unsaturated fatty acid, it is likely at the 2 position and not at the C1 position, otherwise it would be harder to pack close and it would affect membrane structure.

What are ether glycerophospholipids?

They have an ether (R-O-R) linkage instead of an ester linkage at the C1 position of glycerol.

Ex: PAF - platelet activating factor

What is a plasmalogen?

It is an ether glycerophospholipid with an unsaturated alkyl chain, likely at C1.