Phosphate esters of many monosaccharides, not just ATP, participate in metabolic pathways. Hydrolysis of these monosaccharides yields varying amounts of energy depending on the free energy of the molecule, with ATP having the largest free energy of hydrolysis. Like polypeptides and polynucleotides, polysaccharides are metastable. Their hydrolysis is thermodynamically favorable, but kinetically slow, and catalyzed by specific enzymes. Another similarity between polysaccharides and proteins is their use within organisms. Plants use structural sugars like cellulose where animals would use structural proteins such as keratin or collagen. The repetitive monosaccharide sequence of some structural polysaccharides are reminiscent of the repetitive amino acid structures of collagen (Gly-X-Y, X being mostly proline, Y being mostly hydroxyproline) and silk fibroin (mostly Gly, some Ala and Ser). I appreciated the numerous comparisons made between cellulose and silk fibroin, including that both pack in ribbons with H bonds between them. Also how chitin and collagen serve similar functions within the skeletons of invertebrates and vertebrates. I guess if a system "works" in nature, it gets used as much as possible..

Unlike polypeptides and polynucleotides, however, polysaccharides are not formed from template molecules such as RNA or DNA. Instead, the addition of each monosaccharide to the end of the growing chain is catalyzed by enzymes specific to the linkage between the particular pair of monosaccharides being connected. Each monosaccharide can form several different linkages due to the multiple hydroxyl groups around the ring.

In high school biology, we learned that some proteins carried carbohydrate "tags" that told them where to go in the cell, and helped phagocytes identify them; this was revisited on page 309. This chapter also included a lot of organic chemistry, in its discussions of carbohydrate stereochemistry. It was interesting to note that different enantiomers of monosaccharides were used in different places in various organisms (page 282). I thought it was especially interesting to learn about how cells store glucose by building it into the polymer glycogen, which is "branched" so that many branch ends at once can be attacked by enzymes to "nibble" glucose off for fast usage.

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I found these sections extremely easy as well as interesting to

read. General organic chemistry knowledge really helped understand the

conformational concepts. I did not know there were 2 types of striated

muscles, but I now understand why there is a difference between the white

and the dark meat on a chicken. I also think it is interesting how

formaldehyde is the empirical formular for "sugar," yet is absolutely

nothing like a sugar. I also think it is interesting that nature prefers

the L-amino acids, yet the D-sugars. Overall, I enjoyed these sections a

lot.

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Chapter 8 looks at the structure and function of molecular motors.

The begining of the chapter discusses the importance of actin and

myosine in the contraction of muscles, as well as in cell division

at the end of mitosis. Do they also act in cell cleavage in meiosis?

I found it really interesting that the Ca2+ influx from the muscle

impulse is what triggered the muscle contration, I had learned the

importance of Ca in both systems previously but had not connected the

to. The chapter then looks at the function of microtubules both in

protien transport and in the mobility ofbacterium, as well as the

rotating bacterial motor. I think it would be really neat to see a

movie or something of the way a bacterium rotates by changing the way

its flagellum spin.

Chapter 9 looks at the structure and function of carbohydrates. It

begins by discussing the chiral forms of carbohydrates and the

differences between them. It focuses on nomenclature, identifying

the two main forms of carboyhdrates aas aldoses and ketoses. The

chapter then looks at more stuctural componants of carbohydrates and

the polysacrides they can form. I had a little trouble following the

ways to tell disacchrides apart, and I still don't have a clear

understanding of how it is done. The chapter then looks at the

structure of the bacterial cell wall and finishes by discussing

glycoproteins. I had a little trouble understanding the section on

glycoproteins and what they are exactly. I found the discusion of

lectins to be especally confusing.

***

chapter eight is about the motion of proteins. specifically contractile

systems and molecular motors. the interatction are based on two major

proteins, actin and myosin. the movement of chromosomes is the

interactions with microtubules which is made of tubulin. there are

variety of molecular motors that carry molecules and vesicles by

filaments. because energy released by hydrolysis of ATP can be converted

into work through the production of motion in parts of protein, it can act

as a energy transducer. actin can exist as F-actin, which is a long

helical polymer, or G-actin, which is a globular protein monomer. The

G-actin bind ATP leading to polymerization, hydrolyzing the ATP. ADP is

held in actin filament. the F-actin having assymetric subunits, has two

ends, plus and minus end. the plus end grows more rapidly. actin

filament has sites in the subunit can bind to myosin. myosin, composed of

six polypeptide chain (2 identical heavy chains, 2 of 2 kinds of light

chains), can be cleaved by proteases. the tail domain can be cleaved by

trypsin to be light meromyosin and heavy meromyosin. the cleavage of the

heavy meromyosin by papin cuts it to be two S1 fragments and S2, the

stalk. myosin and actin can react with each other to form different

filament.

there three morphologically distinct kinds of muscle: straiated, smooth,

and cardiac. myofibers, which contain myofibrils that exhibits dark A

bands with a cenral H zone alternating with lighter I bands having Z

disks, is called the sarcomere. thin filaments of actin interdigitate

with myosin thick filaments. the cross-bridges between myosin and actin

filaments are the key to muscle contraction. the mechanism of contraction

is the sliding filament model. the myosin headpieces are presumed to

"walk" along the interdigitated actin filaments, pulling them past, which

shortens the sarcomere. the energy comes from ATP hydrolysis that causes

the release of actin-myosin interaction. calcium cases the stimulation of

contraction. troponins I, C, and T are bound to tropomyosin which preents

binding of myosin heads to actin with calcium. myofiber, which are

surrounded by sarcoplasmic reticulum that has high concentrations of

Ca+2. through transverse tubules the signal is transmitted to the

sarcoplasmic reticulum.

red muscle primary energy is the oxidation of fat, while white muscle

relies on glycogen. When ATP levels fall, an intermediary which

phosphorylates ADP efficiently is creatine kinase. actin and myosin can

also be found in eukaryotic cells. actin is a major component of

cytoskeleton giving specific shape to cell. cytokinesis is the

intracellular actin-myosin contractile complex that is the division of

cells in the final stages of mitosis. ctokinesis can be completely

blocked without myosin. cilia is held dwon by an anchoring structure,

basal body. the motion of cilia and flagella is cytoplasmic dynein.

bacterial flagellum composed of flagellin rotates in motion. they also

respond to chemicals, chemotaxis, going towards nutrients and repels from

poisons.

chapter nine goes into carbohydrates also known as saccharides. there are

monosaccarides, disaccharides, oligosaccharides, and polysaccharides

containing the stoichiometric formula (CH2O)n. monosaccharides are the

simple monomeric sugars such as glucose. the smalles molecules are

trioses, n=3, glyceraldehyde and dihydroxyacetone. the first being in the

class of aldoses and the latter in the ketoses. these exist as

enantiomers, D- or L-glyceraldehyde. also R-S convention can be

used. monosaccharides existas enantiomers in nature. tetrose have two

chiral carbons, existing as diastereomers, opposite orientations about the

carbons. there are pentoses, aldopentose have three chiral

centers. ketopentose have two chiral carbons and four isomers. hexose

having six carbons can have many orientations. the pentose and hexoses

can also exist as ring structures. the five memember ring is furanose and

six as pyranose. there can also be stereoisomers with beta and alpha

rotation. if its only at carbon 1, it is an anomer. it can convert

between the two forms, mutarotation. the enzyme mutarotase catalyzes the

process. the cyclic sugar can be represented through Haworth

projection. hexose rings can also be represented in alpha and beta

form. it can be in the stable form, chair, or less favored boat

form. there is also the existance of longer chained carbons, but play a

minor part in nature. there are derivative of monosaccharides. phosphate

esters, acids and lacetons, alditols, amino sugars, and

glycosides. disaccharides have four major distinguishing features. two

specific sugar monomers and their seteroconfigurations, carbons in

linkage, order of the two monoer units, and anomeric configuration of

hydroxyl group of carbon 1. the glycosidic bond is stabile, forming

between two monomers by elimination of a water molecule. ploysaccharides

serve mainly to store for energy. they are unually stored as amylose and

amylopectin. plants rely of special polysaccharides while animals use and

synthesize and use these fibrous structural proteins. cellulose is the

most abundant single polymer. chitin is like cellulose, but it

sonstitutes the major structural material for exoskeltons, an d a matrix

for vertebrate bones. glycosaminoglycans are connective tissue and

skin. jproteoglycan is a carbohydrate complex in cartilage which extend

to core protein noncovalently. this can also be sulfated, heparin, which

is a natural anticoagulant found in body tissues. inhibits blood clotting

process. bacteria have a cell wall of polysaccharide,

peptidoglycan. glycoprotein serve many different functions. there are

N-linked are in intracellular targeting in eukaryotic organisms. O-linked

glycans can serve as antifreeze in fish, and mucins are found in salivary

secretions. also in blood group antigens. the lipid molecule is in form

of a glycolipid, which helps anchor the antigen to the outside surface of

erthrocyte membranes. oligosaccharides are cell markers. there are

certain proteins that bind them. basically carbohydrates in some form in

part of everything in our body, which let us exist.

***

Myosin and actin proteins work together to create a contractile motion

system. Crossbridges of headpieces of the myosin molecules between the

myosin and actin filaments are the key to muscle contraction. The sliding

filament model describes the myosin headpieces „walking‰ along the

interdigited actin filaments as thin and thick filaments slid past one

another. I imagine a sheet of interlocking zippers. The formation of

crossbridges between myosin and actin depend on the presence of high enough

levels of calcium in the system. This contractile motion is driven by a

cycle of ATP hydrolysis and rephosphorilation.

Contractile motion systems are important for other biological systems

because including the mobility of eukaryotic cells via cilia and flagellum

and the movement of sperm. Contained within cilia and flagellum are a

highly organized bumdle of microtubules called an axoneme encased within a

plasma membrane. The axoneme is connected to a basal body embedded within

the cell. This system is again propelled by reaction with ATP. The

flagellum of bateria ehibit motility through a different system. The

flagellum consist almost entirely of one fibrous protein flagellum. The

protein rotates and thus creating mobility for the bacteriaThe driving force

comes from the creation of a prtein gradient generated by ATP hydrolysis as

protons move across the bacterial inner membrane. The flagellum can

rotateeither clockwise or counterclockwise creating some directionality of

motion. Bacteria can also exhibit chemotaxis, a response to chemicals. These

bacteria move toward attractants and away from repellants.

While I can see the design of the contractile motion system, I do not fully

understand how the ATP binds and fuels the system.

The presence of carbohydrates are important biologically because they are

required in both photosynthesis and respiration. They are categorized by

the number of sugar units and their stereochemistry. The number of

possible stereoisomers is dependent upon the number of stereocenters

contained within the molecule. a molecule with n stereocenters will have 2n

stereoisomers. Thus the larger the sugar the exponentially larger numbers

of possible stereoisomers. Sugar phosphates are important intermediates in

metabolism, functioning as activation synthases. Glycosaminoglycans are

important as connective tissue. Cellulose is the major polysachharide in

woody and fibrous plants. It contains primarily a linear polymer of

D-glucose. While similar structurally to starch, animals who can cleave

starch molecules cannot cleave cellulose. Saccharide cahins can be linked to

proteins through glycan bonds. N linked glycans are attached through

N-acetylglucoamine to an asparagines residue. O-linked glycans are attached

by N-acetylgalactosamine and hydroxyl group of threonine or serine residue.

Some of us are just trying to get through the day without breaking anything