Term
| there are, in essence, two types of carbohydrates, name them and determine how they differ from each other |
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Definition
there is ketoses where the carbonyl group is attached to any carbon but the terminal carbon
there is aldose where the carbonyl group and oxygen are attached to the terminal carbon of the carbohydrate chain |
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Term
| last exam we discussed amino acids which had a single chiral center, no we're discussing sugars, but what is different about their chirality |
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Definition
| since carbohydrates are composed carbon chains (~5-6 carbons), they have several chiral centers and are optically active |
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Term
| is there a way that we can determine how many possible isomers there can be from one carbohydrate chain |
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Definition
yes, 2^(n)
n being the number of chiral carbons in the chain |
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Term
| epimers are essentially isomers but differ from each other how |
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Definition
| epimers are isomers but vary at a single carbon, that is, they are identically similar but one carbon is stereochemically different to the other |
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Term
| we mentioned that sugars have a higher propensity to do chemistry, how so |
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Definition
| carbohydrates are composed of carbons Chains, have multiple chiral centers, have many hydroxyl groups good for hydrogen bonding, and will perform hemiacetal reactions internally on itself |
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Term
| it was determined earlier that sugars can do internal reactions, but why wouldn't reactions occur with carbon 1 and carbon 2 |
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Definition
| the reaction between carbond 1 and carbon 2 is so unfavorable that it would likely not occur, however, a carbon further down, say carbon 5 would be most favorable because of the small amount of steric strain |
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Term
| what determines whether a reaction occurs between carbon 1 and 2, carbon 1 and 3, etc. |
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Definition
steric strain, which ever has the least amount will be most favorable
unless of course something else acts on the sugar |
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Term
| once an internal reaction occurs, what structures are formed and how can you tell them apart |
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Definition
five and six carbon ring structures are formed, but specifically, alpha & beta-antomers are formed
the only way that you can tell the difference between them is to tell which way the hydroxyl group is pointing (this is apparent because those carbons are still optically active-it has stereochemistry)
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Term
| what is the relationship between the alpha and beta-antomers called and what does it entail |
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Definition
| their relationship is called a mutaroational relationship, which is basically the optical rotation ratio between alpha and beta antomers |
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Term
| how does changing the properties of carbohydrates beneficial |
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Definition
| by changing the properties of sugars, changes the chemistry of the molecule, and therefore, changes the way it interacts with it's environment |
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Term
| what types of modifications can we do to sugars and why is it so readily possible to do modifications |
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Definition
| can have acidic sugars, can phosphorylate, and all this can happen because nature has many hydroxyl groups to use and decorate |
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Term
| when sugars are in their linear forms, what types of reactions can we use to find quantitative conclusions |
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Definition
| we can do redox reactions to discover how many reducing ends we have |
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Term
| why cant we do redox reactions when the sugar is in it's cyclic form |
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Definition
| because when its in the cyclic form, its locked |
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Term
| We've learned that we cannot run redox reactions when sugars are in their cyclic form, then why should we run it anyways? |
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Definition
| it can be beneficial to run the assay to determine if there are any non-reducing disaccahrides |
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Term
| based on the placement of the hydroxyl groups on a sugar, what can suppose will differ in the structure's of sugars |
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Definition
| polysaccharides will have different 3-D structures depending on which hydroxyl groups are involved in the hemiacetal chemistry |
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Term
| why is chitin characterized as a structural polysaccharide |
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Definition
| it is a modified sugar that can resist degradation from environmental elements |
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Term
| dense polysacchride sugars are also found all over the cell walls of cells and the more delicate organelles within the cells, what purposes do they often serve there |
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Definition
| depending on the alterations of sugars, dense polysacchrides can act as antibiotics, resist pH changes and even counter osmotic pressures |
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Term
| agarose is another altered polysacchride, how is it altered and what does the alteration serve to do |
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Definition
| the long polymers are sulfinated and act as insulation, also used in electrophoresis gel agar |
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Term
| altered polysacchrides are also present in the extracellular matricies of cells, what purposes do these sugar polymers serve way out of the cell |
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Definition
they form a meshwork of polysacchrides (semi-permeable membrane), like a net, that increase the overall surface area to which water can bind
therefore, when the proteins of these cells are in solution they have more of an affinity towards protein-ligand binding
remember that water keeps cells together (non-polar form close together to reduce their hydrophobic surface are to water)
It is also important that cells stay hydrated to maintain mobility |
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Term
| like our cells, bacteria also have extracellular matricies that also act as a meshwork or net, sugars are attached to enzymes that target these EM, what is it and how does it work |
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Definition
the enzyme called lysozyme have sugars that recognize specific sequences on bacterial extracellular matricies and target them and break them down
these are located at every orphaces of the human body |
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Term
| hyaluronan is a carbohydrate polymer that serves specific functions in a specific area of the eye, where in the eye and what does it do |
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Definition
| hyaluronan forms a clear viscous solution that hydrates your eyes and is found predominately in the vitreous humor |
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Term
what can be found in cartilage, tendons, and walls of the aorta
its function is to add tensile strength, and is most prevalent in areas of high stress
this is a carbohydrate polymer and glycosaminoglycan |
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Definition
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Term
| what is the problem with all glycosaminoglycan edible supplements |
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Definition
| how does it get to the right area in the body, once it enters the stomach, it could be broken down and utilized in a number of ways, how do we know that it makes it to the desired location? |
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Term
another glycosaminoglycan is found in nails, hooves and bone and horns
what is it called and based on the areas it is most prevalent, what does it act to do |
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Definition
| keratin sulfate and it is hard, external and gives a rigid structure on the body |
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Term
another gylcosaminoglycan can inhibit coagulation and is often used in unclogging IV lines
what is it and why can it sometimes be too dangerous |
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Definition
| this is called heparin and its dangerous because it prevents coagulation (blood forms clots) and sometimes nurses and doctors administer too much, for example give a adult dosage instead of a infant dosage to infants |
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Term
| based on the few glycosaminoglycans we discussed, what can we purpose about sugars and their structures |
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Definition
| polysacchrides have many structures and these structures provide for many different functions internally and externally in the body |
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Term
| at this point, you know that structure plays a important role in determining function, what component of structure can you look at more closely now |
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Definition
geometry and structure, Phi and Si = 170 and -170 degrees
begin to think about sugar's structure and function by the degrees of freedom between polymers
the plot for polysacchrides is 3-dimensional, the thhird dimension is sigma |
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Term
| what will polysacchrides do to increase their surface area and why will they do it |
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Definition
| polysacchrides will begin to form helices to increase their surface area and this helps them increase the affinity between the hydroxyls on the sugar and the water, this increase the sugar and water "dance" |
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Term
| besides being structural, what else can sugars be |
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Definition
| they can be information carriers and convey information by thehir sequence and the sequence is determined by how it is put together |
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Term
| by now we know that glycosaminoglycan are composed of repeating dissachrides, but there is another group of these proteins that are highly glycosylated, what are they |
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Definition
proteoglycans are found at the cells surface and made up of covalently bound glycosaminoglycan, which is typicalled a Ser
to illustrate, it looks like a small polypeptide with large sugar attachments |
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Term
| in discussing proteoglycans, we discovered that Ser is the amino acid residue involved in the covalently bound protein to the glycosaminoglycans, what reaction makes this possible |
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Definition
| a condensation reaction with serine to make covalent bond occurs |
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Term
| a syndecan is an example of an intergral protein, what glycosaminoglycans are attached to this protein, and what is their purpose besides the covalently bound interaction |
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Definition
glycosaminoglycan like chondroitin sulfate and heparin sulfate
besides the covalent interaction with the peptide, the glycosaminoglycan dont have any other interactions with the peptide itself
however, they do have carboxyl groups that have charge and want to interact with other opposite charged molecules in solution |
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Term
| by now you've learned about syndecans, an integral protein, what other integral protein have you learned about |
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Definition
glypicans are dense and rigid portions of the extracellular wall that give hydration and structure
the can be visualized as an extension of the cell wall that provides a buffer or mesh from nig molecules like bacteria and viruses |
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Term
| when discussing glypicans, you may wonder why they dont just float away, why is that |
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Definition
| the reason they don't float away is because the network of integral proteins acts like a a net and some of them are anchored into the cell wall, and by anchored, I mean covalently bound |
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Term
| illustrate what a hyaluronate looks like |
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Definition
| this proteoglycan is a long polypeptide with other smaller proteins hanging off of it that have keratan sulfate and chondroitin sulfate glycosaminoglycan attached |
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Term
| what is the difference between glycosaminoglycan and glycoproteins |
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Definition
| glycoproteins provide for more diversity than glycosaminoglycan through O-linkages and N-linkages |
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Term
| what are the differences between O-linkages and N-linkages |
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Definition
O-linkages: are through the amino acid residues Ser and Thr and are all made in the ER
N-linkages: Asn is created by use of the amine group on this amino acid residue
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Term
what is the term given to the conjugation of proteins and a small # of sugars
and what is the term given to this formation and where does it happen |
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Definition
| glycoproteins are formed through glycosylation which happens in the ER, where specific amino acid residues are used (O-linked & N-linked), and then these go to the Golgi for repackaging and exportation to both external and internal areas of the cell |
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Term
| now you know where glycoproteins are created, but where can addition sugars be added to the glycoprotein |
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Definition
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Term
| you know that the principles of biochemistry are very complex, so besides glycoprotein formation, what other kind of conjugations can occur |
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Definition
glycolipids can also be formed, for example, gangliosides are lipids of the outer membrane that have sugars added to help our cells differentiate between our own cells and also invading cells
also blood cells are another example |
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Term
| you've learned that red blood cells are an exmaple of glycolipids, why is that |
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Definition
depending on your personal blood type, you have a sequence of sugars attached to the out lipid membrane of your red blood cells, erthrocytes, that extend from the membrane
your body uses this sequence to determine if you're cells are invasive or safe
thats why O is the universal blood donor because it only has the core sequence of sugars attached to it |
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Term
| by now you know that your red blood cells have glycolipids on their outer membranes, what do gram negative bacteria have that is very similar and what do they do |
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Definition
gram negative bacteria have lipopolysacchrides which are long chains of polysacchrides that increase the affinity for water and other molecules
these can also be toxic-these sugars have been known to create sepsis and kill invading molecules |
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Term
| at this point there is some indication that function and sequence of carbohydrates (sugars) are related to each other, what ideas can you make from this |
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Definition
the idea of a sugar code, like that of the amino acid code, there is a relationship between the sequence of the sugar and the function of it as well
for example, a six carbon sugar has five potential hydroxyl groups that can be altered chemically to change the overal function of the sugar |
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Term
| the sugar code presents another phenomena, which is |
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Definition
there is a large diversity with sugars
for example, there are 1.44 x 10^15 possible combinations of hexameric oligosacchrides |
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Term
| so now that you have this idea of the sugar code, what is the purpose of the sugar code, why have it at all |
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Definition
there is a giant post of cellular compartments that need function and there must be a way to identify, mark, package and send sugars to them
this includes cell-cell communication, cell across tissue communication
think of the sugar code as a barcode system for intracellular targeting, and communication |
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Term
| when discussing the purpose of the sugar code, like cell to cell communication and cell targeting, what do you really mean by cell targeting |
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Definition
| more specifically it could mean cell differentiation, like the interaction with certain hormones, which cell will act with the release of a specific cascade of chemical reactions and which cells will get attacked that are invasive |
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Term
| you've been going on and on about this sugar code and how benficial it is for cell to cell communication and differentiation, but what is so great about a sugar code that cannot be read? there must also be an equally great receptor that can read this complex sugar code, what is it |
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Definition
Lectins have the ability to read the sugar code, and like the vast variaty of sugar combinations, there are many different types of lectins out there: cell to cell recognition, signaling and targeting
lectins have a very high specificity and affinity towards sugars |
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Term
| as a biochemist, it is to our benefit to begin thinking about how we can use nature to our advantage, what can lectins do for us experimentally |
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Definition
| you can use lectins to determine the half-life because they make physical interactions with red blood cells, erthyrocytes, and there is a possibility of sugar breaking off, this loss of information will be marked for an uptake reaction and termination of a physiological response. |
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Term
| other than using lectins in the laboratory, how are lectins utilized in the world of food preseveration and food display and how are they physically able to do this |
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Definition
lectins are amphipathic, which means they have both polar and non-polar regions associated with their structures, and are often used in salad dressing that contain lipids, water and sugar
lectins will partially interact with the oil and sugar, then the sugar becomes an amulsification |
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Term
| why does your body never need to physically injest carbohydrates |
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Definition
| gluconeogenisus is the formation of carbohydrates from fat within the body, and from fats and meats injested |
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Term
| there is a specific kind of lectin that are bound to the membranes of cells, what are they called and what function do they serve |
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Definition
| selectins are a specialized class of lectins that mediate cell to cell recognition |
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Term
| how to selectins, one, interact with an invading cell, and two, how do they provoke white blood cells to attack |
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Definition
| selectins are placed throughout the cell membranes of the capillary walls, so when an infection reaches a cell, they start to give off invasive signaling because the receptors of the selectins do not match those of the cell's sugar code, so these invasive interactions with our selectins provoke the white blood cells to attack the invading cells |
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Term
| as a biochemist, what could you do to help determine the selectivity and function of the sugar code, sugar sequence in general |
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Definition
| I could manipulate the active site of lectins |
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Term
| we understand that we can manipulate lectins active site to find out the function of sugar codes, but what does this tell us about the nature of lectins without our intervention |
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Definition
| lectins manipulate the geometry of suagrs to accentuate the polar and non-polar affinities |
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Term
| how do biochemists isolate sugars and characterize them |
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Definition
| use chemical reactions, mass spec., size exclusion chromatography, and NMR to isolate and identify |
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