Daily Newsletter: September 6, 2013 - Carbohydrates and Lipids

Daily Newsletter

September 6, 2013    Carbohydrates and Lipids

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Carbohydrates

While carbohydrates are mainly used as chemical energy storage, carbohydrates are also used as modifiers of proteins and in forming cellular receptors and anchors. One of your goals is to gain a good understanding of the structure of carbohydrates, and a little about their naming.

A topic that will come up throughout the semester is how carbons are numbered in carbohydrates. This is important as we will find carbohydrates being components of monomers and when we move through the carbohydrate catabolism. The following image from Rensselaer Polytechnic Institute shows the linear form of glucose, and the two possible cyclic (pyranose ring) isomers.

The formation is based on aldehyde chemistry, so we will leave some of this discussion to organic chemistry and biochemistry. For our purpose this semester, what is important is that we number carbons from the aldehyde. Notice in the above diagram that carbon 1 is to the left of the oxygen, we go around to carbon 5, and then carbon 6 is outside of the ring. If you see the expression 3', it is referring to the third carbon. 5' the fifth carbon. 6' the sixth carbon, and so forth.

Notice also, that when the ring was formed, there were differences in the groups coming off of carbon 1. These differences are important, and can influence how the sugar is metabolized. We say that these different forms are isomers (if you don't know what an isomer is, look it up and add the definition to your notebook).

One critical difference comes when linking two monosaccharides together to form disaccharides and polysaccharides. For instance (again from rpi.edu), here is maltose:

This is an α 1-4 glycosidic linkage. We have an α Maltose (look at carbon 1) bound from carbon 1 to carbon 4. Since the maltose on the left hand side is α at the 1 carbon, we form an α linkage. In comparison, look at cellobiose:

Cellobiose has a β 1-4 glycosidic linkage. The designation of β comes from the sugar unit that donates carbon 1 to the bond.

So, what is the big deal? Maltose is digestible by humans, cellobiose is not. Just this slight isomeric difference changes the metabolism.
All carbohydrate monomers are connected through glycosidic linkages, whether it is a disaccharide, oligosaccharide or a polysaccharide. Make sure that you learn the different types of carbohydrates.

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Lipids

Lipids are an odd group of biomolecules. Proteins, Carbohydrates and Nucleic Acids are all formed through polymerization reactions; they have monomeric units that join to make polymers. Lipids do not polymerize, and they have no monomers. Instead, Lipid is a word that defines a class of hydrophobic organic compounds found in living systems. There are a number of important groups of Lipids, such as the triglycerides, phospholipids and cholesterols. Today, we are going to concentrate on the triglycerides and the phospholipids.
Both triglycerides and phospholipids possess a glycerol molecule and fatty acids. Glycerol is a 3 carbon compound that we will see from time to time. It acts as the backbone or schaffold of the triglycerides and phospholipids. As you can see, on each carbon atom, there is a hydroxyl group (-OH). This hydroxyl group is where other molecules can bond. Another thing to note is that there is free rotation around the carbon atoms. When you take organic chemistry, you will learn more about free rotation, why it is important, and how it can affect a molecule. For now, just note that there can be free rotation.
Fatty acids are long hydrocarbon chains with a carboxyl group (-COOH) at one end. To the left is a diagram of palmitic acid, a typical saturated fatty acid. In this diagram, each angle on the line represents a carbon atom, and off of these carbon atoms are hydrogens. This is one of many ways that organic chemicals are depicted. Below the first depiction is a molecular model. Carbon atoms are in black, and the white balls are hydrogens. What you will begin to recognize in these diagrams is that there are only single bonds between the carbon atoms. This means that the maximum number of hydrogen atoms are attached to the fatty acid. In other words, they are saturated with hydrogen.
In contrast, an unsaturated fatty acid does not have the maximum number of hydrogen atoms. This occurs when double bonds (two electrons from each carbon are shared) occur in the carbon chain. To the right is a diagram of oleic acid. Note that there is a double bond in the carbon chain. Notice that the chain is bent, or kinked. This creates a very different structure for lipids that carry unsaturated fatty acids.
As a general rule, saturated fatty acids are solid at room temperature, and unsaturated fatty acids are liquid in room temperature. But one thing is the same in both: the carbon chains are HYDROPHOBIC!
In a triglyceride, the carboxyl end of the fatty acid will react with the hydroxyl end of the glycerol. As you can see in the diagram, the two molecules are joined together through an oxygen molecule. As with other biosynthetic reactions, this is a dehydration synthesis (water is released). The resulting bond, as noted in the diagram, is an ester bond. You will learn more about this bond in organic chemistry, so for now I just want you to remember the general look of it. Why is this so critical? Because not all living organisms make triglycerides and phospholipids this way. Member of domain Archaea use an ether bond.
So, what is the difference between a triglyceride and a phospholipid? Recall the look of the glycerol, and note that there are three locations where an ester bond can be formed. In a triglyceride, a fatty acid will be bound to each of the carbon atoms by ester bonds. Tri- means three, so we have three fatty acids attached to the glycerol. The image to the right is an example of a triglyceride, and please note, you can have more than one type of fatty acid in a triglyceride.
The phospholipid in contrast only has two fatty acids. The third binding location will be used for a "phosphate head". This head contains a phosphate group and usually a diglyceride and some small charged organic structure. Phosphytidyl choline is a commonly studied phospholipid that uses choline as the charged organic structure. NOTE: both the phosphate group and the organic structure carry a charge. This phosphate head is charged, thus it is hydrophillic (water loving). The phospholipid contains non-polar, hydrophobic fatty acids (usually referred to as the tails) and a polar, charged, hydrophillic head. This molecule is both hydrophobic and hydrophillic. Amphiphathic is the word we use to describe a molecule with both hydrophobic and hydrophillic properties. A main use for the phospholipid is in biological membranes, as shown in the image to the right.

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Daily Challenge

Proteins, carbohydrates and nucleic acids have the ability to form complex polymers.  Proteins and nucleic acids have their function is determined by the sequence of monomers.  Phospholipids can spontaneously form sealed spheres that create an inside vs. an outside.  All life functions rest upon the diversity of these chemicals.  The basics of biochemistry that you have learned this week will be expanded upon throughout the coming weeks.  You will see further examples of proteins, carbohydrates, nucleic acids and lipids.

Your goal is to start building mental models of what they are and how they interact.  Draw out the structures, write out a full dehydration synthesis or hydrolysis.  What factors cause proteins to fold?  What would occur if you used saturated fatty acids in a phospholipid?  What about non-saturated fatty acids?  Take some time and really build an idea about each of these molecules, and appreciate the diversity.
After spending time, write in the discussion forum your thoughts and ideas about these biochemicals.  (This is a free form discussion where you can write about proteins,carbohydrates and lipids.  The focus is for you to express your understanding of the structure and function of the three biochemical categories, but you are also welcome to pose questions regarding what you do not understand about these chemicals.)
Link to Discussion Forum

Daily Newsletter: September 4, 2012 Phospholipid Bilayer & Passive Transport

Daily Newsletter

September 4, 2012 The Phospholipid Bilayer & Passive Transport

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The basic structure of the cellular membrane is composed of Phospholipids. You will recall the introduction to phospholipids found in Daily Newsletter: August 29, 2012 - Carbohydrates and Lipids. The amphipathic nature of phospholipids means that they will naturally associate with one another. Specifically, the hydrophobic tails want to be with other hydrophobic compounds, and exclude polar compounds (Hydrophobic Exclusion-This is a good concise discussion of the topic by Stephen T. Abedon, Ph.D. at Ohio State). Below is a brief movie that shows what happens when phospholipids in water begin to interact.

Phospholipid Movie: Bilayer formation through molecular self-assembly

The resulting phospholipid bilayer is polar (hydrophilic) on the outside, while the middle is non-polar (hydrophobic). The sides interact with water, but the middle excludes polar substances. This creates a selectively permeable barrier, and is the basis of the membranes function. Changing phospholipids and adding sterols (like cholesterol) will change the integrity and stability of this basic membrane structure.
Selective permeability means that only certain classes of chemical can make it through the phsopholipid bilayer. For other chemicals, we need to provide a protein to serve as a pore, channel or transporter.
In general, there are two ways that a chemical can be moved across the membrane: Down the chemical's concentration gradient (diffusion), or Against the chemical's concentration gradient. When a chemical moves down it's concentration gradient, we do not need to add energy to the process. The concentration gradient and the kinetic energy of the molecule (Brownian Motion) provided the needed energy. We call this form of movement Passive Transport.

There are three basic forms of passive transport through the membrane:

1. Diffusion - Using the inherent Brownian motion of molecules, chemicals move from points of high concentration to points of low concentration.

• Every chemical has a unique concentration gradient.
• The concentration gradient of one molecule will not interfer with the concentration gradient of another molecule.
• What interfers is the ability to move across the cellular membrane (phospholipid bilayer).
• Molecules with high polarity, ions, and large molecules are excluded by the phospholipid tails, and thus can not cross.
• Water*, CO₂, O₂, and nonpolar compounds (lipids) can cross though diffusion.
• Water moves through very slowly; water moves across more readily due to porins (protein pores) possessed by cells to make sure water and small polar compounds can cross readily.

Osmosis - The movement of water across a selectively permeable membrane.

• Water goes to where the party is, meaning it will move to a compartment that has a higher solute concentration.
• Since we are talking about two fluid compartments on either side of a membrane, we are ultimately talking about relative solute concentrations.
• REMEMBER: you are looking at two fluid compartments, so when we are looking at osmosis, we are discussing the movement of water across a selectively permeable membrane from one fluid compartment to a second fluid compartment.
• In biology we always use the inside of the cell as our reference, so:
  • An isotonic fluid has the same solute concentration as the inside of the cell.
  • A hypertonic solution has a solute concentration that is higher than the solute concentration inside the cell.
  • A hypotonic solution has a solute concentration that is lower than the solute concentration inside the cell.

• Remember that we are looking at solute concentrations, not the concentration of a single chemical.
  • Diffusion gradients are specific for each chemical.
  • Osmosis is determined by total solute concentration on each side of a selectively permeable membrane.

Facilitated Diffusion - Ultimately, this is diffusion, but the cell has had to provide a passage for the chemical. So, this only applies to chemicals that can not normally pass through the phospholipid bilayer.

• The cell provides a protein channel or pore for the chemical to pass through.
• Each channel or pore is specific to a single chemical or set of chemicals.
• Since this is an protein (enzyme) mediated action, the ability to transport follows standard enzyme kinetics.
• The core idea about facilitated diffusion following enzyme kinetics is that diffusion becomes limited by the number of channels or pore available.
• Note: You will generally build up a large concentration of a compound on one side of the membrane. We will refer to this as a steep gradient (high on one side, low on the other).
• The facilitator proteins will allow molecules from the HIGH side to move toward the LOW side; hence the use of the word diffusion.
• Rarely will the channel or pore (facilitator) allow transport in the reverse direction for the same ion.

In each case, the cell does not need to expend energy to move the chemical across the membrane. The motive force is built in to the chemical gradients. Remember, the cell membrane is going to provide an internal vs. an external space (compartment). Each side of the membrane will have a unique chemical profile. As such, there will be concentration gradients across the membrane.

Osmosis Movie

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Important Memes

Occassionly, there will be a phrase that I want you to remember to help you as you move through biology.

1. Water goes to where the party is! (This is a great way to remember in what direction water will flow across a selectively permeable membrane in response to changes in osmolarity, aka, solute concentration).
2. The phospholipid bilayer establishes the structure of the membranes, but the proteins provide the function. (The proteins embedded in the membrane will determine the functional capabilities of the membrane).
3. When something is added to a protein, the protein changes shape.

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Daily Challenge: Passive transport

In your own words, describe passive transport. Concentrate on osmosis and facilitated diffusion by providing an example that illustrates each action. Make sure you use an example that uses a cell (not beakers, flasks, etc...).

Daily Newsletter: August 29, 2012 - Carbohydrates and Lipids

Daily Newsletter

August 29, 2012 Carbohydrates and Lipids

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Carbohydrates

While carbohydrates are mainly used as chemical energy storage, carbohydrates are also used as modifiers of proteins and in forming cellular receptors and anchors. One of your goals is to gain a good understanding of the structure of carbohydrates, and a little about their naming.

A topic that will come up throughout the semester is how carbons are numbered in carbohydrates. This is important as we will find carbohydrates being components of monomers and when we move through the carbohydrate catabolism. The following image from Rensselaer Polytechnic Institute shows the linear form of glucose, and the two possible cyclic (pyranose ring) isomers.

The formation is based on aldehyde chemistry, so we will leave some of this discussion to organic chemistry and biochemistry. For our purpose this semester, what is important is that we number carbons from the aldehyde. Notice in the above diagram that carbon 1 is to the left of the oxygen, we go around to carbon 5, and then carbon 6 is outside of the ring. If you see the expression 3', it is referring to the third carbon. 5' the fifth carbon. 6' the sixth carbon, and so forth.

Notice also, that when the ring was formed, there were differences in the groups coming off of carbon 1. These differences are important, and can influence how the sugar is metabolized. We say that these different forms are isomers (if you don't know what an isomer is, look it up and add the definition to your notebook).

One critical difference comes when linking two monosaccharides together to form disaccharides and polysaccharides. For instance (again from rpi.edu), here is maltose:

This is an α 1-4 glycosidic linkage. We have an α Maltose (look at carbon 1) bound from carbon 1 to carbon 4. Since the maltose on the left hand side is α at the 1 carbon, we form an α linkage. In comparison, look at cellobiose:

Cellobiose has a β 1-4 glycosidic linkage. The designation of β comes from the sugar unit that donates carbon 1 to the bond.

So, what is the big deal? Maltose is digestible by humans, cellobiose is not. Just this slight isomeric difference changes the metabolism.
All carbohydrate monomers are connected through glycosidic linkages, whether it is a disaccharide, oligosaccharide or a polysaccharide. Make sure that you learn the different types of carbohydrates.

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Lipids

Lipids are an odd group of biomolecules. Proteins, Carbohydrates and Nucleic Acids are all formed through polymerization reactions; they have monomeric units that join to make polymers. Lipids do not polymerize, and they have no monomers. Instead, Lipid is a word that defines a class of hydrophobic organic compounds found in living systems. There are a number of important groups of Lipids, such as the triglycerides, phospholipids and cholesterols. Today, we are going to concentrate on the triglycerides and the phospholipids.
Both triglycerides and phospholipids possess a glycerol molecule and fatty acids. Glycerol is a 3 carbon compound that we will see from time to time. It acts as the backbone or schaffold of the triglycerides and phospholipids. As you can see, on each carbon atom, there is a hydroxyl group (-OH). This hydroxyl group is where other molecules can bond. Another thing to note is that there is free rotation around the carbon atoms. When you take organic chemistry, you will learn more about free rotation, why it is important, and how it can affect a molecule. For now, just note that there can be free rotation.
Fatty acids are long hydrocarbon chains with a carboxyl group (-COOH) at one end. To the left is a diagram of palmitic acid, a typical saturated fatty acid. In this diagram, each angle on the line represents a carbon atom, and off of these carbon atoms are hydrogens. This is one of many ways that organic chemicals are depicted. Below the first depiction is a molecular model. Carbon atoms are in black, and the white balls are hydrogens. What you will begin to recognize in these diagrams is that there are only single bonds between the carbon atoms. This means that the maximum number of hydrogen atoms are attached to the fatty acid. In other words, they are saturated with hydrogen.
In contrast, an unsaturated fatty acid does not have the maximum number of hydrogen atoms. This occurs when double bonds (two electrons from each carbon are shared) occur in the carbon chain. To the right is a diagram of oleic acid. Note that there is a double bond in the carbon chain. Notice that the chain is bent, or kinked. This creates a very different structure for lipids that carry unsaturated fatty acids.
As a general rule, saturated fatty acids are solid at room temperature, and unsaturated fatty acids are liquid in room temperature. But one thing is the same in both: the carbon chains are HYDROPHOBIC!
In a triglyceride, the carboxyl end of the fatty acid will react with the hydroxyl end of the glycerol. As you can see in the diagram, the two molecules are joined together through an oxygen molecule. As with other biosynthetic reactions, this is a dehydration synthesis (water is released). The resulting bond, as noted in the diagram, is an ester bond. You will learn more about this bond in organic chemistry, so for now I just want you to remember the general look of it. Why is this so critical? Because not all living organisms make triglycerides and phospholipids this way. Member of domain Archaea use an ether bond.
So, what is the difference between a triglyceride and a phospholipid? Recall the look of the glycerol, and note that there are three locations where an ester bond can be formed. In a triglyceride, a fatty acid will be bound to each of the carbon atoms by ester bonds. Tri- means three, so we have three fatty acids attached to the glycerol. The image to the right is an example of a triglyceride, and please note, you can have more than one type of fatty acid in a triglyceride.
The phospholipid in contrast only has two fatty acids. The third binding location will be used for a "phosphate head". This head contains a phosphate group and usually a diglyceride and some small charged organic structure. Phosphytidyl choline is a commonly studied phospholipid that uses choline as the charged organic structure. NOTE: both the phosphate group and the organic structure carry a charge. This phosphate head is charged, thus it is hydrophillic (water loving). The phospholipid contains non-polar, hydrophobic fatty acids (usually referred to as the tails) and a polar, charged, hydrophillic head. This molecule is both hydrophobic and hydrophillic. Amphiphathic is the word we use to describe a molecule with both hydrophobic and hydrophillic properties. A main use for the phospholipid is in biological membranes, as shown in the image to the right.

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Administrative Notes

I have rearranged a few things on the BOLO site to help in navigation. When you are on the main course screen, you will note a box on the top left that tells you about upcoming assignments. Currently it is showing Quiz 1 and Milestone Paper 1. Below the newsletter link is a new link for an archive. In the archive you will find links to all previous forums. Use the archive to recover anything you have written.
Completion check marks: There were issues with the completion check marks for the first week. I changed settings, and they seem to be working for week 2. Remember that you will need to start one discussion and then comment on three different discussions to receive the check mark.
You may have noticed that in each forum, it provides a link for you to download your post for an ePortfolio. This was included so that you can download material as you wish. Remember that the forum posts will help you write your milestone paper.
In the newsletter, if you come across a word that you don't know, make a note of it. Look it up and keep it in your notes. As you will note, I sometimes will tell you that another class will take you deeper into a concept. This is not telling you that it is not useful now, it is just telling you that it will come back up in later classes. Consider this as a topic you will need to pay close attention to in your next class. For our purpose, you will only need a superficial understanding of the concept. It will come back though in multiple different courses.

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Daily Challenge

This was a long newsletter, but it covers the basics of carbohydrates and lipids. What you need to do now is put these foundational concepts into your brain. We consume examples of both of these biomolecules. So what I want you to do is discuss the polymerization and breakdown of carbohydrates, and the formation and breakdown of triglycerides.