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BIS2A Ireland Lecture 4

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    Biomolecules:  Carbohydrates

    Carbohydrates are one of the four main classes of macromolecules that make up all cells and are an essential part of our diet; grains, fruits, and vegetables are all natural sources. While we may be most familiar with the role carbohydrates play in nutrition, they also have a variety of other essential functions in humans, animals, plants, and bacteria. In this section, we will discuss and review basic concepts of carbohydrate structure and nomenclature, as well as a variety of functions they play in cells.

    Molecular structures

    In their simplest form, carbohydrates can be represented by the stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule. For simple carbohydrates, the ratio of carbon-to-hydrogen-to-oxygen in the molecule is 1:2:1. This formula also explains the origin of the term “carbohydrate”: the components are carbon (“carbo”) and the components of water (“hydrate”). Simple carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides, which will be discussed below. While simple carbohydrates fall nicely into this 1:2:1 ratio, carbohydrates can also be structurally more complex. For example, many carbohydrates contain functional groups (remember them from our basic discussion about chemistry) besides the obvious hydroxyl. For example, carbohydrates can have phosphates or amino groups substituted at a variety of sites within the molecule. These functional groups can provide additional properties to the molecule and will alter its overall function. However, even with these types of substitutions, the basic overall structure of the carbohydrate is retained and easily identified.

    Nomenclature

    One issue with carbohydrate chemistry is the nomenclature. Here are a few quick and simple rules:

    1. Simple carbohydrates, such as glucose, lactose, or dextrose, end with an "-ose." 
    2. Simple carbohydrates can be classified based on the number of carbon atoms in the molecule, as with triose (three carbons), pentose (five carbons), or hexose (six carbons).
    3. Simple carbohydrates can be classified based on the functional group found in the molecule, i.e ketose (contains a ketone) or aldose (contains an aldehyde).
    4. Polysaccharides are often organized by the number of sugar molecules in the chain, such as in a monosaccharide, disaccharide, or trisaccharide.

    For a short video on carbohydrate classification, see the 10-minute Khan Academy video by clicking here.

    Monosaccharides

    Monosaccharides ("mono-" = one; "sacchar-" = sweet) are simple sugars; the most common is glucose. In monosaccharides, the number of carbons usually ranges from three to seven. If the sugar has an aldehyde group (the functional group with the structure R-CHO), it is known as an aldose; if it has a ketone group (the functional group with the structure RC(=O)R'), it is known as a ketose.

    Figure 1. Monosaccharides are classified based on the position of their carbonyl group and the number of carbons in the backbone. Aldoses have a carbonyl group (indicated in green) at the end of the carbon chain and ketoses have a carbonyl group in the middle of the carbon chain. Trioses, pentoses, and hexoses have three, five, and six carbons in their backbones, respectively. Attribution: Marc T. Facciotti (own work)

    Glucose versus galactose

    Galactose (part of lactose, or milk sugar) and glucose (found in sucrose, glucose disaccharride) are other common monosaccharides. The chemical formula for glucose and galactose is C6H12O6; both are hexoses, but the arrangements of the hydrogens and hydroxyl groups are different at position C4. Because of this small difference, they differ structurally and chemically and are known as chemical isomers because of the different arrangement of functional groups around the asymmetric carbon; both of these monosaccharides have more than one asymmetric carbon (compare the structures in the figure below).

    Fructose versus both glucose and galactose

    A second comparison can be made when looking at glucose, galactose, and fructose (the second carbohydrate that with glucose makes up the disaccharide sucrose and is a common sugar found in fruit). All three are hexoses; however, there is a major structural difference between glucose and galactose versus fructose: the carbon that contains the carbonyl (C=O).

    In glucose and galactose, the carbonyl group is on the C1 carbon, forming an aldehyde group. In fructose, the carbonyl group is on the C2 carbon, forming a ketone group. The former sugars are called aldoses based on the aldehyde group that is formed; the latter is designated as a ketose based on the ketone group. Again, this difference gives fructose different chemical and structural properties from those of the aldoses, glucose, and galactose, even though fructose, glucose, and galactose all have the same chemical composition: C6H12O6.

    Figure 2. Glucose, galactose, and fructose are all hexoses. They are structural isomers, meaning they have the same chemical formula (C6H12O6) but a different arrangement of atoms.

    Linear versus ring form of the monosaccharides

    Monosaccharides can exist as a linear chain or as ring-shaped molecules. In aqueous solutions, monosaccharides are usually found in ring form (Figure 3). Glucose in a ring form can have two different arrangements of the hydroxyl group (OH) around the anomeric carbon (C1 that becomes asymmetric in the process of ring formation). If the hydroxyl group is below C1 in the sugar, it is said to be in the alpha (α) position, and if it is above C1 in the sugar, it is said to be in the beta (β) position.

    Figure 3. Five- and six-carbon monosaccharides exist in equilibrium between linear and ring form. When the ring forms, the side chain it closes on is locked into an α or β position. Fructose and ribose also form rings, although they form five-membered rings as opposed to the six-membered ring of glucose.

    Disaccharides

    Disaccharides ("di-" = two) form when two monosaccharides undergo a dehydration reaction (also known as a condensation reaction or dehydration synthesis). During this process, the hydroxyl group of one monosaccharide combines with the hydrogen of another monosaccharide, releasing a molecule of water and forming a covalent bond. A covalent bond formed between a carbohydrate molecule and another molecule (in this case, between two monosaccharides) is known as a glycosidic bond. Glycosidic bonds (also called glycosidic linkages) can be of the alpha or the beta type.

    Figure 4. Sucrose is formed when a monomer of glucose and a monomer of fructose are joined in a dehydration reaction to form a glycosidic bond. In the process, a water molecule is lost. By convention, the carbon atoms in a monosaccharide are numbered from the terminal carbon closest to the carbonyl group. In sucrose, a glycosidic linkage is formed between the C1 carbon in glucose and the Ccarbon in fructose.

    Common disaccharides include lactose, maltose, and sucrose (Figure 5). Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found naturally in milk. Maltose, or malt/grain sugar, is a disaccharide formed by a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose.

    Figure 5. Common disaccharides include maltose (grain sugar), lactose (milk sugar), and sucrose (table sugar).

    Polysaccharides

    A long chain of monosaccharides linked by glycosidic bonds is known as a polysaccharide ("poly-" = many). The chain may be branched or unbranched, and it may contain different types of monosaccharides. The molecular weight may be 100,000 Daltons or more, depending on the number of monomers joined. Starch, glycogen, cellulose, and chitin are primary examples of polysaccharides.

    Starch is the stored form of sugars in plants and is made up of a mixture of amylose and amylopectin; both are polymers of glucose. Plants are able to synthesize glucose. Excess glucose, the amount synthesized that is beyond the plant’s immediate energy needs, is stored as starch in different plant parts, including roots and seeds. The starch in the seeds provides food for the embryo as it germinates and can also act as a source of food for humans and animals who may eat the seed. Starch that is consumed by humans is broken down by enzymes, such as salivary amylases, into smaller molecules, such as maltose and glucose.

    Starch is made up of glucose monomers that are joined by 1-4 or 1-6 glycosidic bonds; the numbers 1-4 and 1-6 refer to the carbon number of the two residues that have joined to form the bond. As illustrated in Figure 6, amylose is starch formed by unbranched chains of glucose monomers (only 1-4 linkages), whereas amylopectin is a branched polysaccharide (1-6 linkages at the branch points).

    Figure 6. Amylose and amylopectin are two different forms of starch. Amylose is composed of unbranched chains of glucose monomers connected by 1-4 glycosidic linkages. Amylopectin is composed of branched chains of glucose monomers connected by 1-4 and 1-6 glycosidic linkages. Because of the way the subunits are joined, the glucose chains have a helical structure. Glycogen (not shown) is similar in structure to amylopectin but more highly branched.

    Glycogen

    Glycogen is a common stored form of glucose in humans and other vertebrates. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever blood glucose levels decrease, glycogen is broken down to release glucose in a process known as glycogenolysis.

    Cellulose

    Cellulose is the most abundant natural biopolymer. The cell wall of plants is mostly made of cellulose, which provides structural support to the cell. Wood and paper are mostly cellulosic in nature. Cellulose is made up of glucose monomers that are linked by β 1-4 glycosidic bonds.

    Figure 7. In cellulose, glucose monomers are linked in unbranched chains by β 1-4 glycosidic linkages. Because of the way the glucose subunits are joined, every glucose monomer is flipped relative to the next one, resulting in a linear, fibrous structure.

    Note: possible discussion

    Cellulose is not very soluble in water in its crystalline state; this can be approximated by the stacked cellulose fiber depiction above. Can you suggest a reason for why (based on the types of interactions) it might be so insoluble?

     

    As shown in the figure above, every other glucose monomer in cellulose is flipped over, and the monomers are packed tightly as extended, long chains. This gives cellulose its rigidity and high tensile strength—which is so important to plant cells. While the β 1-4 linkage cannot be broken down by human digestive enzymes, herbivores such as cows, koalas, buffalos, and horses are able, with the help of the specialized flora in their stomach, to digest plant material that is rich in cellulose and use it as a food source. In these animals, certain species of bacteria and protists reside in the rumen (part of the digestive system of herbivores) and secrete the enzyme cellulase. The appendix of grazing animals also contains bacteria that digest cellulose, giving it an important role in the digestive systems of ruminants. Cellulases can break down cellulose into glucose monomers that can be used as an energy source by the animal. Termites are also able to break down cellulose because of the presence of other organisms in their bodies that secrete cellulases.

    Interactions with carbohydrates

    We have just discussed the various types and structures of carbohydrates found in biology. The next thing to address is how these compounds interact with other compounds. The answer to that is that it depends on the final structure of the carbohydrate. Because carbohydrates have many hydroxyl groups associated with the molecule, they are therefore excellent H-bond donors and acceptors. Monosaccharides can quickly and easily form H-bonds with water and are readily soluble. All of those H-bonds also make them quite "sticky". This is also true for many disaccharides and many short-chain polymers. Longer polymers may not be readily soluble.

    Finally, the ability to form a variety of H-bonds allows polymers of carbohydrates or polysaccharides to form strong intramolecular and intermolocular bonds. In a polymer, because there are so many H-bonds, this can provide a lot of strength to the molecule or molecular complex, especially if the polymers interact. Just think of cellulose, a polymer of glucose, if you have any doubts.

    Biomolecules:  Nucleic acids 

    There are two types of nucleic acids in biology: DNA and RNA. DNA carries the heritable genetic information of the cell and is composed of two antiparallel strands of nucleotides arranged in a helical structure. Each nucleotide subunit is composed of a pentose sugar (deoxyribose), a nitrogenous base, and a phosphate group. The two strands associate via hydrogen bonds between chemically complementary nitrogenous bases. Interactions known as "base stacking" interactions also help stabilize the double helix. By contrast to DNA, RNA can be either be single stranded, or double stranded. It too is composed of a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is a molecule of may tricks. It is involved in protein synthesis as a messenger, regulator, and catalyst of the process. RNA is also involved in various other cellular regulatory processes and helps to catalyze some key reactions (more on this later). With respect to RNA, in this course we are primarily interested in (a) knowing the basic molecular structure of RNA and what distinguishes it from DNA, (b) understanding the basic chemistry of RNA synthesis that occurs during a process called transcription, (c) appreciating the various roles that RNA can have in the cell, and (d) learning the major types of RNA that you will encounter most frequently (i.e. mRNA, rRNA, tRNA, miRNA etc.) and associating them with the processes they are involved with. In this module we focus primarily on the chemical structures of DNA and RNA and how they can be distinguished from one another.

    Nucleotide structure

    The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA and RNA are made up of monomers known as nucleotides. Individual nucleotides condense with one another to form a nucleic acid polymer. Each nucleotide is made up of three components: a nitrogenous base (for which there are five different types), a pentose sugar, and a phosphate group. These are depicted below. The main difference between these two types of nucleic acids is the presence or absence of a hydroxyl group at the C2 position, also called the 2' position (read "two prime"), of the pentose (see Figure 1 legend and section on the pentose sugar for more on carbon numbering). RNA has a hydroxyl functional group at that 2' position of the pentose sugar; the sugar is called ribose, hence the name ribonucleic acid. By contrast, DNA lacks the hydroxyl group at that position, hence the name, "deoxy" ribonucleic acid. DNA has a hydrogen atom at the 2' position.  

    Figure 1. A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and one or more phosphate groups. Carbons in the pentose are numbered 1′ through 5′ (the prime distinguishes these residues from those in the base, which are numbered without using a prime notation). The base is attached to the 1′ position of the ribose, and the phosphate is attached to the 5′ position. When a polynucleotide is formed, the 5′ phosphate of the incoming nucleotide attaches to the 3′ hydroxyl group at the end of the growing chain. Two types of pentose are found in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose, but it has an -H instead of an -OH at the 2′ position. Bases can be divided into two categories: purines and pyrimidines. Purines have a double ring structure, and pyrimidines have a single ring.
    Attribution: Marc T. Facciotti (original work)

    The nitrogenous base

    The nitrogenous bases of nucleotides are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus acting as a base by decreasing the hydrogen ion concentration in the local environment. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T). By contrast, RNA contains adenine (A), guanine (G) cytosine (C), and uracil (U) instead of thymine (T). 

    Adenine and guanine are classified as purines. The primary distinguishing structural feature of a purine is double carbon-nitrogen ring. Cytosine, thymine, and uracil are classified as pyrimidines. These are structurally distinguished by a single carbon-nitrogen ring. You will be expected to recognize that each of these ring structures is decorated by functional groups that may be involved in a variety of chemistries and interactions.

    Note: practice

    Take a moment to review the nitrogenous bases in Figure 1. Identify functional groups as described in class. For each functional group identified, describe what type of chemistry you expect it to be involved in. Try to identify whether the functional group can act as either a hydrogen bond donor, acceptor, or both?

    The pentose sugar

    The pentose sugar contains five carbon atoms. Each carbon atom of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”). The two main functional groups that are attached to the sugar are often named in reference to the carbon to whch they are bound. For example, the phosphate residue is attached to the 5′ carbon of the sugar and the hydroxyl group is attached to the 3′ carbon of the sugar. We will often use the carbon number to refer to functional groups on nucleotides so be very familiar with the structure of the pentose sugar. 

    The pentose sugar in DNA is called deoxyribose, and in RNA, the sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the 2' carbon of the ribose and its absence on the 2' carbon of the deoxyribose. You can, therefore, determine if you are looking at a DNA or RNA nucleotide by the presence or absence of the hydroxyl group on the 2' carbon atom—you will likely be asked to do so on numerous occasions, including exams.

    The phosphate group

    There can be anywhere between one and three phosphate groups bound to the 5' carbon of the sugar. When one phosphate is bound, the nucleotide is referred to as a Nucleotide MonoPhosphate (NMP). If two phosphates are bound the nucleotide is referred to as Nucleotide DiPhosphate (NDP). When three phosphates are bound to the nucleotide it is referred to as a Nucleotide TriPhosphate (NTP). The phosphoanhydride bonds between that link the phosphate groups to each other have specific chemical properties that make them good for various biological functions. The hydrolysis of the bonds between the phosphate groups is thermodynamically exergonic in biological conditions; nature has evolved numerous mechanisms to couple this negative change in free energy to help drive many reactions in the cell. Figure 2 shows the structure of the nucleotide triphosphate Adenosine Triphosphate, ATP, that we will discuss in greater detail in other chapters.

    Note: "high-energy" bonds

    The term "high-energy bond" is used A LOT in biology. This term is, however, a verbal shortcuts that can cause some confusion. The term refers to the amount of negative free energy associated with the hydrolysis of the bond in question. The water (or other equivalent reaction partner) is an important contributor to the energy calculus. In ATP, for instance, simply "breaking" a phosphoanhydride bond - say with imaginary molecular tweezers - by pulling off a phosphate would not be energetically favorable. We must, therefore, be careful not to say that breaking bonds in ATP is energetically favorable or that it "releases energy". Rather, we should be more specific, noting that they hydrolysis of the bond is energetically favorable. Some of this common misconception is tied to, in our opinion, the use of the term "high energy bonds". While in Bis2a we have tried to minimize the use of the vernacular "high energy" when referring to bonds, trying instead to describe biochemical reactions by using more specific terms, as students of biology you will no doubt encounter the potentially misleading - though admittedly useful - short cut "high energy bond" as you continue in your studies.  So, keep the above in mind when you are reading or listening to various discussions in biology. Heck, use the term yourself. Just make sure that you really understand what it refers to.

     

    Figure 2. ATP (adenosine triphosphate) has three phosphate groups that can be removed by hydrolysis to form ADP (adenosine diphosphate) or AMP (adenosine monophosphate). Attribution: Marc T. Facciotti (original work)

    Double helix structure of DNA

    DNA has a double helix structure (shown below) created by two strands of covalently linked nucleotide subunits. The sugar and phosphate groups of each strand of nucleotides are positioned on the outside of the helix, forming the backbone of the DNA (highlighted by the orange ribbons in Figure 3). The two strands of the helix run in opposite directions, meaning that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand (See Figures 4 and 5). We referred to this orientation of the two strands as antiparallel. Note too that phosphate groups are depicted in Figure 3 as orange and red "sticks" protruding from the ribbon. The phosphates are negatively charged at physiological pHs and therefore give the backbone of the DNA a strong local negatively charged character. By contrast, the nitrogenous bases are stacked in the interior of the helix (these are depicted as green, blue, red, and white sticks in Figure 3). Pairs of nucleotides interact with one another through specific hydrogen bonds (shown in Figure 5). Each pair of separated from the next base pair in the ladder by 0.34 nm and this close stacking and planar orientation gives rise to energetically favorable base-stacking interactions. The specific chemistry associated with these interactions is beyond the content of Bis2a but is described in more detail here for the curious or more advanced students. We do expect, however, that students are aware that the stacking of the nitrogenous bases contributes to the stability of the double helix and defer to your upper-division genetics and organic chemistry instructors to fill in the chemical details. 

    Figure 3. Native DNA is an antiparallel double helix. The phosphate backbone (indicated by the curvy lines) is on the outside, and the bases are on the inside. Each base from one strand interacts via hydrogen bonding with a base from the opposing strand. Attribution: Marc T. Facciotti (original work)

    In a double helix, certain combinations of base pairing are chemically more favored than others based on the types and locations of functional groups on the nitrogenous bases of each nucleotide. In biology we find that:

    Adenine (A) is chemically complementary with thymidine (T) (A pairs with T)

    and

    Guanine (G) is chemically complementary with cytosine (C) (G pairs with C).

    We often refer to this pattern as "base complementarity" and say that the antiparallel strands are complementary to each other. For example, if the sequence of one strand is of DNA is 5'-AATTGGCC-3', the complementary strand would have the sequence 5'-GGCCAATT-3'. 

    We sometimes choose to represent complementary double-helical structures in text by stacking the complementary strands on top of on another as follows:

    5' - GGCCAATTCCATACTAGGT - 3'

    3' - CCGGTTAAGGTATGATCCA - 5'

    Note that each strand has its 5' and 3' ends labeled and that if one were to walk along each strand starting from the 5' end to the 3' end that the direction of travel would be opposite the other for each strand; the strands are antiparallel. We commonly say things like "running 5-prime to 3-prime" or "synthesized 5-prime to 3-prime" to refer to the direction we are reading a sequence or the direction of synthesis. Start getting yourself accustomed to this nomenclature.

    Figure 4. Panel A. In a double-stranded DNA molecule, the two strands run antiparallel to one another so that one strand runs 5′ to 3′ and the other 3′ to 5′. Here the strands are depicted as blue and green lines pointing in the 5' to 3' orientation. Complementary base pairing is depicted with a horizontal line between complementary bases. Panel B. The two antiparallel strands are depicted in double-helical form. Note that the orientation of the strands is still represented. Moreover, note that the helix is right-handed - the "curl" of the helix, depicted in purple, winds in the direction of the fingers of the hand if the right hand is used and the direction of the helix points towards the thumb. Panel C. This representation shows two structural features that arise from the assembly of the two strands called the major and minor grooves. These grooves can also be seen in Figure 3.  
    Attribution: Marc T. Facciotti (original work)

     

     

    base_pairing_labeled2.png

    Figure 5. A zoomed-in molecular-level view of the antiparallel strands in DNA. In a double-stranded DNA molecule, the two strands run antiparallel to one another so that one strand runs 5′ to 3′ and the other 3′ to 5′. The phosphate backbone is located on the outside, and the bases are in the middle. Adenine forms hydrogen bonds (or base pairs) with thymine, and guanine base pairs with cytosine. 
    Attribution: Marc T. Facciotti (original work)

    Functions and roles of nucleotides and nucleic acids to look out for in Bis2a

    In addition to their structural roles in DNA and RNA, nucleotides such as ATP and GTP also serve as mobile energy carriers for the cell. Some students are surprised when they learn to appreciate that the ATP and GTP molecules we discuss in the context of bioenergetics are the same as those involved in the formation of nucleic acids. We will cover this in more detail when we discuss DNA and RNA synthesis reactions.  Nucleotides also play important roles as co-factors in many enzymatically catalyzed reactions.

    Nucleic acids, RNA in particular, play a variety of roles in in cellular process besides being information storage molecules. Some of the roles that you should keep an eye out for as we progress through the course include: (a) Riboprotein complexes - RNA-Protein complexes in which the RNA serves both catalytic and structural roles. Examples of such complexes include, ribosomes (rRNA), RNases, splicesosome complexes, and telomerase. (b) Information storage and transfer roles. These roles include molecules like DNA, messenger RNA (mRNA), transfer RNA (tRNA). (c) Regulatory roles. Examples of these include various non-coding (ncRNA). Wikipedia has a comprehensive summary of the different types of known RNA molecules that we recommend browsing to get a better sense of the great functional diversity of these molecules.

    Biomolecules: Lipids

    Lipids are a diverse group of hydrophobic compounds that include molecules like fats, oils, waxes, phospholipids, and steroids. Most lipids are at their core hydrocarbons, molecules that include many nonpolar carbon-carbon or carbon-hydrogen bonds. The abundance of nonpolar functional groups give lipids a degree of hydrophobic (“water fearing”) character and most lipids have low solubility in water.  Depending on their physical properties (encoded by their chemical structure), lipids can serve many functions in biological systems including energy storage, insulation, barrier formation, cellular signaling. The diversity of lipid molecules and their range of biological activities are perhaps surprisingly large to most new students of biology. Let's start by developing a core understanding of this class of biomolecules. 

    Fats and oils

    A common fat molecule or triglyceride. These types of molecules are generally hydrophobic and, while they have numerous functions, are probably best known for their roles in body fat and plant oils.  A triglyceride molecule derived from two types of molecular components—a polar "head" group and a nonpolar "tail" group. The "head" group of a triglyceride is derived from a single glycerol molecule. Glycerol, a carbohydrate, is composed of three carbons, five hydrogens, and three hydroxyl (-OH) functional groups. The nonpolar fatty acid "tail" group consists of three hydrocarbons (a functional group composed of C-H bonds) that also have a polar carboxyl functional group (hence the term "fatty acid"—the carboxyl group is acidic at most biologically relevant pHs). The number of carbons in the fatty acid may range from 4–36; most common are those containing 12–18 carbons.

    Figure 1. Triacylglycerol is formed by the joining of three fatty acids to a glycerol backbone in a dehydration reaction. Three molecules of water are released in the process. 
    Attribution: Marc T. Facciotti (own work)

    Note: possible discussion

    The models of the triglycerides shown above depict the relative positions of the atoms in the molecule. If you Google for images of triglycerides you will find some models that show the phospholipid tails in different positions from those depicted above. Using your intuition, give an opinion for which model you think is a more correct representation of real life. Why?

    Figure 2. Stearic acid is a common saturated fatty acid; oleic acid and linolenic acid are common unsaturated fatty acids.
    Attribution: Marc T. Facciotti (own work)

    Note: possible discussion

    Natural fats like butter, canola oil, etc., are composed mostly of triglycerides.  The physical properties of these different fats vary depending on two factors:  
    1) The number of carbons in the hydrocarbon chains;  
    2) The number of desaturations, or double bonds, in the hydrocarbon chains.  
    The first factor influences how these molecules interact with each other and with water, while the second factor dramatically influences their shape. The introduction of a double bond causes a "kink" in the otherwise relatively "straight" hydrocarbon, depicted in a slightly exaggerated was in Figure 3.

    Based on what you can understand from this brief description, propose a rationale—in your own words—to explain why butter is solid at room temperature while vegetable oil is liquid.  

    Here is an important piece of information that could help you with the quesion: butter has a greater percentage of longer and saturated hydrocarbons in its triglycerides than does vegetable oil.

    Figure 3. The straight saturated fatty acid versus the "bent"/"kinked" unsaturated fatty acid. 
    Attribution: Marc T. Facciotti (own work)

    Sterols

    Steroids are lipids with a fused ring structure. Although they do not resemble the other lipids discussed here, they are designated as lipids because they are also largely composed of carbons and hydrogens, are hydrophobic, and are insoluble in water. All steroids have four linked carbon rings.  Many steroids also have the -OH functional group which puts them in the alcohol classification of sterols. Several steroids, like cholesterol, have a short tail. Cholesterol is the most common steroid. It is mainly synthesized in the liver and is the precursor to many steroid hormones such as testosterone. It is also the precursor to Vitamin D and of bile salts which help in the emulsification of fats and their subsequent absorption by cells. Although cholesterol is often spoken of in negative terms, it is necessary for the proper functioning of many animal cells, particularly in its role as a component of the plasma membrane where it is known to modulate membrane structure, organization, and fluidity.

    Figure 4. Cholesterol is a modified lipid molecule that is synthesized by animal cells and is a key structural element in cellular membranes. Cortisol is a hormone (signaling molecule) that is often released in response to stress.
    Attribution: Marc T. Facciotti (own work)

    Note: possible discussion

    In the molecule of cortisol above, what parts of the molecule would you classify as functional groups? Is there any disagreement over what should and should not be included as a functional group?

    Phospholipids

    Phospholipids are major constituents of the cell membrane, the outermost layer of cells. Like fats, they are composed of fatty acid chains attached to glycerol molecule. Unlike the triacylglycerols, phospholipids have two fatty acid tails and a phosphate group attached to the sugar. Phospholipid are therefore amphipathic molecules, meaning it they have a hydrophobic part and a hydrophilic part. The two fatty acid chains extending from the glycerol are hydrophobic and cannot interact with water, whereas the phosphate-containing head group is hydrophilic and interacts with water. Can you identify the functional groups on the phospholipid below that give each part of the phospholipid its properties?

    Note

    Make sure to note in Figure 5 that the phosphate group has an R group linked to one of the oxygen atoms. R is a variable commonly used in these types of diagrams to indicate that some other atom or molecule is bound at that position. That part of the molecule can be different in different phospholipids—and will impart some different chemistry to the whole molecule. At the moment, however, you are responsible for being able to recognize this type of molecule (no matter what the R group is) because of the common core elements—the glycerol backbone, the phosphate group, and the two hydrocarbon tails.

     

    Figure 5. A phospholipid is a molecule with two fatty acids and a modified phosphate group attached to a glycerol backbone. The phosphate may be modified by the addition of charged or polar chemical groups. Several chemical R groups may modify the phosphate. Choline, serine, and ethanolamine are shown here. These attach to the phosphate group at the position labeled R via their hydroxyl groups.
    Attribution: Marc T. Facciotti (own work)

    In the presence of water, some phospholipids will spontaneously arrange themselves into a micelle (Figure 6). The lipids will be arranged such that their polar groups will be on the outside of the micelle, and the nonpolar tails will be on the inside. Under other conditions, a lipid bilayer can also form.  This structure, only a few nanometers thick, is composed of two opposing layers of phospholipids such that all the hydrophobic tails align face-to-face in the center of the bilayer and are surrounded by the hydrophilic head groups. A phospholipid bilayer forms as the basic structure of most cell membranes and are responsible for the dynamic nature of the plasma membrane. 

     

    Figure 6. In the presence of water, some phospholipids will spontaneously arrange themselves into a micelle. 
    Source: Created by Erin Easlon (own work)

     

    Note: possible discussion

    As mentioned above, if you were to take some pure phospholipids and drop them into water that some of the phospholipid would spontaneously form into micelles. This sounds like a process that could be described by an Energy Story.

    Go back to the Energy Story rubric and try to create an Energy Story for this process — I expect that the steps involving the description of energy might be difficult at this point (we'll come back to that later) but you should be able to do at least the first three steps. You can also constructively critique each other's work to create an optimized story.

     

    The phospholipid membrane is discussed in detail in a later module. It will be important to remember the chemical properties associated with the functional groups in the phospholipid in order to understand the function of the cell membrane.

    Membranes

    Plasma membranes enclose and define the borders between the inside and the outside of cells. They are typically composed of dynamic bilayers of phospholipids into which various other lipid soluble molecules and proteins have also been embedded. These bilayers are asymmetric—the outer leaf being different than the inner leaf in lipid composition and in the proteins and carbohydrates that are displayed to either the inside or outside of the cell. Various factors influence the fluidity, permeability, and various other physical properties of the membrane. These include the temperature, the configuration of the fatty acid tails (some kinked by double bonds), the presence of sterols (i.e., cholesterol) embedded in the membrane, and the mosaic nature of the proteins embedded within it. The cell membrane has selectivity; it allows only some substances through while excluding others. In addition, the plasma membrane must, in some cases, be flexible enough to allow certain cells, such as amoebae, to change shape and direction as they move through the environment, hunting smaller, single-celled organisms. 

    Amoebae Hunting Video

    Cellular membranes

    A subgoal in our "build-a-cell" design challenge is to create a boundary that separates the "inside" of the cell from the environment "outside". This boundary needs to serve multiple functions that include:

    1. Act as a barrier by blocking some compounds from moving in and out of the cell. 
    2. Be selectively permeable in order to transport specific compounds into and out of the cell. 
    3. Receive, sense, and transmit signals from the environment to inside of the cell. 
    4. Project "self" to others by communicating identity to other nearby cells.

    Figure 1. The diameter of a typical balloon is 25cm and the thickness of the plastic of the balloon of around 0.25mm. This is a 1000X difference. A typical eukaryotic cell will have a cell diameter of about 50µm and a cell membrane thickness of 5nm. This is a 10,000X difference.

    Note: possible discussion

    The ratio of membrane thickness compared to the size of an average eukaryotic cell is much greater compared to that of a balloon stretched with air. To think that the boundary between life and nonlife is so small, and seemingly fragile, more so than a balloon, suggests that structurally the membrane must be relatively stable. Discuss why cellular membranes are stable. You will need to pull from information we have already covered in this class.

    Fluid mosaic model

    The existence of the plasma membrane was identified in the 1890s, and its chemical components were identified in 1915. The principal components identified at that time were lipids and proteins. The first widely accepted model of the plasma membrane’s structure was proposed in 1935 by Hugh Davson and James Danielli; it was based on the “railroad track” appearance of the plasma membrane in early electron micrographs. They theorized that the structure of the plasma membrane resembles a sandwich, with protein being analogous to the bread, and lipids being analogous to the filling. In the 1950s, advances in microscopy, notably transmission electron microscopy (TEM), allowed researchers to see that the core of the plasma membrane consisted of a double, rather than a single, layer. A new model that better explains both the microscopic observations and the function of that plasma membrane was proposed by S.J. Singer and Garth L. Nicolson in 1972.

    The explanation proposed by Singer and Nicolson is called the fluid mosaic model. The model has evolved somewhat over time, but it still best accounts for the structure and functions of the plasma membrane as we now understand them. The fluid mosaic model describes the structure of the plasma membrane as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character. Plasma membranes range from 5 to 10 nm in thickness. For comparison, human red blood cells, visible via light microscopy, are approximately 8 µm wide, or approximately 1,000 times wider than a plasma membrane.

    Figure 2. The fluid mosaic model of the plasma membrane describes the plasma membrane as a fluid combination of phospholipids, cholesterol, and proteins. Carbohydrates attached to lipids (glycolipids) and to proteins (glycoproteins) extend from the outward-facing surface of the membrane.

     

    The principal components of a plasma membrane are lipids (phospholipids and cholesterol), proteins, and carbohydrates. The proportions of proteins, lipids, and carbohydrates in the plasma membrane vary with organism and cell type, but for a typical human cell, proteins account for about 50 percent of the composition by mass, lipids (of all types) account for about 40 percent of the composition by mass, and carbohydrates account for the remaining 10 percent of the composition by mass. However, the concentration of proteins and lipids varies with different cell membranes. For example, myelin, an outgrowth of the membrane of specialized cells, insulates the axons of the peripheral nerves, contains only 18 percent protein and 76 percent lipid. The mitochondrial inner membrane contains 76 percent protein and only 24 percent lipid. The plasma membrane of human red blood cells is 30 percent lipid. Carbohydrates are present only on the exterior surface of the plasma membrane and are attached to proteins, forming glycoproteins, or to lipids, forming glycolipids.

    Phospholipids

    Phospholipids are major constituents of the cell membrane, the outermost layer of cells. Like fats, they are composed of fatty acid chains attached to a polar head group. Specifically, there are two fatty acid tails and a phosphate group as the polar head group. The phospholipid is an amphipathic molecule, meaning it has a hydrophobic part and a hydrophilic part. The fatty acid chains are hydrophobic and cannot interact with water, whereas the phosphate-containing head group is hydrophilic and interacts with water.

    Note

    Make sure to note in Figure 3 that the phosphate group has an R group linked to one of the oxygen atoms. R is a variable commonly used in these types of diagrams to indicate that some other atom or molecule is bound at that position. That part of the molecule can be different in different phospholipids—and will impart some different chemistry to the whole molecule. At the moment, however, you are responsible for being able to recognize this type of molecule (no matter what the R group is) because of the common core elements—the glycerol backbone, the phosphate group, and the two hydrocarbon tails.

    Figure 3. A phospholipid is a molecule with two fatty acids and a modified phosphate group attached to a glycerol backbone. The phosphate may be modified by the addition of charged or polar chemical groups. Several chemical R groups may modify the phosphate. Choline, serine, and ethanolamine are shown here. These attach to the phosphate group at the position labeled R via their hydroxyl groups.
    Attribution: Marc T. Facciotti (own work)

    A phospholipid bilayer forms as the basic structure of the cell membrane. The fatty acid tails of phospholipids face inside, away from water, whereas the phosphate group faces outside, hydrogen bonding with water. Phospholipids are responsible for the dynamic nature of the plasma membrane.

     

    Figure 4. In the presence of water, some phospholipids will spontaneously arrange themselves into a micelle. The lipids will be arranged such that their polar groups will be on the outside of the micelle, and the nonpolar tails will be on the inside. A lipid bilayer can also form, a two layered sheet only a few nanometers thick. The lipid bilayer consists of two layers of phospholipids organized in a way that all the hydrophobic tails align side by side in the center of the bilayer and are surrounded by the hydrophilic head groups.  
    Source: Created by Erin Easlon (own work)

    Note: possible discussion

    Above it says that if you were to take some pure phospholipids and drop them into water that some if it would spontaneously (on its own) form into micelles. This sounds a lot like something that could be described by an energy story. Go back to the energy story rubric and try to start creating an energy story for this process—I expect that the steps involving the description of energy might be difficult at this point (we'll come back to that later) but you should be able to do at least the first three steps. You can constructively critique (politely) each other's work to create an optimized story.

    Note: possible discussion

    Note that the phospholipid depicted above has an R group linked to the phosphate group. Recall that this designation is generic—these can be different than the R groups on amino acids. What might be a benefit/purpose of "functionalizing" or "decorating" different lipids with different R groups? Think of the functional requirements for membranes stipulated above.

    Membrane proteins

    Proteins make up the second major component of plasma membranes. Integral membrane proteins are, as their name suggests, integrated completely into the membrane structure, and their hydrophobic membrane-spanning regions interact with the hydrophobic region of the the phospholipid bilayer. Single-pass integral membrane proteins usually have a hydrophobic transmembrane segment that consists of 20–25 amino acids. Some span only part of the membrane—associating with a single layer—while others stretch from one side of the membrane to the other, and are exposed on either side.  This type of protein has a hydrophilic region or regions, and one or several mildly hydrophobic regions. This arrangement of regions of the protein tends to orient the protein alongside the phospholipids, with the hydrophobic region of the protein adjacent to the tails of the phospholipids and the hydrophilic region or regions of the protein protruding from the membrane and in contact with the cytosol or extracellular fluid. 

    Peripheral proteins are found on either the exterior or interior surfaces of membranes; and weakly or temporarily associated with the membranes. They can  interact with either integral membrane proteins or simply interact weakly with the phospholipids within the membrane.

    Figure 5. Integral membranes proteins may have one or more α-helices (pink cylinders) that span the membrane (examples 1 and 2), or they may have β-sheets (blue rectangles) that span the membrane (example 3). (credit: “Foobar”/Wikimedia Commons)

    Carbohydrates

    Carbohydrates are the third major component of plasma membranes. They are always found on the exterior surface of cells and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids). These carbohydrate chains may consist of 2–60 monosaccharide units and can be either straight or branched. Along with peripheral proteins, carbohydrates form specialized sites on the cell surface that allow cells to recognize each other (one of the core functional requirements noted above in "cellular membranes"). 

    Membrane fluidity

    The mosaic characteristic of the membrane, described in the fluid mosaic model, helps to illustrate its nature. The integral proteins and lipids exist in the membrane as separate molecules and they "float" in the membrane, moving somewhat with respect to one another. The membrane is not like a balloon, however, in that can expand and contract dramatically; rather, it is fairly rigid and can burst if penetrated or if a cell takes in too much water. However, because of its mosaic nature, a very fine needle can easily penetrate a plasma membrane without causing it to burst, and the membrane will flow and self-seal when the needle is extracted.

    The mosaic characteristics of the membrane explain some but not all of its fluidity. There are two other factors that help maintain this fluid characteristic. One factor is the nature of the phospholipids themselves. In their saturated form, the fatty acids in phospholipid tails are saturated with hydrogen atoms. There are no double bonds between adjacent carbon atoms. This results in tails that are relatively straight. By contrast, unsaturated fatty acids do not have a full complement of hydrogen atoms on their fatty acid tails, and therefore contain some double bonds between adjacent carbon atoms; a double bond results in a bend in the string of carbons of approximately 30 degrees.

    Figure 6. Any given cell membrane will be composed of a combination of saturated and unsaturated phospholipids. The ratio of the two will influence the permeability and fluidity of the membrane. A membrane composed of completely saturated lipids will be dense and less fluid, and a membrane composed of completely unsaturated lipids will be very loose and very fluid.

    Note: possible discussion

    Organisms can be found living in extreme temperature conditions. Both in extreme cold or extreme heat. What types of differences would you expect to see in the lipid composition of organisms that live at these extremes?

     

    Saturated fatty acids, with straight tails, are compressed by decreasing temperatures, and they will press in on each other, making a dense and fairly rigid membrane. When unsaturated fatty acids are compressed, the “kinked” tails elbow adjacent phospholipid molecules away, maintaining some space between the phospholipid molecules. This “elbow room” helps to maintain fluidity in the membrane at temperatures at which membranes with high concentrations of saturated fatty acid tails would “freeze” or solidify. The relative fluidity of the membrane is particularly important in a cold environment.  Many organisms (fish are one example) are capable of adapting to cold environments by changing the proportion of unsaturated fatty acids in their membranes in response to the lowering of the temperature.

    Cholesterol

    Animals have an additional membrane constituent that assists in maintaining fluidity. Cholesterol, which lies alongside the phospholipids in the membrane, tends to dampen the effects of temperature on the membrane. Thus, this lipid functions as a "fluidity buffer", preventing lower temperatures from inhibiting fluidity and preventing increased temperatures from increasing fluidity too much. Thus, cholesterol extends, in both directions, the range of temperature in which the membrane is appropriately fluid and consequently functional. Cholesterol also serves other functions, such as organizing clusters of transmembrane proteins into lipid rafts.

     

    Figure 7. Cholesterol fits between the phospholipid groups within the membrane.

    Review of the components of the membrane

    Archaeal membranes

    One major difference between archaea and either eukaryotes or bacteria is the lipid composition of the archaeal membranes. Unlike eukaryotes and bacteria, archaeal membranes are not made up of fatty acids attached to a glycerol backbone. Instead, the polar lipids consist of isoprenoid (molecules derived from the five carbon lipid isoprene) chains of 20–40 carbons in length. These chains, which are usually saturated, are attached by ether bonds to the glycerol carbons at the 2 and 3 positions on the glycerol backbone, instead of the more familiar ester linkage found in bacteria and eukaryotes. The polar head groups differ based on the genus or species of the Archaea and consist of mixtures of glyco groups (mainly disaccharides), and/or phospho groups primarily of phosphoglycerol, phosphoserine, phosphoethanolamine or phosphoinositol. The inherent stability and unique features of archaeal lipids have made them a useful biomarker for archaea within environmental samples, though approaches based on genetic markers are now more commonly used. 

    A second difference between bacterial and archaeal membranes that is associated with some archaea is the presence of monolayer membranes, as depicted below. Notice that the isoprenoid chain is attached to the glycerol backbones at both ends, forming a single molecule consisting of two polar head groups attached via two isoprenoid chains.

     

    Figure 8. The exterior surface of the archaeal plasma membrane is not identical to the interior surface of the same membrane.

    Figure 9. Comparisons of different types of archaeal lipids and bacterial/eukaryotic lipids

    Note: possible discussion

    In many cases—though not all—the archaea are relatively abundant in environments that represent extremes for life (e.g., high temperature, high salt). What possible advantage could monolayered membranes provide?

    Transport across the membrane


    Design challenge problem and subproblems

    General Problem: The cell membrane must simultaneously act as a barrier between "IN" and "OUT" and control specifically which substances enter and leave the cell and how quickly and efficiently they do so.

    Subproblems: The chemical properties of molecules that must enter and leave the cell are highly variable. Some subproblems associated with this are:  (a) Large and small molecules or collections of molecules must be able to pass across the membrane.  (b) Both hydrophobic and hydrophilic substances must have access to transport.  (c) Substances must be able to cross the membrane with and against concentration gradients.  (d) Some molecules look very similar (e.g. Na+ and K+) but transport mechanisms must still be able to distinguish between them.  

    Energy story perspective

    Later in the course, you will be introduced to the "energy story."  Like the Design challenge, it is a way to think about cellular processes.   Every chemical reaction and cellular process has a beginning, a middle and an end and requires some input of energy.  For example, let's use a simple, everyday example.  You purchase a cup of coffee and decide to add sugar.  The beginning of the "reaction" is when you add the sugar to the coffee.  The middle is when the sugar is dissolving and this may require some input of energy (stirring/heating the coffee).  Eventually, the amount of dissolved sugar will reach a "steady state."   (If you added too much sugar, some of the sugar won't dissolve and will be at the bottom of your cup.) 

    Transport across a membrane can be considered from an energy story perspective; it is a process after all.  For instance, at the beginning of the process a generic substance X may be either on the inside or outside of the cell.  At the end of the process, the substance will be on the opposite side from which it started.  

    e.g. X(in) ---> X(out), 

    where in and out refer to inside the cell and outside the cell, respectively.

    At the beginning the matter in the system might be a very complicated collection of molecules inside and outside of the cell but with one molecule of X more inside the cell than out.  At the end, there is one more molecule of X on the outside of the cell and one less on the inside.  The energy in the system at the beginning is stored largely in the molecular structures and their motions and in electrical and chemical concentration imbalances across the cell membrane.  The transport of X out of the cell will not change the energies of the molecular structures significantly but it will change the energy associated with the imbalance of concentration and or charge across the membrane.  Finally, some mechanism or sets of mechanisms of transport will need to be described.  


    Selective permeability

    One of the great wonders of the cell membrane is its ability to regulate the concentration of substances inside the cell. These substances include: ions such as Ca2+, Na+, K+, and Cl; nutrients including sugars, fatty acids, and amino acids; and waste products, particularly carbon dioxide (CO2), which must leave the cell. 

    The membrane’s lipid bilayer structure provides the first level of control. The phospholipids are tightly packed, and the membrane has a hydrophobic interior. This structure alone creates what is known as a selectively permeable barrier, one that only allows substances meeting certain physical criteria to pass through it.  In the case of the cell membrane, only relatively small, nonpolar materials can move through the lipid bilayer at biologically relevant rates (remember, the lipid tails of the membrane are nonpolar).

    Selective permeability of the cell membrane refers to its ability to differentiate between different types of molecules, only allowing some molecules through while blocking others. Some of this selective property stems from the intrinsic diffusion rates for different molecules across a membrane. A second factor affecting the relative rates of movement of various substances across a biological membrane is activity of various protein-based membrane transporters, both passive and active, that will be discussed in more detail in subsequent sections. First, we take on the notion of intrinsic rates of diffusion across the membrane. 

    Relative permeability

    The fact that different substances might cross a biological membrane at different rates should be relatively intuitive. There are differences in the mosaic composition of membranes in biology and differences in the sizes, flexibility, and chemical properties of molecules so it stands to reason that the permeability rates vary. It is a complicated landscape. The permeability of a substance across a biological membrane can be measured experimentally and the rate of movement across a membrane can be reported in what are known as membrane permeability coefficients. 

    Membrane permeability coefficients

    Below, a variety of compounds are plotted with respect to their membrane permeability coefficients (MPC) as measured against a simple biochemical approximation of a real biological membrane. The reported permeability coefficient for this system is the rate at which simple diffusion through a membrane occurs and is reported in units of centimeters per second (cm/s). The permeability coefficient is proportional to the partition coefficient and is inversely proportional to the membrane thickness. 

    It is important that you are able to read and interpret the diagram below. The larger the coefficient, the more permeable the membrane is to the solute. For example, hexanoic acid is very permeable, a MPC of 0.9; acetic acid, water, and ethanol have MPCs between 0.01 and 0.001, and they are less permeable than hexanoic acid. Where as ions, such as sodium (Na+), have an MPC of 10-12, and cross the membrane at a comparatively slow rate.

    Figure 1. Membrane permeability coefficient diagram. The diagram was taken from BioWiki and can be found at http://biowiki.ucdavis.edu/Biochemis...e_Permeability.

    While there are certain trends or chemical properties that can be roughly associated with different compound permeability (small thing go through "fast", big things "slowly", charged things not at all etc.), we caution against over-generalizing. The molecular determinants of membrane permeability are complicated and involve numerous factors including: the specific composition of the membrane, temperature, ionic composition, hydration; the chemical properties of the solute; the potential chemical interactions between the solute in solution and in the membrane; the dielectric properties of materials; and the energy trade-offs associated with moving substances into and out of various environments. So, in this class, rather than try to apply "rules" and try to develop too many arbitrary "cut-offs", we will strive to develop a general sense of some properties that can influence permeability and leave the assignment of absolute permeability to experimentally reported rates. In addition, we will also try to minimize the use of vocabulary that depends on a frame of reference. For instance, saying that compound A diffuses "quickly" or "slowly" across a bilayer only means something if the terms "quickly" or "slowly" are numerically defined or the biological context is understood.

    Energetics of transport

    All substances that move through the membrane do so by one of two general methods, which are categorized based on whether or not the transport process is exergonic or endergonic.   

    • "An exergonic reaction is a reaction that releases free energy. Because this type of reaction releases energy rather than consuming it, it can occur spontaneously, without being forced by outside factors." https://biologydictionary.net/exergonic-reaction/
    • "An endergonic reaction is a reaction in which energy is absorbed. In chemistry terms, this means that the net change in free energy is positive – there is more energy in the system at the end of the reaction than at the beginning of it."  https://biologydictionary.net/endergonic-reaction/

    Passive transport is the exergonic movement of substances across the membrane. In contrast, active transport is the endergonic movement of substances across the membrane that is coupled to an exergonic reaction.

    Passive transport

    Passive transport does not require the cell to expend energy. In passive transport, substances move from an area of higher concentration to an area of lower concentration, down their concentration gradient                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        . Depending on the chemical nature of the substance, different processes may be associated with passive transport.

    Diffusion

    Diffusion is a passive process of transport. A single substance tends to move from an area of high concentration to an area of low concentration until the concentration is equal across a space. You are familiar with diffusion of substances through the air. For example, think about someone opening a bottle of ammonia in a room filled with people. The ammonia gas is at its highest concentration in the bottle; its lowest concentration is at the edges of the room. The ammonia vapor will diffuse, or spread away, from the bottle; gradually, more and more people will smell the ammonia as it spreads. Materials move within the cell’s cytosol by diffusion, and certain materials move through the plasma membrane by diffusion.

     

     

     

    Figure 2. Diffusion through a permeable membrane moves a substance from an area of high concentration (extracellular fluid, in this case) down its concentration gradient (into the cytoplasm). Each separate substance in a medium, such as the extracellular fluid, has its own concentration gradient, independent of the concentration gradients of other materials. In addition, each substance will diffuse according to that gradient. Within a system, there will be different rates of diffusion of the different substances in the medium.(credit: modification of work by Mariana Ruiz Villareal)
    Factors that affect diffusion

    If unconstrained, molecules will move through and explore space randomly at a rate that depends on their size, their shape, their environment, and their thermal energy. This type of movement underlies the diffusive movement of molecules through whatever medium they are in. The absence of a concentration gradient does not mean that this movement will stop, just that there may be no net movement of the number of molecules from one area to another, a condition known as dynamic equilibrium

    Factors influencing diffusion include:

    • Extent of the concentration gradient: The greater the difference in concentration, the more rapid the diffusion. The closer the distribution of the material gets to equilibrium, the slower the rate of diffusion becomes. 
    • Shape, size and mass of the molecules diffusing: Large and heavier molecules move more slowly; therefore, they diffuse more slowly. The reverse is typically true for smaller, lighter molecules. 
    • Temperature: Higher temperatures increase the energy and therefore the movement of the molecules, increasing the rate of diffusion. Lower temperatures decrease the energy of the molecules, thus decreasing the rate of diffusion. 
    • Solvent density: As the density of a solvent increases, the rate of diffusion decreases. The molecules slow down because they have a more difficult time getting through the denser medium. If the medium is less dense, rates of diffusion increase. Since cells primarily use diffusion to move materials within the cytoplasm, any increase in the cytoplasm’s density will decrease the rate at which materials move in the cytoplasm. 
    • Solubility: As discussed earlier, nonpolar or lipid-soluble materials pass through plasma membranes more easily than polar materials, allowing a faster rate of diffusion. 
    • Surface area and thickness of the plasma membrane: Increased surface area increases the rate of diffusion, whereas a thicker membrane reduces it. 
    • Distance traveled: The greater the distance that a substance must travel, the slower the rate of diffusion. This places an upper limitation on cell size. A large, spherical cell will die because nutrients or waste cannot reach or leave the center of the cell, respectively. Therefore, cells must either be small in size, as in the case of many prokaryotes, or be flattened, as with many single-celled eukaryotes.

    Facilitated transport

    In facilitated transport, also called facilitated diffusion, materials diffuse across the plasma membrane with the help of membrane proteins. A concentration gradient exists that allows these materials to diffuse into or out of the cell without expending cellular energy. In the case that the materials are ions or polar molecules (compounds that are repelled by the hydrophobic parts of the cell membrane), facilitated transport proteins help shield these materials from the repulsive force of the membrane, allowing them to diffuse into the cell.

    Note: possible discussion

    Compare and contrast passive diffusion and facilitated diffusion.

    Channels

    The integral proteins involved in facilitated transport are collectively referred to as transport proteins, and they function as either channels for the material or carriers. In both cases, they are transmembrane proteins. Different channel proteins have different transport properties. Some have evolved to have very high specificity for the substance that is being transported while others transport a variety of molecules sharing some common characteristic(s). The interior "passageway" of channel proteins have evolved to provide a low energetic barrier for transport of substances across the membrane through the complementary arrangement of amino acid functional groups (of both backbone and side-chains). Passage through the channel allows polar compounds to avoid the nonpolar central layer of the plasma membrane that would otherwise slow or prevent their entry into the cell. While at any one time significant amounts of water crosses the membrane both in and out, the rate of individual water molecule transport may not be fast enough to adapt to changing environmental conditions. For such cases Nature has evolved a special class of membrane proteins called aquaporins that allow water to pass through the membrane at a very high rate.

     

    Figure 3. Facilitated transport moves substances down their concentration gradients. They may cross the plasma membrane with the aid of channel proteins. (credit: modification of work by Mariana Ruiz Villareal)

    Channel proteins are either open at all times or they are “gated.” The latter controls the opening of the channel. Various mechanisms may be involved in the gating mechanism. For instance, the attachment of a specific ion or small molecule to the channel protein may trigger opening. Changes in local membrane "stress" or changes in voltage across the membrane may also be triggers to open or close a channel. 

    Different organisms and tissues in multicellular species express different sets of channel proteins in their membranes depending on the environments they live in or specialized function they play in an organisms. This provides each type of cell with a unique membrane permeability profile that is evolved to complement its "needs" (note the anthropomorphism). For example, in some tissues, sodium and chloride ions pass freely through open channels, whereas in other tissues a gate must be opened to allow passage. This occurs in the kidney, where both forms of channels are found in different parts of the renal tubules. Cells involved in the transmission of electrical impulses, such as nerve and muscle cells, have gated channels for sodium, potassium, and calcium in their membranes. Opening and closing of these channels changes the relative concentrations on opposing sides of the membrane of these ions, resulting a change in electrical potential across the membrane that lead to message propagation in the case of nerve cells or in muscle contraction in the case of muscle cells.

    Carrier proteins

    Another type of protein embedded in the plasma membrane is a carrier protein. This aptly named protein binds a substance and, in doing so, triggers a change of its own shape, moving the bound molecule from the outside of the cell to its interior; depending on the gradient, the material may move in the opposite direction. Carrier proteins are typically specific for a single substance. This selectivity adds to the overall selectivity of the plasma membrane. The molecular-scale mechanism of function for these proteins remains poorly understood.

     

    Figure 4. Some substances are able to move down their concentration gradient across the plasma membrane with the aid of carrier proteins. Carrier proteins change shape as they move molecules across the membrane. (credit: modification of work by Mariana Ruiz Villareal)

    Carrier protein play an important role in the function of kidneys. Glucose, water, salts, ions, and amino acids needed by the body are filtered in one part of the kidney. This filtrate, which includes glucose, is then reabsorbed in another part of the kidney with the help of carrier proteins. Because there are only a finite number of carrier proteins for glucose, if more glucose is present in the filtrate than the proteins can handle, the excess is not reabsorbed and it is excreted from the body in the urine. In a diabetic individual, this is described as “spilling glucose into the urine.” A different group of carrier proteins called glucose transport proteins, or GLUTs, are involved in transporting glucose and other hexose sugars through plasma membranes within the body.

    Channel and carrier proteins transport material at different rates. Channel proteins transport much more quickly than do carrier proteins. Channel proteins facilitate diffusion at a rate of tens of millions of molecules per second, whereas carrier proteins work at a rate of a thousand to a million molecules per second.

    Active transport

    Active transport mechanisms require the use of the cell’s energy, usually in the form of adenosine triphosphate (ATP). If a substance must move into the cell against its concentration gradient—that is, if the concentration of the substance inside the cell is greater than its concentration in the extracellular fluid (and vice versa)—the cell must use energy to move the substance. Some active transport mechanisms move small-molecular weight materials, such as ions, through the membrane. Other mechanisms transport much larger molecules.

    Moving against a gradient

    To move substances against a concentration or electrochemical gradient, the cell must use energy. This energy is harvested from ATP generated through the cell’s metabolism. Active transport mechanisms, collectively called pumps, work against electrochemical gradients. Small substances constantly pass through plasma membranes. Active transport maintains concentrations of ions and other substances needed by living cells in the face of these passive movements. Much of a cell’s supply of metabolic energy may be spent maintaining these processes. (Most of a red blood cell’s metabolic energy is used to maintain the imbalance between exterior and interior sodium and potassium levels required by the cell.) Because active transport mechanisms depend on a cell’s metabolism for energy, they are sensitive to many metabolic poisons that interfere with the supply of ATP.

    Two mechanisms exist for the transport of small-molecular weight material and small molecules. Primary active transport moves ions across a membrane and creates a difference in charge across that membrane, which is directly dependent on ATP. Secondary active transport describes the movement of material that is due to the electrochemical gradient established by primary active transport that does not directly require ATP.

    Carrier proteins for active transport

    An important membrane adaption for active transport is the presence of specific carrier proteins or pumps to facilitate movement: there are three types of these proteins or transporters. A uniporter carries one specific ion or molecule. A symporter carries two different ions or molecules, both in the same direction. An antiporter also carries two different ions or molecules, but in different directions. All of these transporters can also transport small, uncharged organic molecules like glucose. These three types of carrier proteins are also found in facilitated diffusion, but they do not require ATP to work in that process. Some examples of pumps for active transport are Na+-K+ ATPase, which carries sodium and potassium ions, and H+-K+ ATPase, which carries hydrogen and potassium ions. Both of these are antiporter carrier proteins. Two other carrier proteins are Ca2+ATPase and H+ ATPase, which carry only calcium and only hydrogen ions, respectively. Both are pumps.

     Figure 5. A uniporter carries one molecule or ion. A symporter carries two different molecules or ions, both in the same direction. An antiporter also carries two different molecules or ions, but in different directions. (credit: modification of work by “Lupask”/Wikimedia Commons)

    Primary active transport

    In primary active transport, the energy is often - though not exclusively - derived directly from the hydrolysis of ATP. Often, primary active transport, such as that shown below,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  which functions to transport sodium and potassium ions allows secondary active transport to occur (discussed in the section below). The second transport method is still considered active because it depends on the use of energy from the primary transport.

    Figure 6. Primary active transport moves ions across a membrane, creating an electrochemical gradient (electrogenic transport). (credit: modification of work by Mariana Ruiz Villareal)

    One of the most important pumps in animal cells is the sodium-potassium pump (Na+-K+ ATPase), which maintains the electrochemical gradient (and the correct concentrations of Na+and K+) in living cells. The sodium-potassium pump moves K+ into the cell while moving Na+ out at the same time, at a ratio of three Na+ for every two K+ ions moved in. The Na+-K+ATPase exists in two forms depending on its orientation to the interior or exterior of the cell and its affinity for either sodium or potassium ions. The process consists of the following six steps.

    1. With the enzyme oriented towards the interior of the cell, the carrier has a high affinity for sodium ions. Three ions bind to the protein. 
    2. ATP is hydrolyzed by the protein carrier and a low-energy phosphate group attaches to it. 
    3. As a result, the carrier changes shape and re-orients itself towards the exterior of the membrane. The protein’s affinity for sodium decreases and the three sodium ions leave the carrier. 
    4. The shape change increases the carrier’s affinity for potassium ions, and two such ions attach to the protein. Subsequently, the low-energy phosphate group detaches from the carrier. 
    5. With the phosphate group removed and potassium ions attached, the carrier protein repositions itself towards the interior of the cell. 
    6. The carrier protein, in its new configuration, has a decreased affinity for potassium, and the two ions are released into the cytoplasm. The protein now has a higher affinity for sodium ions, and the process starts again.

    Several things have happened as a result of this process. At this point, there are more sodium ions outside of the cell than inside and more potassium ions inside than out. For every three ions of sodium that move out, two ions of potassium move in. This results in the interior being slightly more negative relative to the exterior. This difference in charge is important in creating the conditions necessary for the secondary process. The sodium-potassium pump is, therefore, an electrogenic pump (a pump that creates a charge imbalance), creating an electrical imbalance across the membrane and contributing to the membrane potential.

    Link to learning

    Visit the site to see a simulation of active transport in a sodium-potassium ATPase.

    Secondary active transport (co-transport)

    Secondary active transport brings sodium ions, and possibly other compounds, into the cell. As sodium ion concentrations build outside of the plasma membrane because of the action of the primary active transport process, an electrochemical gradient is created. If a channel protein exists and is open, the sodium ions will be pulled through the membrane. This movement is used to transport other substances that can attach themselves to the transport protein through the membrane. Many amino acids, as well as glucose, enter a cell this way. This secondary process is also used to store high energy hydrogen ions in the mitochondria of plant and animal cells for the production of ATP. The potential energy that accumulates in the stored hydrogen ions is translated into kinetic energy as the ions surge through the channel protein ATP synthase, and that energy is used to convert ADP into ATP.

     

    Figure 7. An electrochemical gradient, created by primary active transport, can move other substances against their concentration gradients, a process called co-transport or secondary active transport. (credit: modification of work by Mariana Ruiz Villareal)

    Osmosis

    Osmosis is the movement of water through a semipermeable membrane according to the concentration gradient of water across the membrane, which is inversely proportional to the concentration of solutes. While diffusion transports material across membranes and within cells, osmosis transports only water across a membrane and the membrane limits the diffusion of solutes in the water. Not surprisingly, the aquaporins that facilitate water movement play a large role in osmosis, most prominently in red blood cells and the membranes of kidney tubules.

    Mechanism

    Osmosis is a special case of diffusion. Water, like other substances, moves from an area of high concentration to one of low concentration. An obvious question is what makes water move at all? Imagine a beaker with a semipermeable membrane separating the two sides or halves. On both sides of the membrane the water level is the same, but there are different concentrations of a dissolved substance, or solute, that cannot cross the membrane (otherwise the concentrations on each side would be balanced by the solute crossing the membrane). If the volume of the solution on both sides of the membrane is the same, but the concentrations of solute are different, then there are different amounts of water, the solvent, on either side of the membrane.

    Figure 8. In osmosis, water always moves from an area of higher water concentration to one of lower concentration. In the diagram shown, the solute cannot pass through the selectively permeable membrane, but the water can.

    To illustrate this, imagine two full glasses of water. One has a single teaspoon of sugar in it, whereas the second one contains one-quarter cup of sugar. If the total volume of the solutions in both cups is the same, which cup contains more water? Because the large amount of sugar in the second cup takes up much more space than the teaspoon of sugar in the first cup, the first cup has more water in it.

    Returning to the beaker example, recall that it has a mixture of solutes on either side of the membrane. A principle of diffusion is that the molecules move around and will spread evenly throughout the medium if they can. However, only the material capable of getting through the membrane will diffuse through it. In this example, the solute cannot diffuse through the membrane, but the water can. Water has a concentration gradient in this system. Thus, water will diffuse down its concentration gradient, crossing the membrane to the side where it is less concentrated. This diffusion of water through the membrane—osmosis—will continue until the concentration gradient of water goes to zero or until the hydrostatic pressure of the water balances the osmotic pressure. Osmosis proceeds constantly in living systems.

    Tonicity

    Tonicity describes how an extracellular solution can change the volume of a cell by affecting osmosis. A solution's tonicity often directly correlates with the osmolarity of the solution. Osmolarity describes the total solute concentration of the solution. A solution with low osmolarity has a greater number of water molecules relative to the number of solute particles; a solution with high osmolarity has fewer water molecules with respect to solute particles. In a situation in which solutions of two different osmolarities are separated by a membrane permeable to water, though not to the solute, water will move from the side of the membrane with lower osmolarity (and more water) to the side with higher osmolarity (and less water). This effect makes sense if you remember that the solute cannot move across the membrane, and thus the only component in the system that can move—the water—moves along its own concentration gradient. An important distinction that concerns living systems is that osmolarity measures the number of particles (which may be molecules) in a solution. Therefore, a solution that is cloudy with cells may have a lower osmolarity than a solution that is clear if the second solution contains more dissolved molecules than there are cells.

    Hypotonic solutions

    Three terms—hypotonic, isotonic, and hypertonic—are used to relate the osmolarity of a cell to the osmolarity of the extracellular fluid that contains the cells. In a hypotonic situation, the extracellular fluid has lower osmolarity than the fluid inside the cell, and water enters the cell (in living systems, the point of reference is always the cytoplasm, so the prefix hypo- means that the extracellular fluid has a lower concentration of solutes, or a lower osmolarity, than the cell cytoplasm). It also means that the extracellular fluid has a higher concentration of water in the solution than does the cell. In this situation, water will follow its concentration gradient and enter the cell.

    Hypertonic solutions

    As for a hypertonic solution, the prefix hyper- refers to the extracellular fluid having a higher osmolarity than the cell’s cytoplasm; therefore, the fluid contains less water than the cell does. Because the cell has a relatively higher concentration of water, water will leave the cell.

    Isotonic solutions

    In an isotonic solution, the extracellular fluid has the same osmolarity as the cell. If the osmolarity of the cell matches that of the extracellular fluid, there will be no net movement of water into or out of the cell, although water will still move in and out. Blood cells and plant cells in hypertonic, isotonic, and hypotonic solutions take on characteristic appearances.

    Connection

    Figure 9. Osmotic pressure changes the shape of red blood cells in hypertonic, isotonic, and hypotonic solutions. (credit: Mariana Ruiz Villareal)

    A doctor injects a patient with what the doctor thinks is an isotonic saline solution. The patient dies, and an autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?

    Link to learning

    For a video illustrating the process of diffusion in solutions, visit this site.

    Tonicity in living systems

    In a hypotonic environment, water enters a cell, and the cell swells. In an isotonic condition, the relative concentrations of solute and solvent are equal on both sides of the membrane. There is no net water movement; therefore, there is no change in the size of the cell. In a hypertonic solution, water leaves a cell and the cell shrinks. If either the hypo- or hyper- condition goes to excess, the cell’s functions become compromised, and the cell may be destroyed.

    A red blood cell will burst, or lyse, when it swells beyond the plasma membrane’s capability to expand. Remember, the membrane resembles a mosaic, with discrete spaces between the molecules composing it. If the cell swells, and the spaces between the lipids and proteins become too large, and the cell will break apart.

    In contrast, when excessive amounts of water leave a red blood cell, the cell shrinks, or crenates. This has the effect of concentrating the solutes left in the cell, making the cytosol denser and interfering with diffusion within the cell. The cell’s ability to function will be compromised and may also result in the death of the cell.

    Various living things have ways of controlling the effects of osmosis—a mechanism called osmoregulation. Some organisms, such as plants, fungi, bacteria, and some protists, have cell walls that surround the plasma membrane and prevent cell lysis in a hypotonic solution. The plasma membrane can only expand to the limit of the cell wall, so the cell will not lyse. In fact, the cytoplasm in plants is always slightly hypertonic to the cellular environment, and water will always enter a cell if water is available. This inflow of water produces turgor pressure, which stiffens the cell walls of the plant. In nonwoody plants, turgor pressure supports the plant. Conversely, if the plant is not watered, the extracellular fluid will become hypertonic, causing water to leave the cell. In this condition, the cell does not shrink because the cell wall is not flexible. However, the cell membrane detaches from the wall and constricts the cytoplasm. This is called plasmolysis. Plants lose turgor pressure in this condition and wilt.

    Figure 10. The turgor pressure within a plant cell depends on the tonicity of the solution that it is bathed in. (credit: modification of work by Mariana Ruiz Villareal)

     

    Figure 11. Without adequate water, the plant on the left has lost turgor pressure, visible in its wilting; the turgor pressure is restored by watering it (right). (credit: Victor M. Vicente Selvas)

    Tonicity is a concern for all living things. For example, paramecia and amoebas, which are protists that lack cell walls, have contractile vacuoles. This vesicle collects excess water from the cell and pumps it out, keeping the cell from bursting as it takes on water from its environment.

    Figure 12. A paramecium’s contractile vacuole, here visualized using bright field light microscopy at 480x magnification, continuously pumps water out of the organism’s body to keep it from bursting in a hypotonic medium. (credit: modification of work by NIH; scale-bar data from Matt Russell)

     

    Many marine invertebrates have internal salt levels matched to their environments, making them isotonic with the water in which they live. Fish, however, must spend approximately five percent of their metabolic energy maintaining osmotic homeostasis. Freshwater fish live in an environment that is hypotonic to their cells. These fish actively take in salt through their gills and excrete diluted urine to rid themselves of excess water. Saltwater fish live in the reverse environment, which is hypertonic to their cells, and they secrete salt through their gills and excrete highly concentrated urine.

    In vertebrates, the kidneys regulate the amount of water in the body. Osmoreceptors are specialized cells in the brain that monitor the concentration of solutes in the blood. If the levels of solutes increase beyond a certain range, a hormone is released that retards water loss through the kidney and dilutes the blood to safer levels. Animals also have high concentrations of albumin, which is produced by the liver, in their blood. This protein is too large to pass easily through plasma membranes and is a major factor in controlling the osmotic pressures applied to tissues.

    
    
    The components and functions of the plasma membrane
    Component Location
    Phospholipid Main fabric of the membrane
    Cholesterol Between phospholipids and between the two phospholipid layers of animal cells
    Integral proteins (e.g., integrins) Embedded within the phospholipid layer(s); may or may not penetrate through both layers
    Peripheral proteins On the inner or outer surface of the phospholipid bilayer; not embedded within the phospholipids
    Carbohydrates (components of glycoproteins and glycolipids) Generally attached to proteins on the outside membrane layer