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Ireland 2019 Lecture 4 - Biology

Ireland 2019 Lecture 4 - Biology


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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. 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 C2 carbon 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.

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. 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. 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)

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.

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. 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. 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. 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. 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?

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.

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

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. That is the transport will, like all other reactions, be either exergonic or endergonic. 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. 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)
The components and functions of the plasma membrane
ComponentLocation
PhospholipidMain fabric of the membrane
CholesterolBetween 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 proteinsOn 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

Lecture series

Access to accurate health information is an important resource to empower people with the tools to maintain their health and well-being.

The RCSI MyHealth Lecture Series aims to demystify common health concerns by drawing expertise and insight from our team of researchers and international health experts at the cutting-edge of medical and healthcare developments.

Open to those who want to learn more about common illnesses and health-related topics directly from leading healthcare experts, the series explores a wide range of areas in health and well-being, including child health, women&rsquos health and positive psychology.

View our past lectures below:

Gender is fundamental to many decisions in healthcare systems around the world, and this puts transgender people in vulnerable and complex positions.

Transgender people are individuals whose gender identity or gender expression is different from the sex assigned at birth. Gender identity is the internal sense of being male, female, neither or both. Transgender people have a variety of needs relating to their healthcare including access to mental health, medical transition and primary care services that are sensitive to their identities and experiences.

During this RCSI MyHealth discussion, the panel addresses the role of primary care and access to gender-affirming care, services, and support.

You can also watch the discussion on YouTube here: https://youtu.be/2neY0kzHQKo

Useful resources

Professor Martin Seligman, considered to be the founder of positive psychology, delivers an RCSI MyHealth guest talk on &lsquoPositive Psychology, Agency and Human Progress&rsquo. Professor Seligman, who is Director of the Positive Psychology Center at University of Pennsylvania, shares his insights into the concept of agency, which is a belief that we can make a positive difference in the world, and its role in human flourishing.

You can also watch the discussion on YouTube here: https://youtu.be/TjWrL1MJbj0 .

During this discussion, the panel addresses the clinical aspects of MS, the experience of living with MS, as well as exploring the research and treatments available for MS patients.

You can also watch the discussion on YouTube here: https://youtu.be/bkAjVEiHAcA.

Useful resources

A panel of RCSI experts address some of the most commonly asked questions they encounter from patients about fertility and pregnancy health, as well as focusing on ways to optimise and support fertility and pregnancy health.

You can also watch the discussion on YouTube here: https://youtu.be/3ojZmqwAZ38

Useful resources

Hosted by the RCSI Centre for Positive Psychology and Health, Future-Proofing our Youth is the third and final event in the three-part Positive Health mini-series for 2021. A panel of RCSI experts discussed ideas from strengths-based parenting and growth mindset work and provide examples of how we can help our children develop ways of thinking about stress, adversity and challenge that builds confidence and capability. The discussion was chaired by Dr Mary Collins, Chartered Psychologist and Senior Executive Development Specialist at the RCSI Institute of Leadership.

Useful resources

With the COVID-19 vaccination rollout now underway in Ireland and across the globe, a panel of RCSI experts discussed and addressed many of the common questions and genuine concerns people have about vaccine safety and getting vaccinated. This panel discussion was chaired by Professor Steve Kerrigan, Deputy Head of School (Research) in the RCSI School of Pharmacy and Biomolecular Sciences.

Useful resources

Hosted by the RCSI Centre for Positive Psychology and Health, &lsquoManaging Coronaphobia &ndash Stay Present&rsquo is the second event in the three-part Positive Health mini-series for 2021.

A panel of RCSI experts discuss techniques to help strengthen our capacity to remain present as an antidote to an uncertain future. The discussion was chaired by Dr Mary Collins, Chartered Psychologist and Senior Executive Development Specialist at the RCSI Institute of Leadership.

Useful resources

Hosted by the RCSI Centre for Positive Psychology and Health, &lsquoThe Science of Happiness&rsquo is the first event in the three-part Positive Health mini-series for 2021.

A panel of RCSI experts look at how to define and understand happiness, as well as examine research that shows us how to increase our own happiness and that of others.

The discussion was chaired by Dr Mary Collins, Chartered Psychologist and Senior Executive Development Specialist at the RCSI Institute of Leadership.

Useful resources

Supporting Child and Youth Health this Winter&rsquo is the third event in the RCSI MyHealth Series 2020/2021. A panel of RCSI experts provide practical advice and information to how best to support child and youth health this winter. The discussion is chaired by Professor Ciaran O&rsquoBoyle, Director of the RCSI Centre for Positive Psychology and Health.

Useful resources

&lsquoA Toolkit for Winter Readiness&rsquo is the second event in the RCSI MyHealth Series 2020/2021. The panel discussion, which was chaired by Professor Ciaran O&rsquoBoyle, Director of the RCSI Centre for Positive Psychology and Health, addressed the winter flu season, what we should expect and how we can stay well this winter.

The first event of the RCSI MyHealth Series 2020/2021, 'Living with the New Normal' was broadcast on 29 September 2020.

The panel discussion, which was chaired by Professor Ciaran O&rsquoBoyle, Director of the RCSI Centre for Positive Psychology and Health, addressed the significant impact that sudden and extreme change can have on people&rsquos lives, what we can do to make change easier to accept, and how to talk to our children about COVID-19.

Hosted by the newly established RCSI Centre for Positive Psychology and Health, the ‘Stress Management, Mindfulness and Relaxation' lecture focused on the importance of enhancing you well-being with leading experts addressing the topics of stress management, mindfulness and relaxation.

Dr Frank Doyle describes the information and misinformation available in the media regarding stress management, and shows how you can access the best scientific information and apply it to your own needs to find what stress management option works best for you.

Mindfulness represents just one type of meditation practice. Dr Pádraic Dunne, describes the different types of meditations and how they might be used, not only for relaxation and mental health but also to help alleviate physical symptoms of disease and improve overall health.

A round table discussion – chaired by Dr Ciara Kelly, GP, TV and radio broadcaster and columnist – followed the lecture. Watch it in full below.

The 'Tobacco and Alcohol' lecture was the second in a three-part series of Positive Health lectures at RCSI.

Hosted by the RCSI Centre for Positive Psychology and Health, the lecture focused on tobacco and alcohol with leading experts addressing these topics.

Dr Gráinne Cousins, Senior Lecturer in the School of Pharmacy and Biomolecular Sciences in the RCSI and Dr Ross Morgan, Consultant in Respiratory Medicine Beaumont Hospital, Dublin addressed the real effects of alcohol, tobacco and vaping on your health. The discussion was chaired by broadcaster Dr Ciara Kelly. Watch the full lecture below followed by the round table discussion.

In this lecture, which focused on positive health via exercise and nutrition, we heard from Prof. Suzanne McDonough, Head of the School of Physiotherapy, who discussed the beneficial effects of exercise on health and illness and addressed the barriers to active living and Dr Robert Kelly, a consultant cardiologist and Ireland&rsquos only certified lifestyle medicine consultant, who highlighted the importance of nutrition in the prevention and treatment of disease. Watch the lecture below followed by the round table discussion.

Prof. Karina Butler is a consultant paediatrician and infectious disease specialist with Children&rsquos Health Ireland at Crumlin and Temple Street. She discussed the history of opposition to vaccinations, a movement that started as far back as the 1850s and is still prevalent today. She explained how vaccinations have supported the global decline of diseases like smallpox, polio and diptheria.

Prof. Sam McConkey is Associate Professor and Head of the Department of International Health and Tropical Medicine at the RCSI. He highlighted the success of vaccines by sharing three personal experiences.

Finally, Prof. James Paul O&rsquoNeill, a graduate and fellow of RCSI, is Professor of Otolaryngology, Head and Neck Surgery at RCSI Beaumont Hospital, Dublin. In his presentation, he produced the evidence and facts that show how effective the HPV vaccine has been in preventing cancer.

The lecture and following roundtable discussion was chaired by broadcaster Dr Ciara Kelly.

Dr David Ansell – social epidemiologist, health activist and author of County: Life, Death and Politics at Chicago’s Public Hospital and The Death Gap: How Inequality Kills delivered the RCSI MyHealth public lecture in November 2019.

In his lecture, Dr Ansell addressed the theme of healthcare inequality, drawing from his experience as a physician and his role as senior vice president for community health equity at Rush University Medical Centre, Chicago.

Adopting healthy habits empowers people to take control of their own wellness, according to lifestyle medicine pioneer Dr Beth Frates who delivered an RCSI MyHealth public lecture on 'Paving the Path to Wellness' in April 2019.

Dr Frates is a pioneer in lifestyle medicine education and an award-winning teacher at Harvard University. She currently works with patients to help them adopt and sustain healthy habits, focusing on the core pillars of exercise, nutrition, sleep and stress management.

During the lecture, Dr Frates looked into how healthy habits are formed &ndash drawing from her background in psychology and biology.

Arthritis is the most common cause of disability in Ireland, affecting approximately one in five Irish adults, equating to 915,000 people. Speakers at the MyHealth Lecture ‘Arthritis – My Joint Health’ dispelled several myths that exist around the condition, including the belief that arthritis is a disease reserved for older people and that surgery is inevitable for those who suffer with arthritis.

RCSI clinical experts joined the panel and discussed the signs and symptoms of arthritis and also shared guidance on how best the condition can be managed.

The MyHealth Lecture, 'Cannabis and Youth Health – The Evidence' provided a platform for a discussion on the health issues associated with the use of cannabis, including the use of cannabinoids as a treatment in certain medical conditions, such as epilepsy, and the mental health issues connected with the use of cannabis.

The lecture was delivered by Alex Berenson – former New York Times journalist and author of the best-selling book, Tell Your Children: The Truth about Marijuana, Mental Illness and Violence and Prof. Norman Delanty, FutureNeuro Research Centre at RCSI, who addressed the use of cannabinoids as a treatment in certain medical conditions.

Both speakers were joined by Prof. Mary Cannon, RCSI Professor of Psychiatry Dr Garret McGovern, Medical Director of the Priority Medical Clinic and Prof. Susan Smith, Department of General Practice, RCSI for a panel discussion chaired by television and radio broadcaster Miriam O’Callaghan

Sepsis, otherwise known as blood poisoning, is a silent killer because it is unpredictable, rapid and can go undiagnosed due to its non-specific signs and symptoms.

This RCSI MyHealth Lecture aimed to enable the general public to recognise the signs and symptoms of sepsis, and empowers them with the information they need to ask the right questions if they have a concern about sepsis.

Part 1: Prof. Steve Kerrigan is Associate Professor in Pharmacology at RCSI and inventor of InnovoSep, a potential new breakthrough therapy in the fight against sepsis. Prof. Kerrigan is a passionate advocate for educating people about the signs of sepsis.

Part 2: Ciarán Staunton of the Rory Staunton Foundation tells his son's story. In 2012, 12-year-old Rory developed sepsis after cutting his arm playing basketball. Tragically, Rory's sepsis went undiagnosed until it was too late, and sadly he passed away. Ciarán and his wife Orlaith established the Rory Staunton Foundation to raise public awareness of sepsis, ensuring that no other child or young adult dies of sepsis resulting from the lack of a speedy diagnosis and immediate medical treatment.

Part 3: Prof. Ger Curley, RCSI Professor of Critical Care Medicine and Anaesthesia, discusses the devastating effects of sepsis, current treatment strategies available and highlights new innovative treatments currently being developed and trialed globally.

Part 4: Dr Fidelma Fitzpatrick, RCSI Senior Lecturer and Consultant Microbiologist, will outline the national strategy and guidelines as part of the Patient Safety First Initiative. This initiative aims to facilitate early recognition in order to maximise survival opportunity and minimise the burden of chronic sequelae.

Dr Bennet Omalu, a forensic pathologist/neuropathologist, discovered a brain disease, brought on by concussions and blows to the head from high-impact sports, named chronic traumatic encephalopathy (CTE).

Dr Omalu discovered CTE when he performed autopsies and examined the brains of American football players and World Wrestling Entertainment wrestlers. His work resulted in the understanding of traumatic brain injury and how repetitive and innocuous impacts to the head can result in permanent brain damage and dementia.

In his MyHealth Lecture, Dr Omalu speaks about his life and research, which inspired the book and film Concussion, in which he was played by Will Smith.

Following his lecture, Dr Omalu was joined for a panel discussion by Prof. John O&rsquoByrne, orthopaedic surgeon and FAI Team Surgeon Dr Rod McLoughlin, IRFU Head of Medical Services Dr Pat O'Neill, Medical Consultant in Orthopaedic and Sports Medicine Aisling Daly, retired professional mixed martial artist and founder of Safe MMA Ireland and Bernard Jackman, former Irish international rugby player. The debate was facilitated by RTÉ presenter, Des Cahill.


Research Expertise

Projects

  • Title
    • Gene expression level as a keystone to understanding gene duplication: evolutionary constraints, opportunities, and disease
    • ERC
    • 01/01/2019
    • 30/12/2023
    • Title
      • SFI ERC Supplement
      • Science Foundation Ireland
      • 01/01/2019
      • 30/12/2023
      • Title
        • Dosage-sensitive genes in evolution and disease
        • European Research Council
        • Jan 2013
        • Dec 2018
        • Title
          • SFI ERC Supplement
          • Science Foundation Ireland
          • 1 Jan 2013
          • 31 Dec 2018
          • Title
            • Origin and Evolution of Vertebrate de novo Genes
            • Science Foundation Ireland
            • 2010
            • 2014
            • Title
              • Gene Gains, Losses and Relocations during Vertebrate Evolution
              • Science Foundation Ireland
              • October 2005
              • September 2010
              • Title
                • Supplement to Gene Gains, Losses and Relocations in Vertebrate Evolution
                • Additional funding provided after midway review of SFI PIYRA grant as the grant was exceeding expectations and producing excellent results.
                • Science Foundation Ireland
                • Title
                  • The Origin of New Genes in Poxviruses
                  • IRCSET
                  • October 2005
                  • September 2008
                  • Title
                    • Systematic search of RegulAtory elements coNtrOlling autosomal Monoallelic expression (RANDOM)
                    • Marie Skłodowska Curie Actions
                    • Title
                      • INTEGRATE
                      • Additional funding for Genomics Data Science CRT
                      • Marie Skłodowska Curie Actions
                      • Title
                        • Genomics Data Science CRT
                        • Centre for Research Training (CRT) for Genomics Data Science PhD. Value to TCD is an estimate and depends on numbers of PhD students who take up their projects here.
                        • Science Foundation Ireland
                        • 2019
                        • 2026

                        Keywords

                        ACCELERATED SEQUENCE EVOLUTION ANCIENT Biocomputing BIOINFORMATICS COEVOLUTION COMPARATIVE GENOMICS COMPLETE NUCLEOTIDE-SEQUENCE CONCERTED EVOLUTION Evolution EVOLUTION RATE Evolutionary Biology EVOLUTIONARY CHANGES EVOLUTIONARY RELATIONSHIPS EVOLUTIONARY SIGNIFICANCE GENES Genetics Genomes, Genomics Genomics HIGH-FREQUENCY RETROTRANSPOSITION Human Evolution HYPOTHESIS LINKAGE Molecular evolution Molecular Genetics MONOAMINE-OXIDASE-A PATTERN POLYPLOIDS RECEPTOR SEQUENCE VERTEBRATE EVOLUTION


                        Lecture Schedule, Spring 2021

                        DateTopicReadingSlidesStudy QuestionsVideo
                        1/11Lecture 1: What is a virus?Flint Vol I Chp 1
                        •The evolving concept of virus
                        •Cell size and scale
                        •Pandoravirus
                        pdfWordYouTube
                        1/13Lecture 2: The infectious cycleFlint Vol I Chp 2
                        •Counting Viruses
                        •Viral RNA is not infectious virus
                        •I tested positive
                        •My antibody result
                        pdfWordYouTube
                        1/20Lecture 3: Genomes and geneticsFlint Vol I Chp 3
                        •The Baltimore scheme
                        •ViralZone
                        pdfWordYouTube
                        1/25Lecture 4: StructureFlint Vol I Chp 4
                        •Buckyball Viruses (YouTube)
                        •Virus images at ViperDB
                        pdfWordYouTube
                        1/27Lecture 5: Attachment and entryFlint Vol I Chp 5
                        •A portal for RNA exit
                        •A human rhinovirus in chimpanzees
                        pdfWordYouTube
                        2/1Lecture 6: RNA directed RNA synthesisFlint Vol I Chp 6
                        •Influenza viral RNA synthesis
                        pdfWordYouTube
                        2/3Lecture 7: Transcription and RNA processingFlint Vol I Chp 8 through p277 Chp 10 through p364pdfWordYouTube
                        2/8Lecture 8: Viral DNA replicationFlint Vol I Chp 9
                        •No primer needed
                        pdfWordYouTube
                        2/10Lecture 9: Reverse transcription and integrationFlint Vol I Chp 7
                        •Museum pelts help date the Koala retrovirus
                        •Aretrovirus makes chicken eggshells blue
                        •Reverse transcription animation
                        •Retroviral influence on human embryonic development
                        pdfWordYouTube
                        2/15Lecture 10: AssemblyFlint Vol I Chapters 12 and 13
                        •Packaging of the segmented influenza virus genome
                        •What if influenza virus did not reassort?
                        pdfWordYouTube
                        2/17Lecture 11: The infected cellFlint Vol I Chp 14
                        •Metabolic manipulations in virus-infected cells
                        •Rhinoviruses have a sweet tooth
                        pdfWordYouTube
                        2/22Lecture 12: Infection basicsFlint Vol II Chapters 1 and 2
                        •Transmission of influenza
                        •Slow motion sneezing
                        •Chikungunya an exotic virus on the move
                        •How mosquitoes spread viruses
                        pdfWordYouTube
                        2/24Lecture 13: Intrinsic and innate defensesFlint Vol II Chapter 3
                        •The inflammatory response
                        •Natural antibody protects against viral infection
                        pdfWordYouTube
                        3/1Spring recess
                        3/3Spring recess
                        3/8Lecture 14: Adaptive immunityFlint Vol II Chapter 4
                        My at-home SARS-CoV-2 antibody test result
                        pdfWordYouTube
                        3/10Lecture 15: Mechanisms of pathogenesisFlint Vol II Chapter 5pdfWordYouTube
                        3/15Lecture 16: Acute infectionsFlint Vol II Chapter 5
                        •Acute viral infections
                        •Chronology of an acute infection
                        pdfWordYouTube
                        3/17Lecture 17: Persistent infectionsFlint Vol II Chapter 5pdfWordYouTube
                        3/22Lecture 18: Transformation and oncogenesisFlint Vol II Chapter 6pdfWordYouTube
                        3/24Lecture 19: VaccinesFlint Vol II Chapter 8
                        •Influenza virus-like particle vaccine
                        •Poliovirus vaccine safety
                        pdfWordYouTube
                        3/29Lecture 20: AntiviralsFlint Vol II Chapter 9
                        •A new drug for influenza
                        pdfWordYouTube
                        3/31Lecture 21: EvolutionFlint Vol II Chapter 10
                        •Virulence – a positive or negative trait for evolution?
                        •Increased fidelity reduces viral fitness
                        •Why do viruses cause disease?
                        SARS-CoV-2 variants of concern
                        pdfWordYouTube
                        4/5Lecture 22: Emerging virusesFlint Vol II Chapter 11
                        •MERS-coronavirus in camels
                        •Nipah virus at 20
                        pdfWordYouTube
                        4/12Lecture 23: HIV and AIDSFlint Vol II Chapter 6
                        •The London Patient
                        •Interview with Beatrice Hahn
                        pdfWordYouTube
                        4/14Lecture 24: Unusual infectious agentsFlint Vol II Chapter 12
                        •Is chronic wasting disease a threat to humans?
                        •Prion contamination in the emergency room
                        pdfWordYouTube
                        5/4Lecture 25: Therapeutic virusesFlint Vol I Chapter 3
                        •TWiV 350: Viral gene therapy with Katherine High
                        •Virus Watch: Cancer killing viruses
                        pdfWordYouTube

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                        This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.


                        ISMB provides support for major international meetings in matrix biology. To apply for meeting support, conference organizers are requested to apply at least 6 months before the meeting. Applications should include full details of the meeting being organized, its relevance to matrix biology and the purpose for which the proposed ISMB contribution will be used. Deadlines: January 1, April 1, July 1 and October 1. Applications for meeting support should be sent to the ISMB secretary.

                        Meetings currently supported by ISMB :

                        Gordon Research Conference on Proteoglycans (12-17 July 2020 Proctor Academy, NH, USA) [This conference has now been postponed and will be supported in 2022]

                        Previous meetings supported by ISMB:

                        2019
                        Cartilage Biology and Pathology GRC/GRS, 16-22 March 2019, Galveston, Texas, USA
                        GRC/GRS Metalloproteases, 11-17 May 2019, Lucca (Barga), Italy
                        GRC/GRS on Collagen 2019, 13-19 July 2019, Colby Sawyer College, USA
                        FASEB Conference on Matricellular Proteins in Tissue Remodeling and Inflammation, 14-19 July, 2019. Lisbon, Portugual
                        11th International Conference on Proteoglycans, September 28th to October 3rd 2019, Kanazawa, Japan.

                        2018
                        ASMB Biennial Meeting, October 13-17, 2018, Red Rock Resort, Las Vegas, NV, USA
                        FEBS Advanced Lecture Course on Extracellular Matrix, 27 September - 2 October 2018, Patras, Greece
                        Matrix Biology Europe, July 21-24, 2018, Manchester, UK
                        GRC: Proteoglycans, 8-13 July 2018, Andover, NH, USA

                        2017
                        Seven Lakes Proteoglycans Conference September 10-14, 2017, Varese, Italy
                        Gordon Research Seminar/Gordon Research Conference on Collagens, July 15-21, 2017, New London, NH, USA
                        Jefferson Matrix Biology and Pathology Symposium on Fibrosis and Fibrotic Diseases, June 4-6, 2017, Philadelphia, PA, USA
                        FEBS Advanced Lecture Course on Matrix Pathobiology, Signaling & Molecular Targets, May 25-30, 2017, Spetses, Greece

                        2016
                        American Society for Matrix Biology, November 13-16, 2016, St Petersburg, FL, USA
                        Metalloproteinases and their inhibitors: beginning, past and future, August 4-5, 2016, Oxford, UK
                        Matrix Biology Europe, June 11-14, 2016, Athens, Greece

                        2015
                        Matrix Biology Ireland, December 2-4, 2015, Dublin, Ireland
                        Matrix Pathobiology, Signaling & Molecular Targets (FEBS Advanced Lecture Course), September 24-29, 2015, Rhodes, Greece
                        9th International Conference on Proteoglycans/10th Pan Pacific Connective Tissue Societies Symposium, August 23-27 2015, Seoul, Korea
                        Gordon Research Conference on Matrix Metalloproteinases, August 2-7, 2015, Newry, ME, USA
                        Gordon Research Seminar/Conference on Collagen, July 12-17, 2015, New London, NH, USA
                        Gordon Research Conference on Cartilage Biology and Pathology, March 22-27, 2015, Galveston, TX, USA

                        2014
                        Inaugural meeting of Matrix Biology Ireland, Galway, Ireland, November 19-21, 2014
                        American Society for Matrix Biology, October 12-15, 2014, Cleveland, Ohio, USA
                        Gordon Research Conference on Proteoglycans, July 6-11, 2014, Andover, NH, USA
                        Matrix Biology Europe (formerly FECTS), June 21-24, 2014, Rotterdam, The Netherlands

                        2013
                        Pan Pacific Connective Tissue Societies Symposium, November 24-27, 2013, Hong Kong
                        International Conference on Proteoglycans, August 25-29, 2013, Frankfurt/Main, Germany
                        FASEB Meeting on Matricellular Proteins in Development, Health, and Disease, July 28 – August 2, 2013, Saxtons River, Vermont, USA
                        Gordon Research Conference on Elastin, Elastic Fibers and Microfibrils, July 21-26, 2013, Biddeford, ME, USA
                        Gordon Research Conference on Collagen, July 14-19, 2013, Colby-Sawyer College, New London, NH, USA
                        Gordon Research Conference on Matrix Metalloproteinases, May 19-24, 2013, Renaissance Tuscany Il Ciocco Resort, Lucca (Barga), Italy

                        2012
                        American Society for Matrix Biology Meeting, November 11-14, 2012, San Diego, USA
                        Federation of the European Connective Tissue Societies, August 25-29, 2012, Katowice, Poland

                        2011
                        Extracellular Matrix in Health and Disease, April 14-15, Boston, 2011, USA

                        2010
                        American Society for Matrix Biology Meeting, December 7-10, 2010, Charleston, USA
                        Federation of the European Connective Tissue Societies, July 3-7, 2010, Davos, Switzerland


                        4th Edition of Global Conference on Plant Science and Molecular Biology

                        Plant Science Conference 2019 will provide a dedicated platform to peer researchers, young inspired scientists, academicians, and industrialists to meet, discuss and share the knowledge that&rsquos still more to be revealed in the field of Plant Science, Plant Biology and Plant Molecular Biology.

                        Contact: [email protected]
                        Dates: September 19-21, 2019
                        Venue: London, UK

                        Recommended Plant Science Conferences 2019 : | Plant Science Conferences | Plant Biology Conferences 2019 | Plant Biology Conferences | Plant Conferences | Botany Conferences | Biology Conferences | Plant Science Conference

                        Plant Science Conference 2019 Scientific Sessions:
                        Plant Biology
                        Plant Molecular Biology
                        Plant Sciences and Plant Research
                        Plant Physiology and Biochemistry
                        Plant Biochemistry and Biosystems
                        Plant Genetics and Genomics
                        Plant Ecology and Taxonomy
                        Plant Nutrition and Soil Sciences
                        Plant Diseases and Bryology
                        Microbiology and Phycology
                        Plant Tissue Culture
                        Plant Biotechnology
                        Agronomy and Agricultural Research
                        Plant Science: Antibodies, Antigens and Antibiotics
                        Plant Pathology and Mycology
                        Plant Metabolic Engineering
                        Plant anatomy and morphology
                        Plant and Environment
                        Phytochemical Analysis
                        Plant Hormones
                        Plant Neurobiology


                        News & Event Highlights

                        April 1st 2019 - The Irish Environmental History Network invites you to its 47th public meeting, featuring a lecture from very special guest Dr Christine Corton of the University of Cambridge. Read More

                        March 5th 2019 - The Trinity Centre for Environmental Humanities invites you to a lecture by Dr Niall Brady (Archaeological Diving Company) organised by Trinity Centre for Environmental History in association with the School of History. The lecture will take place on 5th of March in the Neill lecture theatre of the Trinity Long Room Hub from 6-8 PM. Read More

                        January 22nd 2019 - The Trinity Centre for Environmental Humanities invites you to a roundtable discussion on “Ireland’s Peatlands: How to balance natural and cultural heritage in the context of climate change?”, featuring Luke Ming Flanagan (Member of the European Parliament), Flo Renou-Wilson (School of Biology & Environmental Science, University College Dublin), Deirdre O'Mahony (independent artist) and Adrian Kane (SIPTU). Read More

                        January 22nd 2019 - The Irish Environmental History Network invites you to its 45th public meeting, featuring a guest lecture given by Dr Paul Montgomery of the Arctic Studies Center in Liaocheng, University Shandong, China. The lecture will take place on Tuesday the 22nd January at 6pm in the Ui Chadhain Theatre in the Arts Building TCD. ". Read More

                        November 21st 2018 - The 44th public meeting of the Irish Environmental History Network will take place on the 21st of November 2018 in the Swift Theatre of the Arts Building TCD and will take place from 6-8pm. It will feature a guest lecture given by Marianna Dudley of the University of Bristol. This lecture will be entitled "Limits of Power: Wind energy, Orkney, and the postwar British state". Read More

                        October 17th 2018 - The Irish Environmental History Network invites you to its 43rd Public meeting, featuring a guest lecture from Bruno Esperante of University of Santiago de Compostela. The lecture is entitled "Exporting the Green Revolution from the US to Francoist Spain (1950-1962)". Read More

                        October 3rd 2018 - The Irish Environmental History Network (IEHN) invites you to its 42nd public meeting, featuring a guest lecture from Dr Fiona Smyth, a Research Fellow in the School of Engineering at Trinity College Dublin. The lecture is entitled "Music, Munitions, and Misunderstandings: Architectural Acoustics and Environmental Design in 1920s Britain". Read More

                        September 18th 2018 - The 41st Public Lecture of the Irish Environmental History Network will be presented by Dr Heli Huhtaama of Heidelberg Centre for the Environment, University of Heidelberg. This lecture will take place at 6pm, Tuesday 18th September 2018, in the Swift Theatre, Arts Building, Trinity College Dublin. This lecture will be entitled "Climate and human crises on the northern Baltic Sea region in 17th century". Read More

                        September 3rd 2018 - The 40th Public Lecture of the Irish Environmental History Network will be presented by Dr Peter Peregrine of Lawrence University. This lecture will take place at 6pm, Monday 3rd September 2018, in the Swift Theatre, Arts Building, Trinity College Dublin. This lecture will be entitled "Exploring Social Resilience to Climate-Related Disasters: The A.D. 536 Atmospheric Event". Dr Peregrine is Professor of Anthropology at Lawrence University.

                        April 25 2018 - The 39th Public Lecture of the Irish Environmental History Network was presented by Dr James Smith of of University of York. This lecture took place at 6pm, Wednesday 25th April 2018, in the TRiSS Seminar Room, 6th Floor Arts Building, Trinity College Dublin. This lecture was entitled "Engineering the Soul: Landscape, Technology and Energy in Medieval Intellectual Culture". More details.

                        April 3 2018 - The 38th Public Lecture of the Irish Environmental History Network was presented by Dr Julia Lajus of National Research University Higher School of Economics, Moscow, 5pm, Tuesday 3rd April 2018, in the Neill Theatre, Trinity Long Room Hub, Trinity College Dublin. This lecture was entitled "Nature’s experts under Soviet power". More details.

                        March 14 2018 - The 37th Public Lecture of the Irish Environmental History Network was presented by Dr Dr James H. Barrett of University of Cambridge, at 6pm, Wednesday 14th March 2018, in the TRISS seminar room, Arts Building, Trinity College Dublin. More details

                        March 7 2018 - The 36th Public Lecture of the Irish Environmental History Network was presented by Dr Tønnes Bekker-Nielsen of University of Southern Denmark, at 6pm, Wednesday 7th March 2018, in the Uí Chadhain Theatre, Arts Building, Trinity College Dublin. More details

                        Feb. 15 2018 - The Trinity Centre for Environmental Humanities (TCEH) held its official launch on Thursday, 15h of February 2018 from 5-7pm in the Trinity Research in Social Sciences (TRiSS) seminar room on the 6th floor of the Arts Building. This event featured a guest lecture by Dr Christine Hansen of Gothenburg University, which was entitled "Big Fire and other Australian seasons: the forgotten Aboriginal Calendar", followed by a wine reception and launch of the Centre. More details.

                        Jan. 26 2018 - 35th Public Lecture of the Irish Environmental History Network, featuring a lecture by Dr. Ronan Foley of Maynooth University. The lecture was entitled “Therapeutic Environments in 18th and 19th Century Ireland: Hybrid Spaces and Practices”. More details

                        17 February, 2017: Trinity College Dublin

                        A Roundtable Discussion organized by Dr. Derek Gladwin (UBC), entitled: "Is Global Climate Action Trumped?" The event will take place in Trinity College Dublin, Davis Lecture Theatre, Arts Block, from 6pm. The event is sponsored by the TCD Environmental Humanities Initiative, and will be open to the public, but booking your place ahead of time is essential. More details.


                        Labs on hold but never fear, Virtual Geochemistry is here!

                        2020 will certainly be memorable, but sadly not for the 50 th anniversary meeting of the Geochemistry Group…

                        We know that this is a challenging time for many. Early career researchers, in particular, are at heightened risk of loneliness. Motivation to work can be a challenge.

                        All this got me thinking about our motivations more generally. Why am I on the committee of the Geochemistry Group? What actually gives meaning to life?

                        Image credit: Nishant Choksi

                        Around the turn of the 20 th century, William James, the “Father of American Psychology” (according to Wikipedia) wrote:

                        ‘The deepest principle in human nature is the craving to be appreciated’

                        And Abraham Maslow put belonging into his famous Hierarchy of Needs in 1943.

                        I think that, at a basic level, these ideas (i.e. being appreciated, belonging) boil down to not being forgotten.

                        So, we just wanted to say this:

                        The Geochemistry Group have not forgotten you! – Our amazing community of UK and international geochemists.

                        We are absolutely thrilled that more than 520 of you joined our scientific writing webinar, hosted in collaboration with Elsevier. Thanks so much to all of you, to our star coordinator Marc-Alban Millet, and to Tessa da Roo and Andrew Kerr for co-hosting with Marc-Alban. If you missed it (or if you didn’t!), you can find a fantastic diversity of skills based content on the Researcher Academy pages at Elsevier.

                        And we want to hear from you! What can we do for you in the coming months? If you have ideas, please reply to this post, tweet us @geochemgroup, or use the Facebook group.

                        GGRiP will return, in some form, at some point (TBC…).

                        In the meantime, don’t forget that Virtual Goldschmidt 2020 is coming up. Registration for student members is only $25 (a fantastic saving compared to a flight to Hawaii!).


                        Watch the video: Lecture 4 Patterns of Chromosomal Inheritance (June 2022).


Comments:

  1. Sachio

    yourself, you have invented such incomparable answer?

  2. Eadweald

    I do not know how to whom, I liked it!

  3. Hamal

    How do you feel about Putin, everyone?



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