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2.3: Atomic Bonds - Biology


What you’ll learn to do: Classify different types of atomic bonds

When atoms bond together, they create molecules: a sodium atom bonds with a chlorine atom to create salt (sodium chloride), two hydrogen atoms bond with an oxygen atom to create water (hydrogen dioxide). However, not all atomic bonds are the same; in fact salt and water are created with two very different types of bonds (ionic and polar covalent bonds respectively).

The different types of bonds (ionic, polar covalent, and non-polar covalent bonds) behave differently, and these differences have an impact on the molecules they create. Understanding the types of bonds that create living things can help us understand those living things themselves.

Learning Objectives

  • Define the octet rule and its role in chemical bonds
  • Describe the characteristics of ionic bonds and identify common ions
  • Describe the characteristics of covalent bonds and differentiate between polar and nonpolar bonds
  • Model a Hydrogen bond and identify its unique qualities
  • Model van der Waals interactions identify their unique qualities
  • Describe the properties of water that are critical to maintaining life

Chemical Bonding

Not all elements have enough electrons to fill their outermost shells, but an atom is at its most stable when all of the electron positions in the outermost shell are filled. Because of these vacancies in the outermost shells, we see the formation of chemical bonds, or interactions between two or more of the same or different elements that result in the formation of molecules. To achieve greater stability, atoms will tend to completely fill their outer shells and will bond with other elements to accomplish this goal by sharing electrons, accepting electrons from another atom, or donating electrons to another atom. Because the outermost shells of the elements with low atomic numbers (up to calcium, with atomic number 20) can hold eight electrons, this is referred to as the octet rule. An element can donate, accept, or share electrons with other elements to fill its outer shell and satisfy the octet rule.

An early model of the atom was developed in 1913 by the Danish scientist Niels Bohr (1885–1962). The Bohr model shows the atom as a central nucleus containing protons and neutrons, with the electrons in circular electron shells at specific distances from the nucleus, similar to planets orbiting around the sun. Each electron shell has a different energy level, with those shells closest to the nucleus being lower in energy than those farther from the nucleus. By convention, each shell is assigned a number and the symbol n—for example, the electron shell closest to the nucleus is called 1n. In order to move between shells, an electron must absorb or release an amount of energy corresponding exactly to the difference in energy between the shells. For instance, if an electron absorbs energy from a photon, it may become excited and move to a higher-energy shell; conversely, when an excited electron drops back down to a lower-energy shell, it will release energy, often in the form of heat.

Bohr model of an atom, showing energy levels as concentric circles surrounding the nucleus. Energy must be added to move an electron outward to a higher energy level, and energy is released when an electron falls down from a higher energy level to a closer-in one. Image credit: modified from OpenStax Biology

Atoms, like other things governed by the laws of physics, tend to take on the lowest-energy, most stable configuration they can. Thus, the electron shells of an atom are populated from the inside out, with electrons filling up the low-energy shells closer to the nucleus before they move into the higher-energy shells further out. The shell closest to the nucleus, 1n, can hold two electrons, while the next shell, 2n, can hold eight, and the third shell, 3n, can hold up to eighteen.

The number of electrons in the outermost shell of a particular atom determines its reactivity, or tendency to form chemical bonds with other atoms. This outermost shell is known as the valence shell, and the electrons found in it are called valence electrons. In general, atoms are most stable, least reactive, when their outermost electron shell is full. Most of the elements important in biology need eight electrons in their outermost shell in order to be stable, and this rule of thumb is known as the octet rule. Some atoms can be stable with an octet even though their valence shell is the 3n shell, which can hold up to 18 electrons. We will explore the reason for this when we discuss electron orbitals below.

Examples of some neutral atoms and their electron configurations are shown below. In this table, you can see that helium has a full valence shell, with two electrons in its first and only, 1n, shell. Similarly, neon has a complete outer 2n shell containing eight electrons. These electron configurations make helium and neon very stable. Although argon does not technically have a full outer shell, since the 3n shell can hold up to eighteen electrons, it is stable like neon and helium because it has eight electrons in the 3n shell and thus satisfies the octet rule. In contrast, chlorine has only seven electrons in its outermost shell, while sodium has just one. These patterns do not fill the outermost shell or satisfy the octet rule, making chlorine and sodium reactive, eager to gain or lose electrons to reach a more stable configuration.

Bohr diagrams of various elements Image credit: OpenStax Biology

Electron configurations and the periodic table

Elements are placed in order on the periodic table based on their atomic number, how many protons they have. In a neutral atom, the number of electrons will equal the number of protons, so we can easily determine electron number from atomic number. In addition, the position of an element in the periodic table—its column, or group, and row, or period—provides useful information about how those electrons are arranged.

If we consider just the first three rows of the table, which include the major elements important to life, each row corresponds to the filling of a different electron shell: helium and hydrogen place their electrons in the 1n shell, while second-row elements like Li start filling the 2n shell, and third-row elements like Na continue with the 3n shell. Similarly, an element’s column number gives information about its number of valence electrons and reactivity. In general, the number of valence electrons is the same within a column and increases from left to right within a row. Group 1 elements have just one valence electron and group 18 elements have eight, except for helium, which has only two electrons total. Thus, group number is a good predictor of how reactive each element will be:

  • Helium (He), neon (Ne), and argon (Ar), as group 18 elements, have outer electron shells that are full or satisfy the octet rule. This makes them highly stable as single atoms. Because of their non-reactivity, they are called the inert gases or noble gases.
  • Hydrogen (H), lithium (Li), and sodium (Na), as group 1 elements, have just one electron in their outermost shells. They are unstable as single atoms, but can become stable by losing or sharing their one valence electron. If these elements fully lose an electron—as Li and Na typically do—they become positively charged ions: Li+, Na+.
  • Fluorine (F) and chlorine (Cl), as group 17 elements, have seven electrons in their outermost shells. They tend to achieve a stable octet by taking an electron from other atoms, becoming negatively charged ions: F and Cl.
  • Carbon (C), as a group 14 element, has four electrons in its outer shell. Carbon typically shares electrons to achieve a complete valence shell, forming bonds with multiple other atoms.

Thus, the columns of the periodic table reflect the number of electrons found in each element’s valence shell, which in turn determines how the element will react.

Ionic Bonds

Some atoms are more stable when they gain or lose an electron (or possibly two) and form ions. This fills their outermost electron shell and makes them energetically more stable. Because the number of electrons does not equal the number of protons, each ion has a net charge. Cations are positive ions that are formed by losing electrons. Negative ions are formed by gaining electrons and are called anions. Anions are designated by their elemental name being altered to end in “-ide”: the anion of chlorine is called chloride, and the anion of sulfur is called sulfide, for example.

This movement of electrons from one element to another is referred to as electron transfer. As Figure 1 illustrates, sodium (Na) only has one electron in its outer electron shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons, 11 neutrons, and only 10 electrons, leaving it with an overall charge of +1. It is now referred to as a sodium ion. Chlorine (Cl) in its lowest energy state (called the ground state) has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons, 17 neutrons, and 18 electrons, giving it a net negative (–1) charge. It is now referred to as a chloride ion. In this example, sodium will donate its one electron to empty its shell, and chlorine will accept that electron to fill its shell. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium cation) or –1 (chloride anion) charge. Note that these transactions can normally only take place simultaneously: in order for a sodium atom to lose an electron, it must be in the presence of a suitable recipient like a chlorine atom.

Ionic bonds are formed between ions with opposite charges. For instance, positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge.

Certain salts are referred to in physiology as electrolytes (including sodium, potassium, and calcium), ions necessary for nerve impulse conduction, muscle contractions and water balance. Many sports drinks and dietary supplements provide these ions to replace those lost from the body via sweating during exercise.

Learning Objectives

This video shows how ionic compounds form from anions and cations.

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Covalent Bonds

Another way the octet rule can be satisfied is by the sharing of electrons between atoms to form covalent bonds. These bonds are stronger and much more common than ionic bonds in the molecules of living organisms. Covalent bonds are commonly found in carbon-based organic molecules, such as our DNA and proteins. Covalent bonds are also found in inorganic molecules like H2O, CO2, and O2. One, two, or three pairs of electrons may be shared, making single, double, and triple bonds, respectively. The more covalent bonds between two atoms, the stronger their connection. Thus, triple bonds are the strongest.

The strength of different levels of covalent bonding is one of the main reasons living organisms have a difficult time in acquiring nitrogen for use in constructing their molecules, even though molecular nitrogen, N2, is the most abundant gas in the atmosphere. Molecular nitrogen consists of two nitrogen atoms triple bonded to each other and, as with all molecules, the sharing of these three pairs of electrons between the two nitrogen atoms allows for the filling of their outer electron shells, making the molecule more stable than the individual nitrogen atoms. This strong triple bond makes it difficult for living systems to break apart this nitrogen in order to use it as constituents of proteins and DNA.

The formation of water molecules provides an example of covalent bonding. The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds. The electron from the hydrogen splits its time between the incomplete outer shell of the hydrogen atoms and the incomplete outer shell of the oxygen atoms. To completely fill the outer shell of oxygen, which has six electrons in its outer shell but which would be more stable with eight, two electrons (one from each hydrogen atom) are needed: hence the well-known formula H2O. The electrons are shared between the two elements to fill the outer shell of each, making both elements more stable.

View this short video to see an animation of ionic and covalent bonding.

A link to an interactive elements can be found at the bottom of this page.

Polar and Nonpolar Covalent Bonds

There are two types of covalent bonds: polar and nonpolar. Nonpolar covalent bonds form between two atoms of the same element or between different elements that share the electrons equally. For example, an oxygen atom can bond with another oxygen atom to fill their outer shells. This association is nonpolar because the electrons will be equally distributed between each oxygen atom. Two covalent bonds form between the two oxygen atoms because oxygen requires two shared electrons to fill its outermost shell. Nitrogen atoms will form three covalent bonds (also called triple covalent) between two atoms of nitrogen because each nitrogen atom needs three electrons to fill its outermost shell. Another example of a nonpolar covalent bond is found in the methane (CH4) molecule. The carbon atom has four electrons in its outermost shell and needs four more to fill it. It gets these four from four hydrogen atoms, each atom providing one. These elements all share the electrons equally, creating four nonpolar covalent bonds.

In a polar covalent bond, the electrons shared by the atoms spend more time closer to one nucleus than to the other nucleus. Because of the unequal distribution of electrons between the different nuclei, a slightly positive (δ+) or slightly negative (δ–) charge develops. The covalent bonds between hydrogen and oxygen atoms in water are polar covalent bonds. The shared electrons spend more time near the oxygen nucleus, giving it a small negative charge, than they spend near the hydrogen nuclei, giving these molecules a small positive charge. Polar covalent bonds form more often when atoms that differ greatly in size share electrons.

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Learning Objectives

Watch this video for another explanation of covalent bonds and how they form:

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Hydrogen Bonds

Ionic and covalent bonds between elements require energy to break. Iconic bonds are not as strong as covalent, which determines their behavior in biological systems. However, not all bonds are ionic or covalent bonds. Weaker bonds can also form between molecules. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. Without these two types of bonds, life as we know it would not exist. Hydrogen bonds provide many of the critical, life-sustaining properties of water and also stabilize the structures of proteins and DNA, the building block of cells.

When polar covalent bonds containing hydrogen form, the hydrogen in that bond has a slightly positive charge because hydrogen’s electron is pulled more strongly toward the other element and away from the hydrogen. Because the hydrogen is slightly positive, it will be attracted to neighboring negative charges. When this happens, a weak interaction occurs between the δ+ of the hydrogen from one molecule and the δ– charge on the more electronegative atoms of another molecule, usually oxygen or nitrogen, or within the same molecule.

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This interaction is called a hydrogen bond. This type of bond is common and occurs regularly between water molecules. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and in organic polymers, creating a major force in combination. Hydrogen bonds are also responsible for zipping together the DNA double helix.

Learning Objectives

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Van der Waals Interactions

Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. They are also called inter-molecular forces. They occur between polar, covalently bound atoms in different molecules. Some of these weak attractions are caused by temporary partial charges formed when electrons move around a nucleus. These weak interactions between molecules are important in biological systems and occur based on physical proximity.

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Have you or anyone you know ever had a magnetic resonance imaging (MRI) scan, a mammogram, or an X-ray? These tests produce images of your soft tissues and organs (as with an MRI or mammogram) or your bones (as happens in an X-ray) by using either radiowaves or special isotopes (radiolabeled or fluorescently labeled) that are ingested or injected into the body. These tests provide data for disease diagnoses by creating images of your organs or skeletal system.

MRI imaging works by subjecting hydrogen nuclei, which are abundant in the water in soft tissues, to fluctuating magnetic fields, which cause them to emit their own magnetic field. This signal is then read by sensors in the machine and interpreted by a computer to form a detailed image.

Some radiography technologists and technicians specialize in computed tomography, MRI, and mammography. They produce films or images of the body that help medical professionals examine and diagnose. Radiologists work directly with patients, explaining machinery, preparing them for exams, and ensuring that their body or body parts are positioned correctly to produce the needed images. Physicians or radiologists then analyze the test results.

Radiography technicians can work in hospitals, doctors’ offices, or specialized imaging centers. Training to become a radiography technician happens at hospitals, colleges, and universities that offer certificates, associate’s degrees, or bachelor’s degrees in radiography.

Why Life Depends on Water

Do you ever wonder why scientists spend time looking for water on other planets? It is because water is essential to life; even minute traces of it on another planet can indicate that life could or did exist on that planet. Water is one of the more abundant molecules in living cells and the one most critical to life as we know it. Approximately 60–70 percent of your body is made up of water. Without it, life simply would not exist.

Water Is Polar

The hydrogen and oxygen atoms within water molecules form polar covalent bonds. The shared electrons spend more time associated with the oxygen atom than they do with hydrogen atoms. There is no overall charge to a water molecule, but there is a slight positive charge on each hydrogen atom and a slight negative charge on the oxygen atom. Because of these charges, the slightly positive hydrogen atoms repel each other and form the unique shape seen in Figure 6. Each water molecule attracts other water molecules because of the positive and negative charges in the different parts of the molecule. Water also attracts other polar molecules (such as sugars), forming hydrogen bonds. When a substance readily forms hydrogen bonds with water, it can dissolve in water and is referred to as hydrophilic (“water-loving”). Hydrogen bonds are not readily formed with nonpolar substances like oils and fats (Figure 5). These nonpolar compounds are hydrophobic (“water-fearing”) and will not dissolve in water.

Water Stabilizes Temperature

The hydrogen bonds in water allow it to absorb and release heat energy more slowly than many other substances. Temperature is a measure of the motion (kinetic energy) of molecules. As the motion increases, energy is higher and thus temperature is higher. Water absorbs a great deal of energy before its temperature rises. Increased energy disrupts the hydrogen bonds between water molecules. Because these bonds can be created and disrupted rapidly, water absorbs an increase in energy and temperature changes only minimally. This means that water moderates temperature changes within organisms and in their environments. As energy input continues, the balance between hydrogen-bond formation and destruction swings toward the destruction side. More bonds are broken than are formed. This process results in the release of individual water molecules at the surface of the liquid (such as a body of water, the leaves of a plant, or the skin of an organism) in a process called evaporation. Evaporation of sweat, which is 90 percent water, allows for cooling of an organism, because breaking hydrogen bonds requires an input of energy and takes heat away from the body.

Conversely, as molecular motion decreases and temperatures drop, less energy is present to break the hydrogen bonds between water molecules. These bonds remain intact and begin to form a rigid, lattice-like structure (e.g., ice) (Figure 7a). When frozen, ice is less dense than liquid water (the molecules are farther apart). This means that ice floats on the surface of a body of water (Figure 7b). In lakes, ponds, and oceans, ice will form on the surface of the water, creating an insulating barrier to protect the animal and plant life beneath from freezing in the water. If this did not happen, plants and animals living in water would freeze in a block of ice and could not move freely, making life in cold temperatures difficult or impossible.

Water Is an Excellent Solvent

Because water is polar, with slight positive and negative charges, ionic compounds and polar molecules can readily dissolve in it. Water is, therefore, what is referred to as a solvent—a substance capable of dissolving another substance. The charged particles will form hydrogen bonds with a surrounding layer of water molecules. This is referred to as a sphere of hydration and serves to keep the particles separated or dispersed in the water. In the case of table salt (NaCl) mixed in water (Figure 8), the sodium and chloride ions separate, or dissociate, in the water, and spheres of hydration are formed around the ions.

A positively charged sodium ion is surrounded by the partially negative charges of oxygen atoms in water molecules. A negatively charged chloride ion is surrounded by the partially positive charges of hydrogen atoms in water molecules. These spheres of hydration are also referred to as hydration shells. The polarity of the water molecule makes it an effective solvent and is important in its many roles in living systems.

Water Is Cohesive

Have you ever filled up a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water actually forms a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of cohesion. In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together at the liquid-air (gas) interface, although there is no more room in the glass. Cohesion gives rise to surface tension, the capacity of a substance to withstand rupture when placed under tension or stress. When you drop a small scrap of paper onto a droplet of water, the paper floats on top of the water droplet, although the object is denser (heavier) than the water. This occurs because of the surface tension that is created by the water molecules. Cohesion and surface tension keep the water molecules intact and the item floating on the top. It is even possible to “float” a steel needle on top of a glass of water if you place it gently, without breaking the surface tension (Figure 9).

These cohesive forces are also related to the water’s property of adhesion, or the attraction between water molecules and other molecules. This is observed when water “climbs” up a straw placed in a glass of water. You will notice that the water appears to be higher on the sides of the straw than in the middle. This is because the water molecules are attracted to the straw and therefore adhere to it.

Cohesive and adhesive forces are important for sustaining life. For example, because of these forces, water can flow up from the roots to the tops of plants to feed the plant.

Learning Objectives

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Practice Question

Which of the following statements is not true?

  1. Water is polar.
  2. Water stabilizes temperature.
  3. Water is essential for life.
  4. Water is the most abundant atom in Earth’s atmosphere.

[reveal-answer q=”335873″]Show Answer[/reveal-answer]
[hidden-answer a=”335873″]Statement d is not true. Water is not the most abundant atom in Earth’s atmosphere—nitrogen is.[/hidden-answer]

Check Your Understanding

Answer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does not count toward your grade in the class, and you can retake it an unlimited number of times.

Use this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section.


2.3 Carbon

By the end of this section, you will be able to do the following:

  • Explain why carbon is important for life
  • Describe the role of functional groups in biological molecules

Many complex molecules called macromolecules, such as proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids comprise cells. The macromolecules are a subset of organic molecules (any carbon-containing liquid, solid, or gas) that are especially important for life. The fundamental component for all of these macromolecules is carbon. The carbon atom has unique properties that allow it to form covalent bonds to as many as four different atoms, making this versatile element ideal to serve as the basic structural component, or “backbone,” of the macromolecules.

Individual carbon atoms have an incomplete outermost electron shell. With an atomic number of 6 (six electrons and six protons), the first two electrons fill the inner shell, leaving four in the second shell. Therefore, carbon atoms can form up to four covalent bonds with other atoms to satisfy the octet rule. The methane molecule provides an example: it has the chemical formula CH4. Each of its four hydrogen atoms forms a single covalent bond with the carbon atom by sharing a pair of electrons. This results in a filled outermost shell.

Hydrocarbons

Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane (CH4) described above. We often use hydrocarbons in our daily lives as fuels—like the propane in a gas grill or the butane in a lighter. The many covalent bonds between the atoms in hydrocarbons store a great amount of energy, which releases when these molecules burn (oxidize). Methane, an excellent fuel, is the simplest hydrocarbon molecule, with a central carbon atom bonded to four different hydrogen atoms, as Figure 2.21 illustrates. The shape of its electron orbitals determines the shape of the methane molecule's geometry, where the atoms reside in three dimensions. The carbons and the four hydrogen atoms form a tetrahedron, with four triangular faces. For this reason, we describe methane as having tetrahedral geometry.

As the backbone of the large molecules of living things, hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both. Furthermore, individual carbon-to-carbon bonds may be single, double, or triple covalent bonds, and each type of bond affects the molecule's geometry in a specific way. This three-dimensional shape or conformation of the large molecules of life (macromolecules) is critical to how they function.

Hydrocarbon Chains

Successive bonds between carbon atoms form hydrocarbon chains. These may be branched or unbranched. Furthermore, a molecule's different geometries of single, double, and triple covalent bonds alter the overall molecule's geometry as Figure 2.22 illustrates. The hydrocarbons ethane, ethene, and ethyne serve as examples of how different carbon-to-carbon bonds affect the molecule's geometry. The names of all three molecules start with the prefix “eth-,” which is the prefix for two carbon hydrocarbons. The suffixes “-ane,” “-ene,” and “-yne” refer to the presence of single, double, or triple carbon-carbon bonds, respectively. Thus, propane, propene, and propyne follow the same pattern with three carbon molecules, butane, butene, and butyne for four carbon molecules, and so on. Double and triple bonds change the molecule's geometry: single bonds allow rotation along the bond's axis whereas, double bonds lead to a planar configuration and triple bonds to a linear one. These geometries have a significant impact on the shape a particular molecule can assume.

Hydrocarbon Rings

So far, the hydrocarbons we have discussed have been aliphatic hydrocarbons , which consist of linear chains of carbon atoms. Another type of hydrocarbon, aromatic hydrocarbons , consists of closed rings of carbon atoms with alternating single and double bonds. We find ring structures in aliphatic hydrocarbons, sometimes with the presence of double bonds, which we can see by comparing cyclohexane's structure to benzene in Figure 2.23. Examples of biological molecules that incorporate the benzene ring include some amino acids and cholesterol and its derivatives, including the hormones estrogen and testosterone. We also find the benzene ring in the herbicide 2,4-D. Benzene is a natural component of crude oil and has been classified as a carcinogen. Some hydrocarbons have both aliphatic and aromatic portions. Beta-carotene is an example of such a hydrocarbon.

Isomers

The three-dimensional placement of atoms and chemical bonds within organic molecules is central to understanding their chemistry. We call molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds isomers . Structural isomers (like butane and isobutane in Figure 2.24a) differ in the placement of their covalent bonds: both molecules have four carbons and ten hydrogens (C4H10), but the different atom arrangement within the molecules leads to differences in their chemical properties. For example, butane is suited for use as a fuel for cigarette lighters and torches whereas, isobutane is suited for use as a refrigerant and a propellant in spray cans.

Geometric isomers , alternatively have similar placements of their covalent bonds but differ in how these bonds are made to the surrounding atoms, especially in carbon-to-carbon double bonds. In the simple molecule butene (C4H8), the two methyl groups (CH3) can be on either side of the double covalent bond central to the molecule, as Figure 2.24b illustrates. When the carbons are bound on the same side of the double bond, this is the cis configuration. If they are on opposite sides of the double bond, it is a trans configuration. In the trans configuration, the carbons form a more or less linear structure whereas, the carbons in the cis configuration make a bend (change in direction) of the carbon backbone.

Visual Connection

Which of the following statements is false?

  1. Molecules with the formulas CH3CH2COOH and C3H6O2 could be structural isomers.
  2. Molecules must have a double bond to be cis-trans isomers.
  3. To be enantiomers, a molecule must have at least three different atoms or groups connected to a central carbon.
  4. To be enantiomers, a molecule must have at least four different atoms or groups connected to a central carbon.

In triglycerides (fats and oils), long carbon chains known as fatty acids may contain double bonds, which can be in either the cis or trans configuration, as Figure 2.25 illustrates. Fats with at least one double bond between carbon atoms are unsaturated fats. When some of these bonds are in the cis configuration, the resulting bend in the chain's carbon backbone means that triglyceride molecules cannot pack tightly, so they remain liquid (oil) at room temperature. Alternatively, triglycerides with trans double bonds (popularly called trans fats), have relatively linear fatty acids that are able to pack tightly together at room temperature and form solid fats. In the human diet, trans fats are linked to an increased risk of cardiovascular disease, so many food manufacturers have reduced or eliminated their use in recent years. In contrast to unsaturated fats, we call triglycerides without double bonds between carbon atoms saturated fats, meaning that they contain all the hydrogen atoms available. Saturated fats are a solid at room temperature and usually of animal origin.

Enantiomers

Enantiomers are molecules that share the same chemical structure and chemical bonds but differ in the three-dimensional placement of atoms so that they are non-superimposable mirror images. Figure 2.26 shows an amino acid alanine example, where the two structures are nonsuperimposable. In nature, the L-forms of amino acids are predominant in proteins. Some D forms of amino acids are seen in the cell walls of bacteria and polypeptides in other organisms. Similarly, the D-form of glucose is the main product of photosynthesis and we rarely see the molecule's L-form in nature.

Functional Groups

Functional groups are groups of atoms that occur within molecules and confer specific chemical properties to those molecules. We find them along the “carbon backbone” of macromolecules. Chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen form this carbon backbone. Molecules with other elements in their carbon backbone are substituted hydrocarbons .

The functional groups in a macromolecule are usually attached to the carbon backbone at one or several different places along its chain and/or ring structure. Each of the four types of macromolecules—proteins, lipids, carbohydrates, and nucleic acids—has its own characteristic set of functional groups that contributes greatly to its differing chemical properties and its function in living organisms.

A functional group can participate in specific chemical reactions. Figure 2.27 shows some of the important functional groups in biological molecules. They include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl. These groups play an important role in forming molecules like DNA, proteins, carbohydrates, and lipids. We usually classify functional groups as hydrophobic or hydrophilic depending on their charge or polarity characteristics. An example of a hydrophobic group is the nonpolar methyl molecule. Among the hydrophilic functional groups is the carboxyl group in amino acids, some amino acid side chains, and the fatty acids that form triglycerides and phospholipids. This carboxyl group ionizes to release hydrogen ions (H + ) from the COOH group resulting in the negatively charged COO - group. This contributes to the hydrophilic nature of whatever molecule on which it is found. Other functional groups, such as the carbonyl group, have a partially negatively charged oxygen atom that may form hydrogen bonds with water molecules, again making the molecule more hydrophilic.

Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning. Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding of an enzyme to its substrate, as Figure 2.28 illustrates.


Ionic Bonds

Some atoms are more stable when they gain or lose an electron (or possibly two) and form ions. This fills their outermost electron shell and makes them energetically more stable. Because the number of electrons does not equal the number of protons, each ion has a net charge. Cations are positive ions that are formed by losing electrons. Negative ions are formed by gaining electrons and are called anions. Anions are designated by their elemental name being altered to end in “-ide”: the anion of chlorine is called chloride, and the anion of sulfur is called sulfide, for example.

This movement of electrons from one element to another is referred to as electron transfer. As Figure 1 illustrates, sodium (Na) only has one electron in its outer electron shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons, 11 neutrons, and only 10 electrons, leaving it with an overall charge of +1. It is now referred to as a sodium ion. Chlorine (Cl) in its lowest energy state (called the ground state) has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons, 17 neutrons, and 18 electrons, giving it a net negative (–1) charge. It is now referred to as a chloride ion. In this example, sodium will donate its one electron to empty its shell, and chlorine will accept that electron to fill its shell. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium cation) or –1 (chloride anion) charge. Note that these transactions can normally only take place simultaneously: in order for a sodium atom to lose an electron, it must be in the presence of a suitable recipient like a chlorine atom.

Figure 1. In the formation of an ionic compound, metals lose electrons and nonmetals gain electrons to achieve an octet. Ionic bonds are formed between ions with opposite charges. For instance, positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge.

Ionic bonds are formed between ions with opposite charges. For instance, positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge.

Certain salts are referred to in physiology as electrolytes (including sodium, potassium, and calcium), ions necessary for nerve impulse conduction, muscle contractions and water balance. Many sports drinks and dietary supplements provide these ions to replace those lost from the body via sweating during exercise.

Video Review

This video shows how ionic compounds form from anions and cations.


Ionic Bonds

Some atoms are more stable when they gain or lose an electron (or possibly two) and form ions. This fills their outermost electron shell and makes them energetically more stable. Because the number of electrons does not equal the number of protons, each ion has a net charge. Cations are positive ions that are formed by losing electrons. Negative ions are formed by gaining electrons and are called anions. Anions are designated by their elemental name being altered to end in “-ide”: the anion of chlorine is called chloride, and the anion of sulfur is called sulfide, for example.

This movement of electrons from one element to another is referred to as electron transfer. As Figure 1 illustrates, sodium (Na) only has one electron in its outer electron shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons, 11 neutrons, and only 10 electrons, leaving it with an overall charge of +1. It is now referred to as a sodium ion. Chlorine (Cl) in its lowest energy state (called the ground state) has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons, 17 neutrons, and 18 electrons, giving it a net negative (–1) charge. It is now referred to as a chloride ion. In this example, sodium will donate its one electron to empty its shell, and chlorine will accept that electron to fill its shell. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium cation) or –1 (chloride anion) charge. Note that these transactions can normally only take place simultaneously: in order for a sodium atom to lose an electron, it must be in the presence of a suitable recipient like a chlorine atom.

Figure 1. In the formation of an ionic compound, metals lose electrons and nonmetals gain electrons to achieve an octet. Ionic bonds are formed between ions with opposite charges. For instance, positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge.

Ionic bonds are formed between ions with opposite charges. For instance, positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge.

Certain salts are referred to in physiology as electrolytes (including sodium, potassium, and calcium), ions necessary for nerve impulse conduction, muscle contractions and water balance. Many sports drinks and dietary supplements provide these ions to replace those lost from the body via sweating during exercise.

Video Review

This video shows how ionic compounds form from anions and cations.


2.3 Carbon

In this section, you will investigate the following questions:

  • Why is carbon important for life?
  • How do functional groups determine the properties of biological molecules?

Connection for AP ® Courses

The unique properties of carbon make it a central part of biological molecules. With four valence electrons, carbon can covalently bond to oxygen, hydrogen, and nitrogen to form the many molecules important for cellular function. Carbon and hydrogen can form either hydrocarbon chains or rings. Functional groups , such as –CH3 (methyl) and –COOH (carboxyl), are groups of atoms that give specific properties to hydrocarbon chains or rings that define their overall chemical characteristics and function. For example, the attachment of a carboxyl group (-COOH) makes a molecule more acidic, whereas the presence of an amine group (NH2) makes a molecule more basic. (As we will explore in the next chapter, amino acids have both a carboxyl group and an amine group.) Isomers are molecules with the same molecular formula (i.e., same kinds and numbers of atoms), but different molecular structures resulting in different properties or functions. (Don’t confuse “isomer” with “isotope”!)

The information presented and examples highlighted in this section support concepts and Learning Objectives outlined in Big Idea 2 of the AP ® Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices.

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis.
Enduring Understanding 2.A Growth, reproduction and maintenance of living systems require free energy and matter.
Essential Knowledge 2.A.3 Organisms must exchange matter with the environment to grow, reproduce and maintain organization.
Science Practice 4.1 The student can justify the selection of the kind of data needed to answer a particular scientific question.
Learning Objective 2.8 The student is able to justify the selection of data regarding the types of molecules that an animal, plant, or bacterium will take up as necessary building blocks and excrete as waste products.

Teacher Support

As a class, discuss how important carbon is in life forms. Include in the discussion how proteins, DNA, carbohydrates, biological molecules that distinguish life from inanimate materials, are composed of carbon. You can challenge students to consider a life form based on silicon instead of carbon, using this article as a catalyst.

Cells are made of many complex molecules called macromolecules, such as proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids. The macromolecules are a subset of organic molecules (any carbon-containing liquid, solid, or gas) that are especially important for life. The fundamental component for all of these macromolecules is carbon. The carbon atom has unique properties that allow it to form covalent bonds to as many as four different atoms, making this versatile element ideal to serve as the basic structural component, or “backbone,” of the macromolecules.

Individual carbon atoms have an incomplete outermost electron shell. With an atomic number of 6 (six electrons and six protons), the first two electrons fill the inner shell, leaving four in the second shell. Therefore, carbon atoms can form up to four covalent bonds with other atoms to satisfy the octet rule. The methane molecule provides an example: it has the chemical formula CH4. Each of its four hydrogen atoms forms a single covalent bond with the carbon atom by sharing a pair of electrons. This results in a filled outermost shell.

Hydrocarbons

Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane (CH4) described above. We often use hydrocarbons in our daily lives as fuels—like the propane in a gas grill or the butane in a lighter. The many covalent bonds between the atoms in hydrocarbons store a great amount of energy, which is released when these molecules are burned (oxidized). Methane, an excellent fuel, is the simplest hydrocarbon molecule, with a central carbon atom bonded to four different hydrogen atoms, as illustrated in Figure 2.23. The geometry of the methane molecule, where the atoms reside in three dimensions, is determined by the shape of its electron orbitals. The carbons and the four hydrogen atoms form a shape known as a tetrahedron, with four triangular faces for this reason, methane is described as having tetrahedral geometry.

As the backbone of the large molecules of living things, hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both. Furthermore, individual carbon-to-carbon bonds may be single, double, or triple covalent bonds, and each type of bond affects the geometry of the molecule in a specific way. This three-dimensional shape or conformation of the large molecules of life (macromolecules) is critical to how they function.

Hydrocarbon Chains

Hydrocarbon chains are formed by successive bonds between carbon atoms and may be branched or unbranched. Furthermore, the overall geometry of the molecule is altered by the different geometries of single, double, and triple covalent bonds, illustrated in Figure 2.24. The hydrocarbons ethane, ethene, and ethyne serve as examples of how different carbon-to-carbon bonds affect the geometry of the molecule. The names of all three molecules start with the prefix “eth-,” which is the prefix for two carbon hydrocarbons. The suffixes “-ane,” “-ene,” and “-yne” refer to the presence of single, double, or triple carbon-carbon bonds, respectively. Thus, propane, propene, and propyne follow the same pattern with three carbon molecules, butane, butene, and butyne for four carbon molecules, and so on. Double and triple bonds change the geometry of the molecule: single bonds allow rotation along the axis of the bond, whereas double bonds lead to a planar configuration and triple bonds to a linear one. These geometries have a significant impact on the shape a particular molecule can assume.

Hydrocarbon Rings

So far, the hydrocarbons we have discussed have been aliphatic hydrocarbons , which consist of linear chains of carbon atoms. Another type of hydrocarbon, aromatic hydrocarbons , consists of closed rings of carbon atoms. Ring structures are found in hydrocarbons, sometimes with the presence of double bonds, which can be seen by comparing the structure of cyclohexane to benzene in Figure 2.25. Examples of biological molecules that incorporate the benzene ring include some amino acids and cholesterol and its derivatives, including the hormones estrogen and testosterone. The benzene ring is also found in the herbicide 2,4-D. Benzene is a natural component of crude oil and has been classified as a carcinogen. Some hydrocarbons have both aliphatic and aromatic portions beta-carotene is an example of such a hydrocarbon.

Isomers

The three-dimensional placement of atoms and chemical bonds within organic molecules is central to understanding their chemistry. Molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds are known as isomers. Structural isomers (like butane and isobutane shown in figurea) differ in the placement of their covalent bonds: both molecules have four carbons and ten hydrogens (C4H10), but the different arrangement of the atoms within the molecules leads to differences in their chemical properties. For example, due to their different chemical properties, butane is suited for use as a fuel for torches, whereas isobutane is suited for use as a refrigerant and a propellant in spray cans.

Geometric isomers , on the other hand, have similar placements of their covalent bonds but differ in how these bonds are made to the surrounding atoms, especially in carbon-to-carbon double bonds. In the simple molecule butene (C4H8), the two methyl groups (CH3) can be on either side of the double covalent bond central to the molecule, as illustrated in figureb. When the carbons are bound on the same side of the double bond, this is the cis configuration if they are on opposite sides of the double bond, it is a trans configuration. In the trans configuration, the carbons form a more or less linear structure, whereas the carbons in the cis configuration make a bend (change in direction) of the carbon backbone.

Visual Connection

  1. Molecules with the formulas ext_3 ext_2 ext and ext_3 ext_6 ext_2 could be structural isomers.
  2. Molecules must have a double bond to be cis-trans isomers.
  3. To be enantiomers, a molecule must have at least three different atoms or groups connected to a central carbon.
  4. To be enantiomers, a molecule must have at least four different atoms or groups connected to a central carbon.

In triglycerides (fats and oils), long carbon chains known as fatty acids may contain double bonds, which can be in either the cis or trans configuration, illustrated in Figure 2.27. Fats with at least one double bond between carbon atoms are unsaturated fats. When some of these bonds are in the cis configuration, the resulting bend in the carbon backbone of the chain means that triglyceride molecules cannot pack tightly, so they remain liquid (oil) at room temperature. On the other hand, triglycerides with trans double bonds (popularly called trans fats), have relatively linear fatty acids that are able to pack tightly together at room temperature and form solid fats. In the human diet, trans fats are linked to an increased risk of cardiovascular disease, so many food manufacturers have reduced or eliminated their use in recent years. In contrast to unsaturated fats, triglycerides without double bonds between carbon atoms are called saturated fats, meaning that they contain all the hydrogen atoms available. Saturated fats are a solid at room temperature and usually of animal origin.

Enantiomers

Enantiomers are molecules that share the same chemical structure and chemical bonds but differ in the three-dimensional placement of atoms so that they are mirror images. As shown in Figure 2.28, an amino acid alanine example, the two structures are non-superimposable. In nature, only the L-forms of amino acids are used to make proteins. Some D forms of amino acids are seen in the cell walls of bacteria, but never in their proteins. Similarly, the D-form of glucose is the main product of photosynthesis and the L-form of the molecule is rarely seen in nature.

Functional Groups

Functional groups are groups of atoms that occur within molecules and confer specific chemical properties to those molecules. They are found along the “carbon backbone” of macromolecules. This carbon backbone is formed by chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen. Molecules with other elements in their carbon backbone are substituted hydrocarbons .

The functional groups in a macromolecule are usually attached to the carbon backbone at one or more different places along its chain and/or ring structure. Each of the four types of macromolecules—proteins, lipids, carbohydrates, and nucleic acids—has its own characteristic set of functional groups that contributes greatly to its differing chemical properties and its function in living organisms.

A functional group can participate in specific chemical reactions. Some of the important functional groups in biological molecules are shown in Figure 2.29 they include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl. These groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids. Functional groups are usually classified as hydrophobic or hydrophilic depending on their charge or polarity characteristics. An example of a hydrophobic group is the non-polar methyl molecule. Among the hydrophilic functional groups is the carboxyl group found in amino acids, some amino acid side chains, and the fatty acids that form triglycerides and phospholipids. This carboxyl group ionizes to release hydrogen ions (H + ) from the COOH group resulting in the negatively charged COO - group this contributes to the hydrophilic nature of whatever molecule it is found on. Other functional groups, such as the carbonyl group, have a partially negatively charged oxygen atom that may form hydrogen bonds with water molecules, again making the molecule more hydrophilic.

Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning. Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding of an enzyme to its substrate, as illustrated in Figure 2.30.

Science Practice Connection for AP® Courses

Activity

Carbon forms the backbone of important biological molecules. Create a mini-poster of a simple food chain that shows how carbon enters and exits each organism on the chain. Based on the food chain you created, make a prediction regarding the impact of human activity on the supply of carbon in the food chain.

Teacher Support

This activity is an application of Learning Objectives 2.8 and Science Practice 4.1 because the student is describing the types of molecules that organisms take up as necessary building blocks or excrete as wastes.

The carbon cycle involves the movement of carbon between the atmosphere, biosphere, and oceans. Human activities have an effect on the carbon cycle, resulting in the rise of carbon dioxide in the atmosphere and acidification of the oceans due to the burning of fossil fuels. Deforestation leads to decreased absorption of carbon dioxide by plants for photosynthesis.

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    Covalent Bonds and Hydrogen

    Covalent bonds and hydrogen go hand-in-hand. It is always easiest to use hydrogen if you want to keep covalent bonding simple. Hydrogen has atomic number one. We already know that this number indicates a nucleus with one proton and we can surmise that hydrogen also has one electron. With one negative charge (electron) and one positive charge (proton), the hydrogen of the periodic table is a neutral atom, not an ion. It is a gas, not a metal. Hydrogen is, therefore, a candidate for covalent bonding.

    As we have already seen, hydrogen does not remain single for long and is always ready to find a partner. This is because its single shell has one atom where there is place for two. H2 is a gas that forms when two hydrogen atoms bind by way of a covalent bond. It is also known as dihydrogen or molecular hydrogen. A single molecule of H2 contains two protons and two electrons. It is the most common form of hydrogen because it is extremely stable. What can be confusing is the term hydrogen bond. This is not a covalent bond and does not describe H2 but specific bonds between a hydrogen atom and fluorine, oxygen, or nitrogen. We won’t look at hydrogen bonds here, just covalent ones.

    Dihydrogen molecules form when two H atoms collide. As both atoms’ K-shells only host a single electron, if each atom shares one electron and borrows another, they will both enjoy the stability of a complete valence shell. To form a covalent bond, an element may not be in its ionic form, must be a non-metal or transitional metal, and must be similar in form and charge to its new partner. Furthermore, the non-metal atoms should be partially unstable noble gases with full valence shells hardly ever form molecules or have ionic forms.

    Only when two atoms of the same element form a covalent bond will their electrons be equally shared. If different elements share electrons through covalent bonding, one atom’s electrons will have higher electronegativity (higher pulling power) thanks to the closer distance atom nucleus to its surrounding electrons. The closer a valence shell is to the nucleus, the greater its electronegativity. When one atom forms a bond with an atom of a different type, the result is a polar covalent bond. Where the levels of electronegativity are the same, nonpolar covalent bonds will be formed. You can find separate articles for these types of bonds that describe them in detail. Alternatively, this article gives a short summary that looks at how the presence of electronegativity can determine the covalent bond type.


    A covalent bond is one in which one or more pairs of electrons are shared by two atoms. The illustration to the right shows two atoms of oxygen that are covalently bonded by the sharing of two pairs of electrons as illustrated in the shaded area.

    The figure below shows a series of molecules formed by covalent binding. Mouse over each molecule to see a brief description.

    Water is a Polar Molecule

    Note also that the sharing of electrons is not always equal. For example, in a water molecule, the negatively charged electrons spend more time in the vicinity of the heavier oxygen atom.

    The net result is that the water molecule has one end that is more negative relative to the other end. Water is therefore a "polar" molecule. We will see that this polarity has important implications for many biological phenomena including cell structure. You may have heard the expression "like dissolves like." What this means is that polar molecules dissolve well in polar fluids like water. Sugars (e.g., glucose) and salts are polar molecules, and they dissolve in water, because the positive and negative parts of the two types of molecules can distribute themselves comfortably among one another.


    Contents

    2,3-BPG is formed from 1,3-BPG by the enzyme BPG mutase. It can then be broken down by 2,3-BPG phosphatase to form 3-phosphoglycerate. Its synthesis and breakdown are, therefore, a way around a step of glycolysis, with the net expense of one ATP per molecule of 2,3-BPG generated as the high-energy carboxylic acid-phosphate mixed anhydride bond is cleaved by bisphosphoglycerate mutase.

    The normal glycolytic pathway generates 1,3-BPG, which may be dephosphorylated by phosphoglycerate kinase (PGK), generating ATP, or it may be shunted into the Luebering-Rapoport pathway, where bisphosphoglycerate mutase catalyzes the transfer of a phosphoryl group from C1 to C2 of 1,3-BPG, giving 2,3-BPG. 2,3-BPG, the most concentrated organophosphate in the erythrocyte, forms 3-PG by the action of bisphosphoglycerate phosphatase. The concentration of 2,3-BPG varies proportionately to the [H+].

    There is a delicate balance between the need to generate ATP to support energy requirements for cell metabolism and the need to maintain appropriate oxygenation/deoxygenation status of hemoglobin. This balance is maintained by isomerisation of 1,3-BPG to 2,3-BPG, which enhances the deoxygenation of hemoglobin.

    When 2,3-BPG binds to deoxyhemoglobin, it acts to stabilize the low oxygen affinity state (T state) of the oxygen carrier. It fits neatly into the cavity of the deoxy- conformation, exploiting the molecular symmetry and positive polarity by forming salt bridges with lysine and histidine residues in the ß subunits of hemoglobin. The R state, with oxygen bound to a heme group, has a different conformation and does not allow this interaction.

    By itself, hemoglobin has sigmoid-like kinetics. In selectively binding to deoxyhemoglobin, 2,3-BPG stabilizes the T state conformation, making it harder for oxygen to bind hemoglobin and more likely to be released to adjacent tissues. 2,3-BPG is part of a feedback loop that can help prevent tissue hypoxia in conditions where it is most likely to occur. Conditions of low tissue oxygen concentration such as high altitude (2,3-BPG levels are higher in those acclimated to high altitudes), airway obstruction, or congestive heart failure will tend to cause RBCs to generate more 2,3-BPG, because changes in pH and oxygen modulate the enzymes that make and degrade it. [2] The accumulation of 2,3-BPG decreases the affinity of hemoglobin for oxygen. Ultimately, this mechanism increases oxygen release from RBCs under circumstances where it is needed most. This release is potentiated by the Bohr effect, in which hemoglobin's binding affinity for oxygen is also reduced by a lower pH and high concentration of carbon dioxide. In tissues with high energetic demands, oxygen is rapidly consumed, which increases the concentration of H + and carbon dioxide. Through the Bohr effect, hemoglobin is induced to release more oxygen to supply cells that need it. In contrast, 2,3-BPG has no effect on the related compound myoglobin.(reference required)

    In pregnant women, there is a 30% increase in intracellular 2,3-BPG. This lowers the maternal hemoglobin affinity for oxygen, and therefore allows more oxygen to be offloaded to the fetus in the maternal uterine arteries. The fetus has a low sensitivity to 2,3-BPG, so its hemoglobin has a higher affinity for oxygen. Therefore, although the pO2 in the uterine arteries is low, the fetal umbilical artery (which carries deoxygenated blood) can still get oxygenated from them.

    Fetal hemoglobin (HbF) exhibits a low affinity for 2,3-BPG, resulting in a higher binding affinity for oxygen. This increased oxygen-binding affinity relative to that of adult hemoglobin (HbA) is due to HbF's having two α/γ dimers as opposed to the two α/β dimers of HbA. The positive histidine residues of HbA β-subunits that are essential for forming the 2,3-BPG binding pocket are replaced by serine residues in HbF γ-subunits. Like that, histidine nº143 gets lost, so 2,3-BPG has difficulties in linking to the fetal hemoglobin, and it looks like the pure hemoglobin. That’s the way O2 flows from the mother to the fetus. As we can see in the following image, fetal hemoglobin has more affinity to oxygen than adult hemoglobin. Moreover, myoglobin has the highest affinity to oxygen.

    Differences between myoglobin (Mb), fetal hemoglobin (Hb F), adult hemoglobin (Hb A)

    A 2004 study checked the effects of thyroid hormone on 2,3-BPG levels. The result was that the hyperthyroidism modulates in vivo 2,3-BPG content in erythrocytes by changes in the expression of phosphoglycerate mutase (PGM) and 2,3-BPG synthase. This result shows that the increase in the 2,3-BPG content of erythrocytes observed in hyperthyroidism doesn’t depend on any variation in the rate of circulating hemoglobin, but seems to be a direct consequence of the stimulating effect of thyroid hormones on erythrocyte glycolytic activity. [3]

    Red cells increase their intracellular 2,3-BPG concentration as much as five times within one to two hours in patients with chronic anemia, when the oxygen carrying capacity of the blood is diminished. This results in a rightward shift of the oxygen dissociation curve and more oxygen being released to the tissues.

    Chronic respiratory disease with hypoxia

    Recently, scientists have found similarities between low amounts of 2,3-BPG with the occurrence of high altitude pulmonary edema at high altitudes.

    CONCENTRATION OF 2,3-BPG ERYTHROCYTE FOUND IN DIFFERENT CLINICAL SITUATIONS STUDIED
    n Hb (g/dl) 2,3-BPG (mM)
    1 Normality 120 14.2 ± 1.6 4.54 ± 0.57
    2 Hyperthyroidism 35 13.7 ± 1.4 5.66 ± 0.69
    3 Iron deficiency anaemia 40 10.0 ± 1.7 5.79 ± 1.02
    4 Chronic respiratory disease with hypoxia 47 16.4 ± 2.2 5.29 ± 1.13

    In a 1998 study, erythrocyte 2,3-BPG concentration was analyzed during the hemodialysis process. The 2,3-BPG concentration was expressed relative to the hemoglobin tetramer (Hb4) concentration as the 2,3-BPG/Hb4 ratio. Physiologically, an increase in 2,3-BPG levels would be expected to counteract the hypoxia that is frequently observed in this process. Nevertheless, the results show a 2,3-BPG/Hb4 ratio decreased. This is due to the procedure itself: mechanical stress on the erythrocytes is believed to cause the 2,3-BPG escape, which is then removed by hemodialysis. The concentrations of calcium, phosphate, creatinine, urea and albumin did not correlate significantly with the total change in 2,3-BPG/Hb4 ratio. However, the ratio sampled just before dialysis correlated significantly and positively with the total weekly dosage of erythropoietin (main hormone in erythrocyte formation) given to the patients. [4]


    Atomic bonds

    Once the way atoms are put together is understood, the question of how they interact with each other can be addressed—in particular, how they form bonds to create molecules and macroscopic materials. There are three basic ways that the outer electrons of atoms can form bonds:

    The first way gives rise to what is called an ionic bond. Consider as an example an atom of sodium, which has one electron in its outermost orbit, coming near an atom of chlorine, which has seven. Because it takes eight electrons to fill the outermost shell of these atoms, the chlorine atom can be thought of as missing one electron. The sodium atom donates its single valence electron to fill the hole in the chlorine shell, forming a sodium chloride system at a lower total energy level.

    An atom that has more or fewer electrons in orbit than protons in its nucleus is called an ion. Once the electron from its valence shell has been transferred, the sodium atom will be missing an electron it therefore will have a positive charge and become a sodium ion. Simultaneously, the chlorine atom, having gained an extra electron, will take on a negative charge and become a chlorine ion. The electrical force between these two oppositely charged ions is attractive and locks them together. The resulting sodium chloride compound is a cubic crystal, commonly known as ordinary table salt.

    The second bonding strategy listed above is described by quantum mechanics. When two atoms come near each other, they can share a pair of outermost electrons (think of the atoms as tossing the electrons back and forth between them) to form a covalent bond. Covalent bonds are particularly common in organic materials, where molecules often contain long chains of carbon atoms (which have four electrons in their valence shells).

    Finally, in some materials each atom gives up an outer electron that then floats freely—in essence, the electron is shared by all of the atoms within the material. The electrons form a kind of sea in which the positive ions float like marbles in molasses. This is called the metallic bond and, as the name implies, it is what holds metals together.

    There are also ways for atoms and molecules to bond without actually exchanging or sharing electrons. In many molecules the internal forces are such that the electrons tend to cluster at one end of the molecule, leaving the other end with a positive charge. Overall, the molecule has no net electric charge—it is just that the positive and negative charges are found at different places. For example, in water (H2O) the electrons tend to spend most of their time near the oxygen atom, leaving the region of the hydrogen atoms with a positive charge. Molecules whose charges are arranged in this way are called polar molecules. An atom or ion approaching a polar molecule from its negative side, for example, will experience a stronger negative electric force than the more-distant positive electric force. This is why many substances dissolve in water: the polar water molecule can pull ions out of materials by exerting electric forces. A special case of polar forces occurs in what is called the hydrogen bond. In many situations, when hydrogen forms a covalent bond with another atom, electrons move toward that atom, and the hydrogen acquires a slight positive charge. The hydrogen, in turn, attracts another atom, thereby forming a kind of bridge between the two. Many important molecules, including DNA, depend on hydrogen bonds for their structure.

    Finally, there is a way for a weak bond to form between two electrically neutral atoms. Dutch physicist Johannes van der Waals first theorized a mechanism for such a bond in 1873, and it is now known as van der Waals forces. When two atoms approach each other, their electron clouds exert repulsive forces on each other, so that the atoms become polarized. In such situations, it is possible that the electrical attraction between the nucleus of one atom and the electrons of the other will overcome the repulsive forces between the electrons, and a weak bond will form. One example of this force can be seen in ordinary graphite pencil lead. In this material, carbon atoms are held together in sheets by strong covalent bonds, but the sheets are held together only by van der Waals forces. When a pencil is drawn across paper, the van der Waals forces break, and sheets of carbon slough off. This is what creates the dark pencil streak.


    2.3. Chemistry of Water

    A. First Cells Evolved in Water
    1. All living things are 70.90% water.
    2. Because water is a polar molecule, water molecules are hydrogen bonded to each other.
    3. With hydrogen bonding, water is liquid between 0o C and 100 C which is critical for life.

    B. Properties of Water
    1. The temperature of liquid water rises and falls more slowly than that of most other liquids..
    a. Calorie is amount of heat energy required to raise temperature of one gram of water 1o C.
    b. Because water holds more heat, its temperature falls more slowly than other liquids this protects
    organisms from rapid temperature changes and helps them maintain normal temperatures.

    2. Water has a high heat of vaporization.
    a. Hydrogen bonds between water molecules require a large amount of heat to break.
    b. This property moderates earthfs surface temperature permits living systems to exist here.
    c. When animals sweat, evaporation of the sweat takes away body heat, thus cooling the animal.

    3. Water is universal solvent, facilitates chemical reactions both outside of and within living systems..
    a. Water is a universal solvent because it dissolves a great number of solutes.
    b. Ionized or polar molecules attracted to water are hydrophilic.
    c. Nonionized and nonpolar molecules that cannot attract water are hydrophobic.

    4. Water molecules are cohesive and adhesive..
    a. Cohesion allows water to flow freely without molecules separating, due to hydrogen bonding.
    b. Adhesion is ability to adhere to polar surfaces water molecules have positive, negative poles.

    • Surface of water has structure, think of skipping a rock, or insects that walk on water
    • Water sticks to itself, this allows water to be moved from the roots to leaves in plants
    • Water becomes less dense when it freezes, so it floats

    1. Covalently bonded water molecules ionize the atoms dissociate into ions.
    2. When water ionizes or dissociates, it releases a small (107 moles/liter) but equal number of H+ and OH
    ions thus, its pH is neutral.
    3. Water dissociates into hydrogen and hydroxide ions:
    4. Acid molecules dissociate in water, releasing hydrogen ions (H+) ions: HCl ¨ H+ + Cl-.
    5. Bases are molecules that take up hydrogen ions or release hydroxide ions. NaOH ¨ Na+ + OH-.
    6. The pH scale indicates acidity and basicity (alkalinity) of a solution.

    1) One mole of water has 107 moles/liter of hydrogen ions therefore, has neutral pH of 7.
    2) Acid is a substance with pH less than 7 base is a substance with pH greater than 7.
    3) As logarithmic scale, each lower unit has 10 times the amount of hydrogen ions as next higher pH unit


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