Nutritional Biochemistry - Principles of Chemistry: Carbon, the Backbone of Life - PDF

Nutritional Biochemistry Principles of chemistry: carbon, the backbone of life DIET413/BHCS1019 Dr Nathaniel Clark FHEA RNutr MRSB [email protected] 1 Previously...

Nutritional Biochemistry Principles of chemistry: carbon, the backbone of life DIET413/BHCS1019 Dr Nathaniel Clark FHEA RNutr MRSB [email protected] 1 Previously 1 Water contains an unequal distribution of electrons, giving rise to electronegativity in the oxygen and creating a polar molecule. The properties of water arise from attractions between its polar molecules. The positive H of one molecule are attracted to the slightly negative O of a nearby water molecule. The important properties of water include cohesion, moderation of temperature and solvency. Hydrophilic substance interact with water whereas hydrophobic do not. Moles is a useful unit for measuring solute concentrations in solutions. 2 Previously 2 A water molecule can transfer H+ to another water molecules to form H3O+ and OH-. The concentration of H+ is expressed as pH. Buffers in biological fluids (e.g., blood) resist the changes in pH. A buffer consists of an acid-base pair that combines reversibly wit hydrogen ions. Diffusion is moving from an area of high concentration to low concentration, down its concentration gradient. Water specific diffusion is called osmosis, and this plays a major role in the bodies water balance. 3 Last time - Quiz 1. Water is polar. What does this mean? 2. What are the three important properties of water? 3. Sucrose has the formula C12H22O11. What is its formula weight and how much do you need to weigh out to make 0.5 L of 1 M sucrose? 4. What happens when water dissociates? What molecules are (briefly) made? 5. Some chemical reactions are reversible and form a dynamic equilibrium. What does this mean? 6. Which water molecules are not able to move during osmosis? 4 Learning outcomes 1. Understand and describe the formation of bonds with carbon. 2. Describe the molecular diversity arising from carbon skeleton variation (hydrocarbons, isomers). 3. Describe and list the types of chemical groups that are key to the functioning of biological molecules. 5 1. Carbon: the backbone of life Although water is the universal medium for life on Earth, living things are made up of chemicals that are mostly based on the element carbon. Carbon enters the biosphere through the action of plants, which use solar energy to transform CO2 into other molecules. Of all chemical elements, carbon is unparalleled in its ability to form molecules that are large, complex and diverse. Proteins, DNA, carbohydrates, lipids that distinguish living matter from inert matter are all composed of C atoms bonded to one another or to other elements. 6 1. Carbon can bind to four other atoms Carbon (C) has 6 electrons – 2 in the first electron shell (lecture 1) and 4 in the second electron shell (that can carry up to 8). Thus, C can donate or accept 4 electrons to complete its valence shell and become an ion. Instead, a C atom usually completes its valence shell by sharing its 4 electrons with other atoms in covalent bonds so that 8 electrons are present. 7 1. Carbon bonding These bonds can be single or double covalent bonds. Sharing electrons = creating a bond (creating a tether/rope between). Each C acts as an intersection point from which a molecule can branch off in as many as four directions. This tetravalence is one facet of C’s versatility that makes large, complex molecules possible. 8 1. Single carbon bonds When a C atom forms 4 single covalent bonds, the arrangement of its electrons causes the bonds to angle toward the corners of an imaginary tetrahedron. 3D orientation versus Fischer projection. The bond angles in methane (CH4) are 109.5o, and they are roughly the same in any group of atoms where C has 4 single bonds. Ball and stick models (3D orientation). E.g., ethane (C2H6) is shaped like two overlapping tetrahedrons. 9 1. Double carbon bonds In molecules with more C’s, every grouping of a C bonded to 4 other atoms has a tetrahedral shape. Top compound shown. When two C atoms are joined by a double bond, all bonds around those carbons are in the same plane. E.g., ethene (C2H4) is a flat molecule; all its atoms lie in the same plane. Therefore, the 3D structure has changed. Important in fatty acids. 10 1. Valency of carbon The electron configuration of C gives it covalent compatibility with many different elements. These are the most frequent partners of C and their valences. These are the four major atomic components of organic molecules (Lecture 1). These valences are the basis for the rules of covalent bonding in organic chemistry. Valence = number of potential bonds. 11 1. Covalent bonds other than H Consider how the rules of covalent bonding apply to C atoms with partners other than hydrogen: carbon dioxide (CO2) and urea. CO2 is a single carbon atom joined to two atoms of O by a double covalent bond. The structural formula for CO2 is: O=C=O 12 1. Covalent bonds other than H (2) Each line in the formula represents a pair of shared electrons. The two double bonds formed by the carbon atom are the equivalent of four single covalent bonds. The arrangement completes the valence shells of all atoms in the molecules. 13 1. Covalent bonds other than H (3) Urea, CO(NH2)2, is the organic compound found in urine. Each atom has the required number of covalent bonds. In this case, one carbon atom is involved in both single and double bonds. Urea and CO2 are molecules with one C atom. But a C atom can also use one or more valence electrons to form covalent bonds to other carbon atoms, linking the atoms into chains of seemingly infinite variety. 14 2. Molecular diversity arising from C skeleton C chains (like the previous slide) form the skeletons of most organic molecules. The skeletons vary in length and may be straight, branched or arranged in closed rings. Some carbon skeletons have double bonds, which vary in number and location in the molecule. Such variation in C skeletons is one important source of the molecular complexity and diversity that characterise living matter. 15 2. Hydrocarbons All the molecules from the previous slide are hydrocarbons (C and H only). Atoms of H are attached to the C skeleton wherever electrons are available for covalent bonding. Major component of fossil fuels/petroleum. Although hydrocarbons are not prevalent in living organisms, many of a cell’s organic molecules have regions consisting of only C and H. E.g., fat molecules have long tails that are HC’s. 16 2. Hydrocarbons (2) Neither petroleum nor fat dissolves in water; both are hydrophobic compounds because the great majority of their bonds are relatively nonpolar carbon-to-hydrogen linkages. Reflect: what does this mean about the electronegativity (lecture 1)? Another HC characteristic is they can undergo reactions that release a relatively large amount of energy. The gasoline that fuels a car consists of HCs, and the HC tails of fat molecules serve as stored fuel for cells. 17 2. Hydrocarbons: Aliphatic compounds Hydrocarbons are divided into two classes: aromatic compounds and aliphatic compounds. Aliphatic compounds can be saturated (all C-C bonds are single), like hexane, or unsaturated like hexene. Open-chain compounds, whether straight or branched, and which contain no rings are always aliphatic. Important in odour/food detection. Aldehyde (Lecture 2). 18 2. Hydrocarbons: Aromatic compounds An aromatic ring contains a set of covalently bound atoms with specific characteristics: Alternating single and double bonds. Coplanar (flat) structure. Atoms arranged in one or more rings. Important in amino acid properties/chemistry (Lecture 4). 19 2. Isomers Variation in the architecture of organic molecules can be seen in isomers. Compounds that have the same number of atoms of the same elements but different structures and hence different properties. Compare glucose and fructose as 6 carbon compounds. Both have the molecular formula C 6H12O6, but they differ in the covalent arrangement of their carbon skeleton. There are three types of isomers: structural isomers, geometric isomers and enantiomers. 20 2. Structural isomers These differ in the covalent arrangements of their atoms (e.g., gluc, fruc). The number of possible isomers increases as the C skeletons increase in size. There are only three forms of C5H12 (top) but there are 18 variations of C8H18 and 366,319 possible structural isomers of C20H42. Structural isomers may also differ in the location of double bonds. 21 2. Geometric isomers These have the same covalent bonds, but they differ in their spatial arrangement. Same groups/atoms. The differences arise from the inflexibility of double bonds. Single bonds allow the atoms they join to rotate freely about the bond axis without changing the compound. 22 2. Geometric isomers (2) In contrast, double bonds do not rotate, resulting in the possibility of geometric isomers. If a double bond joins two carbon atoms, and each C also has two different atoms (or groups) attached to it, then two distinct geometric isomers are possible. 23 2. Geometric isomers – cis/trans We also need to consider the placement of each group (Lecture 4). In the butene example here, if the CH3 groups are both on the same side, it is called a cis isomer. If the CH3 groups are on opposite sides, they are called trans isomers. The subtle difference in shape between geometric isomers can dramatically affect the biological activities of organic molecules. E.g., the biochemistry of vision involves a light-induced change of rhodopsin from cis isomer to the trans isomer. 24 2. Geometric isomers – examples in the gut Dietary lycopene is in the trans configuration but in tissues it is cis. Cis is better absorbed. Implications still unclear, but geometry of the molecule is important for uptake. 25 2. Geometric isomers – examples in the gut (2) Trans-resveratrol, a well- known plant phenolic compound, has relatively low bioavailability. Metabolised before uptake – affects bioavailability. 26 2. Enantiomers These are isomers that are a mirror image of one another. In this example, the middle (chiral) carbon is called an asymmetric carbon because it is attached to four different atoms or groups of atoms. The four groups can be arranged in space around the asymmetric carbon in two different ways that mirror image one another. They have a left-handed and right-handed versions of the molecule. Like a glove. Usually one isomer is biologically active (does stuff) and one is not. https://www.youtube.com/watch?v=q3pw-keMQGY 27 2. Enantiomers - pharmacology The idea of enantiomers is important in the pharmaceutical industry because two enantiomers of a drug may not be equally effective. In some cases, one of the isomers may even produce harmful effects. E.g., thalidomide, a drug prescribed for thousands of pregnant women in the late 1950’s and early 60’s. Mixture of two enantiomers. One reduced morning sickness (desired effect). One caused birth defects. Other examples shown. The differing effects of enantiomers in the body demonstrate that we are sensitive to even the most subtle variations in molecular architecture. 28 Summary 1 The valence of carbon allows it to bond with up to four other elements/atoms. Double bonds can change the configuration of the molecule, so it is flat. Carbon forms the skeleton of most organic molecules. Such variation in C skeletons is one important source of the molecular complexity and diversity that characterise living matter. In hydrocarbons, all the atoms are C and H. Isomers exist where the formula of more than one molecule is the same, but the spatial orientation is different. These can be structural (gluc/fruc), geometric (cis/trans in fatty acids) or enantiomers (asymmetric carbon). Atomic structure is important for nutrient uptake. 29 10 min break 30 Activity 1. Draw a structural formula for C2H4. 2. Which molecules in this figure are isomers? For each pair, identify the type of isomer. 3. How are gasoline and fat similar? 4. Can propane form isomers? 31 Answers 1.. H H C =C H H 2. The forms in B are structural isomers, as those in C. 3. Both consist largely of hydrocarbon chains. 4. No. There is not enough diversity in the atoms. It can’t form structural isomers because there is only one way for three carbons to attach to each other (in a line). There are no double bonds, so geometric isomers are not possible. Each carbon has at least two hydrogen attached to it, so the molecule is symmetrical and cannot have enantiomeric isomers. 32 3. Chemical groups in biological molecules The distinct properties of an organic molecule depend not only on the arrangement of its carbon skeleton but also on the molecular components attached to that skeleton. We have touched on this through isomers. Think of hydrocarbons as the simplest of molecules, but the underlying framework is used for more complex molecules. Several chemical groups can replace one or more of the hydrogen bonded to the carbon skeleton of the hydrocarbon. Some groups include atoms of the carbon skeleton. 33 3. Chemical groups in biological molecules (2) These groups may participate in chemical reactions or may contribute to function indirectly by their effects of molecular shape. The number and arrangement of the groups help give each molecule its unique properties. Important for Lecture 4 and 5 and your summative assessment. 34 3. Important chemical groups Consider the difference in structure of estradiol/oestrogen and testosterone. What are they? Both are steroid, organic molecules with a carbon skeleton in the form of four fused rings. These sex hormones differ only in the chemical group attached to the rings. The different actions of these two molecules in the body help produce the contrasting features of males and females. 35 3. Important chemical groups - shape In this example of sex hormones, different chemical groups contribute to function by affecting the molecules shape. In other cases, the chemical groups affect molecular function by being directly involved in chemical reactions. These important chemical groups are known as functional groups. Each functional group participates in chemical reactions in a characteristic way, from one organic molecule to another. 36 3. Functional groups The seven chemical groups most important in biological processes are the: 1. Hydroxyl 2. Carbonyl 3. Carboxyl 4. Amino 5. Sulfhydryl 6. Phosphate 7. Methyl groups. The first 6 groups can act as a functional groups; they are also hydrophilic, and this increases the solubility of organic compounds in water. The methyl group is not reactive, but instead often acts as a recognizable tag on biological molecules. 37  3. Functional groups (2) Where have you seen hydroxyl and carbonyl (ketone and aldehyde) groups today? 38 3. Functional groups (3) 39 3. Functional groups (4) 40 3. ATP an important source of energy The phosphate row in the previous table shows a simple example of an organic phosphate molecule. A more complicated organic phosphate, adenosine triphosphate, or ATP, is worth mentioning because its function in the cell is so important. ATP consists of an organic molecule called adenosine attached to a string of three phosphate. 41 3. ATP an important source of energy (2) When three phosphates are present in series, one phosphate may be split off because of a reaction with water. This inorganic phosphate ion (HOPO 32-, is often abbreviated to Pi. Having lost one phosphate, ATP becomes diphosphate, or ADP. Although ATP is said to “store” energy, it is more accurate to think of it as “storing” the potential to react with water. This reaction releases energy that be used by cells (Metabolism Lectures). 42 Summary 2 The distinct properties of an organic molecule depend not only on the arrangement of its carbon skeleton but also on the molecular components attached to that skeleton. These functional groups may participate in chemical reactions or may contribute to function indirectly by their effects of molecular shape – 7 of them. Two are common in carbohydrates. Three are common in amino acids. One is common in ATP/enzymes. One is common in DNA. 43 Questions 1. Carbon commonly forms how many bonds with other atoms? 2. What happens to the orientation of atoms when carbon forms a double bond with another carbon? 3. What is an isomer? What are the three main types found? 4. Identify two sugars that are isomers. 5. What are the 7 functional groups that give rise to biological molecules? What molecules are rich in these? 6. What does the term amino acid signify about the structure of such a molecule? 44 Before next time... Consult textbooks for further reading. Re-read the lecture notes from today. Read the next sessions lecture notes before attending. Definitions for next time: ionization, hydrophilic, hydrophobic, polar, charge (positive, negative), amine group, carboxylic group. Further reading: Campbell and Reece, Biology, Chapter 4. 45