Lecture 7 - Building Blocks and Shapes of Biomolecules 2018-19 PDF

# Elements that occur frequently in biomolecules (e.g. amino acids, DNA) ## 1) Focus on important elements in biology: | Element | Symbol | |---|---| | Carbon | - C | | Hydrogen | - H | | Nitrogen | - N | | Phosphorus | - P | | Oxygen | - O | | Sulfur | - S | ## Metals & Halogens (F,Cl, Br, I al...

# Elements that occur frequently in biomolecules (e.g. amino acids, DNA) ## 1) Focus on important elements in biology: | Element | Symbol | |---|---| | Carbon | - C | | Hydrogen | - H | | Nitrogen | - N | | Phosphorus | - P | | Oxygen | - O | | Sulfur | - S | ## Metals & Halogens (F,Cl, Br, I also found in biology) # How many bonds can an atom form? The number of bonds an atom can form is its valency. ## 1) Focus on important elements in biology: | Element | Symbol | Bonds | |---|---|---| | Carbon | - C | 4 | | Hydrogen | - H | 1 | | Nitrogen | - N | 3 | | Phosphorus | - P | 5 (sometimes 3) | | Oxygen | - O | 2 | | Sulfur | - S | 2 (sometimes 6 or 4) | # These elements occur within functional groups in biomolecules (1) - **Carboxylic acid** - Ethanoic acid - **Aldehyde** - Ethanal - **Ketone** - Propanone - **Ester** - Methyl ethanoate Biomolecules containing (C=O) are called carbonyls. # More important functional groups (2) - **Acid anhydride** - Ethanoic anhydride - **Amide** - Ethanamide - **Thioester** - S-methyl thioethanoate **More examples of carbonyl functional groups** # More important functional groups (3) - **Acid chloride** - Ethanoyl chloride - **Haloalkane** - Chloroethane - **Haloarene** - Bromobenzene **Halogenated functional groups (halogens: F, Cl, Br, I)** # More important functional groups (4) - **Primary alcohol** - Ethanol - **Secondary alcohol** - 2-propanol - **Tertiary alcohol** - 2-methyl-2-propanol **Varieties of alcohol – primary, secondary & tertiary** # More important functional groups (5) - **Primary amine** - Ethylamine - **Secondary amine** - Diethylamine - **Tertiary amine** - Triethylamine **Varieties of amine – primary, secondary & tertiary** # More important functional groups (6) - **Phenol** - Phenol - **Thiol** - Ethanethiol - **Phosphodiester** - Dimethyl phosphate **Phosphodiester linkages are found in DNA & RNA** # How many bonds can an atom form? The number of bonds an atom can form is its valency. ## 1) Focus on important elements in biology: | Element | Symbol | Bonds | |---|---|---| | Carbon | - C | 4 | | Hydrogen | - H | 1 | | Nitrogen | - N | 3 | | Phosphorus | - P | 5 (sometimes 3) | | Oxygen | - O | 2 | | Sulfur | - S | 2 (sometimes 6 or 4) | # How many bonds should carbon have? The normal valency of neutral carbon is 4 (C has 4 bonds) - H - H - C - H - H **This depiction does not adequately represent the 3D structure of methane** Methane ($CH_4$) is formed by microbes called Archaea. # When neutral carbon has only single bonds (sp³ C) arrangement is tetrahedral - H - H - C - H - H - H - H - C - H - H **Tetrahedral orientation of bonds around C (angle 109.5°)** Methane ($CH_4$) is formed by microbes called Archaea. # When neutral carbon has only single bonds (sp³ C) bonds have a tetrahedral orientation - A diagram of a tetrahedron shape. - H - C - H - H - C - H angles = 109.5° **Bond arrangement at saturated C (only single bonds)** # If 4 atoms or groups around carbon are the same (e.g. H) mirror image is the same - H - C - H - H - H - A diagram of an empty rectangle - H - C - H - H - H **mirror** **Mirror image of methane is identical (still methane)** # If 3 atoms or groups around carbon are the same (e.g. H) mirror image is the same - HO - C - H - H - H - A diagram of an empty rectangle - OH - C - H - H - H **mirror** **Mirror image of methanol is identical (still methanol)** # If 2 atoms or groups around carbon are the same (e.g. H) mirror image is the same - HO - C - H - CH3 H - A diagram of an empty rectangle - OH - C - H - H CH3 **mirror** **Mirror image of ethanol is identical (still ethanol)** # If all 4 atoms or groups around carbon are different, the mirror image is not the same - HO - C - CO2H - CH3 H - A diagram of an empty rectangle - OH - C - CH3 - HO2C H **mirror** **Lactic acid has 2 non-identical forms (optical isomers)** # With 4 different atoms or groups around C it is necessary to use 1 dash and 1 wedge bond - HO - C - CO2H - CH3 H - A diagram of an empty rectangle - OH - C - CH3 - HO2C H **mirror** **Wedge is a bond in front of the plane & dash is behind** # How do we describe each mirror image form? One is called the (R) form & the other the (S) - HO - C - CO2H - CH3 H - A diagram of an empty rectangle - OH - C - CH3 - HO2C H **(R) enantiomer or (R) optical isomer** **(S) enantiomer or (S) optical isomer** # How do we decide which is (R) & which (S)? - HO - C - CO2H - CH3 H - A diagram of an empty rectangle - OH - C - CH3 - HO2C H **(R) enantiomer or (R) optical isomer** **(S) enantiomer or (S) optical isomer** # To assign (R) & (S) we must prioritise each of the 4 groups surrounding carbon - HO - C - CO2H - CH3 H # First look at each atom around the central C. The atom with highest atomic number is '1' - H - O1 - H - C - C=O - H - C - H - H H H **Oxygen has the highest atomic number, so OH = 1** # Next look at each atom around the central C. The atom with lowest atomic number is '4' - H - O1 - H - C - C=O - H - C - H - H H4 H **Hydrogen has the lowest atomic number, so H = 4** # Then look at the remaining 2 atoms around the central C to decide '2' and '3' - H - O1 - ? - C - C=O - H - C - H - H H4 H **Both remaining atoms are carbon, so how to prioritise?** # We can decide between the 2 remaining groups by looking at next atom out from C - H - O1 - H3 - C - C=O - H - C - H - H H4 H **Hydrogen loses, Oxygen wins: O has higher atomic No.** # Now, join the numbers 1 & 2 with an arrow if we go clockwise, i.e. to the right = (R) - H - O1 - H3 - C - C=O - H - C - H - H H4 H **1→2 goes to the right (Latin, rectus) then (R)** # Let us now assign the other optical isomer of lactic acid (we know it must be (S)- isomer) - OH - C - CH3 - HO2C H **Use Cahn-Ingold-Prelog rules to assign (S) configuration** # Oxygen has the highest atomic number, so OH has the highest priority (1) - 1 - OH - C - CH3 - HO2C H **Note that the dash & wedge bonds must be adjacent** # Hydrogen has the lowest atomic number and so has the lowest priority (4) - 1 - OH - C - CH3 - HO2C H4 **View structure so lowest priority group is at back (dash)** # Carbon linked to oxygen has higher priority than carbon linked to hydrogen - H - O1 - HO - C - C=O - H - C - H - H H4 H **Carboxylic acid is assigned priority of 2 by CIP rules** # An arrow from 1 to 2 goes anticlockwise (left). Latin for left is 'sinister', so (S) - H - O1 - HO - C - C=O - H - C - H - H H4 H **This optical isomer (enantiomer) has (S) configuration** # Carbon chains in biomolecules An image of a pine forest **LS4002** # A chain of single carbon-carbon bonds & C-H bonds is called an alkane - CH3-CH2-CH2-CH2-CH2-CH2-CH3 - 1 2 3 4 5 6 7 **The 7-carbon alkane, heptane is found in the pitch of the Jeffrey pine tree** - 2C chain = ethane, 3C chain = propane, 4C chain = butane, 5C chain = pentane, 6C chain = hexane # In alkanes a low-energy zig-zag orientation keeps the bonds far apart - CH3-CH2-CH2-CH2-CH2-CH2-CH3 - HHHHHHHH - H - H - H - HH - HH H **The most stable arrangement is to rotate the bonds into a zig-zag chain (known as an extended conformation)** # Bond rotation occurs readily in alkanes - H - H - HHHHHHHH - H - H - H - H - H - HH HH - H - H - H - H - H - H - H - H **Most stable 'zig-zag'** **Other conformations also form all of the time** **All of the bonds can freely rotate to give a wide variety of different 'conformations' that readily interconvert at 25 °C** # We normally draw a 'skeletal structure' - A diagram that shows a straight, zig-zagged line. - A diagram that shows a non-straight zig-zagged line. **Most stable ‘zig-zag’** **Other conformations also form all of the time** **In a skeletal structure the hydrogens are not drawn on but are assumed to be present (only the carbon chain is drawn)** # If a carbon-carbon double bond is present, this is called an alkene - CH-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3 - 9 8 7 6 5 4 3 2 1 - CH-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CO2H - 10 11 12 13 14 15 16 17 18 **Esters of the 18-carbon alkene, oleic acid are found in olive oil** **Alkanes have maximum number of hydrogens & so are 'saturated'. Alkenes have fewer H atoms, so are 'unsaturated'** # Oleic acid is a ‘monounsaturated' fatty acid because it has 1 C=C double bond. - omega 9 8 7 6 5 4 3 2 1 omega - CH-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3 - CH-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CO2H - 10 11 12 13 14 15 16 17 18 **Esters of the 18-carbon alkene, oleic acid are found in olive oil** **Carbon farthest from the CO₂H is signified by the last Greek letter, omega (1). Counting upwards, we see C=C is omega (9)** # Oleic acid is an omega-9 monounsaturated fatty acid (very healthy!) - omega 9 8 7 6 5 4 3 2 1 omega - A diagram that shows a zig-zagged line with a double bond. - CO2H - 10 11 12 13 14 15 16 17 18 **The skeletal formula shows the alkene C=C clearly – the carbon chains are on the same side of the double bond** # In oleic acid, carbon chains are on the same side of the alkene (a 'cis' double bond) - A diagram that shows a zig-zagged line with a double bond. - CO2H **Another possibility (a trans double bond) can occur if oleic esters are treated with metal catalysts to form margarine** # Trans double bonds occur when carbon chains are on opposite sides of the C=C double bond. - A diagram that shows a zig-zagged line with a double bond. - CO2R cis double bond - A diagram that shows a zig-zagged line with a double bond. - CO2R trans double bond **While cis monounsaturates are very healthy, eating so-called 'trans fats' is linked to cardiovascular disease (R = glycerol)**