Biochemistry of Macromolecules PDF

MOLECULES TO MICROBES BIOCHEMISTR Y OF MACROMOLECULES BERNA SAYAN , PhD [email protected]  Blackboard tests will be available shortly on the topics covered today and my other lectures. Key resource: “Life, the science of biology”. If you want to learn more about chemistry: “Essent...

MOLECULES TO MICROBES BIOCHEMISTR Y OF MACROMOLECULES BERNA SAYAN , PhD [email protected]  Blackboard tests will be available shortly on the topics covered today and my other lectures. Key resource: “Life, the science of biology”. If you want to learn more about chemistry: “Essential chemistry for biochemistry”. In today’s lecture… 1- What are macromolecules? 2- Molecular composition of macromolecules 3- Key concepts (saturation, electronegativity, polarity) 4- Isomerism 1 – What are macromolecules? Nucleic acids Proteins Carbohydrates Lipids A macromolecule is a very large molecule that consists of many structural units with similar chemical properties.  How much of each macromolecule in a cell?   Structure of biological macromolecules. Except for lipids, macromolecules are polymers. A large molecule composed of multiple (chemically repeating (chemically similar) similar) subunits, called monomers – that are attached to each other through covalent bonds.covalent bonds monomer polymer  Monomer Polymer Nucleic Acids (polymers) nucleotide DNA strand Nucleic acids are formed from four kinds of nucleotide monomers (adenine, guanine, thymidine, cytosine) linked together by covalent bonds in long chains.  Monomer Polymer Proteins (polymers) amino acids protein Proteins are formed from 20 kinds of amino acid monomers linked together by covalent bonds in long chains.  Monomer Polymer Carbohydrates (polymers) sugar cellulose Carbohydrates are formed from monosaccharide (sugar) monomers linked together by covalent bonds in giant structures.  Monomer NOT A Polymer Lipids (not polymers) fatty acid Triglyceride Lipids are formed from a small set of smaller molecules, but in this case noncovalent forces maintain the interactions between the fatty acid monomers.  Molecular basis of polymer formation.  Condensation reactions form polymers from monomers (polymerization). H monomer OH + H monomer OH H + OH H2O H monomer monomer OH A new covalent bond is formed.  Molecular basis of polymer break down.  Hydrolysis reactions break down polymers into monomers. H monomer monomer OH H2O H monomer OH + H monomer OH SUMMAR Y A macromolecule is a very large molecule that consists of many structural units with similar chemical structures. A polymer is a large molecule composed of multiple repeating subunits, called monomers. Nucleic acids, proteins and carbohydrates are polymers, as the subunits are attached to each other by covalent bonds. Lipids are not polymers as noncovalent bonds hold monomers together. The chemical process by which polymers are constructed is called polymerisation. Polymers are constructed through condensation reactions. Polymers are broken down through hydrolysis reactions. In a condensation reaction, when a monomer is added to the chain, water is produced. In a hydrolysis reaction, when a monomer is removed from the chain, water is used to replace the H and OH at the ends of the monomers. 2 – Molecular composition of macromolecules?  Which elements – which macromolecules? carbohydrates lipids proteins nucleic acids C H C H N C H N C H O O O P O  The elements that make macromolecules. Life on earth is ___________ based. a) Nitrogen Carbon containing molecules/compounds are called b) Oxygen organic molecules/compounds. c) Carbon carbon d) Hydrogen e) Phosphorus   Properties of Carbon 1 2 3 4 5 6 7 8 Group 4 element Carbon can make 4 covalent bonds. Each carbon can bond to 4 other atoms and this molecule always adopts a tetrahedral shape. Fischer projection Wedge and dash model (In the wedge and dash, wedge means the atom is directed towards you, dash means it extends behind the carbon.) Most common elements in order of prevalence 1- C arbon - 2- Hy drogen 3- N itrogen 4- O xygen 5- P hosphorus 6- S ulfur Most common elements in order Number of covalent bonds they typically of prevalence form 1- C arbon ------------------------- 4 2- Hy drogen ----------------- 1 3- N itrogen ---------------------- 3 4- O xygen ------------------------- 2 NS CO H 5- P hosphorus ---------------- 5 6- S ulfur -------------------------- 2  c a p Re  What is a covalent bond? Covalent bonds are formed when elements share electrons.  Why do elements form bonds? To become stable. 16 They want to have a full outer shell. O Oxygen O 8  c a p Re One oxygen atom + two hydrogen atoms H O H X X hydrogen atom oxygen atom hydrogen atom H2 0 H O H  c a p Re  Elements can share one, two, or three pairs of electrons. When elements share 1 pair of electrons, a single covalent bond is formed. H H H H H2 X One line for each pair of shared electrons.  c a p Re When elements share 2 pairs of electrons, a double covalent bond is formed. X O X O X O O O2 X X X One line for each pair of shared electrons.  c a p Re When elements share 3 pairs of electrons, a triple covalent bond is formed. X N XX X N N N N2 X One line for each pair of shared electrons. Carbon-carbon bonds can be single, double or triple covalent bonds. H H H H C C C C C C H H alkane alkene alkyne 3- Key concepts  Saturated - unsaturated  Electronegativity  Polar – Nonpolar  Hydrophobic – Hydrophilic  How do functional groups confer hydrophobicity/ hydrophilicity?  Saturated - unsaturated  Saturated molecules There is a SINGLE covalent bond between carbons. H H C C This is a SATURATED molecule. H H You cannot possibly add more H atoms to this molecule alkane Alkanes are carbon-based molecules with single covalent bonds between carbons. These are called saturated molecules. Single bonds = saturated  Unsaturated molecules There are DOUBLE/TRIPLE covalent H H H H bonds between carbons. These are UNSATURATED molecules. C C C C These double or triple bonds can be broken, H H H H and more hydrogen atoms can be added to these molecules. alkene alkyne Alkenes and alkynes are unsaturated molecules – alkenes have double bonds; alkynes have triple bonds. Double/triple bonds = unsaturated Example: fatty acids  Electronegativity 1 2 3 4 5 6 7 8 F e- O e- N e- F e- d- O e- O polar bonds N e - e - e - e- e- + H H d d+ Water is a polar molecule. Why is electronegativity/polarity important in biology? Polarity enables molecules to form hydrogen bonds.  Polar molecules have slightly more positive or negative regions that can interact with water through hydrogen bonding..  These molecules are called ‘hydrophilic’ molecules.  O - O  In non-polar molecules charge is equally distributed C throughout the molecule. = They DO NOT HAVE slightly more negative/positive regions that can interact H C H with water. H C H H C H  Non-polar molecules CANNOT form hydrogen H C H bonds with water. H C H  These molecules are called ‘hydrophobic’ molecules. CH3 Some biological macromolecules have polar (hydrophilic) and non-polar (hydrophobic) regions. Example: fatty acids polar region (hydrophilic) nonpolar region (hydrophobic) Quick test… Bond Polar/Nonpolar Hydrogen bonding C-C Nonpolar No C-H Nonpolar No O-H Polar Yes N-H Polar Yes C=O Very Polar Yes  How do functional groups confer hydrophobicity/ hydrophilicity? What is a functional group? Groups of atoms in organic molecules that determine the physical and chemical properties of molecules. In general, a functional group will make a macromolecule more hydrophilic because most functional groups have polarity (charge). Functional group Formula Polarity Hydroxyl R-OH Polar Amino R-NH2 Polar Carboxyl R-COOH Polar Phosphate R-PO4- Polar “R” denotes any group of atoms Aromatic ring structured hydrocarbons are typically hydrophobic. example: Benzene structure  SUMMAR Y – Part 1 Saturated molecules contain only single bonds. They have the maximum number of hydrogens that can bond with the carbons. Saturated: no double bonds in chain Unsaturated molecules have one or more double or triple bonds. These molecules do not have the maximum number of hydrogens. Unsaturated: at least one double bond in chain SUMMAR Y – Part 2 Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons. The higher the electronegativity, the more the atom likes to keep hold of electrons. Electronegativity creates polar bonds (positive charge at one end, negative charge at the other). Molecules that have polar covalent bonds can interact with water through hydrogen bonding. These are hydrophilic molecules. Molecules that do not have polar bonds cannot interact with water through hydrogen bonding. These are hydrophobic molecules. SUMMAR Y – Part 3 Functional groups typically confer hydrophilic characteristics. Aromatic structures typically confer hydrophobic characteristics. A is a functional group. NH2 makes it polar. This region of the molecule is hydrophilic. B is an aromatic ring. This region of the molecule is hydrophobic. C is a functional group. OH makes it polar. This region of the molecule is hydrophilic.  4- Isomerism – Key concept The atoms in a functional group can be arranged differently – which will result in differences in structural, functional and chemical properties. Main types of isomerism. 1- Structural isomerism 2- Stereoisomerism Type 1: Geometric isomerism (cis-trans) Type 2: Optical isomerism 1- Structural isomerism Structural isomers are compounds that have the same molecular formulae but different structural formulae. Example 1: Butane and isobutane - C4H10 H H H H H H C H H H C C C C H C C H H H H H H H H C H butane isobutane H Example 2: Glucose and fructose - C6H12O6 H H O C H C OH H C OH C O H C OH H C OH H C OH H C OH H C OH H C OH H C OH H C OH H H Glucose Fructose 2- Stereoisomerism  2a- Geometric (cis-trans) isomers cis- and trans- isomers are compounds that have the same atoms connected to each other, however the atoms are differently arranged in space. Example 1: cis-2-Butene and trans-2-Butene - C4H8 H H CH3 H C C C C H3 C H3 C H CH3 cis-2-Butene trans-2-Butene Example 2: cisplatin and transplatin Cl NH3 H3 N Cl Pt Pt Cl NH3 Cl NH3 cisplatin transplatin cisplatin has been an important anti-cancer drug since 1978. transplatin has no biological activity. Example 3: cis-glucose (a-glucose) and trans-glucose (b-glucose) CH2OH CH2OH H C O H H C O OH H H C C C C OH H OH H HO C C OH HO C C H H OH H OH a-glucose b-glucose 2b- Optical isomerism Optical isomerism occur when a carbon atom has four different atoms or groups of atoms attached to it. This carbon is called the chiral carbon (chiral centre). Optical isomers are also known as ‘enantiomers’.  c a p Re What is a chiral object? Chiral objects vs achiral objects Key fact: Chiral carbon will have 4 different atoms/groups attached to it. H H H3 C C OH HO C CH3 Br Br How do we distinguish between optical isomers (enantiomers)?  By using light polarization. randomly organized light polarizing filter plane-polarized D-form of the chirallight sample (for example D-glucose) (rotates the plane of polarized light to right - clockwise) D comes from dextrorotary. L-form of the chiral sample (for example L-glucose) (rotates the plane of polarized light to left - anticlockwise) L comes from levorotary. To summarise… Solutions of chiral chemical compounds change the plane in which the light is polarized. Each enantiomer of a pair rotates the plane of the light by the same amount, but the directions of rotation are opposite. If one enantiomer rotates the plane of the light to the right (D-form), the other rotates it to the left (L-form). Most natural sugars are D- (example: D-glucose) For those who want some extra knowledge (and like organic chemistry!): These image shows Fischer projections of the two enantiomers of glucose molecule. If the -OH on the bottom chiral center is on the right- hand side of the Fischer projection, the molecule is “D“. If it is on the left-hand side, the molecule is “L”. Most natural amino acids are L- (example: L-alanine) For those who want some extra knowledge (and like organic chemistry!): These image shows Fischer projections of the two enantiomers of alanine molecule. If the -NH2 on the bottom chiral center is on the right- hand side of the Fischer projection, the molecule is “D“. If it is on the left-hand side, the molecule is “L”. Examples of enantiomers In the late 1950s a German company marketed the drug thalidomide as a sedative. Pregnant women also took it because it was effective at stopping morning sickness. Its use caused >12,000 babies to be born with severe limb defects. This tragedy occurred because of: Poor drug regulation processes at the time. Chirality.  Enantiomers of methamphetamine Recreational drug Nasal decongestant (e.g. Vicks)  t o et rg t o f ! o ’ n ise D rev