BMS 100 Chemistry of Life Lecture 1 PDF

Lecture 1: Chemistry of Life Jan 9, 2023 Dr. Ian Fraser [email protected] BMS 100 Contents Chemistry of life Introduction Atoms Bonds Functional groups Biomolecules Introduction • Over the next few weeks and throughout the course we will be looking at several key biomolecules and their metaboli...

Lecture 1: Chemistry of Life Jan 9, 2023 Dr. Ian Fraser [email protected] BMS 100 Contents Chemistry of life Introduction Atoms Bonds Functional groups Biomolecules Introduction • Over the next few weeks and throughout the course we will be looking at several key biomolecules and their metabolism. ▪ What are some examples of biomolecules? ▪ Why do we care about biomolecules? Introduction - Biomolecules Monosaccharides Amino acids Fatty acid Nucleotide • What atoms do you notice in these biomolecules? Atoms - Carbon • Carbon: C6 ▪ 6 protons (+) in nucleus (atomic number) ▪ 6 electrons (-) that circle the nucleus in “shells” C In general: ▪ the first shell holds up to 2e▪ 2nd shell up to 8 e▪ 3rd shell up to 18 e- Atoms – Carbon continued H • Carbon: C6 ▪ Can make 4 covalent bonds by sharing its 4 outer shell electrons and accommodating 4 shared electrons in its outer shell H C H H Atoms - Hydrogen • Hydrogen: H1 ▪ 1 electron in outer shell ▪ Can make 1 covalent bond by sharing its outer shell electron and accommodating one shared electron in its outer shell H Atoms - Oxygen • Oxygen: O8 ▪ 6 electron in outer shell ▪ What is the maximum number of covalent bonds that can be formed with oxygen? O Atoms - Sulfur • Sulfur: S16 ▪ 6 electron in outer shell ▪ How many covalent bonds can sulfur form? • Has more room than oxygen for making covalent bonds, as electrons have more space in the third shell S Atoms - Nitrogen • Nitrogen: N7 ▪ 5 electron in outer shell ▪ How many covalent bonds can Nitrogen form? N Atoms - Phosphorus • Phosphorous: P15 ▪ 5 electron in outer shell ▪ How many covalent bonds can phosphorus form? P Bonds • Atoms can interconnect with each other via various types of bonds • There are two main types of bonding patterns: ▪ Covalent bonds • Connections that involve sharing of outer shell electrons ▪ Biomolecules are held together via covalent bonds ▪ Non-covalent bonds • Connections that do not involve electron sharing ▪ Hydrogen bonds, Van Der Waals forces, ionic bonds, hydrophobic interactions Bonds – Covalent bonds • Covalent bonds ▪ Can be polar or non-polar in nature • Polar = unequal sharing of electrons ▪ Creates positive and negative dipoles (δ) • The atom of a bonded pair that “hogs” the electrons has a (-) δ, and the other atom has a (+) δ • Non-polar = equal sharing of electrons Bonds – Covalent polar bonds • What determines if a bond is polar or not? ▪ Based on the electronegativities of the atoms forming the covalent bond • Electronegativity = the affinity of an atom for electrons ▪ FYI: Determined by various factors, including: • The number of protons in the nucleus • The distance of the electrons from the nucleus • The shielding of the electrons from the nucleus Bonds – Covalent polar bonds • General rule for determining polarity: ▪ If the difference between the electronegativities of the atoms forming the covalent bond is > 0.5, then the atom with the higher electronegativity will attract more electrons than the other Atom Electronegativity C 2.55 O 3.44 H 2.20 N 3.04 S 2.58 P 2.19 Q: Hydrogen in a covalent bond with which atom(s) in the table creates a polar bond? Bonds – Covalent polar bonds • Q: Hydrogen and oxygen share electrons in a covalent bond. Which part of the water molecule will be more negative and why: the oxygen or the hydrogen? Bonds – Hydrogen bonds • Non-covalent bonds: Hydrogen bonds ▪ Dipole-dipole interactions between a (+)δ H on one molecule and a (-)δ O (or N or sometimes S) on a neighbouring molecule Bonds – Hydrogen bonds • The ability of water to form H-bonds allows for its unique thermal and solvent properties. ▪ Osmosis ▪ Solvent and thermal properties • More to come in more acid & base lecture Water – Thinking questions • 1. How can water dissolve neutral polar molecules? • 2. How can water dissolve ionic molecules? • 3. What happens to hydrophobic molecules in water? ▪ What do the terms hydrophobic and amphipathic mean? Water – Thinking questions • 4. How do the above interactions help determine the bilayer structure of cellular membranes? Water – thinking question • Can a polar/ hydrophilic molecule pass through the phospholipid bilayer structure of a cellular membrane easily? • What about a hydrophobic molecules? Bonds – Van Der Waals Forces • Non-Covalent bonds: Van der Waals forces ▪ Transient electrostatic interactions between permanent or induced dipoles ▪ Can be attractive or repulsive in nature: • Attractive at an optimal van der Waals radius. Bonds – Van Der Waals Forces • There are three types of Van der Waals forces: ▪ 1. Strongest: dipole-dipole • Occurs between two polar bonds ▪ Eg. 1) H-bonding is an example of dipole-dipole interaction ▪ Eg 2) The δ+ of one polar bond attracts the δ- of the other. ▪ 2. Dipole-induced dipole ▪ 3. Weakest: induced dipole-induced dipole Bonds – Hydrophobic interactions • Non-covalent bonds: Hydrophobic interactions ▪ Exclusion of non-polar substances from water • Non-polar molecules form aggregates as opposed to bonding with water Bonds - Ionic • Non-covalent bonds: Ionic interactions ▪ Attractions between oppositely charged molecules (aka “electrostatic interactions) ▪ When they occur between amino acid side chains of proteins, ionic bonds are referred to as “salt bridges” Functional Groups The atoms found in organic molecules form a number of functional groups that have predictable noncovalent bonding patterns based on their polarities Methyl H R– C–H H Ether Anhydride R – C – O – C – R’ O Mixed Anhydride OH R – O – R’ Thioester Ketone Amido Phosphoryl R– C–N Aldehyde O H H R – C – S – R’ O O R – C – O – P – OH O O Phosphoanhydride OH OH R – P – O – P – R’ O O Functional Groups - phosphoryl • A closer look: the phosphoryl group ▪ Important as a group that can be added to or removed from enzymes to turn them on or off O Phosphatase R–O–P–O O - - R – OH Kinase ▪ Why do you think the addition or removal of this group can completely change the function of the molecule? Functional Groups – Phosphoryl group • A closer look: the phosphoryl group ▪ Important as a group that can be cleaved from molecules such as ATP to provide energy Review: What type of functional group is this? • What are some reasons that cleavage of this group can release energy? Biomolecules – an introduction Monosaccharides Fatty acids Amino acids Nucleotides Aldose Monosaccharides Generic name: aldohexose • General Formula: (CH2O)n ▪ Minimum of 3 C’s ▪ Hydroxy groups plus either: • Aldehyde • Ketone ▪ Generic naming is based on number of carbons and whether it has an aldehyde or ketone group Ketose Generic name: ketohexose Monosaccharide • Monosaccharides can exist as linear molecules or be converted into cyclic molecules Pyranose Furanose ▪ 6-atom ring structure is called a pyranose, a 5-atom ring structure a furanose. Monosaccharide • Can form glycosidic bonds to make disaccharides or polysaccharides Fatty acids • General Formula: CH3(CH2)nCOOH ▪ This formula is for a saturated fatty acid • Unsaturated forms will have fewer H’s due to one or more double bonds • Fatty acids are hydrocarbon chains, with what type of functional group on the end? Fatty acids • Can attach to a glycerol backbone to create mono-, di-, or tri-glycerides via ester linkage Ester linkage Amino acids • General structure: ▪ R group varies based on the specific amino acid Amino acids – Polar • You are responsible for being able to draw the structure of the polar amino acids for Quiz 1 Amino acids – non polar • You are responsible for being able to draw the structure of the non-polar amino acids for Quiz 2 Amino acids – charged • You are responsible for being able to draw the structure of the charged amino acids for Quiz 3 Amino acids • Can form peptide bonds to be incorporated into proteins Nucleotides • General Structure: ▪ Nitrogenous base • Purines: ▪ double ring structure ▪ Adenine, Guanine • Pyrimidines: ▪ single ring structure ▪ Thymine, Uracil, Cytosine ▪ 5-C sugar ▪ Phosphate group(s) Nucleotides • Can form nucleic acids via a phosphodiester bond • Types of Nucleic acid: ▪ DNA & RNA Base Base Base Base Phosphodiester bond Base Image Based on: https://upload.wikimedia.org/wikipedia/commons/9/95/DNA_synthesis_PL.png Base At home – identify all the functional groups Monosaccharides Amino acids Fatty acid Nucleotide