BMS 100 Lecture 1: Chemistry of Life Jan 9, 2023 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 metabolism. ▪ Wh...

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