Lecture 4 Basic Chemistry refresher & Macromolecules of all sorts

Latest model of an atom 02_01_atom.jpg 02_01_atom.jpg

02_02_atomic number.jpg Hydrogen -the simplest and smallest of all atoms 02_02_atomic number.jpg Atomic number is the number of proton found in the nucleus

02_03_mole.jpg 02_03_mole.jpg

02_04_element abundance.jpg The most abundant element in the human body is hydrogen Why? The most abundant element making the planet is oxygen Why? 02_04_element abundance.jpg 02_04_element abundance.jpg

02_05_chemical reactivity.jpg

02_06_stable arrangement.jpg Sharing bond Giving bond

02_07_periodic table.jpg Periodic Table of universal elements

02_08_ionic bond.jpg Ionic bond between two elements

02_09_covalent bond.jpg The stability of a covalent bond. Remember that one needs to supply energy to get the two atoms close together in the first place 02_09_covalent bond.jpg 02_09_covalent bond.jpg

02_10_geometries.jpg Properties of the most common bioelements Hydrogen Just one 02_10_geometries.jpg

A single bond allows rotation of the atoms either side, whereas a double bond does not 02_11_C-C double bonds.jpg 02_11_C-C double bonds.jpg

02_12_polar covalent.jpg The angle of the bond is very important It may make a molecule polar, or… 02_12_polar covalent.jpg …non-polar

Proteins rely very heavily on this molecular polarity (as well as other Forces) to function correctly 02_13_Proteins bind.jpg 02_13_Proteins bind.jpg

02_14_Protons on move.jpg Atoms can be on the move constantly…

02_15_organic molecules.jpg What is life made of… ATOMS MOLECULES SPECIAL MOLECULES 02_15_organic molecules.jpg 02_15_organic molecules.jpg These are the four organic classes of molecules

02_16_glucose structure.jpg Glucose has this structure 02_16_glucose structure.jpg 02_16_glucose structure.jpg

Life systems are constantly making and breaking bonds 02_17_disaccharide.jpg 02_17_disaccharide.jpg

Macromolecules Macro = huge Amino acids can build into huge molecules So can carbohydrates So may nucleic acids There is theoretical limit to the size of these

There are three major types of biological macromolecules in mammalian systems. 1. Carbohydrates 2. Nucleic acids 3. Proteins Our tasty friends, fats, do not make the grade because they do not form these immense complexes

FATS Here are some important facts about fats…

Saturated & Unsaturated Fats Fact: we all need fats. Fats helps nutrient absorption, nerve transmission, maintaining cell membrane integrity etc. However, when consumed in excess amount, fats contribute to weight gain, heart disease and certain types of cancer. Fats are not created equal. Some fats promote our health positively while some increase our risks of heart disease and other ailments.

Bad Fats Saturated Fats Saturated fats raise total blood cholesterol as well as LDL cholesterol (the bad cholesterol). Saturated fats are mainly found in animal products such as meat, dairy, eggs and seafood. Some plant foods are also high in saturated fats such as coconut oil, palm oil and palm kernel oil.

Bad Fats 2 Trans Fats Trans fats are invented as scientists began to "hydrogenate" liquid oils so that they can withstand better in food production process and provide a better shelf life. As a result of hydrogenation, trans fatty acids are formed. Trans fatty acids are found in many commercially packaged foods, commercially fried food such as French Fries from some fast food chains, other packaged snacks such as microwaved popcorn as well as in vegetable shortening and hard stick margarine.

Good Fat Monounsaturated Fats Have just one double bond. Monounsaturated fats lower total cholesterol and LDL cholesterol (the bad cholesterol) and increase the HDL cholesterol (the good cholesterol). Nut, canola and olive oils are high in monounsaturated fats.

Good Fat 2 Polyunsaturated Fats Have two or more double bonds. Polyunsaturated fats also lower total cholesterol and LDL cholesterol. Seafood like salmon and fish oil, as well as corn, soy, safflower and sunflower oils are high in polyunsaturated fats. Omega 3 fatty acids belong to this group.

02_18_Fatty acids.jpg 02_18_Fatty acids.jpg

02_19_fatty side chains.jpg

02_20_lipid membranes.jpg 02_20_lipid membranes.jpg

02_21_Alanine.jpg 02_21_Alanine.jpg

02_22_peptide bonds.jpg 02_22_peptide bonds.jpg

Nucleotides DNA and RNA are the two nucleic acids that come to mind first However, there are many other uses for these important compounds….

02_23_ATP.jpg ATP - Adenosine Triphosphate - made of ribose sugar This is the most important molecule for ready energy storage - it can be considered to be the cells’ battery 02_23_ATP.jpg 02_23_ATP.jpg

02_24_energy carrier.jpg 02_24_energy carrier.jpg

02_25_nucleotide residues.jpg

By weight 25% of total bacterial cell contents are macromolecules. They are essential in dictating the character of the cell type, ie. E.coli, Salmonella, heart cells, liver cells, brain cells, etc. 02_26_Macromolecules.jpg

02_27_monomeric subunits.jpg Irrespective of the type of biological macromolecule being made they have a common construction theme: A subunit is added one at a time by a repetitive enzymatic process 02_27_monomeric subunits.jpg 02_27_monomeric subunits.jpg However, unlike a bottle factory, where the same robot performs the identical function, with these biological systems the subunits have to be added in a set sequence because we have more than one flavour! 4 subunits in NA; 20 subunits in P’; many many in polysaccarides

Revision Question - What is this process called? 02_28_adding subunits.jpg By design, macromolecule construction occurs by the addition of the incoming subunit to just one end of the growing molecule, ie. DNA growth only takes place at the 3’OH end of an existing DNA strand. 02_28_adding subunits.jpg These processes are common to the construction of all these macromolecules. YOU MUST REMEMBER THEM!

WOW! Due to these differencing subunits there is the potential to make many many alternative polymers. Consider: Proteins A protein of just 200 amino acids We have 20 amino acids to choose from each time There are then possible 20200 possible combinations! DNA 10,000 base DNA molecule We have just 4 different base types to choose from There are then possible 410000 possible combinations

More molecular interactions We learnt that there are 3 types of atomic interactions between atoms. ACTUALLY there are other forces too; van der Waals attractions - weaker than hydrogen bonds attraction between closely located atoms Hydrophobic interactions - weakest of all 3 dimensional structure of water forces hydrophobic groups together Oil in water

Most P’s and RNA molecules have a stable confirmation which they adopt readily and it is dictated by their primary sequence. 02_31_protein fold.jpg

02_32_Noncovalent bonds.jpg E.g. immunoglobulins (Abs). Heavy chain and light chain are made in various locations and combine readily together.

02_33_macro complexes.jpg 02_33_macro complexes.jpg

Study Requirements Essential Concepts At the end of each chapter there are two resources: Essential Concepts You are required to learn each of these facts for every chapter that we cover (These concepts are essential!) Key Terms You are required to know the definition of each of these regardless of the fact that they did or did not appear on my PowerPoint slides (one needs to be familiar with these terms for subsequent courses)