Biochemistry Lecture Notes PDF

Biochemistry Lecture 1: Covalent Bonding in Biomolecules  1.0 chemistry of life - Some metals are important in catalyzing the chemistry of the cell - V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo. - Other elements have specific roles in one or two specific places like iodine in thyroid hormones-...

Biochemistry Lecture 1: Covalent Bonding in Biomolecules  1.0 chemistry of life - Some metals are important in catalyzing the chemistry of the cell - V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo. - Other elements have specific roles in one or two specific places like iodine in thyroid hormones- I, Se, Si, F, B - Na, Cl and K are important for the ionic balance in the cell and are also important for signalling in nerve cells.  - Relevant chemistry in biochem occurs with 6 elements- H, N, C, O, P, S - These are the only ones that can form large complex molecules - Look at electrons and valence structures for bonding - Electron pairs form covalent bonds - Shared electron pairs that join up atoms to form molecules are what we call covalent bonds.  The number of bonds each element can form are as follows: - H = 1 - O = 2 - N = 3 - C = 4 - S = 2 - P = 5 1.1 Geometry of carbon bonds - Single bonded C forms a tetrahedral arrangement = 109.5° - Double bonded C atoms form a trigonal planar geometry = 120° - Bonds in the plane of the screen are drawn as regular lines  - Bonds that are coming towards us are drawn as a solid wedge  - Bonds behind the plane of the screen are drawn as a dashed wedge - Sometimes called wedge-dash representation - Single bonds allow rotation and can change the structural conformation of the molecule - Not all conformations are energetically favourable/equally likely - Tetrahedral arrangement - Double bonds do not allow rotation - Atoms lie in a singular plane - Isomers will not be identical - No conversion - Trigonal planar arrangement 1.2 Functional groups - Hydrocarbons alone don't react - Functional groups are decorations of the hydrocarbon chain that confer specific chemical properties and reactivity to a molecule - All functional groups have at least one or a combination of the atoms O, N, S or P - Alcohols can be oxidised into aldehydes, ketones and carboxylic acids depending on where the hydroxyl group is in the molecule - H from COOH can dissociate which is why carboxyl groups are acids - When they are deprotonated, they are called carboxylates - Acyl groups can be found in larger carboxylic acids - If a carboxylic acid is any further oxidised = CO~2~ - Amino group is basic & can be protonated so carries a positive charge= NH~3~^+^ - Phosphate group is highly acidic so its practically always deprotonated and negatively charged O-P=OO-    1.3 Common linking bonds in biomolecules Esters - Carboxyl group + hydroxyl group = ester - E.g. neurotransmitter acetylcholine  - Phosphoric acid  - can form ester bonds with 2 different hydroxyl groups to link them together into a diester  - E.g. phosphodiester bonds - Phosphoric acid can also anhydrides  - Anhydrides - Carboxylic acid + carboxylic acid = acid anhydrides - Anhydrides have no role in water and hydrolyse quickly so no role in biochem  - However phospho-anhydrides are very important e.g. ATP which has 2 phospho-anhydride links - Thiols  - Can also form esters → thioester e.g. acetyl coenzyme A - Cystine = only amino acid with a thiol group  - Two of the thiols can be linked together to make disulfide bonds  - Amino acids - Amino group of one amino acid and carboxyl group of another join to form a polypeptide chain  - = amide bond/peptide bond - Carboxyl group can be turned into amide if one of O is swapped for N  - When two hydroxy groups are joined by condensation = ether  - Glycosidic bond between sugar molecules looks like ether bond - C1 carbon atom of glucose engages in this bond- not actually an alcohol but a variation of the more highly oxidised aldehyde group. This variation is called "hemiacetal" in the single sugar and "acetal" in the glycosidic bond. \ \ \ \ \ \ \ \ \ \ \ \ \ Summary & ILOs: - **Define the covalent bond-**  Shared electron pairs that join up atoms to form molecules - **Give the number of bonds commonly formed by carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus-** C=4, H=1, N=3, O=2, S=2, P=5 - **Relate the number of bonds formed by carbon to the number of shared electron pairs-** 4 valence e- so needs to bond 4e- more. Therefore forms 4 covalent bonds. 4 bonds = 4 shared e- pairs - **Describe the direction (geometry) of covalent bonds around a central (especially carbon) atom (e.g., tetrahedral (109°), trigonal planar (120°), linear (180°)-** -  tetrahedral = single bonded carbon & 4 bonding, 0 lone - Trigonal planar = double bonded C & 3 bonding, 0 lone - Linear = when C is sp hybridized, C is triple bonded or has 2 double bonds & 2 bonding, 0 lone - **Predict whether a bond is likely to be able to rotate (e.g., single bond versus double bond) and, therefore, have variable or fixed bond angles between groups attached to participating atoms (important for polypeptide chain conformation -- later lecture)-** single bond = can rotate & variable angles, double bond = can't & fixed angles - **Define a functional group**- additions of the hydrocarbon chain that confer specific chemical properties and reactivity to a molecule with at least one atom or combination of O, N, S, or P - **Recognise (and ideally be able to draw) as many of the functional groups and linking bonds that occur in biological molecules as possible, in particular: hydroxyl (alcohol), sulfhydryl, carbonyl, aldehyde, ketone, acyl, acetyl, carboxylate, amino, phosphoryl, ether, ester, thioester, amide (peptide), disulfide, phosphate ester, phosphodiester, phosphoanhydride, hemiacetal (wrt carbohydrates), glycosidic bond, C=C double bond (in fatty acids, gives unsaturated chain)** Lecture 2: Non-covalent Interactions and Water