Name: __________Helly Patel___________ Name: _________Maninee Kapadia__________ Name: _____________________________ Name: _________________________________ Topic 1 – The Chemical Foundation of Life 1. What kind of interactions occur between molecules? There are 2 types of chemical interactions – Covalent Bonds andnon-covalent bonds. Covalent – sharing the electrons among same/diff atoms – mostly sharevalence electrons – important to build the backbone of the biological molecule. Non-covalent – instead of sharing electrons, the electrons have some sort ofelectrostatic charge. They are not sharing all the electrons – due to theelectrostaticity – important to determine the function and structure of differentmolecules. Ex: proteins – building blocks of proteins – amino acids – to formsecondary structures – alpha helix or beta sheets – to form globular structures– protein folding – disulfide bonds, hydrogen bonds, van der waal interactions– interaction is weaker than covalent bond – its is therefore reversible – onceit binds to the receptor – the receptor goes through a conformational changeand finally results in transcribing – chemical interaction. – Types of non-covalentbondso charge-chargeinteractions – electrostatic charge attracts molecules to each other – mostlybetween ionic bonds.
Ex: Na+ (cation) lose 1 e- and Cl-(anion) gains 1 e- o Dipoleinteractions – always goes from delta (more) negative to delta (more) positive– dipole moment – symmetry of the bonds cancel out the asymmetry of the chargedistribution o ChargedDipole – separation of electronic charges between molecules bonded together –if they are the same, there’s separation of charge – no dipole. o Dipole-Dipole– involves the dipole moment – interact with another molecule that has thedipole moment – measures the polarity – separation at the ends of the molecule– asymmetry – produces size of partial charges. o Induceddipole – they are not as strong as covalent interactions o DispersionForce – molecules with two equally distributed electrons come together –attractive force – induced with each other unevenly – result in unequaldistribution of electrons in both molecules – then they will interact with eachother again – two dipole molecules – thus forming a chemical interaction witheach other – can be done either horizontally or vertically (interactions) o Hydrogenbonds – Hydrogen bonds form between two O2 molecules – two donorsides – each water molecule has two O2 with other two acceptor sites– Hydrogen that covalently bonds with the O2 is known as the donor.It is easier to break the hydrogen bond (the whole thing – molecule) than onecovalent bond in a water molecule. If it takes more energy (the number of E in KJ/mol) to pull apartthe complex – means the bond is stronger – vice versa The sharing of the covalent bonds – of the outer electrons –stronger than non-covalent bonds. 2. Why wateris a good medium for life? Because it has both donor and acceptor side to it. H+serves as the donor site and O2 and OH- serve as theacceptor site.
One H is going to bind to each O2 molecules – twoacceptor sites – they are going to bind to the other donor sites – each singlemolecule is able to attract four other bonds. That is because it has twoacceptor and two donor sites – makes water unique. Water molecules are so mobile and flexible – as a liquid – alwaysforming and breaking hydrogen bonds – encounter a lot of other water moleculesto bind – maintain the liquidity Water is a very good universal solvent because of the polarity andthe tendency to immediately form hydrogen bonds. It serves as a great environment for all the hydrophilicsubstances to move around freely. 3. Whynonpolar moieties aggregate in water? Water is a universal solvent and can readily dissolve ordissociate with other molecules mainly for two reasons: o Because of it’shigh polarity o Because of it’sability to hydrogen bond (H+ bonds to the water are non-covalent)Water, due to these these reasons also has the ability to dissolvesubstances and thus change the molecular structure of that substance.
The segregation of water and non-polar substances is described bythe “hydrophobic effect”, meaning water-fearing. The segregation increases thenumber of hydrogen bonds and thus, decreases the interaction of water with thenon-polar substances. This is best described when oil is mixed with water as itaggregates in an aqueous solution, except for water molecules. This segregationand the apparent repulsion between water and other non-polar substancesdescribes the separation of the mixture of oil and water into its twocomponents.
The hydrophobic molecules aggregate to maintain protein structureby orienting the water molecules with it’s polar ends away from the non-polarmolecules. For instance, if we have a fatty acid chain, that has a polar headgroup and a long hydrocarbon tail, the water molecules will constrain aroundthe lipid tail, highly ordered into cages in comparison to bulk-face moleculeswhere they have more freedom of movement and can rapidly form and re-formhydrogen bonds. That is the hydrophobic effect. 4. Howdissolved molecules alter properties of water? As indicated in the question above, water due to it’s highpolarity and ability to form hydrogen bonds, it makes an excellent solvent, beingable to dissolve various types of molecules. Water tends to dissolve moleculesthat have side groups that can form hydrogen bonds – they have side charges –use their polarity to attract the water molecules.
For example: nucleic acidsand proteins. Water can also compete by forming H+ bonds with othermolecules. When the double helical structure is formed by H+ bonds –when water comes – the water molecule can compete with the H+ bondsand form the chemical bonds and as a result the native H+ bond islost – disrupt the chemical properties and reactions – water has this abilityto dissolve things and also has the ability to change the structure ofmolecules in chemistry. These molecules are known as ‘hydrophilic’ molecules. Thus,water participates here as a solvent and serves as an intra- and extra-cellularmeans for water-loving molecules to freely move around in the vicinity. 5. How weakacids and bases behave in water? · Weak acids and bases don’t dissociate or ionizecompletely in an aqueous solution.
· The ionization of a weak acid or a base in water isdetermined by an equilibrium constant of Ka and Kb foracids and bases, respectively. · The lower the Ka (denominator higher andnumerator lower) – the less dissociation – the weaker the acid · The higher the pKa – the weaker the acid (>15),as it is the negative 10-base logarithm of the acid dissociation constant – Kaof an aqueous solution. For example: HA + H2O ? H3O++ H2O where the reversible arrow indicates that the reaction goesback and forth meaning the interaction is between weak acid and weak base.
6. Howbuffers work and why we need them? · A buffering solution is an aqueous solution consistingof a mixture of weak acids and their conjugate bases. The buffering solution’spH changes very little when a small amount of strong acid or base is added toit and that’s why it is used to prevent changes in the pH of a solution. Theyare able to reduce the effects of pH after the addition of a strong acid or abase because the conjugate acid or base is present to combine the added H+or OH-. · Living systems are sensitive to pH changes so theyrequire a close to neutral pH because activity in the membrane and enzymefunctions have to be maintained.
It is also important to maintain certainreactions in which specific and stable pH ranges are needed for example bloodin our body. 7. How waterparticipates in biochemical reactions? · Water is a universal solvent because it has thetendency to form hydrogen bonds and it has a high polarity.
· Water is a great solvent for ionic compounds becausethe ions become hydrated when dissolved in water; these dissolved ions encagedby the water are called hydration shells. · Cells are mostly made of water and most cells aresurrounded by water so water is the medium in which nearly all of life’schemical reactions occur. Water is often a reactant and a product in thechemical reactions that are needed to support life. · A lot of molecules are staying at the ionization state– not splitting apart – low conductivity – however when the water moleculesdissociates into H+ and O2 – that is going to change thepH which is important for certain biochemical reactions to occur and maintain astable environment in some biochemical reactions – the reassociation and dissociation– takes place super fast. References Retrieved from Class notes and Chris Wang’s biochemistry PowerPointsfor Topic 1 – The chemical foundation of life