Name: bonds o charge-charge interactions – electrostatic charge

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Topic 1 – The Chemical Foundation of Life


1.  What kind of interactions occur between molecules?


There are 2 types of chemical interactions – Covalent Bonds and
non-covalent bonds.


Covalent – sharing the electrons among same/diff atoms – mostly share
valence electrons – important to build the backbone of the biological molecule.


Non-covalent – instead of sharing electrons, the electrons have some sort of
electrostatic charge. They are not sharing all the electrons – due to the
electrostaticity – important to determine the function and structure of different
molecules. Ex: proteins – building blocks of proteins – amino acids – to form
secondary 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 – once
it binds to the receptor – the receptor goes through a conformational change
and finally results in transcribing – chemical interaction.

Types of non-covalent

interactions – electrostatic charge attracts molecules to each other – mostly
between ionic bonds. Ex: Na+ (cation) lose 1 e- and Cl-
(anion) gains 1 e-

interactions – always goes from delta (more) negative to delta (more) positive
– dipole moment – symmetry of the bonds cancel out the asymmetry of the charge

Dipole – separation of electronic charges between molecules bonded together –
if they are the same, there’s separation of charge – no dipole.

– involves the dipole moment – interact with another molecule that has the
dipole moment – measures the polarity – separation at the ends of the molecule
– asymmetry – produces size of partial charges.

dipole – they are not as strong as covalent interactions  

Force – molecules with two equally distributed electrons come together –
attractive force – induced with each other unevenly – result in unequal
distribution of electrons in both molecules – then they will interact with each
other again – two dipole molecules – thus forming a chemical interaction with
each other – can be done either horizontally or vertically (interactions)

bonds – Hydrogen bonds form between two O2 molecules – two donor
sides – 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 one
covalent bond in a water molecule.

If it takes more energy (the number of E in KJ/mol) to pull apart
the 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 water
is 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 the
acceptor site. One H is going to bind to each O2 molecules – two
acceptor sites – they are going to bind to the other donor sites – each single
molecule is able to attract four other bonds. That is because it has two
acceptor and two donor sites – makes water unique.


Water molecules are so mobile and flexible – as a liquid – always
forming and breaking hydrogen bonds – encounter a lot of other water molecules
to bind – maintain the liquidity


Water is a very good universal solvent because of the polarity and
the tendency to immediately form hydrogen bonds.


It serves as a great environment for all the hydrophilic
substances to move around freely.



3.  Why
nonpolar moieties aggregate in water?


Water is a universal solvent and can readily dissolve or
dissociate with other molecules mainly for two reasons:

Because of it’s
high polarity

Because of it’s
ability to hydrogen bond (H+ bonds to the water are non-covalent)

Water, due to these these reasons also has the ability to dissolve
substances and thus change the molecular structure of that substance.

The segregation of water and non-polar substances is described by
the “hydrophobic effect”, meaning water-fearing. The segregation increases the
number of hydrogen bonds and thus, decreases the interaction of water with the
non-polar substances. This is best described when oil is mixed with water as it
aggregates in an aqueous solution, except for water molecules. This segregation
and the apparent repulsion between water and other non-polar substances
describes the separation of the mixture of oil and water into its two
components. The hydrophobic molecules aggregate to maintain protein structure
by orienting the water molecules with it’s polar ends away from the non-polar
molecules. For instance, if we have a fatty acid chain, that has a polar head
group and a long hydrocarbon tail, the water molecules will constrain around
the lipid tail, highly ordered into cages in comparison to bulk-face molecules
where they have more freedom of movement and can rapidly form and re-form
hydrogen bonds. That is the hydrophobic effect.



4.  How
dissolved molecules alter properties of water?


As indicated in the question above, water due to it’s high
polarity and ability to form hydrogen bonds, it makes an excellent solvent, being
able to dissolve various types of molecules. Water tends to dissolve molecules
that have side groups that can form hydrogen bonds – they have side charges –
use their polarity to attract the water molecules. For example: nucleic acids
and proteins. Water can also compete by forming H+ bonds with other
molecules. When the double helical structure is formed by H+ bonds –
when water comes – the water molecule can compete with the H+ bonds
and form the chemical bonds and as a result the native H+ bond is
lost – disrupt the chemical properties and reactions – water has this ability
to dissolve things and also has the ability to change the structure of
molecules in chemistry. These molecules are known as ‘hydrophilic’ molecules. Thus,
water participates here as a solvent and serves as an intra- and extra-cellular
means for water-loving molecules to freely move around in the vicinity.  



5.  How weak
acids and bases behave in water?


·    Weak acids and bases don’t dissociate or ionize
completely in an aqueous solution.

·    The ionization of a weak acid or a base in water is
determined by an equilibrium constant of Ka and Kb for
acids and bases, respectively.

·    The lower the Ka (denominator higher and
numerator 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 – Ka
of an aqueous solution.


For example:


HA + H2O ? H3O+
+ H2O where the reversible arrow indicates that the reaction goes
back and forth meaning the interaction is between weak acid and weak base.



6.  How
buffers work and why we need them?


·    A buffering solution is an aqueous solution consisting
of a mixture of weak acids and their conjugate bases. The buffering solution’s
pH changes very little when a small amount of strong acid or base is added to
it and that’s why it is used to prevent changes in the pH of a solution. They
are able to reduce the effects of pH after the addition of a strong acid or a
base because the conjugate acid or base is present to combine the added H+
or OH-.

·    Living systems are sensitive to pH changes so they
require a close to neutral pH because activity in the membrane and enzyme
functions have to be maintained. It is also important to maintain certain
reactions in which specific and stable pH ranges are needed for example blood
in our body.


7.  How water
participates in biochemical reactions?


·    Water is a universal solvent because it has the
tendency to form hydrogen bonds and it has a high polarity.

·    Water is a great solvent for ionic compounds because
the ions become hydrated when dissolved in water; these dissolved ions encaged
by the water are called hydration shells.

·    Cells are mostly made of water and most cells are
surrounded by water so water is the medium in which nearly all of life’s
chemical reactions occur. Water is often a reactant and a product in the
chemical 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 molecules
dissociates into H+ and O2 – that is going to change the
pH which is important for certain biochemical reactions to occur and maintain a
stable environment in some biochemical reactions – the reassociation and dissociation
– takes place super fast.





Retrieved from Class notes and Chris Wang’s biochemistry PowerPoints
for Topic 1 – The chemical foundation of life




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