Atomic Structure & Chemical Bonds

Two major particles are found in the nucleus of most atoms. Protons (have weight and a
positive charge) and Neutrons (equal weight to a proton and no charge). Outside the
nucleus in shells (subdivided into orbitals) are electrons (no weight and a negative
charge)

Usually Protons = neutrons = electrons and since protons have a positive charge and
electrons have an equal but opposite negative charge atoms are neutral.

Isotopes in most cases are when the proton No. is not identical to the neutron number
(exceptions include Hydrogen). Usually the neutron No. is greater than the proton no.

For a given element the proton number is constant and fixed, if there are isotopes the
neutron number is variable.

Atomic Number is the number of protons in an atom

Mass number is the number of protons + neutrons ( usually twice the atomic number)

Atomic weight is the average of mass numbers of all isotopes of an atom taking into
account their relative proportions in a sample (see examples below)

Element Atomic No.(protons) Mass No.(protons +neutrons) Atomic weight Electrons

Hydrogen 1 1 1

1 2 (1 neutron) 1

1 3 (2 neutrons) 1.008 1

Helium 2 4 4 2

Carbon 6 12 6

6 13 6

6 14 12.01 6

Stability and therefore reactivity and bond formation is a result of the organization of
electrons in the orbitals surrounding the nucleus. See Fig 1. below for the organization of
some common atoms. The number of electrons required to be added to or lost from the
outermost shells dictate the number of bonds that must be formed to make the atoms
stable.

Fig.1 See diagrams in your notes.

Notice, the number of shells in the atoms are variable as are the number of electrons in
the shells. The unstable and therefore reactive atoms are hydrogen, carbon, oxygen,
sodium and chlorine. The stable atom and thus unreactive atom is helium. Given that the
inner most shell of all atoms can only contain two electrons and subsequent shell a
maximum of eight electrons you should be able to see that atoms that do not have the
maximum number of electrons in the outer most orbital are the ones that are unstable and
reactive and also the number of bonds required to be formed to make the atoms stable.
Hydrogen-1, carbon-4, oxygen-2, sodium-1 and chlorine-1.

Bonds:
Three major types of bond are associated with biology, Ionic, covalent and
hydrogen. Ionic are the least important but have intermediate strength. Hydrogen are the
weakest but of import while covalent are the strongest and of most import in biology.

Ionic bonds:

Ionic bonds are formed between ionized atoms (charged). When atoms lose electrons
from the outermost shell to become stable they become positively charged (Cations) due
to an excess of protons in the nucleus. The number of positive charges ( and therefore
potential bonds) is dependant on the number of electrons lost. If atoms gain electrons in
the outer most shell to become stable an excess in negative charge arises dependant on
the number of electrons gained (anion). In the case of sodium chloride (fig 2), sodium
loses the single electron in the outermost shell thus the remaining outer shell is now full.
As a consequence there is a single net positive charge. The chlorine accepts the electron
lost to complete its outermost shell and becomes stable with a net negative charge due to
the excess of electrons. The exchange of electrons has to be complimentary. Magnesium
loses the two electrons in its outer most shell to become stable and thus has two positive
charges. Magnesium can therefore ionically bond with two chlorine atoms since each will
gain one of the two electrons lost. The ionic bonds are actually electrostatic attractions
between the opposite charges of the opposite ions. The bond does not have to permanent
because the charged atoms are stable.

Fig 2 .
Covalent Bonds:

In the following figure are representations of some simple molecules containing covalent
bonds. In all cases the incomplete outer most orbitals of the atoms involved overlap such
that pairs of electrons can be shared to complete the outermost orbitals. For example
hydrogen atoms have a single orbital containing one electron. To be complete the orbitals
require two electrons. By overlapping the orbitals the electrons in each atoms outermost
orbital are also found in the orbital of the other atom. Thus each outer orbital now
theoretically contains two electrons and is thus stable. The resulting covalent bond is a
result of sharing a pair of electrons, one from each atom. The number of covalent bonds
formed is dependant on the number of pairs of electrons that need to be shared to
complete the outermost orbital. In the example below, the carbon atom in methane has
four electrons in the outermost orbital, thus requires four more to be stable. Notice the
carbon covalently bonds with four hydrogen atoms, thus sharing the hydrogens four
electrons, thus completing the outermost orbital. By the same token each hydrogen atom
shares one of the four carbons electrons also becoming stable. In the case of oxygen each
atom shares two pairs of electrons to become stable, and therefore forms two covalent
(double) bonds.

Hydrogen Bonds:

Polar molecules, such as water molecules and amino acids have a weak, partial negative
charge at one region of the molecule (the oxygen atom in water) and a partial positive
charge elsewhere (the hydrogen atoms in water). The polarity is usually the result of
unequal sharing of electrons (due to significant differences in the mass of nuclei of
atoms) during covalent bond formation.

Thus when polar molecules are close together, their positive and negative regions are
attracted to the oppositely-charged regions of nearby molecules. The force of attraction,
shown here as a dotted line, is called a hydrogen bond. Each water molecule is hydrogen
bonded to four others.

The hydrogen bonds that form between water molecules account for some of the essential
— and unique — properties of water.

 The attraction created by hydrogen bonds are primarily responsible for the
properties of water.
 The energy required to break multiple hydrogen bonds causes water to have a
high heat of vaporization; that is, a large amount of energy is needed to convert
liquid water, where the molecules are attracted through their hydrogen bonds, to
water vapor, where they are not.
 Below 00C the hydrogen bonds are permanent, thus water molecules do not move
resulting in the formation of ice where the molecules are spread out, which
decreases the density of water.

Two outcomes of this:

 The evaporation of sweat, used by many mammals to cool themselves, achieves
this by the large amount of heat needed to break the hydrogen bonds between
water molecules.
 Moderating temperature shifts in the ecosystem (which is why the climate is more
moderate near large bodies of water like the ocean)

The hydrogen bond is relatively weak. However, when many hydrogen bonds can form
between molecules (or parts of the same molecule), the resulting union can be sufficiently
strong as to be quite stable.

Macromolecules:
There are three true major macromolecules and thus polymers (carbohydrates, proteins &
nucleic acids) and one that is not truly a macromolecule (lipids). While each may have
several functions each has at least one unique function.

Carbohydrates- Covalent bonds are the major source of energy for cells when broken.
Proteins- Enzymes, the biological catalysts that regulate the reactions of life.
Nucleic Acids – The storage of Genetic information (enzymes) in DNA, and RNA for
the conversion of the genetic information into Protein.
Lipids- Membranes

All theoretical polymers are made of repeating subunits (monomers) covalently bonded
together by a process that usually requires the removal of apart of water from one
monomer and a part from the other monomer involved in the covalent bond. The name of
the covalent bond formed depends on the monomers involved and the macromolecule
formed.

Ex. Monomer A Monomer B

A- O-H + H-O-B
(The italicized atoms are those parts of water to be removed.)
thus, A-O- B + H-O-H

is the resulting reaction, known as a condensation reaction or Dehydration Synthesis.

Carbohydrates.
Saccharide in greek means sugar and is the basis for naming the monomers and
complexes of monomers of the carbohydrates.
The monomers of carbohydrates are grouped into classes based on the following
carbon, hydrogen and oxygen associations
(CH2O)n where n can have the following values:
3 = triose 4 = tetrose 5 = pentose 6 = hexose 7 = heptose

Triose and tetrose monosaccharides are always organized as a linear chain whereas
pentose, hexose and heptose are either organized as linear chains or ring structures,
usually ring structures in biological material. While the number of carbon, hydrogen
and oxygen atoms in a given class are fixed the specific arrangement is variable.
Specific arrangements of atoms give rise to specific monosaccharides within a class.
Glucose and fructose are both hexose monosaccharides with different arrangements of
atoms (Fig 2b) and therefore different properties.

Carbohydrates can be classified as simple – monosaccharides, short chain-

oligosaccharides ( a few monosaccharides covalently bonded together), or complex
carbohydrates- polysaccharides (many monosaccharides covalently bonded together). A
specific short chain carbohydrate with two monosaccharides covalently bonded together
is termed a disaccharide. The formation of the covalent bond to link monosaccharides
together requires making the monosaccharides to be bonded unstable. This is
accomplished by removing specific functional groups or parts of function groups from
the carbon skeleton of the individual monosaccharides to be bonded. An O-H is removed
from one monosaccharide and a H from the other. The unstable parts of the
monosaccharides then share electrons to generate stability in a covalent bond called a
glycosidic bond (Fig 2). Additionally the H and O-H also covalently bond to produce
water. This reaction is a condensation reaction or Dehydration synthesis. To break this
bond the reverse is required- the addition of water or Hydrolysis.

Proteins:
Proteins being polymers are also made of monomers covalently bonded together. In this
case the monomers are called Amino Acids of which there are twenty different ones
available to construct the proteins

The basic structure of an amino acid is presented below:

While it is useful to know all structures, minimally the structure of Cysteine (the
presence of a sulfhydryl group [-H-S] at the terminus of the R group) should be known
because of its importance in the structural organization of proteins. Additionally all the
amino acids have a slight negative charge associated with the –C=O (carboxyl) group and
a slight positive charge associated with the –N-H (amine) group in the protein as a result
of unequal sharing of electrons, and thus have the ability to form hydrogen bonds which
again will be of importance in the structural organization of proteins.

The structures of proteins are more complex than carbohydrates in that there are
potentially four sequential levels of organization (hierarchy) termed Primary, Secondary,
Tertiary and Quaternary structures.

Primary Structure is the linear sequence of Amino acids in a given protein (encoded for in
DNA). The specific sequence of amino acids is maintained by the formation of covalent
bonds in a similar manner to that in carbohydrates. That is parts of water are removed
from the functional groups of adjacent amino acids. –O-H is removed from the –COOH
group of the first amino acid in the sequence and H from the NH2 (of the next Amino
Acid in the sequence) resulting in the sharing of electrons between the two functional
groups of the two amino acids to form a covalent bond termed a Peptide bond (Fig 4).
Since the -H and –O-H combine covalently, just as in the formation of a glycosidic bond,
the process is known as dehydration synthesis. To break this bond the reverse is required,
the addition of water or Hydrolysis.

Secondary Structure:
Is the spiraling in space of the primary structure and is maintained using hydrogen bonds
between the positive charges on the amine groups and negative charges on the carboxyl
groups.

Tertiary structure is the folding of the previous structures and is maintained by covalent
bonds called disulfide bridges between the sulfhydryl groups of two adjacent cysteines.

Quaternary structure requires multiple linear sequences of amino acids (organized as

above to be hydrogen bonded together.

Lipids:

Lipids are not true macromolecules because the monomers are not covalently bonded
together.

Simple lipids are composed of subunits made of fatty acids covalently bonded to a triose
sugar – glycerol.

Monoglycerides One fatty acid

Di Two fatty acids
Tri Three fatty acids

Complex lipid subunits are derivatives of diglycerides called phosphodiglycerides

because they are composed of two fatty acids, one glycerol and a phosphate group
attached to the glycerol. The presence of the phosphate makes the glycerol phosphate
polar and therefore hydrophilic whereas the fatty acids are non polar and therefore
hydrophobic. It is these properties that are responsible for the organization of the
macromolecule into the membrane structure shown below where the circles represent the
polar glycerol phosphate and the squiggly lines the fatty acid side chains.
Nucleic Acids:

There are two main functions of nucleic acids, the storage of genetic information (DNA)
and the conversion of this information into proteins (via RNA). The monomers of
nucleic acids are called nucleotides. In addition to being the monomers of nucleic acids,
specific nucleotides and their derivatives can be used for other purposes including storage
of chemical energy (ATP –made by phosphorylation of ADP) and as coenzymes in major
biochemical reactions (NAD & FAD).

The monomers (nucleotides) are comprised of three components.

1. A pentose sugar (Deoxyribose in DNA & Ribose in RNA)
2. Phosphate attached to the carbon #5 of the sugar
3. A Nitrogen base attached to the carbon #1 of the sugar

The nitrogen bases are classified as either two ringed purines (Adenine and Guanine) or
single ringed pyrimidenes (Thymine, cytosine and Uracil). Both purines (A & G) are
found in DNA along with the pyrimidenes Thymine and Cytosine ( T & C). RNA
contains both purines (A & G) and the pyrimidenes Uracil and Cytosine ( U & C). [see
the figure below].

In both DNA and RNA the nucleotides are covalently bonded together in linear sequences
using phosphodiester bonds between the carbon #3 and the phosphate attached to the
carbon # 5 of adjacent sugars via of dehydration synthesis.

In DNA molecules there are two linear sequences of nucleotides which are connected
using hydrogen bonds between the nitrogen bases of the two strands. This hydrogen
bonding is highly specific, the purine Guanine only hydrogen bonds with pyrimidene
cytosine and the purine Adenine only hydrogen bonds with pyrimidene thymine. In order
to hydrogen bond in such a way one strand of nucleotides has to be upside down and
reversed relative to the other [see the figure below]. The resultant strands in the molecule
are therefore said to be complimentary and antiparallel. The direction of the strands can
be designated therefore as either 5’ to 3’ or 3’ to 5’. If the nucleotide sequence is known
in one strand , by definition it is known in the other.

Ex. 5’_____________________3’
ATT C C GAT C G CA
Hydrogen bonds ->
T A AG G C T A G C G T
3’ 5’
Genetic information for the sequence of amino acids in the protein is stored in the
sequence of N-bases of the nucleotides in only one of the two strands of DNA (sense
strand). Three N-bases (and therefore nucleotides are required to encode for a single
amino acid, hence the term Triplet Codon.

RNA is a single stranded polymer of nucleotides covalently bonded similarly to DNA.

However, remember the four bases found are Guanine, Adenine, Cytosine and Uracil.
There are three types of RNA each with its own unique function:-

mRNA – has the amino acid sequence of the protein in the nucleotide sequence.
rRNA- associates with protein to produce a ribosome whose function is to read mRNA
and form peptide bonds between the amino acids thus creating the protein.
tRNA- is associated with transporting the amino acids required to the site of protein
synthesis. tRNA is unusual in that it is folded uniquely so that complimentary
areas of nucleotides are antiparallel and thus hydrogen bonds form.
DNA Replication:

This process is for copying the genetic information (DNA-chromosome) so new cells can
be created with the same properties as the original cell in which the DNA is replicated.
The process involves a series of enzymes (helicases, ligases and polymerases). Each has
specialized functions in the process- that is to break the hydrogen bonds and unwind the
molecule, fill in any gaps in the new strands to form a continuous strand of nucleotides
and attach free nucleotides to the parent or original DNA template strand. For our
purposes we will collectively call the enzymes DNA polymerase.

In the process the two complimentary anti-parallel strands unwind, separate and expose
the N-bases of the nucleotides. Each strand stays intact and acts as a template for the
formation of a new complimentary anti-parallel strand of nucleotides. The new strand is
formed according to the base pairing rule A to T and G to C. Each new nucleotide N base
forms H bonds with the complimentary base in the old strand and phosphodiester bonds
with adjacent nucleotides in the newly synthesizing strand. As the process occurs the
strands recoil to form helices.

As a consequence of the mechanism each new molecule of DNA possesses an original

strand (old) of nucleotides and a newly synthesized strand. The process is therefore
considered “semi conservative”.
Legend:

A simplified representation of a DNA molecule separating to form two new molecules.

To reproduce, a cell must copy and transmit its genetic information (DNA) to all of its
progeny.
To do so, DNA replicates, following the process of semiconservative replication. Each
strand of the original molecule acts as a template for the synthesis of a new
complementary DNA molecule.

The two strands of the double helix are first separated by enzymes. With the assistance of
other enzymes, spare parts available inside the cell are bound to the individual strands
following the rules of complementary base pairing: adenine (A) to thymine (T) and
guanine (G) to cytosine (C).

Two strands of DNA are obtained from one, having produced two daughter molecules
which are identical to one another and to the parent molecule.
Protein Syntesis:
Protein Synthesis involves two steps

Transcription: RNA polymerase unwinds the DNA Strands to expose the N bases of the
nucleotides to be transcribed to m RNA. The sense strand acts as a template to construct
an anti-parallel complimentary mRNA molecule.

Eg
Nonsense DNA 5’ ________________________3’
ATG GTC CCA CGA

mRNA 5’ _______________________3
AUG GUC CCA CGA
RNA polymerase->
Sense DNA 3’ TAC CAG GGT GCT 5’

Translation : mRNA acts as a template to hydrogen bond tRNA molecules to which have
specific amino acids attached to them, thus lining the Amino acids up in the correct order
to create the protein.
The t RNA molecules have a code that is complimentary and anti-parallel to the triplet
codes in the mRNA.
Using the example above

mRNA 5’ _______________________3
AUG GUC CCA CGA

tRNA codes 3’ UAC CAG GGU GCU 5’

In order to form the hydrogen bonds between the tRNA and mRNA a ribosome has to be
present. It also forms the peptide bond between the Amino acids. Since the ribosome only
sits over two triplet codes on the mRNA, to complete the synthesis of protein it needs to
move along the mRNA – Translocation.

See diagram on next page.