Building Blocks of life
Molecular Structure: DNA, RNA and
amino acids
Lecture 3
Chromosome to DNA molecule
• A chromosome is “essentially” a long strand of dsDNA (double
stranded Deoxyribonucleic acid) wound around proteins; e.g.
histones, and condensed to form a structure called chromatin.
• However it order for the DNA to carry out its function is must be
unwound from the proteins: i.e. chromatin -> long strand of dsDNA
• This dsDNA strands are shaped in the form of a “double Helix”
• Each DNA strand consists of nucleotides which are joined together.
• The DNA “double Helix” is two such strands which are coiled and
connected together via what are referred to as: nucleotide bases or
bases
The Crick and Watson double Helix
• The dsDNA has the following
important features:
• I strand, The primary/sense
strand, runs from 5’ to 3’
• The corresponding strand,
the complimentary/antisense strand, runs 3’ to 5’
• The bases (nucleic acids)
joining the strands;
• Base pairings (always the
same pairings):
– A (adenine) <-> T (Thymine)
– C (Cytosine) <-> G (Guanine)
Adapted from [1] p.194
[you can find the original article by C and W p 195]
RNA: Ribose nucleic acid
• A molecule closely associate with DNA and
which a part of the “gene expression” process
is referred to as RNA
• The RNA [nucleotide] is very similar to DNA
[nucleotide] except:
– Its nucleic acid has a ribose sugar as opposed to a
deoxyribose sugar.
– The Nucleotide base Thymine is replace with an
equivalent base called Uracil (klug p.191)
– The RNA strand is single stranded
Amino acids
• The third important molecule, associated with
genetics, is the “amino acid”
• An amino acid is a molecule that has two main
elements: a constant part [shown in pink in the
next slide] and a variable part. This variable part
has specific chemical properties which are
essential to its function.
• In proteins [chains of amino acids] the constant
regions are referred to as the “backbone” (main
chain) and the variable region as the side chains.
AMINO Acids (AA) and their properties
• Amino acids are grouped
according to properties, refer to
diagram.
• These properties help determine
the final shape of proteins
• For example hydrophobic amino
acids [non polar] tend to stay
away from water and are in the
centre of proteins
• Hydrophilic [polar] tend to be on
the outside surface of proteins
• Two other important amino acids
to note are: cystine which has a
sulphur (S) in the side chain
• Tryptophan which is the largest
amino acid.
An amino acid chain (Polypeptide)
• When two AA are joined
together “peptide” bonds
• A number of AA joined by
peptide bonds are called a
polypeptide chain.
• The polypeptide has two
elements: the main chain
connected via peptide
bonds; and side chains
(associated with
functionality or determine
the final shape).
Secondary and Tertiary structure
• The primary chain (polypeptide
chain) then begins to change its
shape depending on the side
chain properties of the amino
acid to firstly form:
• the secondary structure:
consisting of α helixes and β
sheets both
• The secondary structure then
changes to the tertiary structure
• The diagram shows a myoglobin
[like haemoglobin] molecule with
α helixes and β sheets, the heme
group [blue] contains iron and
does not contain AA and red ball
an oxygen molecule
Secondary to Tertiary structure
• Secondary structures interact with the environment to
form the tertiary or 3-D structure of the protein :
essentially the polypeptide chain is contorted to form the
most thermodynamically stable structure:
• Since most proteins are in water A number of factors affect
the formation:
1. Polar (Hydrophilic) AA try to stay on the outside of the structure
2. Non polar (hydrophobic) stay on the inside
• However in some cases the proteins are in hydrophobic
solution [Lipids in the cell membrane] and in this case the
structure would alter: non polar outside, polar inside.
Exam question
• Describe, using suitable examples, the three
important molecules associated with the
existence of life. [this will form part of a
question]
References
• [1] Klug 7th ed
• [2]
Http://biotech.matcmadison.edu/resources/proteins
/labManual/chapter_2.htm; accessed on the
21/9/2011