Download Lecture 3

Molecules of life:DNA, RNA and
Amino Acids
Molecular Structure
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 is 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)
always from the same
pairings:
– A (adenine) <-> T (Thymine)
– C (Cytosine) <-> G (Guanine)
Adapted from [1] p.194
W p 195]
[you can find the original article by C and
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
DNA version of genetic code table
• Later we will see how gene expression and
protein production [the basis of life] works.
• The process involves the use of a genetic code
where sets of 3, triplets, of nucletides bases
[Codon] is converted into an amino acid [
described shortly]
• The following tables show the code form the
prespective of the DNA codon or RNA codon
The genetic code
RNA conversion table
DNA conversion table
Note: the only difference is T being replaced with U
Adapted from Ref [1] p. 247
Amino acids
• The other important molecule, associated with
genetics, is the “amino acid”
• An amino 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 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 chain or 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
1. 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.
• Another important feature is the formation of disulphide bonds between
two adjacent Cistine AA
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