Molecules of life:DNA, RNA and Amino Acids Molecular Structure Lecture 3.

Molecules of life:DNA, RNA and Amino Acids

Molecular StructureLecture 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/anti-sense 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 [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

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

Adapted from Ref [1] p. 247

Note: the only difference is T being replaced with U

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