Chap 6 Nucleic Acid & Protein Synthesis

Structure of Nucleo des and ATP

Nucleo de

 Basic building blocks of nucleic acids, such as DNA and RNA

 Organic compound of a nitrogenous base, a pentose sugar, and a phosphate group

 Two nucleo des can be joined together by a condensa on reac on to form dinucleo des

 Many nucleo des are linked into a long chain, forming a polynucleo de, either DNA or RNA
(This happens in the nucleus during interphase)

 The covalent sugar–phosphate ester bonds (phosphodiester bonds) link the 5-carbon of one
sugar molecule and the 3-carbon of the next

 The polynucleo de strand is said to have 3΄ and 5΄ ends

 Adenosine Triphosphate (Adenosine = Adenine + Ribose sugar)

 Three components: Adenine (nitrogenous base), Ribose (sugar), phosphate

 Phosphorylated nucleo de

Nitrogenous Bases

 Purines are nitrogenous bases with double-ring structures (adenine and guanine)

 Pyrimidines are nitrogenous bases with single-ring structures (thymine, cytosine, uracil)

 Complementary base pairing between adenine and thymine (or adenine and uracil in RNA)
and between guanine and cytosine

 Adenine and thymine (or uracil in RNA) form 2 hydrogen bonds, and guanine and cytosine
form 3

DNA Structure and Replica on

 DNA comprises two an parallel polynucleo de strands lying side by side, held together by
hydrogen bonds

 One strand is in the 3’ to 5’ direc on, and the other is in the 5’ to 3’ direc on,
hence an parallel.

 It has 4 nitrogenous bases: adenine, thymine, guanine, and cytosine

 The phosphodiester bonds make up a sugar-phosphate backbone, which supports the shape
of the DNA

 Hydrogen bonds between the complementary bases hold the DNA double helix together,
maintain 3D structure, and ensure stability
Replica on of DNA:

 Occurs during interphase (S phase)

 Each new DNA molecule contains one old strand and a complementary new one (hence,
replica on is called semi-conserva ve)

o The DNA double helix unwinds and ‘unzips’ as the hydrogen bonds between the base
pairs break by the DNA helicase enzyme.

o Both strands are used as templates.

o DNA polymerase catalyses the synthesis of the phosphodiester backbone by linking

o DNA polymerase can only add nucleo des in the 5’ to 3’ direc on

o It uses the 3’ to 5’ strand as a template and forms the polynucleo de in a 5’ to 3’

o This strand is con nuously synthesized (Leading strand)

o The new strand synthesized in 5’ to 3’ is made in small Okazaki fragments (Lagging

o The DNA ligase enzyme joins Okazaki fragments together by forming phosphodiester
bonds
RNA

 RNA is a single-stranded polynucleo de chain

 It contains a pentose sugar (ribose)

 Has 4 nitrogenous bases: adenine, uracil, guanine and cytosine

There are different types of RNA, which include:

 mRNA (messenger RNA): Carries the gene c informa on as a template from the nucleus to
the ribosome for transla on, remains as an unfolded strand

 tRNA (transfer RNA): Has a specific amino acid at one end and an an codon at the other; it
fits onto the ribosome mRNA at a complementary codon for protein synthesis, folded into
complex structures

 rRNA (ribosomal RNA): Primary component of ribosomes, synthesised in the nucleolus,

The Gene c Code

Gene:

 A sequence of nucleo des that forms part of a DNA molecule

 A polypep de is coded for by a gene

Codon:
  Each group of three bases in mRNA cons tutes a codon

 There are 4 nucleo de bases, 4 x 4 x 4 = 64 possible amino acids. However, only 20 amino
acids exist; hence the gene c code is:

o Redundant or degenerate - Mul ple codon codes for the same amino acid

 The gene c code is universal - All organisms use the same code

 It has start and stop codons to mark the beginning and end of the gene for protein synthesis

Protein Synthesis

Transcrip on

 Occurs in the nucleus

 DNA unwinds to form two strands (template and non-template)

 Only one strand acts as the template (the template strand)

 Free-ac vated RNA nucleo des line up with their complementary base and form H-bonds

 RNA polymerase catalyses the synthesis of phosphodiester bonds to form a sugar-phosphate

 Hydrogen bonds between the DNA and mRNA strands are then broken

 DNA is reformed

 mRNA strand then leaves the nucleus through the nuclear pores

Post-transcrip onal RNA modifica on

 Exons: Coding sequence

 Introns: Non-coding sequence which is not translated

 Introns are removed from the primary transcript, leaving behind only exons, which will
undertake transla on (this process is called RNA splicing)

 Primary transcript: Original molecule of RNA before splicing

Transla on

 Small ribosomal subunit a aches to mRNA

 tRNA enters the ribosome and a aches to the mRNA

 A codon on the mRNA a aches to a specific an codon on the tRNA

o AUG is the start codon; complementary an codon is UAC, which brings the amino
acid methionine

 Only 2 tRNA molecules can fit in the ribosome at the same me

 Each tRNA carries a specific amino acid

 A pep de bond is formed between the amino acids of 2 adjacent tRNA molecules (at any
me, 2 tRNA molecules can fit in the ribosome)

 The ribosome moves along the mRNA, reading the next codon

 Another tRNA molecule brings a third amino acid, which joins the previous one

 The first tRNA leaves and is reused

 The polypep de chain grows un l a ‘stop’ codon: UAA, UAC or UGA is reached.
Muta on

Gene Muta on

 A change in the sequence of base pairs in a DNA molecule that may result in an altered
polypep de

 Caused by mutagens like radia on, tar, tobacco, etc.

 Random events

 Harmful as it changes the amino acid sequence, which changes the mRNA created

 This further alters the tRNA that a aches to the ribosome, changing the amino acid brought,
and hence alters polypep de forma on

Types of muta ons

 Subs tu on muta on: A nucleo de base is replaced by a different nucleo de base

o E.g., Sickle cell anaemia, where the base thymine is replaced with adenine (CTT →
CAT) so Glutamine becomes Valine
 Elimina on (dele on) muta on: Removal of one or more nucleo des and is not replaced

 Inser on muta on: A nucleo de base is added

 Frame-shi muta on

o Inser on or dele on of one or more nucleo des which results in incorrect reading of
the sequence of triplets in the gene c code due to a shi in the reading frame