B2.7 Gene Expression

Section 1: DNA & RNA

What is Gene Expression? Gene expression is when information in a gene in DNA is used to synthesise a functional protein. This occurs through through the processes of transcription and translation that use the genetic code on the DNA as a template. The polypeptide chain produced in protein synthesis is then folded and modified to produce the final protein.

Nucleic Acids

Nucleic acids are molecules present in living organisms that are composed of nucleotides, which are monomers made up of three components: a sugar, phosphate group and a nitrogenous base. DNA and RNAare the two types of nucleic acids that interact during gene expression.

DNA Structure and Function

DNA is a molecule that carries the genetic code, found in the nucleus. It is a two stranded molecule, made up of repeated nucleotides. The two strands run anti- parallel with each other (they run in opposite directions). The sugar type found in DNA nucleotides is a deoxyribose sugar and the 4 possible bases are: A, T, C & G. The sugar and phosphate groups make up the ‘sugar-phosphate backbone’ and the nitrogenous bases of each strand are in the centre and are complementary to each other. They are held together through hydrogen bonding following the complementary base pairing rule: A – T and G – C. The function of DNA is to carry the genetic code for building proteins which are made in protein synthesis.

RNA Structure and Function
RNA is another type of nucleic acid that is involved in gene expression. It is a molecule
made up of nucleotides just like DNA but with some key differences.
RNA is:
 Single stranded and relatively shorter than DNA
 Contains a ribose sugar instead of a deoxyribose sugar
 Contains the nitrogenous bases: G – C and A – U (no T base)
 Found in the nucleus but mostly in the cytoplasm of a cell
 While DNA is a long lived molecule, RNA is very short lived
RNA Types – there are 3 types of RNA
 mRNA: Messenger RNA
 tRNA: Transfer RNA
 rRNA: Ribosomal RNA

mRNA – Messenger RNA mRNA’s function is to carry the genetic code to build a protein, from the DNA in the nucleus out to the ribosomes in the cytoplasm. It is a long, thin single stranded chain made in the nucleus by using one side of the DNA molecule as a template (the template strand). It is made by using free RNA nucleotides and following the complementary base pairing rule A – U (on RNA) and G – C. tRNA – Transfer RNA tRNA’s is a short strand of RNA that is folded in a t or clover shape. It has an important sequence of 3 bases at the bottom called an anti- codon. tRNA’s function is to carry a specific amino acid from the cytoplasm to the ribosomes and its anticodon is complementary/matches to the codon on the mRNA strand (through hydrogen bonding of A – U and C – G).

rRNA – Ribosomal RNA rRNA’s function is to make up part of the structure of the ribosomes (about 60% of ribosome is rRNA). The ribosome is made of 2 subunits. The small subunit is for mRNA binding and the large subunit carries tRNA and grows the polypeptide chain.

The Importance of complementary bases
The complementary nature of the bases is important as it results in accurate protein synthesis (when the
genetic code from DNA is used to produce a protein).
Why are A – T/U and G – C complementary?
Purines and Pyrimidines The size of the bases determines which bases can bind together. A large (double ring) base can complement only a small (single ring) base. The large/double ring bases are called purines: these are A and G. The small/single ring bases are called pyrimidines: these are C, T & U. For example, A can bind only with T, because A is large and T is small. Adenine and Guanine are both large, so can’t fit together in either DNA or RNA.

Hydrogen bonding between bases

In addition, the placement of hydrogen bonds prevents other bonding combinations. A and T/U form the same number of hydrogen bonds together (2 hydrogen bonds), and C and G form the same number of hydrogen bonds together (3 hydrogen bonds). Adenine can’t bind with cytosine, because they have different numbers of hydrogen bonds and can’t chemically fit together.

Section 2: Protein Synthesis

Purpose of each stage:

Transcription Transcription is the process that copies the code on DNA into an mRNA strand so the code to build a protein can be carried out of the nucleus to the ribosomes. This ensures that the original DNA does not get damaged leaving the nucleus. Transcription occurs in the nucleus and each step is enzyme-controlled.

Translation The purpose of translation is to use the copied code in mRNA to make a polypeptide chain. The polypeptide chain will then fold and form a protein, so that the protein can be used for structural (e.g. ligaments) or catalytic functions (e.g. enzymes). Translation occurs in the cytoplasm, using a ribosome, and each step is enzyme-controlled.

Transcription Process

1. An enzyme unwinds the DNA double helix (breaking the hydrogen bonds between the complementary bases) to expose the bases on the template strand of the DNA. The template strand of the DNA carries the code for making a polypeptide chain/protein that is copied to make mRNA (= the role of DNA in protein synthesis).
2. Transcription starts at a promoter sequence on the template strand. An enzyme begins joining free RNA nucleotides to the exposed bases on the DNA template strand using complementary base pairing of A-U and G-C to build a single stranded mRNA molecule (U replaces T in mRNA nucleotides)
3. Transcription is complete when the enzyme reaches the terminator sequence and the mRNA strand detaches
4. The single strand of mRNA leaves the nucleus (through the nuclear pores) carrying the copied code, to build a polypeptide/protein, out to the ribosomes in the cytoplasm.
   Translation Process
5. The mRNA attaches to a ribosome and protein synthesis begins at the start codon (AUG - Met).
   There is a specific tRNA for each different amino acid, and the tRNAs carry their specific amino acid from the cytoplasm to the ribosomes.
6. The anticodon (3 base sequence) of a tRNA molecule is complementary to a codon (3 base sequence) on the mRNA strand. The code on the mRNA strand is read by the ribosome and a tRNA molecule with the complementary bases, matches with the mRNA codon. The amino acid attached to the tRNA molecule is added to start forming a polypeptide chain.
7. As more amino acids are added, peptide bonds form between neighbouring amino acids, building the polypeptide chain.
   The unloaded tRNAs leave the mRNA-ribosome translation complex and return to the cytoplasm to be reloaded with their specific amino acid by an enzyme.
8. Protein synthesis is terminated by a stop codon in mRNA, and the polypeptide chain is released from the ribosome. When protein synthesis is complete the mRNA is broken down.

Why is DNA not directly translated into a protein?
Ribosomes are used to make polypeptide chains and are not found in the nucleus. Ribosomes are capable of translating only single-stranded mRNA.
DNA is only one copy of the gene but a cell can produce many mRNA via transcription therefore many copies of the same gene / protein in response to cell demands.
If translation was to occur in the nucleus directly from the DNA template strand it would be slow as only one molecule of protein could be produced at a time by each cell as there is only one copy of the needed DNA. As proteins are large molecules these may not be able to leave the nucleus as they would be too large to pass through the pores of the nuclear membrane.
DNA is protected in the nucleus - if it was to be translated into a protein it would need to be at a ribosome and so would have to leave the nucleus. This may damage the DNA. The DNA is also a very long molecule and would potentially be too large to fit through nuclear pores.
Why is tRNA shorter than mRNA?
tRNA is shorter than mRNA, as it is not required to have the total coding length of the gene but only for one anti-codon to attach one amino acid molecule, while mRNA is a longer molecule because contains the whole code (from one gene) to produce a polypeptide chain (protein) which is made a sequence of amino acids.
Why does the cell continually make mRNA molecules but not DNA molecules?
The cell continually makes mRNA because it’s a (relatively) short-lived molecule; DNA is long-lived. DNA is protected and not damaged when making proteins, because it stays in the nucleus and is tightly wound. More proteins can be made simultaneously when there are multiple mRNA molecules made, because the cell may have increased demands for a specific protein; therefore lots of mRNA made (note that mRNA can be read by multiple ribosomes). DNA is only made prior to cell division and mRNA is made continuous whenever proteins are required.
Similarities between transcription and translation include:
● Both use complementary base pairing
● Both have mRNA involved in the process
● Both have a start and stop sequence
● Both are controlled by enzymes
● Code on both read in sets of three bases
Differences between transcription and translation include:
● Transcription occurs in the nucleus and requires DNA, whereas translation occurs in the cytoplasm on a ribosome and involves tRNA and amino acids
● Transcription makes mRNA whereas translation reads mRNA / makes proteins
● Transcription uses DNA as a template, whereas translation uses mRNA as a template ● Transcription involves the pairing of DNA and free RNA nucleotides, whereas translation involves pairing anticodon bases of tRNA and codon mRNA