B2.7 Gene Expression

Gene Expression

The process by which information in a gene in DNA is used to synthesize a functional protein through transcription and translation.

Nucleic acids

Molecules composed of nucleotides, which are monomers made up of a sugar, phosphate group, and a nitrogenous base. DNA and RNA are the two types of nucleic acids involved in gene expression.

DNA Structure

A double-stranded molecule found in the nucleus that carries the genetic code. It is made up of repeated nucleotides with a deoxyribose sugar and four possible bases: A, T, C, and G.

* long-lived

RNA Structure

A single-stranded molecule involved in gene expression, located in nucleus and cytoplasm. It is made up of nucleotides with a ribose sugar and contains the bases G, C, A, and U. There are three types of RNA: mRNA, tRNA, and rRNA.

* short-lived

mRNA

Messenger RNA carries the genetic code from the DNA in the nucleus to the ribosomes in the cytoplasm for protein synthesis.

tRNA

Transfer RNA is a short, folded RNA molecule that carries a specific amino acid from the cytoplasm to the ribosomes. It matches its anticodon to the codon on the mRNA strand.

rRNA

Ribosomal RNA makes up part of the structure of ribosomes. It is the most abundant type of RNA and plays a role in protein synthesis.

Complementary Bases

The bases A-T/U and G-C in DNA and RNA are complementary because they have the right size and hydrogen bonding properties to bind together.

Transcription

The process that copies the code on DNA into an mRNA strand in the nucleus, allowing the code to be carried out of the nucleus to the ribosomes.

Translation

The process of using the code in mRNA to make a polypeptide chain on a ribosome in the cytoplasm, ultimately forming a protein.

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

**1)** 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.* 

**2)** 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. 

**3)** 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.* 

**4)** 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. The DNA is also a very long molecule and would potentially be too large to fit through nuclear pores.
* 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.

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 and differences 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

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● 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

coding strand

Function: to increase the durability of the DNA strand. It reduces the risk that the DNA can be changed and in the event that the template strand is damaged, it acts as a template.

template strand

Function: to provide the correct sequence of amino acids in the protein by being read by enzymes during transcription.

Redundancy of the genetic code

The genetic code has redundancy as two or more mRNA codons can specify the same amino acid (degeneracy)

This means that there are more codons than amin acids so some codons will be redundant.

mutations

Permanent changes in the DNA base sequence

substitution mutations

mutation where the base in a DNA triplet is replaced with another

may result in:

* silent: codon being changed to one that encodes the same amino acid and causes no change in the protein produced
* missense: change a codon to one that encodes a different AA and alters the protein produced and its function
* nonsense: changes an amino acid coding codon to a STOP codon, resulting in an incomplete protein which will likely not function

insertion/deletion mutation

insertion: when a base is added into the base sequence

deletion: when a base is removed from the base sequence

frameshifts

single base insertions or deletions result in frameshifts, changing the reading frame of every DNA triplet from the mutation onwards, thus altering the the mRNA sequence and the amino acids coded for

* may change the structure of the protein, resulting in a non-functioning protein
* or alter start/stop codons, affecting the length of the polypeptide and thus the structure of the protein

if deletion or insertion involves 3 bases, it will affect a single amino acid and not cause a frameshift, but can still have a severe effect on protein structure as the midding/added AA can negatively affect the overall 3d folding of the prtein and the function.

position of a frame shift

A frame shift near the start of the gene will have a greater negative impact on the final protein due to dramatic changes in the AA sequence so more of the protein structure will be altered, especially if an early STOP codon occurs

* results in a non-functioning protein

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A frame shift near the end of the gene will result in most of the protein structure being coded for correctly and thus may still be functional (esp. if active site of enzyme is unaffected)

* however can affect the functioning of an enzyme if ti changes an amino acid in the active site

metabolic pathway

a series of enzyme-controlled biochemical reactions where the product of one reaction becomes the substrate for the next

enzyme

a biological catalyst that aids in chemical reactions by lowering the activation energy needed for the reaction to occur and also creates or controls metabolic pathways.

mutations in metabolic pathways

mutated gene/genotype → non-functional protein (e.g: enzyme) → impacts a step in metabolic pathway → absence of product or build-up of substrate = different phenotype