DNA – Genes, Transcription, Translation and Inheritance

The Central Dogma

DNA encodes mRNA – synthesised by transcription. mRNA encodes for proteins (amino acids) – synthesised by
translation. Triplet code is used - every 3 nucleotides on mRNA (codon) codes for an amino acid. Template strand – used
as a template for mRNA synthesis, we generally write the sequence code for the final protein on the coding strand (runs
5’-3’). mRNA is synthesised in the 5’-3’ direction but the template strand is read 3’-5’.

Gene

Has various definitions. The basic unit of inheritance, by which hereditary characteristics are transmitted from parent to
offspring. At molecular level – consists of a length of DNA (in some viruses, RNA) which exerts influence on organisms
form and function by encoding and directing the synthesis of a proteins, tRNA, rRNA or other structural RNA.

In its simplest form – a gene is a DNA sequence with a start/stop codon that is transcribed into mRNA and translated into
a polypeptide. Start/Stop codon – starts and stop transcription marking the start and end of the gene. The start codon of
any protein will always code for the amino acid “Met”. This makes the reading frame (where the translation of the first
codon begins) very important – single base shift will change amino acid sequence completely and may introduce new
stop codons.

Most amino acids are coded for by multiple codons – this gives the genetic code redundancy, allowing for some mistakes
to be make during transcription or in the code itself (silent mutation) as same amino acid may be produced. Transcription
starts upstream and continues downstream from the regions defined by stop/start codons – these are called 5’ and 3’
UTRs.

Prokaryotic genes are organised into operons. This is a series of genes which share a single enhancer, operator,
promoter, and silencer. The mRNA produced will have multiple protein coding regions (therefore multiple open reading
frames) that are translated into multiple proteins. This saves energy/time as these often code for enzymes/proteins
involved in the same pathway – this is polycistronic mRNA. Eukaryotic genes have a single ORF – each one having its own
promoter, enhancer etc. Also contains introns and exons, with the introns being spliced in various ways (junk DNA)
following transcription. This allows for alternative splicing, meaning one gene can code for multiple types of proteins.

Transcription

In prokaryotes – the entire central dogma is carried out in cytoplasm. In Eukaryotes – transcription occurs in the nucleus
– mRNA moves out to cytoplasm to bind to ribosomes. Transcription has 3 key steps.

Initiation: RNA pol binds to the promoter region of gene, specifically the TATA box – this contains bases with only 2 H
bonds holding them together – weaker than the 3 used in G/C bonding – easier to break apart. The DNA strands then
separate and unwind allowing RNA pol to synthesise a RNA transcript using the template strand of DNA. Elongation: the
RNA transcript continues to synthesise as RNA pol moves downstream. Termination – RNA pol reaches termination
sequence – drops off and the transcript is completed.

In prokaryotes – transcript can used for protein synthesis right away – in Eukaryotes this whole process is more
complicated. Firstly, transcription factors bind with RNA pol to create a transcription initiation complex – this is
necessary for transcription to start. Additionally, the mRNA produced is modified – non-coding sections of DNA are cut
out. Certain introns are spliced in different ways to make a variety of different transcripts from single coding sequence.
Additionally, a 5’ cap and 3’ poly-a tail are added for protection of the protein coding segment.
Translation

Once transcript is made – cell can use it for protein synthesis. In Eukaryotes – transcript must leave nucleus (following
RNA processing) before translation can take place. In Prokaryotes, protein synthesis happens right away, with no cap or
tail added. Additionally, mRNA may be polycistronic – producing multiple proteins.

mRNA binds to ribosomes subunits. The ribosomes bring tRNA to bind to mRNA with use of their anticodon. tRNA
carries amino acids that are associated/coded for by the codons present on mRNA. Within the ribosome 2 tRNA’s are
brought close enough together to allow for the addition of an amino acid to the growing polypeptide chain, once the
chain is passed on, the ribosome continues to move in the 5’ – 3’ direction and the now “empty” tRNA is discarded.

The proteins produced may have more than one domain. These domains serve different functions within that protein –
however these cross codon boundaries. Proteins then naturally fold into their secondary/tertiary structures – this may
be aided by the enzyme chaperonin. Post translational modifications also take place, with amino acids being altered by
adding sugars, lipids and phosphate groups. Proteins may also be cleaved or have subunits added to form a quaternary
structure (e.g. haemoglobin).

Types of DNA and Location

DNA – found in chloroplasts and mitochondria – these are endosymbionts which still maintain their own genome. In
prokaryotes there is Plasmid DNA – small circular pieces of self-replicating DNA. We also have environmental DNA
(eDNA) – found in soils, water, faeces and even air. These come from shed cells. Very useful for ecological surveying –
can use molecular methods to sequence DNA to work out what species exist in that area – “forensic ecology”. This can
also be used to identify what is in our food.

Prokaryotic genomes are arranged into nucleoids – this simply where the genome DNA is within the cytoplasm – a single
circular chromosome. It is supercoiled with help of architectural proteins (not histones). Non-essential genes are usually
found in the single circular DNA plasmids in the cytoplasm. Eukaryotic organelles resemble prokaryotes in their genome
organisation. Most prokaryotes contain only one copy of each gene – haploid. These genomes also contain less repetitive
DNA

In eukaryotes genomes – DNA in linear – packaged into multiple chromosomes with the aid of histone proteins. DNA +
histones make chromatin – which in then looped in domains to make chromosomes. All DNA in human cell would stretch
to 2m if not for this packing. Eukaryotes mostly contain two copies of each gene (diploid). There is also a significant
amount of noncoding and repetitive DNA.

Inheritance of DNA

Mendelian genetics covers the inheritance of chromosomal DNA – what about all the other types?

Mitochondrial DNA (mtDNA) – only comes down maternal line. This is because when the egg is fertilised – sperm does
not contribute a mitochondria to the cell. The Y chromosome only comes from the male side of the ancestors – this is
because females cannot inherit, and therefore pass on Y chromosomes without becoming a male.

Plasmids use a lateral method to be inherited. This is how bacteria have sex and are able to mix up genes, as their
primary mode of replication, asexual reproduction, does not allow this. This allows bacteria to adapt quickly to changing
environments. This involves plasmids called F plasmids (fertility) – have genes necessary for conjugation. Within this
plasmid are the genes to make a mating bridge from an F+ cell (a cell with the F plasmid) to an F- cell. The plasmid DNA
breaks at an indicated point and one of the strands peels off and transfers through the mating bridge. Both cells now
have a single strand they use as a template to make a complimentary second strand – meaning the F plasmid has been
inherited and both cells are now F+. In this way, antibiotic resistance can spread through bacteria populations.