BMS04 - Genes and genetic expression :lock: (Nucleic Acids: DNA structure,…
BMS04 - Genes and genetic expression :lock:
Nucleic Acids: DNA structure
The structure of DNA contains these elements; Carbon, Hydrogen, Oxygen, Nitrogen and Phosphate.
The structure and features of DNA was able to be discovered by a number of important experiments often using bacteria as they're easily manipulated and reproduce quickly.
Griffith et al
Avery et al
Maurice and Wilkins
Watson and Crick
The structure of DNA for a long time was disputed due to every concept seeming too simple.
The information will also be able to store large quantities of information.
Sequencing genomes of RNA/DNA is an important tool. A genome is the entire set of genes in the chromosomes of an organism.
The information stored must be able to be expressed.
Genetic material needs the ability to replicate.
Genetic material needs the ability to have variation; this is done by mutations.
DNA is an anti-parallel double helix with the basic unit being a nucleotide. The major difference between a nucleoside and a nucleotide is that a nucleotide has a phosphate. A nucleotide consists of:
A pentose sugar e.g a ribose for RNA or a deoxyribose for DNA.
Phosphate group(s), there can be more than one phosphate group and these give nucleic acids their acidity.
A nitrogenous base; either the purines (which are adenine and guanine) or the pyrimidines (Cytosine, Thymine and Uracil).
These are in the middle of the strand paired by hydrogen bonds. Certain bases are complementary with eachother (A with T and C with G).
The G-C pairing requires more energy to cleave as there are three hydrogen bonds compared to the A-T pairing which has two hydrogen bonds.
A nucleoside is phosphorylated by specific kinases; deoxynucleotide triphosphates (dNTPs) are the basis of building DNA.
These dNTPs are able to form strong phosphodiester bonds with eachother. The 3' hydroxyl with the 5' hydroxyl of another dNTP via a phosphate group.
DNA is unidirectional. It is read in a single direction from the 5' end to the 3' end. This is due to the polarity of the strand caused by phosphodiester bonds.
The double helix consists of two complementary strands coiled around a central axis. It is described as antiparallel as the 5' of one strand is paired to the 3' end of the other.
The helix is right handed with 10 nucleotides per turn with each turn being 3.4nm with a diameter of 2nm.
The helix can be separated by denaturation. This the disruption of the hydrogen bonds holding the strands together.
DNA comes in three forms and the transition between these forms namely B and Z is thought to be crucial to regulating gene expression.
A form - This form is similar to the B form but has been moderately dehydrated. This has 11 base pairs per turn and is found in DNA and RNA hybrids.
Z form - This is a left-handed helix with 12 pairs per turn. This the phosphodiester backbone 'zig-zags' and this form is caused by DNA have regions of alternating purines and pyrimidines.
B form - The form of DNA we are used to seeing. This is a right-handed helix described by Watson and Crick. Chromosomal DNA is predominantly B type.
DNA is found in the nucleus and mitochondria of eukaryotes. Whilst in prokaryotes e.g. bacteria, it is found in the cytoplasm. In plants however, DNA is found in the chloroplasts and nucleus.
Eukaryotic DNA is packed into chromosomes. These are long linear molecules of double-stranded DNA bonded to proteins called histones to form chromatin.
Prokaryotes have their DNA in a circular chromosome. This chromosome is single-stranded and super- coiled bonded to proteins to form nucleoids. They also have extra-chromasomal DNA in the form of plasmids.
Chloroplasts and mitochondria have closed, circular DNA.
The transfer of genetic information all stems from DNA.
DNA can be used to pass on genetic traits by inheritance. In this instance, DNA is used in
, in order to get more copies.
DNA replication is the mechanism in which DNA makes a 'copy' of itself during cell division and proof-reads itself to maintain a high fidelity.
DNA replication occurs in specialized regions of a cell, requiring many proteins found in the nucleus often called a 'replication factory'.
DNA replication is
. This means that each of the daughter strands contain a single parent strand.
In order for replication, the DNA needs to be unwinded and this done using
, which breaks the hydrogen bonds between bases. Each single parent strand will become a template for a new DS DNA.
The mechanism was discovered by studying E.Coli.
DNA polymerase uses DNA as a template to make exact copies and works from the 5' to 3' direction. Adds deoxynucleotide triphosphates to the 3' prime end of the sugar-phosphate backbone with pyrophosphate being released.
DNA polymerase is able to proof-read from the 3' to 5' direction using an exonuclease enzyme.
DNA polymerase requires certain ingredients to work effectively however, on it's own it is
capable of only extending a DNA strand
Single-stranded binding proteins
are tetramers which bind to SS DNA to ensure it cannot anneal back together.
releases supercoils in DNA.
unwinds the DNA helix into two separate strands.
is an RNA polymerase which makes short-chained RNA primers required to get replication started.
The DNA sliding clamp
help the DNA polymerase remain on the strand it's copying.
helps remove the RNA primers.
links strands together by the formation of phosphodiester bond.
DNA replication must occur
mitosis/meiosis so each daughter cell can be given a genome. Therefore, it occurs in the S stage of cell division usually taking 8-9 hours.
DNA is also required for the
of genes. To do this, RNA must be made and from here -
DNA polymerase can make mistakes. Approximately 1 in a million base pairs are wrong but thanks to the the exonuclease proof reading, the chance is reduced. Nevertheless, there is always a low risk of mutation. Mutations can be bad leading to a higher predisposition to diseases e.g. Colon cancer.
For replication to begin, the strands are separated using a helicase. This then creates a site known as the 'origin of replication'.
There will be many of these sites along the DNA helix which will then form a replication fork.
Single stranded binding proteins prevent the SS's from annealing. Replication begins here in both directions forming complementary strands of DNA.
DNA polymerase can only go from the 5' to 3' direction so how can DNA be replicated on both strands simultaneously if one is in the wrong orientation? It relies on
using Okazaki fragments.
One strand is copied like normal or continuously which is called the
whilst the other is done discontinuously in small fragments (Okazaki fragments) due to the unidirectionality of DNA polymerase; this is the
The lagging strand will have a series of Okazaki fragments and RNA primers. Once the primers are removed, there are missing phosphodiester bonds which DNA ligase is able to join.
Discontinuous rep. 1
Discontinuous rep. 2
Origin of replication and replication forks
As DNA polymerase can only go from 5' to 3', the end of the lagging strand will not be able to be copied, this is potentially problematic. To combat this, chromosomes have
Telomeres are repeat sequences at the end of chromosomes. Telomerase is the enzyme required to add these sequences on. Defects with the telomerase enzyme is thought to be involved in ageing.
OVERALL, DNA replication processes here.
Transcription and Translation
The central dogma of molecular biology is that DNA makes RNA via transcription and that RNA codes for proteins using translation. However, due to reverse transcriptase - information doesn't have to flow in a single direction.
DNA is used to make mRNA. mRNA can then be translated into proteins - this is how protein synthesis occurs from DNA. DNA is composed of four bases (ATGC) which make three-lettered combinations called
Individual codons code for an individual amino acid. The entire genetic code consists of 64 codons - these 64 codons are used to synthesise the essential amino acids. The code is not entirely universal in all organisms; an exception being mitochondria.
The genetic code has a degeneracy. This means that an amino acid can be coded by
more than one codon
except methionine. This is usually due to variation in the third base (3rd base wobble).
of a peptide is important. As reading from a different starting point can drastically change a protein - each protein has
different reading frames.
There are three types of RNA which are distinguished using gel electrophoresis.
tRNA (Transfer RNA) is the second most abundant form of RNA (15%).
tRNA is rather small in size and has a distinct cloverleaf structure due to internal hydrogen bonding.
It transfers an amino acid from the amino acid pool in the cytoplasm to a ribosome
. It is able to interpret the codons on mRNA and presents an
. The anti-codon then binds to the mRNA, releasing the amino-acid to the ribosome for protein synthesis.
mRNA is the least abundant form of RNA in the body (3%).
mRNA acts as a 'messenger' by carrying genetic information from DNA to the ribosomes. They tend to have a PolyA tail on their 3' end, ORF is the coding portion whilst UTR is the non-coding portion.
rRNA (Ribosomal RNA) is the most abundant in the body (71%).
This form of RNA is structurally important in ribosomes.
Transcription is the process in which RNA is made from DNA.
DNA unwinds and exposes a portion of the bases on each strand.
One strand then acts as a template for transcription to begin.
RNA transcript is elongated; one nucleotide at a time. As the chain is made, DNA slowly begins to reform. The singly-stranded RNA is then released. This will only code for a
gene in eukaryotes.
RNA production in bacteria is quite different and relies on
to produce a copy of DNA.
It is a three step process that results in a '
' which is able to code for more than one gene.
In reality, transcription is a lot more involved and has a number of important steps.
For eukaryotes, transcription is more complex. RNA is made in the nucleus but transcription requires the formation of a
transcription initiation complex (in prokaryotes also)
RNA polymerase II
. mRNA also requires a few maturation processes.
is the first maturation process. It involves the addition of a 'cap' by chemically modifying the 5' end. It requires a 5' to 5' linkage triphosphate bridge by the addition of 7-methyl guanosine- this prevents the RNA from being degraded by exonucleases and assists in transport.
The pre-mRNA must also go under
. DNA contains discontinuous genes with both coding regions (exons) and non-coding regions (introns) and so during transcription, all is copied. Usually all introns are removed but also exons may be selectively removed to alter the final peptide.
also occurs. It depends on a number of proteins which add on a PolyA tail at the 3' end. This aids primarily with transport and stabilisation.