DNA, Genes and Protein Synthesis
Structure of Nucleotides
A nucleotide is made out of three components: a sugar, a phosphate and a base.
The sugar is a pentose sugar. It is either ribose (found in RNA) or deoxyribose (found in DNA)
The base is one of 5 different organic nitrogenous bases. In DNA, these are either Adenine, Guanine, Cytosine or Thymine.
In RNA, thymine is replaced by uracil.
Cytosine, Thymine, and Uracil are categorised as pyrimidines (they have a single-ringed structure), whilst Adenine and Guanine are both purines (double-ringed structure.
Structure of ATP
All living organisms need energy to stay alive. This energy comes from the sun.
Plants use solar energy to combine water and carbon dioxide to form complex organic molecules during photosynthesis.
Both animals and plants break down these molecules in order to form adenosine trisphosphate (ATP).
ATP is the energy that is needed to maintain life on this earth.
ATP contains adenine (a base), ribose sugar and three phosphate groups.
Energy is defined as the “ability to work”.
It comes in a variety of forms, like for example heat, light, sound, electrical, chemical, and mechanical energy.
Energy can be changed from one type of energy to another.
Energy cannot be made or destroyed.
Energy is measured in J (Joules).
Energy is needed for a variety of things like for example:
Metabolism: all reactions in an organism
Building macromolecules from monomers
Movement: both within and of the organism
Energy for the movement of muscle filaments in a muscle contraption
Active transport of ions and molecules against a concentration gradient
Changing the shape of carrier proteins in plasma membranes.
Production of substances – e.g., hormones and enzymes
Maintenance of body temperature – in birds and animals because they are endothermic and need energy to replace that lost as heat to the environment.
Secretion – needed to form lysosomes for the secretion of cell products
Activation of molecules: when a Pi (inorganic phosphate) is transferred from ATP to another molecule, it makes it more reactive and therefore lowers its activation energy. ATP therefore allows enzyme catalysed reactions to occur more readily.
The reaction is reversible. ATP can be broken down into ADP (adenosine diphosphate) and Pi (inorganic phosphate), or it can be resynthesised again.
Bonds store energy, and when they are broken, they release it. ATP contains 3 phosphate groups which are unstable and so have low activation energy.
There are 3 ways the synthesis to ATP from ADP can occur
Photophosphorylation: this means it happens during photosynthesis in the chlorophyll
Oxidative phosphorylation: this happens in mitochondria during electron transfer.
Substrate-level phosphorylation: this happens in plants and animals when phosphate groups are transferred from donor molecules to make ATP from ADP
Due to the phosphate group's instability, it makes ATP an ineffective long-term energy store. It is therefore classed as an immediate energy source of a cell.
ATP can only supply energy for a few seconds.
This is not a problem because it can rapidly reform from ADP + Pi.
The features of an ATP molecule make it an biologically useful source of energy.
It allows energy to be released in suitably small amounts.
It releases energy on breakdown: it only needs a bond broken in a hydrolysis reaction, single-step
It is a useful energy carrier and can be used in many different chemical reactions
It is mobile and transports chemical energy to where it is needed in the cell.
Nucleic acids
Nucleotides join by bond formation between the sugar of one and the phosphate of the next to form a phosphodiester bond. This condensation reaction results in a chain of nucleotides called a nucleic acid, e.g., RNA and DNA.
RNA Molecules form single-stranded polynucleotide molecules.
DNA molecules consist of 2 polynucleotide strands twisted around each other in a double helix shape.
The strands twist in opposite ways. This makes them antiparallel to each other.
DNA Replication
DNA replicates using a process called semi-conservative replication.
This means: every new DNA molecule will have one original strand and one newly synthesized strand. The original DNA molecule acts as a template for the formation of the new strand.
Firstly, the two strands unzip. The hydrogen bonds are broken. This is all catalysed by the enzyme DNA helicase.
The exposed bases attract free nucleotides and new bonds are being formed.
Once in place, DNA polymerase catalyses linking up the nucleotides and DNA ligase catalyses phosphodiester bond formation between the two DNA strands.
This creates two new strands of DNA identical to the original molecule. These strands now coil up into a double helix structure.
Meselson and Stahl
Initially there were two ideas on how DNA replication could happen: either conservative or semi-conservative.
To test this theory Meselson and Stahl analysed DNA from multiple generations of E. coli bacteria.
They grew the bacteria with different isotopes of nitrogen.
They were exposed to N15 for several generations until they were exposed to a lighter N14.
Scientists could then distinguish between the different DNA by centrifuging it.
Any original DNA would be heavier and drop to the bottom, any new DNA would be lighter and be at the top
They discovered that the DNA in E. coli bacteria was semi-conservative.
Genetic code
DNA acts as genetic material and carries the information needed to make new proteins.
Using the DNA code, 20 amino acids are being put together in countless combinations to make many different proteins.
A gene is a section of DNA that contains the coded information for making polypeptides and functional RNA. Genes determine the inherited characters by coding for polypeptides.
This code is hidden in the bases along the DNA molecule and as DNA determines the sequence of amino acids.
The sequence of nucleotide bases forms a code.
Each code has three letters and is known as a triplet.
Each code codes for or represents a specific amino acid.
The code can be quoted as DNA triplets or RNA codons.
There are three features of the genetic code:
Non-overlapping code - the code is read in one direction, in 3s, and each base is only in 1 triplet.
Degenerate code - There are 64 codons however, only actually 20 amino acids; therefore, most amino acids are coded for by more than one triplet.
Universal code - The same code for every organism.
Parts of the gene that don’t take part in amino acid sequences are called introns. Parts that do are called exons.
Structures of RNA
Messenger RNA is also referred to as mRNA. mRNA is formed in the Nucleus and carries instructions for more than one protein.
Strands of mRNA form on the anti-sense strand of DNA during the process of transcription.
The mRNA is single-stranded and relatively short.
Transfer RNA (tRNA) is a clover-shaped molecule that is responsible for bringing in the required amino acids during translation.
It contains a binding site for the amino acid at one end and an anticodon at the other.
The anticodon consists of three bases that match up with the codon on the mRNA. This decides the order of amino acids in the resulting polypeptide chain.
DNA and Protein Synthesis
Transcription: The gene from which the cell wants the information to make a protein unwinds to expose the bases.
Free mRNA nucleotides in the nucleus base pair with one strand of the unwound DNA molecule. The mRNA copy is made with RNA polymerase.
This enzyme joins up the mRNA strands to make a mRNA strand. This strand is complimentary to the DNA strand.
The mRNA molecule leaves the nucleus via a nuclear pore into the cytoplasm.
Translation: First step, the mRNA attaches to a ribosome. Six bases of the mRNA are exposed.
A complimentary tRNA molecule with its attached amino acid (methionine) base pairs via its anticodon in the first position.
Another tRNA base pairs with the other three mRNA bases in the ribosome at the second position.
The enzyme peptidyl transferase forms a peptide bond between the two amino acids.
The first tRNA (without its amino acid) leaves the ribosome.
The ribosome moves along the mRNA to the next codon (three bases). The second tRNA molecule moves into the first position. Another tRNA molecule pairs with the mRNA, bringing its amino acid. A growing polypeptide is formed in this way until a stop codon is reached
The protein is finally formed.
Gene Mutation
Any change in the quantity or structure of the DNA is known as a mutation.
Silent mutations do not cause a change in the primary sequence of the polypeptide chain.
Mutations that occur during the formation of gametes may be inherited.
That causes discontinuous variation.
Any change in the sequence of bases is called a gene mutation.
Mutations have both advantages and disadvantages.
They provide genetic diversity necessary for natural selection and speciation.
They can also provide organisms that are well suited to their environment or those that can be lethal.
Substitutions: a DNA nucleotide is replaced by another.
Sickle cell anaemia is caused by a substitution point mutation which results in humans having abnormal haemoglobin.
The red blood cells become sickle shaped which impairs their ability to transport oxygen efficiently.
Deletion: a nucleotide is lost in the DNA sequence. This is known as a frameshift mutation. The reading frame that contains the three letters for the triplet has shifted. A deletion at the start of a sequence could alter every triplet that follows, whereas a deletion at the end may have fewer consequences.
Insertions: another base is added. This could be a repetition of a base or a different base entirely.
Chromosomal mutations can be changes in the number of chromosomes, usually arising in three or more sets of chromosomes rather than the usual two. This is known as polyploidy and occurs mostly in plants. We can also have a change in just one chromosome due to an individual pair of homologous chromosomes not separating during meiosis.
This is known as non-disjunction, resulting in the gamete having one more or one less chromosome, e.g., down syndrome, where a sufferer has 3 chromosome 21s.