Nucleotides
Both DNA and RNA are made up of monomers called nucleotides |
Each nucleotide contains a phosphate group, a nitrogen-containing organic base, and a pentose (5-carbon) sugar: either ribose (RNA) of deoxyribose (DNA) |
There are 2 groups of organic bases: Pyrimidines (single ring) and purines (double ring) |
For nitrogenous bases found in DNA: |
- Guanine (Purine) |
- Cytosine (pyrimidine) |
- Adenine (purine) |
- Thymine (pyrimidine) |
In RNA the pyrimidine uracil replaces thymine |
ATP
Adenine triphosphate is also a nucleotide: it has a ribose sugar joined to the adenine base, with three phosphate groups attached. |
When the high-energy bond between the second and third phosphate group is broken via hydrolysis by the enzyme ATPase, 30.6Kg of energy is released for use in the cell, and adenine diphosphate is formed. |
This reaction is reversible, requiring energy from respiration of glucose to reform the bond |
Structure of DNA
DNA consists of 2 polynucleotide strands that are arranged into a double helix. |
First a dinucleotide is formed when a condensation reaction occurs between 2 nucleotides: |
The 5th carbon atom of a deoxyribose sugar is joined to the 3rd carbon atom of the deoxyribose sugar of the nucleotide above it, via the phosphate molecule. |
This continues, building a single strand of DNA in the 5'-3' direction. |
DNA then forms a double-stranded molecule from two strands: one strand runs in the opposite direction to the other (anti-parallel). |
Both strands are held together by hydrogen bonds that form between complimentary nitrogenous bases. |
The double strand then twists to form a double helix. |
Bases between both stands pair up in a certain way which is called the complementary base pairing rule: |
Guanine forms hydrogen bonds with an adjacent cytosine molecule and adenineforms hydrogen bonds with an adjacent thymine molecule. |
Hydrogen bonds are weak, but the sheer number of them present in a molecule of DNA over a million nucleotides long, means that collectively they are very strong. |
In fact you would need to heat DNA to over 95 degrees C to break them all. |
Advantages and roles of ATP
Advantages of ATP: |
Energy is released quickly from a one-step reaction involving just one enzyme (hydrolysis of glucose takes many steps) |
Energy is released in small amounts, 30.6KJ where it is needed. By contrast just one molecule of glucose contains 1880KJ which couldn't safely be released all at once. |
It is the 'universal energy currency', i.e. it's a common source of energy for all reactions in all living things. |
Roles of ATP in cells: |
Used in many anabolic reactions, e.g. DNA and protein synthesis |
Active transport |
Muscle contraction |
Nerve impulse transmission |
Key Term
Codon |
The triplet of bases in mRNA that codes for a particular amino acid, or a punctuation signal. |
Introns |
Non-coding nucleotide sequence in DNA and pre-mRNA, that is removed from pre-mRNA, to produce mature mRNA. |
Exons |
Nucleotide sequence on one strand of the DNA molecule and the corresponding mRNA that codes for the production of a specific polypeptide. |
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Extracting DNA
DNA can be easily extracted from cells by grinding up a sample in a solution of ice cold salt and washing up liquid. |
The detergent dissolves the lipids in the phospholipid membranes, allowing DNA to be released, and the cold temperature protects the DNA from cellular DNAases. |
Addition of protease will digest any remaining cellular enzymes and the histones that the DNA is wound around. |
Finally, adding ethanol to the salt already present, will cause the DNA to precipitate out from the solution. |
Structure of RNA
RNA is usually shorter than DNA and single-stranded. |
Nucleotides also differ in that the sugar is ribose, the one base thymine replaced with uracil. |
Three different types of RNA are involved in protein synthesis. |
Types of RNA
mRNA |
Messenger RNA is a single-stranded molecule typically 300-2000 nucleotides long. It is produced in the nucleus using one of the DNA strands as a template during transcription. |
rRNA |
Ribosomal RNA forms ribosomes with the addition of protein. |
tRNA |
Transfer RNA is a small molecule that winds itself into a cloverleaf shape. It has an anticodon at one end, and an amino acid at the other. As the name suggests, it 'transfers' the correct amino acid to the growing polypeptide during translation. |
Process of semi-conservative DNA replication
The process requires ATP, free nucleotides and enzymes. |
- DNA helicase breaks the hydrogen bonds between the bases causing the double helix to unwind and separate into two strands. |
- The exposed bases bind to free floating nucleotides in the nucleoplasm. |
- DNA polymerase binds the complimentary nucleotides (forming the phosphodiester bond). |
- One strand acts as the template for the new molecule, so newly synthesised DNA contains one parent strand and a complimentary newly synthesised strand. |
Functions of DNA
DNA has 2 main functions in organisms |
1. Protein synthesis - the sequence of bases in one strand, called the template strand, determines the order of amino acids in the polypeptide (primary structure). |
2. Replication - when cells divide, a complete copy of the DNA in the cell needs to be made. Both DNA strands separate and each strand acts as a template to synthesise a complimentary strand. |
Three theories for how DNA replicates have been proposed: |
1. Conservative replication: original parent stranded molecule is conserved, and a new double-stranded DNA molecule synthesised from it. |
2. Semi-conservative replication: parental strands separate, and each strands acts as a template to synthesise a new strand. The new molecule consists of one original parent strand and one newly synthesised strand. |
3. Dispersive: the newly synthesised molecules contain fragments from the original parent strand and newly synthesised DNA. |
Key Term
Silent Mutation |
A change in the sequence of nucleotide bases without a subsequent change in the amino acid. |
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Meselson-stahl experiment
1. Grow bacteria on a 15N is a heavy isotope of nitrogen so all DNA produced would be a heavier weight than normal. When DNA was extracted by centrifuging in caesium chloride, the DNA band appeared low down in the tube. |
2. Bacteria were then grown on a 14N medium (normal weight nitrogen), and after one generation the DNA extracted formed an intermediate band half way up the tube. This is because the DNA molecule contained one strand from the heavy parent and one newly synthesised light DNA strand. (Because one band was produced this rules out conservative replication). |
3. The bacteria were grown for a further generation using 14N medium. The DNA extracted formed an intermediate band half way up the tube, and a lighter band towards the top of the tube. Because half of the DNA was intermediate weight and half light, this rules out dispersive replication. |
4. DNA therefore replicates semi-conservatively. |
5. If grown for further generations using 14N medium, whilst intermediate weight DNA would remain, the proportion of light DNA produced would increase. |
Meselson-stahl experiment diagram
DNA replication theories
The Genetic code
The sequence of nucleotide bases forms a code. |
Each 'code word' has 3 letters called a triplet code or codon, which codes for a specific amino acid. |
Genetic code examples:
DNA codon |
mRNA codon |
Amino acid that is coded for |
Amino acid abbreviation |
GGG |
CCC |
Proline |
Pro |
CGG |
GCC |
Glycine |
Gly |
ATG |
UAC |
Tyrosine |
Tyr |
TAC |
AUG |
Methionine |
Met |
ACT |
UGA |
Stop |
The Genetic code part 2
There are 20 amino acids that are coded by 4power3 bases, i.e. 64 different combinations of A, G, C, T(U). |
Therefore, there are 'spare' base codes. |
This is referred to as degeneracy or the 'degenerate code'. |
This code is universal, i.e. it is the same in all living things. |
One codon acts as a START codon, marking the point on the DNA where transcription begins - this is AUG on the mRNA and codes for methionine. |
Each gene found on the DNA will code for a different polypeptide: this is called the one gene, one polypeptide hypothesis. |
Post-translational modification
Translation produces a polypeptide, but further modification is needed in order to produce a protein with a secondary, tertiary or quaternary structure. |
This modification occurs within the Golgi body. |
Modification also occurs to produce molecules such as glycoproteins, lipoproteins, and complex quaternary structures such as haemoglobin. |
To form haemoglobin, 2 alpha chains and 2 beta chains (coded by 2 different genes) need to be assembled together with iron as a prosthetic group. |
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Protein Synthesis
Transcription occurs in the nucleus. |
Translation occurs at the ribosomes. |
Post-translational modification occurs in the Golgi apparatus prior to packaging of the protein into vesicles. |
Transcription
DNA acts as a template for the production of mRNA. |
DNA helicase acts on a specific region of the DNA molecule called the cistron, breaking the hydrogen bonds between both DNA strands, causing the strands to separate and unwind, exposing nucleotide bases. |
Free RNA nucleotide pair to exposed bases on the DNA template strand and RNA polymerase joins them by forming the phosphodiester bonds between the phosphate group on one nucleotide and the ribose sugar on the next. |
This continues until the RNA polymerase reaches a STOP codon, when the RNA polymerase detaches and production of mRNA is complete. |
The mRNA strand leaves the nucleus via the nuclear pores and moves to the ribosomes. |
Introns and Exons
In eukaryotes, introns are present within many genes so are also transcribed producing pre-mRNA. |
The coding regions are referred to as exons. |
The pre-mRNA is spliced to remove the non-coding regions before passing to the ribosomes. In prokaryotes, the DNA does not contain introns, and so the mRNA is produced directly from the DNA template. |
Translation
Involves another specific RNA molecule called transfer RNA (tRNA). |
At one end of the tRNA molecule there are 3 exposed bases called the anticodon, these are complimentary to the mRNA codon. |
At the opposite end of the tRNA molecule is an amino acid attachment site where the relevant amino acid is found. |
The attachment of the relevant amino acid to the attachment site is called amino acid aviation and requires ATP. |
Translation involves converting the codons on the mRNA into a sequence of amino acids known as a polypeptide. |
Each ribosome (found free in the cytoplasm, or attached to the rough endoplasmic reticulum) is made up of 2 subunits made from ribosomal RNA and protein. |
The mRNA binds to the smaller subunit, whilst tRNA to one of 2 attachment sites on the larger subunit. |
The process of translation
Initiation: ribosome attaches to the START codon. |
tRNA molecule with a complimentary anticodon to the first codon to the first codon, binds to the first attachment site on the ribosome. |
A second tRNA molecule joins to the second attachment site, and a ribosomal enzyme catalyses the formation of a peptide bond between the 2 amino acids. This is known as elongation. |
The first tRNA molecule is released and the ribosome now moves one codon along the mRNA, which exposes a free attachment site and another tRNA molecule joins and the process is repeated. |
This repeats until a STOP codon is reached, when the polypeptide is released. This is called termination. |
Usually several ribosomes bind to a single mRNA strand at the same time. This is called a polysome. |
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