ATP

• ATP is a nucleotide.

• ATP stands for adeninosine triphosphate, as it contains the base adenine, the sugar ribose and three phosphate groups.

Energy

• When ATP is required in the bond, the enzyme ATPase hydrolyses the bond between the second and third phosphate groups, making adeninosine disulphate (ADP) and one inorganic phosphate ion.

• Every mole of ATP releases 30.6 kJ of energy, making it an exergonic reaction (releases energy).

• This reaction is reversible. This is done through a condensation reaction, with the enzyme ATP synthetase, ADP and an inorganic phosphate ion. It results in ATP and a water molecule.

• This reaction, the addition of phosphate to ADP is known as phosphorylation and is a endergonic reaction, as it takes in energy from it's surroundings.

• ATP transfers energy from energy-rich compounds such as glucose to where they are needed in cellular reactions.

• These transfers are inefficient and produce heat energy, which would destroy cells if uncontrolled.

• Therefore energy is released gradually in a series of small steps called respiration, which produces ATP.

ATP vs glucose

• ATP only needs one reaction to produce energy, where glucose requires many intermediates and takes longer.

• ATP needs one enzyme, while glucose requires many.

• ATP releases small amount of energy where and when it is needed, glucose releases it in large amounts.

• ATP is a common source of energy of energy for many chemical reactions, increasing cell control and efficiency.

Roles

• Metabolic processes.

• Active transport.

• Movement.

• Nerve transmissions.

• Secretion.

DNA

Structure

• The structure was discovered by Watson and Crick, although they used Franklin’s work without credit.

• DNA stands for Deoxyribose Nucleic Acid, as it contains deoxyribose as it’s pentose sugar.

• DNA is a polymer, built up of nucleotide monomers. Each nucleotide consists of one phosphate, one sugar and one organic base. This makes it a polynucleotide.

• There are four different bases, and two complementary base pairings; adenine and thymine, and cytosine and guanine.

  • The complementary bases are held together by weak hydrogen bonds, which therefore hold the two polynucleotide strands together.

  • Adenine and thymine have two hydrogen bonds, guanine and cytosine three.

  • The largest bases, adenine and guanine, are described as purines. This is because they have two nitrogen containing rings.

  • The smallest bases, thymine and cytosine, are described as pyrimidines. This is because they have a single nitrogen containing ring.

• Nucleotides form strong covalent bonds with the phosphate of one nucleotide and the phosphate of another.

  • The chains run in opposite directions to each other, known as antiparallel strands.

  • The distance between the two backbones doesn’t vary along the length of the whole molecule, which perfectly accommodates the space needed for a purine-pyrimidine pair.

  • The strands are coiled into a double helix.

Triplet code

• DNA codes for proteins, by copying to DNA and using to sequence to decide the amino acids.

• There is 20 amino acids, and each ones have different codes.

• It is also known as a degenerate code, as amino acids can be coded for by more than one triplet code.

• The codes are made of three letters, with 64 different possibilities. One of these triplet is known as a codon.

• There is a start code that is the same for each protein, known as met. There are also three end codes.

• This code was discovered by Crick and colleagues.

Replication

• DNA replicates in order to perform meiosis and mitosis, which are needed for growth, repair and reproduction.

• DNA uses a semi-conservative replication, known as this as half of the two new strands are built up of the old strand.

• There are three enzymes used during the replication.

• The enzyme DNA helicase attaches to the DNA molecule and moves along its length.

  • This separates the hydrogen bonds holding together the strand, and splits it apart.

• Free nucleotides are attracted to the exposed strand, with ATP activating their movement.

  • Nucleotides are attracted to the complementary base pairing, so A to T and C to G.

  • DNA ligase is used to help match and lay down nucleotides to build the new daughter strand.

• DNA polymerase binds the DNA fragments together by forming phosphate bridges.

• This process was proven by Meselson and Stahl.

  • They used e-coli bacteria and created parent DNA molecules of N15, which is a heavy isotope of nitrogen. This was created by growing e-coli on a N15 medium for many generations.

  • They then placed it in a growing medium where only N14 nitrogen existed.

  • Between each generation, they used a density gradient centrifugation. This is when the tubes are spun in a centrifuge, and observed under only UV light. During the process, the DNA molecules move to where their density corresponds with caesium chloride solution.

• They looked at four generations:

  • Parent generation - contained only N15 only DNA.

  • F1 - contained hybrid N15 and N14 DNA.

  • F2 - contained half hybrid N14 and N15 DNA and half N14 only DNA.

  • F3 - contained 25% hybrid N15 DNA and 75% N14 DNA.

• This was done as there were three main theories of DNA replication at the time:

  • Conservative - the old strand remains as a completely identical strand is made.

  • Dispersive - DNA strands are made from fragments of new and old strands.

  • Semi-conservative - one old strand remains, and one is completely new.

• This proved semi-conservative, as there was new DNA created and the DNA didn’t remain hybrid.

Function

• DNA is extremely stable and information asses virtually unchanged.

• It is a large molecule as it carries a large amount of genetic information.

• The two strands can easily separate due to weak hydrogen bonds, allowing for easier replication.

• The base pairs are protected by the deoxyribose-phosphate backbones.

RNA

Overview

• RNA stands for ribonucleic acid.

• It is a single stranded polynucleotide, resembling a singular DNA strand.

• It uses the pentose sugar ribose.

• It uses adenine and guanine as purine bases and cytosine and uracil as pyrimidine bases, excluding thymine.

• The main role of RNA is protein synthesis.

• There are three types:

Messenger RNA (mRNA)

• It is synthesised in the nucleus and carries the genetic code from the DNA to the ribosomes in the cytoplasm.

• These strands are different lengths based on the lengths of the genes they are transcribed from.

Ribosomal RNA (rRNA)

• Found in the cytoplasm and comprises large, complex molecules.

• They make up ribosomes, along with protein. They are the site of translation of the genetic code into protein.

Transfer RNA (tRNA)

• A small molecule, made up of 75-90 nucleotides and forms a ‘clover-leaf‘ shape.

• It folds so that in certain places there are complementary base pairings.

• It has an anticodon, which allows it to interact with molecules of mRNA.

• At the opposite end of the molecule is an amino acid binding site, which are carried and eventually form polypeptide chains during protein synthesis.

  • This is done as the tRNA transfers them to ribosomes during protein synthesis.

Protein synthesis

• There are two stages:

  • Transcription - a strand of DNA acts as a template for mRNA production, this occurs in the nucleus.

  • Translation - the mRNA strand moves to a ribosome and acts as a template for complementary tRNA molecules to deposit amino acids, which are linked to form a polypeptide.

Transcription

• Transcription rewrites DNA as a new strand in order to transport it out of the cell, as DNA is too large and valuable to leave the nucleus.

• This happens in 4 steps:

  • DNA helicase splits hydrogen bonds between the bases, unwinding the strands and exposing the bases.

  • RNA polymerase binds to the template strand of DNA to copy it. Free ribonucleotides align with the bases in complementary pairs, with uracil bonding to adenine instead of thymine.

  • RNA polymerase forms bonds to add bases to the RNA strand, synthesising a molecule of mRNA along the DNA behind the RNA polymerase, the DNA strands reform the double helix.

  • Once a stop codon is reached, the RNA polymerase separates from the template strand. Production of mRNA is complete and it moves out of the nuclear pores towards a ribosome.

Exons and introns

• In eukaryotes, RNA must be processed before synthesising a polypeptide.

• Before it is processed, it is known as pre-mRNA, and is much longer than the final strand.

• Some parts, known as introns, do not code for any polypeptides. It is also known as junk DNA, and is suspected to be evolutionary leftovers. Around 97% of DNA is introns.

  • These parts are removed by RNA polymerase using endonucleases.

• The parts that are left behind do code for polypeptides and are known as exons.

  • These are spliced together using ligases.

Translation

• Translation begins once the mRNA has reached a ribosome. It occurs using the sequence of codons to organise the amino acids, which forms a polypeptide.

  • Also used in this process is tRNA.

• The ribosome has two subunits, one larger as it has two sites for tRNA attachment and one smaller which binds to the mRNA strand.

• The ribosome moves along the mRNA and adds one amino acid at a time, holding the codon-anticodon complex together until they bind. This occurs in three stages.

  • Initiation:

    • The ribosome attaches to the start codon on the mRNA.

    • A tRNA with a complementary anti-codon to the first mRNA codon attaches to the ribosome. The bases bond together using hydrogen bonds, creating a codon-anticodon complex.

    • A second tRNA attaches at the other attachment site, which is complementary to the second mRNA codon.

  • Elongation:

    • The two amino acids are close enough for a ribosomal enzyme to catalyse a peptide bond between them.

    • The first tRNA leaves the ribosome and therefore it’s attachment site vacant. It returns to the cytoplasm and binds to another copy of its specific amino acid.

      • This requires ATP, and is a process known as amino acid activation.

    • The ribosome then moves one codon along the mRNA strand and the next tRNA binds to the attachment site.

  • Termination:

    • The first two processes repeat until a stop codon is reached.

    • The ribosome-mRNA-polypeptide complex separates.

• Usually several ribosomes are attached to one mRNA strand, all reading the information at the same time. This is called a polysome.

• Each ribosome produces a separate polypeptide.

Post-translational modification

• The polypeptide chain is only a primary structure protein, and while usually functional, must be chemically modified or folded into secondary, tertiary and quaternary structures in order to fit it’s purpose.

  • It is chemically modified in the golgi body and folded in the ER.

  • It can be modified to combine with non-proteins, such as carbohydrates to make glycoproteins, lipids to make lipoproteins and phosphate to make phospho-proteins.

Theories

• In the 1940s research began into how DNA encoded information. Experiments on fungi showed that radiation damage to DNA prevented a single enzyme from being made, leading to the one gene-one enzyme hypothesis.

  • As enzymes are a type of protein, this was expanded to become the one gene one-protein hypothesis.

• However, as some proteins require multiple polypeptides, this became the one gene one-polypeptide hypothesis.

  • This defines a gene biochemically: a sequence of DNA bases that codes for a polypeptide.