 How does information flows in the cell?  What controls cell function?  Is it DNA, RNA, Proteins, Genes, Chromosomes or the Nucleus?

 All living things inherit genes from their parents.  The different types of genes, composed of segments of deoxyribonucleic acid (DNA) which distinguish one species from another.

DNA replication (S phase) occurs between two phases of growth (G1 and G2). G1 phase - cell makes many biochemicals and organelles. S phase – the enzyme DNA helicase unzips the helix of double-stranded DNA, exposing the nucleotide bases. The hydrogen bonds that hold the two strands of the DNA molecule are weak and the enzyme is easily able to separate them. The junction between the unwound single strands of DNA and the intact double helix is called the replication fork. The replication fork moves along the parental DNA strand so that there is a continuous unwinding of the parental strands.

 With in the nucleus, the stockpiles of free nucleotides attach to the exposed bases according to the base-pairing rule with the help of the enzyme DNA polymerase.  Another enzyme, DNA ligase, seals the new short stretches of nucleotides into a continuous strand that rewinds.

 Outcome of DNA replication = Two double - helix DNA molecules - one parental strand and one new strand.  One of the two strands is retained from one generation to the next, while the other strand is new.  This process is referred to as semi-conservative replication.

 In 1953, James Watson and Francis Crick suggested a possible structure for DNA. This was based observations of other scientists’ experiments.  Watson and Crick suggested that DNA consisted of two chains twisted around each other to form a double helix ladder, cross-linked by nitrogenous bases, of which there are four types: adenine (A), cytosine ( C ), guanine (G) and thymine ( T).  The discovery of DNA was a turning point in studies of inheritance.

 Coded information in DNA must be translated into a protein.  Proteins provide the essential link between DNA and the functioning cell.  The central role of DNA is to determine what proteins the cell makes. A protein consists of subunits of amino acids. Amino acid arrangement gives a protein its individuality and functionality. The DNA determines in what sequence the 20 different types of amino acids are put together in the protein.

 A single nitrogenous base does not specify a single amino acid.  Three nitrogenous bases (64 possible combinations) code for the 20 different amino acids commonly found in cells.  This triplet of bases is known as a codon; codons, or triplet codes, form the basis of the genetic code.

 DNA = instructions in the chromosomes in the nucleus  Ribosomes in the cytoplasm = make proteins.  Information on the codons in the DNA has to be conveyed from the nucleus through the nuclear membrane to the sites of protein synthesis in the cytoplasm.  The DNA stays in the nucleus and another molecule (mRNA) acts as a messenger and carries instructions from the DNA to the cytoplasm.  Messenger RNA, like DNA, consists of a string of nucleotides however differs from DNA in four ways:  RNA: DNA:  Contains the sugar ribose, - Contains sugar deoxyribose  Single-stranded- Double-stranded  Contains Uracil- Contains Thyamine  Shorter than DNA- Much longer than RNA

 Transcription of DNA generates a single- stranded RNA molecule that is identical in sequence with one of the strands of the double helix but with one difference.  DNA: Thymine usually pairs with Adenine  RNA: Uracil pairs with Adenine.  Transcription is similar to DNA replication  a small section of the DNA molecule unwinds and free-floating nucleotides bind to the strand. The sequence is complementary to the DNA strand.

 Transcription is different from DNA replication by:  Only a small part of a DNA strand is used as the template for the RNA strand.  Coding region of the DNA is a gene - DNA replication, involves the whole DNA molecule as the template.  The enzymes involved with holding the RNA nucleotides together are RNA polymerases rather than the DNA polymerases involved in DNA replication.  Only single-stranded RNA is produced in transcription. It is found both in the nucleus and cytoplasm in eukaryotic cells. DNA formed by replication is double-stranded and found only in the nucleus.

 The DNA first unwinds and then unzips exposing the nucleotide bases of both strands.  Only one strand used to direct the synthesis of mRNA - the template strand.  Other strand, of DNA origin, has the same sequence as the mRNA (except for T bases instead of U) and is called the non-template strand.  There is nucleotide sequence at the start of the gene, called a promoter which signals the start of a gene.  Proteins position RNA polymerase on to the DNA to bind with the promoter.  Complementary RNA nucleotides are progressively joined together by RNA polymerase moving along the length of DNA.  A base sequence at the end of the gene serves as a stop signal.  The mRNA is released as a single strand into the nucleus - called pre-mRNA  The DNA zips up and twists itself back into a double helix again once the mRNA has peeled off

 Before the mRNA leaves the nucleus a methylated cap is added to the 5’ end & about 100–200 adenine nucleotides (A) are added to the 3’ end – a poly-A tail.  After these additions some segments are removed.  Most eukaryotic genes have regions of base sequences that are not translated into the amino acids of proteins:  Introns - non coding & interspersed with regions of DNA  Exons – regions of DNA that contain the actual information for protein formation. Both the exons and introns are transcribed into pre-mRNA, but introns are removed by RNA splicing before the mRNA leaves the nucleus.  The average mRNA strand is about 1000–2000 bases long, including a methylated cap and 100–200 adenine bases in the poly-A tail.

Translation  The synthesis of proteins from mRNA  The process by which a ribosome assembles amino acids in a particular sequence to synthesise a specific polypeptide coded by the mRNA.  mRNA attaches itself to a ribosome (in cytoplasm)  amino acids assembled in a particular order.  Ribosomes are made up of two subunits, one small and one large. The nucleus assembles them both from ribosomal RNA (rRNA) and proteins in the nucleus so to participate in translation.

 Needed for protein synthesis.  Transfer or carry amino acids to ribosomes.  Exist as free-floating molecules within the cytoplasm  Do not have a line ararrangement of nucleotide bases. They are folded back on themselves to form a compact three-dimensional structure like a clover leaf  Has three nucleotide bases at the bottom called the anticodon, and an amino acid binding site at the top.  The anticodon of the tRNA is complementary to the codon of the mRNA.  Cells possess over 20 different types of tRNAs – more than enough for the different types of amino acids.  The type of amino acid picked up by RNA is related to the sequence of the anticodon. E.g. ACG = Cysteine (see figure 8.14, pg253)

 A small ribosome subunit loaded with an initiator tRNA (one that can start the process) recognises an mRNA strand as it leaves the nucleus and travels to the cytoplasm.  The ribosome subunit bonds to the methylated cap on the mRNA and moves along it ‘scanning’ for a n AUG start - once found, a large ribosomal subunit joins with the small one.  Ribosome passes along the mRNA strand and, as it passes each codon in the mRNA, a tRNA, carrying the appropriate amino acid, moves to the ribosome.  The three bases in the mRNA codon bond to the complementary anticodon on the tRNA molecule.  The ribosome then moves along adding more amino acids to the growing polypeptide chain.  Once aligned, peptide bonds form between adjacent amino acids  polypeptide chain.  The completed polypeptide chain peels off from the tRNA molecules and then the tRNA molecules detach themselves from the mRNA and return to the pool of tRNAs in the cytoplasm.  On reaching a stop codon the ribosome releases the mRNA strand and the newly synthesised polypeptide chain.

 The genetic code shows the relationship between the triplets of bases in mRNA (i.e. the codons) and the amino acids that are translated from the mRNA code.  Most amino acids are coded for by more than one codon.  Three of the codons do not code for an amino acid, instead they stop the polypeptide chain at that point – called stop codons.