Revise Passage of information from parents to offspring for Cambridge 9700 (16.1)

Deoxyribonucleic acid (DNA) is the primary genetic material in all living organisms. It's a polymer made of repeating monomer units called nucleotides. Each DNA nucleotide comprises three components:

1. A deoxyribose sugar (a pentose).
2. A phosphate group.
3. One of four nitrogenous bases: Adenine (A), Guanine (G), Cytosine (C), or Thymine (T).

DNA exists as a double helix, a spiral ladder structure. The 'uprights' of the ladder are formed by alternating sugar and phosphate groups, linked by strong covalent phosphodiester bonds – this forms the sugar-phosphate backbone. The 'rungs' are formed by pairs of nitrogenous bases, joined by weaker hydrogen bonds. Adenine always pairs with Thymine (A-T) via two hydrogen bonds, and Guanine always pairs with Cytosine (G-C) via three hydrogen bonds. This specific pairing is known as complementary base pairing. The greater number of hydrogen bonds in G-C pairs makes regions of DNA rich in G-C content more stable than A-T rich regions.

The two strands of the DNA helix run in opposite directions, meaning they are antiparallel. One strand runs in the 5' to 3' direction, while the other runs 3' to 5'. The 5' and 3' designations refer to the carbon number on the deoxyribose sugar to which the phosphate group (5' carbon) or a hydroxyl group (3' carbon) is attached.

Before a cell divides, its DNA must be accurately replicated to ensure each daughter cell receives a complete set of genetic instructions. DNA replication is a semi-conservative process, meaning each new DNA molecule consists of one original (parental) strand and one newly synthesised strand.

The process unfolds in several key steps:

1. Unwinding: The enzyme DNA helicase unwinds the double helix at a specific origin of replication by breaking the hydrogen bonds between complementary base pairs, separating the two DNA strands. Single-strand binding proteins attach to the separated strands to prevent them from re-annealing.
2. Template strands: Each separated strand then acts as a template for the synthesis of a new complementary strand.
3. Elongation: Free nucleotides in the nucleoplasm align with their complementary bases on the exposed template strands (A with T, G with C).
4. Polymerisation: The enzyme DNA polymerase catalyses the formation of phosphodiester bonds between the sugar and phosphate groups of adjacent new nucleotides. It adds nucleotides to the 3' end of the growing strand, thus synthesising the new strand in the 5' to 3' direction.
5. Rewinding: The newly synthesised strands wind together with their template strands to form two new, identical DNA double helices.

Leading and Lagging Strands

Because the two DNA strands are antiparallel and DNA polymerase can only synthesise in the 5' to 3' direction, replication occurs differently on each strand.

• Leading Strand: One template strand (the 3' to 5' strand) is replicated continuously. DNA polymerase follows the replication fork, synthesising a single, long new strand called the leading strand.
• Lagging Strand: The other template strand (the 5' to 3' strand) is replicated discontinuously. Synthesis occurs in the direction away from the replication fork in short sections called Okazaki fragments. Each fragment is initiated by a short RNA primer. After the fragments are synthesised, the RNA primers are removed and replaced with DNA. Finally, the enzyme DNA ligase joins the Okazaki fragments together by forming phosphodiester bonds, creating a single, continuous strand.

The information encoded in DNA ultimately dictates the production of proteins, which carry out most cellular functions. This flow of information from DNA to RNA to protein is known as the central dogma of molecular biology and involves two main processes: transcription and translation.

Transcription is the synthesis of an RNA molecule from a DNA template. It occurs in the nucleus of eukaryotic cells.

1. Initiation: The enzyme RNA polymerase binds to a specific region on the DNA known as the promoter, upstream of the gene to be transcribed.
2. Elongation: RNA polymerase unwinds a short section of the DNA double helix. It then moves along the template strand (also known as the antisense strand), adding complementary RNA nucleotides to build a new messenger RNA (mRNA) molecule. Uracil (U) replaces Thymine (T) in RNA, so A pairs with U, and G pairs with C.
3. Termination: When RNA polymerase reaches a specific terminator sequence on the DNA, transcription stops. The newly synthesised RNA molecule detaches from the DNA, and the DNA strands rewind.

Post-transcriptional Modification in Eukaryotes

In eukaryotic cells, the initial RNA transcript, called pre-mRNA, undergoes processing before it can be translated. This modification occurs in the nucleus.

• Splicing: Eukaryotic genes contain non-coding regions called introns interspersed among coding regions called exons. Splicing removes the introns and joins the exons together to form a continuous coding sequence. This process is carried out by a complex called the spliceosome.
• Capping and Tailing: A modified guanine nucleotide, known as the 5' cap, is added to the 5' end of the mRNA. At the 3' end, a poly-A tail, consisting of 50-250 adenine nucleotides, is added. These modifications protect the mRNA from degradation by enzymes in the cytoplasm, facilitate its export from the nucleus, and help ribosomes attach to the 5' end for translation.

Translation is the process where the genetic information carried by mature mRNA is used to synthesise a polypeptide (protein). This occurs on ribosomes in the cytoplasm. Ribosomes are composed of a large and a small subunit and have three binding sites for tRNA: the A (aminoacyl) site, the P (peptidyl) site, and the E (exit) site.

1. Initiation: The small ribosomal subunit binds to the 5' end of the mRNA and moves along it until it finds the start codon (usually AUG). The initiator transfer RNA (tRNA), carrying the amino acid methionine, binds to the start codon in the P site. The large ribosomal subunit then joins to form the complete translation initiation complex.
2. Elongation: A second tRNA, with an anticodon complementary to the next mRNA codon, binds to the A site. A peptide bond is formed between the amino acid in the P site and the new amino acid in the A site. The ribosome then translocates one codon down the mRNA. The tRNA from the P site moves to the E site and is released, while the tRNA from the A site (now carrying the growing polypeptide chain) moves to the P site. The A site is now free for the next tRNA.
3. Termination: This elongation cycle repeats until a stop codon (UAA, UAG, or UGA) enters the A site. Release factor proteins bind to the stop codon, causing the polypeptide chain to be released from the tRNA in the P site. The ribosome then dissociates from the mRNA, and the subunits are free to start another round of translation.

The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins. It has three crucial characteristics:

1. Degenerate (or Redundant): Most amino acids are specified by more than one codon (e.g., Leucine is coded by six different codons). This redundancy provides a degree of protection against point mutations, as a change in the third base of a codon often does not change the specified amino acid.
2. Non-overlapping: The codons are read sequentially from a fixed starting point, three bases at a time, without any overlap. Each base is part of only one codon.
3. Universal: With very few minor exceptions (e.g., in mitochondria), the same codons specify the same amino acids in all organisms, from bacteria to humans. This universality is strong evidence for a common ancestor for all life on Earth.

Not all genes are expressed all the time. Gene expression is tightly controlled. Structural genes code for proteins involved in cell structure or function, while regulatory genes code for proteins that control the expression of other genes. A classic example of gene regulation in prokaryotes is the lac operon in E. coli.

An operon is a cluster of genes under the control of a single promoter. The lac operon contains genes that code for enzymes needed to metabolise lactose. It consists of:

• Promoter: A DNA sequence where RNA polymerase binds.
• Operator: A DNA sequence that acts as a switch. A repressor protein can bind here.
• Structural Genes: lacZ, lacY, and lacA, which code for enzymes involved in lactose breakdown.
• Regulatory Gene (lacI): Located elsewhere, this gene codes for a repressor protein.

Functioning of the lac operon:

1. When lactose is absent: The lacI gene is constitutively expressed, producing the lac repressor protein. This repressor protein binds to the operator region. This binding physically blocks RNA polymerase from transcribing the structural genes. The operon is 'switched off'.
2. When lactose is present: Lactose (or its isomer, allolactose) acts as an inducer. It binds to the lac repressor protein, causing a conformational (shape) change. This altered repressor can no longer bind to the operator. With the operator free, RNA polymerase can bind to the promoter and transcribe the structural genes (lacZ, lacY, lacA). The enzymes for lactose metabolism are produced. The operon is 'switched on'.

In eukaryotic cells, the vast amount of DNA must be packaged into compact structures called chromosomes to fit inside the nucleus. A chromosome consists of a long, continuous DNA molecule tightly coiled around basic proteins called histones. These histone proteins are positively charged, allowing them to bind strongly to the negatively charged phosphate groups of DNA. The DNA-histone complex forms repeating units called nucleosomes, which look like 'beads on a string'. These nucleosomes are further coiled and folded into a more compact structure called chromatin, which is then supercoiled to form the highly condensed chromosome structure visible during cell division.