IB Biology HL Chapter 7 Notes

DNA Structure and Packaging

Your DNA needs to fit inside a tiny cell nucleus, which is like cramming 3 metres of thread into a space the size of a pinhead! Nucleosomes are the solution - they're like molecular spools where DNA wraps around eight histone proteins.

Think of histones as protective packaging that keeps DNA safe from damage and allows it to coil up super tightly. This process is called supercoiling, and it's brilliant because it makes DNA compact enough for cell division and can even switch genes off when they're not needed.

DNA replication follows the semiconservative model - each new DNA molecule contains one original strand and one newly made strand. The process happens much faster in eukaryotes because it starts at multiple points along the chromosome, whilst prokaryotes only start from one spot.

Key Point: The leading strand copies continuously in the 5' to 3' direction, but the lagging strand has to copy in short fragments called Okazaki fragments because DNA can only be built in one direction.

DNA Replication Process

The DNA replication machinery works like a well-coordinated factory line. RNA primase starts things off by adding short RNA primers, giving DNA polymerase III something to grab onto as it adds new nucleotides.

On the leading strand, replication flows smoothly in one direction. But the lagging strand is trickier - it creates Okazaki fragments that need to be stitched together by DNA ligase after DNA polymerase I removes the RNA primers.

DNA sequencing uses a clever trick called the dideoxy method. Scientists add special nucleotides without the crucial 3'OH group, which stops replication dead in its tracks. Each base gets a different coloured fluorescent tag, so when replication stops, they can see exactly which base caused it.

Remember: DNA polymerase absolutely needs that 3'OH group to keep adding nucleotides - it's like needing the right connector to plug in the next piece!

Non-Coding DNA and Profiling

Not all your DNA codes for proteins - loads of it has other crucial jobs! Non-coding regions include promoters that tell RNA polymerase where to start, enhancers that speed up gene expression, and silencers that slow it down.

Tandem repeats are like DNA's fingerprint - short sequences that repeat different numbers of times in different people. These repeats are why DNA profiling works so well for identification, since everyone has their own unique pattern.

The process involves extracting DNA, amplifying it using PCR, then separating the fragments by electrophoresis. Telomeres are special tandem repeats that protect chromosome ends, getting shorter each time cells divide.

Rosalind Franklin used X-ray diffraction to photograph DNA crystals, creating the famous 'Photo 51' that proved DNA's helical structure. Her work was absolutely crucial for Watson and Crick's double helix model.

Fun Fact: Your tandem repeats are so unique that the chances of two unrelated people having identical patterns are about 1 in several billion!

Proving DNA as Genetic Material

The Hershey-Chase experiment brilliantly proved that DNA, not protein, carries genetic information. They used the fact that DNA contains phosphorus but no sulfur, whilst proteins contain sulfur but no phosphorus.

Using bacteriophages (viruses that infect bacteria), they created two versions - one with radioactive phosphorus in the DNA and another with radioactive sulfur in the protein coat. When the virus infected bacteria, only the DNA entered the cell whilst the protein coat stayed outside.

The results were crystal clear: bacteria infected with radioactive DNA became radioactive and passed this to their offspring. But bacteria infected with viruses having radioactive protein coats showed no radioactivity inside the cells.

This experiment was a game-changer because it definitively settled the debate about what genetic material actually was, paving the way for all modern molecular biology.

Think About It: Before this experiment, many scientists thought proteins were too complex to be genetic material - DNA seemed too simple!

Transcription Process

Transcription is where your DNA recipe gets copied into mRNA so it can leave the nucleus. RNA polymerase does all the heavy lifting, binding to the promoter region and unwinding the DNA strands.

The process has three clear stages: initiation (RNA polymerase binds and starts), elongation (mRNA grows as nucleotides are added in the 5' to 3' direction), and termination (everything detaches when the stop signal is reached).

Only the antisense strand gets transcribed - think of it as the template that creates a complementary mRNA copy. The sense strand has the same sequence as the mRNA (except T instead of U).

RNA polymerase reads the DNA template and adds complementary ribonucleotide triphosphates, building the mRNA molecule one base at a time until it hits the termination sequence.

Key Difference: Unlike DNA replication, transcription only copies one strand and doesn't need a primer to get started!

Transcription Regulation and Processing

Prokaryotes and eukaryotes handle transcription very differently. In prokaryotes, translation starts immediately because there's no nucleus to separate the processes.

Eukaryotes need post-transcriptional modification - the initial pre-mRNA gets a 5' cap and poly(A) tail added for protection, then splicing removes introns (non-coding sequences) and joins exons (coding sequences) together.

Spliceosomes are the molecular machines that do this cutting and pasting. Alternative splicing is brilliant because it lets one gene make several different proteins by including different combinations of exons.

The lac operon in bacteria shows how gene regulation works. When lactose is absent, a repressor protein blocks RNA polymerase from accessing the promoter. When lactose appears, it binds to the repressor, changing its shape so transcription can proceed.

Cool Fact: Alternative splicing means humans can make over 100,000 different proteins from only about 20,000 genes!

Epigenetic Regulation

Histones aren't just DNA packaging - they're also gene switches! Acetylation adds acetyl groups to histone tails, loosening DNA packing so genes can be transcribed. Deacetylation does the opposite, silencing genes.

DNA methylation involves adding methyl groups to cytosine bases, particularly in CpG sequences near promoter regions. Methylated genes get switched off and stay off, even through cell divisions.

Epigenetics studies how environmental factors can change gene expression without altering the actual DNA sequence. Your diet, age, and lifestyle can influence methylation patterns, affecting which genes are active.

These changes can be inherited, which explains why identical twins can become more different as they age. DNA methylation levels are highest at birth and change throughout your lifetime.

Mind-Blowing: Your grandmother's diet during pregnancy might have affected your dad's genes, which could influence your health today!

Translation Machinery

Translation is where mRNA finally becomes protein. Ribosomes are the protein factories, made of rRNA and proteins, with a small subunit that binds mRNA and a large subunit with three crucial binding sites.

The ribosome's A, P, and E sites work like a conveyor belt: tRNA enters at A (aminoacyl), moves to P (peptidyl) after forming peptide bonds, then exits at E (exit). It's a beautifully coordinated dance!

Bound ribosomes attach to the endoplasmic reticulum and make proteins destined for export or membrane insertion. Free ribosomes float in the cytoplasm and make proteins that stay inside the cell.

Translation starts when mRNA binds to the small ribosomal subunit, and the first tRNA (carrying methionine) pairs with the start codon AUG. The large subunit then joins to complete the ribosome.

Remember: Every protein in every organism starts with methionine - it's like the universal "start here" signal!

Translation Process

Translation initiation begins when the initiator tRNA carrying methionine base-pairs with the AUG start codon. The large ribosomal subunit then binds to form the complete translation complex.

During elongation, tRNA molecules bring amino acids to the A site, where they match their anticodons with mRNA codons. Peptide bonds form between adjacent amino acids as the ribosome moves along the mRNA.

The process involves translocation - the ribosome shifts one codon at a time, moving tRNA from A to P to E sites. Used tRNA molecules exit at the E site and can be recycled for another round.

Each step requires energy and precise coordination. The growing polypeptide chain emerges from the ribosome and begins folding into its final protein shape even before translation finishes.

Efficiency Tip: One mRNA can have multiple ribosomes translating it simultaneously, making lots of protein copies quickly!

Translation Completion

Translation termination happens when a stop codon (UAG, UAA, or UGA) enters the ribosome's A site. These don't code for amino acids - instead, release factors recognise them and trigger disassembly.

The completed polypeptide gets released, and the ribosomal subunits separate from the mRNA. Everything can be recycled for another round of protein synthesis, making the process incredibly efficient.

The translation complex disassembles in an organised way, with the mRNA remaining intact and ready for more ribosomes to use. This means one mRNA molecule can produce many copies of the same protein.

Once released, the new protein may need additional modifications like folding assistance from chaperones or chemical modifications before it becomes fully functional.

Final Thought: From DNA to protein, this entire process happens thousands of times per second in your cells - it's molecular machinery at its finest!