DNA Organization Lecture Notes PDF

# LECTURE: DNA ORGANIZATION PART 1 ## Introduction to Telomeres In an experiment, fibroblasts from a 70-year-old lady and a 13-year-old girl were taken and grown in culture media with a mitogenic stimulus and all nutrients required for growth. Surprisingly, the fibroblast from an elderly lady wi...

# LECTURE: DNA ORGANIZATION PART 1 ## Introduction to Telomeres In an experiment, fibroblasts from a 70-year-old lady and a 13-year-old girl were taken and grown in culture media with a mitogenic stimulus and all nutrients required for growth. Surprisingly, the fibroblast from an elderly lady will grow about 10-20 times and stop multiplying; meanwhile, the fibroblast from a young girl will grow about 40-50 times and stop proliferating. It was concluded that older people's cells have less replicative properties and younger people's cells have more replicative properties. With advancements in genetic research, it was discovered that when a cell multiplies, its chromosomes become shorter from ends. With every replicative cycle, the ends of chromosomes become short and in fibroblast after almost 50 replications, ends are lost and further shortening of the chromosome will disturb the essential genes and the cell will stop replicating. In younger girls, total replication cycles are less than in elderly ladies, and in the elderly ladies, telomeres have shortened, so further replicative property is less. ## Structure of Telomeres When we open up its DNA at the end of the chromosome, there is a 3' end and a 5' end. 3' is a longer end that folds on itself, associated with certain proteins responsible for maintaining this folding. This area is rich in certain nucleotide sequences. These ends are called telomeres. ## Shortening of Telomeres According to basic principles of replication, enzymes concerned with replication read from 3 to 5′ end. * A primer is placed at the 3′ end, and new DNA is formed along it. When a new strand is made from the parent strand, at the 5′ end of the new strand there is no means to remove the primer. * It means if the primer is not removed in the new strand, the 5′ end has been shortened. When DNA replicates in eukaryotic cells, the new strands at the 5′ end are shortened because of primer DNA. ## Purpose of Telomeres Telomeres provide extra ends at the chromosomes so that if some ends are shortened during every replicative cycle, the cell can still undergo many replicative cycles until cellular aging is achieved. With age, telomeres are shortened because of multiple replicative cycles. In some cells capacity to proliferate is unusually big such as zygote, germ cells, and cancer cells. ## Telomerase Enzyme Telomerase enzyme is found in cells that have more replicative properties. * Whenever telomerase is at work, it keeps on elongating the end of the DNA double-stranded molecule. These are responsible for telomeres' elongation, making cells undergo more replicative cycles. * Telomerase has a special type of nucleotide sequence, usually the A,C sequence, with a short stretch of RNA. * Telomeres are usually rich in the T, G nucleotide sequence. The RNA of telomerase undergoes hydrogen bonding with the 3′ end of the telomere at one domain. On the other domain, it will read points of RNA and polymerize DNA. This DNA piece is complementary to the RNA present in the telomerase enzyme. * One domain provides the RNA template; the other domain reads the RNA and polymerizes DNA. Such enzyme activity is called RNA-dependent DNA polymerase activity * The domain that reads RNA and polymerizes DNA is called reverse transcriptase. * Telomerase enzyme will repeat this functional cycle many times until the DNA telomeric end has been significantly elongated. Every cell has a gene to synthesize telomerase, but many cells inhibit this process, which results in rapid aging. Telomerase enzymes are pathologically present in excess in cancer cells. ## Reverse Transcriptase HIV is responsible for producing the clinical syndrome of AIDS at an advanced stage. After entering the body, it specifically attacks T helper cells. * HIV has a single-strand RNA genome with a double copy, which is injected into a T-helper cell along with viral reverse transcriptase enzyme, which can read RNA and polymerize DNA. * Another enzyme digests its RNA, leaving single-stranded DNA. * Another enzyme reads this DNA strand and polymerizes it, eventually making viral double-stranded DNA. This viral double-stranded DNA genome is integrated into the human genome. In humans, reverse transcriptase is present in telomerase. ## DNA PACKING In one cell, the total length of DNA is one meter and it is packed in our cells in a special way that it can be transcribed and replicated while remaining in the nucleus. DNA present in chromosomes is compressed an average of 8000 times. * In DNA, nitrogenous bases are attached to sugar molecules and phosphates called nucleotides converted into a polymer called a single strand of DNA. * The complementary strand, with an anti-parallel arrangement, forms double-stranded DNA, which is coiled to form a double helix structure. * The double-stranded DNA molecule is negatively charged because of the phosphate backbone. Histones are special nucleoproteins that are positively charged because of the presence of amino acids rich in extra protons, such as lysine and arginine with magnesium ions. * Histones play a major role in the wrapping of DNA. * Histones are divided into H1, H2A, H2B, H3, and H4 types. Dimers of these types except H1 collectively make a structure known as an octamer. ## HIGH-YIELD POINTS ### TELOMERES * **Fibroblast Experiment:** Fibroblasts from an elderly individual replicate fewer times (~10-20) than those from a younger person (~40-50) que to shorter telomeres. * **Replication and Telomere Shortening:** DNA replication enzymes cannot fully replicate the 5′ ends of new strands, causing progressive telomere shortening with each cell division. * **Structure of Telomeres:** Telomeres consist of a 3′ end, rich in T and G nucleotide sequences, stabilized by specific proteins. * **Telomerase Function:** Telomerase, an RNA-dependent DNA polymerase, extends telomeres by adding repetitive sequences, enabling prolonged replicative cycles in zygotes, germ cells, and cancer cells. * **Reverse Transcriptase Activity:** Telomerase uses its RNA template to synthesize complementary DNA, a process similar to the reverse transcriptase mechanism seen in HIV. * **Telomerase and Cancer:** Excessive telomerase activity is a hallmark of cancer cells, allowing them to bypass cellular aging. ### DNA PACKING * **DNA Packing:** DNA is highly compacted in chromosomes (~8000x compression) using histone proteins to fit into the nucleus while remaining functional for replication and transcription. * **Histones:** DNA wraps around histone octamers (H2A, H2B, H3, and H4) to form nucleosomes.