GIM 201 Lesson 1 - Intro and DNA PDF

phosphate on CS it would Bases so This slide explains the different types of DNA in the human genome and how they are distributed. Here’s a simpler breakdown: 1. Types of DNA: Dispersed repetitive DNA: Makes up about 45% of the genome. These sequenc...

phosphate on CS it would Bases so This slide explains the different types of DNA in the human genome and how they are distributed. Here’s a simpler breakdown: 1. Types of DNA: Dispersed repetitive DNA: Makes up about 45% of the genome. These sequences are repeated in various places but not clustered. SINEs (Short Interspersed Elements): These are short DNA sequences, 90–500 base pairs (bp) long. A common example is the Alu element, which makes up about 10% of the genome. LINEs (Long Interspersed Elements): These are longer sequences, up to 7,000 bp long, scattered throughout the genome. Exons: These are the coding parts of the DNA that are used to make proteins. Surprisingly, they only make up 1-2% of the genome. 2. Other elements: Introns: Non-coding regions within genes. Tandem repeats and Alpha-satellite DNA: Specific sequences repeated many times in a row, often found in important structural parts of chromosomes (e.g., centromeres). Other dispersed repeats: Include transposons and other repetitive DNA. 3. Pie Chart: This shows the proportion of each DNA type in the genome. Most of the genome is made up of repetitive sequences, not coding DNA. 4. Illustrations: The first bar shows single-copy DNA, which is unique and scattered (45% of the genome). The second bar represents dispersed repetitive DNA (also 45%). The third bar shows satellite DNA, which clusters in specific areas (10%). In short, only a tiny portion of your DNA codes for proteins. Most of it consists of repeated sequences with various functions or unknown roles. Here’s a simpler explanation. 1. DNA Types: Repetitive DNA: Makes up almost half of your DNA (45%). These are repeated sequences scattered throughout your genome. SINEs (Short Repeats): Small pieces of DNA, like the Alu element, which is very common and makes up about 10% of your DNA. LINEs (Long Repeats): Longer pieces of DNA, up to 7,000 letters long, also scattered around. Exons: The useful part of DNA that makes proteins. This is only 1-2% of your whole DNA! 2. Other Stuff: Introns: Extra pieces inside genes that don’t make proteins. Tandem Repeats and Alpha-satellite DNA: Repeated DNA found in specific spots, like the centers of chromosomes. 3. Big Picture: Most of your DNA (90%) is repetitive or doesn’t code for proteins. Only a tiny bit (1-2%) actually makes the proteins your body needs. Think of your DNA like a big library: only a few books (the exons) are useful for instructions, while most of the library is filled with repeated books and extra material. Why compaction is necessary: If we stretched out all the DNA in one cell, it would be about 2 meters long! To fit inside a tiny cell nucleus, DNA is tightly packed into structures called chromatin. How DNA is compacted: 1. Nucleosomes: DNA wraps around 8 proteins called histones to form a nucleosome. Each nucleosome is about 150 base pairs of DNA, with 20-60 base pairs of linker DNA connecting them. 2. Solenoid Structure: Nucleosomes coil together, forming a solenoid, which looks like a spring with 6 nucleosomes per turn. 3. Chromatin Loops: The solenoid coils further into loops, about 100 kilobase pairs each, supported by scaffold proteins. Key Takeaway: This organization is efficient and allows DNA to be easily accessed when needed for replication or transcription while still fitting into the nucleus. pngs.at This slide is about histone tail modifications, which control how tightly or loosely DNA is packed, affecting whether genes can be turned on or off. Here’s the simple explanation: 1. What are histones? DNA wraps around proteins called histones, like thread around a spool. Histones have “tails” that can be modified to either loosen or tighten how DNA is wrapped. 2. How do modifications work? The tails of histones are positively charged, so they attract DNA (which is negatively charged), making the DNA tightly wrapped. Certain enzymes can modify these tails: Acetylation: Adds an “acetyl” group to the tail, which weakens its grip on DNA. This makes the DNA looser and allows genes to be active (transcription can happen). Methylation: Adds “methyl” groups, which can make the DNA tighter and inactive (genes are silenced). 3. Key Enzymes: HATs (Histone Acetyltransferases): Add acetyl groups to loosen DNA and make genes active. HDACs (Histone Deacetylases): Remove acetyl groups to tighten DNA and turn genes off. HMTs (Histone Methyltransferases): Add methyl groups to silence genes. Iii L 4. Two States of DNA: Active (euchromatin): DNA is loose, and genes can be read (transcribed). Inactive (heterochromatin): DNA is tightly packed, and genes are silent. In short: Histone modifications act like a switch, controlling whether genes are “on” or “off” by changing how tightly DNA is wrapped around histones. DNA replication is the process of copying DNA to ensure that each new cell gets an exact genetic copy during cell division. 1. Overview: DNA replication is semi-conservative: each new DNA molecule has one old strand and one new strand. 2. Steps of DNA Replication: Unwinding: DNA helicase separates the double helix into two single strands. This creates a replication fork. Stabilizing the strands: Single-stranded binding proteins (SSBs) keep the strands apart and stable. Primer synthesis: DNA primase makes a short RNA primer to provide a starting point for DNA polymerase. Elongation: DNA polymerase adds new nucleotides to the 3’ end of the primer, building the new DNA strand. The leading strand is synthesized continuously, while the lagging strand is synthesized in short fragments (Okazaki fragments). Joining fragments: DNA ligase seals gaps between Okazaki fragments on the lagging strand. 3. Proofreading and Error Correction: DNA polymerase has a proofreading function that checks and fixes errors during replication. This keeps the error rate extremely low (about 1 error per billion nucleotides). 4. Supercoiling Problem: As the DNA unwinds, supercoiling occurs ahead of the replication fork. Topoisomerases solve this: Type I: Makes single-strand nicks to relieve tension. Type II: Makes double-strand breaks to untangle DNA. Key Takeaways: Histone Tail Modification regulates gene activity by loosening or tightening DNA packaging. DNA Replication ensures precise duplication of DNA with high fidelity, using enzymes like helicase, polymerase, and ligase, while addressing structural challenges like supercoiling. Each incoming nucleotide has three phosphate groups. When the new nucleotide attaches, two phosphates (called pyrophosphate) are removed. This releases energy needed to create the bond. 8 DNA polymerase Here’s a simplified explanation of the points in the image: 1. DNA replication is highly accurate: Mistakes during copying (replication) happen only about once every 10 billion nucleotides (the building blocks of DNA). 2. Mechanisms to fix errors: DNA polymerase, the enzyme that builds new DNA strands, has ways to check and fix errors. 3. Pause for correction: If the wrong nucleotide is added, the process pauses, giving the enzyme a chance to fix the mistake. 4. Proofreading activity: DNA polymerase has a “proofreading” function. It can find and remove incorrectly paired nucleotides using a process called exonuclease activity. 5. Exonuclease activity: This means the enzyme can cut out nucleotides from the end of the DNA strand if they are incorrect. 6. Endonuclease activity: Sometimes, the enzyme can also cut out nucleotides from inside the DNA strand if needed. 7. Improved accuracy: This proofreading and cutting function improves the accuracy of DNA replication by 100 to 1,000 times. In short, DNA polymerase acts like a careful editor, checking for errors during DNA replication and fixing them to ensure the DNA copy is almost perfect. Key source error Exactly the same molecular make up but just a different shape aplin.MY DNA Pathway