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Biochemistry-II - Eukaryotic Genes

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    Study Guide Biochemistry - II – Eukaryotic Genes 1. DNA and Genomes in Eukaryotes What Is a Genome? The genome is the complete set of DNA found in an organism. Scientists can estimate how much DNA an organism has by using physical measurement techniques . Even though DNA is microscopic, the total amount inside a cell is surprisingly large. 1 . Different Types of DNA in Eukaryotes In higher organisms, especially eukaryotes , DNA is not all the same. Scientists classify DNA based on its complexity , which means how many unique (independent) DNA sequences it contains. Eukaryotic DNA can be divided into three main classes based on this complexity. 1. Highly Complex (Unique) DNA • This type makes up about 50% of the DNA in mammals . • These sequences usually appear only once per genome . • They contain functional genes , which are responsible for making proteins. • This DNA is essential for normal cell function and development. 2. Moderately Repetitive DNA • This group accounts for about 20% of the total DNA . • These sequences are repeated hundreds to thousands of times in the genome. • Some of these sequences are actively transcribed . • A key example is ribosomal RNA (rRNA) genes , which are needed to make ribosomes. 3. Highly Repetitive DNA • This DNA is repeated millions of times per genome . • It is rarely transcribed into RNA. • Many of these sequences are believed to help with chromosome structure and stability rather than coding for proteins.

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    Study Guide What Is “Junk DNA”? All three DNA categories contain sequences sometimes called “junk DNA.” • These sequences do not usually code for proteins . • Some come from ancient viruses that entered the genome long ago. • Over time, these viral sequences became inactive , but they remain in the DNA. • Even though they are not expressed, they are still part of the genome. 2. How Does All This DNA Fit Inside the Cell? The amount of DNA inside a eukaryotic cell is enormous: • One chromosome contains a single DNA molecule that can be several centimeters long . • The total DNA in one cell can be up to 3 meters long . • However, the nucleus that holds this DNA is only about 10 ⁻ ⁵ meters (10 micrometers) in diameter . This means the DNA must be tightly packed and highly organized . 3. Chromatin: The Condensed Form of DNA To fit inside the nucleus, DNA wraps around proteins and becomes compact. This condensed DNA - protein structure is called chromatin . Chromatin allows: • Efficient storage of DNA • Proper gene regulation • Accurate cell division Key Takeaways Even though eukaryotic cells contain huge amounts of DNA , they organize it efficiently using different DNA types and compact structures like chromatin . Each DNA fraction — unique, moderately repetitive, and highly repetitive — plays an important role in genome organization and function.

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    Study Guide 2. Structure of Chromatin Figure 1 1. What Is Chromatin? Chromatin is the material inside the nucleus that makes up chromosomes. It is made of DNA and proteins . Chromatin does not look the same all the time. Depending on how tightly it is packed, it can be seen in different forms under a microscope. 2. Types of Chromatin Based on Appearance When chromatin is stained and viewed under a light microscope, it appears in two main forms .

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    Study Guide Heterochromatin • This type of chromatin is tightly packed . • It stays condensed throughout the entire cell cycle . • Under the microscope, it looks dark and clumped . • Genes in heterochromatin are not transcribed (not active). Euchromatin • This chromatin is loosely packed . • It appears lighter and more spread out under the microscope. • Actively transcribed genes are found here. 3. Types of Heterochromatin Heterochromatin can be further divided into two types . Facultative Heterochromatin • This type is condensed only in certain cells , not in all cells. • Example: In animals, the genes that make β - globin are condensed in cells that do not develop into blood cells. • This means these genes can be turned on or off depending on the cell type . Constitutive Heterochromatin • This type is always condensed in all cells of an organism. • It contains highly repeated DNA sequences . • It is commonly found in: o Centromeres (regions where chromosomes attach to the mitotic spindle) o Telomeres (the ends of chromosomes)

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    Study Guide 4. Levels of Chromatin Organization Refer the same image here , especially the parts labeled DNA (2 nm), nucleosome (11 nm), and condensed fiber (30 nm) . Chromatin is organized in several structural levels , becoming more compact at each step. 5. The Nucleosome: The Basic Unit of Chromatin The nucleosome is the basic building block of chromatin, found in both euchromatin and heterochromatin. • Each nucleosome contains: o 146 base pairs of DNA o Wrapped almost two complete turns around a core of proteins • The protein core is called a histone octamer . The histone octamer contains: • 2 copies each of: o H2A o H2B o H3 o H4 This structure looks like beads on a string when viewed under an electron microscope. 6. Role of Linker DNA and Histone H1 • Nucleosomes are connected by linker DNA , which is about 65 base pairs long . • Another histone protein, H1 , binds to this linker DNA. • Histone H1 helps pull nucleosomes closer together. • Because H1 binds cooperatively , many H1 molecules can attach one after another, allowing a whole gene region to be “zipped up” quickly.

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    Study Guide 7. Higher Levels of Chromatin Packing Nucleosomes are packed even more tightly to form larger structures. 30 nm Fiber • The nucleosome chain coils into a helix - like structure called the 30 nm fiber . • (1 nanometer = 10 ⁻ ⁹ meters) Chromatin Loops and Scaffold • Scaffolding proteins hold chromatin into organized domains. • In active genes: o Chromatin forms loops o The actively transcribed DNA is located on the looped - out, brush - like regions o DNA between genes is attached to the scaffold 8. Role of Nonhistone Proteins • Nonhistone proteins help control: o Chromatin condensation o Chromatin decondensation • These proteins play a key role in gene regulation . • Active genes are always found in less condensed chromatin regions . Key Takeaways • Chromatin exists as euchromatin (active) and heterochromatin (inactive) • The nucleosome is the basic unit of chromatin • DNA wraps around histone octamers • Histone H1 helps pack nucleosomes tightly • Chromatin becomes more condensed through 30 nm fibers and looped domains • Gene activity depends on how tightly chromatin is packed

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    Study Guide 3. Chromatin Replication 1. What Is Chromatin Replication? Chromatin replication in eukaryotic cells involves two closely linked processes : • DNA replication , and • Assembly of chromatin , which includes histone proteins. DNA replication in eukaryotes is similar to that in prokaryotes because each DNA strand acts as a template for the synthesis of a new strand. However, unlike prokaryotes, eukaryotic DNA replication occurs only during one specific stage of the cell cycle called the S phase . 2. The Eukaryotic Cell Cycle Figure 1 The eukaryotic cell cycle is divided into several well - defined phases: M Phase (Mitosis) • This is the phase where cell division occurs . • It is considered the “start” of the cell cycle.

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    Study Guide G1 Phase (First Gap Phase) • Begins immediately after cell division. • The cell grows and carries out metabolic activities and enzyme synthesis . • Some animal cells can remain arrested in G1 for years without dividing. • Regulation of this phase is important for understanding cancer , which results from uncontrolled cell division. S Phase (Synthesis Phase) • DNA replication occurs only during this phase . • Entry into S phase commits the cell to divide. G2 Phase (Second Gap Phase) • Occurs after DNA replication. • Prepares the cell for mitosis. 3. Role of Cyclins and Cell Cycle Control The transitions between different phases of the cell cycle are controlled by special proteins called cyclins . • Cyclins act as kinases . • They phosphorylate specific target proteins. • This phosphorylation triggers key events such as: o Start of DNA replication o Entry into mitosis o Progression through mitosis Different cyclins operate at different stages of the cell cycle to ensure proper timing and regulation .

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    Study Guide 4. Origins of DNA Replication in Eukaryotes Figure 2 Unlike prokaryotic cells, which have a single origin of replication , eukaryotic chromosomes have multiple origins . Key points: • DNA replication starts simultaneously at many origins along the chromosome. • Replication proceeds in both directions from each origin (bidirectional replication). • Replication forks are often attached to the nuclear membrane , and the DNA may move through these fixed sites. 5. DNA Polymerases and Replication Forks Several DNA polymerases are present in the eukaryotic nucleus. One important enzyme involved in replication is DNA polymerase δ . • Polymerase δ becomes fully active when it binds to a special protein called PCNA (Proliferating Cell Nuclear Antigen) . • PCNA helps the polymerase stay attached to DNA, allowing it to synthesize long DNA strands without falling off .

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    Study Guide As in prokaryotes: • Leading strand synthesis is continuous. • Lagging strand synthesis is discontinuous. • Overall DNA replication is semiconservative , meaning each daughter DNA molecule contains: o One parental strand o One newly synthesized strand 6. Nucleosome Assembly During Replication Figure 3 Chromatin assembly differs from DNA replication in an important way. • During cell division, histone content doubles , just like DNA content. • On the leading strand: o Existing histone octamers temporarily detach o They then reattach to the newly formed DNA double helix • Newly synthesized histones also assemble into new nucleosome core particles on both strands

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