Biochemistry-II - Eukaryotic Genes - Quick Guides

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Study GuideBiochemistry-II–Eukaryotic Genes1.DNA and Genomes in EukaryotesWhat Is a Genome?Thegenomeis the complete set of DNA found in an organism. Scientists can estimate how muchDNA an organism has by usingphysical measurement techniques. Even though DNA ismicroscopic, the total amount inside a cell is surprisingly large.1.Different Types of DNA in EukaryotesIn higher organisms, especiallyeukaryotes, DNA is not all the same. Scientists classify DNA basedon itscomplexity, which meanshow many unique (independent) DNA sequencesit contains.Eukaryotic DNA can be divided intothree main classesbased on this complexity.1. Highly Complex (Unique) DNA•This type makes upabout 50% of the DNA in mammals.•These sequences usually appearonly once per genome.•They containfunctional genes, which are responsible for making proteins.•This DNA is essential for normal cell function and development.2. Moderately Repetitive DNA•This group accounts forabout 20% of the total DNA.•These sequences are repeatedhundreds to thousands of timesin the genome.•Some of these sequences areactively transcribed.•A key example isribosomal RNA (rRNA) genes, which are needed to make ribosomes.3. Highly Repetitive DNA•This DNA is repeatedmillions of times per genome.•It israrely transcribedinto RNA.•Many of these sequences are believed to help withchromosome structure and stabilityrather than coding for proteins.

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Study GuideWhat Is “Junk DNA”?All three DNA categories contain sequences sometimes called“junk DNA.”•These sequences donot usually code for proteins.•Some come fromancient virusesthat entered the genome long ago.•Over time, these viral sequences becameinactive, 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 chromosomecontains a single DNA molecule that can beseveral centimeters long.•Thetotal DNA in one cellcan beup to 3 meters long.•However, the nucleus that holds this DNA is only about10⁻⁵meters (10 micrometers) indiameter.This means the DNA must betightly packed and highly organized.3.Chromatin: The Condensed Form of DNATo fit inside the nucleus, DNA wraps around proteins and becomes compact.This condensed DNA-protein structure is calledchromatin.Chromatin allows:•Efficientstorage of DNA•Propergene regulation•Accuratecell divisionKey TakeawaysEven though eukaryotic cells containhuge amounts of DNA, they organize it efficiently usingdifferent DNA types and compact structures likechromatin. Each DNA fraction—unique, moderatelyrepetitive, and highly repetitive—plays an important role in genome organization and function.

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Study Guide2.Structure of ChromatinFigure 11. What Is Chromatin?Chromatin is the material inside the nucleus that makes up chromosomes. It is made ofDNA andproteins.Chromatin does not look the same all the time. Depending on how tightly it is packed, it can be seenin different forms under a microscope.2. Types of Chromatin Based on AppearanceWhen chromatin is stained and viewed under a light microscope, it appears intwo main forms.

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Study GuideHeterochromatin•This type of chromatin istightly packed.•It stays condensed throughout theentire cell cycle.•Under the microscope, it looksdark and clumped.•Genes in heterochromatin are not transcribed(not active).Euchromatin•This chromatin isloosely packed.•It appearslighter and more spread outunder the microscope.•Actively transcribed genesare found here.3. Types of HeterochromatinHeterochromatin can be further divided intotwo types.Facultative Heterochromatin•This type is condensedonly in certain cells, not in all cells.•Example:In animals, the genes that makeβ-globinare condensed in cells that do not develop into bloodcells.•This means these genes can be turnedon or off depending on the cell type.Constitutive Heterochromatin•This type isalways condensedinall cellsof an organism.•It containshighly repeated DNA sequences.•It is commonly found in:oCentromeres(regions where chromosomes attach to the mitotic spindle)oTelomeres(the ends of chromosomes)

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Study Guide4. Levels of Chromatin OrganizationRefer the same image here, especially the parts labeledDNA (2 nm), nucleosome (11 nm), andcondensed fiber (30 nm).Chromatin is organized inseveral structural levels, becoming more compact at each step.5. The Nucleosome: The Basic Unit of ChromatinThenucleosomeis the basic building block of chromatin, found in both euchromatin andheterochromatin.•Each nucleosome contains:o146 base pairs of DNAoWrapped almosttwo complete turnsaround a core of proteins•The protein core is called ahistone octamer.The histone octamer contains:•2 copies each of:oH2AoH2BoH3oH4This structure looks likebeads on a stringwhen viewed under an electron microscope.6. Role of Linker DNA and Histone H1•Nucleosomes are connected bylinker DNA, which is about65 base pairs long.•Another histone protein,H1, binds to this linker DNA.•Histone H1 helps pull nucleosomes closer together.•Because H1 bindscooperatively, many H1 molecules can attach one after another, allowinga whole gene region to be“zipped up”quickly.

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Study Guide7. Higher Levels of Chromatin PackingNucleosomes are packed even more tightly to form larger structures.30 nm Fiber•The nucleosome chain coils into ahelix-like structurecalled the30 nm fiber.•(1 nanometer = 10⁻⁹meters)Chromatin Loops and Scaffold•Scaffolding proteinshold chromatin into organized domains.•In active genes:oChromatin formsloopsoThe actively transcribed DNA is located on thelooped-out, brush-like regionsoDNA between genes is attached to the scaffold8. Role of Nonhistone Proteins•Nonhistone proteinshelp control:oChromatin condensationoChromatin decondensation•These proteins play a key role ingene regulation.•Active genesare always found inless condensed chromatin regions.Key Takeaways•Chromatin exists aseuchromatin (active)andheterochromatin (inactive)•Thenucleosomeis the basic unit of chromatin•DNA wraps aroundhistone octamers•Histone H1helps pack nucleosomes tightly•Chromatin becomes more condensed through30 nm fibers and looped domains•Gene activity depends on how tightly chromatin is packed

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Study Guide3.Chromatin Replication1. What Is Chromatin Replication?Chromatin replication in eukaryotic cells involvestwo closely linked processes:•DNA replication, and•Assembly of chromatin, which includes histone proteins.DNA replication in eukaryotes is similar to that in prokaryotes becauseeach DNA strand acts as atemplatefor the synthesis of a new strand. However, unlike prokaryotes, eukaryotic DNA replicationoccursonly during one specific stageof the cell cycle called theS phase.2. The Eukaryotic Cell CycleFigure 1The eukaryotic cell cycle is divided into several well-defined phases:M Phase (Mitosis)•This is the phase wherecell division occurs.•It is considered the “start” of the cell cycle.

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Study GuideG1 Phase (First Gap Phase)•Begins immediately after cell division.•The cell grows and carries outmetabolic activities and enzyme synthesis.•Some animal cells can remainarrested in G1 for yearswithout dividing.•Regulation of this phase is important for understandingcancer, which results fromuncontrolled 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 ControlThe transitions between different phases of the cell cycle are controlled by special proteins calledcyclins.•Cyclins act askinases.•They phosphorylate specific target proteins.•This phosphorylation triggers key events such as:oStart of DNA replicationoEntry into mitosisoProgression through mitosisDifferent cyclins operate at different stages of the cell cycle to ensureproper timing and regulation.

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Study Guide4. Origins of DNA Replication in EukaryotesFigure 2Unlike prokaryotic cells, which havea single origin of replication, eukaryotic chromosomes havemultiple origins.Key points:•DNA replication starts simultaneously atmany originsalong the chromosome.•Replication proceeds inboth directionsfrom each origin (bidirectional replication).•Replication forks are oftenattached to the nuclear membrane, and the DNA may movethrough these fixed sites.5. DNA Polymerases and Replication ForksSeveral DNA polymerases are present in the eukaryotic nucleus. One important enzyme involved inreplication isDNA polymeraseδ.•Polymeraseδbecomes fully active when it binds to a special protein calledPCNA(Proliferating Cell Nuclear Antigen).•PCNA helps the polymerase stay attached to DNA, allowing it to synthesizelong DNAstrands without falling off.

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Study GuideAs in prokaryotes:•Leading strandsynthesis is continuous.•Lagging strandsynthesis is discontinuous.•Overall DNA replication issemiconservative, meaning each daughter DNA moleculecontains:oOne parental strandoOne newly synthesized strand6. Nucleosome Assembly During ReplicationFigure 3Chromatin assembly differs from DNA replication in an important way.•During cell division,histone content doubles, just like DNA content.•On the leading strand:oExisting histone octamers temporarily detachoThey then reattach to the newly formed DNA double helix•Newly synthesized histones also assemble intonew nucleosome core particleson bothstrands

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