L3 Slides F24 - DNA Replication PDF

Self-Review: Bonds and interactions in solution (and in cells) Types of chemical bonds: Covalent bond: Typical “bond” between atoms Example: the bonds between atoms in CO2: O=C=O Covalent bonds are much stronger than all of the following bonds and interactions Non-covalent bonds: Ion...

Self-Review: Bonds and interactions in solution (and in cells) Types of chemical bonds: Covalent bond: Typical “bond” between atoms Example: the bonds between atoms in CO2: O=C=O Covalent bonds are much stronger than all of the following bonds and interactions Non-covalent bonds: Ionic bond: Bond dissociated by water, resulting in ions (charged atoms or molecules) Example: the bond between atoms in NaCl For biochemical molecules, we call interactions between ions “electrostatic interactions” Hydrogen-bond aka “H-bond”: Bond in which a hydrogen atom is “shared” non-covalently This is the basis for the genetic code!: interactions between bases in DNA and RNA (later in lecture) Other important interactions: van der Waals interactions Atoms like to be in contact with other atoms! Molecules will interact with each other strongly if they have complementary shapes. Hydrophobic interactions Hydrophobic parts of molecules associate with each other to avoid water molecules drives protein folding (in next lecture) See Panels 2-1, 2-2, and 2-3 (pages 70-75) for more details Please log into PollEv using your NetID biomg1350fall24 https://pollev.com/biomg1350fall24  Nucleic acids (DNA) Reading: ECB6 82-83, 179-192, 209-225 This is an animation of the amazing process of DNA replication Learning Objectives Know the different classes of molecules in cells Know the types of monomers that make up biological macromolecules Understand how base-pairing is used in nucleic acid structure and DNA replication Appreciate the complexity of eukaryotic DNA genome organization  Today’s lecture The “central dogma” The macromolecules found in cells Nucleic acids DNA The “Central Dogma” of Molecular Biology DNA sequence nucleus mRNA sequence cytosol Protein sequence  Macromolecules are abundant in cells Macromolecules are a signature of life Figure 2-29 Essential Cell Biology ype of macromolecule is a polymer constructe specific types of monomers monomer macromolecule monosaccharide polysaccharide (dozens) amino acid polypeptide (protein) (20) nucleotide nucleic acid (DNA/RNA) (4) Figure 2-30 Essential Cell Biology  Biological polymers (“macromolecules”) are formed by ‘condensation’ of monomers monomer growing polymer 'Condensation’ reaction: a molecule of water is released during the reaction The building blocks of nucleic acid (DNA) Nucleic acids (DNA and RNA) monomer macromolecule nucleotide nucleic acid (DNA/RNA) (4) DNA – deoxyribonucleic acid the genetic material RNA – ribonucleic acid information transfer other functions we discuss later he monomers in DNA are the “deoxynucleotide H deoxynucleoside (base + sugar) deoxynucleotide (deoxynucleoside + phosphate) Deoxynucleotides in DNA use deoxyribose 5’ H 4’ 1’ 3’ 2’ H 2’ carbon carries a second hydrogen (instead of an OH group) Deoxynucleotides in DNA use 4 different bases H eoxynucleotides in DNA carry phosphate group monophosphate diphosphate H triphosphate “deoxynucleoside-mono-/di-/triphosphate”  Deoxynucleotides form polymers by phosphodiester linkage monomer monomer dimer condensation H 2O 5’ 5’ 3’ condensation 3’ phosphodiester linkage 5’ H 2O + 5’ O- 3’ 3’ Panel 2-6 Essential Cell Biology  The deoxynucleotide polymer: DNA sugar-phosphate backbone (acidic) 5’ end guanine deoxyribose phosphodiester linkage adenine deoxyribose phosphodiester linkage thymine deoxyribose phosphodiester linkage cytosine 5’-GATC-3’ deoxyribose or just: GATC 3’ end when 5' and 3' not specified Figure 2-25 Essential Cell Biology The structure of DNA n chromosomes forms “anti-parallel” double st base-pairs Hydrogen bond C pairs with G T pairs with A Hydrogen bonds define the genetic code! Figure 5-2d and 5-6a Essential Cell Biology n chromosomes forms “anti-parallel” double st sugar-phosphate backbon base-pairs base-pairs sugar-phosphate backbone is on the outside base-pairs are on the inside Figure 5-2d and 5-6a Essential Cell Biology n chromosomes forms “anti-parallel” double st base-pairs base-pairs One turn (10 bases-pairs) 5'-CATTGCCAGT-3’ 3’-GTAACGGTCA-5’ Figure 5-2d and 5-6a Essential Cell Biology n chromosomes forms “anti-parallel” double st Figure 5-2d and 5-6a Essential Cell Biology DNA replication  The daunting task of DNA replication The total XX human genome Single cell to human body (diploid, 23 chromosome pairs) Estimate for the human body 6,369,418,890 bp is: (6.4 billion base pairs, 6.4*109 bp) 30,000,000,000,000 cells (30 trillion cells, 3*1013 cells) in total 2.1 m (~7 feet) long (and 2 nm wide) ~200,000,000,000,000,000,000,000 bp (2 sextillion base pairs, 2*1023 bp) With as few mistakes as possible!!! (you don’t need to memorize these numbe  DNA replication is semi-conservative (one old strand templates one new strand) Figure 6-2 Essential Cell Biology  DNA acts as a template for its own replication DNA incoming polymerase deoxynucleoside triphosphate DNA polymerase always adds deoxynucleotides to the 3’ end => DNA synthesis occurs only in the 5’-to-3’ direction! DNA polymerase is highly accurate makes only 1 error in 10,000,000 bases (it is highly selective for the right deoxynucleotide and can remove wrong ones) => BUT, DNA it would still polymerase take(100 is fast about 2 years to replicate the (diploid) deoxynucleotides/second) human genome Key steps of DNA replication DNA Synthesis begins at “Replication Origins” (20,000 replication origins in the human genome) Replication bubble with right and left ‘replication forks’ Many replication origins speed up DNA replication in chromosomes  Key steps of DNA replication DNA Synthesis begins at “Replication Origins” (20,000 replication origins in the human genome) Replication bubble with right& left ‘replicatio forks’ DNA polymerase needs 3’-OH group for DNA synthesis How do cells solve this problem?  Key steps of DNA replication DNA Synthesis begins at “Replication Origins” (20,000 replication origins in the human genome) Replication bubble RNA primers: 3’HO- 5’ Primase synthesizes short RNA primers (~10 5’ -OH 3’ nucleotides), Template is ready for DNA synthesis which provide free 3’-OH groups for DNA by DNA polymerase synthesis  Key steps of DNA replication RNA primers: synthesized DNA: 5’ DNA polymerase uses 3’-OH group of the primer and starts DNA synthesis 3’ in 5’-3’ direction Replication is delayed and fragmented on the lagging is Replication strand continuous on the leading strand 5’ 3’ DNA fragments on the lagging 5’ 3’ strand are called “Okazaki fragments” Okazaki fragments DNA replication in action  Key steps of DNA replication RNA primers: synthesized DNA: Okazaki fragments 5’ 3’ DNA fragments on the lagging 5’ 3’ strand are called “Okazaki fragments” RNA primers are removed, replace with DNA and gaps are sealed 5’ 3’ end of the chromosome 5’ 3’ The “end-replication problem” The leading strand is synthesized in its entirety. The lagging strand cannot be replicated to the end without a special mechanism ~100 bp Telomeres and telomerase prevent chromosomes shortening  DNA organization in cells Nuclear DNA: Chromosomes and their architecture w do you fit DNA in chromosomes into the nucle Largest human DNA Chromosome 1 ~1.6 x 1011 Da ~7.5 x 109 atoms The total XX human genome (diploid, 23 chromosome pairs) 6,369,418,890 bp 2.1 m (~7 feet) long 0.00001 m (10 mm) n chromosomes is highly compacted in the nuc Histone proteins enable formation of “chromatin” The structure of a “nucleosome” histone octamer DNA double helix (2 copies of each 4 different histones) (grey) n chromosomes is highly compacted in the nuc Histone proteins enable formation of “chromatin” “beads-on-a-string” chromatin in EM: chromatin fiber n chromosomes is highly compacted in the nuc rphase chromosomes occupy their own territories in the nuc Here, individual chromosome have been stained with different fluorescence n chromosomes is highly compacted in the nuc During mitosis, chromosomes are in their most compact form mitotic chromosomes in humans (karyotyp  This week’s section activity is FLUORESCENCE MICROSCOPY Remember homework is due tonight!