BMS1025 - Cell Biology - the nucleus 2024 - lecture 2.pdf

BMS1025 – CELL BIOLOGY April Chloe Terrazas ; Cellular Biology: organelles, structure, function DR PENNY LYMPANY [email protected] 28AY04 DNA STRUCTURE...

BMS1025 – CELL BIOLOGY April Chloe Terrazas ; Cellular Biology: organelles, structure, function DR PENNY LYMPANY [email protected] 28AY04 DNA STRUCTURE This Photo by Unknown Author is licensed under CC BY DNA – SOME KEY POINTS Deoxyribonucleic acid (DNA) - two long polynucleotide chains composed of four types of nucleotide subunits Each chain is a “DNA strand” The two strands run antiparallel with hydrogen bonds between the base portions of the nucleotides A nucleotide is composed of a five-carbon sugar to which a phosphate group and a nitrogen-containing base are attached The nucleotides are covalently linked together in a chain through the sugars and phosphates, to form a “backbone” of alternating sugar–phosphate–sugar– phosphate NUCLEOTIDES Nucleoside A nucleotide consists of a nitrogen containing base, a five-carbon sugar (ribose) and a phosphate group The phosphate makes the nucleotide negatively charged. Glycosidic bond  DNA STRUCTURE Alberts et al. Molecular Biology of the Cell 7th Ed In DNA, the deoxyribose attached to a phosphate group (deoxyribonucleic acid), and the base may be either adenine (A), cytosine (C), guanine (G), or thymine (T). SUGARS  NUCLEIC ACID POLYMERS Nucleotides joined together by phosphodiester bonds between the 5' and 3' carbon atoms of adjacent sugar rings – forms polymer Linear sequence of nucleotides - one-letter code e.g. AGCTT, starting with the 5' end of the chain. Nucleoside/Base Abbreviation Adenosine A Guanosine G Cytidine C Thymine/Uracil T/U CREATING THE PHOSPHODIESTER BOND Nucleotide 1 The 5' group of a nucleotide triphosphate is held close to the free 3' hydroxyl group of a nucleotide chain. Nucleotide 2 The 3' hydroxyl group forms a bond to the phosphorus atom of the free nucleotide closest to the 5' oxygen atom. Meanwhile, the bond between the first phosphorus atom and the oxygen atom linking it to the next phosphate group breaks. A new phosphodiester bond now joins the two nucleotides. A pyrophosphate group has been liberated. The pyrophosphate group is hydrolyzed (split by the addition of water), releasing a great deal of energy and driving the reaction forward to completion. THE DOUBLE HELIX Nucleotides - covalently linked Strands are held together by hydrogen bonds between base pairs All bases the inside of the double helix, sugar–phosphate backbones on the outside The strands run anti-parallel Source: Fig 4-3 Alberts et al. Molecular Biology of the Cell 7th Ed  BASE PAIRING Two-ring base (a purine) is paired with a single-ring base (a pyrimidine) - most energetically favourable Each base pair is of similar width - sugar–phosphate backbones a constant distance apart A. Two hydrogen bonds form between A and T, whereas three form between G and C. The bases can pair in this way only if the two polynucleotide chains that contain them are antiparallel B. A short section of the double helix viewed from its side. Base pairs are perpendicular to the axis of the helix. Source: Fig 4-5 Alberts et al. Molecular Biology of the Cell 7th Ed THE ALPHA HELIX Double stranded DNA molecule winds into a right-handed double helix –efficiency of base pairing One complete turn per 10.4 bp Two grooves, the major and minor groove Source: Fig 4-6 Alberts et al. Molecular Biology of the Cell 7th Ed DNA packaging THE CHROMOSOME Eukaryotes - 22 pairs of homologous chromosomes and 1 pair of non-homologous Exception - gametes (eggs and sperm) and some highly specialized cell types Chromosome - single long linear DNA molecule + proteins that fold the DNA into compact structure Chromosomes associated with other proteins (as well as numerous RNA molecules) required for the processes of gene expression, DNA replication, and DNA repair The complex of DNA and tightly bound protein = chromatin  KARYOTYPE centromeres A – chromosomes “painted” and visualised as they were obtained from a lysed cell B – lined up in numerical order – showing the Karyotype Chromosomes 1–22 numbered in approximate order of size. The red knobs (chromosomes 13, 14, 15, 21, and 22) indicate the positions of genes that code for the large ribosomal RNAs and form the nucleolus (Adapted from U. Francke, Cytogenet. Cell Genet. 31:24–32, 1981.) CENTROMERES AND TELOMERES Centromere Attachment site for the two halves of each replicated chromosome (sister chromatids) Not always in centre of chromosome Keeps chromosomes properly aligned during cell division Telomeres Repetitive stretches of DNA located at the ends of linear chromosomes Arms Protect the ends of chromosomes to keep them from unravelling – think shoelaces In many types of cells, telomeres lose a bit of their DNA every time a cell divides. When all of the telomere DNA is gone, the cell cannot replicate and dies WBC and other rapidly dividing cells have an enzyme (Telomerase) that prevents their chromosomes from losing their telomeres – cells live longer Telomerase adds TTAGGG repeats to the ends of chromosomes Role in cancer - chromosomes of malignant cells usually do not lose their telomeres – fuels the uncontrolled growth  CELL CYCLE Interphase Cell actively expressing genes and synthesising proteins DNA is replicated – sister chromatids M phase Occurs when DNA replication complete Nucleus divided into two daughter nuclei Chromosomes condense Nuclear envelope breaks down, mitotic spindle forms from microtubules and other proteins Condensed mitotic chromosomes captured by mitotic spindle and complete set of chromosomes is pulled to each end of the cell separating the members of each daughter chromatid pair Nuclear envelope reforms around each chromosome set Cell divides into two daughter cells This phase is brief in mammalian cells (~1 hour) - rest of time spent in interphase CELL DIVISION mitosis - chromosomes more easily distinguished Replicated chromosomes are linked together  DNA – SIZE IS IMPORTANT Most important function of DNA - form genes - including information about when, where and how much of each RNA molecule and protein is to be made. If the double helices of all 46 chromosomes in a human cell could be laid end to end, they would reach approximately 2 meters BUT the nucleus is ~6 μm in diameter. This is equivalent to packing 40 km (24 miles) of extremely fine thread into a tennis ball. DNA packaging uses specialized proteins that bind to the DNA and fold it - series of organized coils and loops DNA tightly compacted but remains accessible to the enzymes in the cell that replicate it, repair it, and use its genes to produce RNA molecules and proteins HOW IS IT DONE? Human genome DNA length – 3.1 x 109 nucleotide pairs Number of genes coding for proteins - ~20,000 Largest gene coding for proteins – 2.5 x 106 nucleotide pairs Source: Fig 4-16 Alberts et al. Molecular Biology of the Cell 7th Ed  DNA IN CHROMOSOMES If chromosome 22 was laid out as one long double helix, it would extend to around 1.5 cm But at mitosis, it measures only 2 µm Compaction of 7000x How? – proteins which coil and fold the DNA DNA of interphase chromosomes is still tightly packed but can decondense to allow access to specific sequences for gene expression, DNA repair and replication and then recondense  CHROMATIN - EUKARYOTES Chromatin - diffuse mass of DNA at interphase What is interphase? period in cell cycle characterised by - G1 phase - cell undergoes growth, S phase - cell makes a copy of its DNA G2 phase - cell continues to grow, and prepares for cell division Heterochromatin - chromatin regions that are condensed during interphase and transcriptionally inactive Euchromatin - chromatin regions that are decondensed and DNA sequences are being transcribed into RNA Heterochromatin stains more densely than euchromatin Histology Guide © Faculty of Biological Sciences, University of Leeds NUCLEOSOMES - EUKARYOTES Basic structural unit of DNA packaging - DNA wound round proteins Fundamental subunit of chromatin Proteins binding to DNA to form chromosomes divided into – Histones Non-histone Complex of both classes of protein with nuclear DNA = chromatin This Photo by Unknown Author is licensed under CC BY HISTONES A – EM of interphase nuclei showing chromatin in form of a fibre B – unfolded chromatin showing a DNA string with beads (nucleosome core particle – DNA wound round a histone core Source: Fig 4-21 Alberts et al. Molecular Biology of the Cell 7th Ed NUCLEOSOMES - CONT Each nucleosome core particle - complex of eight histone proteins—two molecules each of histones H2A, H2B, H3, and H4—and double-stranded DNA that is 147 nt pairs long This histone octamer forms a protein core around which the double-stranded DNA is wound 147 nt pairs wraps 1.7 times around the histone core Each nucleosome separated from next by linker DNA (few nt up to about 80) Nucleosomes repeat at intervals of approx. 200 nucleotide pairs. Source: Fig 4-22 Alberts et al. Molecular Biology of the Cell 7th Ed nt – nucleotide pairs STRUCTURE OF NUCLEOSOME CORE PARTICLE NUCLEOSOMES PACKED INTO A CHROMATIN FIBRE – THE ZIGZAG MODEL Source: Fig 4-28 Alberts et al. Molecular Biology of the Cell 7th Ed Chromatin in a living cell probably rarely adopts the “beads on a string” form Nucleosomes packed on top of each other – DNA more condensed Nucleosome to nucleosome linkages formed by histone tails, notably H4 tail LOOPED DOMAINS 30 nm fibre pulled into loops – “looped domains”  DNA PACKAGING - OVERVIEW WHAT WE HAVE COVERED Nucleus Nuclear envelope Nuclear lamina DNA DNA packaging THAT’S ALL FOLKS Remember – for more information Alberts B et al. Molecular Biology of the Cell or your favourite Molecular Cell Biology text book The module discussion board Email – [email protected] This Photo by Unknown Author is licensed under CC BY-NC