Topic 1 & 2 - Components, DNA Structure, Replication PDF

🕵🏾 Topic 1 & 2 - Components, DNA Structure, Replication Lecture 1.1 - Introduction to cell and its components Central Dogma of Biology The central dogma of molecular biology is a theory stating that genetic...

🕵🏾 Topic 1 & 2 - Components, DNA Structure, Replication Lecture 1.1 - Introduction to cell and its components Central Dogma of Biology The central dogma of molecular biology is a theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein. Prokaryote Cell no nucleus + membrane bound organelles genome is found as circular plasmid DNA plasmid is important for gene modification Topic 1 & 2 - Components, DNA Structure, Replication 1  Eukaryotic Cell Structure organelle - compartment of a cell with a specific function. Nucleus Contains DNA, nucleoproteins (nucleic acids bonded to a protein) & RNA. Function: stores DNA and co-ordinate the cell’s activities, such as growth, metabolism, protein synthesis and cell division. TEM images of the nucleus reveal that DNA is found in two forms. Heterochromatin → condensed, tightly packed DNA (chromatin) -> APPEARS DARK- heterochromatin has no active RNA synthesis as it is condensed Euchromatin → uncondensed DNA → APPEARS LIGHT - has active RNA synthesis). Topic 1 & 2 - Components, DNA Structure, Replication 2  Nucleolus Found within the nucleus, Function: site of ribosomal RNA (rRNA) synthesis. Nuclear Envelope A double layered membrane, Contains nuclear pores - allows macromolecules to pass through when entering or exiting the nucleus. Function: controls what enters and exits the nucleus. Cytoplasm - metabolism of carbohydrates, amino acids & nucleotides, fatty acid synthesis Cytosol Metabolism, protein synthesis (free ribosomes) Endoplasmic Reticulum (ER) Rough ER Translation of mRNA into membrane associated proteins or for secretion out of the cell. Topic 1 & 2 - Components, DNA Structure, Replication 3  A series of interconnecting membranes, vesicles & cisternae (flattened sacs), continuous throughout the cytoplasm. Ribosomes are attached to the outer surface of the membranes, making this ER "rough". nascent protein (plural nascent proteins)= A protein as it is being formed by a ribosome before it folds into its active shape. Smooth ER The lack of embedded ribosomes classifies this ER as smooth. Function: Synthesis of lipids, Ca 2+ storage, steroid production Golgi Apparatus Topic 1 & 2 - Components, DNA Structure, Replication 4  Modifies and packaging of proteins and lipids for delivery to other organelles within the cell or for secretion out of the cell shaped stacks of cisternae. The Golgi bodies have polarity - proteins move from the convex/cis (entry point) to concave/trans end of the stack and are modified as they move. Vesicles leave from the concave/trans face of the Golgi body Mitochondria Topic 1 & 2 - Components, DNA Structure, Replication 5  Mitochondria are double-membraned organelles with an smooth outer and a folded inner lipid bilayer membrane. The inner membrane forms folds called cristae, which boost the surface area for ATP production. matrix houses the Krebs cycle, along with mitochondrial DNA, ribosomes, and enzymes. These enzymes are crucial for ATP generation through the Krebs cycle and oxidative phosphorylation. Cells with high energy demands, like muscle and sperm cells, possess more mitochondria to meet their ATP needs. Ribosome Composed of two rRNA subunits (40s+60s for eukaryotes + 50s +30s for prokaryotes) that wrap around mRNA to begin translation and protein synthesis. Function: site of protein synthesis (translation) within the cell. Lysosomes Membrane bound organelles that contains acid hydrolases at pH 5 Topic 1 & 2 - Components, DNA Structure, Replication 6  Function: Intracellular digestion dark stain colour Peroxisomes membrane bound organelle that undergoes chemical detoxification and lipid metabolism. Proteosome Degradation of intracellular proteins Endosome - sorting and delivery of lipid vesicles and their contents to and from the plasma membrane. Plasma Membrane 1. Acts as a selective barrier, allowing only small, non-polar molecules to pass through passively 2. Facilitates communication with other molecules and cells Amphipathic (Polar Hydrophoillic Head) (Hydrophobic fatty acid tail region) Topic 1 & 2 - Components, DNA Structure, Replication 7  Cytoskeleton crucial role in changing cell shape and movement by providing structural support. + intracellular transport. consists of three main components: microfilaments, intermediate filaments, and microtubules. Name the 6 types of Stem Cells Totipotent – These cells can produce all of the cell types necessary to give rise to a new organism. Pluripotent – Can produce nearly all cell types. Typically, they can form almost all of the cells of the three ‘germ layers’ (endoderm, mesoderm, ectoderm). Multipotent – Can produce cells of a closely related family Oligopotent – Can only produce a few cell types of the same family e.g. lymphoid cells Unipotent – Can only produce one type of cell. They can self renew so don’t rely on a separate stem cell pool for replenishment Describe the DNA Organisation starting from the Nucleus to Chromosome. And describe how the DNA Helix appears Topic 1 & 2 - Components, DNA Structure, Replication 8  In the nucleus, each double stranded DNA molecule is wrapped around histones to form nucleosomes, which form ‘beads on a string DNA’. Nucleosomes can also tightly pack into solenoid structures, forming 30nm fibres. Solenoid fibres are compacted into several ‘hierarchical loops’ to create highly condensed structures, which are chromosomes. Topic 1 & 2 - Components, DNA Structure, Replication 9  Which groove is most important for DNA-protein binding major → more base pairs exposed → larger area for protein binding Describe the arrangement of nucleotides and codons. Nucleotides are composed of a pentose ring (deoxyribose) conjugated to a nitrogenous base. These are linked via a phosphate group at the 5’ end of the pentose ring. Bases bind via hydrogen bonding. GC base pairing → more stable than AT base pairing Genes are coded for by 4 bases (A, T (U), G, C) which form 3-lettered codons – give instructions about amino acid incorporation into nascent proteins. ATG (AUG) is the first codon in every gene. – Codes for methionine Explain how a stem cell differentiates in a basic manner Environmental cues by signalling molecules causes a stem cell to change its genome since genes are activated, this causes cell remodelling → Differentiation REVISION QUESTIONS Topic 1 & 2 - Components, DNA Structure, Replication 10  https://prod-files-secure.s3.us-west-2.amazonaws.com/28809373-1787-41ca -b20b-bcbe176b6898/85e1e320-1fe5-48a1-ab6e-420ba5e82984/Revision_ Questions.pdf MICROSCOPE CELL BOOKLET good notes Lecture 2.1 - DNA structure and replication Explain the 3 models of DNA replication Semiconservative Model of DNA Replication: each strand of the original DNA molecule serves as a template for the synthesis of a new complementary strand. each newly formed DNA molecule consists of one parental strand and one daughter strand. Conservative Model of DNA Replication: In the conservative model, the original DNA molecule remains intact, and an entirely new DNA molecule is synthesized. Dispersive Model of DNA replication during DNA replication, the original parental DNA molecule would break into fragments, and these fragments would then serve as templates for the synthesis of new DNA. Meselson-Stahl Experiment 1. Isotope Labelling: E. coli bacteria were grown in a medium containing a heavy isotope of nitrogen, N-15, which was incorporated into the bacterial DNA, making it denser. 2. Transfer to Light Isotope Medium: The labeled bacteria were then transferred to a medium containing a lighter isotope of nitrogen, N-14, and allowed to replicate their DNA in this new medium. 3. Sampling at Intervals: DNA samples were collected at various time intervals after the switch to the lighter isotope medium. Topic 1 & 2 - Components, DNA Structure, Replication 11  4. Density Gradient Centrifugation: The collected DNA samples were subjected to density gradient centrifuge, separating DNA molecules based on density. 5. Observation: The centrifuged DNA was observed. An intermediate band containing a mix of N-15 and N-14 DNA was observed, supporting the semiconservative model. This indicated that DNA replication involves the synthesis of new strands complementary to the old ones. What was Arthur Kornberg’s discovery in 1957 Arthur Kornberg demonstrated the existence of a DNA polymerase - DNA polymerase I DNA Polymerase I has THREE different enzymatic activities in a single polypeptide: a 5’ to 3’ DNA polymerizing activity a 3’ to 5’ exonuclease (enzyme which removes successive nucleotides from the end of a polynucleotide molecule.) activity a 5’ to 3’ exonuclease (enzyme) activity Topic 1 & 2 - Components, DNA Structure, Replication 12  Explain Semi-Conservative DNA Replication DNA Replication - occurs in the Synthesis phase (S phase) of the cell cycle 1. Initiation DNA Helicase untwists the DNA strands by breaking their hydrogen bonds. Primase makes a short RNA primer that matches the single-stranded DNA. DNA polymerase needs this primer to start replicating DNA. The primer is later removed by DNA polymerase's exonuclease function. 2. Elongation Diagram - The first part of DNA replication showing a replication fork DNA replication involves two strands: 3' to 5' and 5' to 3'. DNA polymerase continuously builds a new 5' to 3' strand on the 3' to 5' strand (leading). On the 5' to 3' strand (lagging), new DNA polymerases start due to helicase action, creating Okazaki fragments. DNA ligase joins Okazaki fragments on the lagging strand into a continuous chain. Topic 1 & 2 - Components, DNA Structure, Replication 13  3. Termination DNA ligase connects the remaining Okazaki fragments and the sections where forks have met, by creating phosphodiester bonds between sugar and phosphate groups. The end result is two complete DNA molecules, each consisting of one original DNA strand and one new DNA strand, following the semi-conservative replication model. Topic 1 & 2 - Components, DNA Structure, Replication 14  Diagram - DNA replication continued Describe the difference between exonuclease vs endonuclease endonucleases = enzymes that remove successive nucleotides within the polynucleotide molecules exonucleases = enzymes that remove successive nucleotides from the ends of a polynucleotide molecules What is the function of an exonuclease domain in DNA Polymerase? The exonuclease activity serves a proofreading function exonuclease removes incorrectly matched bases DNA Polymerase I stalls if the incorrect ntd is added - it can’t add the next ntd in the chain Explain why DNA P 1 was not the main replication enzyme Topic 1 & 2 - Components, DNA Structure, Replication 15  too slow to replicate genome moderately processive (processivity → number of dNTP’s (Nucleostide Triphosphate - nucleotides with multiple phosphate groups) added to a growing DNA chain before the enzyme dissociates from the template There is more DNA polymerases in E. coli. A total of 5 DNA Ps So if it’s not the chief replication enzyme then what does DNAP I do? functions in processes that require short lengths of DNA synthesis major role in DNA repair its role in DNA replication is to remove primers and fill in the gaps left behind Types of DNA P + their functions Explain the arrangement From the double helix to visible chromosomes In the nucleus each double stranded DNA molecule is wrapped around histones to form nucleosomes, which form ‘beads on a string DNA’. Nucleosomes can also tightly pack into solenoid structures, forming 30nm fibres. These fibres are compacted into several ‘hierarchical loops’ to create highly condensed structures, which are chromosomes. Topic 1 & 2 - Components, DNA Structure, Replication 16  Explain how DNA and RNA are polymers Both DNA and Ribonucleic Acid (RNA) are nucleic acids (polymer of nucleotides) NucleoSide = base + sugar NucleoTide = base + sugar + phosphate Topic 1 & 2 - Components, DNA Structure, Replication 17  The pentose sugar in DNA is 2-deoxyribose whereas the pentose sugar in RNA is ribose. 2-deoxyribose has only a hydrogen atom on the second carbon (therefore no extra oxygen hence deoxyribose), whereas ribose has a hydroxyl group on second carbon instead. ribose = left, deoxyribose = right The nucleic acids DNA and RNA are polynucleotides. DNA is a polymer of deoxyribonucleotides and RNA is a polymer of ribonucleotides. A nucleotide is composed of a nitrogenous base, a sugar and a phosphate. Nucleotides are covalently linked together via phosphodiester bonds.. " Acetylation of histone tails neutralizes the positive charges" why does this occur Acetylation of histone tails involves adding acetyl groups, which are negatively charged, to positively charged histones. This neutralization of charges reduces the tight binding between histones and DNA, —> DNA more accessible for processes like gene expression and regulation. Essentially, histone acetylation helps loosen the chromatin structure and open it up, facilitating DNA-related cellular activities. Name 2 enzymes involved in acetylation/deacetylation histone deacetylase - removes acetyl groups to condense chromatin Histone Acetyltransferases - acetylates histones to open chromatin Topic 1 & 2 - Components, DNA Structure, Replication 18  What are telomeric repeats - telomere (compound structure at the end of a chromosome) Clusters of repeated 6bp TTAGGG in humans protects integrity of chromosomes and loss of DNA Allow the replication of the extreme ends of chromosomes Explain how telomeres are maintained Telomeres are specialized DNA sequences located at the ends of linear chromosomes. Telomeres are composed of repeated sequences (e.g., TTAGGG in humans) and associated proteins. 1. End Replication Problem: , the end of the lagging strand (telomeres) cannot be replaced by DNA, creating a gap at the 3' end of the chromosome. 2. Telomerase Enzyme: Telomerase enzyme contains both RNA and protein components. The RNA component serves as a template for synthesizing the missing DNA sequence at the telomere. 3. Extension of Telomeres: Telomerase extends the telomeric DNA by adding repeat sequences to the 3' end of the chromosome. This action effectively Topic 1 & 2 - Components, DNA Structure, Replication 19  compensates for the lost DNA during replication and prevents the shortening of the telomeres. 4. Cell Division: Telomere maintenance allows cells to undergo multiple rounds of cell division without losing essential genetic material → important in stem cells and rapidly dividing cells. 5. Limited Replication in Somatic Cells: While telomerase is active in germ cells, stem cells, and certain immune cells, most somatic (body) cells have limited telomerase activity. Consequently, with each round of cell division, telomeres gradually shorten. This process is thought to contribute to cellular aging → cell senescence or apoptosis (cell death). In summary, telomeres are maintained by the action of telomerase, which adds repetitive DNA sequences to the ends of chromosomes on the 3’ of the lagging strand during DNA replication. Topic 1 & 2 - Components, DNA Structure, Replication 20  Define gene A gene is a region of DNA that codes for a specific protein Define locus gene has a specific location on a specific chromosome REVISION QUESTIONS https://prod-files-secure.s3.us-west-2.amazonaws.com/28809373-1787-41ca -b20b-bcbe176b6898/bc412b3d-e083-41a6-9ddb-8b5d5cdb8184/Cell_Cycle _Group_work_Session_2.pdf Topic 1 & 2 - Components, DNA Structure, Replication 21 Topic 1 & 2 - Components, DNA Structure, Replication 22