Basic Cell and Molecular Biology Past Paper PDF 2021 (Rijksuniversiteit Groningen)

lOMoARcPSD|46413053 Basic Cell and Molecular Biology Basic Cell and Molecular Biology (Rijksuniversiteit Groningen) Scannen om te openen op Studeersnel Studeersnel wordt niet gesponsord of ondersteund door een...

lOMoARcPSD|46413053 Basic Cell and Molecular Biology Basic Cell and Molecular Biology (Rijksuniversiteit Groningen) Scannen om te openen op Studeersnel Studeersnel wordt niet gesponsord of ondersteund door een hogeschool of universiteit Gedownload door Pranav Ashok ([email protected])  lOMoARcPSD|46413053 Basic cell and Molecular Biology Exam 15-10-2021 14:00-17:00 Made by Arjen Zijlstra Gedownload door Pranav Ashok ([email protected])  lOMoARcPSD|46413053 Molecular Biology 2 Reading Material Subject Molecular Biology of the Cell 1. Cells and genomes Chapter 1 pp 1‐39 2. Introduction Cell Chemistry Chapter 2 pp 43‐50; and Proteins Ch.3 pp 109‐118 (+ Fig. 3‐38) 3. DNA, Chromosomes Chapter 4 pp 173‐187 (+ Fig. 4‐61) 4. 5. DNA Replication Chapter 5 pp 237‐254 6. DNA Replication, DNA Repair Chapter 5 pp 254‐276 7. How Cells Read the Genome: Chapter 6 pp 299‐320, 324‐327 From DNA to RNA 8. How Cells Read the Genome: Chapter 6 pp 333‐349, 351 (+ Fig. 6‐87) from RNA to protein 9. Analyzing Molecules (DNA) Chapter 8 pp 463‐477 top; 483 10. Microscopy Chapter 9 pp 529‐546, 554‐556 11. Membranes Chapter 10 pp 565‐590 (583‐589 not for exam) 12. Intracellular Compartments Chapter 12 pp 641‐681, 683‐684 and Protein Transport 13. Intracellular Membrane Tra c Chapter 13 pp 695‐742 Lecture 1 - Molecular Biology: Introduction Cell Biology (39 pages) 27-9-2021 Lecture 2 - Molecular biology: Introduction Cell Chemistry and Proteins (21 pages) 28-9-2021 Lecture 3 - Molecular Biology: DNA, Chromosomes (16 pages) 29-9-2021 Lecture 4 & 5 - Molecular Biology: DNA Replication and Repair (40 pages) 30-9-2021 Lecture 6 & 7- Molecular Biology: How Cells Read the Genome: From DNA to Protein. (44 pages) Lecture 8 - Molecular Biology: Analyzing Molecules (DNA). (15 pages) Lecture 9 - Cell Biology: Microscopy (27 pages) Lecture 10 - Cell Biology: Membrane structure (19 pages) Lecture 11 - Cell Biology: Intracellular compartments and Protein sorting (43 pages) Lecture 12 - Cell Biology: Intracellular membrane traffic (48 pages) Gedownload door Pranav Ashok ([email protected])  lOMoARcPSD|46413053 Molecular Biology 3 Summaries Molecular Biology Pages 4 - 34) Cell Biology Pages: 35 - end Gedownload door Pranav Ashok ([email protected])  lOMoARcPSD|46413053 Molecular Biology 4 Molecular Biology Gedownload door Pranav Ashok ([email protected])  lOMoARcPSD|46413053 Molecular Biology 5 Chapter 1: Cells and genomes The universal features of cells on earth. All cells store their hereditary information in the same linear chemical code: DNA All cells replicate their hereditary information by templated polymerization. All cells transcribe portions of their hereditary information into the same intermediary form: RNA. All cells use proteins as catalysts All cells translate RNA into Protein the same way Each protein is encoded by a speciûc gene All cells function as biochemical factories dealing with the same basic molecular building blocks. All cells are enclosed in a plasma membrane across which nutrients and waste materials must pass. A living cell can exist with fewer than 500 genes Di erences among cells: Source of energy - Lithotrophic: Energy from (energy-rich) inorganic chemicals - Phototrophic: Energy from sunlight - Organotropic: Energy from other cells and organic cell-products Diversity in shape and size - Spherical - Rod-shaped - Spiral Cells Prokaryote or eukaryote - Prokaryote: One compartment - Eukaryote: Many membrane-bound compartments (organelles), and has a nucleus The number of genes di ers Gedownload door Pranav Ashok ([email protected])  lOMoARcPSD|46413053 Molecular Biology 6 Summary: The individual cell is the minimal self-reproducing unit of living matter, and it consists of a self-replicating collection of catalysts. Central to this reproduction is the transmission of genetic information to progeny cells. Every cell on our planet stores its genetic information in the same chemical form4as double-stranded DNA. The cell replicates its information by separating the paired DNA strands and using each as a template for polymerization to make a new DNA strand with a complementary sequence of nucleotides. The same strategy of templated polymerization is used to transcribe portions of the information from DNA into molecules of the closely related polymer, RNA. These RNA molecules in turn guide the synthesis of protein molecules by the more complex machinery of translation, involving a large multimolecular machine, the ribosome. Proteins are the principal catalysts for almost all the chemical reactions in the cell; their other functions include the selective import and export of small molecules across the plasma membrane that forms the cell9s boundary. The speciûc function of each protein depends on its amino acid sequence, which is speciûed by the nucleotide sequence of a corresponding segment of the DNA4the gene that codes for that protein. In this way, the genome of the cell determines its chemistry; and the chemistry of every living cell is fundamentally similar because it must provide for the synthesis of DNA, RNA, and protein. The simplest known cells can survive with about 400 genes. The Diversity of Genomes and the Tree of Life. Cells can be powered by a variety of free-energy sources Some cells ûx nitrogen and carbon dioxide for others The tree of life has three primary branches: 1. Bacteria 2. Archaea 3. Eukaryotes Some genes evolve rapidly, others are highly conserved Most bacteria and Archaea have 1000-6000 genes New genes are generated from preexisting genes 1. Intragenic mutation: an existing gene can be randomly modiûed by changes in its DNA sequence, through various types of error that occur mainly in the process of DNA replication. 2. Gene duplication: an existing gene can be accidentally duplicated so as to create a pair of initially identical genes within a single cell; these two genes may then diverge in the course of evolution. 3. DNA segment shu ing: two or more existing genes can break and rejoin to make a hybrid gene consisting of DNA segments that originally belonged to separate genes. 4. Horizontal (intercellular) transfer: a piece of DNA can be transferred from the genome of one cell to that of Gedownload door Pranav Ashok ([email protected])  lOMoARcPSD|46413053 Molecular Biology 7 another4even to that of another species. This process is in contrast with the usual vertical transfer of genetic information from parent to progeny. Gene duplications give rise to families of related genes within a single cell Genes can be transferred between organisms, both in the laboratory and in nature Sex results in horizontal exchanges of genetic information within a species The function of a gene can often be deduced from its sequence More than 200 gene families are common to all three primary branches of the tree of life Mutations reveal the functions of genes Molecular Biology began with a spotlight on E. coli. Gene homology: Ortholog: Homologous genes with the same function in two species Paralog: Homologous genes with di erent functions in the same species. Summary: Prokaryotes (cells without a distinct nucleus) are biochemically the most diverse organisms and include species that can obtain all their energy and nutrients from inorganic chemical sources, such as the reactive mixtures of minerals released at hydrothermal vents on the ocean üoor4the sort of diet that may have nourished the ûrst living cells 3.5 billion years ago. DNA sequence comparisons reveal the family relationships of living organisms and show that the prokaryotes fall into two groups that diverged early in the course of evolution: the bacteria (or eubacteria) and the archaea. Together with the eukaryotes (cells with a membrane-enclosed nucleus), these constitute the three primary branches of the tree of life. Most bacteria and archaea are small unicellular organisms with compact genomes comprising 100036000 genes. Many of the genes within a single organism show strong family resemblances in their DNA sequences, implying that they originated from the same ancestral gene through gene duplication and divergence. Family resemblances (homologies) are also clear when gene sequences are compared between di erent species, and more than 200 gene families have been so highly conserved that they can be recognized as common to most species from all three domains of the living world. Thus, given the DNA sequence of a newly discovered gene, it is often possible to deduce the gene9s function from the known function of a homologous gene in an intensively studied model organism, such as the bacterium E. coli. Genetic information in eukaryotes Eukaryotic cells may have originated as predators Modern eukaryotic cells evolved from a symbiosis Eukaryotic have hybrid genomes Eukaryotic genomes are big Eukaryotic genomes are rich in regulatory DNA The genome deûnes the program of multicellular development Many eukaryotes live as solitary cells Gedownload door Pranav Ashok ([email protected])  lOMoARcPSD|46413053 Molecular Biology 8 A yeast serves as a minimal model eukaryote The expression levels of all the genes of an organism can be monitored simultaneously Arabidopsis has been chosen out of 300,000 species as a model plant The world of animal cells is represented by a worm, a üy a ûsh, a mouse, and a human Studies in drosophila provide a key to genetics The vertebrate genome is a product of repeated duplications The frog and the zebraûsh provide accessible models for vertebrate development The mouse is the predominant mammalian model organism Humans report on their own particularities We are all di erent in detail Understanding cells and organisms will require mathematics, computers, and quantitative information Summary: Eukaryotic cells, by deûnition, keep their DNA in a separate membrane-enclosed compartment, the nucleus. They have, in addition, a cytoskeleton for support and movement, elaborate intracellular compartments for digestion and secretion, the capacity (in many species) to engulf other cells, and metabolism that depends on the oxidation of organic molecules by mitochondria. These properties suggest that eukaryotes may have originated as predators on other cells. Mitochondria4and, in plants, chloroplasts4contain their own genetic material, and they evidently evolved from bacteria that were taken up into the cytoplasm of ancient cells and survived as symbionts. Eukaryotic cells typically have 3330 times as many genes as prokaryotes, and often thousands of times more noncoding DNA. The noncoding DNA allows for great complexity in the regulation of gene expression, as required for the construction of complex multicellular organisms. Many eukaryotes are, however, unicellular4among them the yeast Saccharomyces cerevisiae, which serves as a simple model organism for eukaryotic cell biology, revealing the molecular basis of many fundamental processes that have been strikingly conserved during a billion years of evolution. A small number of other organisms have also been chosen for intensive study: a worm, a üy, a ûsh, and the mouse serve as