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The course From molecules to cells provides a definition of life in the context of biochemistry and cell biology. It
covers the basics of molecular mechanisms behind the complexity, sustainability and heredity of the living organisms including evolutionary principles and phenomenon of the origin of life. It covers the biology of prokaryotes and eukaryotes emphasizing the interplay between the structure and function on the seminal topics like biosynthesis and transformation of cellular components and organelles; cell growth and oncogenic transformation; transport, receptors, and cell signaling; the cytoskeleton, the extracellular matrix, and cell movements; chromatin structure and RNA synthesis. The course From molecules to cells set the stage for follow-up courses, particularly From cells to organisms. The course is built from topical blocks (see Syllabus) each of them consisting of lecture (3h) and workshop focused on primary literature as a Q&A session(1h). Poslední úprava: Půta František, doc. RNDr., CSc. (06.02.2022)
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1. Molecular Biology of the Cell, 7th Edition, ISBN-13: 978-0393884821, 2022 Poslední úprava: Šebková Nataša, RNDr., Ph.D. (31.05.2022)
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Final mark is based on the oral examination (67%) and results of tests taken during the course (33%). Oral examination takes place during the examination period and students must first obtain the evaluation for Q&A sessions and take-home exercises. Poslední úprava: Půta František, doc. RNDr., CSc. (06.02.2022)
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Definition of life Origin of life Sustainability of life - metabolism Strategies of energetic metabolism Information molecules From nucleic acid to protein - central dogma of molecular biology Protein biology Concept of conformation change - regulation of enzyme activity, molecular machines Cytoskeleton and cell mobility Vesicular trafficking Cell signalling Cell cycle and its regulation E pluribus unum - general cell biology principles under specific conditions (in differentiated organism in particular cell types or separate taxa) Poslední úprava: Půta František, doc. RNDr., CSc. (06.02.2022)
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Study outcomes are structured according to the syllabus. By the end of the course, students should be able to prove that they can: (1) Definition of Life; Origin of Life Define fundamental characteristics of living systems and distinguish them from non-living entities. Explain the metaphor “Life is like riding a bicycle. To keep your balance, you must keep moving” in the context of biological systems. Compare living systems with borderline cases such as viruses, fire, or crystals, and argue whether they fulfill the criteria of life. Describe the relationships between entropy, chaos, and thermal energy in open biological systems. Outline the most probable steps and intermediates in current theories of the origin of life. Evaluate environmental limits of life (temperature, pH, radiation) and discuss the concept of robustness. Distinguish between biogenic and non-biogenic elements and explain their relevance for living matter.
(2) Sustainability of Life Define life as a phenomenon. List and describe the fundamental characteristics of living systems. Explain the following features including: Teleonomic character State-dependent rules Nontrivial replication Emergence of structural organization Far from equilibrium systems under kinetic control Persistence in time Apparent tendency for increasing complexity. Discuss the question of the origin of life and express in your own words why the current theories face difficulties. Define the basic principles of metabolism. List the molecules of coupling of exergonic and endergonic reactions. Outline the basic scheme of energetic metabolism. Explain the importance of oxidation-reduction reactions. Describe the steps of glycolysis and explain the logic of the pathway using Lehninger’s e-book. Describe the Krebs cycle reactions and explain the logic of the pathway using Lehninger’s e-book. Discuss how metabolism can impact physiology.
(3) Cell Membranes Explain why membranes are essential for all living organisms and how they enable cellular life. Discuss the functional logic of membranes in enveloped viruses and compare it to cellular membranes. List and describe the major functions associated with the plasma membrane. Relate membrane structure to function, including the roles of phospholipids, glycolipids, and cholesterol. Describe unique features of membrane organization in Archaea. Explain the principles determining membrane fluidity and predict its biological consequences. Distinguish membrane asymmetry and domain formation, including phase separation and epithelial polarity. Classify membrane proteins according to their anchors and functions. Compare different modes of transport across membranes and explain the role of electrochemical gradients. Describe the molecular mechanism of the Na⁺/K⁺-ATPase and explain its physiological importance. Evaluate experimental methods used for membrane characterization (cryo-EM, FRAP, FLIM, AFM, patch clamp, etc.) and select appropriate techniques for specific biological questions.
(4) Nucleic Acids at the Center of Life Describe the key historical experiments that led to the discovery of DNA as genetic material. Explain the composition of a bacterial cell with emphasis on nucleic acids. Describe primary, secondary, and tertiary structures of nucleic acids and the factors stabilizing them. Explain the importance of hydration, ribose pucker, base pairing, and nucleotide modifications for helix formation. Discuss tautomeric forms of bases and their significance for mutations and evolution. Interpret DNA denaturation curves and define the concept of melting temperature (Tm). Explain DNA topology, the role of supercoiling, and the function of topoisomerases. Compare genome organizations in bacteria, archaea, eukaryotes, and organelles.
(5) Central Dogma of Molecular Biology State and explain the central dogma of molecular biology and its modern extensions. Define the concept of a gene and discuss its evolving interpretation. Classify DNA and RNA polymerases and explain the principles of enzymatic nucleic acid synthesis. Describe the organization of DNA replication, including the replication origin and replication fork. Compare transcription mechanisms in bacteria, archaea, and eukaryotes. Analyze interactions among replication, transcription, and DNA repair. Explain post-transcriptional RNA processing, including splicing and rRNA modification. Describe translation in prokaryotes and eukaryotes and evaluate the action of antibiotics on this process. Classify types of mutations and explain basic DNA repair mechanisms. Describe mechanisms of mRNA surveillance and quality control.
(6) Cytoskeleton and cell motility Identify the major building blocks of cytoskeletal networks Describe principles and dynamics of assembly for actin filaments, microtubules, and intermediate filaments Discuss the similarities and differences in cytoskeletal networks. Diagram the structure of key cytoskeletal elements in eukaryotic cells, including selected associated proteins and crosslinkers, and predict their roles in maintaining cell shape and intracellular transport. Assess the mechanisms of molecular motors (e.g., kinesins, dyneins, myosins) in terms of processivity, directionality, and cooperation Design an experiment to investigate molecular motors´ contribution to cellular motility. Compare the cytoskeleton in bacteria, including the bacterial flagellum, to eukaryotic systems and evaluate examples of diseases or syndromes (e.g., cytoskeletal disorders like muscular dystrophy) linked to cytoskeletal dysfunction.
(7) Cell organelles, vesicular trafficking Explain the (dis)advantages of cellular compartments Describe the role of signal sequences involved in protein sorting to various compartments (e.g., nucleus, mitochondria, chloroplasts, endoplasmic reticulum). Summarize the role of the nuclear pore complex and Ran gradient in nuclear import/export. Analyze the protein secretory pathway regarding posttranslational modifications Discuss the ways in which protein can be degraded, including the roles of proteasome, ubiquitin, lysosomes, and autophagosomes. Compare different vesicular trafficking mechanisms involving molecules like clathrin, COPI, COPII, dynamin, Rab proteins, and SNAREs. Prepare a model illustrating inter-organelle connections in the eukaryotic cell. Critically compare the structure, function, and evolutionary origins of mitochondria and chloroplasts.
(8) Cell Signaling Describe the complexity of signaling cascades, including feedback loops, signal multiplication, integration, and selectivity. Classify types of intercellular communication. Compare key pathways such as G-protein coupled receptors with second messengers, kinase-linked pathways, proteolysis-dependent pathways (e.g., Wnt, Notch), and those with intracellular receptors. Distinguish early versus delayed cellular responses to the signals. Evaluate how signaling pathways achieve specificity and integration. Propose an experiment enabling scientists to understand the position of a particular signaling molecule in the signaling network. Deduce the possible outcomes of such experiment.
(9) Proteins – from amino acids to protein structure Deduce the properties of water as a solvent from the characteristics of the molecule. List proteinogenic amino acids; draw their structures. Discuss their characteristics as sets of rules with intersections. Explain their acid base properties, chirality. Explain the properties of the peptide bond. Outline the spatial arrangements of major types of secondary structures. Discuss their stability with respect to amino acid composition. Deduce the hierarchical organization of protein structures – from secondary structures to domains. Critically discuss the number of folds known in Nature. Discuss major forces stabilizing protein structures. Present explanations why protein conformations are only marginally stable. Describe the system of protein homeostasis. Explain how proteins attain stable conformation using the concept of folding landscape. Explain folding upon binding versus conformation selection. Distinguish thermodynamic versus kinetic stability of a protein.
(10) Protein functions I - ligand binding, cooperativity, allostery Explain allostery, cooperativity. Give examples. Explain in your own words Perutz’s mechanism of hemoglobin cooperativity. Argue why oxygen transport proteins exist as oligomers. Discuss hemoglobin changes during short-term high-altitude adaptation. Explain the Bohr effect – the role of H+ and Cl- in contributing to oxygen unloading in tissue capillaries.
(11) Protein functions II - enzymatic catalysis; energy transduction in membrane systems List the key properties of enzymes important for life. List and explain the principles whereby enzymes can be regulated in cells. Explain key principles of catalysis; illustrate them with examples. Describe the chemiosmotic mechanism for ATP synthesis – outline key principles, key discoveries. Draw the anatomy of mitochondria and respirasome. Explain the concept of the standard reduction potential (E’°) of a redox pair and of the protonmotive force. List major carriers of reducing equivalents and characterize them based on their E’° values. Propose an experiment to prove the role of a proton gradient in ATP synthesis. Recall the spatial and functional architecture of each of the complexes I to IV (redox centers, components, proton transport versus electron translocation). Explain the principle of the Q cycle. Present an overview of the functioning of the ATP synthase. Explain how the binding sites for nucleotides in the alpha/beta head change during the rotation of the gamma subunit. Explain what exactly causes the Fo c-ring to rotate.
(12) Cell Cycle and Its Regulation Describe the logic of cell cycle phases and predict the consequences of their modification. Compare mitosis and meiosis in terms of purpose and mechanism. Explain checkpoint control and experimental methods for cell-cycle analysis. Interpret the concept of nucleo-cytosolic ratio and its developmental implications. Analyze the balance between proliferation, apoptosis, and senescence. Explain the role of telomeres and telomerase in proliferation control. Describe the molecular regulation of CDK activity. Interpret oncogenes and tumor suppressors using molecular examples (p53, Rb, APC). Explain mechanisms and pathways of apoptosis. Evaluate genetic and environmental mechanisms of carcinogenesis. Discuss principles of modern personalized anticancer therapies. Poslední úprava: Libusová Lenka, RNDr., Ph.D. (03.02.2026)
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